pdb id class method authors reference annotation
10mh transferase-DNA X-ray (2.55 Å) Sheikhnejad G, Brank A, Christman JK, Goddard A, Alvarez E, Ford Jr H, Marquez VE, Marasco CJ, Sufrin JR, O'gara M, Cheng X (1999) "Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine." J.Mol.Biol., 285, 2021-2034. doi: 10.1006/jmbi.1998.2426. Ternary structure of hhai methyltransferase with adohcy and hemimethylated DNA containing 5,6-dihydro-5-azacytosine at the target. SNAP output
173d DNA-antibiotic X-ray (3.0 Å) Kamitori S, Takusagawa F (1994) "Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2-Actinomycin D Complexes and its Host DNA." J.Am.Chem.Soc., 116, 4154. doi: 10.1021/JA00089A002. Multiple binding modes of anticancer drug actinomycin d: x-ray, molecular modeling, and spectroscopic studies of d(gaagcttc)2-actinomycin d complexes and its host DNA. SNAP output
185d DNA-antibiotic NMR Addess KJ, Feigon J (1994) "Sequence Specificity of Quinoxaline Antibiotics. 1. Solution Structure of a 1:1 Complex between Triostin a and [D(Gacgtc)]2 and Comparison with the Solution Structure of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2 Complex." Biochemistry, 33, 12386. doi: 10.1021/BI00207A005. Sequence specificity of quinoxaline antibiotics. 1. solution structure of a 1:1 complex between triostin a and [d(gacgtc)]2 and comparison with the solution structure of the [n-mecys3, n-mecys7]tandem-[d(gatatc)]2 complex. SNAP output
193d DNA-antibiotic NMR Chen H, Patel DJ (1995) "Solution Structure of a Quinomycin Bisintercalator-DNA Complex." J.Mol.Biol., 246, 164. doi: 10.1006/JMBI.1994.0074. Solution structure of a quinomycin bisintercalator-DNA complex. SNAP output
1a02 transcription-DNA X-ray (2.7 Å) Chen L, Glover JN, Hogan PG, Rao A, Harrison SC (1998) "Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA." Nature, 392, 42-48. doi: 10.1038/32100. Structure of the DNA binding domains of nfat, fos and jun bound to DNA. SNAP output
1a0a transcription-DNA X-ray (2.8 Å) Shimizu T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y, Ogawa N, Oshima Y, Hakoshima T (1997) "Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition." EMBO J., 16, 4689-4697. doi: 10.1093/emboj/16.15.4689. Phosphate system positive regulatory protein pho4-DNA complex. SNAP output
1a1f transcription-DNA X-ray (2.1 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Dsnr (zif268 variant) zinc finger-DNA complex (gacc site). SNAP output
1a1g transcription-DNA X-ray (1.9 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Dsnr (zif268 variant) zinc finger-DNA complex (gcgt site). SNAP output
1a1h transcription-DNA X-ray (1.6 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Qgsr (zif268 variant) zinc finger-DNA complex (gcac site). SNAP output
1a1i transcription-DNA X-ray (1.6 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Radr (zif268 variant) zinc finger-DNA complex (gcac site). SNAP output
1a1j transcription-DNA X-ray (2.0 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Radr (zif268 variant) zinc finger-DNA complex (gcgt site). SNAP output
1a1k transcription-DNA X-ray (1.9 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Radr (zif268 variant) zinc finger-DNA complex (gacc site). SNAP output
1a1l transcription-DNA X-ray (2.3 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Zif268 zinc finger-DNA complex (gcac site). SNAP output
1a1v hydrolase-DNA X-ray (2.2 Å) Kim JL, Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA, Murcko MA, Lin C, Caron PR (1998) "Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding." Structure, 6, 89-100. doi: 10.1016/S0969-2126(98)00010-0. Hepatitis c virus ns3 helicase domain complexed with single stranded sDNA. SNAP output
1a31 isomerase-DNA X-ray (2.1 Å) Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) "Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA." Science, 279, 1504-1513. doi: 10.1126/science.279.5356.1504. Human reconstituted DNA topoisomerase i in covalent complex with a 22 base pair DNA duplex. SNAP output
1a35 isomerase-DNA X-ray (2.5 Å) Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) "Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA." Science, 279, 1504-1513. doi: 10.1126/science.279.5356.1504. Human topoisomerase i-DNA complex. SNAP output
1a36 isomerase-DNA X-ray (2.8 Å) Stewart L, Redinbo MR, Qiu X, Hol WG, Champoux JJ (1998) "A model for the mechanism of human topoisomerase I." Science, 279, 1534-1541. doi: 10.1126/science.279.5356.1534. Topoisomerase i-DNA complex. SNAP output
1a3q transcription-DNA X-ray (2.1 Å) Cramer P, Larson CJ, Verdine GL, Muller CW (1997) "Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution." EMBO J., 16, 7078-7090. doi: 10.1093/emboj/16.23.7078. Human nf-kappa-b p52 bound to DNA. SNAP output
1a66 transcription-DNA NMR Zhou P, Sun LJ, Dotsch V, Wagner G, Verdine GL (1998) "Solution structure of the core NFATC1/DNA complex." Cell(Cambridge,Mass.), 92, 687-696. doi: 10.1016/S0092-8674(00)81136-8. Solution NMR structure of the core nfatc1-DNA complex, 18 structures. SNAP output
1a6b viral protein-DNA NMR Schuler W, Dong C, Wecker K, Roques BP (1999) "NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes." Biochemistry, 38, 12984-12994. doi: 10.1021/bi990378d. NMR structure of the complex between the zinc finger protein ncp10 of moloney murine leukemia virus and a sequence of the psi-packaging domain of hiv-1, 20 structures. SNAP output
1a6y transcription-DNA X-ray (2.3 Å) Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F (1998) "Structural elements of an orphan nuclear receptor-DNA complex." Mol.Cell, 1, 849-861. doi: 10.1016/S1097-2765(00)80084-2. Reverba orphan nuclear receptor-DNA complex. SNAP output
1a73 hydrolase-DNA X-ray (1.8 Å) Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI." Nature, 394, 96-101. doi: 10.1038/27952. Intron-encoded endonuclease i-ppoi complexed with DNA. SNAP output
1a74 hydrolase-DNA X-ray (2.2 Å) Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI." Nature, 394, 96-101. doi: 10.1038/27952. I-ppol homing endonuclease-DNA complex. SNAP output
1aay transcription-DNA X-ray (1.6 Å) Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO (1996) "Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions." Structure, 4, 1171-1180. doi: 10.1016/S0969-2126(96)00125-6. Zif268 zinc finger-DNA complex. SNAP output
1ahd DNA binding protein-DNA NMR Billeter M, Qian YQ, Otting G, Muller M, Gehring W, Wuthrich K (1993) "Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex." J.Mol.Biol., 234, 1084-1097. doi: 10.1006/jmbi.1993.1661. Determination of the NMR solution structure of an antennapedia homeodomain-DNA complex. SNAP output
1ais transcription-DNA X-ray (2.1 Å) Kosa PF, Ghosh G, DeDecker BS, Sigler PB (1997) "The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box." Proc.Natl.Acad.Sci.USA, 94, 6042-6047. doi: 10.1073/pnas.94.12.6042. Tata-binding protein-transcription factor (ii)b-tata-box complex from pyrococcus woesei. SNAP output
1akh DNA binding protein-DNA X-ray (2.5 Å) Li T, Jin Y, Vershon AK, Wolberger C (1998) "Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract." Nucleic Acids Res., 26, 5707-5718. doi: 10.1093/nar/26.24.5707. Mat a1-alpha2-DNA ternary complex. SNAP output
1am9 transcription-DNA X-ray (2.3 Å) Parraga A, Bellsolell L, Ferre-D'Amare AR, Burley SK (1998) "Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution." Structure, 6, 661-672. doi: 10.1016/S0969-2126(98)00067-7. Human srebp-1a bound to ldl receptor promoter. SNAP output
1an2 transcription-DNA X-ray (2.9 Å) Ferre-D'Amare AR, Prendergast GC, Ziff EB, Burley SK (1993) "Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain." Nature, 363, 38-45. doi: 10.1038/363038a0. Recognition by max of its cognate DNA through a dimeric b-hlh-z domain. SNAP output
1an4 transcription-DNA X-ray (2.9 Å) Ferre-D'Amare AR, Pognonec P, Roeder RG, Burley SK (1994) "Structure and function of the b/HLH/Z domain of USF." EMBO J., 13, 180-189. Structure and function of the b-hlh-z domain of usf. SNAP output
1aoi DNA binding protein-DNA X-ray (2.8 Å) Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) "Crystal structure of the nucleosome core particle at 2.8 A resolution." Nature, 389, 251-260. doi: 10.1038/38444. Complex between nucleosome core particle (h3,h4,h2a,h2b) and 146 bp long DNA fragment. SNAP output
1apl DNA binding protein-DNA X-ray (2.7 Å) Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo CO (1991) "Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions." Cell(Cambridge,Mass.), 67, 517-528. doi: 10.1016/0092-8674(91)90526-5. Crystal structure of a mat-alpha2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. SNAP output
1au7 transcription-DNA X-ray (2.3 Å) Jacobson EM, Li P, Leon-del-Rio A, Rosenfeld MG, Aggarwal AK (1997) "Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility." Genes Dev., 11, 198-212. Pit-1 mutant-DNA complex. SNAP output
1awc transcription-DNA X-ray (2.15 Å) Batchelor AH, Piper DE, de la Brousse FC, McKnight SL, Wolberger C (1998) "The structure of GABPalpha/beta: an ETS domain- ankyrin repeat heterodimer bound to DNA." Science, 279, 1037-1041. doi: 10.1126/science.279.5353.1037. Mouse gabp alpha-beta domain bound to DNA. SNAP output
1az0 hydrolase-DNA X-ray (2.0 Å) Perona JJ, Martin AM (1997) "Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis." J.Mol.Biol., 273, 207-225. doi: 10.1006/jmbi.1997.1315. Ecorv endonuclease-DNA complex. SNAP output
1azp DNA binding protein-DNA X-ray (1.6 Å) Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The hyperthermophile chromosomal protein Sac7d sharply kinks DNA." Nature, 392, 202-205. doi: 10.1038/32455. Hyperthermophile chromosomal protein sac7d bound with kinked DNA duplex. SNAP output
1azq DNA binding protein-DNA X-ray (1.94 Å) Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The hyperthermophile chromosomal protein Sac7d sharply kinks DNA." Nature, 392, 202-205. doi: 10.1038/32455. Hyperthermophile chromosomal protein sac7d bound with kinked DNA duplex. SNAP output
1b01 gene regulation-DNA X-ray (2.56 Å) Gomis-Ruth FX, Sola M, Acebo P, Parraga A, Guasch A, Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll M (1998) "The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator." EMBO J., 17, 7404-7415. doi: 10.1093/emboj/17.24.7404. Transcriptional repressor copg-DNA complex. SNAP output
1b3t protein-DNA X-ray (2.2 Å) Bochkarev A, Bochkareva E, Frappier L, Edwards AM (1998) "The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1." J.Mol.Biol., 284, 1273-1278. doi: 10.1006/jmbi.1998.2247. Ebna-1 nuclear protein-DNA complex. SNAP output
1b69 integrase-DNA NMR Wojciak JM, Connolly KM, Clubb RT (1999) "NMR structure of the Tn916 integrase-DNA complex." Nat.Struct.Biol., 6, 366-373. doi: 10.1038/7603. The solution structure of tn916 integrase n-terminal domain-DNA complex. SNAP output
1b72 protein-DNA X-ray (2.35 Å) Piper DE, Batchelor AH, Chang CP, Cleary ML, Wolberger C (1999) "Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation." Cell(Cambridge,Mass.), 96, 587-597. doi: 10.1016/S0092-8674(00)80662-5. Pbx1, homeobox protein hox-b1-DNA ternary complex. SNAP output
1b8i transcription-DNA X-ray (2.4 Å) Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK (1999) "Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex." Nature, 397, 714-719. doi: 10.1038/17833. Structure of the homeotic ubx-exd-DNA ternary complex. SNAP output
1b94 hydrolase-DNA X-ray (1.9 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Restriction endonuclease ecorv with calcium. SNAP output
1b95 hydrolase-DNA X-ray (2.05 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group. SNAP output
1b96 hydrolase-DNA X-ray (2.3 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group. SNAP output
1b97 hydrolase-DNA X-ray (1.9 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group. SNAP output
1bbx DNA binding protein-DNA NMR Agback P, Baumann H, Knapp S, Ladenstein R, Hard T (1998) "Architecture of Nonspecific Protein-DNA Interactions in the Sso7D-DNA Complex." Nat.Struct.Biol., 5, 579-584. doi: 10.1038/836. Non-specific protein-DNA interactions in the sso7d-DNA complex, NMR, 1 structure. SNAP output
1bc7 transcription-DNA X-ray (2.01 Å) Mo Y, Vaessen B, Johnston K, Marmorstein R (1998) "Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins." Mol.Cell, 2, 201-212. doi: 10.1016/S1097-2765(00)80130-6. Serum response factor accessory protein 1a (sap-1)-DNA complex. SNAP output
1bc8 transcription-DNA X-ray (1.93 Å) Mo Y, Vaessen B, Johnston K, Marmorstein R (1998) "Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins." Mol.Cell, 2, 201-212. doi: 10.1016/S1097-2765(00)80130-6. Structures of sap-1 bound to DNA sequences from the e74 and c-fos promoters provide insights into how ets proteins discriminate between related DNA targets. SNAP output
1bdh transcription-DNA X-ray (2.7 Å) Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan RG (1996) "A Positively Charged Residue Bound in the Minor Groove Does not Alter the Bending of a DNA Duplex." J.Am.Chem.Soc., 118, 13073-13074. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1bdi transcription-DNA X-ray (3.0 Å) Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan RG (1996) "A Positively Charged Residue Bound in the Minor Groove Does not Alter the Bending of a DNA Duplex." J.Am.Chem.Soc., 118, 13073-13074. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1bdt gene regulation-DNA X-ray (2.5 Å) Schildbach JF, Karzai AW, Raumann BE, Sauer RT (1999) "Origins of DNA-binding specificity: role of protein contacts with the DNA backbone." Proc.Natl.Acad.Sci.USA, 96, 811-817. doi: 10.1073/pnas.96.3.811. Wild type gene-regulating protein arc-DNA complex. SNAP output
1bdv gene regulation-DNA X-ray (2.8 Å) Schildbach JF, Karzai AW, Raumann BE, Sauer RT (1999) "Origins of DNA-binding specificity: role of protein contacts with the DNA backbone." Proc.Natl.Acad.Sci.USA, 96, 811-817. doi: 10.1073/pnas.96.3.811. Arc fv10 cocrystal. SNAP output
1bf4 DNA-binding protein-DNA X-ray (1.6 Å) Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA." Nat.Struct.Biol., 5, 782-786. doi: 10.1038/1822. Chromosomal DNA-binding protein sso7d-d(gcgaacgc) complex. SNAP output
1bf5 gene regulation-DNA X-ray (2.9 Å) Chen X, Vinkemeier U, Zhao Y, Jeruzalmi D, Darnell Jr JE, Kuriyan J (1998) "Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA." Cell(Cambridge,Mass.), 93, 827-839. doi: 10.1016/S0092-8674(00)81443-9. Tyrosine phosphorylated stat-1-DNA complex. SNAP output
1bg1 transcription-DNA X-ray (2.25 Å) Becker S, Groner B, Muller CW (1998) "Three-dimensional structure of the Stat3beta homodimer bound to DNA." Nature, 394, 145-151. doi: 10.1038/28101. Transcription factor stat3b-DNA complex. SNAP output
1bgb hydrolase-DNA X-ray (2.0 Å) Horton NC, Perona JJ (1998) "Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts." J.Biol.Chem., 273, 21721-21729. doi: 10.1074/jbc.273.34.21721. Ecorv endonuclease complex with 5'-cgggatatccc DNA. SNAP output
1bhm hydrolase-DNA X-ray (2.2 Å) Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK (1995) "Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding." Science, 269, 656-663. Restriction endonuclease bamhi complex with DNA. SNAP output
1bj6 viral protein-DNA NMR Morellet N, Demene H, Teilleux V, Huynh-Dinh T, de Rocquigny H, Fournie-Zaluski MC, Roques BP (1998) "Structure of the complex between the HIV-1 nucleocapsid protein NCp7 and the single-stranded pentanucleotide d(ACGCC)." J.Mol.Biol., 283, 419-434. doi: 10.1006/jmbi.1998.2098. 1h NMR of (12-53) ncp7-d(acgcc) complex, 10 structures. SNAP output
1bl0 transcription-DNA X-ray (2.3 Å) Rhee S, Martin RG, Rosner JL, Davies DR (1998) "A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator." Proc.Natl.Acad.Sci.USA, 95, 10413-10418. doi: 10.1073/pnas.95.18.10413. Multiple antibiotic resistance protein (mara)-DNA complex. SNAP output
1bnk hydrolase-DNA X-ray (2.7 Å) Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T (1998) "Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision." Cell(Cambridge,Mass.), 95, 249-258. doi: 10.1016/S0092-8674(00)81755-9. Human 3-methyladenine DNA glycosylase complexed to DNA. SNAP output
1bnz DNA binding protein-DNA X-ray (2.0 Å) Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA." Nat.Struct.Biol., 5, 782-786. doi: 10.1038/1822. Sso7d hyperthermophile protein-DNA complex. SNAP output
1bp7 transcription-DNA X-ray (3.0 Å) Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI." Mol.Cell, 2, 469-476. doi: 10.1016/S1097-2765(00)80146-X. Group i mobile intron endonuclease i-crei complexed with homing site DNA. SNAP output
1bpx transferase-DNA X-ray (2.4 Å) Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) "Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism." Biochemistry, 36, 11205-11215. doi: 10.1021/bi9703812. DNA polymerase beta-DNA complex. SNAP output
1bpy transferase-DNA X-ray (2.2 Å) Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) "Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism." Biochemistry, 36, 11205-11215. doi: 10.1021/bi9703812. Human DNA polymerase beta complexed with gapped DNA and ddctp. SNAP output
1bpz transferase-DNA X-ray (2.6 Å) Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) "Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism." Biochemistry, 36, 11205-11215. doi: 10.1021/bi9703812. Human DNA polymerase beta complexed with nicked DNA. SNAP output
1brn hydrolase-DNA X-ray (1.76 Å) Buckle AM, Fersht AR (1994) "Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution." Biochemistry, 33, 1644-1653. doi: 10.1021/bi00173a005. Subsite binding in an rnase: structure of a barnase-tetranucleotide complex at 1.76 angstroms resolution. SNAP output
1bss hydrolase-DNA X-ray (2.15 Å) Horton NC, Newberry KJ, Perona JJ (1998) "Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases." Proc.Natl.Acad.Sci.USA, 95, 13489-13494. doi: 10.1073/pnas.95.23.13489. Ecorv-t93a-DNA-ca2+. SNAP output
1bsu hydrolase-DNA X-ray (2.0 Å) Martin AM, Sam MD, Reich NO, Perona JJ (1999) "Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease." Nat.Struct.Biol., 6, 269-277. doi: 10.1038/6707. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. SNAP output
1bua hydrolase-DNA X-ray (2.15 Å) Martin AM, Sam MD, Reich NO, Perona JJ (1999) "Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease." Nat.Struct.Biol., 6, 269-276. doi: 10.1038/6707. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. SNAP output
1bvo complex (transcription factor-DNA) X-ray (2.7 Å) Cramer P, Varrot A, Barillas-Mury C, Kafatos FC, Muller CW (1999) "Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA." Structure Fold.Des., 7, 841-852. doi: 10.1016/S0969-2126(99)80107-5. Dorsal homologue gambif1 bound to DNA. SNAP output
1by4 gene regulation-DNA X-ray (2.1 Å) Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B, Rastinejad F (2000) "Structural basis of RXR-DNA interactions." J.Mol.Biol., 296, 509-520. doi: 10.1006/jmbi.1999.3457. Structure and mechanism of the homodimeric assembly of the rxr on DNA. SNAP output
1c0w gene regulation-DNA X-ray (3.2 Å) Pohl E, Holmes RK, Hol WG (1999) "Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain." J.Mol.Biol., 292, 653-667. doi: 10.1006/jmbi.1999.3073. Crystal structure of the cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal binding sh-like domain. SNAP output
1c7u transcription-DNA NMR Huang K, Louis JM, Donaldson L, Lim FL, Sharrocks AD, Clore GM (2000) "Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors." Embo J., 19, 2615-2628. doi: 10.1093/emboj/19.11.2615. Complex of the DNA binding core domain of the transcription factor mef2a with a 20mer oligonucleotide. SNAP output
1c7y recombination-DNA X-ray (3.1 Å) Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H, Morikawa K (2000) "Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer." Proc.Natl.Acad.Sci.USA, 97, 8257-8262. doi: 10.1073/pnas.140212997. E.coli ruva-holliday junction complex. SNAP output
1c8c DNA binding protein-DNA X-ray (1.45 Å) Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH (2000) "Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs." J.Mol.Biol., 303, 395-403. doi: 10.1006/jmbi.2000.4112. Crystal structures of the chromosomal proteins sso7d-sac7d bound to DNA containing t-g mismatched base pairs. SNAP output
1c9b transcription-DNA X-ray (2.65 Å) Tsai FT, Sigler PB (2000) "Structural basis of preinitiation complex assembly on human pol II promoters." EMBO J., 19, 25-36. doi: 10.1093/emboj/19.1.25. Crystal structure of a human tbp core domain-human tfiib core domain complex bound to an extended, modified adenoviral major late promoter (admlp). SNAP output
1ca5 structural protein-DNA X-ray (2.2 Å) Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH-J (2000) "Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs." J.Mol.Biol., 303, 395-403. doi: 10.1006/jmbi.2000.4112. Intercalation site of hyperthermophile chromosomal protein sso7d-sac7d bound to DNA. SNAP output
1ca6 structural protein-DNA X-ray (2.2 Å) Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH-J (2000) "Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs." J.Mol.Biol., 303, 395-403. doi: 10.1006/jmbi.2000.4112. Intercalation site of hyperthermophile chromosomal protein sso7d-sac7d bound to DNA. SNAP output
1cbv immune system-DNA X-ray (2.66 Å) Herron JN, He XM, Ballard DW, Blier PR, Pace PE, Bothwell AL, Voss Jr EW, Edmundson AB (1991) "An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex." Proteins, 11, 159-175. doi: 10.1002/prot.340110302. An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded fab and a deoxynucleotide-fab complex. SNAP output
1cdw transcription-DNA X-ray (1.9 Å) Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK (1996) "Crystal structure of a human TATA box-binding protein/TATA element complex." Proc.Natl.Acad.Sci.USA, 93, 4862-4867. doi: 10.1073/pnas.93.10.4862. Human tbp core domain complexed with DNA. SNAP output
1cez transferase-DNA X-ray (2.4 Å) Cheetham GM, Jeruzalmi D, Steitz TA (1999) "Structural basis for initiation of transcription from an RNA polymerase-promoter complex." Nature, 399, 80-83. doi: 10.1038/19999. Crystal structure of a t7 RNA polymerase-t7 promoter complex. SNAP output
1cf7 transcription-DNA X-ray (2.6 Å) Zheng N, Fraenkel E, Pabo CO, Pavletich NP (1999) "Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP." Genes Dev., 13, 666-674. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor e2f-dp. SNAP output
1cgp transcription-DNA X-ray (3.0 Å) Schultz SC, Shields GC, Steitz TA (1991) "Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees." Science, 253, 1001-1007. Catabolite gene activator protein (cap)-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1cit transcription-DNA X-ray (2.7 Å) Meinke G, Sigler PB (1999) "DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B." Nat.Struct.Biol., 6, 471-477. doi: 10.1038/8276. DNA-binding mechanism of the monomeric orphan nuclear receptor ngfi-b. SNAP output
1cjg transcription-DNA NMR Spronk CA, Bonvin AM, Radha PK, Melacini G, Boelens R, Kaptein R (1999) "The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator." Structure Fold.Des., 7, 1483-1492. doi: 10.1016/S0969-2126(00)88339-2. NMR structure of lac repressor hp62-DNA complex. SNAP output
1ckq protein-DNA X-ray (1.85 Å) Horvath M, Choi J, Kim Y, Wilkosz PA, Chandrasekhar K, Rosenberg JM "The Integration of Recognition and Cleavage: X-Ray Structures of Pre- Transition State and Post-Reactive DNA-Eco Ri Endonuclease Complexes." Pre-transition state eco ri endonuclease-cognate DNA (tcgcgaattcgcg) complex. SNAP output
1ckt gene regulation-DNA X-ray (2.5 Å) Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ (1999) "Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins." Nature, 399, 708-712. doi: 10.1038/21460. Crystal structure of hmg1 domain a bound to a cisplatin-modified DNA duplex. SNAP output
1cl8 protein-DNA X-ray (1.8 Å) Horvath M, Rosenberg JM "Iap (Inner-Adenine to Purine): A Cognate EcoRI-DNA Base Analog Complex." A pre-transition state eco ri endonuclease-cognate DNA (tcgcgapttcgcg) complex with DNA base analog purine (p). SNAP output
1clq transferase-DNA X-ray (2.7 Å) Shamoo Y, Steitz TA (1999) "Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex." Cell(Cambridge,Mass.), 99, 155-166. doi: 10.1016/S0092-8674(00)81647-5. Crystal structure of a replication fork DNA polymerase editing complex at 2.7 Å resolution. SNAP output
1cma transcription-DNA X-ray (2.8 Å) Somers WS, Phillips SE (1992) "Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands." Nature, 359, 387-393. doi: 10.1038/359387a0. Met repressor-DNA complex + s-adenosyl-methionine. SNAP output
1co0 transcription NMR Brocchieri L, Zhou GP, Jardetzky O (2002) "Allostery and Induced Fit, NMR and Molecular Modeling Study of the trp-repressor - mtr DNA complex." Structures and Mechanisms, ACS Symposium Series, 827, 340-366. NMR study of trp repressor-mtr operator DNA complex. SNAP output
1cqt gene regulation-DNA X-ray (3.2 Å) Chasman D, Cepek K, Sharp PA, Pabo CO (1999) "Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface." Genes Dev., 13, 2650-2657. doi: 10.1101/gad.13.20.2650. Crystal structure of a ternary complex containing an oca-b peptide, the oct-1 pou domain, and an octamer element. SNAP output
1crx replication-DNA X-ray (2.4 Å) Guo F, Gopaul DN, van Duyne GD (1997) "Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse." Nature, 389, 40-46. doi: 10.1038/37925. Cre recombinase-DNA complex reaction intermediate i. SNAP output
1cw0 hydrolase-DNA X-ray (2.3 Å) Tsutakawa SE, Jingami H, Morikawa K (1999) "Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex." Cell(Cambridge,Mass.), 99, 615-623. doi: 10.1016/S0092-8674(00)81550-0. Crystal structure analysis of very short patch repair (vsr) endonuclease in complex with a duplex DNA. SNAP output
1cyq hydrolase-DNA X-ray (1.93 Å) Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat Jr RJ, Stoddard BL (1999) "A novel endonuclease mechanism directly visualized for I-PpoI." Nat.Struct.Biol., 6, 1096-1099. doi: 10.1038/70027. Intron encoded homing endonuclease i-ppoi (h98a)-DNA homing site complex. SNAP output
1cz0 hydrolase-DNA X-ray (2.1 Å) Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat Jr RJ, Stoddard BL (1999) "A novel endonuclease mechanism directly visualized for I-PpoI." Nat.Struct.Biol., 6, 1096-1099. doi: 10.1038/70027. Intron encoded homing endonuclease i-ppoi-DNA complex lacking catalytic metal ion. SNAP output
1d02 hydrolase-DNA X-ray (1.7 Å) Deibert M, Grazulis S, Janulaitis A, Siksnys V, Huber R (1999) "Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution." EMBO J., 18, 5805-5816. doi: 10.1093/emboj/18.21.5805. Crystal structure of muni restriction endonuclease in complex with cognate DNA. SNAP output
1d0e transferase-DNA X-ray (3.0 Å) Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM (2000) "Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain." J.Mol.Biol., 296, 613-632. doi: 10.1006/jmbi.1999.3477. Crystal structures of the n-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. SNAP output
1d1u hydrolase-DNA X-ray (2.3 Å) Cote ML, Yohannan SJ, Georgiadis MM (2000) "Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs." Acta Crystallogr.,Sect.D, 56, 1120-1131. doi: 10.1107/S0907444900008246. Use of an n-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing g-a mispairs. SNAP output
1d2i hydrolase-DNA X-ray (1.7 Å) Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK (2000) "Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution." Nat.Struct.Biol., 7, 134-140. doi: 10.1038/72405. Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer. SNAP output
1d3u gene regulation-DNA X-ray (2.4 Å) Littlefield O, Korkhin Y, Sigler PB (1999) "The structural basis for the oriented assembly of a TBP/TFB/promoter complex." Proc.Natl.Acad.Sci.USA, 96, 13668-13673. doi: 10.1073/pnas.96.24.13668. Tata-binding protein-transcription factor (ii)b-bre+tata-box complex from pyrococcus woesei. SNAP output
1d5y transcription-DNA X-ray (2.7 Å) Kwon HJ, Bennik MH, Demple B, Ellenberger T (2000) "Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA." Nat.Struct.Biol., 7, 424-430. doi: 10.1038/75213. Crystal structure of the e. coli rob transcription factor in complex with DNA. SNAP output
1d66 transcription-DNA X-ray (2.7 Å) Marmorstein R, Carey M, Ptashne M, Harrison SC (1992) "DNA recognition by GAL4: structure of a protein-DNA complex." Nature, 356, 408-414. doi: 10.1038/356408a0. DNA recognition by gal4: structure of a protein-DNA complex. SNAP output
1d8y transferase-DNA X-ray (2.08 Å) Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M (1999) "Structural origins of the exonuclease resistance of a zwitterionic RNA." Proc.Natl.Acad.Sci.USA, 96, 14240-14245. doi: 10.1073/pnas.96.25.14240. Crystal structure of the complex of DNA polymerase i klenow fragment with DNA. SNAP output
1dc1 hydrolase-DNA X-ray (1.7 Å) van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM (2001) "Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis." Structure, 9, 133-144. doi: 10.1016/S0969-2126(01)00564-0. Restriction enzyme bsobi-DNA complex structure: encirclement of the DNA and histidine-catalyzed hydrolysis within a canonical restriction enzyme fold. SNAP output
1dct transferase-DNA X-ray (2.8 Å) Reinisch KM, Chen L, Verdine GL, Lipscomb WN (1995) "The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing." Cell(Cambridge,Mass.), 82, 143-153. doi: 10.1016/0092-8674(95)90060-8. DNA (cytosine-5) methylase from haeiii covalently bound to DNA. SNAP output
1ddn gene regulation-DNA X-ray (3.0 Å) White A, Ding X, vanderSpek JC, Murphy JR, Ringe D (1998) "Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex." Nature, 394, 502-506. doi: 10.1038/28893. Diphtheria tox repressor (c102d mutant)-tox DNA operator complex. SNAP output
1de8 lyase-DNA X-ray (2.95 Å) Mol CD, Izumi T, Mitra S, Tainer JA (2000) "DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected." Nature, 403, 451-456. doi: 10.1038/35000249. Human apurinic-apyrimidinic endonuclease-1 (ape1) bound to abasic DNA. SNAP output
1de9 lyase-DNA X-ray (3.0 Å) Mol CD, Izumi T, Mitra S, Tainer JA (2000) "DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination." Nature, 403, 451-456. doi: 10.1038/35000249. Human ape1 endonuclease with bound abasic DNA and mn2+ ion. SNAP output
1dew lyase-DNA X-ray (2.65 Å) Mol CD, Izumi T, Mitra S, Tainer JA (2000) "DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination." Nature, 403, 451-456. doi: 10.1038/35000249. Crystal structure of human ape1 bound to abasic DNA. SNAP output
1dfm hydrolase-DNA X-ray (1.5 Å) Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK (2000) "Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution." Nat.Struct.Biol., 7, 134-140. doi: 10.1038/72405. Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer. SNAP output
1dgc transcription-DNA X-ray (3.0 Å) Konig P, Richmond TJ (1993) "The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility." J.Mol.Biol., 233, 139-154. doi: 10.1006/jmbi.1993.1490. The x-ray structure of the gcn4-bzip bound to atf-creb site DNA shows the complex depends on DNA flexibility. SNAP output
1dh3 transcription-DNA X-ray (3.0 Å) Schumacher MA, Goodman RH, Brennan RG (2000) "The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding." J.Biol.Chem., 275, 35242-35247. doi: 10.1074/jbc.M007293200. Crystal structure of a creb bzip-cre complex reveals the basis for creb faimly selective dimerization and DNA binding. SNAP output
1diz hydrolase-DNA X-ray (2.5 Å) Hollis T, Ichikawa Y, Ellenberger T (2000) "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO J., 19, 758-766. doi: 10.1093/emboj/19.4.758. Crystal structure of e. coli 3-methyladenine DNA glycosylase (alka) complexed with DNA. SNAP output
1dmu hydrolase-DNA X-ray (2.2 Å) Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE (1998) "Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence." EMBO J., 17, 5466-5476. doi: 10.1093/emboj/17.18.5466. Crystal structure of the restriction endonuclease bgli (e.c.3.1.21.4) bound to its DNA recognition sequence. SNAP output
1dnk hydrolase-DNA X-ray (2.3 Å) Weston SA, Lahm A, Suck D (1992) "X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution." J.Mol.Biol., 226, 1237-1256. doi: 10.1016/0022-2836(92)91064-V. The x-ray structure of the dnase i-d(ggtatacc)2 complex at 2.3 angstroms resolution. SNAP output
1dp7 transcription-DNA X-ray (1.5 Å) Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W, Mach B, Burley SK (2000) "Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding." Nature, 403, 916-921. doi: 10.1038/35002634. Cocrystal structure of rfx-dbd in complex with its cognate x-box binding site. SNAP output
1drg hydrolase, ligase-DNA X-ray (2.55 Å) Woods KC, Martin SS, Chu VC, Baldwin EP (2001) "Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction." J.Mol.Biol., 313, 49-69. doi: 10.1006/jmbi.2001.5012. Crystal structure of trimeric cre recombinase-lox complex. SNAP output
1dsc DNA-antibiotic NMR Lian C, Robinson H, Wang AH-J (1996) "Structure of Actinomycin D Bound with (Gaagcttc)2 and (Gatgcttc)2 and its Binding to the (Cag)N:(Ctg)N Triplet Sequence by NMR Analysis." J.Am.Chem.Soc., 118, 8791. doi: 10.1021/JA961631P. NMR study of DNA (5'-d(*gp*ap*ap*gp*cp*tp*tp*c)-3') self-complementary duplex complexed with actinomycin d, minimized average structure. SNAP output
1dsd DNA-antibiotic NMR Lian C, Robinson H, Wang AH-J (1996) "Structure of Actinomycin D Bound with (Gaagcttc)2 and (Gatgcttc)2 and its Binding to the (Cag)N:(Ctg)N Triplet Sequence by NMR Analysis." J.Am.Chem.Soc., 118, 8791. doi: 10.1021/JA961631P. NMR study of DNA (5'-d(*gp*ap*tp*gp*cp*tp*tp*c)-3') t:t mismatched duplex complexed with actinomycin d, minimized average structure. SNAP output
1dsz transcription-DNA X-ray (1.7 Å) Rastinejad F, Wagner T, Zhao Q, Khorasanizadeh S (2000) "Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1." EMBO J., 19, 1045-1054. doi: 10.1093/emboj/19.5.1045. Structure of the rxr-rar DNA-binding domain heterodimer in complex with the retinoic acid response element dr1. SNAP output
1du0 transcription-DNA X-ray (2.0 Å) Grant RA, Rould MA, Klemm JD, Pabo CO (2000) "Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A." Biochemistry, 39, 8187-8192. doi: 10.1021/bi000071a. Engrailed homeodomain q50a variant DNA complex. SNAP output
1dux transcription-DNA X-ray (2.1 Å) Mo Y, Vaessen B, Johnston K, Marmorstein R (2000) "Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA." Nat.Struct.Biol., 7, 292-297. doi: 10.1038/74055. Elk-1-DNA structure reveals how residues distal from DNA-binding surface affect DNA-recognition. SNAP output
1e3m DNA binding X-ray (2.2 Å) Lamers MH, Perrakis A, Enzlin JH, Winterwerp HHK, De Wind N, Sixma TK (2000) "The Crystal Structure of DNA Mismatch Repair Protein Muts Binding to a G X T Mismatch." Nature, 407, 711. doi: 10.1038/35037523. The crystal structure of e. coli muts binding to DNA with a g:t mismatch. SNAP output
1e3o transcription X-ray (1.9 Å) Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A, Reinbold R, Scholer HR, Wilmanns M (2001) "Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping." Mol.Cell, 8, 569. doi: 10.1016/S1097-2765(01)00336-7. Crystal structure of oct-1 pou dimer bound to more. SNAP output
1ea4 gene regulation-DNA X-ray (2.95 Å) Costa M, Sola M, Del G, Eritja R, Hernaindez-Arriaga AM, Espinosa M, Gomis-Rueth FX, Coll M (2001) "Plasmid Transcriptional Repressor Copg Oligomerises to Render Helical Superstructures Unbound and in Complexes with Oligonucleotides." J.Mol.Biol., 310, 403. doi: 10.1006/JMBI.2001.4760. Transcriptional repressor copg-22bp dsDNA complex. SNAP output
1ebm lyase-DNA X-ray (2.1 Å) Bruner SD, Norman DP, Verdine GL (2000) "Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA." Nature, 403, 859-866. doi: 10.1038/35002510. Crystal structure of the human 8-oxoguanine glycosylase (hogg1) bound to a substrate oligonucleotide. SNAP output
1ecr replication-DNA X-ray (2.7 Å) Kamada K, Horiuchi T, Ohsumi K, Shimamoto N, Morikawa K (1996) "Structure of a replication-terminator protein complexed with DNA." Nature, 383, 598-603. doi: 10.1038/383598a0. Escherichia coli replication terminator protein (tus) complexed with DNA. SNAP output
1efa transcription-DNA X-ray (2.6 Å) Bell CE, Lewis M (2000) "A closer view of the conformation of the Lac repressor bound to operator." Nat.Struct.Biol., 7, 209-214. doi: 10.1038/78907. Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf. SNAP output
1egw transcription-DNA X-ray (1.5 Å) Santelli E, Richmond TJ (2000) "Crystal structure of MEF2A core bound to DNA at 1.5 A resolution." J.Mol.Biol., 297, 437-449. doi: 10.1006/jmbi.2000.3568. Crystal structure of mef2a core bound to DNA. SNAP output
1ehl immune system X-ray (2.4 Å) Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O (2000) "Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation." J.Mol.Biol., 299, 711-723. doi: 10.1006/jmbi.2000.3772. 64m-2 antibody fab complexed with d(5ht)(6-4)t. SNAP output
1ej9 isomerase-DNA X-ray (2.6 Å) Redinbo MR, Champoux JJ, Hol WG (2000) "Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA." Biochemistry, 39, 6832-6840. doi: 10.1021/bi992690t. Crystal structure of human topoisomerase i DNA complex. SNAP output
1emh hydrolase-DNA X-ray (1.8 Å) Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) "Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects." Proc.Natl.Acad.Sci.USA, 97, 5083-5088. doi: 10.1073/pnas.97.10.5083. Crystal structure of human uracil-DNA glycosylase bound to uncleaved substrate-containing DNA. SNAP output
1emj hydrolase-DNA X-ray (2.0 Å) Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) "Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects." Proc.Natl.Acad.Sci.USA, 97, 5083-5088. doi: 10.1073/pnas.97.10.5083. Uracil-DNA glycosylase bound to DNA containing a 4'-thio-2'deoxyuridine analog product. SNAP output
1eo3 hydrolase-DNA X-ray (2.0 Å) Horton NC, Connolly BA, Perona JJ (2000) "Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study." J.Am.Chem.Soc., 122, 3314-3324. doi: 10.1021/ja993719j. Inhibition of ecorv endonuclease by deoxyribo-3'-s-phosphorothiolates: a high resolution x-ray crystallographic study. SNAP output
1eo4 hydrolase-DNA X-ray (1.9 Å) Horton NC, Connolly BA, Perona JJ (2000) "Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study." J.Am.Chem.Soc., 122, 3314-3324. doi: 10.1021/ja993719j. Ecorv bound to mn2+ and cognate DNA containing a 3's substition at the cleavage site. SNAP output
1eon hydrolase-DNA X-ray (1.6 Å) Horton NC, Connolly BA, Perona JJ (2000) "Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study." J.Am.Chem.Soc., 122, 3314-3324. doi: 10.1021/ja993719j. Ecorv bound to 3'-s-phosphorothiolate DNA and ca2+. SNAP output
1eoo hydrolase-DNA X-ray (2.16 Å) Horton NC, Perona JJ (2000) "Crystallographic snapshots along a protein-induced DNA-bending pathway." Proc.Natl.Acad.Sci.USA, 97, 5729-5734. doi: 10.1073/pnas.090370797. Ecorv bound to cognate DNA. SNAP output
1eop hydrolase-DNA X-ray (2.6 Å) Horton NC, Perona JJ (2000) "Crystallographic snapshots along a protein-induced DNA-bending pathway." Proc.Natl.Acad.Sci.USA, 97, 5729-5734. doi: 10.1073/pnas.090370797. Ecorv bound to cognate DNA. SNAP output
1eqz structural protein-DNA X-ray (2.5 Å) Harp JM, Hanson BL, Timm DE, Bunick GJ (2000) "Asymmetries in the nucleosome core particle at 2.5 A resolution." Acta Crystallogr.,Sect.D, 56, 1513-1534. doi: 10.1107/S0907444900011847. X-ray structure of the nucleosome core particle at 2.5 Å resolution. SNAP output
1eri hydrolase-DNA X-ray (2.5 Å) Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM (1990) "Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing." Science, 249, 1307-1309. X-ray structure of the DNA-eco ri endonuclease-DNA recognition complex: the recognition network and the integration of recognition and cleavage. SNAP output
1esg hydrolase-DNA X-ray (1.9 Å) Viadiu H, Aggarwal AK (2000) "Structure of BamHI bound to nonspecific DNA: a model for DNA sliding." Mol.Cell, 5, 889-895. doi: 10.1016/S1097-2765(00)80329-9. Restriction endonuclease bamhi bound to a non-specific DNA.. SNAP output
1evw hydrolase-DNA X-ray (3.1 Å) Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat Jr RJ, Stoddard BL (2000) "Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site." J.Mol.Biol., 300, 877-887. doi: 10.1006/jmbi.2000.3874. L116a mutant of the homing endonuclease i-ppoi complexed to homing site DNA.. SNAP output
1ewn hydrolase-DNA X-ray (2.1 Å) Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T (2000) "Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG." Proc.Natl.Acad.Sci.USA, 97, 13573-13578. doi: 10.1073/pnas.97.25.13573. Crystal structure of the human aag DNA repair glycosylase complexed with 1,n6-ethenoadenine-DNA. SNAP output
1ewq replication-DNA X-ray (2.2 Å) Obmolova G, Ban C, Hsieh P, Yang W (2000) "Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA." Nature, 407, 703-710. doi: 10.1038/35037509. Crystal structure taq muts complexed with a heteroduplex DNA at 2.2 Å resolution. SNAP output
1exi transcription-DNA X-ray (3.12 Å) Heldwein EE, Brennan RG (2001) "Crystal structure of the transcription activator BmrR bound to DNA and a drug." Nature, 409, 378-382. doi: 10.1038/35053138. Crystal structure of transcription activator bmrr, from b. subtilis, bound to 21 base pair bmr operator and tpsb. SNAP output
1exj transcription-DNA X-ray (3.0 Å) Heldwein EE, Brennan RG (2001) "Crystal structure of the transcription activator BmrR bound to DNA and a drug." Nature, 409, 378-382. doi: 10.1038/35053138. Crystal structure of transcription activator bmrr, from b. subtilis, bound to 21 base pair bmr operator and tpp. SNAP output
1eyg replication-DNA X-ray (2.8 Å) Raghunathan S, Kozlov AG, Lohman TM, Waksman G (2000) "Structure of the DNA binding domain of E. coli SSB bound to ssDNA." Nat.Struct.Biol., 7, 648-652. doi: 10.1038/77943. Crystal structure of chymotryptic fragment of e. coli ssb bound to two 35-mer single strand dnas. SNAP output
1eyu hydrolase-DNA X-ray (1.78 Å) Horton JR, Cheng X (2000) "PvuII endonuclease contains two calcium ions in active sites." J.Mol.Biol., 300, 1049-1056. doi: 10.1006/jmbi.2000.3938. High resolution structure of the pvuii endonculease-cognate DNA complex at ph 4.6. SNAP output
1f0o hydrolase-DNA X-ray (2.5 Å) Horton JR, Cheng X (2000) "PvuII endonuclease contains two calcium ions in active sites." J.Mol.Biol., 300, 1049-1056. doi: 10.1006/jmbi.2000.3938. Pvuii endonuclease-cognate DNA complex (glutaraldehyde-crosslinked crystal) at ph 7.5 with two calcium ions at each active site. SNAP output
1f0v hydrolase-DNA X-ray (1.7 Å) Liu YS, Gotte G, Libonati M, Eisenberg DS (2001) "A domain-swapped RNase A dimer with implications for amyloid formation." Nat.Struct.Biol., 8, 211-214. doi: 10.1038/84941. Crystal structure of an rnase a dimer displaying a new type of 3d domain swapping. SNAP output
1f2i transcription-DNA X-ray (2.35 Å) Wang BS, Grant RA, Pabo CO (2001) "Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA." Nat.Struct.Biol., 8, 589-593. doi: 10.1038/89617. Cocrystal structure of selected zinc finger dimer bound to DNA. SNAP output
1f44 hydrolase, ligase-DNA X-ray (2.05 Å) Woods KC, Martin SS, Chu VC, Baldwin EP (2001) "Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction." J.Mol.Biol., 313, 49-69. doi: 10.1006/jmbi.2001.5012. Crystal structure of trimeric cre recombinase-lox complex. SNAP output
1f4k replication-DNA X-ray (2.5 Å) Wilce JA, Vivian JP, Hastings AF, Otting G, Folmer RH, Duggin IG, Wake RG, Wilce MC (2001) "Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest." Nat.Struct.Biol., 8, 206-210. doi: 10.1038/84934. Crystal structure of the replication terminator protein-b-site DNA complex. SNAP output
1f4r hydrolase-DNA X-ray (2.4 Å) Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T (2000) "Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG." Proc.Natl.Acad.Sci.USA, 97, 13573-13578. doi: 10.1073/pnas.97.25.13573. Crystal structure of the human aag DNA repair glycosylase complexed with 1,n6-ethenoadenine-DNA. SNAP output
1f4s transcription-DNA NMR Cahuzac B, Cerdan R, Felenbok B, Guittet E (2001) "The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein." Structure, 9, 827-836. doi: 10.1016/S0969-2126(01)00640-2. Structure of transcriptional factor alcr in complex with a target DNA. SNAP output
1f5e transcription-DNA NMR Cahuzac B, Cerdan R, Felenbok B, Guittet E (2001) "The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein." Structure, 9, 827-836. doi: 10.1016/S0969-2126(01)00640-2. Structure of transcriptional factor alcr in complex with a target DNA. SNAP output
1f5t transcription-DNA X-ray (3.0 Å) Chen CS, White A, Love J, Murphy JR, Ringe D (2000) "Methyl groups of thymine bases are important for nucleic acid recognition by DtxR." Biochemistry, 39, 10397-10407. doi: 10.1021/bi0009284. Diphtheria tox repressor (c102d mutant) complexed with nickel and dtxr consensus binding sequence. SNAP output
1f66 structural protein-DNA X-ray (2.6 Å) Suto RK, Clarkson MJ, Tremethick DJ, Luger K (2000) "Crystal structure of a nucleosome core particle containing the variant histone H2A.Z." Nat.Struct.Biol., 7, 1121-1124. doi: 10.1038/81971. 2.6 a crystal structure of a nucleosome core particle containing the variant histone h2a.z. SNAP output
1f6o hydrolase-DNA X-ray (2.4 Å) Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T (2000) "Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG." Proc.Natl.Acad.Sci.USA, 97, 13573-13578. doi: 10.1073/pnas.97.25.13573. Crystal structure of the human aag DNA repair glycosylase complexed with DNA. SNAP output
1fiu hydrolase-DNA X-ray (1.6 Å) Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R (2000) "Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA." Nat.Struct.Biol., 7, 792-799. doi: 10.1038/79032. Tetrameric restriction endonuclease ngomiv in complex with cleaved DNA. SNAP output
1fja DNA-antibiotic NMR Chen H, Liu X, Patel DJ (1996) "DNA Bending and Unwinding Associated with Actinomycin D Antibiotics Bound to Partially Overlapping Sites on DNA." J.Mol.Biol., 258, 457. doi: 10.1006/JMBI.1996.0262. NMR study of deoxyribonucleic acid complexed with actinomycin d. SNAP output
1fjl transcription-DNA X-ray (2.0 Å) Wilson DS, Guenther B, Desplan C, Kuriyan J (1995) "High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA." Cell(Cambridge,Mass.), 82, 709-719. doi: 10.1016/0092-8674(95)90468-9. Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide. SNAP output
1fjx transferase-DNA X-ray (2.26 Å) Vilkaitis G, Dong A, Weinhold E, Cheng X, Klimasauskas S (2000) "Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase." J.Biol.Chem., 275, 38722-38730. Structure of ternary complex of hhai methyltransferase mutant (t250g) in complex with DNA and adohcy. SNAP output
1flo ligase, lyase-DNA X-ray (2.65 Å) Chen Y, Narendra U, Iype LE, Cox MM, Rice PA (2000) "Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping." Mol.Cell, 6, 885-897. doi: 10.1016/S1097-2765(00)00086-1. Flp recombinase-holliday junction complex i. SNAP output
1fn7 hydrolase-DNA X-ray (2.6 Å) Norman DP, Bruner SD, Verdine GL (2001) "Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein." J.Am.Chem.Soc., 123, 359-360. doi: 10.1021/ja003144m. Coupling of damage recognition and catalysis by a human base-excision DNA repair protein. SNAP output
1fok hydrolase-DNA X-ray (2.8 Å) Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK (1997) "Structure of the multimodular endonuclease FokI bound to DNA." Nature, 388, 97-100. doi: 10.1038/40446. Structure of restriction endonuclease foki bound to DNA. SNAP output
1fos transcription-DNA X-ray (3.05 Å) Glover JN, Harrison SC (1995) "Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA." Nature, 373, 257-261. doi: 10.1038/373257a0. Two human c-fos:c-jun:DNA complexes. SNAP output
1fw6 replication-DNA X-ray (2.7 Å) Junop MS, Obmolova G, Rausch K, Hsieh P, Yang W (2001) "Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repair." Mol.Cell, 7, 1-12. doi: 10.1016/S1097-2765(01)00149-6. Crystal structure of a taq muts-DNA-adp ternary complex. SNAP output
1fyl transcription-DNA X-ray (2.1 Å) Littlefield O, Nelson HC (2001) "Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex." Proteins, 45, 219-228. doi: 10.1002/prot.1142. Serendipitous crystal structure containing the heat shock transcription factor's DNA binding domain and cognate DNA in a head-to-head orientation. SNAP output
1fym transcription-DNA X-ray (2.2 Å) Littlefield O, Nelson HC (2001) "Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex." Proteins, 45, 219-228. doi: 10.1002/prot.1142. Serendipitous crystal structure containing the heat shock transcription factor's DNA binding domain and cognate DNA in a tail-to-tail orientation. SNAP output
1g2d transcription-DNA X-ray (2.2 Å) Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO (2001) "Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes." Structure, 9, 717-723. doi: 10.1016/S0969-2126(01)00632-3. Structure of a cys2his2 zinc finger-tata box complex (clone #2). SNAP output
1g2f transcription-DNA X-ray (2.0 Å) Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO (2001) "Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes." Structure, 9, 717-723. doi: 10.1016/S0969-2126(01)00632-3. Structure of a cys2his2 zinc finger-tata box complex (tatazf;clone #6). SNAP output
1g38 transferase-DNA X-ray (2.0 Å) Goedecke K, Pignot M, Goody RS, Scheidig AJ, Weinhold E (2001) "Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog." Nat.Struct.Biol., 8, 121-125. doi: 10.1038/84104. Adenine-specific methyltransferase m. taq i-DNA complex. SNAP output
1g3x DNA X-ray (2.7 Å) Malinina L, Soler-Lopez M, Aymami J, Subirana JA (2002) "Intercalation of an acridine-peptide drug in an AA/TT base step in the crystal structure of [d(CGCGAATTCGCG)](2) with six duplexes and seven Mg(2+) ions in the asymmetric unit." Biochemistry, 41, 9341-9348. doi: 10.1021/bi020135c. Intercalation of an 9acridine-peptide drug in a DNA dodecamer. SNAP output
1g4d viral protein-DNA NMR Wojciak JM, Iwahara J, Clubb RT (2001) "The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove." Nat.Struct.Biol., 8, 84-90. doi: 10.1038/89582. NMR structure of the mu bacteriophage repressor DNA-binding domain-DNA complex. SNAP output
1g9y hydrolase-DNA X-ray (2.05 Å) Chevalier BS, Monnat Jr RJ, Stoddard BL (2001) "The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites." Nat.Struct.Biol., 8, 312-316. doi: 10.1038/86181. Homing endonuclease i-crei - DNA substrate complex with calcium. SNAP output
1g9z hydrolase-DNA X-ray (1.8 Å) Chevalier BS, Monnat Jr RJ, Stoddard BL (2001) "The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites." Nat.Struct.Biol., 8, 312-316. doi: 10.1038/86181. Laglidadg homing endonuclease i-crei - DNA product complex with magnesium. SNAP output
1ga5 transcription-DNA X-ray (2.4 Å) Sierk ML, Zhao Q, Rastinejad F (2001) "DNA Deformability as a Recognition Feature in the RevErb Response Element." Biochemistry, 40, 12833-12843. doi: 10.1021/bi011086r. Crystal structure of the orphan nuclear receptor rev-erb(alpha) DNA-binding domain bound to its cognate response element. SNAP output
1gat transcription-DNA NMR Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM (1993) "NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1." Science, 261, 438-446. doi: 10.1021/bi00131a004. Solution structure of the specific DNA complex of the zinc containing DNA binding domain of the erythroid transcription factor gata-1 by multidimensional NMR. SNAP output
1gau transcription-DNA NMR Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM (1993) "NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1." Science, 261, 438-446. doi: 10.1021/bi00131a004. Solution structure of the specific DNA complex of the zinc containing DNA binding domain of the erythroid transcription factor gata-1 by multidimensional NMR. SNAP output
1gcc transcription-DNA NMR Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M (1998) "A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA." EMBO J., 17, 5484-5496. doi: 10.1093/emboj/17.18.5484. Solution NMR structure of the complex of gcc-box binding domain of aterf1 and gcc-box DNA, minimized average structure. SNAP output
1gd2 transcription-DNA X-ray (2.0 Å) Fujii Y, Shimizu T, Toda T, Yanagida M, Hakoshima T (2000) "Structural basis for the diversity of DNA recognition by bZIP transcription factors." Nat.Struct.Biol., 7, 889-893. doi: 10.1038/82822. Crystal structure of bzip transcription factor pap1 bound to DNA. SNAP output
1gdt DNA binding protein-DNA X-ray (3.0 Å) Yang W, Steitz TA (1995) "Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site." Cell(Cambridge,Mass.), 82, 193-207. doi: 10.1016/0092-8674(95)90307-0. Crystal structure of a site-specific recombinase, gamma-delta resolvase complexed with a 34 bp cleavage site. SNAP output
1gji transcription-DNA X-ray (2.85 Å) Huang DB, Chen YQ, Ruetsche M, Phelps CB, Ghosh G (2001) "X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2." Structure, 9, 669-678. doi: 10.1016/S0969-2126(01)00635-9. Crystal structure of c-rel bound to DNA. SNAP output
1glu transcription-DNA X-ray (2.9 Å) Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) "Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA." Nature, 352, 497-505. doi: 10.1038/352497a0. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. SNAP output
1gm5 helicase X-ray (3.24 Å) Singleton MR, Scaife S, Wigley DB (2001) "Structural Analysis of DNA Replication Fork Reversal by Recg." Cell(Cambridge,Mass.), 107, 79. doi: 10.1016/S0092-8674(01)00501-3. Structure of recg bound to three-way DNA junction. SNAP output
1gt0 transcription X-ray (2.6 Å) Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR, Wilmanns M (2003) "Crystal Structure of a POU/Hmg/DNA Ternary Complex Suggests Differential Assembly of Oct4 and Sox2 on Two Enhancers." Genes Dev., 17, 2048. doi: 10.1101/GAD.269303. Crystal structure of a pou-hmg-DNA ternary complex. SNAP output
1gtw transcription-DNA X-ray (1.85 Å) Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer bound to a DNA fragment from the tom-1a promoter. SNAP output
1gu4 transcription-DNA X-ray (1.8 Å) Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer bound to a high affinity DNA fragment. SNAP output
1gu5 transcription-DNA X-ray (2.1 Å) Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer bound to a DNA fragment from the mim-1 promoter. SNAP output
1gxp transcriptional activator X-ray (2.5 Å) Blanco AG, Sola M, Gomis-Ruth FX, Coll M (2002) "Tandem DNA Recognition by Two-Component Signal Transduction Transcriptional Activator Phob." Structure, 10, 701. doi: 10.1016/S0969-2126(02)00761-X. Phob effector domain in complex with pho box DNA.. SNAP output
1h0m transcription-DNA X-ray (3.0 Å) Vannini A, Volpari C, Gargioli C, Muraglia E, Cortese R, De Francesco R, Neddermann P, Di Marco S (2002) "The Crystal Structure of the Quorum Sensing Protein Trar Bound to its Autoinducer and Target DNA." Embo J., 21, 4393. doi: 10.1093/EMBOJ/CDF459. Three-dimensional structure of the quorum sensing protein trar bound to its autoinducer and to its target DNA. SNAP output
1h38 transferase X-ray (2.9 Å) Tahirov TH, Temiakov D, Anikin M, Patlan V, Mcallister WT, Vassylyev DG, Yokoyama S (2002) "Structure of a T7 RNA Polymerase Elongation Complex at 2.9 A Resolution." Nature, 420, 43. doi: 10.1038/NATURE01129. Structure of a t7 RNA polymerase elongation complex at 2.9a resolution. SNAP output
1h6f transcription factor X-ray (1.7 Å) Coll M, Seidman JG, Muller CW (2002) "Structure of the DNA-Bound T-Box Domain of Human Tbx3, a Transcription Factor Responsible for Ulnar- Mammary Syndrome." Structure, 10, 343. doi: 10.1016/S0969-2126(02)00722-0. Human tbx3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site. SNAP output
1h88 transcription-DNA X-ray (2.8 Å) Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2002) "Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter." Cell(Cambridge,Mass.), 108, 57. doi: 10.1016/S0092-8674(01)00636-5. Crystal structure of ternary protein-DNA complex1. SNAP output
1h89 transcription-DNA X-ray (2.45 Å) Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2002) "Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter." Cell(Cambridge,Mass.), 108, 57. doi: 10.1016/S0092-8674(01)00636-5. Crystal structure of ternary protein-DNA complex2. SNAP output
1h8a transcription-DNA X-ray (2.23 Å) Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2002) "Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter." Cell(Cambridge,Mass.), 108, 57. doi: 10.1016/S0092-8674(01)00636-5. Crystal structure of ternary protein-DNA complex3. SNAP output
1h9d transcription factor X-ray (2.6 Å) Bravo J, Li Z, Speck NA, Warren AJ (2001) "The Leukemia-Associated Aml1 (Runx1)-Cbfbeta Complex Functions as a DNA-Induced Molecular Clamp." Nat.Struct.Biol., 8, 371. doi: 10.1038/86264. Aml1-cbf-beta-DNA complex. SNAP output
1h9t transcriptional regulation X-ray (3.25 Å) Van Aalten DMF, Dirusso CC, Knudsen J (2001) "The Structural Basis of Acyl Coenzyme A-Dependent Regulation of the Transcription Factor Fadr." Embo J., 20, 2041. doi: 10.1093/EMBOJ/20.8.2041. Fadr, fatty acid responsive transcription factor from e. coli in complex with fadb operator. SNAP output
1hao hydrolase-hydrolase inhibitor-DNA X-ray (2.8 Å) Padmanabhan K, Tulinsky A (1996) "An ambiguous structure of a DNA 15-mer thrombin complex." Acta Crystallogr.,Sect.D, 52, 272-282. doi: 10.1107/S0907444995013977. Complex of human alpha-thrombin with a 15mer oligonucleotide ggttggtgtggttgg (based on NMR model of DNA). SNAP output
1hap hydrolase-hydrolase inhibitor-DNA X-ray (2.8 Å) Padmanabhan K, Tulinsky A (1996) "An ambiguous structure of a DNA 15-mer thrombin complex." Acta Crystallogr.,Sect.D, 52, 272-282. doi: 10.1107/S0907444995013977. Complex of human alpha-thrombin with a 15mer oligonucleotide ggttggtgtggttgg (based on x-ray model of DNA). SNAP output
1hbx gene regulation X-ray (3.15 Å) Hassler M, Richmond TJ (2001) "The B-Box Dominates Sap-1/Srf Interactions in the Structure of the Ternary Complex." Embo J., 20, 3018. doi: 10.1093/EMBOJ/20.12.3018. Ternary complex of sap-1 and srf with specific sre DNA. SNAP output
1hcq transcription-DNA X-ray (2.4 Å) Schwabe JW, Chapman L, Finch JT, Rhodes D (1993) "The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements." Cell(Cambridge,Mass.), 75, 567-578. doi: 10.1016/0092-8674(93)90390-C. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. SNAP output
1hcr DNA binding protein-DNA X-ray (2.3 Å) Feng JA, Johnson RC, Dickerson RE (1994) "Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions." Science, 263, 348-355. Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions. SNAP output
1hdd transcription-DNA X-ray (2.8 Å) Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO (1990) "Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions." Cell(Cambridge,Mass.), 63, 579-590. doi: 10.1016/0092-8674(90)90453-L. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 angstroms resolution: a framework for understanding homeodomain-DNA interactions. SNAP output
1hf0 transcription X-ray (2.7 Å) Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A, Reinbold R, Scholer HR, Wilmanns M (2001) "Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping." Mol.Cell, 8, 569. doi: 10.1016/S1097-2765(01)00336-7. Crystal structure of the DNA-binding domain of oct-1 bound to DNA as a dimer. SNAP output
1hht RNA polymerase X-ray (2.9 Å) Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI (2001) "A Mechanism for Initiating RNA-Dependent RNA Polymerization." Nature, 410, 235. doi: 10.1038/35065653. RNA dependent RNA polymerase from dsrna bacteriophage phi6 plus template. SNAP output
1hi0 RNA polymerase X-ray (3.0 Å) Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI (2001) "A Mechanism for Initiating RNA-Dependent RNA Polymerization." Nature, 410, 235. doi: 10.1038/35065653. RNA dependent RNA polymerase from dsrna bacteriophage phi6 plus initiation complex. SNAP output
1hjb transcription-DNA X-ray (3.0 Å) Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2001) "Structural Analyses of DNA Recognition by the Aml1/Runx-1 Runt Domain and its Allosteric Control by Cbfbeta." Cell(Cambridge,Mass.), 104, 755. doi: 10.1016/S0092-8674(01)00271-9. Crystal structure of runx-1-aml1-cbfalpha runt domain and c-ebpbeta bzip homodimer bound to a DNA fragment from the csf-1r promoter. SNAP output
1hjc transcription-DNA X-ray (2.65 Å) Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2001) "Structural Analyses of DNA Recognition by the Aml1/Runx-1 Runt Domain and its Allosteric Control by Cbfbeta." Cell(Cambridge,Mass.), 104, 755. doi: 10.1016/S0092-8674(01)00271-9. Crystal structure of runx-1-aml1-cbfalpha runt domain bound to a DNA fragment from the csf-1r promoter. SNAP output
1hlo transcription-DNA X-ray (2.8 Å) Brownlie P, Ceska T, Lamers M, Romier C, Stier G, Teo H, Suck D (1997) "The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control." Structure, 5, 509-520. doi: 10.1016/S0969-2126(97)00207-4. The crystal structure of an intact human max-DNA complex: new insights into mechanisms of transcriptional control. SNAP output
1hlv DNA binding protein-DNA X-ray (2.5 Å) Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi S, Ikuta M, Iwahara J, Okazaki T, Yokoyama S (2001) "Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA." EMBO J., 20, 6612-6618. doi: 10.1093/emboj/20.23.6612. Crystal structure of cenp-b(1-129) complexed with the cenp-b box DNA. SNAP output
1hlz transcription-DNA X-ray (2.8 Å) Sierk ML, Zhao Q, Rastinejad F (2001) "DNA Deformability as a Recognition Feature in the RevErb Response Element." Biochemistry, 40, 12833-12843. doi: 10.1021/bi011086r. Crystal structure of the orphan nuclear receptor rev-erb(alpha) DNA-binding domain bound to its cognate response element. SNAP output
1hry DNA binding protein-DNA NMR Werner MH, Huth JR, Gronenborn AM, Clore GM (1995) "Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex." Cell(Cambridge,Mass.), 81, 704-705. doi: 10.1016/0092-8674(95)90532-4. The 3d structure of the human sry-DNA complex solved by multid-dimensional heteronuclear-edited and-filtered NMR. SNAP output
1hrz DNA binding protein-DNA NMR Werner MH, Huth JR, Gronenborn AM, Clore GM (1995) "Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex." Cell(Cambridge,Mass.), 81, 704-705. doi: 10.1016/0092-8674(95)90532-4. The 3d structure of the human sry-DNA complex solved by multi-dimensional heteronuclear-edited and-filtered NMR. SNAP output
1hu0 hydrolase-DNA X-ray (2.35 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in base-excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Crystal structure of an hogg1-DNA borohydride trapped intermediate complex. SNAP output
1huo transferase-DNA X-ray (2.6 Å) Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK (2001) "Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes." Biochemistry, 40, 5368-5375. doi: 10.1021/bi002176j. Crystal structure of DNA polymerase beta complexed with DNA and cr-tmppcp. SNAP output
1hut hydrolase-hydrolase inhibitor-DNA X-ray (2.9 Å) Padmanabhan K, Padmanabhan KP, Ferrara JD, Sadler JE, Tulinsky A (1993) "The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer." J.Biol.Chem., 268, 17651-17654. The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. SNAP output
1huz transferase-DNA X-ray (2.6 Å) Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK (2001) "Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes." Biochemistry, 40, 5368-5375. doi: 10.1021/bi002176j. Crystal structure of DNA polymerase complexed with DNA and cr-pcp. SNAP output
1hvn viral protein-DNA NMR South TL, Summers MF (1993) "Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC." Protein Sci., 2, 3. Zinc-and sequence-dependent binding to nucleic acids by the n-terminal zinc finger domain of the hiv-1 nucleocapsid protein: NMR structure of the complex with the psi-site analog, d-acgcc. SNAP output
1hvo viral protein-DNA NMR South TL, Summers MF (1993) "Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC." Protein Sci., 2, 3. Zinc-and sequence-dependent binding to nucleic acids by the n-terminal zinc finger domain of the hiv-1 nucleocapsid protein: NMR structure of the complex with the psi-site analog, d-acgcc. SNAP output
1hw2 transcription-DNA X-ray (3.25 Å) Xu Y, Heath RJ, Li Z, Rock CO, White SW (2001) "The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli." J.Biol.Chem., 276, 17373-17379. doi: 10.1074/jbc.M100195200. Fadr-DNA complex: transcriptional control of fatty acid metabolism in echerichia coli. SNAP output
1hwt gene regulation-DNA X-ray (2.5 Å) King DA, Zhang L, Guarente L, Marmorstein R (1999) "Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein." Nat.Struct.Biol., 6, 64-71. doi: 10.1038/4940. Structure of a hap1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein. SNAP output
1hys transferase-DNA-RNA hybrid X-ray (3.0 Å) Sarafianos SG, Das K, Tantillo C, Clark Jr AD, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E (2001) "Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA." EMBO J., 20, 1449-1461. doi: 10.1093/emboj/20.6.1449. Crystal structure of hiv-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. SNAP output
1i3j hydrolase-DNA X-ray (2.2 Å) Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V (2001) "Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate." EMBO J., 20, 3631-3637. doi: 10.1093/emboj/20.14.3631. Crystal structure of the DNA-binding domain of intron endonuclease i-tevi with its substrate. SNAP output
1i3w DNA-antibiotic X-ray (1.7 Å) Robinson H, Gao YG, Yang X, Sanishvili R, Joachimiak A, Wang AH (2001) "Crystallographic Analysis of a Novel Complex of Actinomycin D Bound to the DNA Decamer Cgatcgatcg." Biochemistry, 40, 5587. doi: 10.1021/BI002859Z. Actinomycin d binding to cgatcgatcg. SNAP output
1i6h transcription-DNA-RNA hybrid X-ray (3.3 Å) Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD (2001) "Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution." Science, 292, 1876-1882. doi: 10.1126/science.1059495. RNA polymerase ii elongation complex. SNAP output
1i6j transferase-DNA X-ray (2.0 Å) Cote ML, Georgiadis MM (2001) "Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase." Acta Crystallogr.,Sect.D, 57, 1238-1250. doi: 10.1107/S090744490100943X. Crystal structure of a pseudo-16-mer DNA with stacked guanines and two g-a mispairs complexed with the n-terminal fragment of moloney murine leukemia virus reverse transcriptase. SNAP output
1i7d isomerase-DNA X-ray (2.05 Å) Changela A, DiGate RJ, Mondragon A (2001) "Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule." Nature, 411, 1077-1081. doi: 10.1038/35082615. Noncovalent complex of e.coli DNA topoisomerase iii with an 8-base single-stranded DNA oligonucleotide. SNAP output
1i8m immune system-DNA X-ray (2.1 Å) Tanner JJ, Komissarov AA, Deutscher SL (2001) "Crystal Structure of an Antigen-Binding Fragment Bound to Single-Stranded DNA." J.Mol.Biol., 314, 807-822. doi: 10.1006/jmbi.2001.5178. Crystal structure of a recombinant anti-single-stranded DNA antibody fragment complexed with dt5. SNAP output
1iaw hydrolase-DNA X-ray (2.4 Å) Huai Q, Colandene JD, Topal MD, Ke H (2001) "Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement." Nat.Struct.Biol., 8, 665-669. doi: 10.1038/90366. Crystal structure of naei complexed with 17mer DNA. SNAP output
1ic8 transcription-DNA X-ray (2.6 Å) Chi Y-I, Frantz JD, Oh B-C, Hansen L, Dhe-Paganon S, Shoelson SE (2002) "Diabetes mutations delineate an atypical POU domains in HNF1-Alpha." Mol.Cell, 10, 1129-1137. doi: 10.1016/S1097-2765(02)00704-9. Hepatocyte nuclear factor 1a bound to DNA : mody3 gene product. SNAP output
1id3 structural protein-DNA X-ray (3.1 Å) White CL, Suto RK, Luger K (2001) "Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions." EMBO J., 20, 5207-5218. doi: 10.1093/emboj/20.18.5207. Crystal structure of the yeast nucleosome core particle reveals fundamental differences in inter-nucleosome interactions. SNAP output
1if1 transcription-DNA X-ray (3.0 Å) Escalante CR, Yie J, Thanos D, Aggarwal AK (1998) "Structure of IRF-1 with bound DNA reveals determinants of interferon regulation." Nature, 391, 103-106. doi: 10.1038/34224. Interferon regulatory factor 1 (irf-1) complex with DNA. SNAP output
1ig4 transcription-DNA NMR Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, Shirakawa M (2001) "Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA." Cell(Cambridge,Mass.), 105, 487-497. doi: 10.1016/S0092-8674(01)00324-5. Solution structure of the methyl-cpg-binding domain of human mbd1 in complex with methylated DNA. SNAP output
1ig7 transcription-DNA X-ray (2.2 Å) Hovde S, Abate-Shen C, Geiger JH (2001) "Crystal structure of the Msx-1 homeodomain/DNA complex." Biochemistry, 40, 12013-12021. doi: 10.1021/bi0108148. Msx-1 homeodomain-DNA complex structure. SNAP output
1ig9 transferase-DNA X-ray (2.6 Å) Franklin MC, Wang J, Steitz TA (2001) "Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase." Cell(Cambridge,Mass.), 105, 657-667. doi: 10.1016/S0092-8674(01)00367-1. Structure of the replicating complex of a pol alpha family DNA polymerase. SNAP output
1ign DNA binding protein-DNA X-ray (2.25 Å) Konig P, Giraldo R, Chapman L, Rhodes D (1996) "The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA." Cell(Cambridge,Mass.), 85, 125-136. doi: 10.1016/S0092-8674(00)81088-0. DNA-binding domain of rap1 in complex with telomeric DNA site. SNAP output
1ihf transcription-DNA X-ray (2.5 Å) Rice PA, Yang S, Mizuuchi K, Nash HA (1996) "Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn." Cell(Cambridge,Mass.), 87, 1295-1306. doi: 10.1016/S0092-8674(00)81824-3. Integration host factor-DNA complex. SNAP output
1ijs virus-DNA X-ray (3.25 Å) Llamas-Saiz AL, Agbandje-McKenna M, Parker JS, Wahid AT, Parrish CR, Rossmann MG (1996) "Structural analysis of a mutation in canine parvovirus which controls antigenicity and host range." Virology, 225, 65-71. doi: 10.1006/viro.1996.0575. Cpv (strain d) mutant a300d, complex (viral coat-DNA), vp2, ph=7.5, t=4 degrees c. SNAP output
1ijw DNA binding protein-DNA X-ray (2.4 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations.. SNAP output
1imh transcription-DNA X-ray (2.86 Å) Stroud JC, Lopez-Rodriguez C, Rao A, Chen L (2002) "Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor." Nat.Struct.Biol., 9, 90-94. doi: 10.1038/nsb749. Tonebp-DNA complex. SNAP output
1io4 transcription-DNA X-ray (3.0 Å) Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2001) "Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta." Cell(Cambridge,Mass.), 104, 755-767. doi: 10.1016/S0092-8674(01)00271-9. Crystal structure of runx-1-aml1-cbfalpha runt domain-cbfbeta core domain heterodimer and c-ebpbeta bzip homodimer bound to a DNA fragment from the csf-1r promoter. SNAP output
1ipp transcription-DNA X-ray (2.2 Å) Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI." Nature, 394, 96-101. doi: 10.1038/27952. Homing endonuclease-DNA complex. SNAP output
1iu3 replication inhibitor-DNA X-ray (3.0 Å) Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S (2004) "Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein." Nucleic Acids Res., 32, 82-92. doi: 10.1093/nar/gkh173. Crystal structure of the e.coli seqa protein complexed with hemimethylated DNA. SNAP output
1iv6 DNA binding protein-DNA NMR Nishikawa T, Okamura H, Nagadoi A, Konig P, Rhodes D, Nishimura Y (2001) "Solution structure of a telomeric DNA complex of human TRF1." Structure, 9, 1237-1251. doi: 10.1016/S0969-2126(01)00688-8. Solution structure of the DNA complex of human trf1. SNAP output
1ixy transferase-DNA X-ray (2.5 Å) Lariviere L, Morera S (2002) "A Base-flipping Mechanism for the T4 Phage beta-Glucosyltransferase and Identification of a Transition-state Analog." J.Mol.Biol., 324, 483-490. doi: 10.1016/S0022-2836(02)01091-4. Ternary complex of t4 phage bgt with udp and a 13 mer DNA duplex. SNAP output
1j1v replication-DNA X-ray (2.1 Å) Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S (2003) "Structural basis of replication origin recognition by the DnaA protein." NUCLEIC ACIDS RES., 31, 2077-2086. doi: 10.1093/nar/gkg309. Crystal structure of dnaa domainiv complexed with dnaabox DNA. SNAP output
1j3e replication-DNA X-ray (2.5 Å) Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S (2004) "Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein." Nucleic Acids Res., 32, 82-92. doi: 10.1093/nar/gkh173. Crystal structure of the e.coli seqa protein complexed with n6-methyladenine- guanine mismatch DNA. SNAP output
1j46 transcription-DNA NMR Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM (2001) "Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation." J.Mol.Biol., 312, 481-499. doi: 10.1006/jmbi.2001.4977. 3d solution NMR structure of the wild type hmg-box domain of the human male sex determining factor sry complexed to DNA. SNAP output
1j47 transcription-DNA NMR Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM (2001) "Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation." J.Mol.Biol., 312, 481-499. doi: 10.1006/jmbi.2001.4977. 3d solution NMR structure of the m9i mutant of the hmg-box domain of the human male sex determining factor sry complexed to DNA. SNAP output
1j4w transcription-DNA NMR Braddock DT, Louis JM, Baber JL, Levens D, Clore GM (2002) "Structure and dynamics of KH domains from FBP bound to single-stranded DNA." Nature, 415, 1051-1056. doi: 10.1038/4151051a. Complex of the kh3 and kh4 domains of fbp with a single_stranded 29mer DNA oligonucleotide from the fuse element of the c-myc oncogene. SNAP output
1j59 gene regulation-DNA X-ray (2.5 Å) Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RE, Berman HM (1996) "Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface." J.Mol.Biol., 260, 395-408. doi: 10.1006/jmbi.1996.0409. Catabolite gene activator protein (cap)-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1j5k transcription-DNA NMR Braddock DT, Baber JL, Levens D, Clore GM (2002) "Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA." EMBO J., 21, 3476-3485. doi: 10.1093/emboj/cdf352. Complex of the kh3 domain of hnrnp k with a single_stranded 10mer DNA oligonucleotide. SNAP output
1j5n DNA binding protein-DNA NMR Masse JE, Wong B, Yen Y-M, Allain FH-T, Johnson RC, Feigon J (2002) "The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding." J.Mol.Biol., 323, 263-284. doi: 10.1016/S0022-2836(02)00938-5. Solution structure of the non-sequence-specific hmgb protein nhp6a in complex with sry DNA. SNAP output
1j5o transferase-immune system-DNA X-ray (3.5 Å) Sarafianos SG, Das K, Clark Jr AD, Ding J, Boyer PL, Hughes SH, Arnold E (1999) "Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids." Proc.Natl.Acad.Sci.USA, 96, 10027-10032. doi: 10.1073/pnas.96.18.10027. Crystal structure of met184ile mutant of hiv-1 reverse transcriptase in complex with double stranded DNA template-primer. SNAP output
1j75 immune system-DNA X-ray (1.85 Å) Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich A (2001) "Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins." Nat.Struct.Biol., 8, 761-765. doi: 10.1038/nsb0901-761. Crystal structure of the DNA-binding domain zalpha of dlm-1 bound to z-DNA. SNAP output
1j9n DNA binding protein-DNA NMR Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez C (2003) "Solution structure and stability of tryptophan-containing nucleopeptide duplexes." Chembiochem, 4, 40-49. doi: 10.1002/cbic.200390012. Solution structure of the nucleopeptide [ac-lys-trp-lys-hse(p3*dgcatcg)-ala]-[p5*dcgtagc]. SNAP output
1jb7 DNA-binding protein-DNA X-ray (1.86 Å) Horvath MP, Schultz SC (2001) "DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex." J.Mol.Biol., 310, 367-377. doi: 10.1006/jmbi.2001.4766. DNA g-quartets in a 1.86 Å resolution structure of an oxytricha nova telomeric protein-DNA complex. SNAP output
1je8 transcription-DNA X-ray (2.12 Å) Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE (2002) "Dimerization allows DNA target site recognition by the NarL response regulator." Nat.Struct.Biol., 9, 771-778. doi: 10.1038/nsb845. Two-component response regulator narl-DNA complex: DNA bending found in a high affinity site. SNAP output
1jey DNA binding protein-DNA X-ray (2.5 Å) Walker JR, Corpina RA, Goldberg J (2001) "Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair." Nature, 412, 607-614. doi: 10.1038/35088000. Crystal structure of the ku heterodimer bound to DNA. SNAP output
1jfi transcription-DNA X-ray (2.62 Å) Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley SK (2001) "Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex." Cell(Cambridge,Mass.), 106, 71-81. doi: 10.1016/S0092-8674(01)00417-2. Crystal structure of the nc2-tbp-DNA ternary complex. SNAP output
1jfs transcription-DNA X-ray (2.9 Å) Huffman JL, Lu F, Zalkin H, Brennan RG (2002) "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry, 41, 511-520. doi: 10.1021/bi0156660. Purine repressor mutant-hypoxanthine-purf operator complex. SNAP output
1jft transcription-DNA X-ray (2.5 Å) Huffman JL, Lu F, Zalkin H, Brennan RG (2002) "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry, 41, 511-520. doi: 10.1021/bi0156660. Purine repressor mutant-hypoxanthine-purf operator complex. SNAP output
1jgg transcription-DNA X-ray (2.0 Å) Hirsch JA, Aggarwal AK (1995) "Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity." EMBO J., 14, 6280-6291. Even-skipped homeodomain complexed to at-rich DNA. SNAP output
1jh9 transcription-DNA X-ray (2.55 Å) Huffman JL, Lu F, Zalkin H, Brennan RG (2002) "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry, 41, 511-520. doi: 10.1021/bi0156660. Purine repressor mutant-hypoxanthine-purf operator complex. SNAP output
1jj4 transcription-DNA X-ray (2.4 Å) Kim SS, Tam JK, Wang AF, Hegde RS (2000) "The structural basis of DNA target discrimination by papillomavirus E2 proteins." J.Biol.Chem., 275, 31245-31254. doi: 10.1074/jbc.M004541200. Human papillomavirus type 18 e2 DNA-binding domain bound to its DNA target. SNAP output
1jj6 DNA binding protein-DNA X-ray (2.3 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations.. SNAP output
1jj8 DNA binding protein-DNA X-ray (2.75 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jk1 transcription-DNA X-ray (1.9 Å) Miller JC, Pabo CO (2001) "Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition." J.Mol.Biol., 313, 309-315. doi: 10.1006/jmbi.2001.4975. Zif268 d20a mutant bound to wt DNA site. SNAP output
1jk2 transcription-DNA X-ray (1.65 Å) Miller JC, Pabo CO (2001) "Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition." J.Mol.Biol., 313, 309-315. doi: 10.1006/jmbi.2001.4975. Zif268 d20a mutant bound to the gct DNA site. SNAP output
1jko DNA binding protein-DNA X-ray (2.24 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jkp DNA binding protein-DNA X-ray (2.8 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jkq DNA binding protein-DNA X-ray (2.86 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jkr DNA binding protein-DNA X-ray (2.28 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jmc replication-DNA X-ray (2.4 Å) Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L (1997) "Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA." Nature, 385, 176-181. doi: 10.1038/385176a0. Single stranded DNA-binding domain of human replication protein a bound to single stranded DNA, rpa70 subunit, residues 183-420. SNAP output
1jnm transcription-DNA X-ray (2.2 Å) Kim Y, Podust LM "Crystal Structure of the Jun bZIP homodimer complexed with CRE." Crystal structure of the jun-cre complex. SNAP output
1jt0 transcription-DNA X-ray (2.9 Å) Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG (2002) "Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR." EMBO J., 21, 1210-1218. doi: 10.1093/emboj/21.5.1210. Crystal structure of a cooperative qacr-DNA complex. SNAP output
1jwl transcription-DNA X-ray (4.0 Å) Bell CE, Lewis M (2001) "Crystallographic analysis of Lac repressor bound to natural operator O1." J.Mol.Biol., 312, 921-926. doi: 10.1006/jmbi.2001.5024. Structure of the dimeric lac repressor-operator o1-onpf complex. SNAP output
1jx4 transferase-DNA X-ray (1.7 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2001) "Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication." Cell(Cambridge,Mass.), 107, 91-102. doi: 10.1016/S0092-8674(01)00515-3. Crystal structure of a y-family DNA polymerase in a ternary complex with DNA substrates and an incoming nucleotide. SNAP output
1jxl transferase-DNA X-ray (2.1 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2001) "Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication." Cell(Cambridge,Mass.), 107, 91-102. doi: 10.1016/S0092-8674(01)00515-3. Crystal structure of a y-family DNA polymerase in a ternary complex with DNA substrates and an incoming nucleotide. SNAP output
1k3w hydrolase-DNA X-ray (1.42 Å) Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G (2002) "Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate." EMBO J., 21, 789-800. doi: 10.1093/emboj/21.4.789. Crystal structure of a trapped reaction intermediate of the DNA repair enzyme endonuclease viii with DNA. SNAP output
1k3x hydrolase-DNA X-ray (1.25 Å) Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G (2002) "Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate." EMBO J., 21, 789-800. doi: 10.1093/emboj/21.4.789. Crystal structure of a trapped reaction intermediate of the DNA repair enzyme endonuclease viii with brominated-DNA. SNAP output
1k4s isomerase-DNA X-ray (3.2 Å) Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr AB, Stewart LJ (2002) "The mechanism of topoisomerase I poisoning by a camptothecin analog." Proc.Natl.Acad.Sci.USA, 99, 15387-15392. doi: 10.1073/pnas.242259599. Human DNA topoisomerase i in covalent complex with a 22 base pair DNA duplex. SNAP output
1k4t isomerase-DNA X-ray (2.1 Å) Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr AB, Stewart LJ (2002) "The mechanism of topoisomerase I poisoning by a camptothecin analog." Proc.Natl.Acad.Sci.USA, 99, 15387-15392. doi: 10.1073/pnas.242259599. Human DNA topoisomerase i (70 kda) in complex with the poison topotecan and covalent complex with a 22 base pair DNA duplex. SNAP output
1k61 transcription-DNA X-ray (2.1 Å) Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C (2002) "A Hoogsteen base pair embedded in undistorted B-DNA." NUCLEIC ACIDS RES., 30, 5244-5252. doi: 10.1093/nar/gkf661. Matalpha2 homeodomain bound to DNA. SNAP output
1k6o transcription-DNA X-ray (3.19 Å) Mo Y, Ho W, Johnston K, Marmorstein R (2001) "Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex." J.Mol.Biol., 314, 495-506. doi: 10.1006/jmbi.2001.5138. Crystal structure of a ternary sap-1-srf-c-fos sre DNA complex. SNAP output
1k78 transcription-DNA X-ray (2.25 Å) Garvie CW, Hagman J, Wolberger C (2001) "Structural studies of Ets-1/Pax5 complex formation on DNA." Mol.Cell, 8, 1267-1276. doi: 10.1016/S1097-2765(01)00410-5. Pax5(1-149)+ets-1(331-440)+DNA. SNAP output
1k79 transcription-DNA X-ray (2.4 Å) Garvie CW, Hagman J, Wolberger C (2001) "Structural studies of Ets-1/Pax5 complex formation on DNA." Mol.Cell, 8, 1267-1276. doi: 10.1016/S1097-2765(01)00410-5. Ets-1(331-440)+ggaa duplex. SNAP output
1k7a transcription-DNA X-ray (2.8 Å) Garvie CW, Hagman J, Wolberger C (2001) "Structural studies of Ets-1/Pax5 complex formation on DNA." Mol.Cell, 8, 1267-1276. doi: 10.1016/S1097-2765(01)00410-5. Ets-1(331-440)+ggag duplex. SNAP output
1k82 hydrolase-DNA X-ray (2.1 Å) Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G (2002) "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA." J.Biol.Chem., 277, 19811-19816. doi: 10.1074/jbc.M202058200. Crystal structure of e.coli formamidopyrimidine-DNA glycosylase (fpg) covalently trapped with DNA. SNAP output
1k8g DNA binding protein-DNA X-ray (2.6 Å) Classen S, Ruggles JA, Schultz SC (2001) "Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA." J.Mol.Biol., 314, 1113-1125. doi: 10.1006/jmbi.2000.5191. Crystal structure of the n-terminal domain of oxytricha nova telomere end binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA. SNAP output
1kb2 transcription-DNA X-ray (2.7 Å) Shaffer PL, Gewirth DT (2002) "Structural basis of VDR-DNA interactions on direct repeat response elements." EMBO J., 21, 2242-2252. doi: 10.1093/emboj/21.9.2242. Crystal structure of vdr DNA-binding domain bound to mouse osteopontin (spp) response element. SNAP output
1kb4 transcription-DNA X-ray (2.8 Å) Shaffer PL, Gewirth DT (2002) "Structural basis of VDR-DNA interactions on direct repeat response elements." EMBO J., 21, 2242-2252. doi: 10.1093/emboj/21.9.2242. Crystal structure of vdr DNA-binding domain bound to a canonical direct repeat with three base pair spacer (dr3) response element. SNAP output
1kb6 transcription-DNA X-ray (2.7 Å) Shaffer PL, Gewirth DT (2002) "Structural basis of VDR-DNA interactions on direct repeat response elements." EMBO J., 21, 2242-2252. doi: 10.1093/emboj/21.9.2242. Crystal structure of vdr DNA-binding domain bound to rat osteocalcin (oc) response element. SNAP output
1kbu hydrolase, ligase-DNA X-ray (2.2 Å) Martin SS, Pulido E, Chu VC, Lechner TS, Baldwin EP (2002) "The Order of Strand Exchanges in Cre-LoxP Recombination and its Basis Suggested by the Crystal Structure of a Cre-LoxP Holliday Junction Complex." J.Mol.Biol., 319, 107-127. doi: 10.1016/S0022-2836(02)00246-2. Cre recombinase bound to a loxp holliday junction. SNAP output
1kc6 hydrolase-DNA X-ray (2.6 Å) Horton NC, Dorner LF, Perona JJ (2002) "Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation." Nat.Struct.Biol., 9, 42-47. doi: 10.1038/nsb741. Hincii bound to cognate DNA. SNAP output
1kc8 ribosome X-ray (3.01 Å) Hansen J, Moore PB, Steitz TA (2003) "Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit." J.Mol.Biol., 330, 1061-1075. doi: 10.1016/S0022-2836(03)00668-5. Co-crystal structure of blasticidin s bound to the 50s ribosomal subunit. SNAP output
1kdh transferase-DNA X-ray (3.0 Å) Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C (2002) "Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase." EMBO J., 21, 427-439. doi: 10.1093/emboj/21.3.427. Binary complex of murine terminal deoxynucleotidyl transferase with a primer single stranded DNA. SNAP output
1keg immune system-DNA X-ray (2.4 Å) Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O (2012) "Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides." Acta Crystallogr.,Sect.D, 68, 232-238. doi: 10.1107/S0907444912000327. Antibody 64m-2 fab complexed with dtt(6-4)tt. SNAP output
1kfs transferase-DNA X-ray (2.1 Å) Brautigam CA, Steitz TA (1998) "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J.Mol.Biol., 277, 363-377. doi: 10.1006/jmbi.1997.1586. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1kfv hydrolase-DNA X-ray (2.55 Å) Serre L, Pereira de Jesus K, Boiteux S, Zelwer C, Castaing B (2002) "Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA." EMBO J., 21, 2854-2865. doi: 10.1093/emboj/cdf304. Crystal structure of lactococcus lactis formamido-pyrimidine DNA glycosylase (alias fpg or mutm) non covalently bound to an ap site containing DNA.. SNAP output
1kix DNA binding protein-DNA X-ray (2.7 Å) Peersen OB, Ruggles JA, Schultz SC (2002) "Dimeric structure of the Oxytricha nova telomere end-binding protein alpha-subunit bound to ssDNA." Nat.Struct.Biol., 9, 182-187. Dimeric structure of the o. nova telomere end binding protein alpha subunit with bound ssDNA. SNAP output
1kln transferase-DNA X-ray (3.2 Å) Beese LS, Derbyshire V, Steitz TA (1993) "Structure of DNA polymerase I Klenow fragment bound to duplex DNA." Science, 260, 352-355. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1kqq transcription-DNA NMR Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT (2002) "The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA." EMBO J., 21, 1197-1209. doi: 10.1093/emboj/21.5.1197. Solution structure of the dead ringer arid-DNA complex. SNAP output
1krp transferase-DNA X-ray (2.2 Å) Brautigam CA, Steitz TA (1998) "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J.Mol.Biol., 277, 363-377. doi: 10.1006/jmbi.1997.1586. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1ksp transferase-DNA X-ray (2.3 Å) Brautigam CA, Steitz TA (1998) "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J.Mol.Biol., 277, 363-377. doi: 10.1006/jmbi.1997.1586. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1ksx replication-DNA X-ray (3.2 Å) Enemark EJ, Stenlund A, Joshua-Tor L (2002) "Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex." EMBO J., 21, 1487-1496. doi: 10.1093/emboj/21.6.1487. Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. SNAP output
1ksy replication-DNA X-ray (3.05 Å) Enemark EJ, Stenlund A, Joshua-Tor L (2002) "Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex." EMBO J., 21, 1487-1496. doi: 10.1093/emboj/21.6.1487. Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. SNAP output
1ku7 transcription-DNA X-ray (2.4 Å) Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA (2002) "Structure of the bacterial RNA polymerase promoter specificity sigma subunit." Mol.Cell, 9, 527-539. doi: 10.1016/S1097-2765(02)00470-7. Crystal structure of thermus aquatics RNA polymerase sigmaa subunit region 4 bound to-35 element DNA. SNAP output
1kx3 structural protein-DNA X-ray (2.0 Å) Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution." J.Mol.Biol., 319, 1097-1113. doi: 10.1016/S0022-2836(02)00386-8. X-ray structure of the nucleosome core particle, ncp146, at 2.0 Å resolution. SNAP output
1kx4 structural protein-DNA X-ray (2.6 Å) Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution." J.Mol.Biol., 319, 1097-1113. doi: 10.1016/S0022-2836(02)00386-8. X-ray structure of the nucleosome core particle, ncp146b, at 2.6 Å resolution. SNAP output
1kx5 structural protein-DNA X-ray (1.94 Å) Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution." J.Mol.Biol., 319, 1097-1113. doi: 10.1016/S0022-2836(02)00386-8. X-ray structure of the nucleosome core particle, ncp147, at 1.9 Å resolution. SNAP output
1l1m transcription regulator-DNA NMR Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R, Boelens R, Kaptein R (2002) "Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain." EMBO J., 21, 2866-2876. doi: 10.1093/emboj/cdf318. Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o1. SNAP output
1l1t hydrolase-DNA X-ray (1.8 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg) bound to abasic-site containing DNA. SNAP output
1l1v DNA-antibiotic NMR Chou SH, Chin KH, Chen FM (2002) "Looped Out and Perpendicular: Deformation of Watson-Crick Base Pair Associated with Actinomycin D Binding." Proc.Natl.Acad.Sci.USA, 99, 6625. doi: 10.1073/PNAS.102580399. Unusual actd-dna_ta complex structure. SNAP output
1l1z hydrolase-DNA X-ray (1.7 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg) covalent-DNA intermediate. SNAP output
1l2b hydrolase-DNA X-ray (2.4 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg) DNA end-product structure. SNAP output
1l2c hydrolase-DNA X-ray (2.2 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg)-DNA estranged thymine mismatch recognition complex. SNAP output
1l2d hydrolase-DNA X-ray (2.0 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg)-DNA estranged guanine mismatch recognition complex. SNAP output
1l3l transcription-DNA X-ray (1.66 Å) Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, Molyneaux JM, Anderson JC, Bashkin JK, Winans SC, Joachimiak A (2002) "Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA." Nature, 417, 971-974. doi: 10.1038/nature00833. Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. SNAP output
1l3s transferase-DNA X-ray (1.7 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment complexed to 9 base pairs of duplex DNA.. SNAP output
1l3t transferase-DNA X-ray (1.7 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 10 base pairs of duplex DNA following addition of a single dttp residue. SNAP output
1l3u transferase-DNA X-ray (1.8 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 11 base pairs of duplex DNA following addition of a dttp and a datp residue.. SNAP output
1l3v transferase-DNA X-ray (1.71 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 15 base pairs of duplex DNA following addition of dttp, datp, dctp, and dgtp residues.. SNAP output
1l5u transferase-DNA X-ray (1.95 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 12 base pairs of duplex DNA following addition of a dttp, a datp, and a dctp residue.. SNAP output
1lat transcription-DNA X-ray (1.9 Å) Gewirth DT, Sigler PB (1995) "The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex." Nat.Struct.Biol., 2, 386-394. doi: 10.1038/nsb0595-386. Glucocorticoid receptor mutant-DNA complex. SNAP output
1lau hydrolase-DNA X-ray (1.8 Å) Savva R, McAuley-Hecht K, Brown T, Pearl L (1995) "The structural basis of specific base-excision repair by uracil-DNA glycosylase." Nature, 373, 487-493. doi: 10.1038/373487a0. Uracil-DNA glycosylase. SNAP output
1lb2 gene regulation-DNA X-ray (3.1 Å) Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH (2002) "Structural basis of transcription activation: the CAP-alpha CTD-DNA complex." Science, 297, 1562-1566. doi: 10.1126/science.1076376. Structure of the e. coli alpha c-terminal domain of RNA polymerase in complex with cap and DNA. SNAP output
1lcc gene regulation-DNA NMR Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH, Boelens R, Kaptein R (1993) "Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics." J.Mol.Biol., 234, 446-462. doi: 10.1006/jmbi.1993.1598. Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. SNAP output
1lcd gene regulation-DNA NMR Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH, Boelens R, Kaptein R (1993) "Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics." J.Mol.Biol., 234, 446-462. doi: 10.1006/jmbi.1993.1598. Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. SNAP output
1le5 transcription-DNA X-ray (2.75 Å) Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh G (2002) "The X-ray crystal structure of the NF-kB p50/p65 heterodimer bound to the Interferon beta-kB site." J.Biol.Chem., 277, 24694-24700. doi: 10.1074/jbc.M200006200. Crystal structure of a nf-kb heterodimer bound to an ifnb-kb. SNAP output
1le8 transcription-DNA X-ray (2.3 Å) Ke A, Mathias JR, Vershon AK, Wolberger C (2002) "Structural and Thermodynamic Characterization of the DNA Binding Properties of a Triple Alanine Mutant of MATalpha2." Structure, 10, 961-971. doi: 10.1016/S0969-2126(02)00790-6. Crystal structure of the mata1-matalpha2-3a heterodimer bound to DNA complex. SNAP output
1le9 transcription-DNA X-ray (3.0 Å) Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh G (2002) "The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site." J.Biol.Chem., 277, 24694-24700. doi: 10.1074/jbc.M200006200. Crystal structure of a nf-kb heterodimer bound to the ig-hiv-kb siti. SNAP output
1lei transcription-DNA X-ray (2.7 Å) Chen-Park FE, Huang DB, Noro B, Thanos D, Ghosh G (2002) "The kB DNA sequence from the HIV Long Terminal Repeat functions as an allosteric regulator of HIV transcription." J.Biol.Chem., 277, 24701-24708. doi: 10.1074/jbc.M200007200. The kb DNA sequence from the hlv-ltr functions as an allosteric regulator of hiv transcription. SNAP output
1lfu transcription NMR Sprules T, Green N, Featherstone M, Gehring K (2003) "Lock and Key Binding of the HOX YPWM Peptide to the PBX Homeodomain." J.Biol.Chem., 278, 1053-1058. doi: 10.1074/jbc.M207504200. NMR solution structure of the extended pbx homeodomain bound to DNA. SNAP output
1lli transcription-DNA X-ray (2.1 Å) Lim WA, Hodel A, Sauer RT, Richards FM (1994) "The crystal structure of a mutant protein with altered but improved hydrophobic core packing." Proc.Natl.Acad.Sci.USA, 91, 423-427. doi: 10.1073/pnas.91.1.423. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. SNAP output
1llm transcription-DNA X-ray (1.5 Å) Wolfe SA, Grant RA, Pabo CO (2003) "Structure of a designed dimeric zinc finger protein bound to DNA." Biochemistry, 42, 13401-13409. doi: 10.1021/bi034830b. Crystal structure of a zif23-gcn4 chimera bound to DNA. SNAP output
1lmb transcription-DNA X-ray (1.8 Å) Beamer LJ, Pabo CO (1992) "Refined 1.8 A crystal structure of the lambda repressor-operator complex." J.Mol.Biol., 227, 177-196. doi: 10.1016/0022-2836(92)90690-L. Refined 1.8 angstrom crystal structure of the lambda repressor-operator complex. SNAP output
1lo1 hormone-growth factor receptor-DNA NMR Gearhart MD, Holmbeck SMA, Evans RM, Dyson HJ, Wright PE (2003) "Monomeric Complex of Human Orphan Estrogen Related Receptor-2 with DNA: A Pseudo-dimer Interface Mediates Extended Half-site Recognition." J.Mol.Biol., 327, 819-832. doi: 10.1016/S0022-2836(03)00183-9. Estrogen related receptor 2 DNA binding domain in complex with DNA. SNAP output
1lpq isomerase-DNA X-ray (3.14 Å) Lesher DT, Pommier Y, Stewart L, Redinbo MR (2002) "8-Oxoguanine rearranges the active site of human topoisomerase I." Proc.Natl.Acad.Sci.USA, 99, 12102-12107. doi: 10.1073/pnas.192282699. Human DNA topoisomerase i (70 kda) in non-covalent complex with a 22 base pair DNA duplex containing an 8-oxog lesion. SNAP output
1lq1 transcription-DNA X-ray (2.3 Å) Zhao H, Msadek T, Zapf J, Madhusudan, Hoch JA, Varughese KI (2002) "DNA complexed structure of the key transcription factor initiating development in sporulating bacteria." Structure, 10, 1041-1050. doi: 10.1016/S0969-2126(02)00803-1. DNA complexed structure of the key transcription factor initiating development in sporulation bacteria. SNAP output
1lrr replication inhibitor-DNA X-ray (2.65 Å) Guarne A, Zhao Q, Guirlando R, Yang W (2002) "Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex." NAT.STRUCT.BIOL., 9, 839-843. Crystal structure of e. coli seqa complexed with hemimethylated DNA. SNAP output
1lv5 transferase-DNA X-ray (1.95 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of the closed conformation of bacillus DNA polymerase i fragment bound to DNA and dctp. SNAP output
1lws hydrolase-DNA X-ray (3.5 Å) Moure CM, Gimble FS, Quiocho FA (2002) "Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence." Nat.Struct.Biol., 9, 764-770. doi: 10.1038/nsb840. Crystal structure of the intein homing endonuclease pi-scei bound to its recognition sequence. SNAP output
1lwt hydrolase-DNA X-ray (3.2 Å) Moure CM, Gimble FS, Quiocho FA (2002) "Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence." Nat.Struct.Biol., 9, 764-770. doi: 10.1038/nsb840. Crystal structure of the intein homing endonuclease pi-scei bound to its substrate DNA (ca2+ free). SNAP output
1lwv hydrolase-DNA X-ray (2.3 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in Base Excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Borohydride-trapped hogg1 intermediate structure co-crystallized with 8-aminoguanine. SNAP output
1lww hydrolase-DNA X-ray (2.1 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in Base Excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Borohydride-trapped hogg1 intermediate structure co-crystallized with 8-bromoguanine. SNAP output
1lwy hydrolase-DNA X-ray (2.01 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in Base Excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Hogg1 borohydride-trapped intermediate without 8-oxoguanine. SNAP output
1m07 hydrolase-DNA X-ray (1.8 Å) Leu Y-J, Chern S-S, Wang S-C, Hsiao Y-Y, Amiraslanov I, Liaw Y-C, Liao Y-D (2003) "Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography." J.Biol.Chem., 278, 7300-7309. doi: 10.1074/jbc.M206701200. Residues involved in the catalysis and base specificity of cytotoxic ribonuclease from bullfrog (rana catesbeiana). SNAP output
1m0e transferase-DNA X-ray (2.5 Å) Zhou L, Cheng X, Connolly BA, Dickman MJ, Hurd PJ, Hornby DP (2002) "ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASES." J.MOL.BIOL., 321, 591-599. doi: 10.1016/S0022-2836(02)00676-9. Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferase. SNAP output
1m18 structural protein-DNA X-ray (2.45 Å) Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K (2003) "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands." J.Mol.Biol., 326, 371-380. doi: 10.1016/S0022-2836(02)01407-9. Ligand binding alters the structure and dynamics of nucleosomal DNA. SNAP output
1m19 structural protein-DNA X-ray (2.3 Å) Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K (2003) "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands." J.Mol.Biol., 326, 371-380. doi: 10.1016/S0022-2836(02)01407-9. Ligand binding alters the structure and dynamics of nucleosomal DNA. SNAP output
1m1a structural protein-DNA X-ray (2.65 Å) Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K (2003) "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands." J.MOL.BIOL., 326, 371-380. doi: 10.1016/S0022-2836(02)01407-9. Ligand binding alters the structure and dynamics of nucleosomal DNA. SNAP output
1m3h hydrolase-DNA X-ray (2.05 Å) Chung SJ, Verdine GL (2004) "Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase." Chem.Biol., 11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014. Crystal structure of hogg1 d268e mutant with product oligonucleotide. SNAP output
1m3q hydrolase-DNA X-ray (1.9 Å) Chung SJ, Verdine GL (2004) "Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase." Chem.Biol., 11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014. Crystal structure of hogg1 d268e mutant with base-excised DNA and 8-aminoguanine. SNAP output
1m5r transferase-DNA X-ray (1.8 Å) Lariviere L, Morera S (2002) "A Base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition state analog." J.Mol.Biol., 324, 483-489. doi: 10.1016/S0022-2836(02)01091-4. Ternary complex of t4 phage bgt with udp and a 13 mer DNA duplex. SNAP output
1m5x hydrolase-DNA X-ray (2.25 Å) Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL (2003) "Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI." J.Mol.Biol., 329, 253-269. doi: 10.1016/S0022-2836(03)00447-9. Crystal structure of the homing endonuclease i-msoi bound to its DNA substrate. SNAP output
1m6x ligase, lyase-DNA X-ray (2.8 Å) Conway AB, Chen Y, Rice PA (2003) "Structural Plasticity of the Flp-Holliday Junction Complex." J.Mol.Biol., 326, 425-434. doi: 10.1016/S0022-2836(02)01370-0. Flpe-holliday junction complex. SNAP output
1ma7 hydrolase, ligase-DNA X-ray (2.3 Å) Martin SS, Chu VC, Baldwin EP (2003) "Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination." Biochemistry, 42, 6814-6826. doi: 10.1021/bi0272306. Crystal structure of cre site-specific recombinase complexed with a mutant DNA substrate, loxp-a8-t27. SNAP output
1mdm transcription-DNA X-ray (2.8 Å) Garvie CW, Pufall MA, Graves BJ, Wolberger C (2002) "STRUCTURAL ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN PROTEIN PARTNERSHIPS." J.Biol.Chem., 277, 45529-45536. doi: 10.1074/jbc.M206327200. Inhibited fragment of ets-1 and paired domain of pax5 bound to DNA. SNAP output
1mdy transcription-DNA X-ray (2.8 Å) Ma PC, Rould MA, Weintraub H, Pabo CO (1994) "Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation." Cell(Cambridge,Mass.), 77, 451-459. doi: 10.1016/0092-8674(94)90159-7. Crystal structure of myod bhlh domain bound to DNA: perspectives on DNA recognition and implications for transcriptional activation. SNAP output
1mey transferase-DNA X-ray (2.2 Å) Kim CA, Berg JM (1996) "A 2.2 A Resolution Crystal Structure of a Designed Zinc Finger Protein Bound to DNA." Nat.Struct.Biol., 3, 940-945. doi: 10.1038/nsb1196-940. Crystal structure of a designed zinc finger protein bound to DNA. SNAP output
1mhd complex (transcription activator-DNA) X-ray (2.8 Å) Shi Y, Wang YF, Jayaraman L, Yang H, Massague J, Pavletich NP (1998) "Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling." Cell(Cambridge,Mass.), 94, 585-594. doi: 10.1016/S0092-8674(00)81600-1. Crystal structure of a smad mh1 domain bound to DNA. SNAP output
1mht transferase-DNA X-ray (2.6 Å) Klimasauskas S, Kumar S, Roberts RJ, Cheng X (1994) "HhaI methyltransferase flips its target base out of the DNA helix." Cell(Cambridge,Mass.), 76, 357-369. doi: 10.1016/0092-8674(94)90342-5. Covalent ternary structure of hhai methyltransferase, DNA and s-adenosyl-l-homocysteine. SNAP output
1mj1 ribosome cryo-EM (13.0 Å) Stark H, Rodnina MV, Wieden H-J, Zemlin F, Wintermeyer W, van Heel M (2002) "Ribosome Interactions of Aminoacyl-tRNA and Elongation Factor TU in the Codon Recognition Complex." Nat.Struct.Biol., 9, 849-854. Fitting the ternary complex of ef-tu-trna-gtp and ribosomal proteins into a 13 a cryo-EM map of the coli 70s ribosome. SNAP output
1mj2 transcription-DNA X-ray (2.4 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine repressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to a consensus operator sequence. SNAP output
1mje gene regulation-antitumor protein-DNA X-ray (3.5 Å) Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thoma NH, Zheng N, Chen PL, Lee WH, Pavletich NP (2002) "BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure." Science, 297, 1837-1848. doi: 10.1126/science.297.5588.1837. Structure of a brca2-dss1-ssDNA complex. SNAP output
1mjm transcription-DNA X-ray (2.2 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine aporepressor mutant (q44k) complexed to half of the consensus operator sequence. SNAP output
1mjo transcription-DNA X-ray (2.1 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine holorepressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to the minimal met consensus operator with the central ta step mutated to at. SNAP output
1mjp transcription-DNA X-ray (3.4 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine aporepressor mutant (q44k) complexed to the minimal met consensus operator. SNAP output
1mjq transcription-DNA X-ray (2.4 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine repressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to an altered met consensus operator sequence. SNAP output
1mm8 transcription-DNA X-ray (2.8 Å) Steiniger-White M, Bhasin A, Lovell S, Rayment I, Reznikoff WS (2002) "Evidence for "unseen" Transposase--DNA contacts." J.Mol.Biol., 322, 971-982. doi: 10.1016/S0022-2836(02)00877-X. Crystal structure of tn5 transposase complexed with me DNA. SNAP output
1mnm transcription-DNA X-ray (2.25 Å) Tan S, Richmond TJ (1998) "Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex." Nature, 391, 660-666. doi: 10.1038/35563. Yeast matalpha2-mcm1-DNA ternary transcription complex crystal structure. SNAP output
1mnn transcription-DNA X-ray (1.4 Å) Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN (2002) "Structure of the sporulation-specific transcription factor Ndt80 bound to DNA." Embo J., 21, 5721-5732. doi: 10.1093/emboj/cdf572. Structure of the sporulation specific transcription factor ndt80 bound to DNA. SNAP output
1mnv DNA-antibiotic X-ray (2.6 Å) Hou M-H, Robinson H, Gao Y-G, Wang AH-J (2002) "Crystal Structure of Actinomycin D Bound to the Ctg Triplet Repeat Sequences Linked to Neurological Diseases." Nucleic Acids Res., 30, 4910. doi: 10.1093/NAR/GKF619. Actinomycin d binding to atgctgcat. SNAP output
1mow hydrolase-DNA X-ray (2.4 Å) Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat Jr RJ, Stoddard BL (2002) "Design, Activity and Structure of a Highly Specific Artificial Endonuclease." Mol.Cell, 10, 895-905. doi: 10.1016/S1097-2765(02)00690-1. E-drei. SNAP output
1mq2 transferase-DNA X-ray (3.1 Å) Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH (2003) "Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals Structural Insights into its Coding Potential." Structure, 11, 121-127. doi: 10.1016/S0969-2126(02)00930-9. Human DNA polymerase beta complexed with gapped DNA containing an 8-oxo-7,8-dihydro-guanine and damp. SNAP output
1mq3 transferase-DNA X-ray (2.8 Å) Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH (2003) "Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals Structural Insights into its Coding Potential." Structure, 11, 121-127. doi: 10.1016/S0969-2126(02)00930-9. Human DNA polymerase beta complexed with gapped DNA containing an 8-oxo-7,8-dihydro-guanine template paired with dctp. SNAP output
1mse DNA binding protein-DNA NMR Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y (1994) "Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices." Cell(Cambridge,Mass.), 79, 639-648. doi: 10.1016/0092-8674(94)90549-5. Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices. SNAP output
1msf DNA binding protein-DNA NMR Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y (1994) "Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices." Cell(Cambridge,Mass.), 79, 639-648. doi: 10.1016/0092-8674(94)90549-5. Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices. SNAP output
1msw transcription-DNA-RNA X-ray (2.1 Å) Yin YW, Steitz TA (2002) "Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase." Science, 298, 1387-1395. doi: 10.1126/science.1077464. Structural basis for the transition from initiation to elongation transcription in t7 RNA polymerase. SNAP output
1mtl hydrolase-DNA X-ray (2.8 Å) Barrett TE, Savva R, Barlow T, Brown T, Jiricny J, Pearl LH (1998) "Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct." Nat.Struct.Biol., 5, 697-701. doi: 10.1038/1394. Non-productive mug-DNA complex. SNAP output
1muh transcription-DNA X-ray (2.3 Å) Davies DR, Goryshin IY, Reznikoff WS, Rayment I (2000) "Three-dimensional structure of the Tn5 synaptic complex transposition intermediate." Science, 289, 77-85. doi: 10.1126/science.289.5476.77. Crystal structure of tn5 transposase complexed with transposon end DNA. SNAP output
1mus transcription-DNA X-ray (1.9 Å) Steiniger-White M, Rayment I, Reznikoff WS (2004) "Structure/function insights into Tn5 transposition." Curr.Opin.Struct.Biol., 14, 50-57. doi: 10.1016/j.sbi.2004.01.008. Crystal structure of tn5 transposase complexed with resolved outside end DNA. SNAP output
1mvm virus-DNA X-ray (3.5 Å) Llamas-Saiz AL, Agbandje-McKenna M, Wikoff WR, Bratton J, Tattersall P, Rossmann MG (1997) "Structure determination of minute virus of mice." Acta Crystallogr.,Sect.D, 53, 93-102. doi: 10.1107/S0907444996010566. Mvm(strain i), complex(viral coat-DNA), vp2, ph=7.5, t=4 degrees c. SNAP output
1mw8 isomerase X-ray (1.9 Å) Perry K, Mondragon A (2003) "Structure of a Complex between E. coli DNA Topoisomerase I and Single-Stranded DNA." Structure, 11, 1349-1358. doi: 10.1016/j.str.2003.09.013. Crystal structure of a complex between h365r mutant of 67 kda n-terminal fragment of e. coli DNA topoisomerase i and 5'-acttcgggatg-3'. SNAP output
1mwi hydrolase-DNA X-ray (2.35 Å) Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, Jiricny J, Pearl LH (1998) "Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions." Cell(Cambridge,Mass.), 92, 117-129. doi: 10.1016/S0092-8674(00)80904-6. Crystal structure of a mug-DNA product complex. SNAP output
1mwj hydrolase-DNA X-ray (2.85 Å) Barrett TE, Scharer O, Savva R, Brown T, Jiricny J, Verdine GL, Pearl LH (1999) "Crystal Structure of a thwarted mismatch glycosylase DNA repair complex." Embo J., 18, 6599-6609. doi: 10.1093/emboj/18.23.6599. Crystal structure of a mug-DNA pseudo substrate complex. SNAP output
1n39 hydrolase, lyase-DNA X-ray (2.2 Å) Norman DP, Chung SJ, Verdine GL (2003) "Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase." Biochemistry, 42, 1564-1572. doi: 10.1021/bi026823d. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. SNAP output
1n3a hydrolase, lyase-DNA X-ray (2.2 Å) Norman DP, Chung SJ, Verdine GL (2003) "Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase." Biochemistry, 42, 1564-1572. doi: 10.1021/bi026823d. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. SNAP output
1n3c hydrolase, lyase-DNA X-ray (2.7 Å) Norman DP, Chung SJ, Verdine GL (2003) "Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase." Biochemistry, 42, 1564-1572. doi: 10.1021/bi026823d. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. SNAP output
1n3e hydrolase-DNA X-ray (2.5 Å) Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL (2003) "Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI." J.Mol.Biol., 329, 253-269. doi: 10.1016/S0022-2836(03)00447-9. Crystal structure of i-crei bound to a palindromic DNA sequence i (palindrome of left side of wildtype DNA target sequence). SNAP output
1n3f hydrolase-DNA X-ray (2.0 Å) Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL (2003) "Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI." J.Mol.Biol., 329, 253-269. doi: 10.1016/S0022-2836(03)00447-9. Crystal structure of i-crei bound to a palindromic DNA sequence ii (palindrome of right side of wildtype DNA target sequence). SNAP output
1n48 transferase-DNA X-ray (2.2 Å) Ling H, Boudsocq F, Woodgate R, Yang W "A Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate." Y-family DNA polymerase dpo4 in complex with DNA containing abasic lesion. SNAP output
1n56 transferase-DNA X-ray (2.4 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/s1097-2765(04)00101-7. Y-family DNA polymerase dpo4 in complex with DNA containing abasic lesion. SNAP output
1n5y transferase-immune system-DNA X-ray (3.1 Å) Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E (2002) "Structure of HIV-1 Reverse Transcriptase with Pre-Translocation and Post-Translocation AZTMP-Terminated DNA." Embo J., 21, 6614-6624. doi: 10.1093/emboj/cdf637. Hiv-1 reverse transcriptase crosslinked to post-translocation aztmp-terminated DNA (complex p). SNAP output
1n6j transcription-DNA X-ray (2.2 Å) Han A, Pan F, Stroud JC, Youn HD, Liu JO, Chen L (2003) "Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2." Nature, 422, 730-734. doi: 10.1038/nature01555. Structural basis of sequence-specific recruitment of histone deacetylases by myocyte enhancer factor-2. SNAP output
1n6q transferase-immune system-DNA X-ray (3.0 Å) Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft JJ, Ilankumaran I, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E (2002) "Structures of HIV-1 Reverse Transcriptase with Pre- and Post-translocation AZTMP-terminated DNA." Embo J., 21, 6614-6624. doi: 10.1093/emboj/cdf637. Hiv-1 reverse transcriptase crosslinked to pre-translocation aztmp-terminated DNA (complex n). SNAP output
1nfk transcription-DNA X-ray (2.3 Å) Ghosh G, van Duyne G, Ghosh S, Sigler PB (1995) "Structure of NF-kappa B p50 homodimer bound to a kappa B site." Nature, 373, 303-310. doi: 10.1038/373303a0. Structure of the nuclear factor kappa-b (nf-kb) p50 homodimer. SNAP output
1ng9 DNA binding protein X-ray (2.6 Å) Lamers MH, Winterwerp HHK, Sixma TK (2003) "The alternating ATPase domains of MutS control DNA mismatch repair." Embo J., 22, 746-756. doi: 10.1093/emboj/cdg064. E.coli muts r697a: an atpase-asymmetry mutant. SNAP output
1ngm transcription-DNA X-ray (2.95 Å) Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler PB (2003) "Crystal structure of a transcription factor IIIB core interface ternary complex." Nature, 422, 534-539. doi: 10.1038/nature01534. Crystal structure of a yeast brf1-tbp-DNA ternary complex. SNAP output
1nh2 transcription-DNA X-ray (1.9 Å) Bleichenbacher M, Tan S, Richmond TJ (2003) "Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes." J.Mol.Biol., 332, 783-793. doi: 10.1016/S0022-2836(03)00887-8. Crystal structure of a yeast tfiia-tbp-DNA complex. SNAP output
1nh3 isomerase-DNA X-ray (3.1 Å) Chrencik JE, Burgin AB, Pommier Y, Stewart L, Redinbo MR (2003) "Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex." J.Biol.Chem., 278, 12461-12466. doi: 10.1074/jbc.M212930200. Human topoisomerase i ara-c complex. SNAP output
1njw transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Guanine-thymine mismatch at the polymerase active site. SNAP output
1njx transferase-DNA X-ray (1.65 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Thymine-guanine mismatch at the polymerase active site. SNAP output
1njy transferase-DNA X-ray (2.0 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Thymine-thymine mismatch at the polymerase active site. SNAP output
1njz transferase-DNA X-ray (2.0 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Cytosine-thymine mismatch at the polymerase active site. SNAP output
1nk0 transferase-DNA X-ray (1.7 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Adenine-guanine mismatch at the polymerase active site. SNAP output
1nk2 DNA binding protein-DNA NMR Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA (1997) "Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity." Biochemistry, 36, 5372-5380. doi: 10.1021/bi9620060. Vnd-nk-2 homeodomain-DNA complex, NMR, 20 structures. SNAP output
1nk3 DNA binding protein-DNA NMR Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA (1997) "Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity." Biochemistry, 36, 5372-5380. doi: 10.1021/bi9620060. Vnd-nk-2 homeodomain-DNA complex, NMR, minimized average structure. SNAP output
1nk4 transferase-DNA X-ray (1.6 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Guanine-guanine mismatch at the polymerase active site. SNAP output
1nk5 transferase-DNA X-ray (2.1 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Adenine-adenine mismatch at the polymerase active site. SNAP output
1nk6 transferase-DNA X-ray (2.1 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Cytosine-cytosine mismatch at the polymerase active site. SNAP output
1nk7 transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Guanine-adenine mismatch at the polymerase active site. SNAP output
1nk8 transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after a single round of primer extension, following incorporation of dctp.. SNAP output
1nk9 transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after two rounds of primer extension, following incorporation of dctp and dgtp.. SNAP output
1nkb transferase-DNA X-ray (2.0 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after three rounds of primer extension, following incorporation of dctp, dgtp, and dttp.. SNAP output
1nkc transferase-DNA X-ray (1.8 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after five rounds of primer extension, following incorporation of dctp, dgtp, dttp, and datp.. SNAP output
1nke transferase-DNA X-ray (1.8 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a cytosine-thymine mismatch after a single round of primer extension, following incorporation of dctp.. SNAP output
1nkp transcription-DNA X-ray (1.8 Å) Nair SK, Burley SK (2003) "X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors." Cell(Cambridge,Mass.), 112, 193-205. doi: 10.1016/S0092-8674(02)01284-9. Crystal structure of myc-max recognizing DNA. SNAP output
1nlw transcription-DNA X-ray (2.0 Å) Nair SK, Burley SK (2003) "X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors." Cell(Cambridge,Mass.), 112, 193-205. doi: 10.1016/S0092-8674(02)01284-9. Crystal structure of mad-max recognizing DNA. SNAP output
1nne DNA binding protein-DNA X-ray (3.11 Å) Alani E, Lee JY, Schofield MJ, Kijas AW, Hsieh P, Yang W (2003) "Crystal structure and biochemical analysis of the MutS-ADP-Beryllium Fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair." J.Biol.Chem., 278, 16088-16094. doi: 10.1074/jbc.M213193200. Crystal structure of the muts-adpbef3-DNA complex. SNAP output
1nnj hydrolase X-ray (1.9 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Crystal structure complex between the lactococcus lactis fpg and an abasic site containing DNA. SNAP output
1nop hydrolase-DNA X-ray (2.3 Å) Davies DR, Interthal H, Champoux JJ, Hol WGJ (2003) "Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide." Chem.Biol., 10, 139-147. doi: 10.1016/S1074-5521(03)00021-8. Crystal structure of human tyrosyl-DNA phosphodiesterase (tdp1) in complex with vanadate, DNA and a human topoisomerase i-derived peptide. SNAP output
1noy transferase-DNA X-ray (2.2 Å) Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA (1996) "Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions." Biochemistry, 35, 8110-8119. doi: 10.1021/bi960178r. DNA polymerase (e.c.2.7.7.7)-DNA complex. SNAP output
1nvp transcription-DNA X-ray (2.1 Å) Bleichenbacher M, Tan S, Richmond TJ (2003) "Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes." J.Mol.Biol., 332, 783-793. doi: 10.1016/S0022-2836(03)00887-8. Human tfiia-tbp-DNA complex. SNAP output
1nwq transcription-DNA X-ray (2.8 Å) Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson PF (2003) "Structural Basis for DNA Recognition by the Basic Region Leucine Zipper Transcription Factor CCAAT/enhancer Binding Protein Alpha." J.Biol.Chem., 278, 15178-15184. doi: 10.1074/jbc.M300417200. Crystal structure of c-ebpalpha-DNA complex. SNAP output
1nzb replication-DNA X-ray (3.1 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of wild type cre recombinase-loxp synapse. SNAP output
1o3q gene regulation-DNA X-ray (3.0 Å) Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking." J.Mol.Biol., 314, 63-74. doi: 10.1006/jmbi.2001.5089. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o3r gene regulation-DNA X-ray (3.0 Å) Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking." J.Mol.Biol., 314, 63-74. doi: 10.1006/jmbi.2001.5089. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o3s gene regulation-DNA X-ray (3.0 Å) Chen S, Gunasekera A, Zhang X, Kunkel TA, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking." J.Mol.Biol., 314, 75-82. doi: 10.1006/jmbi.2001.5090. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o3t gene regulation-DNA X-ray (2.8 Å) Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking." J.Mol.Biol., 314, 63-74. doi: 10.1006/jmbi.2001.5089. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o4x transcription-DNA NMR Williams DC, Cai M, Clore GM (2004) "Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex." J.Biol.Chem., 279, 1449-1457. doi: 10.1074/jbc.M309790200. Ternary complex of the DNA binding domains of the oct1 and sox2 transcription factors with a 19mer oligonucleotide from the hoxb1 regulatory element. SNAP output
1oct transcription-DNA X-ray (3.0 Å) Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO (1994) "Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules." Cell(Cambridge,Mass.), 77, 21-32. doi: 10.1016/0092-8674(94)90231-3. Crystal structure of the oct-1 pou domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. SNAP output
1odg hydrolase X-ray (2.8 Å) Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH (2003) "Crystal Structure of the Escherichia Coli Dcm Very-Short-Patch DNA Repair Endonuclease Bound to its Reaction Product-Site in a DNA Superhelix." Nucleic Acids Res., 31, 1633. doi: 10.1093/NAR/GKG273. Very-short-patch DNA repair endonuclease bound to its reaction product site. SNAP output
1odh transcription factor-DNA X-ray (2.85 Å) Cohen SX, Moulin M, Hashemolhosseini S, Kilian K, Wegner M, Muller CW (2003) "Crystal Structure of the Gcm Domain-DNA Complex: A DNA-Binding Domain with a Novel Fold and Mode of Target Site Recognition." Embo J., 22, 1835. doi: 10.1093/EMBOJ/CDG182. Structure of the gcm domain bound to DNA. SNAP output
1oe4 hydrolase-DNA X-ray (2.0 Å) Wibley JEA, Waters TR, Haushalter K, Verdine GL, Pearl LH (2003) "Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1." Mol.Cell, 11, 1647. doi: 10.1016/S1097-2765(03)00235-1. Xenopus smug1, an anti-mutator uracil-DNA glycosylase. SNAP output
1oe5 hydrolase-DNA X-ray (2.3 Å) Wibley JEA, Waters TR, Haushalter K, Verdine GL, Pearl LH (2003) "Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1." Mol.Cell, 11, 1647. doi: 10.1016/S1097-2765(03)00235-1. Xenopus smug1, an anti-mutator uracil-DNA glycosylase. SNAP output
1oe6 hydrolase-DNA X-ray (2.65 Å) Wibley JEA, Waters TR, Haushalter K, Verdine GL, Pearl LH (2003) "Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1." Mol.Cell, 11, 1647. doi: 10.1016/S1097-2765(03)00235-1. Xenopus smug1, an anti-mutator uracil-DNA glycosylase. SNAP output
1oh5 DNA binding X-ray (2.9 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with a c:a mismatch. SNAP output
1oh6 DNA binding X-ray (2.4 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with an a:a mismatch. SNAP output
1oh7 DNA binding X-ray (2.5 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with a g:g mismatch. SNAP output
1oh8 DNA binding X-ray (2.9 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with an unpaired thymidine. SNAP output
1oj8 hydrolase X-ray (1.7 Å) Tsai C-J, Liu J-H, Liao Y-D, Chen L-Y, Cheng P-T, Sun Y-J "Retro and Novel Binding Modes in Cytotoxic Ribonucleases from Rana Catesbeiana of Two Crystal Structures Complexed with (2',5'Cpg) and D(Apcpgpa)." Novel and retro binding modes in cytotoxic ribonucleases from rana catesbeiana of two crystal structures complexed with d(apcpgpa) and (2',5'cpg). SNAP output
1omh transferase-DNA X-ray (1.95 Å) Guasch A, Lucas M, Moncalian G, Cabezas M, Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M (2003) "Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC." Nat.Struct.Biol., 10, 1002-1010. doi: 10.1038/nsb1017. Conjugative relaxase trwc in complex with orit DNA. metal-free structure.. SNAP output
1orn hydrolase-DNA X-ray (1.7 Å) Fromme JC, Verdine GL (2003) "Structure of a Trapped Endonuclease III-DNA Covalent Intermediate." Embo J., 22, 3461-3471. doi: 10.1093/emboj/cdg311. Structure of a trapped endonuclease iii-DNA covalent intermediate: estranged-guanine complex. SNAP output
1orp hydrolase-DNA X-ray (2.2 Å) Fromme JC, Verdine GL (2003) "Structure of a Trapped Endonuclease III-DNA Covalent Intermediate." Embo J., 22, 3461-3471. doi: 10.1093/emboj/cdg311. Structure of a trapped endonuclease iii-DNA covalent intermediate: estranged-adenine complex. SNAP output
1osb transferase-DNA X-ray (2.65 Å) Guasch A, Lucas M, Moncalian G, Cabezas M, Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M (2003) "Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC." Nat.Struct.Biol., 10, 1002-1010. doi: 10.1038/nsb1017. Conjugative relaxase trwc in complex with orit DNA. metal-free structure.. SNAP output
1osl transcription-DNA NMR Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R (2004) "Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes." Science, 305, 386-389. doi: 10.1126/science.1097064. Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence. SNAP output
1otc protein-DNA X-ray (2.8 Å) Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA, Schultz SC (1998) "Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA." Cell(Cambridge,Mass.), 95, 963-974. doi: 10.1016/S0092-8674(00)81720-1. The o. nova telomere end binding protein complexed with single strand DNA. SNAP output
1oup hydrolase-DNA X-ray (2.3 Å) Li C-L, Hor L-I, Chang Z-F, Tsai L-C, Yang W-Z, Yuan HS (2003) "DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site." Embo J., 22, 4014-4025. doi: 10.1093/emboj/cdg377. Crystal structure of the periplasmic endonuclease vvn complexed with octamer double stranded DNA. SNAP output
1ouq replication-DNA X-ray (3.2 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of wild-type cre recombinase-loxp synapse. SNAP output
1ouz transcription-DNA X-ray (2.41 Å) Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA (2003) "Integration Host Factor: putting a twist on protein-DNA recognition." J.Mol.Biol., 330, 493-502. doi: 10.1016/S0022-2836(03)00529-1. Crystal structure of a mutant ihf (betae44a) complexed with a variant h' site (t44a). SNAP output
1ovf DNA-antibiotic NMR Chin K-H, Chen F-M, Chou S-H (2003) "Solution Structure of the Actd-5'-Ccgtt(3)Gtgg-3' Complex: Drug Interaction with Tandem G.T Mismatches and Hairpin Loop Backbone." Nucleic Acids Res., 31, 2622. doi: 10.1093/NAR/GKG353. NMR structure of actd-5'-ccgttttgtgg-3' complex. SNAP output
1owf transcription-DNA X-ray (1.95 Å) Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA (2003) "Integration Host Factor: putting a twist on protein-DNA recognition." J.Mol.Biol., 330, 493-502. doi: 10.1016/S0022-2836(03)00529-1. Crystal structure of a mutant ihf (betae44a) complexed with the native h' site. SNAP output
1owg transcription-DNA X-ray (2.1 Å) Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA (2003) "Integration Host Factor: putting a twist on protein-DNA recognition." J.Mol.Biol., 330, 493-502. doi: 10.1016/S0022-2836(03)00529-1. Crystal structure of wt ihf complexed with an altered h' site (t44a). SNAP output
1owr transcription-DNA X-ray (3.0 Å) Stroud JC, Chen L (2003) "Structure of NFAT Bound to DNA as a Monomer." J.Mol.Biol., 334, 1009-1022. doi: 10.1016/j.jmb.2003.09.065. Crystal structure of human nfat1 bound monomerically to DNA. SNAP output
1ozj transcription-DNA X-ray (2.4 Å) Chai J, Wu J-W, Yan N, Massague J, Pavletich NP, Shi Y (2003) "Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding." J.Biol.Chem., 278, 20327-20331. doi: 10.1074/jbc.C300134200. Crystal structure of smad3-mh1 bound to DNA at 2.4 Å resolution. SNAP output
1p34 structural protein-DNA X-ray (2.7 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3a structural protein-DNA X-ray (3.0 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3b structural protein-DNA X-ray (3.0 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3f structural protein-DNA X-ray (2.9 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3g structural protein-DNA X-ray (2.7 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3i structural protein-DNA X-ray (2.3 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3k structural protein-DNA X-ray (2.9 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3l structural protein-DNA X-ray (2.4 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3m structural protein-DNA X-ray (2.9 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3o structural protein-DNA X-ray (2.75 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3p structural protein-DNA X-ray (2.7 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p47 transcription-DNA X-ray (2.2 Å) Peisach E, Pabo CO (2003) "Constraints for Zinc Finger Linker Design as Inferred from X-ray Crystal Structure of Tandem Zif268-DNA Complexes." J.Mol.Biol., 330, 1-7. doi: 10.1016/S0022-2836(03)00572-2. Crystal structure of tandem zif268 molecules complexed to DNA. SNAP output
1p4e DNA binding protein-recombination-DNA X-ray (2.7 Å) Rice PA, Chen Y (2003) "The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis." J.Biol.Chem., 278, 24800-24807. doi: 10.1074/jbc.M300853200. Flpe w330f mutant-DNA holliday junction complex. SNAP output
1p51 DNA binding protein-DNA X-ray (2.5 Å) Swinger KK, Lemberg KM, Zhang Y, Rice PA (2003) "Flexible DNA bending in HU-DNA cocrystal structures." Embo J., 22, 3749-3760. doi: 10.1093/emboj/cdg351. Anabaena hu-DNA cocrystal structure (ahu6). SNAP output
1p59 hydrolase-DNA X-ray (2.5 Å) Fromme JC, Verdine GL (2003) "Structure of a Trapped Endonuclease III-DNA Covalent Intermediate." Embo J., 22, 3461-3471. doi: 10.1093/emboj/cdg311. Structure of a non-covalent endonuclease iii-DNA complex. SNAP output
1p5w virus-DNA X-ray (3.3 Å) Govindasamy L, Hueffer K, Parrish CR, Agbandje-McKenna M (2003) "Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants." J.Virol., 77, 12211-12221. doi: 10.1128/JVI.77.22.12211-12221.2003. The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants. SNAP output
1p71 DNA binding protein-DNA X-ray (1.9 Å) Swinger KS, Lemberg KM, Zhang Y, Rice PA (2003) "Flexible DNA bending in HU-DNA cocrystal structures." Embo J., 22, 3749-3760. doi: 10.1093/emboj/cdg351. Anabaena hu-DNA corcrystal structure (tr3). SNAP output
1p78 DNA binding protein-DNA X-ray (2.25 Å) Swinger KS, Lemberg KM, Zhang Y, Rice PA (2003) "Flexible DNA bending in HU-DNA cocrystal structures." Embo J., 22, 3749-3760. doi: 10.1093/emboj/cdg351. Anabaena hu-DNA cocrystal structure (ahu2). SNAP output
1p7d DNA binding protein-DNA X-ray (2.95 Å) Aihara H, Kwon HJ, Nunes-Duby SE, Landy A, Ellenberger T (2003) "A Conformational Switch Controls the DNA Cleavage Activity of Lambda Integrase." Mol.Cell, 12, 187-198. doi: 10.1016/S1097-2765(03)00268-5. Crystal structure of the lambda integrase (residues 75-356) bound to DNA. SNAP output
1p7h transcription-DNA X-ray (2.6 Å) Giffin MJ, Stroud JC, Bates DL, von Koenig KD, Hardin J, Chen L (2003) "Structure of NFAT1 bound as a dimer to the HIV-1 LTR kappa B element." Nat.Struct.Biol., 10, 800-806. doi: 10.1038/nsb981. Structure of nfat1 bound as a dimer to the hiv-1 ltr kb element. SNAP output
1p8k hydrolase-DNA X-ray (2.6 Å) Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL (2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor." Genes Dev., 17, 2875-2888. doi: 10.1101/gad.1109003. The structure and DNA recognition of a bifunctional homing endonuclease and group i intron splicing factor. SNAP output
1pa6 DNA binding protein-DNA X-ray (2.45 Å) Theobald DL, Schultz SC (2003) "Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgagg. SNAP output
1par transcription-DNA X-ray (2.6 Å) Raumann BE, Rould MA, Pabo CO, Sauer RT (1994) "DNA recognition by beta-sheets in the Arc repressor-operator crystal structure." Nature, 367, 754-757. doi: 10.1038/367754a0. DNA recognition by beta-sheets in the arc repressor-operator crystal structure. SNAP output
1pdn gene regulation-DNA X-ray (2.5 Å) Xu W, Rould MA, Jun S, Desplan C, Pabo CO (1995) "Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations." Cell(Cambridge,Mass.), 80, 639-650. doi: 10.1016/0092-8674(95)90518-9. Crystal structure of a paired domain-DNA complex at 2.5 angstroms resolution reveals structural basis for pax developmental mutations. SNAP output
1per transcription-DNA X-ray (2.5 Å) Rodgers DW, Harrison SC (1993) "The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites." Structure, 1, 227-240. doi: 10.1016/0969-2126(93)90012-6. The complex between phage 434 repression DNA-binding domain and operator site or3: structural differences between consensus and non-consensus half-sites. SNAP output
1pfe DNA-antibiotic X-ray (1.1 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. Echinomycin-(gcgtacgc)2 complex. SNAP output
1pfi virus fiber diffraction Liu DJ, Day LA (1994) "Pf1 virus structure: helical coat protein and DNA with paraxial phosphates." Science, 265, 671-674. Pf1 virus structure: helical coat protein and DNA with paraxial phosphates. SNAP output
1pgz DNA binding protein-DNA X-ray (2.6 Å) Myers JC, Moore SA, Shamoo Y (2003) "Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures." J.Biol.Chem., 278, 42300-42306. doi: 10.1074/jbc.M306147200. Crystal structure of up1 complexed with d(ttagggttag(6-mi)g); a human telomeric repeat containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6-mi). SNAP output
1ph1 DNA binding protein-DNA X-ray (2.51 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttggggt. SNAP output
1ph2 DNA binding protein-DNA X-ray (3.1 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttg. SNAP output
1ph3 DNA binding protein-DNA X-ray (2.3 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttggtg. SNAP output
1ph4 DNA binding protein-DNA X-ray (2.3 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttggcg. SNAP output
1ph5 DNA binding protein-DNA X-ray (2.3 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttg(3dr)gg. SNAP output
1ph6 DNA binding protein-DNA X-ray (2.1 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgtgg. SNAP output
1ph7 DNA binding protein-DNA X-ray (2.9 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgigg. SNAP output
1ph8 DNA binding protein-DNA X-ray (2.36 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgcgg. SNAP output
1ph9 DNA binding protein-DNA X-ray (2.5 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgagg. SNAP output
1phj DNA binding protein-DNA X-ray (2.5 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA gg(3dr)gttttgggg. SNAP output
1pji hydrolase-DNA X-ray (1.9 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Crystal structure of wild type lactococcus lactis fpg complexed to a 1,3 propanediol containing DNA. SNAP output
1pjj hydrolase-DNA X-ray (1.9 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Complex between the lactococcus lactis fpg and an abasic site containing DNA.. SNAP output
1pm5 hydrolase-DNA X-ray (1.95 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Crystal structure of wild type lactococcus lactis fpg complexed to a tetrahydrofuran containing DNA. SNAP output
1pnr transcription-DNA X-ray (2.7 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Purine repressor-hypoxanthine-purf-operator complex. SNAP output
1po6 RNA binding protein-DNA X-ray (2.1 Å) Myers JC, Moore SA, Shamoo Y (2003) "Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures." J.BIOL.CHEM., 278, 42300-42306. doi: 10.1074/jbc.M306147200. Crystal structure of up1 complexed with d(tagg(6mi)ttaggg): a human telomeric repeat containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6mi). SNAP output
1pp7 transcription-DNA X-ray (2.45 Å) Schumacher MA, Lau AOT, Johnson PJ (2003) "Structural Basis of Core Promoter Recognition in a Primitive Eukaryote." Cell(Cambridge,Mass.), 115, 413-424. doi: 10.1016/S0092-8674(03)00887-0. Crystal structure of the t. vaginalis initiator binding protein bound to the ferredoxin inr. SNAP output
1pp8 transcription-DNA X-ray (3.05 Å) Schumacher MA, Lau AOT, Johnson PJ (2003) "Structural Basis of Core Promoter Recognition in a Primitive Eukaryote." Cell(Cambridge,Mass.), 115, 413-424. doi: 10.1016/S0092-8674(03)00887-0. Crystal structure of the t. vaginalis ibp39 initiator binding domain (ibd) bound to the alpha-scs inr element. SNAP output
1pt3 hydrolase-DNA X-ray (2.5 Å) Hsia KC, Chak KF, Liang PH, Cheng YS, Ku WY, Yuan HS (2004) "DNA binding and degradation by the HNH protein ColE7." STRUCTURE, 12, 205-214. doi: 10.1016/S0969-2126(04)00006-1. Crystal structures of nuclease-cole7 complexed with octamer DNA. SNAP output
1pue transcription-DNA X-ray (2.1 Å) Kodandapani R, Pio F, Ni CZ, Piccialli G, Klemsz M, McKercher S, Maki RA, Ely KR (1996) "A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex." Nature, 380, 456-460. doi: 10.1038/380456a0. Pu.1 ets domain-DNA complex. SNAP output
1puf transcription-DNA X-ray (1.9 Å) LARONDE-LEBLANC NA, Wolberger C (2003) "STRUCTURE OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA RECOGNITION ANTERIOR TO POSTERIOR." Genes Dev., 17, 2060-2072. doi: 10.1101/gad.1103303. Crystal structure of hoxa9 and pbx1 homeodomains bound to DNA. SNAP output
1pv4 transcription-DNA X-ray (3.0 Å) Skordalakes E, Berger JM (2003) "Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading." Cell(Cambridge,Mass.), 114, 135-146. doi: 10.1016/S0092-8674(03)00512-9. X-ray crystal structure of the rho transcription termination factor in complex with single stranded DNA. SNAP output
1pvi hydrolase-DNA X-ray (2.6 Å) Cheng X, Balendiran K, Schildkraut I, Anderson JE (1994) "Structure of PvuII endonuclease with cognate DNA." EMBO J., 13, 3927-3935. Structure of pvuii endonuclease with cognate DNA. SNAP output
1pvp recombination-DNA X-ray (2.35 Å) Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H, Schultz PG, Santoro SW (2003) "A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water." Chem.Biol., 10, 1085-1094. doi: 10.1016/j.chembiol.2003.10.015. Basis for a switch in substrate specificity: crystal structure of selected variant of cre site-specific recombinase, alshg bound to the engineered recognition site loxm7. SNAP output
1pvq recombination-DNA X-ray (2.75 Å) Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H, Schultz PG, Santoro SW (2003) "A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water." Chem.Biol., 10, 1085-1094. doi: 10.1016/j.chembiol.2003.10.015. Basis for a switch in substrate specificity: crystal structure of selected variant of cre site-specific recombinase, lnsgg bound to the engineered recognition site loxm7. SNAP output
1pvr recombination-DNA X-ray (2.65 Å) Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H, Schultz PG, Santoro SW (2003) "A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water." Chem.Biol., 10, 1085-1094. doi: 10.1016/j.chembiol.2003.10.015. Basis for a switch in substrate specificity: crystal structure of selected variant of cre site-specific recombinase, lnsgg bound to the loxp (wildtype) recognition site. SNAP output
1pyi transcription-DNA X-ray (3.2 Å) Marmorstein R, Harrison SC (1994) "Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster." Genes Dev., 8, 2504-2512. Crystal structure of a ppr1-DNA complex: DNA recognition by proteins containing a zn2cys6 binuclear cluster. SNAP output
1pzu transcription-DNA X-ray (3.1 Å) Jin L, Sliz P, Chen L, Macian F, Rao A, Hogan PG, Harrison SC (2003) "An asymmetric NFAT1 dimer on a pseudo-palindromic KB-like DNA site." Nat.Struct.Biol., 10, 807-811. doi: 10.1038/nsb975. An asymmetric nfat1-rhr homodimer on a pseudo-palindromic, kappa-b site. SNAP output
1q0t transferase-DNA X-ray (3.1 Å) Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X, Schlagman SL, Kossykh V, Hattman S, Cheng X (2003) "Structure of the bacteriophage T4 DNA adenine methyltransferase." Nat.Struct.Biol., 10, 849-855. doi: 10.1038/nsb973. Ternary structure of t4dam with adohcy and DNA. SNAP output
1q3f hydrolase-DNA X-ray (1.9 Å) Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT (2003) "Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase." Biochemistry, 42, 12455-12460. doi: 10.1021/bi035372+. Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA. SNAP output
1q3u replication-DNA X-ray (2.9 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of a wild-type cre recombinase-loxp synapse: pre-cleavage complex. SNAP output
1q3v replication-DNA X-ray (2.91 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of a wild-type cre recombinase-loxp synapse: phosphotyrosine covalent intermediate. SNAP output
1q9x transferase,replication-DNA X-ray (2.69 Å) Freisinger E, Grollman AP, Miller H, Kisker C (2004) "Lesion (in)tolerance reveals insights into DNA replication fidelity." Embo J., 23, 1494-1505. doi: 10.1038/sj.emboj.7600158. Crystal structure of enterobacteria phage rb69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA. SNAP output
1q9y transferase, replication-DNA X-ray (2.8 Å) Freisinger E, Grollman AP, Miller H, Kisker C (2004) "Lesion (in)tolerance reveals insights into DNA replication fidelity." Embo J., 23, 1494-1505. doi: 10.1038/sj.emboj.7600158. Crystal structure of enterobacteria phage rb69 gp43 DNA polymerase complexed with 8-oxoguanosine containing DNA. SNAP output
1qai transferase-DNA X-ray (2.3 Å) Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM (2000) "Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain." J.Mol.Biol., 296, 613-622. doi: 10.1006/jmbi.1999.3477. Crystal structures of the n-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. SNAP output
1qaj transferase-DNA X-ray (2.3 Å) Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM (2000) "Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain." J.Mol.Biol., 296, 613-632. doi: 10.1006/jmbi.1999.3477. Crystal structures of the n-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. SNAP output
1qbj hydrolase-DNA X-ray (2.1 Å) Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A (1999) "Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA." Science, 284, 1841-1845. doi: 10.1126/science.284.5421.1841. Crystal structure of the zalpha z-DNA complex. SNAP output
1qln nucleotidyltransferase X-ray (2.4 Å) Cheetham GMT, Steitz TA (1999) "Structure of a Transcribing T7 RNA Polymerase Initiation Complex." Science, 286, 2305. doi: 10.1126/SCIENCE.286.5448.2305. Structure of a transcribing t7 RNA polymerase initiation complex. SNAP output
1qn3 tata box-binding protein (tbp) X-ray (1.95 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the c(-25) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn4 tata box-binding protein (tbp) X-ray (1.86 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-24) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn5 tata box-binding protein (tbp) X-ray (1.93 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the g(-26) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn6 tata box-binding protein (tbp) X-ray (2.1 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-26) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn7 tata box-binding protein (tbp) X-ray (2.3 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-27) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn8 tata box-binding protein (tbp) X-ray (2.1 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-28) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn9 tata box-binding protein (tbp) X-ray (1.9 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the c(-29) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qna tata box-binding protein (tbp) X-ray (1.8 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-30) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qnb tata box-binding protein (tbp) X-ray (2.23 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-25) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qnc tata box-binding protein (tbp) X-ray (2.3 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the a(-31) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qne tata box-binding protein (tbp) X-ray (1.9 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the adenovirus major late promoter tata box bound to wild-type tbp (arabidopsis thaliana tbp isoform 2).. SNAP output
1qp0 transcription-DNA X-ray (2.9 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor-hypoxanthine-palindromic operator complex. SNAP output
1qp4 transcription-DNA X-ray (3.0 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor-hypoxanthine-palindromic operator complex. SNAP output
1qp7 transcription-DNA X-ray (2.9 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1qp9 transcription-DNA X-ray (2.8 Å) Lukens AK, King DA, Marmorstein R (2000) "Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation." Nucleic Acids Res., 28, 3853-3863. doi: 10.1093/nar/28.20.3853. Structure of hap1-pc7 complexed to the uas of cyc7. SNAP output
1qpi transcription-DNA X-ray (2.5 Å) Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W (2000) "Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system." Nat.Struct.Biol., 7, 215-219. doi: 10.1038/73324. Crystal structure of tetracycline repressor-operator complex. SNAP output
1qps hydrolase-DNA X-ray (2.5 Å) Horvath MM, Choi J, Kim Y, Wilkosz P, Rosenberg JM "The Integration of Recognition and Cleavage: X-Ray Structures of Pre- Transition State and Post-Reactive DNA-Eco RI Endonuclease Complexes." The crystal structure of a post-reactive cognate DNA-eco ri complex at 2.50 a in the presence of mn2+ ion. SNAP output
1qpz transcription-DNA X-ray (2.5 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor-hypoxanthine-palindromic operator complex. SNAP output
1qqa gene regulation-DNA X-ray (3.0 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1qqb gene regulation-DNA X-ray (2.7 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1qrh hydrolase-DNA X-ray (2.5 Å) Choi J, Kim Y, Greene P, Hager P, Rosenberg JM "X-Ray Structure of the DNA-Eco RI Endonuclease Complexes with the ED144 and RK145 Mutations." X-ray structure of the DNA-eco ri endonuclease complexes with an r145k mutation at 2.7 a. SNAP output
1qri hydrolase-DNA X-ray (2.6 Å) Choi J, Kim Y, Greene P, Hager P, Rosenberg JM "X-Ray Structure of the DNA-Eco RI Endonuclease Complexes with the ED144 and RK145 Mutations." X-ray structure of the DNA-eco ri endonuclease complexes with an e144d mutation at 2.7 a. SNAP output
1qrv gene regulation-DNA X-ray (2.2 Å) Murphy IV FV, Sweet RM, Churchill ME (1999) "The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition." EMBO J., 18, 6610-6618. doi: 10.1093/emboj/18.23.6610. Crystal structure of the complex of hmg-d and DNA. SNAP output
1qsl transferase-DNA X-ray (2.2 Å) Brautigam CA, Aschheim K, Steitz TA (1999) "Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment." Chem.Biol., 6, 901-908. doi: 10.1016/S1074-5521(00)80009-5. Klenow fragment complexed with single-stranded substrate and europium (iii) ion. SNAP output
1qss transferase-DNA X-ray (2.3 Å) Li Y, Mitaxov V, Waksman G (1999) "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation." Proc.Natl.Acad.Sci.USA, 96, 9491-9496. doi: 10.1073/pnas.96.17.9491. Ddgtp-trapped closed ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
1qsy transferase-DNA X-ray (2.3 Å) Li Y, Mitaxov V, Waksman G (1999) "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation." Proc.Natl.Acad.Sci.USA, 96, 9491-9496. doi: 10.1073/pnas.96.17.9491. Ddatp-trapped closed ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
1qtm transferase-DNA X-ray (2.3 Å) Li Y, Mitaxov V, Waksman G (1999) "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation." Proc.Natl.Acad.Sci.USA, 96, 9491-9496. doi: 10.1073/pnas.96.17.9491. Ddttp-trapped closed ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
1qum hydrolase-DNA X-ray (1.55 Å) Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA (1999) "Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis." Cell(Cambridge,Mass.), 98, 397-408. doi: 10.1016/S0092-8674(00)81968-6. Crystal structure of escherichia coli endonuclease iv in complex with damaged DNA. SNAP output
1qx0 transferase-DNA X-ray (2.26 Å) Guasch A, Lucas M, Moncalian G, Cabezas M, Prez-Luque R, Gomis-Rth FX, de la Cruz F, Coll M (2003) "RECOGNITION AND PROCESSING OF THE ORIGIN OF TRANSFER DNA BY CONJUGATIVE RELAXASE TRWC." Nat.Struct.Biol., 10, 1002-1010. doi: 10.1038/nsb1017. Conjugative relaxase trwc in complex with orit DNA. metal-bound structure. SNAP output
1qzg DNA binding protein-DNA X-ray (1.9 Å) Lei M, Podell ER, Baumann P, Cech TR (2003) "DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA." Nature, 426, 198-203. doi: 10.1038/nature02092. Crystal structure of pot1 (protection of telomere)- ssDNA complex. SNAP output
1qzh DNA binding protein-DNA X-ray (2.4 Å) Lei M, Podell ER, Baumann P, Cech TR (2003) "DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA." Nature, 426, 198-203. doi: 10.1038/nature02092. Crystal structure of pot1 (protection of telomere)- ssDNA complex. SNAP output
1r0a transferase-immune system-DNA X-ray (2.8 Å) Peletskaya EN, Kogon AA, Tuske S, Arnold E, Hughes SH (2004) "Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA." J.Virol., 78, 3387-3397. doi: 10.1128/JVI.78.7.3387-3397.2004. Crystal structure of hiv-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms. SNAP output
1r0n transcription-DNA X-ray (2.6 Å) Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad F (2003) "Structure of the heterodimeric Ecdysone Receptor DNA-binding complex." Embo J., 22, 5827-5840. doi: 10.1093/emboj/cdg569. Crystal structure of heterodimeric ecdsyone receptor DNA binding complex. SNAP output
1r0o transcription-DNA X-ray (2.24 Å) Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad F (2003) "Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex." Embo J., 22, 5827-5840. doi: 10.1093/emboj/cdg569. Crystal structure of the heterodimeric ecdysone receptor DNA-binding complex. SNAP output
1r2y hydrolase-DNA X-ray (2.34 Å) Fromme JC, Verdine GL (2003) "DNA Lesion Recognition by the Bacterial Repair Enzyme MutM." J.Biol.Chem., 278, 51543-51548. doi: 10.1074/jbc.M307768200. Mutm (fpg) bound to 8-oxoguanine (oxog) containing DNA. SNAP output
1r2z hydrolase-DNA X-ray (1.63 Å) Fromme JC, Verdine GL (2003) "DNA Lesion Recognition by the Bacterial Repair Enzyme MutM." J.Biol.Chem., 278, 51543-51548. doi: 10.1074/jbc.M307768200. Mutm (fpg) bound to 5,6-dihydrouracil (dhu) containing DNA. SNAP output
1r49 isomerase-DNA X-ray (3.13 Å) Interthal H, Quigley PM, Hol WG, Champoux JJ (2004) "The role of lysine 532 in the catalytic mechanism of human topoisomerase I." J.Biol.Chem., 279, 2984-2992. doi: 10.1074/jbc.M309959200. Human topoisomerase i (topo70) double mutant k532r-y723f. SNAP output
1r4i transcription-DNA X-ray (3.1 Å) Shaffer PL, Jivan A, Dollins DE, Claessens F, Gewirth DT (2004) "Structural basis of androgen receptor binding to selective androgen response elements." Proc.Natl.Acad.Sci.USA, 101, 4758-4763. doi: 10.1073/pnas.0401123101. Crystal structure of androgen receptor DNA-binding domain bound to a direct repeat response element. SNAP output
1r4o transcription-DNA X-ray (2.5 Å) Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) "Crystallographic Analysis of the Interaction of The Glucocorticoid Receptor with DNA." Nature, 352, 497-505. doi: 10.1038/352497a0. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. SNAP output
1r4r transcription-DNA X-ray (3.0 Å) Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) "Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA." Nature, 352, 497-505. doi: 10.1038/352497a0. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. SNAP output
1r71 transcription-DNA X-ray (2.2 Å) Khare D, Ziegelin G, Lanka E, Heinemann U (2004) "Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB." Nat.Struct.Mol.Biol., 11, 656-663. doi: 10.1038/nsmb773. Crystal structure of the DNA binding domain of korb in complex with the operator DNA. SNAP output
1r7m hydrolase-DNA X-ray (2.25 Å) Moure CM, Gimble FS, Quiocho FA (2003) "The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity." J.Mol.Biol., 334, 685-695. doi: 10.1016/j.jmb.2003.09.068. The homing endonuclease i-scei bound to its DNA recognition region. SNAP output
1r8d transcription-DNA X-ray (2.7 Å) Newberry KJ, Brennan RG (2004) "The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus." J.Biol.Chem., 279, 20356-20362. doi: 10.1074/jbc.M400960200. Crystal structure of mtan bound to DNA. SNAP output
1r8e transcription-DNA X-ray (2.4 Å) Newberry KJ, Brennan RG (2004) "The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus." J.Biol.Chem., 279, 20356-20362. doi: 10.1074/jbc.M400960200. Crystal structure of bmrr bound to DNA at 2.4a resolution. SNAP output
1r9s transcription-DNA-RNA hybrid X-ray (4.25 Å) Westover KD, Bushnell DA, Kornberg RD (2004) "Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center." Cell(Cambridge,Mass.), 119, 481-489. doi: 10.1016/j.cell.2004.10.016. RNA polymerase ii strand separated elongation complex, matched nucleotide. SNAP output
1r9t transcription-DNA-RNA hybrid X-ray (3.5 Å) Westover KD, Bushnell DA, Kornberg RD (2004) "Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center." Cell(Cambridge,Mass.), 119, 481-489. doi: 10.1016/j.cell.2004.10.016. RNA polymerase ii strand separated elongation complex, mismatched nucleotide. SNAP output
1ram transcription-DNA X-ray (2.7 Å) Chen YQ, Ghosh S, Ghosh G (1998) "A novel DNA recognition mode by the NF-kappa B p65 homodimer." Nat.Struct.Biol., 5, 67-73. doi: 10.1038/nsb0198-67. A novel DNA recognition mode by nf-kb p65 homodimer. SNAP output
1rb8 virus-DNA X-ray (3.5 Å) Bernal RA, Hafenstein S, Esmeralda R, Fane BA, Rossmann MG (2004) "The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells." J.Mol.Biol., 337, 1109-1122. doi: 10.1016/j.jmb.2004.02.033. The phix174 DNA binding protein j in two different capsid environments.. SNAP output
1rbj hydrolase-DNA X-ray (2.7 Å) Ko TP, Williams R, McPherson A (1996) "Structure of a ribonuclease B+d(pA)4 complex." Acta Crystallogr.,Sect.D, 52, 160-164. doi: 10.1107/S0907444995009127. Ribonuclease b complex with d(tetra-(deoxy-adenylate)). SNAP output
1rc8 transferase-DNA X-ray (2.75 Å) Eastberg JH, Pelletier J, Stoddard BL (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212. T4 polynucleotide kinase bound to 5'-gtcac-3' ssDNA. SNAP output
1rcn hydrolase-DNA X-ray (2.32 Å) Fontecilla-Camps JC, de Llorens R, le Du MH, Cuchillo CM (1994) "Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition." J.Biol.Chem., 269, 21526-21531. Crystal structure of the ribonuclease a d(aptpapapg) complex : direct evidence for extended substrate recognition. SNAP output
1rcs transcription-DNA NMR Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O (1994) "The solution structures of the trp repressor-operator DNA complex." J.Mol.Biol., 238, 592-614. doi: 10.1006/jmbi.1994.1317. NMR study of trp repressor-operator DNA complex. SNAP output
1rep replication-DNA X-ray (2.6 Å) Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C, Miki K (1999) "Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution." EMBO J., 18, 4597-4607. doi: 10.1093/emboj/18.17.4597. Crystal structure of replication initiator protein repe54 of mini-f plasmid complexed with an iteron DNA. SNAP output
1rff hydrolase-DNA X-ray (1.7 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octapeptide klnyydpr, and tetranucleotide agtt.. SNAP output
1rfi hydrolase-DNA X-ray (2.2 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, pentapeptide klnyk, and tetranucleotide agtc. SNAP output
1rg1 hydrolase-DNA X-ray (2.1 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtt. SNAP output
1rg2 hydrolase-DNA X-ray (2.1 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agta. SNAP output
1rgt hydrolase-DNA X-ray (2.0 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtc. SNAP output
1rgu hydrolase-DNA X-ray (2.22 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. The crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtg. SNAP output
1rh0 hydrolase-DNA X-ray (2.3 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine and trinucleotide gtt. SNAP output
1rh6 DNA binding protein-DNA X-ray (1.7 Å) Sam MD, Cascio D, Johnson RC, Clubb RT (2004) "Crystal structure of the excisionase-DNA complex from bacteriophage lambda." J.Mol.Biol., 338, 229-240. doi: 10.1016/j.jmb.2004.02.053. Bacteriophage lambda excisionase (xis)-DNA complex. SNAP output
1rio transcription-DNA X-ray (2.3 Å) Jain D, Nickels BE, Sun L, Hochschild A, Darst SA (2004) "Structure of a ternary transcription activation complex." Mol.Cell, 13, 45-53. doi: 10.1016/S1097-2765(03)00483-0. Structure of bacteriophage lambda ci-ntd in complex with sigma-region4 of thermus aquaticus bound to DNA. SNAP output
1rm1 transcription-DNA X-ray (2.5 Å) Jin X, Gewirth DT, Geiger JH "High Resolution Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex." Structure of a yeast tfiia-tbp-tata-box DNA complex. SNAP output
1rnb endonuclease X-ray (1.9 Å) Baudet S, Janin J (1991) "Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution." J.Mol.Biol., 219, 123-132. doi: 10.1016/0022-2836(91)90862-Z. Crystal structure of a barnase-d(*gp*c) complex at 1.9 angstroms resolution. SNAP output
1rpe gene regulation-DNA X-ray (2.5 Å) Shimon LJ, Harrison SC (1993) "The phage 434 OR2/R1-69 complex at 2.5 A resolution." J.Mol.Biol., 232, 826-838. doi: 10.1006/jmbi.1993.1434. The phage 434 or2-r1-69 complex at 2.5 angstroms resolution. SNAP output
1rpz transferase-DNA X-ray (2.9 Å) Eastberg JH, Pelletier J, Stoddard BL (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212. T4 polynucleotide kinase bound to 5'-tgcac-3' ssDNA. SNAP output
1rr8 isomerase-DNA X-ray (2.6 Å) Chrencik JE, Staker BL, Burgin AB, Pourquier P, Pommier Y, Stewart L, Redinbo MR (2004) "Mechanisms of camptothecin resistance by human topoisomerase I mutations." J.Mol.Biol., 339, 773-784. doi: 10.1016/j.jmb.2004.03.077. Structural mechanisms of camptothecin resistance by mutations in human topoisomerase i. SNAP output
1rrc transferase-DNA X-ray (2.46 Å) Eastberg JH, Pelletier J, Stoddard BL (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212. T4 polynucleotide kinase bound to 5'-gtc-3' ssDNA. SNAP output
1rrj isomerase-DNA X-ray (2.3 Å) Chrencik JE, Staker BL, Burgin AB, Pourquier P, Pommier Y, Stewart L, Redinbo MR (2004) "Mechanisms of camptothecin resistance by human topoisomerase I mutations." J.Mol.Biol., 339, 773-784. doi: 10.1016/j.jmb.2004.03.077. Structural mechanisms of camptothecin resistance by mutations in human topoisomerase i. SNAP output
1rrq hydrolase-DNA X-ray (2.22 Å) Fromme JC, Banerjee A, Huang SJ, Verdine GL (2004) "Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase." Nature, 427, 652-656. doi: 10.1038/nature02306. Muty adenine glycosylase in complex with DNA containing an a:oxog pair. SNAP output
1rrs hydrolase-DNA X-ray (2.4 Å) Fromme JC, Banerjee A, Huang SJ, Verdine GL (2004) "Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase." Nature, 427, 652-656. doi: 10.1038/nature02306. Muty adenine glycosylase in complex with DNA containing an abasic site. SNAP output
1rta hydrolase-DNA X-ray (2.5 Å) Birdsall DL, McPherson A (1992) "Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A." J.Biol.Chem., 267, 22230-22236. Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease a. SNAP output
1rtd transferase-DNA X-ray (3.2 Å) Huang H, Chopra R, Verdine GL, Harrison SC (1998) "Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance." Science, 282, 1669-1675. doi: 10.1126/science.282.5394.1669. Structure of a catalytic complex of hiv-1 reverse transcriptase: implications for nucleoside analog drug resistance. SNAP output
1run transcription-DNA X-ray (2.7 Å) Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH (1996) "Aromatic hydrogen bond in sequence-specific protein DNA recognition." Nat.Struct.Biol., 3, 837-841. doi: 10.1038/nsb1096-837. Catabolite gene activator protein (cap)-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1ruo transcription-DNA X-ray (2.7 Å) Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH (1996) "Aromatic hydrogen bond in sequence-specific protein DNA recognition." Nat.Struct.Biol., 3, 837-841. doi: 10.1038/nsb1096-837. Catabolite gene activator protein (cap) mutant-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1rv5 hydrolase-DNA X-ray (2.1 Å) Horton NC, Perona JJ (1998) "Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT)." J.Mol.Biol., 277, 779-783. doi: 10.1006/jmbi.1998.1655. Complex of ecorv endonuclease with d(aaagat)-d(atctt). SNAP output
1rva hydrolase-DNA X-ray (2.0 Å) Kostrewa D, Winkler FK (1995) "Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Biochemistry, 34, 683-696. doi: 10.1021/bi00002a036. Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution. SNAP output
1rvb hydrolase-DNA X-ray (2.1 Å) Kostrewa D, Winkler FK (1995) "Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Biochemistry, 34, 683-696. doi: 10.1021/bi00002a036. Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution. SNAP output
1rvc hydrolase-DNA X-ray (2.1 Å) Kostrewa D, Winkler FK (1995) "Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Biochemistry, 34, 683-696. doi: 10.1021/bi00002a036. Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution. SNAP output
1rxv hydrolase-DNA X-ray (2.5 Å) Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA (2004) "Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair." Cell(Cambridge,Mass.), 116, 39-50. doi: 10.1016/S0092-8674(03)01036-5. Crystal structure of a. fulgidus fen-1 bound to DNA. SNAP output
1rxw hydrolase-DNA X-ray (2.0 Å) Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA (2004) "Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair." Cell(Cambridge,Mass.), 116, 39-50. doi: 10.1016/S0092-8674(03)01036-5. Crystal structure of a. fulgidus fen-1 bound to DNA. SNAP output
1ryr transferase-DNA X-ray (2.28 Å) Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W (2003) "Replication of a Cis-Syn Thymine Dimer at Atomic Resolution." Nature, 424, 1083-1087. doi: 10.1038/nature01919. Replication of a cis-syn thymine dimer at atomic resolution. SNAP output
1rys transferase-DNA X-ray (2.03 Å) Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W (2003) "Replication of a Cis-Syn Thymine Dimer at Atomic Resolution." Nature, 424, 1083-1087. doi: 10.1038/nature01919. Replication of a cis-syn thymine dimer at atomic resolution. SNAP output
1rz9 viral protein-DNA X-ray (3.1 Å) Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda F (2004) "The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces." Mol.Cell, 13, 403-414. doi: 10.1016/S1097-2765(04)00023-1. Crystal structure of aav rep complexed with the rep-binding sequence. SNAP output
1rzr transcription-transport protein-DNA X-ray (2.8 Å) Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W, Brennan RG (2004) "Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P." Cell(Cambridge,Mass.), 118, 731-741. doi: 10.1016/j.cell.2004.08.027. Crystal structure of transcriptional regulator-phosphoprotein-DNA complex. SNAP output
1rzt transferase-DNA X-ray (2.1 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel TA, Pedersen LC (2004) "A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology." Mol.Cell, 13, 561-572. doi: 10.1016/S1097-2765(04)00061-9. Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule. SNAP output
1s0m transferase-DNA X-ray (2.7 Å) Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F, Woodgate R, Jerina DM, Yang W (2004) "Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase." Proc.Natl.Acad.Sci.USA, 101, 2265-2269. doi: 10.1073/pnas.0308332100. Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. SNAP output
1s0n transferase-DNA X-ray (2.8 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/S1097-2765(04)00101-7. Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift. SNAP output
1s0o transferase-DNA X-ray (2.1 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/S1097-2765(04)00101-7. Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift. SNAP output
1s0v transferase-DNA-RNA hybrid X-ray (3.2 Å) Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG (2004) "Structural basis for substrate selection by t7 RNA polymerase." Cell(Cambridge,Mass.), 116, 381-391. doi: 10.1016/S0092-8674(04)00059-5. Structural basis for substrate selection by t7 RNA polymerase. SNAP output
1s10 transferase-DNA X-ray (2.1 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/S1097-2765(04)00101-7. Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift. SNAP output
1s32 structural protein-DNA X-ray (2.05 Å) Edayathumangalam RS, Weyermann P, Gottesfeld JM, Dervan PB, Luger K (2004) "Molecular Recognition of the Nucleosomal 'Supergroove'." Proc.Natl.Acad.Sci.USA, 101, 6864-6869. doi: 10.1073/pnas.0401743101. Molecular recognition of the nucleosomal 'supergroove'. SNAP output
1s40 cell cycle-DNA NMR Mitton-Fry RM, Anderson EM, Theobald DL, Glustrom LW, Wuttke DS (2004) "Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13." J.Mol.Biol., 338, 241-255. doi: 10.1016/j.jmb.2004.01.063. Solution structure of the cdc13 DNA-binding domain complexed with a single-stranded telomeric DNA 11-mer. SNAP output
1s6m DNA binding protein-DNA X-ray (2.28 Å) Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F (2006) "Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site." J.Mol.Biol., 358, 857-869. doi: 10.1016/j.jmb.2006.02.018. Conjugative relaxase trwc in complex with orit DNA. metal-bound structure. SNAP output
1s76 transferase X-ray (2.88 Å) Yin YW, Steitz TA (2004) "The structural mechanism of translocation and helicase activity in T7 RNA polymerase." Cell(Cambridge,Mass.), 116, 393-404. doi: 10.1016/S0092-8674(04)00120-5. T7 RNA polymerase alpha beta methylene atp elongation complex. SNAP output
1s77 transferase X-ray (2.69 Å) Yin YW, Steitz TA (2004) "The structural mechanism of translocation and helicase activity in T7 RNA polymerase." Cell(Cambridge,Mass.), 116, 393-404. doi: 10.1016/S0092-8674(04)00120-5. T7 rnap product pyrophosphate elongation complex. SNAP output
1s97 transferase-DNA X-ray (2.4 Å) Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK (2004) "Dpo4 is hindered in extending a G.T mismatch by a reverse wobble." Nat.Struct.Mol.Biol., 11, 457-462. doi: 10.1038/nsmb755. Dpo4 with gt mismatch. SNAP output
1s9f transferase-DNA X-ray (2.0 Å) Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK (2004) "Dpo4 is hindered in extending a G.T mismatch by a reverse wobble." Nat.Struct.Mol.Biol., 11, 457-462. doi: 10.1038/nsmb755. Dpo with at matched. SNAP output
1s9k transcription-DNA X-ray (3.1 Å) Wang D, Stroud JC, Chen L "Crystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site." Crystal structure of human nfat1 and fos-jun on the il-2 arre1 site. SNAP output
1sa3 hydrolase-DNA X-ray (1.95 Å) Xu QS, Kucera RB, Roberts RJ, Guo HC (2004) "An Asymmetric Complex of Restriction Endonuclease MspI on Its Palindromic DNA Recognition Site." STRUCTURE, 12, 1741-1747. doi: 10.1016/j.str.2004.07.014. An asymmetric complex of restriction endonuclease mspi on its palindromic DNA recognition site. SNAP output
1sax transcription-DNA X-ray (2.8 Å) Garcia-Castellanos R, Mallorqui-Fernandez G, Marrero A, Potempa J, Coll M, Gomis-Ruth FX (2004) "On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator." J.Biol.Chem., 279, 17888-17896. doi: 10.1074/jbc.M313123200. Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA. SNAP output
1sc7 isomerase-DNA X-ray (3.0 Å) Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, Burgin AB (2005) "Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex." J.Med.Chem., 48, 2336-2345. doi: 10.1021/jm049146p. Human DNA topoisomerase i (70 kda) in complex with the indenoisoquinoline mj-ii-38 and covalent complex with a 22 base pair DNA duplex. SNAP output
1seu isomerase-DNA X-ray (3.0 Å) Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, Burgin AB (2005) "Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex." J.Med.Chem., 48, 2336-2345. doi: 10.1021/jm049146p. Human DNA topoisomerase i (70 kda) in complex with the indolocarbazole sa315f and covalent complex with a 22 base pair DNA duplex. SNAP output
1sfo transcription-DNA-RNA hybrid X-ray (3.61 Å) Westover KD, Bushnell DA, Kornberg RD (2004) "Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II." Science, 303, 1014-1016. doi: 10.1126/science.1090839. RNA polymerase ii strand separated elongation complex. SNAP output
1sfu DNA binding protein-DNA X-ray (2.0 Å) Ha SC, Lokanath NK, Van Quyen D, Wu CA, Lowenhaupt K, Rich A, Kim YG, Kim KK (2004) "A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA." Proc.Natl.Acad.Sci.USA, 101, 14367-14372. doi: 10.1073/pnas.0405586101. Crystal structure of the viral zalpha domain bound to left-handed z-DNA. SNAP output
1si2 gene regulation-RNA-DNA X-ray (2.6 Å) Ma JB, Ye K, Patel DJ (2004) "Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain." Nature, 429, 318-322. doi: 10.1038/nature02519. Crystal structure of the paz domain of human eif2c1 in complex with a 9-mer sirna-like duplex of deoxynucleotide overhang. SNAP output
1skm transferase-DNA X-ray (2.2 Å) Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X (2004) "Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase." Nucleic Acids Res., 32, 3877-3886. doi: 10.1093/nar/gkh701. Hhai methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site. SNAP output
1skn transcription-DNA X-ray (2.5 Å) Rupert PB, Daughdrill GW, Bowerman B, Matthews BW (1998) "A new DNA-binding motif in the Skn-1 binding domain-DNA complex." Nat.Struct.Biol., 5, 484-491. doi: 10.1038/nsb0698-484. The binding domain of skn-1 in complex with DNA: a new DNA-binding motif. SNAP output
1skr transferase-electron transport-DNA X-ray (2.4 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. T7 DNA polymerase complexed to DNA primer-template and ddatp. SNAP output
1sks transferase-electron transport-DNA X-ray (2.3 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Binary 3' complex of t7 DNA polymerase with a DNA primer-template containing a cis-syn thymine dimer on the template. SNAP output
1skw transferase-electron transport-DNA X-ray (2.3 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Binary 3' complex of t7 DNA polymerase with a DNA primer-template containing a disordered cis-syn thymine dimer on the template. SNAP output
1sl0 transferase-electron transport-DNA X-ray (3.2 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Ternary 3' complex of t7 DNA polymerase with a DNA primer-template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide. SNAP output
1sl1 transferase-electron transport-DNA X-ray (2.2 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Binary 5' complex of t7 DNA polymerase with a DNA primer-template containing a cis-syn thymine dimer on the template. SNAP output
1sl2 transferase-electron transport-DNA X-ray (2.3 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Ternary 5' complex of t7 DNA polymerase with a DNA primer-template containing a cis-syn thymine dimer on the template and an incoming nucleotide. SNAP output
1srs transcription-DNA X-ray (3.2 Å) Pellegrini L, Tan S, Richmond TJ (1995) "Structure of serum response factor core bound to DNA." Nature, 376, 490-498. doi: 10.1038/376490a0. Serum response factor (srf) core complexed with specific sre DNA. SNAP output
1ssp hydrolase-DNA X-ray (1.9 Å) Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA (1998) "Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA." EMBO J., 17, 5214-5226. doi: 10.1093/emboj/17.17.5214. Wild-type uracil-DNA glycosylase bound to uracil-containing DNA. SNAP output
1stx hydrolase-DNA X-ray (2.1 Å) Horton NC, Perona JJ (2004) "DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. Structure of the k38a mutant of ecorv bound to cognate DNA and mn2+. SNAP output
1suz hydrolase-DNA X-ray (1.8 Å) Horton NC, Perona JJ (2004) "DNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. The structure of k92a ecorv bound to cognate DNA and mg2+. SNAP output
1svc transcription-DNA X-ray (2.6 Å) Muller CW, Rey FA, Sodeoka M, Verdine GL, Harrison SC (1995) "Structure of the NF-kappa B p50 homodimer bound to DNA." Nature, 373, 311-317. doi: 10.1038/373311a0. Nfkb p50 homodimer bound to DNA. SNAP output
1sx5 hydrolase-DNA X-ray (1.5 Å) Horton NC, Perona JJ (2004) "DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. K38a ecorv bound to cleaved DNA and mn2+: p1 crystal form. SNAP output
1sx8 hydrolase-DNA X-ray (2.15 Å) Horton NC, Perona JJ (2004) "DNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. Ecorv bound to cognate DNA and mn2+. SNAP output
1sxp transferase-DNA X-ray (2.5 Å) Lariviere L, Morera S (2004) "Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase." J.Biol.Chem., 279, 34715-34720. doi: 10.1074/jbc.M404394200. Bgt in complex with a 13mer DNA containing a central a:g mismatch. SNAP output
1sxq transferase-DNA X-ray (1.8 Å) Lariviere L, Morera S (2004) "Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase." J.Biol.Chem., 279, 34715-34720. doi: 10.1074/jbc.M404394200. Bgt in complex with a 13mer DNA containing a central c:g base pair and udp. SNAP output
1t03 transferase-antibody-DNA X-ray (3.1 Å) Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P, Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH, Arnold E (2004) "Structure of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir." Nat.Struct.Mol.Biol., 11, 469-474. doi: 10.1038/nsmb760. Hiv-1 reverse transcriptase crosslinked to tenofovir terminated template-primer (complex p). SNAP output
1t05 transferase-DNA X-ray (3.0 Å) Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P, Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH, Arnold E (2004) "Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir." Nat.Struct.Mol.Biol., 11, 469-474. doi: 10.1038/nsmb760. Hiv-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate. SNAP output
1t2k transcription-DNA X-ray (3.0 Å) Panne D, Maniatis T, Harrison SC (2004) "Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer." Embo J., 23, 4384-4393. doi: 10.1038/sj.emboj.7600453. Structure of the DNA binding domains of irf3, atf-2 and jun bound to DNA. SNAP output
1t2s nucleic acid binding protein-DNA NMR Lingel A, Simon B, Izaurralde E, Sattler M (2004) "Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain." Nat.Struct.Mol.Biol., 11, 576-577. doi: 10.1038/nsmb777. Structural basis for 3' end recognition of nucleic acids by the drosophila argonaute 2 paz domain. SNAP output
1t2t hydrolase-DNA X-ray (2.5 Å) Edgell DR, Derbyshire V, Van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M (2004) "Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor." Nat.Struct.Mol.Biol., 11, 936-944. doi: 10.1038/nsmb823. Crystal structure of the DNA-binding domain of intron endonuclease i-tevi with operator site. SNAP output
1t38 transferase-DNA X-ray (3.2 Å) Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA (2004) "DNA binding and nucleotide flipping by the human DNA repair protein AGT." Nat.Struct.Mol.Biol., 11, 714-720. doi: 10.1038/nsmb791. Human o6-alkylguanine-DNA alkyltransferase bound to DNA containing o6-methylguanine. SNAP output
1t39 transferase-DNA X-ray (3.3 Å) Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA (2004) "DNA binding and nucleotide flipping by the human DNA repair protein AGT." Nat.Struct.Mol.Biol., 11, 714-720. doi: 10.1038/nsmb791. Human o6-alkylguanine-DNA alkyltransferase covalently crosslinked to DNA. SNAP output
1t3n replication-DNA X-ray (2.3 Å) Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK (2004) "Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing." Nature, 430, 377-380. doi: 10.1038/nature02692. Structure of the catalytic core of DNA polymerase iota in complex with DNA and dttp. SNAP output
1t7p transferase-DNA X-ray (2.2 Å) Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T (1998) "Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution." Nature, 391, 251-258. doi: 10.1038/34593. T7 DNA polymerase complexed to DNA primer-template,a nucleoside triphosphate, and its processivity factor thioredoxin. SNAP output
1t8e transferase-electron transport-DNA X-ray (2.54 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with dctp at the insertion site.. SNAP output
1t8i isomerase-DNA X-ray (3.0 Å) Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, Burgin AB (2005) "Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex." J.Med.Chem., 48, 2336-2345. doi: 10.1021/jm049146p. Human DNA topoisomerase i (70 kda) in complex with the poison camptothecin and covalent complex with a 22 base pair DNA duplex. SNAP output
1t9i hydrolase-DNA X-ray (1.6 Å) Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M, Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL (2004) "Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease." Biochemistry, 43, 14015-14026. doi: 10.1021/bi048970c. I-crei(d20n)-DNA complex. SNAP output
1t9j hydrolase-DNA X-ray (2.0 Å) Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M, Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL (2004) "Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease." Biochemistry, 43, 14015-14026. doi: 10.1021/bi048970c. I-crei(q47e)-DNA complex. SNAP output
1tau transferase-DNA X-ray (3.0 Å) Eom SH, Wang J, Steitz TA (1996) "Structure of Taq ploymerase with DNA at the polymerase active site." Nature, 382, 278-281. doi: 10.1038/382278a0. Taq polymerase (e.c.2.7.7.7)-DNA-b-octylglucoside complex. SNAP output
1tc3 DNA binding protein-DNA X-ray (2.45 Å) van Pouderoyen G, Ketting RF, Perrakis A, Plasterk RH, Sixma TK (1997) "Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA." EMBO J., 16, 6044-6054. doi: 10.1093/emboj/16.19.6044. Transposase tc3a1-65 from caenorhabditis elegans. SNAP output
1tdz hydrolase-DNA X-ray (1.8 Å) Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B (2004) "Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase." J.Biol.Chem., 279, 44074-44083. doi: 10.1074/jbc.M405928200. Crystal structure complex between the lactococcus lactis fpg (mutm) and a fapy-dg containing DNA. SNAP output
1tez lyase-DNA X-ray (1.8 Å) Mees A, Klar T, Gnau P, Hennecke U, Eker APM, Carell T, Essen L-O (2004) "Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair." Science, 306, 1789-1793. doi: 10.1126/science.1101598. Complex between DNA and the DNA photolyase from anacystis nidulans. SNAP output
1tf3 transcription-DNA NMR Foster MP, Wuttke DS, Radhakrishnan I, Case DA, Gottesfeld JM, Wright PE (1997) "Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA." Nat.Struct.Biol., 4, 605-608. doi: 10.1038/nsb0897-605. Tfiiia finger 1-3 bound to DNA, NMR, 22 structures. SNAP output
1tf6 transcription-DNA X-ray (3.1 Å) Nolte RT, Conlin RM, Harrison SC, Brown RS (1998) "Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex." Proc.Natl.Acad.Sci.USA, 95, 2938-2943. doi: 10.1073/pnas.95.6.2938. Co-crystal structure of xenopus tfiiia zinc finger domain bound to the 5s ribosomal RNA gene internal control region. SNAP output
1tgh transcription-DNA X-ray (2.9 Å) Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ, Dickerson RE (1996) "How proteins recognize the TATA box." J.Mol.Biol., 261, 239-254. doi: 10.1006/jmbi.1996.0456. Tata binding protein (tbp)-DNA complex. SNAP output
1tk0 transferase-electron transport-DNA X-ray (2.3 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with 8 oxo guanosine and ddctp at the insertion site. SNAP output
1tk5 transferase-electron transport-DNA X-ray (2.2 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand. SNAP output
1tk8 transferase-electron transport-DNA X-ray (2.5 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with 8 oxo guanosine and damp at the elongation site. SNAP output
1tkd transferase-electron transport-DNA X-ray (2.49 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with 8 oxo guanosine and dcmp at the elongation site. SNAP output
1tl8 isomerase-DNA X-ray (3.1 Å) Ioanoviciu A, Antony S, Pommier Y, Staker BL, Stewart L, Cushman M (2005) "Synthesis and Mechanism of Action Studies of a Series of Norindenoisoquinoline Topoisomerase I Poisons Reveal an Inhibitor with a Flipped Orientation in the Ternary DNA-Enzyme-Inhibitor Complex As Determined by X-ray Crystallographic Analysis." J.Med.Chem., 48, 4803-4814. doi: 10.1021/jm050076b. Human DNA topoisomerase i (70 kda) in complex with the indenoisoquinoline ai-iii-52 and covalent complex with a 22 base pair DNA duplex. SNAP output
1tn9 integrase-DNA NMR Wojciak JM, Connolly KM, Clubb RT (1999) "NMR structure of the Tn916 integrase-DNA complex." Nat.Struct.Biol., 6, 366-373. doi: 10.1038/7603. The solution structure of tn916 integrase n-terminal domain-DNA complex. SNAP output
1tqe transcription-protein binding-DNA X-ray (2.7 Å) Han A, He J, Wu Y, Liu JO, Chen L (2005) "Mechanism of Recruitment of Class II Histone Deacetylases by Myocyte Enhancer Factor-2." J.Mol.Biol., 345, 91-102. doi: 10.1016/j.jmb.2004.10.033. Mechanism of recruitment of class ii histone deacetylases by myocyte enhancer factor-2. SNAP output
1tro transcription-DNA X-ray (1.9 Å) Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB (1988) "Crystal structure of trp repressor/operator complex at atomic resolution." Nature, 335, 321-329. doi: 10.1038/335321a0. Crystal structure of trp repressor operator complex at atomic resolution. SNAP output
1trr transcription-DNA X-ray (2.4 Å) Lawson CL, Carey J (1993) "Tandem binding in crystals of a trp repressor/operator half-site complex." Nature, 366, 178-182. doi: 10.1038/366178a0. Tandem binding in crystals of a trp repressor-operator half-site complex. SNAP output
1tsr antitumor protein-DNA X-ray (2.2 Å) Cho Y, Gorina S, Jeffrey PD, Pavletich NP (1994) "Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations." Science, 265, 346-355. P53 core domain in complex with DNA. SNAP output
1ttu transcription X-ray (2.85 Å) Kovall RA, Hendrickson WA (2004) "Crystal structure of the nuclear effector of Notch signaling, CSL, bound to DNA." Embo J., 23, 3441-3451. doi: 10.1038/sj.emboj.7600349. Crystal structure of csl bound to DNA. SNAP output
1tup antitumor protein-DNA X-ray (2.2 Å) Cho Y, Gorina S, Jeffrey PD, Pavletich NP (1994) "Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations." Science, 265, 346-355. Tumor suppressor p53 complexed with DNA. SNAP output
1tv9 transferase-DNA X-ray (2.0 Å) Krahn JM, Beard WM, Wilson SH (2004) "STRUCTURAL INSIGHTS INTO DNA POLYMERASE BETA DETERRENTS FOR MISINCORPORATION SUPPORT OF AN INDUCED-FIT MECHANISM FOR FIDELITY." Structure, 12, 1823-1832. doi: 10.1016/j.str.2004.08.001. Human DNA polymerase beta complexed with nicked DNA containing a mismatched template adenine and incoming cytidine. SNAP output
1tva transferase-DNA X-ray (2.6 Å) Krahn JM, Beard WA, Wilson SH (2004) "Structural insights into DNA polymerase Beta deterrents for misincorporation support an induced-fit mechanism for fidelity." Structure, 12, 1823-1832. doi: 10.1016/j.str.2004.08.001. Human DNA polymerase beta complexed with nicked DNA containing a mismatched template thymidine and incoming cytidine. SNAP output
1tw8 hydrolase-DNA X-ray (2.8 Å) Etzkorn C, Horton NC (2004) "Ca2+ binding in the active site of HincII: implications for the catalytic mechanism." Biochemistry, 43, 13256-13270. Hincii bound to ca2+ and cognate DNA gtcgac. SNAP output
1tx3 hydrolase-DNA X-ray (2.5 Å) Etzkorn C, Horton NC (2004) "Ca2+ binding in the active site of HincII: implications for the catalytic mechanism." Biochemistry, 43, 13256-13270. doi: 10.1021/bi0490082. Hincii bound to cognate DNA. SNAP output
1u0c hydrolase-DNA X-ray (2.5 Å) Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R, Stoddard BL, Seligman LM (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions." J.Mol.Biol., 342, 31-41. doi: 10.1016/j.jmb.2004.07.031. Y33c mutant of homing endonuclease i-crei. SNAP output
1u0d hydrolase-DNA X-ray (2.9 Å) Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R, Stoddard BL, Seligman LM (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions." J.Mol.Biol., 342, 31-41. doi: 10.1016/j.jmb.2004.07.031. Y33h mutant of homing endonuclease i-crei. SNAP output
1u1k transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtt 7da ggg); a human telomeric repeat containing 7-deaza-adenine. SNAP output
1u1l transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtt prn ggg); a human telomeric repeat containing nebularine. SNAP output
1u1m transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta 7gu gg); a human telomeric repeat containing 7-deaza-guanine. SNAP output
1u1n transport protein-DNA X-ray (2.1 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta (prn)gg); a human telomeric repeat containing nebularine. SNAP output
1u1o transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggttag(di)g); a human telomeric repeat containing inosine. SNAP output
1u1p transport protein-DNA X-ray (1.9 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta 2pr gg); a human telomeric repeat containing 2-aminopurine. SNAP output
1u1q transport protein-DNA X-ray (1.8 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta(di)gg); a human telomeric repeat containing inosine. SNAP output
1u1r transport protein-DNA X-ray (1.8 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggttag(2pr)g); a human telomeric repeat containing 2-aminopurine. SNAP output
1u1y virus-RNA X-ray (2.85 Å) Horn WT, Convery MA, Stonehouse NJ, Adams CJ, Liljas L, Phillips SE, Stockley PG (2004) "The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions." Rna, 10, 1776-1782. doi: 10.1261/rna.7710304. Crystal structure of a complex between wt bacteriophage ms2 coat protein and an f5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position. SNAP output
1u35 structural protein-DNA X-ray (3.0 Å) Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K (2005) "Structural characterization of the histone variant macroH2A." Mol.Cell.Biol., 25, 7616-7624. doi: 10.1128/MCB.25.17.7616-7624.2005. Crystal structure of the nucleosome core particle containing the histone domain of macroh2a. SNAP output
1u3e DNA binding protein-DNA X-ray (2.92 Å) Shen BW, Landthaler M, Shub DA, Stoddard BL (2004) "DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI." J.Mol.Biol., 342, 43-56. doi: 10.1016/j.jmb.2004.07.032. DNA binding and cleavage by the hnh homing endonuclease i-hmui. SNAP output
1u45 transferase-DNA X-ray (2.01 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. 8oxoguanine at the pre-insertion site of the polymerase active site. SNAP output
1u47 transferase-DNA X-ray (2.0 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Cytosine-8-oxoguanine base pair at the polymerase active site. SNAP output
1u48 transferase-DNA X-ray (2.1 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Extension of a cytosine-8-oxoguanine base pair. SNAP output
1u49 transferase-DNA X-ray (2.15 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Adenine-8oxoguanine mismatch at the polymerase active site. SNAP output
1u4b transferase-DNA X-ray (1.6 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Extension of an adenine-8oxoguanine mismatch. SNAP output
1u78 DNA binding protein-DNA X-ray (2.69 Å) Watkins S, van Pouderoyen G, Sixma TK (2004) "Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA." Nucleic Acids Res., 32, 4306-4312. doi: 10.1093/nar/gkh770. Structure of the bipartite DNA-binding domain of tc3 transposase bound to transposon DNA. SNAP output
1u8b metal binding protein-DNA X-ray (2.1 Å) He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dotsch V, Wei H, Gross JD, Lane WS, Wagner G, Verdine GL (2005) "A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada." Mol.Cell, 20, 117-129. doi: 10.1016/j.molcel.2005.08.013. Crystal structure of the methylated n-ada-DNA complex. SNAP output
1u8r metal-binding protein,transcription-DNA X-ray (2.75 Å) Wisedchaisri G, Holmes RK, Hol WGJ (2004) "Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions." J.Mol.Biol., 342, 1155-1169. doi: 10.1016/j.jmb.2004.07.083. Crystal structure of an ider-DNA complex reveals a conformational change in activated ider for base-specific interactions. SNAP output
1ua0 transferase-DNA X-ray (2.1 Å) Hsu GW, Kiefer JR, Burnouf D, Becherel OJ, Fuchs RPP, Beese LS (2004) "Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase." J.Biol.Chem., 279, 50280-50285. doi: 10.1074/jbc.M409224200. Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase. SNAP output
1ua1 transferase-DNA X-ray (2.0 Å) Hsu GW, Kiefer JR, Becherel OJ, Fuchs RPP, Beese LS (2004) "Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase." J.Biol.Chem., 279, 50280-50285. doi: 10.1074/jbc.M409224200. Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site.. SNAP output
1uaa hydrolase-DNA X-ray (3.0 Å) Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman G (1997) "Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP." Cell(Cambridge,Mass.), 90, 635-647. doi: 10.1016/S0092-8674(00)80525-5. E. coli rep helicase-DNA complex. SNAP output
1ubd transcription-DNA X-ray (2.5 Å) Houbaviy HB, Usheva A, Shenk T, Burley SK (1996) "Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator." Proc.Natl.Acad.Sci.USA, 93, 13577-13582. doi: 10.1073/pnas.93.24.13577. Co-crystal structure of human yy1 zinc finger domain bound to the adeno-associated virus p5 initiator element. SNAP output
1unj DNA-antibiotic X-ray (2.5 Å) Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement R, Machinek R, Sheldrick GM, Uson I (2005) "Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)." Acta Crystallogr.,Sect.D, 61, 407. doi: 10.1107/S090744490500082X. Crystal structure of a 7-aminoactinomycin d complex with non-complementary DNA. SNAP output
1unm DNA-antibiotic X-ray (2.0 Å) Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement R, Machinek R, Sheldrick GM, Uson I (2005) "Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)." Acta Crystallogr.,Sect.D, 61, 407. doi: 10.1107/S090744490500082X. Crystal structure of 7-aminoactinomycin d with non-complementary DNA. SNAP output
1urn transcription-RNA X-ray (1.92 Å) Oubridge C, Ito N, Evans PR, Teo CH, Nagai K (1994) "Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin." Nature, 372, 432-438. doi: 10.1038/372432a0. U1a mutant-RNA complex + glycerol. SNAP output
1uut hydrolase-DNA X-ray (2.0 Å) Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda F (2004) "The Nuclease Domain of Adeno-Associated Virus Rep Coordinates Replication Initiation Using Two Distinct DNA Recognition Interfaces." Mol.Cell, 13, 403. doi: 10.1016/S1097-2765(04)00023-1. The nuclease domain of adeno-associated virus rep complexed with the rbe' stemloop of the viral inverted terminal repeat. SNAP output
1v14 hydrolase X-ray (2.9 Å) Mate MJ, Kleanthous C (2004) "Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases." J.Biol.Chem., 279, 34763. doi: 10.1074/JBC.M403719200. Crystal structure of the colicin e9, mutant his103ala, in complex with mg+2 and dsDNA (resolution 2.9a). SNAP output
1v15 hydrolase X-ray (2.4 Å) Mate MJ, Kleanthous C (2004) "Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases." J.Biol.Chem., 279, 34763. doi: 10.1074/JBC.M403719200. Crystal structure of the colicin e9, mutant his103ala, in complex with zn+2 and dsDNA (resolution 2.4a). SNAP output
1vas hydrolase-DNA X-ray (2.75 Å) Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K (1995) "Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition." Cell(Cambridge,Mass.), 83, 773-782. doi: 10.1016/0092-8674(95)90190-6. Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. SNAP output
1vfc structural protein-DNA NMR Hanaoka S, Nagadoi A, Nishimura Y (2005) "Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities." Protein Sci., 14, 119-130. doi: 10.1110/ps.04983705. Solution structure of the DNA complex of human trf2. SNAP output
1vkx transcription-DNA X-ray (2.9 Å) Chen FE, Huang DB, Chen YQ, Ghosh G (1998) "Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA." Nature, 391, 410-413. doi: 10.1038/34956. Crystal structure of the nfkb p50-p65 heterodimer complexed to the immunoglobulin kb DNA. SNAP output
1vol transcription-DNA X-ray (2.7 Å) Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake K, Lee DK, Roeder RG, Burley SK (1995) "Crystal structure of a TFIIB-TBP-TATA-element ternary complex." Nature, 377, 119-128. doi: 10.1038/377119a0. Tfiib (human core domain)-tbp (a.thaliana)-tata element ternary complex. SNAP output
1vpw transcription-DNA X-ray (2.7 Å) Arvidson DN, Lu F, Faber C, Zalkin H, Brennan RG (1998) "The structure of PurR mutant L54M shows an alternative route to DNA kinking." Nat.Struct.Biol., 5, 436-441. doi: 10.1038/nsb0698-436. Structure of the purr mutant, l54m, bound to hypoxanthine and purf operator DNA. SNAP output
1vq5 ribosome X-ray (2.6 Å) Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA (2005) "Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction." Mol.Cell, 20, 437-448. doi: 10.1016/j.molcel.2005.09.006. The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output
1vqp ribosome X-ray (2.25 Å) Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA (2005) "Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction." Mol.Cell, 20, 437-448. doi: 10.1016/j.molcel.2005.09.006. The structure of the transition state analogue "rap" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output
1vrl hydrolase-DNA X-ray (2.5 Å) Fromme JC, Banerjee A, Huang SJ, Verdine GL (2004) "Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase." Nature, 427, 652-656. doi: 10.1038/nature02306. Muty adenine glycosylase in complex with DNA and soaked adenine free base. SNAP output
1vrr hydrolase-DNA X-ray (2.7 Å) Townson SA, Samuelson JC, Xu SY, Aggarwal AK (2005) "Implications for Switching Restriction Enzyme Specificities from the Structure of BstYI Bound to a BglII DNA Sequence." Structure, 13, 791-801. doi: 10.1016/j.str.2005.02.018. Crystal structure of the restriction endonuclease bstyi complex with DNA. SNAP output
1vs2 DNA-antibiotic X-ray (2.0 Å) Wang AH, Ughetto G, Quigley GJ, Rich A (1986) "Interactions of Quinoxaline Antibiotic and DNA: The Molecular Structure of a Triostin A-D(Gcgtacgc) Complex." J.Biomol.Struct.Dyn., 4, 319. Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin a-d(gcgtacgc) complex. SNAP output
1vtg DNA-antibiotic X-ray (1.67 Å) Wang AH, Ughetto G, Quigley GJ, Hakoshima T, van der Marel GA, van Boom JH, Rich A (1984) "The molecular structure of a DNA-triostin A complex." Science, 225, 1115-1121. The molecular structure of a DNA-triostin a complex. SNAP output
1vtl transcription-DNA X-ray (2.25 Å) Kim JL, Nikolov DB, Burley SK (1993) "Co-Crystal Structure of TBP Recognizing the Minor Groove of a TATA Element." Nature, 365, 520-527. doi: 10.1038/365520a0. Co-crystal structure of tbp recognizing the minor groove of a tata element. SNAP output
1vtn transcription-DNA X-ray (2.5 Å) Clark KL, Halay ED, Lai E, Burley SK (1993) "Co-Crystal Structure of the HNF-3/Fork Head DNA-Recognition Motif Resembles Histone H5." Nature, 364, 412-420. doi: 10.1038/364412a0. Co-crystal structure of the hnf-3-fork head DNA-recognition motif resembles histone h5. SNAP output
1vto transcription-DNA X-ray (1.9 Å) Kim JL, Burley SK (1994) "1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG." Nat.Struct.Biol., 1, 638-653. 1.9 Å resolution refined structure of tbp recognizing the minor groove of tataaaag. SNAP output
1w0t DNA binding protein X-ray (2.0 Å) Court RI, Chapman LM, Fairall L, Rhodes D (2005) "How the Human Telomeric Proteins Trf1 and Trf2 Recognize Telomeric DNA: A View from High-Resolution Crystal Structures." Embo Rep., 6, 39. doi: 10.1038/SJ.EMBOR.7400314. Htrf1 DNA-binding domain in complex with telomeric DNA.. SNAP output
1w0u DNA binding protein X-ray (1.8 Å) Court RI, Chapman LM, Fairall L, Rhodes D (2005) "How the Human Telomeric Proteins Trf1 and Trf2 Recognize Telomeric DNA: A View from High-Resolution Crystal Structures." Embo Rep., 6, 39. doi: 10.1038/SJ.EMBOR.7400314. Htrf2 DNA-binding domain in complex with telomeric DNA.. SNAP output
1w36 recombination X-ray (3.1 Å) Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB (2004) "Crystal Structure of Recbcd Enzyme Reveals a Machine for Processing DNA Breaks." Nature, 432, 187. doi: 10.1038/NATURE02988. Recbcd:DNA complex. SNAP output
1w7a DNA binding X-ray (2.27 Å) Lamers MH, Georgijevic D, Lebbink J, Winterwerp HHK, Agianian B, De Wind N, Sixma TK (2004) "ATP Increases the Affinity between Muts ATPase Domains: Implications for ATP Hydrolysis and Conformational Changes." J.Biol.Chem., 279, 43879. doi: 10.1074/JBC.M406380200. Atp bound muts. SNAP output
1wb9 DNA-binding X-ray (2.1 Å) Lebbink JHG, Georgijevic D, Natrajan G, Fish A, Winterwerp HHK, Sixma TK, De Wind N (2006) "Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair." Embo J., 25, 409. doi: 10.1038/SJ.EMBOJ.7600936. Crystal structure of e. coli DNA mismatch repair enzyme muts, e38t mutant, in complex with a g.t mismatch. SNAP output
1wbb DNA-binding X-ray (2.5 Å) Lebbink JHG, Georgijevic D, Natrajan G, Fish A, Winterwerp HHK, Sixma TK, De Wind N (2006) "Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair." Embo J., 25, 409. doi: 10.1038/SJ.EMBOJ.7600936. Crystal structure of e. coli DNA mismatch repair enzyme muts, e38a mutant, in complex with a g.t mismatch. SNAP output
1wbd DNA-binding X-ray (2.4 Å) Lebbink JHG, Georgijevic D, Natrajan G, Fish A, Winterwerp HHK, Sixma TK, De Wind N (2006) "Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair." Embo J., 25, 409. doi: 10.1038/SJ.EMBOJ.7600936. Crystal structure of e. coli DNA mismatch repair enzyme muts, e38q mutant, in complex with a g.t mismatch. SNAP output
1wd0 structural protein-DNA X-ray (1.9 Å) Ko TP, Chu HM, Chen CY, Chou CC, Wang AH (2004) "Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers." Acta Crystallogr.,Sect.D, 60, 1381-1387. doi: 10.1107/S0907444904012065. Crystal structures of the hyperthermophilic chromosomal protein sac7d in complex with DNA decamers. SNAP output
1wd1 structural protein-DNA X-ray (2.2 Å) Ko TP, Chu HM, Chen CY, Chou CC, Wang AH (2004) "Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers." Acta Crystallogr.,Sect.D, 60, 1381-1387. doi: 10.1107/S0907444904012065. Crystal structures of the hyperthermophilic chromosomal protein sac7d in complex with DNA decamers. SNAP output
1wet transcription-DNA X-ray (2.6 Å) Schumacher MA, Glasfeld A, Zalkin H, Brennan RG (1997) "The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity." J.Biol.Chem., 272, 22648-22653. doi: 10.1074/jbc.272.36.22648. Structure of the purr-guanine-purf operator complex. SNAP output
1wtb transcription-DNA NMR Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi S, Ishikawa F, Katahira M (2005) "Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D." J.Biol.Chem., 280, 18862-18870. doi: 10.1074/jbc.M411822200. Complex structure of the c-terminal RNA-binding domain of hnrnp d (auf1) with telomere DNA. SNAP output
1wte hydrolase-DNA X-ray (1.9 Å) Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo N, Kita K, Sato M (2005) "Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA." J.Biol.Chem., 280, 5605-5610. doi: 10.1074/jbc.M411684200. Crystal structure of type ii restrcition endonuclease, ecoo109i complexed with cognate DNA. SNAP output
1wto DNA binding protein-DNA X-ray (1.5 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d double mutant v26f-m29f in complex with DNA gcgatcgc. SNAP output
1wtp DNA binding protein-DNA X-ray (1.9 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29f in complex with DNA gcga(ubr)cgc. SNAP output
1wtq DNA binding protein-DNA X-ray (1.7 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29f in complex with DNA gtaattac. SNAP output
1wtr DNA binding protein-DNA X-ray (1.8 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29a in complex with DNA gcgatcgc. SNAP output
1wtv DNA binding protein-DNA X-ray (1.6 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29a in complex with DNA gtaattac. SNAP output
1wtw DNA binding protein-DNA X-ray (2.2 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant v26a in complex with DNA gcgatcgc. SNAP output
1wtx DNA binding protein-DNA X-ray (2.2 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant v26a in complex with DNA gtaattac. SNAP output
1wvl structural protein-DNA X-ray (2.6 Å) Wu SW, Ko TP, Chou CC, Wang AH (2005) "Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates." Proteins, 60, 617-628. doi: 10.1002/prot.20524. Crystal structure of multimeric DNA-binding protein sac7d-gcn4 with DNA decamer. SNAP output
1x0f transcription-DNA NMR Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi S, Ishikawa F, Katahira M (2005) "Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D." J.Biol.Chem., 280, 18862-18870. doi: 10.1074/jbc.M411822200. Complex structure of the c-terminal RNA-binding domain of hnrnp d(auf1) with telomeric DNA. SNAP output
1x9m transferase-electron transport-DNA X-ray (2.1 Å) Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc.Natl.Acad.Sci.USA, 101, 16186-16191. doi: 10.1073/pnas.0406516101. T7 DNA polymerase in complex with an n-2-acetylaminofluorene-adducted DNA. SNAP output
1x9n ligase-DNA X-ray (3.0 Å) Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T (2004) "Human DNA ligase I completely encircles and partially unwinds nicked DNA." Nature, 432, 473-478. doi: 10.1038/nature03082. Crystal structure of human DNA ligase i bound to 5'-adenylated, nicked DNA. SNAP output
1x9s transferase-electron transport-DNA X-ray (2.7 Å) Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc.Natl.Acad.Sci.Usa, 101, 16186-16191. doi: 10.1073/pnas.0406516101. T7 DNA polymerase in complex with a primer-template DNA containing a disordered n-2 aminofluorene on the template, crystallized with dideoxy-ctp as the incoming nucleotide.. SNAP output
1x9w transferase-electron transport-DNA X-ray (2.3 Å) Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc.Natl.Acad.Sci.Usa, 101, 16186-16191. doi: 10.1073/pnas.0406516101. T7 DNA polymerase in complex with a primer-template DNA containing a disordered n-2 aminofluorene on the template, crystallized with dideoxy-atp as the incoming nucleotide.. SNAP output
1xbr transcription-DNA X-ray (2.5 Å) Muller CW, Herrmann BG (1997) "Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor." Nature, 389, 884-888. doi: 10.1038/39929. T domain from xenopus laevis bound to DNA. SNAP output
1xc8 hydrolase-DNA X-ray (1.95 Å) Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B (2004) "Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase." J.Biol.Chem., 279, 44074-44083. doi: 10.1074/jbc.M405928200. Crystal structure complex between the wild-type lactococcus lactis fpg (mutm) and a fapy-dg containing DNA. SNAP output
1xc9 transferase-DNA X-ray (1.9 Å) Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese LS (2005) "Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication." J.Biol.Chem., 280, 3764-3770. doi: 10.1074/jbc.M411276200. Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication. SNAP output
1xf2 immune system-DNA X-ray (2.3 Å) Schuermann JP, Prewitt SP, Davies C, Deutscher SL, Tanner JJ (2005) "Evidence for Structural Plasticity of Heavy Chain Complementarity-determining Region 3 in Antibody-ssDNA Recognition." J.Mol.Biol., 347, 965-978. doi: 10.1016/j.jmb.2005.02.008. Structure of fab DNA-1 complexed with dt3. SNAP output
1xhu hydrolase-DNA X-ray (2.95 Å) Etzkorn C, Horton NC (2004) "Mechanistic Insights from the Structures of HincII Bound to Cognate DNA Cleaved from Addition of Mg(2+) and Mn(2+)." J.Mol.Biol., 343, 833-849. doi: 10.1016/j.jmb.2004.08.082. Hincii bound to cleaved, cognate DNA containing gtcgac. SNAP output
1xhv hydrolase-DNA X-ray (2.5 Å) Etzkorn C, Horton NC (2004) "Mechanistic Insights from the Structures of HincII Bound to Cognate DNA Cleaved from Addition of Mg(2+) and Mn(2+)." J.Mol.Biol., 343, 833-849. doi: 10.1016/j.jmb.2004.08.082. Hincii bound to cleaved cognate DNA gtcgac and mn2+. SNAP output
1xhz transferase-DNA X-ray (2.7 Å) Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2004) "Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage phi29." Mol.Cell, 16, 609-618. doi: 10.1016/j.molcel.2004.10.019. Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex. SNAP output
1xi1 transferase-DNA X-ray (2.2 Å) Wang J, Kamtekar S, Berman AJ, Steitz TA (2005) "Correction of X-ray intensities from single crystals containing lattice-translocation defects." Acta Crystallogr.,Sect.D, 61, 67-74. doi: 10.1107/S0907444904026721. Phi29 DNA polymerase ssDNA complex, monoclinic crystal form. SNAP output
1xjv transcription-DNA X-ray (1.73 Å) Lei M, Podell ER, Cech TR (2004) "Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection." Nat.Struct.Mol.Biol., 11, 1223-1229. doi: 10.1038/nsmb867. Crystal structure of human pot1 bound to telomeric single-stranded DNA (ttagggttag). SNAP output
1xns hydrolase, ligase-DNA X-ray (2.8 Å) Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD (2005) "Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination." J.Biol.Chem., 280, 8290-8299. doi: 10.1074/jbc.M411668200. Peptide trapped holliday junction intermediate in cre-loxp recombination. SNAP output
1xo0 hydrolase, ligase-DNA X-ray (2.0 Å) Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD (2005) "Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination." J.Biol.Chem., 280, 8290-8299. doi: 10.1074/jbc.M411668200. High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination. SNAP output
1xpx transcription regulation-DNA X-ray (2.8 Å) Yousef MS, Matthews BW (2005) "Structural Basis of Prospero-DNA Interaction: Implications for Transcription Regulationin Developing Cells." STRUCTURE, 13, 601-607. doi: 10.1016/j.str.2005.01.023. Structural basis of prospero-DNA interaction; implications for transcription regulation in developing cells. SNAP output
1xs9 transcription-DNA NMR Dangi B, Gronenborn AM, Rosner JL, Martin RG (2004) "Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA." Mol.Microbiol., 54, 45-59. doi: 10.1111/j.1365-2958.2004.04250.x. A model of the ternary complex formed between mara, the alpha-ctd of RNA polymerase and DNA. SNAP output
1xsd transcription-DNA X-ray (2.7 Å) Safo MK, Zhao Q, Ko T-P, Musayev FN, Robinson H, Scarsdale N, Wang AH-J, Archer GL (2005) "Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons." J.Bacteriol., 187, 1833-1844. doi: 10.1128/JB.187.5.1833-1844.2005. Crystal structure of the blai repressor in complex with DNA. SNAP output
1xsl transferase-DNA X-ray (2.3 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC (2005) "A closed conformation for the Pol lambda catalytic cycle." Nat.Struct.Mol.Biol., 12, 97-98. doi: 10.1038/nsmb876. Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap. SNAP output
1xsn transferase-DNA X-ray (1.95 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC (2005) "A closed conformation for the Pol lambda catalytic cycle." Nat.Struct.Mol.Biol., 12, 97-98. doi: 10.1038/nsmb876. Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddttp. SNAP output
1xsp transferase-DNA X-ray (2.2 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC (2005) "A closed conformation for the Pol lambda catalytic cycle." Nat.Struct.Mol.Biol., 12, 97-98. doi: 10.1038/nsmb876. Crystal structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate. SNAP output
1xvk DNA-antibiotic X-ray (1.26 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. X-ray structure of an echinomycin-(gcgtacgc)2 complex. SNAP output
1xvn DNA-antibiotic X-ray (1.5 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. Echinomycin (acgtacgt)2 complex. SNAP output
1xvr DNA-antibiotic X-ray (1.4 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. Echinomycin (cgtacg)2 complex. SNAP output
1xyi structural protein-DNA X-ray (1.45 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." Nucleic Acids Res., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d double mutant val26ala-met29ala in complex with DNA gcgatcgc. SNAP output
1y1w transcription,transferase-DNA-RNA hybrid X-ray (4.0 Å) Kettenberger H, Armache K-J, Cramer P (2004) "Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS." Mol.Cell, 16, 955-965. doi: 10.1016/j.molcel.2004.11.040. Complete RNA polymerase ii elongation complex. SNAP output
1y6f transferase-DNA X-ray (2.4 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp-glucose and DNA containing an abasic site. SNAP output
1y6g transferase-DNA X-ray (2.8 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp and a 13_mer DNA containing a hmu base at 2.8 Å resolution. SNAP output
1y77 transcription,transferase-DNA-RNA hybrid X-ray (4.5 Å) Kettenberger H, Armache K-J, Cramer P (2004) "Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS." Mol.Cell, 16, 955-965. doi: 10.1016/j.molcel.2004.11.040. Complete RNA polymerase ii elongation complex with substrate analogue gmpcpp. SNAP output
1y8z transferase-DNA X-ray (1.9 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a hmu base at 1.9 Å resolution. SNAP output
1ya6 transferase-DNA X-ray (2.4 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a central a:g mismatch. SNAP output
1yf3 transferase-DNA X-ray (2.29 Å) Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) "Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase." Cell(Cambridge,Mass.), 121, 349-361. doi: 10.1016/j.cell.2005.02.021. T4dam in complex with adohcy and 13-mer oligonucleotide making non- and semi-specific (~1-4) contact. SNAP output
1yfh transferase-DNA X-ray (3.01 Å) Duguid EM, Rice PA, He C (2005) "The structure of the human AGT protein bound to DNA and its implications for damage detection." J.Mol.Biol., 350, 657-666. doi: 10.1016/j.jmb.2005.05.028. Wt human o6-alkylguanine-DNA alkyltransferase bound to DNA containing an alkylated cytosine. SNAP output
1yfi hydrolase-DNA X-ray (2.7 Å) Xu QS, Roberts RJ, Guo H-C (2005) "Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure." Protein Sci., 14, 2590-2600. doi: 10.1110/ps.051565105. Crystal structure of restriction endonuclease mspi in complex with its cognate DNA in p212121 space group. SNAP output
1yfj transferase-DNA X-ray (2.69 Å) Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) "Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase." Cell(Cambridge,Mass.), 121, 349-361. doi: 10.1016/j.cell.2005.02.021. T4dam in complex with adohcy and 15-mer oligonucleotide showing semi-specific and specific contact. SNAP output
1yfl transferase-DNA X-ray (3.09 Å) Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) "Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase." Cell(Cambridge,Mass.), 121, 349-361. doi: 10.1016/j.cell.2005.02.021. T4dam in complex with sinefungin and 16-mer oligonucleotide showing semi-specific and specific contact and flipped base. SNAP output
1ynw transcription-DNA X-ray (3.0 Å) Shaffer PL, Gewirth DT (2004) "Structural analysis of RXR-VDR interactions on DR3 DNA." J.Steroid Biochem.Mol.Biol., 89-90, 215-219. doi: 10.1016/j.jsbmb.2004.03.084. Crystal structure of vitamin d receptor and 9-cis retinoic acid receptor DNA-binding domains bound to a dr3 response element. SNAP output
1yo5 transcription-DNA X-ray (2.0 Å) Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y, Ghosh D, Gulick AM (2005) "Analysis of the 2.0 A Crystal Structure of the Protein-DNA Complex of the Human PDEF Ets Domain Bound to the Prostate Specific Antigen Regulatory Site." Biochemistry, 44, 7095-7106. doi: 10.1021/bi047352t. Analysis of the 2.0a crystal structure of the protein-DNA complex of human pdef ets domain bound to the prostate specific antigen regulatory site. SNAP output
1yqk hydrolase-DNA X-ray (2.5 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA. SNAP output
1yql hydrolase-DNA X-ray (2.6 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Catalytically inactive hogg1 crosslinked with 7-deaza-8-azaguanine containing DNA. SNAP output
1yqm hydrolase-DNA X-ray (2.5 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA. SNAP output
1yqr hydrolase-DNA X-ray (2.43 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxog containing DNA. SNAP output
1yrn DNA binding protein-DNA X-ray (2.5 Å) Li T, Stark MR, Johnson AD, Wolberger C (1995) "Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA." Science, 270, 262-269. Crystal structure of the mata1-matalpha2 homeodomain heterodimer bound to DNA. SNAP output
1ysa transcription-DNA X-ray (2.9 Å) Ellenberger TE, Brandl CJ, Struhl K, Harrison SC (1992) "The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex." Cell(Cambridge,Mass.), 71, 1223-1237. doi: 10.1016/S0092-8674(05)80070-4. The gcn4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. SNAP output
1ytb transcription-DNA X-ray (1.8 Å) Kim Y, Geiger JH, Hahn S, Sigler PB (1993) "Crystal structure of a yeast TBP/TATA-box complex." Nature, 365, 512-520. doi: 10.1038/365512a0. Crystal structure of a yeast tbp-tata-box complex. SNAP output
1ytf transcription-DNA X-ray (2.5 Å) Tan S, Hunziker Y, Sargent DF, Richmond TJ (1996) "Crystal structure of a yeast TFIIA/TBP/DNA complex." Nature, 381, 127-134. doi: 10.1038/381127a0. Yeast tfiia-tbp-DNA complex. SNAP output
1yui DNA binding protein-DNA NMR Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn AM, Clore GM (1997) "The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode." Nat.Struct.Biol., 4, 122-132. doi: 10.1038/nsb0297-122. Solution NMR structure of the gaga factor-DNA complex, regularized mean structure. SNAP output
1yuj DNA binding protein-DNA NMR Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn AM, Clore GM (1997) "The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode." Nat.Struct.Biol., 4, 122-132. doi: 10.1038/nsb0297-122. Solution NMR structure of the gaga factor-DNA complex, 50 structures. SNAP output
1z19 DNA binding protein-DNA X-ray (2.8 Å) Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T (2005) "A structural basis for allosteric control of DNA recombination by lambda integrase." Nature, 435, 1059-1066. doi: 10.1038/nature03657. Crystal structure of a lambda integrase(75-356) dimer bound to a coc' core site. SNAP output
1z1b DNA binding protein-DNA X-ray (3.8 Å) Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T (2005) "A structural basis for allosteric control of DNA recombination by lambda integrase." Nature, 435, 1059-1066. doi: 10.1038/nature03657. Crystal structure of a lambda integrase dimer bound to a coc' core site. SNAP output
1z1c virus-DNA X-ray (3.5 Å) Kontou M, Govindasamy L, Nam HJ, Bryant N, Llamas-Saiz AL, Foces-Foces C, Hernando E, Rubio MP, McKenna R, Almendral JM, Agbandje-McKenna M (2005) "Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice." J.Virol., 79, 10931-10943. doi: 10.1128/JVI.79.17.10931-10943.2005. Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice. SNAP output
1z1g DNA binding protein-DNA X-ray (4.4 Å) Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T (2005) "A structural basis for allosteric control of DNA recombination by lambda integrase." Nature, 435, 1059-1066. doi: 10.1038/nature03657. Crystal structure of a lambda integrase tetramer bound to a holliday junction. SNAP output
1z63 hydrolase-DNA complex X-ray (3.0 Å) Durr H, Korner C, Muller M, Hickmann V, Hopfner KP (2005) "X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA." Cell(Cambridge,Mass.), 121, 363-373. doi: 10.1016/j.cell.2005.03.026. Sulfolobus solfataricus swi2-snf2 atpase core in complex with dsDNA. SNAP output
1z9c transcription-DNA X-ray (2.64 Å) Hong M, Fuangthong M, Helmann JD, Brennan RG (2005) "Structure of an OhrR-ohrA Operator Complex Reveals the DNA Binding Mechanism of the MarR Family." Mol.Cell, 20, 131-141. doi: 10.1016/j.molcel.2005.09.013. Crystal structure of ohrr bound to the ohra promoter: structure of marr family protein with operator DNA. SNAP output
1zaa transcription-DNA X-ray (2.1 Å) Pavletich NP, Pabo CO (1991) "Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A." Science, 252, 809-817. Zinc finger-DNA recognition: crystal structure of a zif268-DNA complex at 2.1 angstroms. SNAP output
1zay transcription-DNA X-ray (2.7 Å) Zheleznova EE, Brennan RG "The Roles of Exocyclic Groups in the Central Base-Pair Step in Modulating the Affinity of PurR for its Operator." Purine repressor-hypoxanthine-modified-purf-operator complex. SNAP output
1zbb structural protein-DNA X-ray (9.0 Å) Schalch T, Duda S, Sargent DF, Richmond TJ (2005) "X-ray structure of a tetranucleosome and its implications for the chromatin fibre." Nature, 436, 138-141. doi: 10.1038/nature03686. Structure of the 4_601_167 tetranucleosome. SNAP output
1zbi hydrolase-RNA-DNA X-ray (1.85 Å) Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005) "Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis." Cell(Cambridge,Mass.), 121, 1005-1016. doi: 10.1016/j.cell.2005.04.024. Bacillus halodurans rnase h catalytic domain mutant d132n in complex with 12-mer RNA-DNA hybrid. SNAP output
1zbl hydrolase-RNA-DNA X-ray (2.2 Å) Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005) "Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis." Cell(Cambridge,Mass.), 121, 1005-1016. doi: 10.1016/j.cell.2005.04.024. Bacillus halodurans rnase h catalytic domain mutant d192n in complex with 12-mer RNA-DNA hybrid. SNAP output
1zet replication-DNA X-ray (2.3 Å) Wang J (2005) "DNA polymerases: Hoogsteen base-pairing in DNA replication?." Nature, 437, E6-7; discussion E7. doi: 10.1038/nature04199. X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota. SNAP output
1zg1 transcription-DNA X-ray (2.3 Å) Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML, Gunsalus RP, Dickerson RE (2005) "Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator." Biochemistry, 44, 14538-14552. doi: 10.1021/bi050734u. Narl complexed to nirb promoter non-palindromic tail-to-tail DNA site. SNAP output
1zg5 transcription-DNA X-ray (2.3 Å) Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML, Gunsalus RP, Dickerson RE (2005) "Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator." Biochemistry, 44, 14538-14552. doi: 10.1021/bi050734u. Narl complexed to narg-89 promoter palindromic tail-to-tail DNA site. SNAP output
1zgw transcription regulator-DNA NMR He C, Hus JC, Sun LJ, Zhou P, Norman DP, Doetsch V, Wei H, Gross JD, Lane WS, Wagner G, Verdine GL (2005) "A Methylation-Dependent Electrostatic Switch Controls DNA Repair and Transcriptional Activation by E. coli Ada." Mol.Cell, 20, 117-129. doi: 10.1016/j.molcel.2005.08.013. NMR structure of e. coli ada protein in complex with DNA. SNAP output
1zjm DNA-lyase-transferase X-ray (2.1 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2005) "Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate." STRUCTURE, 13, 1225-1233. doi: 10.1016/j.str.2005.05.010. Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus. SNAP output
1zjn DNA-lyase-transferase X-ray (2.61 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2005) "Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate." STRUCTURE, 13, 1225-1233. doi: 10.1016/j.str.2005.05.010. Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus with dgtp. SNAP output
1zla structural protein-DNA X-ray (2.9 Å) Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM (2006) "The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA." Science, 311, 856-861. doi: 10.1126/science.1120541. X-ray structure of a kaposi's sarcoma herpesvirus lana peptide bound to the nucleosomal core. SNAP output
1zlk transcription-DNA X-ray (3.1 Å) Wisedchaisri G, Wu M, Rice AE, Roberts DM, Sherman DR, Hol WGJ (2005) "Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency." J.Mol.Biol., 354, 630-641. doi: 10.1016/j.jmb.2005.09.048. Crystal structure of the mycobacterium tuberculosis hypoxic response regulator dosr c-terminal domain-DNA complex. SNAP output
1zm5 DNA binding protein-DNA X-ray (2.5 Å) Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F (2006) "Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of TrwC Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site." J.Mol.Biol., 358, 857-869. doi: 10.1016/j.jmb.2006.02.018. Conjugative relaxase trwc in complex with orit DNA, cooper-bound structure. SNAP output
1zme transcription-DNA X-ray (2.5 Å) Swaminathan K, Flynn P, Reece RJ, Marmorstein R (1997) "Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster." Nat.Struct.Biol., 4, 751-759. doi: 10.1038/nsb0997-751. Crystal structure of put3-DNA complex. SNAP output
1zns hydrolase-DNA X-ray (2.5 Å) Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y, Cheng YS, Yuan HS (2006) "Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+." Protein Sci., 15, 269-280. doi: 10.1110/ps.051903406. Crystal structure of n-cole7-12-bp DNA-zn complex. SNAP output
1zq3 transcription-DNA NMR Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M (2006) "The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site." J.Mol.Biol., 356, 1137-1151. doi: 10.1016/j.jmb.2005.12.007. NMR solution structure of the bicoid homeodomain bound to the consensus DNA binding site taatcc. SNAP output
1zqa transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (150 millimolar) at ph 7.5. SNAP output
1zqb transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of bacl2 (150 millimolar). SNAP output
1zqc transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (15 millimolar). SNAP output
1zqd transferase-DNA X-ray (3.5 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (150 millimolar). SNAP output
1zqe transferase-DNA X-ray (3.7 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of crcl3 (saturated solution). SNAP output
1zqf transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cscl (150 millimolar). SNAP output
1zqg transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of a sodium-free artificial mother liquor at ph 6.5. SNAP output
1zqh transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of a sodium-free artificial mother liquor at ph 7.5. SNAP output
1zqi transferase-DNA X-ray (2.7 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (150 millimolar). SNAP output
1zqj transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (15 millimolar) and mgcl2 (15 millimolar). SNAP output
1zqk transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (75 millimolar) and mgcl2 (75 millimolar). SNAP output
1zql transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of mncl2 (15 millimolar) and mgcl2 (15 millimolar). SNAP output
1zqm transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of mncl2 (15 millimolar). SNAP output
1zqn transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of bacl2 (15 millimolar) and nacl (15 millimolar). SNAP output
1zqo transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (15 millimolar) and nacl (15 millimolar). SNAP output
1zqp transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (75 millimolar) and nacl (75 millimolar). SNAP output
1zqq transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of mncl2 (15 millimolar) and nacl (15 millimolar). SNAP output
1zqr transferase-DNA X-ray (3.7 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of nicl2. SNAP output
1zqs transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of tlcl (0.5 millimolar). SNAP output
1zqt transferase-DNA X-ray (3.4 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (0.01 millimolar) and zncl2 (0.02 millimolar). SNAP output
1zr2 recombination-DNA X-ray (3.9 Å) Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA (2005) "Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs." Science, 309, 1210-1215. doi: 10.1126/science.1112064. Structure of a synaptic gamma-delta resolvase tetramer covalently linked to two cleaved dnas. SNAP output
1zr4 recombination-DNA X-ray (3.4 Å) Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA (2005) "Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs." Science, 309, 1210-1215. doi: 10.1126/science.1112064. Structure of a synaptic gamma-delta resolvase tetramer covalently linked to two cleaved dnas. SNAP output
1zrc gene regulation-DNA X-ray (2.8 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-icap38 DNA. SNAP output
1zrd gene regulation-DNA X-ray (2.8 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6a;17t]icap38 DNA. SNAP output
1zre gene regulation-DNA X-ray (2.8 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6g;17c]icap38 DNA. SNAP output
1zrf gene regulation-DNA X-ray (2.1 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6c;17g]icap38 DNA. SNAP output
1zs4 transcription-DNA X-ray (1.7 Å) Jain D, Kim Y, Maxwell KL, Beasley S, Zhang R, Gussin GN, Edwards AM, Darst SA (2005) "Crystal Structure of Bacteriophage lambdacII and Its DNA Complex." Mol.Cell, 19, 259-269. doi: 10.1016/j.molcel.2005.06.006. Structure of bacteriophage lambda cii protein in complex with DNA. SNAP output
1ztg DNA, RNA binding protein-DNA X-ray (3.0 Å) Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR, Barker A, Leedman PJ, Wilce JA, Wilce MCJ (2012) "Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides." Nucleic Acids Res., 40, 5101-5114. doi: 10.1093/nar/gks058. Human alpha polyc binding protein kh1. SNAP output
1ztt transferase-DNA X-ray (1.85 Å) Goodwin KD, Long EC, Georgiadis MM (2005) "A host-guest approach for determining drug-DNA interactions: an example using netropsin." Nucleic Acids Res., 33, 4106-4116. doi: 10.1093/nar/gki717. Netropsin bound to d(cttaattcgaattaag) in complex with mmlv rt catalytic fragment. SNAP output
1ztw transferase-DNA X-ray (1.8 Å) Goodwin KD, Long EC, Georgiadis MM (2005) "A host-guest approach for determining drug-DNA interactions: an example using netropsin." Nucleic Acids Res., 33, 4106-4116. doi: 10.1093/nar/gki717. D(cttaattcgaattaag) complexed with moloney murine leukemia virus reverse transcriptase catalytic fragment. SNAP output
1zvv transcription-DNA X-ray (2.98 Å) Schumacher MA, Seidel G, Hillen W, Brennan RG (2006) "Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation." J.Biol.Chem., 281, 6793-6800. doi: 10.1074/jbc.M509977200. Crystal structure of a ccpa-crh-DNA complex. SNAP output
1zx4 cell cycle X-ray (2.98 Å) Schumacher MA, Funnell BE (2005) "Structures of ParB bound to DNA reveal mechanism of partition complex formation." Nature, 438, 516-519. doi: 10.1038/nature04149. Structure of parb bound to DNA. SNAP output
1zyq transferase-electron transport-DNA X-ray (2.7 Å) Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T (2005) "A lysine residue in the fingers subdomain of t7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine." Structure, 13, 1653-1659. doi: 10.1016/j.str.2005.07.020. T7 DNA polymerase in complex with 8og and incoming ddatp. SNAP output
1zzi structural protein-DNA X-ray (1.8 Å) Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack S (2005) "X-Ray Crystallographic and NMR Studies of the Third KH Domain of hnRNP K in Complex with Single-Stranded Nucleic Acids." STRUCTURE, 13, 1055-1067. doi: 10.1016/j.str.2005.04.008. Crystal structure analysis of the third kh domain of hnrnp k in complex with ssDNA. SNAP output
1zzj structural protein-DNA X-ray (2.3 Å) Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack S (2005) "X-Ray Crystallographic and NMR Studies of the Third KH Domain of hnRNP K in Complex with Single-Stranded Nucleic Acids." STRUCTURE, 13, 1055-1067. doi: 10.1016/j.str.2005.04.008. Structure of the third kh domain of hnrnp k in complex with 15-mer ssDNA. SNAP output
209d DNA-antibiotic X-ray (3.0 Å) Shinomiya M, Chu W, Carlson RG, Weaver RF, Takusagawa F (1995) "Structural, Physical, and Biological Characteristics of RNA.DNA Binding Agent N8-Actinomycin D." Biochemistry, 34, 8481. doi: 10.1021/BI00026A032. Structural, physical and biological characteristics of RNA:DNA binding agent n8-actinomycin d. SNAP output
2a07 transcription-DNA X-ray (1.9 Å) Stroud JC, Wu Y, Bates DL, Han A, Nowick K, Paabo S, Tong H, Chen L (2006) "Structure of the Forkhead Domain of FOXP2 Bound to DNA." Structure, 14, 159-166. doi: 10.1016/j.str.2005.10.005. Crystal structure of foxp2 bound specifically to DNA.. SNAP output
2a0i hydrolase-DNA X-ray (2.72 Å) Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF (2005) "Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the f factor relaxase." Structure, 13, 1533-1544. doi: 10.1016/j.str.2005.06.013. F factor trai relaxase domain bound to f orit single-stranded DNA. SNAP output
2a3v recombination X-ray (2.8 Å) MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul DN (2006) "Structural basis for broad DNA-specificity in integron recombination." Nature, 440, 1157-1162. doi: 10.1038/nature04643. Structural basis for broad DNA-specificity in integron recombination. SNAP output
2a66 transcription-DNA X-ray (2.2 Å) Solomon IH, Hager JM, Safi R, McDonnell DP, Redinbo MR, Ortlund EA (2005) "Crystal Structure of the Human LRH-1 DBD-DNA Complex Reveals Ftz-F1 Domain Positioning is Required for Receptor Activity." J.Mol.Biol., 354, 1091-1102. doi: 10.1016/j.jmb.2005.10.009. Human liver receptor homologue DNA-binding domain (hlrh-1 dbd) in complex with dsDNA from the hcyp7a1 promoter. SNAP output
2a6o transcription-DNA X-ray (2.6 Å) Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F (2005) "Active site sharing and subterminal hairpin recognition in a new class of DNA transposases." Mol.Cell, 20, 143-154. doi: 10.1016/j.molcel.2005.07.026. Crystal structure of the ishp608 transposase in complex with stem-loop DNA. SNAP output
2ac0 apoptosis-DNA X-ray (1.8 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex i). SNAP output
2acj hydrolase-DNA X-ray (2.6 Å) Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005) "Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases." Nature, 437, 1183-1186. doi: 10.1038/nature04088. Crystal structure of the b-z junction containing DNA bound to z-DNA binding proteins. SNAP output
2adw DNA-antibiotic X-ray (1.6 Å) Cuesta-Seijo JA, Weiss MS, Sheldrick GM (2006) "Serendipitous Sad Phasing of an Echinomycin-(Acgtacgt)2 Bisintercalation Complex." Acta Crystallogr.,Sect.D, 62, 417. doi: 10.1107/S0907444906003763. Crystal structure of echinomycin-(acgtacgt)2 solved by sad. SNAP output
2ady apoptosis-DNA X-ray (2.5 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex iv). SNAP output
2ago transferase-DNA X-ray (2.85 Å) Vaisman A, Ling H, Woodgate R, Yang W (2005) "Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis." Embo J., 24, 2957-2967. doi: 10.1038/sj.emboj.7600786. Fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. SNAP output
2agp transferase-DNA X-ray (2.9 Å) Vaisman A, Ling H, Woodgate R, Yang W (2005) "Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis." Embo J., 24, 2957-2967. doi: 10.1038/sj.emboj.7600786. Fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. SNAP output
2agq transferase-DNA X-ray (2.1 Å) Vaisman A, Ling H, Woodgate R, Yang W (2005) "Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis." Embo J., 24, 2957-2967. doi: 10.1038/sj.emboj.7600786. Fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. SNAP output
2ahi apoptosis-DNA X-ray (1.85 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex iii). SNAP output
2ajq transferase,transcription-DNA X-ray (2.6 Å) Brieba L, Ellenberger T "Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing." Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing. SNAP output
2alz transferase-DNA X-ray (2.5 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) "Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair." Structure, 13, 1569-1577. doi: 10.1016/j.str.2005.08.010. Ternary complex of hpoli with DNA and dctp. SNAP output
2aoq hydrolase-DNA X-ray (2.2 Å) Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W (2005) "MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage." Mol.Cell, 20, 155-166. doi: 10.1016/j.molcel.2005.08.019. Crystal structure of muth-unmethylated DNA complex. SNAP output
2aor hydrolase-DNA X-ray (2.0 Å) Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W (2005) "MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage." Mol.Cell, 20, 155-166. doi: 10.1016/j.molcel.2005.08.019. Crystal structure of muth-hemimethylated DNA complex. SNAP output
2aq4 transferase X-ray (2.32 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) "Rev1 employs a novel mechanism of DNA synthesis using a protein template." Science, 309, 2219-2222. doi: 10.1126/science.1116336. Ternary complex of the catalytic core of rev1 with DNA and dctp.. SNAP output
2as5 transcription-DNA X-ray (2.7 Å) Wu Y, Borde M, Heissmeyer V, Feuerer M, Lapan AD, Stroud JC, Bates DL, Guo L, Han A, Ziegler SF, Mathis D, Benoist C, Chen L, Rao A (2006) "FOXP3 Controls Regulatory T Cell Function through Cooperation with NFAT." Cell(Cambridge,Mass.), 126, 375-387. doi: 10.1016/j.cell.2006.05.042. Structure of the DNA binding domains of nfat and foxp2 bound specifically to DNA.. SNAP output
2asd transferase-DNA X-ray (1.95 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Oxog-modified insertion ternary complex. SNAP output
2asj transferase-DNA X-ray (2.35 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Oxog-modified preinsertion binary complex. SNAP output
2asl transferase-DNA X-ray (2.65 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Oxog-modified postinsertion binary complex. SNAP output
2ata apoptosis-DNA X-ray (2.2 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex ii). SNAP output
2atl transferase-DNA X-ray (2.8 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Unmodified insertion ternary complex. SNAP output
2au0 transferase-DNA X-ray (2.7 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Unmodified preinsertion binary complex. SNAP output
2axy DNA binding protein-DNA X-ray (1.7 Å) Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James TL (2005) "Crystal Structure of the First KH Domain of Human Poly(C)-binding Protein-2 in Complex with a C-rich Strand of Human Telomeric DNA at 1.7 A." J.Biol.Chem., 280, 38823-38830. doi: 10.1074/jbc.M508183200. Crystal structure of kh1 domain of human poly(c)-binding protein-2 with c-rich strand of human telomeric DNA. SNAP output
2ayb transcription-DNA X-ray (3.2 Å) Hooley E, Fairweather V, Clarke AR, Gaston K, Brady RL (2006) "The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein." Nucleic Acids Res., 34, 3897-3908. doi: 10.1093/nar/gkl466. Crystal structure of hpv6a e2 DNA binding domain bound to a 16 base pair DNA target. SNAP output
2ayg transcription-DNA X-ray (3.1 Å) Hooley E, Fairweather V, Clarke AR, Gaston K, Brady RL (2006) "The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein." Nucleic Acids Res., 34, 3897-3908. doi: 10.1093/nar/gkl466. Crystal structure of hpv6a e2 DNA binding domain bound to an 18 base pair DNA target. SNAP output
2b0d hydrolase-DNA X-ray (2.0 Å) Hiller DA, Rodriguez AM, Perona JJ (2005) "Non-cognate Enzyme-DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC." J.Mol.Biol., 354, 121-136. doi: 10.1016/j.jmb.2005.09.046. Ecorv restriction endonuclease-gaattc-ca2+. SNAP output
2b0e hydrolase-DNA X-ray (1.9 Å) Hiller DA, Rodriguez AM, Perona JJ (2005) "Non-cognate Enzyme-DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC." J.Mol.Biol., 354, 121-136. doi: 10.1016/j.jmb.2005.09.046. Ecorv restriction endonuclease-gaautc-ca2+. SNAP output
2b9s isomerase-DNA X-ray (2.27 Å) Davies DR, Mushtaq A, Interthal H, Champoux JJ, Hol WG (2006) "The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA." J.Mol.Biol., 357, 1202-1210. doi: 10.1016/j.jmb.2006.01.022. Crystal structure of heterodimeric l. donovani topoisomerase i-vanadate-DNA complex. SNAP output
2bam hydrolase-DNA X-ray (2.0 Å) Viadiu H, Aggarwal AK (1998) "The role of metals in catalysis by the restriction endonuclease BamHI." Nat.Struct.Biol., 5, 910-916. doi: 10.1038/2352. Restriction endonuclease bamhi complex with DNA and calcium ions (pre-reactive complex).. SNAP output
2bcq transferase, lyase-DNA X-ray (1.65 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired dtmp. SNAP output
2bcr transferase, lyase-DNA X-ray (1.75 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired damp. SNAP output
2bcs transferase, lyase-DNA X-ray (2.2 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired dcmp. SNAP output
2bcu transferase, lyase-DNA X-ray (2.2 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired damp and a t:t mismatch. SNAP output
2bcv transferase, lyase-DNA X-ray (2.0 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with dttp and a DNA duplex containing an unpaired dtmp. SNAP output
2bdp transferase-DNA X-ray (1.8 Å) Kiefer JR, Mao C, Braman JC, Beese LS (1998) "Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal." Nature, 391, 304-307. doi: 10.1038/34693. Crystal structure of bacillus DNA polymerase i fragment complexed to 9 base pairs of duplex DNA. SNAP output
2bgw hydrolase X-ray (2.8 Å) Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF, McDonald NQ (2005) "Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition." EMBO J., 24, 895-905. doi: 10.1038/sj.emboj.7600581. Xpf from aeropyrum pernix, complex with DNA. SNAP output
2bjc transcription regulator NMR Salinas RK, Folkers GE, Bonvin AMJJ, Das D, Boelens R, Kaptein R (2005) "Altered Specificity in DNA Binding by the Lac Repressor: A Mutant Lac Headpiece that Mimics the Gal Repressor." Chembiochem, 6, 1628. doi: 10.1002/CBIC.200500049. NMR structure of a protein-DNA complex of an altered specificity mutant of the lac repressor headpiece that mimics the gal repressor. SNAP output
2bnw DNA-binding-regulatory protein X-ray (2.45 Å) Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W (2006) "Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription." Nucleic Acids Res., 34, 1450. doi: 10.1093/NAR/GKL015. Structural basis for cooperative binding of ribbon-helix-helix omega repressor to direct DNA heptad repeats. SNAP output
2bnz DNA binding protein-DNA X-ray (2.6 Å) Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W (2006) "Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription." Nucleic Acids Res., 34, 1450. doi: 10.1093/NAR/GKL015. Structural basis for cooperative binding of ribbon-helix-helix omega repressor to inverted DNA heptad repeats. SNAP output
2bop transcription-DNA X-ray (1.7 Å) Hegde RS, Grossman SR, Laimins LA, Sigler PB (1992) "Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target." Nature, 359, 505-512. doi: 10.1038/359505a0. Crystal structure at 1.7 angstroms of the bovine papillomavirus-1 e2 DNA-binding domain bound to its DNA target. SNAP output
2bpa virus-DNA X-ray (3.0 Å) McKenna R, Xia D, Willingmann P, Ilag LL, Krishnaswamy S, Rossmann MG, Olson NH, Baker TS, Incardona NL (1992) "Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications." Nature, 355, 137-143. doi: 10.1038/355137a0. Atomic structure of single-stranded DNA bacteriophage phix174 and its functional implications. SNAP output
2bpf transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J (1994) "Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP." Science, 264, 1891-1903. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp. SNAP output
2bpg transferase-DNA X-ray (3.6 Å) Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J (1994) "Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP." Science, 264, 1891-1903. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp. SNAP output
2bq3 transferase X-ray (2.0 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2bqr transferase X-ray (2.37 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2bqu transferase X-ray (2.5 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2br0 transferase X-ray (2.17 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2bsq transcription X-ray (3.0 Å) Mattison K, Wilbur JS, So M, Brennan RG (2006) "Structure of Fitab from Neisseria Gonorrhoeae Bound to DNA Reveals a Tetramer of Toxin-Antitoxin Heterodimers Containing Pin Domains and Ribbon-Helix-Helix Motifs." J.Biol.Chem., 281, 37942. doi: 10.1074/JBC.M605198200. Fitab bound to DNA. SNAP output
2bzf DNA binding protein X-ray (2.87 Å) Bradley CM, Ronning DR, Ghirlando R, Craigie R, Dyda F (2005) "Structural Basis for DNA Bridging by Barrier-to-Autointegration Factor." Nat.Struct.Mol.Biol., 12, 935. doi: 10.1038/NSMB989. Structural basis for DNA bridging by barrier-to-autointegration factor (baf). SNAP output
2c22 polymerase X-ray (2.56 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, Guengerich FP (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c28 polymerase X-ray (2.27 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, P Guengerich F (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c2d polymerase X-ray (2.57 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, P Guengerich F (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c2e polymerase X-ray (2.61 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, P Guengerich F (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c2r polymerase X-ray (2.55 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, Guengerich FP (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c5r DNA-binding protein-DNA X-ray (2.9 Å) Albert A, Munoz-Espin D, Jimenez M, Asensio JL, Hermoso JA, Salas M, Meijer WJJ (2005) "Structural Basis for Membrane Anchorage of Viral Phi 29 DNA During Replication." J.Biol.Chem., 280, 42486. doi: 10.1074/JBC.C500429200. The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA. SNAP output
2c62 transcription X-ray (1.74 Å) Werten S, Moras D (2006) "A Global Transcription Cofactor Bound to Juxtaposed Strands of Unwound DNA." Nat.Struct.Mol.Biol., 13, 181. doi: 10.1038/NSMB1044. Crystal structure of the human transcription cofactor pc4 in complex with single-stranded DNA. SNAP output
2c6y transcription regulation X-ray (2.4 Å) Tsai K-L, Huang C-Y, Chang C-H, Sun Y-J, Chuang W-J, Hsiao C-D (2006) "Crystal Structure of the Human Foxk1A-DNA Complex and its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins." J.Biol.Chem., 281, 17400. doi: 10.1074/JBC.M600478200. Crystal structure of interleukin enhancer-binding factor 1 bound to DNA. SNAP output
2c7a receptor-DNA X-ray (2.5 Å) Roemer SC, Donham DC, Sherman L, Pon VH, Edwards DP, Churchill MEA (2006) "Structure of the Progesterone Receptor-Deoxyribonucleic Acid Complex: Novel Interactions Required for Binding to Half-Site Response Elements." Mol.Endocrinol., 20, 3042. doi: 10.1210/ME.2005-0511. Structure of the progesterone receptor-DNA complex. SNAP output
2c7o transferase-DNA X-ray (1.9 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (pcgc:gmgc) and sah. SNAP output
2c7p transferase-DNA X-ray (1.7 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (gcgc:gmpc) and sah. SNAP output
2c7q transferase-DNA X-ray (1.85 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with g) and sah. SNAP output
2c7r transferase-DNA X-ray (1.9 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase (t250g mutant) complex with oligonucleotide containing 2-aminopurine as a target base (gpgc:gmgc) and sah. SNAP output
2c9l viral protein X-ray (2.25 Å) Petosa C, Morand P, Baudin F, Moulin M, Artero JB, Muller CW (2006) "Structural Basis of Lytic Cycle Activation by the Epstein-Barr Virus Zebra Protein." Mol.Cell, 21, 565. doi: 10.1016/J.MOLCEL.2006.01.006. Structure of the epstein-barr virus zebra protein. SNAP output
2c9n viral protein X-ray (3.3 Å) Petosa C, Morand P, Baudin F, Moulin M, Artero JB, Muller CW (2006) "Structural Basis of Lytic Cycle Activation by the Epstein-Barr Virus Zebra Protein." Mol.Cell, 21, 565. doi: 10.1016/J.MOLCEL.2006.01.006. Structure of the epstein-barr virus zebra protein at approximately 3. 5 angstrom resolution. SNAP output
2cax transcriptional repressor X-ray (2.9 Å) Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W (2006) "Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription." Nucleic Acids Res., 34, 1450. doi: 10.1093/NAR/GKL015. Structural basis for cooperative binding of ribbon-helix-helix repressor omega to mutated direct DNA heptad repeats. SNAP output
2ccz DNA-replication X-ray (2.7 Å) Huang C-Y, Hsu C-H, Sun Y-J, Wu H-N, Hsiao C-D (2006) "Complexed Crystal Structure of Replication Restart Primsome Protein Prib Reveals a Novel Single-Stranded DNA-Binding Mode." Nucleic Acids Res., 34, 3878. doi: 10.1093/NAR/GKL536. Crystal structure of e. coli primosomol protein prib bound to ssDNA. SNAP output
2cdm DNA-DNA-binding protein X-ray (2.7 Å) Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, De La Cruz F (2006) "Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of Trwc Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site." J.Mol.Biol., 358, 857. doi: 10.1016/J.JMB.2006.02.018. The structure of trwc complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. SNAP output
2cgp transcription-DNA X-ray (2.2 Å) Passner JM, Steitz TA (1997) "The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer." Proc.Natl.Acad.Sci.USA, 94, 2843-2847. doi: 10.1073/pnas.94.7.2843. Catabolite gene activator protein-DNA complex, adenosine-3',5'-cyclic-monophosphate. SNAP output
2crx hydrolase, ligase-DNA X-ray (2.5 Å) Gopaul DN, Guo F, Van Duyne GD (1998) "Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination." EMBO J., 17, 4175-4187. doi: 10.1093/emboj/17.14.4175. Structure of the holliday junction intermediate in cre-loxp site-specific recombination. SNAP output
2cv5 structural protein-DNA X-ray (2.5 Å) Tsunaka Y, Kajimura N, Tate S, Morikawa K (2005) "Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle." Nucleic Acids Res., 33, 3424-3434. doi: 10.1093/nar/gki663. Crystal structure of human nucleosome core particle. SNAP output
2d45 transcription-DNA X-ray (3.8 Å) Safo MK, Ko TP, Musayev FN, Zhao Q, Wang AH, Archer GL (2006) "Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec." Acta Crystallogr.,Sect.F, 62, 320-324. doi: 10.1107/S1744309106009742. Crystal structure of the meci-meca repressor-operator complex. SNAP output
2d55 DNA-antibiotic X-ray (3.0 Å) Kamitori S, Takusagawa F (1992) "Crystal Structure of the 2:1 Complex between D(Gaagcttc) and the Anticancer Drug Actinomycin D." J.Mol.Biol., 225, 445. doi: 10.1016/0022-2836(92)90931-9. Structural, physical and biological characteristics of RNA.DNA binding agent n8-actinomycin d. SNAP output
2d5v transcription-DNA X-ray (2.0 Å) Iyaguchi D, Yao M, Watanabe N, Nishihira J, Tanaka I (2007) "DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6." Structure, 15, 75-83. doi: 10.1016/j.str.2006.11.004. Crystal structure of hnf-6alpha DNA-binding domain in complex with the ttr promoter. SNAP output
2d7d hydrolase-DNA X-ray (2.1 Å) Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE (2006) "Structural insights into the cryptic DNA-dependent ATPase activity of UvrB." J.Mol.Biol., 357, 62-72. doi: 10.1016/j.jmb.2005.12.059. Structural insights into the cryptic DNA dependent atp-ase activity of uvrb. SNAP output
2d7g hydrolase X-ray (3.3 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the aa complex of the n-terminal domain of pria. SNAP output
2d7h hydrolase X-ray (3.0 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the ccc complex of the n-terminal domain of pria. SNAP output
2da8 DNA-antibiotic NMR Addess KJ, Sinsheimer JS, Feigon J (1993) "Solution Structure of a Complex between [N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2." Biochemistry, 32, 2498. doi: 10.1021/BI00061A006. Solution structure of a complex between (n-mecys3,n-mecys7)tandem and (d(gatatc))2. SNAP output
2db3 hydrolase-RNA X-ray (2.2 Å) Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S (2006) "Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa." Cell(Cambridge,Mass.), 125, 287-300. doi: 10.1016/j.cell.2006.01.054. Structural basis for RNA unwinding by the dead-box protein drosophila vasa. SNAP output
2ddg hydrolase-DNA X-ray (2.1 Å) Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R (2007) "Crystal structure of family 5 uracil-DNA glycosylase bound to DNA." J.Mol.Biol., 373, 839-850. doi: 10.1016/j.jmb.2007.08.022. Crystal structure of uracil-DNA glycosylase in complex with ap:g containing DNA. SNAP output
2dem hydrolase-DNA X-ray (1.95 Å) Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R (2007) "Crystal structure of family 5 uracil-DNA glycosylase bound to DNA." J.Mol.Biol., 373, 839-850. doi: 10.1016/j.jmb.2007.08.022. Crystal structure of uracil-DNA glycosylase in complex with ap:a containing DNA. SNAP output
2dgc transcription-DNA X-ray (2.2 Å) Keller W, Konig P, Richmond TJ (1995) "Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition." J.Mol.Biol., 254, 657-667. doi: 10.1006/jmbi.1995.0645. Gcn4 basic domain, leucine zipper complexed with atf-creb site DNA. SNAP output
2dlc ligase-trna X-ray (2.4 Å) Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT (2007) "Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms." Nucleic Acids Res., 35, 4289-4300. doi: 10.1093/nar/gkm417. Crystal structure of the ternary complex of yeast tyrosyl-trna synthetase. SNAP output
2dnj hydrolase-DNA X-ray (2.0 Å) Lahm A, Suck D (1991) "DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex." J.Mol.Biol., 222, 645-667. doi: 10.1016/0022-2836(91)90502-W. Dnase i-induced DNA conformation. 2 angstroms structure of a dnase i-octamer complex. SNAP output
2dp6 hydrolase-DNA X-ray (1.8 Å) Kosaka H, Nakagawa N, Masui R, Kuramitsu S "Structure of Family 5 Uracil-DNA Glycosylase Bound to DNA Reveals Insights into the Mechanism for Substrate Recognition and Catalysis." Crystal structure of uracil-DNA glycosylase in complex with ap:c containing DNA. SNAP output
2dpd DNA binding protein-DNA X-ray (3.17 Å) Vivian JP, Wilce J, Wilce MCJ "Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site." Crystal structure of the replication termination protein in complex with a pseudosymmetric b-site. SNAP output
2dpi transferase-DNA X-ray (2.3 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota." Nat.Struct.Mol.Biol., 13, 619-625. doi: 10.1038/nsmb1118. Ternary complex of hpoli with DNA and dctp. SNAP output
2dpj transferase-DNA X-ray (2.3 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota." Nat.Struct.Mol.Biol., 13, 619-625. doi: 10.1038/nsmb1118. Structure of hpoli with DNA and dttp. SNAP output
2dpu DNA binding protein-DNA X-ray (3.1 Å) Vivian JP, Wilce J, Wilce MCJ "Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA." Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer b-site DNA. SNAP output
2drp transcription-DNA X-ray (2.8 Å) Fairall L, Schwabe JW, Chapman L, Finch JT, Rhodes D (1993) "The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition." Nature, 366, 483-487. doi: 10.1038/366483a0. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger-DNA recognition. SNAP output
2dtu transferase-DNA X-ray (2.37 Å) Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie S (2007) "Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family." J.Biol.Chem., 282, 1432-1444. doi: 10.1074/jbc.M605675200. Crystal structure of the beta hairpin loop deletion variant of rb69 gp43 in complex with DNA containing an abasic site analog. SNAP output
2dwl hydrolase-DNA X-ray (3.2 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the pria protein complexed with oligonucleotides. SNAP output
2dwm hydrolase-DNA X-ray (3.15 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the pria protein complexed with oligonucleotides. SNAP output
2dwn hydrolase-DNA X-ray (3.35 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the pria protein complexed with oligonucleotides. SNAP output
2dy4 transferase-DNA X-ray (2.65 Å) Aller P, Rould MA, Hogg M, Wallace SS, Doublie S (2007) "A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol." Proc.Natl.Acad.Sci.USA, 104, 814-818. doi: 10.1073/pnas.0606648104. Crystal structure of rb69 gp43 in complex with DNA containing thymine glycol. SNAP output
2e1c transcription-DNA X-ray (2.1 Å) Yokoyama K, Ishijima SA, Koike H, Kurihara C, Shimowasa A, Kabasawa M, Kawashima T, Suzuki M (2007) "Feast/Famine Regulation by Transcription Factor FL11 for the Survival of the Hyperthermophilic Archaeon Pyrococcus OT3." Structure, 15, 1542-1554. doi: 10.1016/j.str.2007.10.015. Structure of putative hth-type transcriptional regulator ph1519-DNA complex. SNAP output
2e2h transcription,transferase-DNA-RNA hybrid X-ray (3.95 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex at 5 mm mg2+ with gtp. SNAP output
2e2i transcription,transferase-DNA-RNA hybrid X-ray (3.41 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 5 mm mg+2 with 2'-dgtp. SNAP output
2e2j transcription,transferase-DNA-RNA hybrid X-ray (3.5 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 5 mm mg+2 with gmpcpp. SNAP output
2e42 transcription-DNA X-ray (1.8 Å) Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada K, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer v285a mutant bound to a high affinity DNA fragment. SNAP output
2e43 transcription-DNA X-ray (2.1 Å) Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada K, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer k269a mutant bound to a high affinity DNA fragment. SNAP output
2e52 hydrolase-DNA X-ray (2.0 Å) Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I (2009) "Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations." Acta Crystallogr.,Sect.D, 65, 1326-1333. doi: 10.1107/S0907444909041134. Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA at 2.0 angstrom resolution. SNAP output
2ea0 hydrolase-DNA X-ray (1.4 Å) Golan G, Zharkov DO, Grollman AP, Shoham G "Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrate and mutations of critical residues." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli in complex with ap-site containing DNA substrate. SNAP output
2efw replication-DNA X-ray (2.5 Å) Vivian JP, Porter CJ, Wilce JA, Wilce MCJ (2007) "An asymmetric structure of the Bacillus subtilis replication terminator protein in complex with DNA." J.Mol.Biol., 370, 481-491. doi: 10.1016/j.jmb.2007.02.067. Crystal structure of the rtp:nrb complex from bacillus subtilis. SNAP output
2er8 transcription activator-DNA X-ray (2.85 Å) Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB, Marmorstein R (2006) "Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein." Structure, 14, 725-735. doi: 10.1016/j.str.2005.11.025. Crystal structure of leu3 DNA-binding domain complexed with a 12mer DNA duplex. SNAP output
2ere transcription activator-DNA X-ray (3.0 Å) Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB, Marmorstein R (2006) "Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein." Structure, 14, 725-735. doi: 10.1016/j.str.2005.11.025. Crystal structure of a leu3 DNA-binding domain complexed with a 15mer DNA duplex. SNAP output
2erg transcription activator-DNA X-ray (3.15 Å) Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB, Marmorstein R (2006) "Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein." Structure, 14, 725-735. doi: 10.1016/j.str.2005.11.025. Crystal structure of leu3 DNA-binding domain with a single h50c mutation complexed with a 15mer DNA duplex. SNAP output
2es2 gene regulation X-ray (1.78 Å) Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U (2006) "T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB." J.Mol.Biol., 360, 702-714. doi: 10.1016/j.jmb.2006.05.044. Crystal structure analysis of the bacillus subtilis cold shock protein bs-cspb in complex with hexathymidine. SNAP output
2etw cell cycle-DNA X-ray (1.67 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Principles of protein-DNA recognition revealed in the structural analysis of ndt80-mse DNA complexes. SNAP output
2euv cell cycle-DNA X-ray (1.94 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Principles of protein-DNA recognition revealed in the structural analysis of ndt80-mse DNA complexes. SNAP output
2euw cell cycle-DNA X-ray (1.68 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma4t). SNAP output
2eux cell cycle-DNA X-ray (1.57 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse variant va4g). SNAP output
2euz cell cycle-DNA X-ray (1.56 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant mc5t). SNAP output
2evf cell cycle-DNA X-ray (1.56 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma6t). SNAP output
2evg cell cycle-DNA X-ray (1.55 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma7t). SNAP output
2evh cell cycle-DNA X-ray (1.989 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma7g). SNAP output
2evi cell cycle-DNA X-ray (1.8 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma8t). SNAP output
2evj cell cycle-DNA X-ray (1.89 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of an ndt80-DNA complex (mse mutant ma9c). SNAP output
2ewj replication-DNA X-ray (2.7 Å) Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon C, Hill TM, Dixon NE (2006) "A molecular mousetrap determines polarity of termination of DNA replication in E. coli." Cell(Cambridge,Mass.), 125, 1309-1319. doi: 10.1016/j.cell.2006.04.040. Escherichia coli replication terminator protein (tus) complexed with DNA- locked form. SNAP output
2ex5 hydrolase-DNA X-ray (2.2 Å) Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux C, Stoddard BL (2006) "The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold." Structure, 14, 869-880. doi: 10.1016/j.str.2006.03.009. Group i intron-encoded homing endonuclease i-ceui complexed with DNA. SNAP output
2exf viral protein-DNA NMR Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF, Roques BP, Mely Y, Bouaziz S, Morellet N (2008) "How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription." J.Mol.Biol., 383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046. Solution structure of the hiv-1 nucleocapsid (ncp7(12-55)) complexed with the DNA (-) primer binding site. SNAP output
2ezd DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the second DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, minimized average structure. SNAP output
2eze DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the second DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, 35 structures. SNAP output
2ezf DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the third DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, minimized average structure. SNAP output
2ezg DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the third DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, 35 structures. SNAP output
2ezv hydrolase-DNA X-ray (2.4 Å) Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S, Schildkraut I, Aggarwal AK (2005) "A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA." Embo J., 24, 4198-4208. doi: 10.1038/sj.emboj.7600880. Crystal structure of tetrameric restriction endonuclease sfii bound to cognate DNA.. SNAP output
2f03 hydrolase-DNA X-ray (3.05 Å) Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S, Schildkraut I, Aggarwal AK (2005) "A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA." Embo J., 24, 4198-4208. doi: 10.1038/sj.emboj.7600880. Crystal structure of tetrameric restriction endonuclease sfii in complex with cognate DNA (partial bound form). SNAP output
2f55 hydrolase-DNA X-ray (3.3 Å) Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora B, Sharma SD, Cameron CE, Raney KD, Sakon J (2006) "Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus." J.Biol.Chem., 281, 3528-3535. doi: 10.1074/jbc.M512100200. Two hepatitis c virus ns3 helicase domains complexed with the same strand of DNA. SNAP output
2f5n hydrolase-DNA X-ray (2.0 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Mutm crosslinked to undamaged DNA sampling a:t base pair ic1. SNAP output
2f5o hydrolase-DNA X-ray (2.05 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Mutm crosslinked to undamaged DNA sampling g:c base pair ic3. SNAP output
2f5p hydrolase-DNA X-ray (2.0 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Mutm crosslinked to undamaged DNA sampling a:t base pair ic2. SNAP output
2f5q hydrolase-DNA X-ray (2.35 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Catalytically inactive (e3q) mutm crosslinked to oxog:c containing DNA cc2. SNAP output
2f5s hydrolase-DNA X-ray (2.35 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Catalytically inactive (e3q) mutm crosslinked to oxog:c containing DNA cc1. SNAP output
2f8n structural protein-DNA X-ray (2.9 Å) Chakravarthy S, Luger K "Nucleosomes containing the histone domain of macroH2A: In vitro possibilities." 2.9 angstrom x-ray structure of hybrid macroh2a nucleosomes. SNAP output
2f8x transcription-DNA X-ray (3.25 Å) Nam Y, Sliz P, Song L, Aster JC, Blacklow SC (2006) "Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes." Cell(Cambridge,Mass.), 124, 973-983. doi: 10.1016/j.cell.2005.12.037. Crystal structure of activated notch, csl and maml on hes-1 promoter DNA sequence. SNAP output
2fcc hydrolase X-ray (2.3 Å) Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G (2006) "Structure of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine Covalent Complex with Abasic Site-containing DNA." J.Mol.Biol., 362, 241-258. doi: 10.1016/j.jmb.2006.06.059. Crystal structure of t4 pyrimidine dimer glycosylase (t4-pdg) covalently complexed with a DNA substrate containing abasic site. SNAP output
2fd8 oxidoreductase-DNA X-ray (2.3 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
2fdc DNA binding protein-DNA X-ray (3.3 Å) Truglio JJ, Karakas E, Rhau B, Wang H, DellaVecchia MJ, Van Houten B, Kisker C (2006) "Structural basis for DNA recognition and processing by UvrB." Nat.Struct.Mol.Biol., 13, 360-364. doi: 10.1038/nsmb1072. Structural basis of DNA damage recognition and processing by uvrb: crystal structure of a uvrb-DNA complex. SNAP output
2fdf oxidoreductase-DNA X-ray (2.1 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with co(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
2fdg oxidoreductase-DNA X-ray (2.2 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), succinate, and methylated trinucleotide t-mea-t. SNAP output
2fdh oxidoreductase-DNA X-ray (2.1 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with mn(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
2fdi oxidoreductase-DNA X-ray (1.8 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t (air 3 hours). SNAP output
2fdk oxidoreductase-DNA X-ray (2.3 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t (air 9 days). SNAP output
2ff0 hormone-growth factor-DNA NMR Little TH, Zhang Y, Matulis CK, Weck J, Zhang Z, Ramachandran A, Mayo KE, Radhakrishnan I (2006) "Sequence-specific deoxyribonucleic Acid (DNA) recognition by steroidogenic factor 1: a helix at the carboxy terminus of the DNA binding domain is necessary for complex stability." Mol.Endocrinol., 20, 831-843. doi: 10.1210/me.2005-0384. Solution structure of steroidogenic factor 1 DNA binding domain bound to its target sequence in the inhibin alpha-subunit promoter. SNAP output
2fio transcription-DNA X-ray (2.7 Å) Badia D, Camacho A, Perez-Lago L, Escandon C, Salas M, Coll M (2006) "The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA." Mol.Cell, 22, 73-81. doi: 10.1016/j.molcel.2006.02.019. Phage phi29 transcription regulator p4-DNA complex. SNAP output
2fj7 structural protein-DNA X-ray (3.2 Å) Bao Y, White CL, Luger K (2006) "Nucleosome Core Particles Containing a Poly(dA.dT) Sequence Element Exhibit a Locally Distorted DNA Structure." J.Mol.Biol., 361, 617-624. doi: 10.1016/j.jmb.2006.06.051. Crystal structure of nucleosome core particle containing a poly (da.dt) sequence element. SNAP output
2fjv transferase-DNA X-ray (2.05 Å) Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC (2006) "A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine." J.Am.Chem.Soc., 128, 7846-7854. doi: 10.1021/ja0600936. Rt29 bound to d(cttaattcgaattaag) in complex with mmlv rt catalytic fragment. SNAP output
2fjw transferase-DNA X-ray (1.95 Å) Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC (2006) "A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine." J.Am.Chem.Soc., 128, 7846-7854. doi: 10.1021/ja0600936. D(cttgaatgcattcaag) in complex with mmlv rt catalytic fragment. SNAP output
2fjx transferase-DNA X-ray (1.8 Å) Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC (2006) "A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine." J.Am.Chem.Soc., 128, 7846-7854. doi: 10.1021/ja0600936. Rt29 bound to d(cttgaatgcattcaag) in complex with mmlv rt catalytic fragment. SNAP output
2fkc hydrolase-DNA X-ray (2.39 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Crystal form i of pre-reactive complex of restriction endonuclease hinp1i with cognate DNA and calcium ion. SNAP output
2fkh hydrolase-DNA X-ray (3.09 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Crystal form ii of pre-reactive complex of restriction endonuclease hinp1i with cognate DNA and calcium ions. SNAP output
2fl3 hydrolase-DNA X-ray (2.39 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Binary complex of restriction endonuclease hinp1i with cognate DNA. SNAP output
2flc hydrolase-DNA X-ray (2.59 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Post-reactive complex of restriction endonuclease hinp1i with nicked cognate DNA and magnesium ions. SNAP output
2fld hydrolase-DNA X-ray (2.0 Å) Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D (2006) "Computational redesign of endonuclease DNA binding and cleavage specificity." Nature, 441, 656-659. doi: 10.1038/nature04818. I-msoi re-designed for altered DNA cleavage specificity. SNAP output
2fll replication-DNA X-ray (2.6 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site." Structure, 14, 749-755. doi: 10.1016/j.str.2006.01.010. Ternary complex of human DNA polymerase iota with DNA and dttp. SNAP output
2fln replication-DNA X-ray (2.5 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site." Structure, 14, 749-755. doi: 10.1016/j.str.2006.01.010. Binary complex of catalytic core of human DNA polymerase iota with DNA (template a). SNAP output
2flp replication-DNA X-ray (2.4 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site." Structure, 14, 749-755. doi: 10.1016/j.str.2006.01.010. Binary complex of the catalytic core of human DNA polymerase iota with DNA (template g). SNAP output
2fmp transferase-DNA X-ray (1.65 Å) Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH (2006) "Magnesium-induced assembly of a complete DNA polymerase catalytic complex." Structure, 14, 757-766. doi: 10.1016/j.str.2006.01.011. DNA polymerase beta with a terminated gapped DNA substrate and ddctp with sodium in the catalytic site. SNAP output
2fmq transferase-DNA X-ray (2.2 Å) Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH (2006) "Magnesium-induced assembly of a complete DNA polymerase catalytic complex." Structure, 14, 757-766. doi: 10.1016/j.str.2006.01.011. Sodium in active site of DNA polymerase beta. SNAP output
2fms transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH (2006) "Magnesium-induced assembly of a complete DNA polymerase catalytic complex." Structure, 14, 757-766. doi: 10.1016/j.str.2006.01.011. DNA polymerase beta with a gapped DNA substrate and dumpnpp with magnesium in the catalytic site. SNAP output
2fo1 gene regulation-signalling protein-DNA X-ray (3.12 Å) Wilson JJ, Kovall RA (2006) "Crystal structure of the CSL-Notch-Mastermind ternary complex bound to DNA." Cell(Cambridge,Mass.), 124, 985-996. doi: 10.1016/j.cell.2006.01.035. Crystal structure of the csl-notch-mastermind ternary complex bound to DNA. SNAP output
2fqz hydrolase-DNA X-ray (2.0 Å) Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V (2006) "Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease." Embo J., 25, 2219-2229. doi: 10.1038/sj.emboj.7601096. Metal-depleted ecl18ki in complex with uncleaved DNA. SNAP output
2fr4 immune system-DNA X-ray (1.95 Å) Ou Z, Bottoms CA, Henzl MT, Tanner JJ (2007) "Impact of DNA hairpin folding energetics on antibody-ssDNA association." J.Mol.Biol., 374, 1029-1040. doi: 10.1016/j.jmb.2007.09.084. Structure of fab DNA-1 complexed with a stem-loop DNA ligand. SNAP output
2fvp transferase-DNA X-ray (2.25 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2fvq transferase-DNA X-ray (2.3 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2fvr transferase-DNA X-ray (2.2 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2fvs transferase-DNA X-ray (2.35 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2g1p transferase-DNA X-ray (1.89 Å) Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X (2006) "Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase." J.Mol.Biol., 358, 559-570. doi: 10.1016/j.jmb.2006.02.028. Structure of e. coli DNA adenine methyltransferase (dam). SNAP output
2g8f hydrolase-RNA-DNA X-ray (1.65 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain e188a mutant in complex with mg2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8h hydrolase-RNA-DNA X-ray (1.85 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d192n mutant in complex with mg2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8i hydrolase-RNA-DNA X-ray (1.65 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d192n mutant in complex with mn2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8k hydrolase-RNA-DNA X-ray (1.65 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d192n mutant in complex with ca2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8u hydrolase-RNA-DNA X-ray (2.7 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d132n mutant in complex with mg2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8v hydrolase-RNA-DNA X-ray (1.85 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain e188a mutant in complex with mg2+ and RNA-DNA hybrid (reaction product). SNAP output
2g8w hydrolase-RNA-DNA X-ray (2.05 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain e188a mutant in complex with ca2+ and RNA-DNA hybrid. SNAP output
2gat transcription-DNA NMR Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) "Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution." Nat.Struct.Biol., 4, 732-738. doi: 10.1038/nsb0997-732. Solution structure of the c-terminal domain of chicken gata-1 bound to DNA, NMR, regularized mean structure. SNAP output
2gb7 hydrolase-DNA X-ray (1.7 Å) Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V (2006) "Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease." Embo J., 25, 2219-2229. doi: 10.1038/sj.emboj.7601096. Metal-depleted ecl18ki in complex with uncleaved, modified DNA. SNAP output
2ge5 hydrolase-DNA X-ray (2.4 Å) Hiller DA, Perona JJ (2006) "Positively Charged C-Terminal Subdomains of EcoRV Endonuclease: Contributions to DNA Binding, Bending, and Cleavage." Biochemistry, 45, 11453-11463. doi: 10.1021/bi0606400. Ecorv restriction endonuclease c-terminal deletion mutant-gatatc-ca2+. SNAP output
2geq transcription-DNA X-ray (2.3 Å) Ho WC, Fitzgerald MX, Marmorstein R (2006) "Structure of the p53 Core Domain Dimer Bound to DNA." J.Biol.Chem., 281, 20494-20502. doi: 10.1074/jbc.M603634200. Crystal structure of a p53 core dimer bound to DNA. SNAP output
2gie hydrolase-DNA X-ray (2.6 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Hincii bound to cognate DNA gttaac. SNAP output
2gig hydrolase-DNA X-ray (1.83 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Alteration of sequence specificity of the type ii restriction endonuclease hincii through an indirect readout mechanism. SNAP output
2gih hydrolase-DNA X-ray (2.5 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Q138f hincii bound to cognate DNA gtcgac and ca2+. SNAP output
2gii hydrolase-DNA X-ray (2.3 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Q138f hincii bound to cognate DNA gttaac. SNAP output
2gij hydrolase-DNA X-ray (1.93 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Q138f hincii bound to cognate DNA gttaac and ca2+. SNAP output
2gkd toxin-DNA NMR Singh S, Hager MH, Zhang C, Griffith BR, Lee MS, Hallenga K, Markley JL, Thorson JS (2006) "Structural insight into the self-sacrifice mechanism of enediyne resistance." Acs Chem.Biol., 1, 451-460. doi: 10.1021/cb6002898. Structural insight into self-sacrifice mechanism of enediyne resistance. SNAP output
2gli transcription-DNA X-ray (2.6 Å) Pavletich NP, Pabo CO (1993) "Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers." Science, 261, 1701-1707. Five-finger gli-DNA complex. SNAP output
2glo transcription-DNA NMR Cordier F, Hartmann B, Rogowski M, Affolter M, Grzesiek S (2006) "DNA recognition by the brinker repressor - an extreme case of coupling between binding and folding." J.Mol.Biol., 361, 659-672. doi: 10.1016/j.jmb.2006.06.045. Solution structure of the brinker DNA binding domain in complex with the omb enhancer. SNAP output
2gm4 recombination, DNA X-ray (3.5 Å) Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV, Boocock MR, Grindley ND, Steitz TA (2006) "Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination." Proc.Natl.Acad.Sci.Usa, 103, 10642-10647. doi: 10.1073/pnas.0604062103. An activated, tetrameric gamma-delta resolvase: hin chimaera bound to cleaved DNA. SNAP output
2gws transferase-DNA X-ray (2.4 Å) Picher AJ, Garcia-Diaz M, Bebenek K, Pedersen LC, Kunkel TA, Blanco L (2006) "Promiscuous mismatch extension by human DNA polymerase lambda." Nucleic Acids Res., 34, 3259-3266. doi: 10.1093/nar/gkl377. Crystal structure of human DNA polymerase lambda with a g-g mismatch in the primer terminus. SNAP output
2gxa replication-DNA X-ray (3.15 Å) Enemark EJ, Joshua-Tor L (2006) "Mechanism of DNA translocation in a replicative hexameric helicase." Nature, 442, 270-275. doi: 10.1038/nature04943. Crystal structure of papillomavirus e1 hexameric helicase with ssDNA and mgadp. SNAP output
2gzk DNA-structural protein NMR Stott K, Tang GS, Lee KB, Thomas JO (2006) "Structure of a Complex of Tandem HMG Boxes and DNA." J.Mol.Biol., 360, 90-104. doi: 10.1016/j.jmb.2006.04.059. Structure of a complex of tandem hmg boxes and DNA. SNAP output
2h1k transcription-DNA X-ray (2.42 Å) Longo A, Guanga GP, Rose RB (2007) "Structural basis for induced fit mechanisms in DNA recognition by the pdx1 homeodomain." Biochemistry, 46, 2948-2957. doi: 10.1021/bi060969l. Crystal structure of the pdx1 homeodomain in complex with DNA. SNAP output
2h1o gene regulation-DNA complex X-ray (3.0 Å) Mattison K, Wilbur JS, So M, Brennan RG (2006) "Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs." J.Biol.Chem., 281, 37942-37951. doi: 10.1074/jbc.M605198200. Structure of fitab bound to ir36 DNA fragment. SNAP output
2h27 transferase-DNA X-ray (2.3 Å) Lane WJ, Darst SA (2006) "The structural basis for promoter -35 element recognition by the group IV sigma factors." Plos Biol., 4, e269. doi: 10.1371/journal.pbio.0040269. Crystal structure of escherichia coli sigmae region 4 bound to its-35 element DNA. SNAP output
2h3a immune system-DNA NMR Madl T, Van Melderen L, Mine N, Respondek M, Oberer M, Keller W, Khatai L, Zangger K (2006) "Structural Basis for Nucleic Acid and Toxin Recognition of the Bacterial Antitoxin CcdA." J.Mol.Biol., 364, 170-185. doi: 10.1016/j.jmb.2006.08.082. Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda. SNAP output
2h3c immune system-DNA NMR Madl T, Van Melderen L, Mine N, Respondek M, Oberer M, Keller W, Khatai L, Zangger K (2006) "Structural Basis for Nucleic Acid and Toxin Recognition of the Bacterial Antitoxin CcdA." J.Mol.Biol., 364, 170-185. doi: 10.1016/j.jmb.2006.08.082. Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda. SNAP output
2h7f isomerase-DNA X-ray (2.7 Å) Perry K, Hwang Y, Bushman FD, Van Duyne GD (2006) "Structural basis for specificity in the poxvirus topoisomerase." Mol.Cell, 23, 343-354. doi: 10.1016/j.molcel.2006.06.015. Structure of variola topoisomerase covalently bound to DNA. SNAP output
2h7g isomerase-DNA X-ray (1.9 Å) Perry K, Hwang Y, Bushman FD, Van Duyne GD (2006) "Structural basis for specificity in the poxvirus topoisomerase." Mol.Cell, 23, 343-354. doi: 10.1016/j.molcel.2006.06.015. Structure of variola topoisomerase non-covalently bound to DNA. SNAP output
2h7h viral protein-DNA X-ray (2.3 Å) Kim Y, Borovilos M "Crystal structure of the JUN BZIP homodimer complexed with AP-1 DNA." Crystal structure of the jun bzip homodimer complexed with ap-1 DNA. SNAP output
2h8c hydrolase-DNA X-ray (3.1 Å) Macmaster R, Sedelnikova S, Baker PJ, Bolt EL, Lloyd RG, Rafferty JB (2006) "RusA Holliday junction resolvase: DNA complex structure--insights into selectivity and specificity." Nucleic Acids Res., 34, 5577-5584. doi: 10.1093/nar/gkl447. Structure of rusa d70n in complex with DNA. SNAP output
2h8r transcription activator-DNA X-ray (3.2 Å) Lu P, Rha GB, Chi YI (2007) "Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta." Biochemistry, 46, 12071-12080. doi: 10.1021/bi7010527. Hepatocyte nuclear factor 1b bound to DNA: mody5 gene product. SNAP output
2han transcription-DNA X-ray (1.95 Å) Jakob M, Kolodziejczyk R, Orlowski M, Krzywda S, Kowalska A, Dutko-Gwozdz J, Gwozdz T, Kochman M, Jaskolski M, Ozyhar A (2007) "Novel DNA-binding element within the C-terminal extension of the nuclear receptor DNA-binding domain." Nucleic Acids Res., 35, 2705-2718. doi: 10.1093/nar/gkm162. Structural basis of heterodimeric ecdysteroid receptor interaction with natural response element hsp27 gene promoter. SNAP output
2hap gene regulation-DNA X-ray (2.5 Å) King DA, Zhang L, Guarente L, Marmorstein R (1999) "Structure of HAP1-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation." Nat.Struct.Biol., 6, 22-27. doi: 10.1038/4893. Structure of a hap1-18-DNA complex reveals that protein-DNA interactions can have direct allosteric effects on transcriptional activation. SNAP output
2hax gene regulation-DNA X-ray (1.29 Å) Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U (2007) "Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus." Febs J., 274, 1265-1279. doi: 10.1111/j.1742-4658.2007.05672.x. Crystal structure of bacillus caldolyticus cold shock protein in complex with hexathymidine. SNAP output
2hdc protein-DNA NMR Jin C, Marsden I, Chen X, Liao X (1999) "Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex." J.Mol.Biol., 289, 683-690. doi: 10.1006/jmbi.1999.2819. Structure of transcription factor genesis-DNA complex. SNAP output
2hdd transcription-DNA X-ray (1.9 Å) Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO (1997) "Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity." Structure, 5, 1047-1054. doi: 10.1016/S0969-2126(97)00256-6. Engrailed homeodomain q50k variant DNA complex. SNAP output
2heo immune system-DNA X-ray (1.7 Å) Magis C, Gasparini D, Lecoq A, Le Du MH, Stura E, Charbonnier JB, Mourier G, Boulain JC, Pardo L, Caruana A, Joly A, Lefranc M, Masella M, Menez A, Cuniasse P (2006) "Structure-based secondary structure-independent approach to design protein ligands: Application to the design of Kv1.2 potassium channel blockers." J.Am.Chem.Soc., 128, 16190-16205. doi: 10.1021/ja0646491. General structure-based approach to the design of protein ligands: application to the design of kv1.2 potassium channel blockers.. SNAP output
2hhq transferase-DNA X-ray (1.8 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. O6-methyl-guanine:t pair in the polymerase-10 basepair position. SNAP output
2hhs transferase-DNA X-ray (1.8 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. O6-methyl:c pair in the polymerase-10 basepair position. SNAP output
2hht transferase-DNA X-ray (2.05 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. C:o6-methyl-guanine pair in the polymerase-2 basepair position. SNAP output
2hhu transferase-DNA X-ray (1.8 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. C:o6-methyl-guanine in the polymerase postinsertion site (-1 basepair position). SNAP output
2hhv transferase-DNA X-ray (1.55 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. T:o6-methyl-guanine in the polymerase-2 basepair position. SNAP output
2hhw transferase-DNA X-ray (1.88 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. Ddttp:o6-methyl-guanine pair in the polymerase active site, in the closed conformation. SNAP output
2hhx transferase-DNA X-ray (2.26 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. O6-methyl-guanine in the polymerase template preinsertion site. SNAP output
2hmi immune system-DNA X-ray (2.8 Å) Ding J, Das K, Hsiou Y, Sarafianos SG, Clark Jr AD, Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E (1998) "Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution." J.Mol.Biol., 284, 1095-1111. doi: 10.1006/jmbi.1998.2208. Hiv-1 reverse transcriptase-fragment of fab 28-DNA complex. SNAP output
2hof recombination-DNA X-ray (2.4 Å) Ghosh K, Guo F, Van Duyne GD (2007) "Synapsis of loxP sites by Cre recombinase." J.Biol.Chem., 282, 24004-24016. doi: 10.1074/jbc.M703283200. Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination. SNAP output
2hoi recombination-DNA X-ray (2.601 Å) Ghosh K, Guo F, Van Duyne GD (2007) "Synapsis of loxP sites by Cre recombinase." J.Biol.Chem., 282, 24004-24016. doi: 10.1074/jbc.M703283200. Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination. SNAP output
2hos transcription-DNA X-ray (1.9 Å) Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM (2006) "Structure and properties of a re-engineered homeodomain protein-DNA interface." Acs Chem.Biol., 1, 755-760. doi: 10.1021/cb6003756. Phage-selected homeodomain bound to unmodified DNA. SNAP output
2hot transcription-DNA X-ray (2.19 Å) Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM (2006) "Structure and properties of a re-engineered homeodomain protein-DNA interface." Acs Chem.Biol., 1, 755-760. doi: 10.1021/cb6003756. Phage selected homeodomain bound to modified DNA. SNAP output
2hr1 transferase-DNA X-ray (1.96 Å) Shieh FK, Youngblood B, Reich NO (2006) "The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI." J.Mol.Biol., 362, 516-527. doi: 10.1016/j.jmb.2006.07.030. Ternary structure of wt m.hhai c5-cytosine DNA methyltransferase with unmodified DNA and adohcy. SNAP output
2ht0 transcription-DNA X-ray (2.0 Å) Swinger KK, Rice PA (2007) "Structure-based Analysis of HU-DNA Binding." J.Mol.Biol., 365, 1005-1016. doi: 10.1016/j.jmb.2006.10.024. Ihf bound to doubly nicked DNA. SNAP output
2hvh transferase-DNA X-ray (2.492 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. Ddctp:o6meg pair in the polymerase active site (0 position). SNAP output
2hvi transferase-DNA X-ray (1.98 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. Ddctp:g pair in the polymerase active site (0 position). SNAP output
2hvr ligase-RNA-DNA X-ray (2.45 Å) Nandakumar J, Shuman S, Lima CD (2006) "RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward." Cell(Cambridge,Mass.), 127, 71-84. doi: 10.1016/j.cell.2006.08.038. Structure of t4 RNA ligase 2 with nicked 5'-adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick. SNAP output
2hvs ligase-DNA-RNA X-ray (2.5 Å) Nandakumar J, Shuman S, Lima CD (2006) "RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward." Cell(Cambridge,Mass.), 127, 71-84. doi: 10.1016/j.cell.2006.08.038. Structure of t4 RNA ligase 2 with nicked 5'-adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick. SNAP output
2hvy isomerase-biosynthetic protein-RNA X-ray (2.3 Å) Li L, Ye K (2006) "Crystal structure of an H/ACA box ribonucleoprotein particle." Nature, 443, 302-307. doi: 10.1038/nature05151. Crystal structure of an h-aca box rnp from pyrococcus furiosus. SNAP output
2hw3 transferase-DNA X-ray (1.98 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. T:o6-methyl-guanine pair in the polymerase postinsertion site (-1 basepair position). SNAP output
2hzv metal binding protein-DNA X-ray (3.1 Å) Schreiter ER, Wang SC, Zamble DB, Drennan CL (2006) "NikR-operator complex structure and the mechanism of repressor activation by metal ions." Proc.Natl.Acad.Sci.Usa, 103, 13676-13681. doi: 10.1073/pnas.0606247103. Nikr-operator DNA complex. SNAP output
2i05 replication-DNA X-ray (2.6 Å) Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE "Polarity of Termination of DNA Replication in E. coli." Escherichia coli replication terminator protein (tus) complexed with tera DNA. SNAP output
2i06 replication-DNA X-ray (2.2 Å) Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE "Polarity of Termination of DNA Replication in E. coli." Escherichia coli replication terminator protein (tus) complexed with DNA- locked form. SNAP output
2i0q structural protein-DNA X-ray (1.91 Å) Buczek P, Horvath MP (2006) "Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova." J.Biol.Chem., 281, 40124-40134. doi: 10.1074/jbc.M607749200. Crystal structure of a telomere single-strand DNA-protein complex from o. nova with full-length alpha and beta telomere proteins. SNAP output
2i13 DNA binding protein-DNA X-ray (1.96 Å) Segal DJ, Crotty JW, Bhakta MS, Barbas CF, Horton NC (2006) "Structure of Aart, a Designed Six-finger Zinc Finger Peptide, Bound to DNA." J.Mol.Biol., 363, 405-421. doi: 10.1016/j.jmb.2006.08.016. Aart, a six finger zinc finger designed to recognize ann triplets. SNAP output
2i3p hydrolase-DNA X-ray (2.3 Å) Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb B, Sussman D, Stoddard BL, Seligman LM (2006) "Homing endonuclease I-CreI derivatives with novel DNA target specificities." Nucleic Acids Res., 34, 4791-4800. doi: 10.1093/nar/gkl645. K28r mutant of homing endonuclease i-crei. SNAP output
2i3q hydrolase-DNA X-ray (2.3 Å) Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb B, Sussman D, Stoddard BL, Seligman LM (2006) "Homing endonuclease I-CreI derivatives with novel DNA target specificities." Nucleic Acids Res., 34, 4791-4800. doi: 10.1093/nar/gkl645. Q44v mutant of homing endonuclease i-crei. SNAP output
2i5s hydrolase-DNA X-ray (1.9 Å) Lee JE, Bae E, Bingman CA, Phillips Jr GN, Raines RT (2008) "Structural basis for catalysis by onconase." J.Mol.Biol., 375, 165-177. doi: 10.1016/j.jmb.2007.09.089. Crystal structure of onconase with bound nucleic acid. SNAP output
2i5w hydrolase, lyase-DNA X-ray (2.6 Å) Banerjee A, Verdine GL (2006) "A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex." Proc.Natl.Acad.Sci.Usa, 103, 15020-15025. doi: 10.1073/pnas.0603644103. Structure of hogg1 crosslinked to DNA sampling a normal g adjacent to an oxog. SNAP output
2i9g transferase-DNA X-ray (2.1 Å) Batra VK, Shock DD, Prasad R, Beard WA, Hou EW, Pedersen LC, Sayer JM, Yagi H, Kumar S, Jerina DM, Wilson SH (2006) "Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features." Proc.Natl.Acad.Sci.Usa, 103, 17231-17236. doi: 10.1073/pnas.0605069103. DNA polymerase beta with a benzo[c]phenanthrene diol epoxide adducted guanine base. SNAP output
2i9k transferase-DNA X-ray (2.65 Å) Youngblood B, Shieh FK, De Los Rios S, Perona JJ, Reich NO (2006) "Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI." J.Mol.Biol., 362, 334-346. doi: 10.1016/j.jmb.2006.07.031. Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase m.hhai. SNAP output
2i9t transcription-DNA X-ray (2.8 Å) Escalante CR, Shen L, Thanos D, Aggarwal AK (2002) "Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter." Structure, 10, 383-391. doi: 10.1016/S0969-2126(02)00723-2. Structure of nf-kb p65-p50 heterodimer bound to prdii element of b-interferon promoter. SNAP output
2ia6 transferase-DNA X-ray (2.5 Å) Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H (2007) "A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment." Proc.Natl.Acad.Sci.Usa, 104, 14905-14910. doi: 10.1073/pnas.0700717104. Bypass of major benzopyrene-dg adduct by y-family DNA polymerase with unique structural gap. SNAP output
2ibk transferase-DNA X-ray (2.25 Å) Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H (2007) "A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment." Proc.Natl.Acad.Sci.Usa, 104, 14905-14910. doi: 10.1073/pnas.0700717104. Bypass of major benzopyrene-dg adduct by y-family DNA polymerase with unique structural gap. SNAP output
2ibs transferase-DNA X-ray (2.4 Å) Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden DTF, Scheidig AJ, Jones AC, Weinhold E (2007) "2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence." J.Am.Chem.Soc., 129, 6240-6248. doi: 10.1021/ja069366n. Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing 2-aminopurine at the target position. SNAP output
2ibt transferase-DNA X-ray (1.7 Å) Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden DTF, Scheidig AJ, Jones AC, Weinhold E (2007) "2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence." J.Am.Chem.Soc., 129, 6240-6248. doi: 10.1021/ja069366n. Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position. SNAP output
2ief DNA binding protein-DNA X-ray (2.601 Å) Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson RC, Clubb RT (2007) "Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly." Proc.Natl.Acad.Sci.Usa, 104, 2109-2114. doi: 10.1073/pnas.0607820104. Structure of the cooperative excisionase (xis)-DNA complex reveals a micronucleoprotein filament. SNAP output
2ih2 transferase-DNA X-ray (1.61 Å) Lenz T, Scheidig AJ, Weinhold E "Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing 5-methylpyrimidin-2(1h)-one at the target base partner position. SNAP output
2ih4 transferase-DNA X-ray (2.1 Å) Lenz T, Scheidig AJ, Weinhold E "Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing pyrrolo-dc at the target base partner position. SNAP output
2ih5 transferase-DNA X-ray (1.8 Å) Lenz T, Scheidig AJ, Weinhold E "Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing an abasic site analog at the target base partner position. SNAP output
2ihm transferase-DNA X-ray (2.4 Å) Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC (2007) "Structural insight into the substrate specificity of DNA Polymerase mu." Nat.Struct.Mol.Biol., 14, 45-53. doi: 10.1038/nsmb1180. Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide. SNAP output
2ihn hydrolase-DNA X-ray (3.0 Å) Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC (2007) "Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how FEN-1 family nucleases bind their substrates." J.Biol.Chem., 282, 31713-31724. doi: 10.1074/jbc.M703209200. Co-crystal of bacteriophage t4 rnase h with a fork DNA substrate. SNAP output
2iie recombination-DNA X-ray (2.41 Å) Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA (2007) "A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending." J.Mol.Biol., 367, 731-740. doi: 10.1016/j.jmb.2006.09.082. Single chain integration host factor protein (scihf2) in complex with DNA. SNAP output
2iif recombination-DNA X-ray (2.72 Å) Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA (2007) "A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending." J.Mol.Biol., 367, 731-740. doi: 10.1016/j.jmb.2006.09.082. Single chain integration host factor mutant protein (scihf2-k45ae) in complex with DNA. SNAP output
2imw transferase-DNA X-ray (2.05 Å) Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor JS, Yang W, Suo Z (2007) "Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase." J.Mol.Biol., 365, 590-602. doi: 10.1016/j.jmb.2006.10.008. Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. SNAP output
2irf gene regulation-DNA X-ray (2.2 Å) Fujii Y, Shimizu T, Kusumoto M, Kyogoku Y, Taniguchi T, Hakoshima T (1999) "Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences." EMBO J., 18, 5028-5041. doi: 10.1093/emboj/18.18.5028. Crystal structure of an irf-2-DNA complex.. SNAP output
2is1 hydrolase-DNA X-ray (2.9 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA-so4 complex. SNAP output
2is2 hydrolase-DNA X-ray (3.0 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA binary complex. SNAP output
2is4 hydrolase-DNA X-ray (2.6 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA-adpnp ternary complex. SNAP output
2is6 hydrolase-DNA X-ray (2.2 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA-adpmgf3 ternary complex. SNAP output
2iso transferase-DNA X-ray (2.1 Å) Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF (2007) "Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta." Biochemistry, 46, 461-471. doi: 10.1021/bi061517b. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-difluoromethylene triphosphate. SNAP output
2isp transferase-DNA X-ray (2.2 Å) Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF (2007) "Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta." Biochemistry, 46, 461-471. doi: 10.1021/bi061517b. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-methylene triphosphate. SNAP output
2isz transcription-DNA X-ray (2.403 Å) Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG (2007) "Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis." Biochemistry, 46, 436-447. doi: 10.1021/bi0609826. Crystal structure of a two-domain ider-DNA complex crystal form i. SNAP output
2it0 transcription-DNA X-ray (2.6 Å) Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG (2007) "Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis." Biochemistry, 46, 436-447. doi: 10.1021/bi0609826. Crystal structure of a two-domain ider-DNA complex crystal form ii. SNAP output
2itl DNA binding protein-DNA X-ray (1.65 Å) Bochkareva E, Martynowski D, Seitova A, Bochkarev A (2006) "Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA." Embo J., 25, 5961-5969. doi: 10.1038/sj.emboj.7601452. The origin binding domain of the sv40 large t antigen bound to the functional pen palindrome DNA (23 bp). SNAP output
2ivh hydrolase X-ray (2.8 Å) Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS (2007) "Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases." Nucleic Acids Res., 35, 584. doi: 10.1093/NAR/GKL621. Crystal structure of the nuclease domain of cole7 (h545q mutant) in complex with an 18-bp duplex DNA. SNAP output
2ivk hydrolase X-ray (2.9 Å) Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS (2007) "Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases." Nucleic Acids Res., 35, 584. doi: 10.1093/NAR/GKL621. Crystal structure of the periplasmic endonuclease vvn complexed with a 16-bp DNA. SNAP output
2j6s transferase-DNA X-ray (2.5 Å) Eoff RL, Irimia A, Egli M, Guengerich FP (2007) "Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred." J.Biol.Chem., 282, 1456. doi: 10.1074/JBC.M609661200. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, o6- methylguanine modified DNA, and datp.. SNAP output
2j6t transferase-DNA X-ray (2.6 Å) Eoff RL, Irimia A, Egli M, Guengerich FP (2007) "Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred." J.Biol.Chem., 282, 1456. doi: 10.1074/JBC.M609661200. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, o6- methylguanine modified DNA, and datp.. SNAP output
2j6u transferase-DNA X-ray (2.5 Å) Eoff RL, Irimia A, Egli M, Guengerich FP (2007) "Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred." J.Biol.Chem., 282, 1456. doi: 10.1074/JBC.M609661200. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, o6- methylguanine modified DNA, and dgtp.. SNAP output
2ja5 transferase X-ray (3.8 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "Cpd Damage Recognition by Transcribing RNA Polymerase II." Science, 315, 859. doi: 10.1126/SCIENCE.1135400. Cpd lesion containing RNA polymerase ii elongation complex a. SNAP output
2ja6 transferase X-ray (4.0 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "CPD damage recognition by transcribing RNA polymerase II." Science, 315, 859-862. doi: 10.1126/science.1135400. Cpd lesion containing RNA polymerase ii elongation complex b. SNAP output
2ja7 transferase X-ray (3.8 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "Cpd Damage Recognition by Transcribing RNA Polymerase II." Science, 315, 859. doi: 10.1126/SCIENCE.1135400. Cpd lesion containing RNA polymerase ii elongation complex c. SNAP output
2ja8 transferase X-ray (3.8 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "Cpd Damage Recognition by Transcribing RNA Polymerase II." Science, 315, 859. doi: 10.1126/SCIENCE.1135400. Cpd lesion containing RNA polymerase ii elongation complex d. SNAP output
2jea hydrolase-RNA X-ray (2.33 Å) Lorentzen E, Dziembowski A, Lindner D, Seraphin B, Conti E (2007) "RNA Channelling by the Archaeal Exosome." Embo Rep., 8, 470. doi: 10.1038/SJ.EMBOR.7400945. Structure of a 9-subunit archaeal exosome bound to RNA. SNAP output
2jef transferase-DNA X-ray (2.17 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleotide triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state and x-ray crystallography of correct and incorrect pairing. SNAP output
2jeg transferase X-ray (2.38 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleoside triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state kinetics and x- ray crystallography of correct and incorrect pairing. SNAP output
2jei transferase X-ray (2.39 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleoside triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state kinetics and x- ray crystallography of correct and incorrect pairing. SNAP output
2jej transferase X-ray (1.86 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleoside triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state kinetics and x- ray crystallography of correct and incorrect pairing. SNAP output
2jg3 transferase-DNA X-ray (1.9 Å) Pljevaljcic G, Schmidt F, Scheidig AJ, Lurz R, Weinhold E (2007) "Quantitative Labeling of Long Plasmid DNA with Nanometer Precision." Chembiochem, 8, 1516. doi: 10.1002/CBIC.200700294. Mtaqi with baz. SNAP output
2jlg transferase X-ray (2.8 Å) Poranen MM, Salgado PS, Koivunen MRL, Wright S, Bamford DH, Stuart DI, Grimes JM (2008) "Structural Explanation for the Role of Mn2+ in the Activity of {Phi}6 RNA-Dependent RNA Polymerase." Nucleic Acids Res., 36, 6633. doi: 10.1093/NAR/GKN632. Structural explanation for the role of mn in the activity of phi6 RNA-dependent RNA polymerase. SNAP output
2jp9 transcription-DNA NMR Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE (2007) "Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA." J.Mol.Biol., 372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017. Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. SNAP output
2jpa transcription-DNA NMR Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE (2007) "Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA." J.Mol.Biol., 372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017. Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. SNAP output
2jx1 transcription-DNA NMR Gamsjaeger R, Swanton MK, Kobus FJ, Lehtomaki E, Lowry JA, Kwan AH, Matthews JM, Mackay JP "Structure of the fifth zinc finger of Myelin Transcription Factor 1 in complex with RARE DNA." Structure of the fifth zinc finger of myelin transcription factor 1 in complex with rare DNA. SNAP output
2jxi DNA binding protein, DNA NMR Halouska S, Zhou Y, Becker DF, Powers R (2008) "Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex." Proteins, 75, 12-27. doi: 10.1002/prot.22217. Solution structure of the DNA-binding domain of pseudomonas putida proline utilization a (puta) bound to gttgca DNA sequence. SNAP output
2jzw viral protein-DNA NMR Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF, Roques BP, Mely Y, Bouaziz S, Morellet N (2008) "How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription." J.Mol.Biol., 383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046. How the hiv-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription. SNAP output
2k1n transcription-DNA NMR Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J (2008) "Insights into the Nature of DNA Binding of AbrB-like Transcription Factors." Structure, 16, 1702-1713. doi: 10.1016/j.str.2008.08.014. DNA bound structure of the n-terminal domain of abrb. SNAP output
2k7f replication-DNA NMR Kobayashi M, Ab E, Bonvin AM, Siegal G (2010) "Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex." J.Biol.Chem., 285, 10087-10097. doi: 10.1074/jbc.M109.054106. Haddock calculated model of the complex between the brct region of rfc p140 and dsDNA. SNAP output
2kae transcription-DNA NMR Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH, Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP (2009) "Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition by GATA-type Zinc Finger Domains." J.Biol.Chem., 284, 5827-5835. doi: 10.1074/jbc.M808712200. Data-driven model of med1:DNA complex. SNAP output
2kdz transcription-DNA NMR Lou YC, Wei SY, Rajasekaran M, Chou CC, Hsu HM, Tai JH, Chen C (2009) "NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis." Nucleic Acids Res. doi: 10.1093/nar/gkp097. Structure of the r2r3 DNA binding domain of myb1 protein from protozoan parasite trichomonas vaginalis in complex with mre-1-mre-2r DNA. SNAP output
2kei transcription-DNA NMR Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R (2009) "Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes." J.Mol.Biol., 390, 478-489. doi: 10.1016/j.jmb.2009.05.022. Refined solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o1. SNAP output
2kej transcription-DNA NMR Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R (2009) "Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes." J.Mol.Biol., 390, 478-489. doi: 10.1016/j.jmb.2009.05.022. Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o2. SNAP output
2kek transcription-DNA NMR Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R (2009) "Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes." J.Mol.Biol., 390, 478-489. doi: 10.1016/j.jmb.2009.05.022. Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o3. SNAP output
2kfn transferase-DNA X-ray (2.03 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with bridging-sulfur substrate and manganese. SNAP output
2kfz transferase-DNA X-ray (2.03 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with bridging-sulfur substrate and zinc only. SNAP output
2kkf DNA binding protein-DNA NMR Cierpicki T, Risner LE, Grembecka J, Lukasik SM, Popovic R, Omonkowska M, Shultis DD, Zeleznik-Le NJ, Bushweller JH (2010) "Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia." Nat.Struct.Mol.Biol., 17, 62-68. doi: 10.1038/nsmb.1714. Solution structure of mll cxxc domain in complex with palindromic cpg DNA. SNAP output
2kmk DNA binding protein-DNA NMR Lee S, Doddapaneni K, Hogue A, McGhee L, Meyers S, Wu Z (2010) "Solution structure of Gfi-1 zinc domain bound to consensus DNA." J.Mol.Biol., 397, 1055-1066. doi: 10.1016/j.jmb.2010.02.006. Gfi-1 zinc fingers 3-5 complexed with DNA. SNAP output
2kn7 hydrolase-DNA NMR Das D, Folkers GE, van Dijk M, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R (2012) "The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition." Structure, 20, 667-675. doi: 10.1016/j.str.2012.02.009. Structure of the xpf-single strand DNA complex. SNAP output
2ko0 transcription-DNA NMR Campagne S, Saurel O, Gervais V, Milon A (2010) "Structural determinants of specific DNA-recognition by the THAP zinc finger." Nucleic Acids Res. doi: 10.1093/nar/gkq053. Solution structure of the thap zinc finger of thap1 in complex with its DNA target. SNAP output
2ktq transferase-DNA X-ray (2.3 Å) Li Y, Korolev S, Waksman G (1998) "Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation." EMBO J., 17, 7514-7525. doi: 10.1093/emboj/17.24.7514. Open ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
2kv6 DNA binding protein-DNA NMR Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP (2010) "Minor Groove Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the Acrolein-Derived 1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a Trimethylene Linkage ." Biochemistry, 49, 6155-6164. doi: 10.1021/bi100364f. Tetrapeptide kwkk conjugated to oligonucleotide duplex by a trimethylene tether. SNAP output
2ky8 transcription-DNA NMR Scarsdale JN, Webb HD, Ginder GD, Williams DC (2011) "Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence." Nucleic Acids Res., 39, 6741-6752. doi: 10.1093/nar/gkr262. Solution structure and dynamic analysis of chicken mbd2 methyl binding domain bound to a target methylated DNA sequence. SNAP output
2kzm transferase-DNA X-ray (2.6 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with normal substrate and zinc and manganese. SNAP output
2kzz transferase-DNA X-ray (2.25 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with normal substrate and zinc only. SNAP output
2l1g transcription-DNA NMR Campagne S, Gervais V, Saurel O, Milon A "RDC refined solution structure of the THAP zinc finger of THAP1 in complex with its 16bp RRM1 DNA target." Rdc refined solution structure of the thap zinc finger of thap1 in complex with its 16bp rrm1 DNA target. SNAP output
2l45 viral protein-DNA NMR Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell NP (2012) "Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7." Biochemistry, 51, 1752-1761. doi: 10.1021/bi201834g. C-terminal zinc knuckle of the hivncp7 with DNA. SNAP output
2l46 viral protein-DNA NMR Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell NP (2012) "Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7." Biochemistry, 51, 1752-1761. doi: 10.1021/bi201834g. C-terminal zinc finger of the hivncp7 with platinated DNA. SNAP output
2l4l viral protein-DNA NMR Bazzi A, Zargarian L, Chaminade F, Boudier C, De Rocquigny H, Rene B, Mely Y, Fosse P, Mauffret O (2011) "Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC." Nucleic Acids Res., 39, 3903-3916. doi: 10.1093/nar/gkq1290. Structural insights into the ctar DNA recognition by the hiv-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of nc. SNAP output
2ld5 transcription-DNA NMR Zhang Y, Larsen CA, Stadler HS, Ames JB (2011) "Structural basis for sequence specific DNA binding and protein dimerization of HOXA13." Plos One, 6, e23069. doi: 10.1371/journal.pone.0023069. Solution NMR-derived complex structure of hoxa13 DNA binding domain bound to DNA. SNAP output
2lef gene regulation-DNA NMR Love JJ, Li X, Case DA, Giese K, Grosschedl R, Wright PE (1995) "Structural basis for DNA bending by the architectural transcription factor LEF-1." Nature, 376, 791-795. doi: 10.1038/376791a0. Lef1 hmg domain (from mouse), complexed with DNA (15bp), NMR, 12 structures. SNAP output
2lev transcription regulator-DNA multiple methods: solution nmr, solution scattering Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M (2011) "Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler." Plos Pathog., 7, e1002380. doi: 10.1371/journal.ppat.1002380. Structure of the DNA complex of the c-terminal domain of ler. SNAP output
2lex transcription-DNA NMR Yamasaki K, Kigawa T, Watanabe S, Inoue M, Yamasaki T, Seki M, Shinozaki K, Yokoyama S (2012) "Structural basis for sequence-spscific DNA recognition by an Arabidopsis WRKY transcription factor." J.Biol.Chem. doi: 10.1074/jbc.M111.279844. Complex of the c-terminal wrky domain of atwrky4 and a w-box DNA. SNAP output
2lkx transcription-DNA NMR Chaney BA, Clark-Baldwin K, Dave V, Ma J, Rance M (2005) "Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome." Biochemistry, 44, 7497-7511. doi: 10.1021/bi0473253. NMR structure of the homeodomain of pitx2 in complex with a taatcc DNA binding site. SNAP output
2lt7 metal binding protein-DNA NMR Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE (2012) "Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso." Proc.Natl.Acad.Sci.USA, 109, 15229-15234. doi: 10.1073/pnas.1213726109. Solution NMR structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA. SNAP output
2ltt transcription, DNA binding protein-DNA NMR Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW, Janjua H, Xiao R, Acton TB, Montelione GT (2013) "Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome." Nucleic Acids Res., 41, 2756-2768. doi: 10.1093/nar/gks1348. Solution NMR structure of ydbc:dt19g1 complex. northeast structural genomics consortium (nesg) target kr150. SNAP output
2m2w transferase-DNA NMR Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD (2014) "How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation." J.Am.Chem.Soc., 136, 4927-4937. doi: 10.1021/ja4102375. Ternary complex of asfv pol x with DNA and mgdgtp. SNAP output
2map transcription-DNA NMR Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH (2014) "Structural basis for -10 promoter element melting by environmentally induced sigma factors." Nat.Struct.Mol.Biol., 21, 269-276. doi: 10.1038/nsmb.2777. Solution structure of the complex formed by the region 2 of e. coli sigmae and its cognate -10 promoter element non template strand tgtcaaa.. SNAP output
2me6 transcription-DNA NMR Proudfoot A, Wuthrich K, Serrano P, Geralt M "NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens in complex with the DNA sequence CGACTAATTAGTCG." NMR structure of the homeodomain transcription factor gbx1 from homo sapiens in complex with the DNA sequence cgactaattagtcg. SNAP output
2mf8 metal binding protein-DNA NMR Gamsjaeger R, O'Connell MR, Cubeddu L, Shepherd NE, Lowry JA, Kwan AH, Vandevenne M, Swanton MK, Matthews JM, Mackay JP (2013) "A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers." J.Biol.Chem., 288, 35180-35191. doi: 10.1074/jbc.M113.482075. Haddock model of myt1 f4f5 - DNA complex. SNAP output
2mna DNA binding protein-DNA NMR Gamsjaeger R, Kariawasam R, Gimenez AX, Touma C, McIlwain E, Bernardo RE, Shepherd NE, Ataide SF, Dong Q, Richard DJ, White MF, Cubeddu L (2015) "The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus." Biochem.J., 465, 337-346. doi: 10.1042/BJ20141140. The structural basis of DNA binding by the single-stranded DNA-binding protein from sulfolobus solfataricus. SNAP output
2moe hydrolase-DNA NMR Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN, Williams DC (2015) "Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches." Nucleic Acids Res., 42, 11218-11232. doi: 10.1093/nar/gku782. Solution structure of mbd4 methyl-cytosine binding domain bound to methylated DNA. SNAP output
2mru DNA binding protein-DNA NMR Zorzini V, Buts L, Schrank E, Sterckx YG, Respondek M, Engelberg-Kulka H, Loris R, Zangger K, van Nuland NA (2015) "Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding." Nucleic Acids Res., 43, 1241-1256. doi: 10.1093/nar/gku1352. Structure of truncated ecmaze-DNA complex. SNAP output
2mxf transcription regulator-DNA NMR Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B (2015) "A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT." Plos Pathog., 11, e1004967. doi: 10.1371/journal.ppat.1004967. Structure of the DNA complex of the c-terminal domain of mvat. SNAP output
2n21 hydrolase-DNA NMR Heddi B, Cheong VV, Martadinata H, Phan AT (2015) "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex." Proc.Natl.Acad.Sci.USA, 112, 9608-9613. doi: 10.1073/pnas.1422605112. Solution structure of complex between DNA g-quadruplex and g-quadruplex recognition domain of rhau. SNAP output
2n8a transferase NMR Eustermann S, Wu WF, Langelier MF, Yang JC, Easton LE, Riccio AA, Pascal JM, Neuhaus D (2015) "Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1." Mol.Cell, 60, 742-754. doi: 10.1016/j.molcel.2015.10.032. 1h, 13c and 15n chemical shift assignments and solution structure for parp-1 f1f2 domains in complex with a DNA single-strand break. SNAP output
2nbj DNA binding protein-DNA NMR Paquet F, Loth K, Landon C "First 3D structure of an atypical protein-DNA complex." DNA-archeal mc1 protein complex structure by NMR. SNAP output
2nl8 DNA binding protein-DNA X-ray (2.3 Å) Bochkareva E, Martynowski D, Seitova A, Bochkarev A (2006) "Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA." Embo J., 25, 5961-5969. doi: 10.1038/sj.emboj.7601452. The origin binding domain of the sv40 large t antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3). SNAP output
2nll transcription-DNA X-ray (1.9 Å) Rastinejad F, Perlmann T, Evans RM, Sigler PB (1995) "Structural determinants of nuclear receptor assembly on DNA direct repeats." Nature, 375, 203-211. doi: 10.1038/375203a0. Retinoid x receptor-thyroid hormone receptor DNA-binding domain heterodimer bound to thyroid response element DNA. SNAP output
2nmv hydrolase-DNA X-ray (2.95 Å) Waters TR, Eryilmaz J, Geddes S, Barrett TE (2006) "Damage detection by the UvrABC pathway: crystal structure of UvrB bound to fluorescein-adducted DNA." Febs Lett., 580, 6423-6427. doi: 10.1016/j.febslet.2006.10.051. Damage detection by the uvrabc pathway: crystal structure of uvrb bound to fluorescein-adducted DNA. SNAP output
2nny transcription-DNA X-ray (2.58 Å) Lamber EP, Vanhille L, Textor LC, Kachalova GS, Sieweke MH, Wilmanns M (2008) "Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization." Embo J., 27, 2006-2017. doi: 10.1038/emboj.2008.117. Crystal structure of the ets1 dimer DNA complex.. SNAP output
2nob hydrolase, lyase-DNA X-ray (2.1 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive h270a human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA. SNAP output
2noe hydrolase, lyase-DNA X-ray (2.2 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive g42a human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA. SNAP output
2nof hydrolase, lyase-DNA X-ray (2.35 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of q315f human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA. SNAP output
2noh hydrolase, lyase-DNA X-ray (2.01 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive q315a human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA. SNAP output
2noi hydrolase, lyase-DNA X-ray (2.35 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of g42a human 8-oxoguanine glycosylase crosslinked to undamaged g-containing DNA. SNAP output
2nol hydrolase, lyase-DNA X-ray (2.57 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxog DNA. SNAP output
2noz hydrolase, lyase-DNA X-ray (2.43 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of q315f human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA. SNAP output
2np2 DNA binding protein-DNA X-ray (3.02 Å) Mouw KW, Rice PA (2007) "Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb." Mol.Microbiol., 63, 1319-1330. doi: 10.1111/j.1365-2958.2007.05586.x. Hbb-DNA complex. SNAP output
2np6 transferase-DNA X-ray (2.1 Å) Lenz T, Scheidig AJ, Weinhold E "Caught in the act II: Visualization of an intermediate in the DNA base-flipping pathway induced by the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing an abasic site analog at the target position. SNAP output
2np7 transferase-DNA X-ray (1.9 Å) Lenz T, Scheidig AJ, Weinhold E "Caught in the act II: Visualization of an intermediate in the DNA base-flipping pathway induced by the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing an abasic site analog at the target position and pyrrolo-dc at the target base partner position. SNAP output
2nq9 hydrolase-DNA X-ray (1.45 Å) Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA (2008) "DNA apurinic-apyrimidinic site binding and excision by endonuclease IV." Nat.Struct.Mol.Biol., 15, 515-522. doi: 10.1038/nsmb.1414. High resolution crystal structure of escherichia coli endonuclease iv (endo iv) y72a mutant bound to damaged DNA. SNAP output
2nqb structural protein-DNA X-ray (2.3 Å) Chakravarthy S, Luger K "Comparative analysis of nucleosome structures from different species." Drosophila nucleosome structure. SNAP output
2nqj hydrolase X-ray (2.45 Å) Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA (2008) "DNA apurinic-apyrimidinic site binding and excision by endonuclease IV." Nat.Struct.Mol.Biol., 15, 515-522. doi: 10.1038/nsmb.1414. Crystal structure of escherichia coli endonuclease iv (endo iv) e261q mutant bound to damaged DNA. SNAP output
2nqp isomerase-RNA X-ray (3.5 Å) Hur S, Stroud RM (2007) "How U38, 39, and 40 of Many tRNAs Become the Targets for Pseudouridylation by TruA." Mol.Cell, 26, 189-203. doi: 10.1016/j.molcel.2007.02.027. Crystal structure of pseudoudirinde synthase trua in complex with leucyl trna. SNAP output
2nr0 isomerase-RNA X-ray (3.9 Å) Hur S, Stroud RM (2007) "How U38, 39, and 40 of Many tRNAs Become the Targets for Pseudouridylation by TruA." Mol.Cell, 26, 189-203. doi: 10.1016/j.molcel.2007.02.027. Crystal structure of pseudoudirinde synthase trua in complex with leucyl trna. SNAP output
2nra replication-DNA X-ray (3.1 Å) Swan MK, Bastia D, Davies C (2006) "Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication." Proc.Natl.Acad.Sci.Usa, 103, 18481-18486. doi: 10.1073/pnas.0609046103. Crystal structure of pi initiator protein in complex with iteron DNA. SNAP output
2ntc DNA binding protein-DNA X-ray (2.4 Å) Meinke G, Phelan P, Moine S, Bochkareva E, Bochkarev A, Bullock PA, Bohm A (2007) "The Crystal Structure of the SV40 T-Antigen Origin Binding Domain in Complex with DNA." Plos Biol., 5, e23. doi: 10.1371/journal.pbio.0050023. Crystal structure of sv40 large t antigen origin binding domain with DNA. SNAP output
2ntz cell cycle-DNA X-ray (3.35 Å) Schumacher MA, Mansoor A, Funnell BE (2007) "Structure of a four-way bridged ParB-DNA complex provides insight into P1 segrosome assembly." J.Biol.Chem., 282, 10456-10464. doi: 10.1074/jbc.M610603200. Structure of a parb-DNA complex reveals a double b-box interaction. SNAP output
2nvq transcription,transferase-DNA-RNA hybrid X-ray (2.9 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 150 mm mg+2 with 2'dutp. SNAP output
2nvt transcription,transferase-DNA-RNA hybrid X-ray (3.36 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 150 mm mg+2 with gmpcpp. SNAP output
2nvx transcription,transferase-DNA-RNA hybrid X-ray (3.6 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 5 mm mg+2 with 2'-dutp. SNAP output
2nvz transcription,transferase-DNA-RNA hybrid X-ray (4.3 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex with utp, updated 11-2006. SNAP output
2nzd structural protein-DNA X-ray (2.65 Å) Ong MS, Richmond TJ, Davey CA (2007) "DNA stretching and extreme kinking in the nucleosome core." J.Mol.Biol., 368, 1067-1074. doi: 10.1016/j.jmb.2007.02.062. Nucleosome core particle containing 145 bp of DNA. SNAP output
2o19 isomerase-DNA X-ray (2.45 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomersae iii in complex with an 8-base single stranded oligonucleotide. frozen in glycerol at ph 5.5. SNAP output
2o49 transcription-DNA X-ray (2.0 Å) Yamasaki K, Akiba T, Yamasaki T, Harata K (2007) "Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1." Nucleic Acids Res., 35, 5073-5084. doi: 10.1093/nar/gkm504. Crystal structure of the n-terminal cut domain of satb1 bound to matrix attachment region DNA. SNAP output
2o4a transcription-DNA X-ray (1.75 Å) Yamasaki K, Akiba T, Yamasaki T, Harata K (2007) "Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1." Nucleic Acids Res., 35, 5073-5084. doi: 10.1093/nar/gkm504. Crystal structure of the n-terminal cut domain of satb1 bound to matrix attachment region DNA. SNAP output
2o4i hydrolase-DNA X-ray (3.5 Å) Brucet M, Querol-Audi J, Serra M, Ramirez-Espain X, Bertlik K, Ruiz L, Lloberas J, Macias MJ, Fita I, Celada A (2007) "Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains." J.Biol.Chem., 282, 14547-14557. doi: 10.1074/jbc.M700236200. Structure of trex1 in complex with DNA. SNAP output
2o54 isomerase-DNA X-ray (2.5 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glycerol at ph 7.0. SNAP output
2o59 isomerase-DNA X-ray (2.5 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glycerol ph 8.0. SNAP output
2o5c isomerase-DNA X-ray (2.35 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glucose ph 5.5. SNAP output
2o5e isomerase-DNA X-ray (2.5 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glucose ph 7.0. SNAP output
2o5i transferase-DNA-RNA hybrid X-ray (2.5 Å) Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I (2007) "Structural basis for transcription elongation by bacterial RNA polymerase." Nature, 448, 157-162. doi: 10.1038/nature05932. Crystal structure of the t. thermophilus RNA polymerase elongation complex. SNAP output
2o5j transferase-DNA-RNA hybrid X-ray (3.0 Å) Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R (2007) "Structural basis for substrate loading in bacterial RNA polymerase." Nature, 448, 163-168. doi: 10.1038/nature05931. Crystal structure of the t. thermophilus rnap polymerase elongation complex with the ntp substrate analog. SNAP output
2o61 transcription-DNA X-ray (2.8 Å) Panne D, Maniatis T, Harrison SC (2007) "An Atomic Model of the Interferon-beta Enhanceosome." Cell(Cambridge,Mass.), 129, 1111-1123. doi: 10.1016/j.cell.2007.05.019. Crystal structure of nfkb, irf7, irf3 bound to the interferon-b enhancer. SNAP output
2o6g transcription-DNA X-ray (3.1 Å) Panne D, Maniatis T, Harrison SC (2007) "An Atomic Model of the Interferon-beta Enhanceosome." Cell(Cambridge,Mass.), 129, 1111-1123. doi: 10.1016/j.cell.2007.05.019. Crystal structure of irf-3 bound to the interferon-b enhancer. SNAP output
2o6m hydrolase-DNA X-ray (2.3 Å) Eastberg JH, Eklund J, Monnat R, Stoddard BL (2007) "Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism." Biochemistry, 46, 7215-7225. doi: 10.1021/bi700418d. H98q mutant of the homing endonuclease i-ppoi complexed with DNA. SNAP output
2o8b DNA binding protein-DNA X-ray (2.75 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to adp and a g t mispair. SNAP output
2o8c DNA binding protein-DNA X-ray (3.37 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to adp and an o6-methyl-guanine t mispair. SNAP output
2o8d DNA binding protein-DNA X-ray (3.0 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to adp and a g du mispair. SNAP output
2o8e DNA binding protein-DNA X-ray (3.3 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to a g t mispair, with adp bound to msh2 only. SNAP output
2o8f DNA binding protein-DNA X-ray (3.25 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to DNA with a single base t insert. SNAP output
2o8k transcription-DNA NMR Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE (2007) "Structural basis of DNA recognition by the alternative sigma-factor, sigma54." J.Mol.Biol., 369, 1070-1078. doi: 10.1016/j.jmb.2007.04.019. NMR structure of the sigma-54 rpon domain bound to the-24 promoter element. SNAP output
2o93 transcription-DNA X-ray (3.05 Å) Bates DL, Barthel KK, Wu Y, Kalhor R, Stroud JC, Giffin MJ, Chen L (2008) "Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element." Structure, 16, 684-694. doi: 10.1016/j.str.2008.01.020. Crystal structure of nfat bound to the hiv-1 ltr tandem kappab enhancer element. SNAP output
2o9l RNA polymerase sigma factor rpon-DNA NMR Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE (2007) "Structural basis of DNA recognition by the alternative sigma-factor, sigma54." J.Mol.Biol., 369, 1070-1078. doi: 10.1016/j.jmb.2007.04.019. Amber refined NMR structure of the sigma-54 rpon domain bound to the-24 promoter element. SNAP output
2oa8 hydrolase-DNA X-ray (2.1 Å) de Silva U, Choudhury S, Bailey SL, Harvey S, Perrino FW, Hollis T (2007) "The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals a Polyproline II Helix for Protein Partnering." J.Biol.Chem., 282, 10537-10543. doi: 10.1074/jbc.M700039200. Crystal structure of mtrex1 with ssDNA. SNAP output
2oaa hydrolase-DNA X-ray (1.5 Å) Kaus-Drobek M, Czapinska H, Sokolowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) "Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically." Nucleic Acids Res., 35, 2035-2046. doi: 10.1093/nar/gkm064. Restriction endonuclease mvai-cognate DNA substrate complex. SNAP output
2odi hydrolase-DNA X-ray (1.45 Å) Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) "Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA." J.Mol.Biol., 369, 722-734. doi: 10.1016/j.jmb.2007.03.018. Restriction endonuclease bcni-cognate DNA substrate complex. SNAP output
2oeh transcription-DNA NMR Cai S, Zhu L, Zhang Z, Chen Y (2007) "Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling." Biochemistry, 46, 4943-4950. doi: 10.1021/bi061738h. Determination of the three-dimensional structure of the mrf2-DNA complex using paramagnetic spin labeling. SNAP output
2ofi 3-methyladenine DNA glycosylase i-DNA X-ray (1.85 Å) Metz AH, Hollis T, Eichman BF (2007) "DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG)." Embo J., 26, 2411-2420. doi: 10.1038/sj.emboj.7601649. Crystal structure of 3-methyladenine DNA glycosylase i (tag) bound to DNA-3ma. SNAP output
2og0 DNA binding protein-DNA X-ray (1.9 Å) Papagiannis CV, Sam MD, Abbani MA, Yoo D, Cascio D, Clubb RT, Johnson RC (2007) "Fis targets assembly of the xis nucleoprotein filament to promote excisive recombination by phage lambda." J.Mol.Biol., 367, 328-343. doi: 10.1016/j.jmb.2006.12.071. Crystal structure of the lambda xis-DNA complex. SNAP output
2oh2 transferase-DNA X-ray (3.05 Å) Lone S, Townson SA, Uljon SN, Johnson RE, Brahma A, Nair DT, Prakash S, Prakash L, Aggarwal AK "Ternary complex of the catalytic core of human DNA polymerase Kappa with DNA and dTT." Ternary complex of human DNA polymerase. SNAP output
2ok0 immune system-DNA X-ray (1.89 Å) Sanguineti S, Centeno Crowley JM, Lodeiro Merlo MF, Cerutti ML, Wilson IA, Goldbaum FA, Stanfield RL, de Prat-Gay G (2007) "Specific recognition of a DNA immunogen by its elicited antibody." J.Mol.Biol., 370, 183-195. doi: 10.1016/j.jmb.2007.04.046. Fab ed10-DNA complex. SNAP output
2opf hydrolase-DNA X-ray (1.85 Å) Golan G, Zharkov DO, Grollman AP, Shoham G "Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli (r252a) in complex with ap-site containing DNA substrate. SNAP output
2oq4 hydrolase-DNA X-ray (2.6 Å) Golan G, Zharkov DO, Grollman AP, Shoham G "Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli (e2q) in complex with ap-site containing DNA substrate. SNAP output
2or1 gene regulation-DNA X-ray (2.5 Å) Aggarwal AK, Rodgers DW, Drottar M, Ptashne M, Harrison SC (1988) "Recognition of a DNA operator by the repressor of phage 434: a view at high resolution." Science, 242, 899-907. Recognition of a DNA operator by the repressor of phage 434. a view at high resolution. SNAP output
2ost hydrolase-DNA X-ray (3.1 Å) Zhao L, Bonocora RP, Shub DA, Stoddard BL (2007) "The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif." Embo J., 26, 2432-2442. doi: 10.1038/sj.emboj.7601672. The structure of a bacterial homing endonuclease : i-ssp6803i. SNAP output
2owo ligase-DNA X-ray (2.3 Å) Nandakumar J, Nair PA, Shuman S (2007) "Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate." Mol.Cell, 26, 257-271. doi: 10.1016/j.molcel.2007.02.026. Last stop on the road to repair: structure of e.coli DNA ligase bound to nicked DNA-adenylate. SNAP output
2oxm hydrolase-DNA X-ray (2.5 Å) Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT (2007) "Enzymatic capture of an extrahelical thymine in the search for uracil in DNA." Nature, 449, 433-437. doi: 10.1038/nature06131. Crystal structure of a ung2-modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping. SNAP output
2oxv hydrolase-DNA X-ray (1.95 Å) Sapienza PJ, Rosenberg JM, Jen-Jacobson L (2007) "Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease." Structure, 15, 1368-1382. doi: 10.1016/j.str.2007.09.014. Structure of the a138t promiscuous mutant of the ecori restriction endonuclease bound to its cognate recognition site.. SNAP output
2oyq transferase-DNA X-ray (2.86 Å) Zahn KE, Belrhali H, Wallace SS, Doublie S (2007) "Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with 5-nimp opposite an abasic site analog. SNAP output
2oyt hydrolase-DNA X-ray (2.0 Å) Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT (2007) "Enzymatic capture of an extrahelical thymine in the search for uracil in DNA." Nature, 449, 433-437. doi: 10.1038/nature06131. Crystal structure of ung2-DNA(tm). SNAP output
2ozm transferase-DNA X-ray (2.86 Å) Zahn KE, Belrhail H, Wallace SS, Doublie S (2007) "Caught Bending the A-Rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with 5-nitp opposite an abasic site analog. SNAP output
2ozs transferase-DNA X-ray (2.75 Å) Zahn KE, Belrhali H, Wallace SS, Doublie S (2007) "Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with datp opposite dtmp. SNAP output
2p0j hydrolase-DNA X-ray (2.1 Å) Townson SA, Samuelson JC, Bao Y, Xu SY, Aggarwal AK (2007) "BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning." Structure, 15, 449-459. doi: 10.1016/j.str.2007.03.002. Structure of restriction endonuclease bstyi bound to non-cognate DNA. SNAP output
2p2r RNA and DNA binding protein-DNA X-ray (1.6 Å) Fenn S, Du Z, Lee JK, Tjhen R, Stroud RM, James TL (2007) "Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution." Nucleic Acids Res., 35, 2651-2660. doi: 10.1093/nar/gkm139. Crystal structure of the third kh domain of human poly(c)-binding protein-2 in complex with c-rich strand of human telomeric DNA. SNAP output
2p5g transferase-DNA X-ray (2.8 Å) Zahn KE, Belrhali H, Wallace SS, Doublie S (2007) "Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with damp opposite an abasic site analog in a 21mer template. SNAP output
2p5l transcription repressor X-ray (2.85 Å) Garnett JA, Marincs F, Baumberg S, Stockley PG, Phillips SE (2008) "Structure and function of the arginine repressor-operator complex from Bacillus subtilis." J.Mol.Biol., 379, 284-298. doi: 10.1016/j.jmb.2008.03.007. Crystal structure of a dimer of n-terminal domains of ahrc in complex with an 18bp DNA operator site. SNAP output
2p5o transferase-DNA X-ray (2.8 Å) Hogg M, Wallace SS, Doublie S (2004) "Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site." Embo J., 23, 1483-1493. doi: 10.1038/sj.emboj.760015. Crystal structure of rb69 gp43 in complex with DNA containing an abasic site analog. SNAP output
2p66 transferase, lyase-DNA X-ray (2.5 Å) Prasad R, Batra VK, Yang X-P, Krahn JM, Pedersen LC, Beard WA, Wilson SH (2005) "Structural insight into the DNA Polymerase beta deoxyribose phosphate lyase mechanism." DNA REPAIR, 4, 1347-1357. doi: 10.1016/j.dnarep.2005.08.009. Human DNA polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA. SNAP output
2p6r DNA binding protein-DNA X-ray (3.0 Å) Buttner K, Nehring S, Hopfner KP (2007) "Structural basis for DNA duplex separation by a superfamily-2 helicase." Nat.Struct.Mol.Biol., 14, 647-652. doi: 10.1038/nsmb1246. Crystal structure of superfamily 2 helicase hel308 in complex with unwound DNA. SNAP output
2p7c transcription regulator NMR Boudet J, Duval V, Van Melckebeke H, Blackledge M, Amoroso A, Joris B, Simorre JP (2007) "Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against beta-lactam antibiotics." Nucleic Acids Res., 35, 4384-4395. doi: 10.1093/nar/gkm448. Solution structure of the bacillus licheniformis blai monomeric form in complex with the blap half-operator.. SNAP output
2pe5 transcription-DNA X-ray (3.5 Å) Daber R, Stayrook S, Rosenberg A, Lewis M (2007) "Structural analysis of lac repressor bound to allosteric effectors." J.Mol.Biol., 370, 609-619. doi: 10.1016/j.jmb.2007.04.028. Crystal structure of the lac repressor bound to onpg in repressed state. SNAP output
2pfj hydrolase-DNA X-ray (3.1 Å) Hadden JM, Declais AC, Carr SB, Lilley DM, Phillips SE (2007) "The structural basis of Holliday junction resolution by T7 endonuclease I." Nature, 449, 621-624. doi: 10.1038/nature06158. Crystal structure of t7 endo i resolvase in complex with a holliday junction. SNAP output
2pfn transferase, lyase-DNA X-ray (1.9 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. Na in the active site of DNA polymerase lambda. SNAP output
2pfo transferase, lyase-DNA X-ray (2.0 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. DNA polymerase lambda in complex with DNA and dupnpp. SNAP output
2pfp transferase, lyase-DNA X-ray (2.1 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. DNA polymerase lambda in complex with DNA and dctp. SNAP output
2pfq transferase, lyase-DNA X-ray (2.1 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal. SNAP output
2pi0 transcription activator-DNA X-ray (2.31 Å) Escalante CR, Nistal-Villan E, Shen L, Garcia-Sastre A, Aggarwal AK (2007) "Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer." Mol.Cell, 26, 703-716. doi: 10.1016/j.molcel.2007.04.022. Crystal structure of irf-3 bound to the prdiii-i regulatory element of the human interferon-b enhancer. SNAP output
2pi4 transferase-DNA X-ray (2.5 Å) Kennedy WP, Momand JR, Yin YW (2007) "Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase." J.Mol.Biol., 370, 256-268. doi: 10.1016/j.jmb.2007.03.041. T7rnap complexed with a phi10 protein and initiating gtps.. SNAP output
2pi5 transferase-DNA X-ray (2.9 Å) Kennedy WP, Momand JR, Yin YW (2007) "Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase." J.Mol.Biol., 370, 256-268. doi: 10.1016/j.jmb.2007.03.041. T7 RNA polymerase complexed with a phi10 promoter. SNAP output
2pjr hydrolase-DNA X-ray (2.9 Å) Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB (1999) "Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism." Cell(Cambridge,Mass.), 97, 75-98. doi: 10.1016/S0092-8674(00)80716-3. Helicase product complex. SNAP output
2ppb transferase-DNA-RNA X-ray (3.0 Å) Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R (2007) "Structural basis for substrate loading in bacterial RNA polymerase." Nature, 448, 163-168. doi: 10.1038/nature05931. Crystal structure of the t. thermophilus rnap polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin. SNAP output
2pqu RNA and DNA binding protein-DNA X-ray (2.12 Å) Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James TL (2007) "X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2." Rna, 13, 1043-1051. doi: 10.1261/rna.410107. Crystal structure of kh1 domain of human pcbp2 complexed to single-stranded 12-mer telomeric DNA. SNAP output
2prt transcription-DNA X-ray (3.15 Å) Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE (2007) "Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA." J.Mol.Biol., 372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017. Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. SNAP output
2pua transcription-DNA X-ray (2.9 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pub transcription-DNA X-ray (2.7 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2puc transcription-DNA X-ray (2.6 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pud transcription-DNA X-ray (2.6 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pue transcription-DNA X-ray (2.7 Å) Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998) "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry, 37, 971-982. doi: 10.1021/bi971942s. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2puf transcription-DNA X-ray (3.0 Å) Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998) "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry, 37, 971-982. doi: 10.1021/bi971942s. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pug transcription-DNA X-ray (2.7 Å) Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998) "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry, 37, 971-982. doi: 10.1021/bi971942s. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pvi hydrolase-DNA X-ray (1.76 Å) Horton JR, Bonventre J, Cheng X (1998) "How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?." J.Biol.Chem., 379, 451-458. Pvuii endonuclease complexed to an iodinated cognate DNA. SNAP output
2pxi lyase, transferase-DNA X-ray (2.1 Å) McKenna CE, Kashemirov BA, Upton TG, Batra VK, Goodman MF, Pedersen LC, Beard WA, Wilson SH (2007) "(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta." J.Am.Chem.Soc., 129, 15412-15413. doi: 10.1021/ja072127v. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate. SNAP output
2py5 replication, transferase-DNA X-ray (1.6 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with single-stranded DNA. SNAP output
2pyj replication, transferase-DNA X-ray (2.03 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex). SNAP output
2pyl replication, transferase-DNA X-ray (2.2 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex). SNAP output
2pyo structural protein-DNA X-ray (2.43 Å) Clapier CR, Chakravarthy S, Petosa C, Fernandez-Tornero C, Luger K, Muller CW (2007) "Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer." Proteins, 71, 1-7. doi: 10.1002/prot.21720. Drosophila nucleosome core. SNAP output
2pzs replication, transferase-DNA X-ray (2.6 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with primer-template DNA (post-translocation binary complex). SNAP output
2q10 hydrolase-DNA X-ray (1.75 Å) Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) "Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA." J.Mol.Biol., 369, 722-734. doi: 10.1016/j.jmb.2007.03.018. Restriction endonuclease bcni (wild type)-cognate DNA substrate complex. SNAP output
2q2k DNA binding protein-DNA X-ray (3.0 Å) Schumacher MA, Glover TC, Brzoska AJ, Jensen SO, Dunham TD, Skurray RA, Firth N (2007) "Segrosome structure revealed by a complex of ParR with centromere DNA." Nature, 450, 1268-1271. doi: 10.1038/nature06392. Structure of nucleic-acid binding protein. SNAP output
2q2t ligase-DNA X-ray (2.3 Å) Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S (2007) "Structural basis for nick recognition by a minimal pluripotent DNA ligase." Nat.Struct.Mol.Biol., 14, 770-778. doi: 10.1038/nsmb1266. Structure of chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick. SNAP output
2q2u ligase-DNA X-ray (3.0 Å) Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S (2007) "Structural basis for nick recognition by a minimal pluripotent DNA ligase." Nat.Struct.Mol.Biol., 14, 770-778. doi: 10.1038/nsmb1266. Structure of chlorella virus DNA ligase-product DNA complex. SNAP output
2qby replication-DNA X-ray (3.35 Å) Dueber EL, Corn JE, Bell SD, Berger JM (2007) "Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex." Science, 317, 1210-1213. doi: 10.1126/science.1143690. Crystal structure of a heterodimer of cdc6-orc1 initiators bound to origin DNA (from s. solfataricus). SNAP output
2qfj transcription repressor-DNA X-ray (2.1 Å) Crichlow GV, Zhou H, Hsiao H-H, Frederick KB, Debrosse M, Yang Y, Folta-Stogniew EJ, Chung H-J, Fan C, De La Cruz EM, Levens D, Lolis E, Braddock D (2007) "Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition." EMBO J., 27, 277-289. doi: 10.1038/sj.emboj.7601936. Crystal structure of first two rrm domains of fir bound to ssDNA from a portion of fuse. SNAP output
2qhb DNA binding protein-DNA X-ray (2.4 Å) Cho H-S, Byun J-S, Jun S-H, Han W, Lee W "Complex structure of plant telomere bindig protein, NgTRF and telomere DNA." Crystal structure of ngtrf complexed with telomeric DNA. SNAP output
2qk9 hydrolase-DNA-RNA X-ray (2.55 Å) Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W (2007) "Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription." Mol.Cell, 28, 264-276. doi: 10.1016/j.molcel.2007.08.015. Human rnase h catalytic domain mutant d210n in complex with 18-mer RNA-DNA hybrid. SNAP output
2qkb hydrolase-DNA-RNA X-ray (2.4 Å) Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W (2007) "Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription." Mol.Cell, 28, 264-276. doi: 10.1016/j.molcel.2007.08.015. Human rnase h catalytic domain mutant d210n in complex with 20-mer RNA-DNA hybrid. SNAP output
2qkk hydrolase-DNA-RNA X-ray (3.2 Å) Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W (2007) "Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription." Mol.Cell, 28, 264-276. doi: 10.1016/j.molcel.2007.08.015. Human rnase h catalytic domain mutant d210n in complex with 14-mer RNA-DNA hybrid. SNAP output
2ql2 transcription-DNA X-ray (2.5 Å) Longo A, Guanga GP, Rose RB (2008) "Crystal structure of E47-NeuroD1/beta2 bHLH domain-DNA complex: heterodimer selectivity and DNA recognition." Biochemistry, 47, 218-229. doi: 10.1021/bi701527r. Crystal structure of the basic-helix-loop-helix domains of the heterodimer e47-neurod1 bound to DNA. SNAP output
2qnc hydrolase-DNA X-ray (3.1 Å) Biertumpfel C, Yang W, Suck D (2007) "Crystal structure of T4 endonuclease VII resolving a Holliday junction." Nature, 449, 616-620. doi: 10.1038/nature06152. Crystal structure of t4 endonuclease vii n62d mutant in complex with a DNA holliday junction. SNAP output
2qnf hydrolase-DNA X-ray (3.0 Å) Biertumpfel C, Yang W, Suck D (2007) "Crystal structure of T4 endonuclease VII resolving a Holliday junction." Nature, 449, 616-620. doi: 10.1038/nature06152. Crystal structure of t4 endonuclease vii h43n mutant in complex with heteroduplex DNA containing base mismatches. SNAP output
2qoj hydrolase-DNA X-ray (2.4 Å) Scalley-Kim M, McConnell-Smith A, Stoddard BL (2007) "Coevolution of a homing endonuclease and its host target sequence." J.Mol.Biol., 372, 1305-1319. doi: 10.1016/j.jmb.2007.07.052. Coevolution of a homing endonuclease and its host target sequence. SNAP output
2qsg DNA binding protein-DNA X-ray (3.1 Å) Min J-H, Pavletich NP (2007) "Recognition of DNA damage by the Rad4 nucleotide excision repair protein." Nature, 449, 570-575. doi: 10.1038/nature06155. Crystal structure of rad4-rad23 bound to a uv-damaged DNA. SNAP output
2qsh DNA binding protein-DNA X-ray (2.805 Å) Min J-H, Pavletich NP (2007) "Recognition of DNA damage by the Rad4 nucleotide excision repair protein." Nature, 449, 570-575. doi: 10.1038/nature06155. Crystal structure of rad4-rad23 bound to a mismatch DNA. SNAP output
2r0q recombination-DNA X-ray (3.2 Å) Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA (2008) "Architecture of a serine recombinase-DNA regulatory complex." Mol.Cell, 30, 145-155. doi: 10.1016/j.molcel.2008.02.023. Crystal structure of a serine recombinase- DNA regulatory complex. SNAP output
2r1j transcription-DNA X-ray (1.53 Å) Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams LD (2008) "P22 c2 repressor-operator complex: mechanisms of direct and indirect readout." Biochemistry, 47, 2325-2338. doi: 10.1021/bi701826f. Crystal structure of the p22 c2 repressor protein in complex with the synthetic operator 9t. SNAP output
2r2r transferase-DNA X-ray (2.1 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. D(attagttataactaat) complexed with mmlv rt catalytic fragment. SNAP output
2r2s transferase-DNA X-ray (2.8 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. Co(iii)bleomycinb2 bound to d(attagttataactaat) complexed with mmlv rt catalytic fragment. SNAP output
2r2t transferase-DNA X-ray (2.0 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. D(atttagttaactaaat) complexed with mmlv rt catalytic fragment. SNAP output
2r2u transferase-DNA X-ray (2.3 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. Co(iii)bleomycinb2 bithiazole-c-terminal tail domain bound to d(atttagttaactaaat) complexed with mmlv rt catalytic fragment. SNAP output
2r5y transcription-DNA X-ray (2.6 Å) Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS (2007) "Functional specificity of a Hox protein mediated by the recognition of minor groove structure." Cell(Cambridge,Mass.), 131, 530-543. doi: 10.1016/j.cell.2007.09.024. Structure of scr-exd complex bound to a consensus hox-exd site. SNAP output
2r5z transcription-DNA X-ray (2.6 Å) Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS (2007) "Functional specificity of a Hox protein mediated by the recognition of minor groove structure." Cell(Cambridge,Mass.), 131, 530-543. doi: 10.1016/j.cell.2007.09.024. Structure of scr-exd complex bound to a DNA sequence derived from the fkh gene. SNAP output
2r7y hydrolase-RNA-DNA X-ray (1.8 Å) Jiang J-S, Gerlits O, Huang Z "Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N." Selenium derivatized RNA-DNA hybrid in complex with rnase h catalytic domain mutant d132n. SNAP output
2r7z transcription-DNA-RNA hybrid X-ray (3.8 Å) Damsma GE, Alt A, Brueckner F, Carell T, Cramer P (2007) "Mechanism of transcriptional stalling at cisplatin-damaged DNA." Nat.Struct.Mol.Biol., 14, 1127-1133. doi: 10.1038/nsmb1314. Cisplatin lesion containing RNA polymerase ii elongation complex. SNAP output
2r8g replication, transferase-DNA X-ray (2.7 Å) Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP (2008) "Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV." Biochemistry, 47, 7322-7334. doi: 10.1021/bi800152j. Selectivity of nucleoside triphosphate incorporation opposite 1,n2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase. SNAP output
2r8h replication, transferase-DNA X-ray (2.48 Å) Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP (2008) "Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV." Biochemistry, 47, 7322-7334. doi: 10.1021/bi800152j. Selectivity of nucleoside triphosphate incorporation opposite 1,n2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase. SNAP output
2r8i replication, transferase-DNA X-ray (2.38 Å) Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP (2008) "Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV." Biochemistry, 47, 7322-7334. doi: 10.1021/bi800152j. Selectivity of nucleoside triphosphate incorporation opposite 1,n2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase. SNAP output
2r8j replication, transferase-DNA X-ray (3.1 Å) Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T (2007) "Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta." Science, 318, 967-970. doi: 10.1126/science.1148242. Structure of the eukaryotic DNA polymerase eta in complex with 1,2-d(gpg)-cisplatin containing DNA. SNAP output
2r8k replication, transferase-DNA X-ray (3.3 Å) Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T (2007) "Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta." Science, 318, 967-970. doi: 10.1126/science.1148242. Structure of the eukaryotic DNA polymerase eta in complex with 1,2-d(gpg)-cisplatin containing DNA. SNAP output
2r9l transferase-DNA X-ray (2.4 Å) Brissett NC, Pitcher RS, Juarez R, Picher AJ, Green AJ, Dafforn TR, Fox GC, Blanco L, Doherty AJ (2007) "Structure of a NHEJ polymerase-mediated DNA synaptic complex." Science, 318, 456-459. doi: 10.1126/science.1145112. Polymerase domain from mycobacterium tuberculosis ligase d in complex with DNA. SNAP output
2ram transcription-DNA X-ray (2.4 Å) Chen YQ, Ghosh S, Ghosh G (1998) "A novel DNA recognition mode by the NF-kappa B p65 homodimer." Nat.Struct.Biol., 5, 67-73. doi: 10.1038/nsb0198-67. A novel DNA recognition mode by nf-kb p65 homodimer. SNAP output
2rba hydrolase-DNA X-ray (2.79 Å) Maiti A, Morgan MT, Pozharski E, Drohat AC (2008) "Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition." Proc.Natl.Acad.Sci.Usa, 105, 8890-8895. doi: 10.1073/pnas.0711061105. Structure of human thymine DNA glycosylase bound to abasic and undamaged DNA. SNAP output
2rbf oxidoreductase-DNA X-ray (2.25 Å) Zhou Y, Larson JD, Bottoms CA, Arturo EC, Henzl MT, Jenkins JL, Nix JC, Becker DF, Tanner JJ (2008) "Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA." J.Mol.Biol., 381, 174-188. doi: 10.1016/j.jmb.2008.05.084. Structure of the ribbon-helix-helix domain of escherichia coli puta (puta52) complexed with operator DNA (o2). SNAP output
2rdj transferase-DNA X-ray (2.2 Å) Wong JH, Fiala KA, Suo Z, Ling H (2008) "Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4." J.Mol.Biol., 379, 317-330. doi: 10.1016/j.jmb.2008.03.038. Snapshots of a y-family DNA polymerase in replication: dpo4 in apo and binary-ternary complex forms. SNAP output
2rgr isomerase-DNA X-ray (3.0 Å) Dong KC, Berger JM (2007) "Structural basis for gate-DNA recognition and bending by type IIA topoisomerases." Nature, 450, 1201-1205. doi: 10.1038/nature06396. Topoisomerase iia bound to g-segment DNA. SNAP output
2rve hydrolase-DNA X-ray (3.0 Å) Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS (1993) "The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments." EMBO J., 12, 1781-1795. The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA segments. SNAP output
2ssp protein-DNA X-ray (2.25 Å) Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA (1998) "Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA." EMBO J., 17, 5214-5226. doi: 10.1093/emboj/17.17.5214. Leucine-272-alanine uracil-DNA glycosylase bound to abasic site-containing DNA. SNAP output
2stt DNA binding protein-DNA NMR Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM (1997) "Correction of the NMR structure of the ETS1/DNA complex." J.Biomol.NMR, 10, 317-328. doi: 10.1023/A:1018399711996. Solution NMR structure of the human ets1-DNA complex, 25 structures. SNAP output
2stw DNA binding protein-DNA NMR Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L, Shiloach J, Gronenborn AM (1997) "Correction of the NMR structure of the ETS1/DNA complex." J.Biomol.NMR, 10, 317-328. doi: 10.1023/A:1018399711996. Solution NMR structure of the human ets1-DNA complex, restrained regularized mean structure. SNAP output
2up1 gene regulation-DNA X-ray (2.1 Å) Ding J, Hayashi MK, Zhang Y, Manche L, Krainer AR, Xu RM (1999) "Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA." Genes Dev., 13, 1102-1115. Structure of up1-telomeric DNA complex. SNAP output
2uvr transferase X-ray (2.9 Å) Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP (2007) "Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 282, 19831. doi: 10.1074/JBC.M702290200. Crystal structures of mutant dpo4 DNA polymerases with 8-oxog containing DNA template-primer constructs. SNAP output
2uvu transferase X-ray (2.7 Å) Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP (2007) "Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 282, 19831. doi: 10.1074/JBC.M702290200. Crystal structures of mutant dpo4 DNA polymerases with 8-oxog containing DNA template-primer constructs. SNAP output
2uvv transferase X-ray (2.2 Å) Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP (2007) "Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 282, 19831. doi: 10.1074/JBC.M702290200. Crystal structures of mutant dpo4 DNA polymerases with 8-oxog containing DNA template-primer constructs. SNAP output
2uvw transferase X-ray (2.09 Å) Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP (2007) "Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 282, 19831. doi: 10.1074/JBC.M702290200. Crystal structures of mutant dpo4 DNA polymerases with 8-oxog containing DNA template-primer constructs. SNAP output
2uyc transferase X-ray (2.0 Å) Daujotyte D, Grazulis S "HhaI DNA Methyltransferase R163N Mutant Complex with 13mer Gcgc-Gmgc Oligonucleotide and Sah." Hhai DNA methyltransferase r163n mutant complex with 13mer gcgc-gmgc oligonucleotide and sah. SNAP output
2uyh transferase X-ray (2.63 Å) Daujotyte D, Grazulis S "HhaI DNA Methyltransferase S87Q-Q237S Mutant Complex with 13mer Gcgc-Gmgc Oligonucleotide and Sah." Hhai DNA methyltransferase s87q-q237s mutant complex with 13mer gcgc- gmgc oligonucleotide and sah. SNAP output
2uz4 transferase X-ray (2.1 Å) Daujotyte D, Leinartaite L, Grazulis S "DNA Methyltransferase R165N Mutant." Hhai DNA methyltransferase r165n mutant complex with 13mer gcgc-gmgc oligonucleotide and sah. SNAP output
2uzk transcription X-ray (2.7 Å) Tsai K-L, Sun Y-J, Huang C-Y, Yang J-Y, Hung M-C, Hsiao C-D (2007) "Crystal Structure of the Human Foxo3A-Dbd/DNA Complex Suggests the Effects of Post-Translational Modification." Nucleic Acids Res., 35, 6984. doi: 10.1093/NAR/GKM703. Crystal structure of the human foxo3a-dbd bound to DNA. SNAP output
2v1u replication X-ray (3.1 Å) Gaudier M, Schuwirth BS, Westcott SL, Wigley DB (2007) "Structural Basis of DNA Replication Origin Recognition by an Orc Protein." Science, 317, 1213. doi: 10.1126/SCIENCE.1143664. Structure of the aeropyrum pernix orc1 protein in complex with DNA. SNAP output
2v2t transcription X-ray (3.05 Å) Moorthy AK, Huang DB, Wang VY, Vu D, Ghosh G (2007) "X-Ray Structure of a NF-kappaB p50/Relb/DNA Complex Reveals Assembly of Multiple Dimers on Tandem kappaB Sites." J.Mol.Biol., 373, 723. doi: 10.1016/J.JMB.2007.08.039. X-ray structure of a nf-kb p50-relb-DNA complex. SNAP output
2v4q transferase X-ray (2.6 Å) Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ (2009) "Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct." Biochemistry, 48, 7079. doi: 10.1021/BI9003588. Post-insertion complex of the y-family DNA polymerase dpo4 with m1dg containing template DNA. SNAP output
2v4r transferase X-ray (2.5 Å) Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M, Guengerich FP, Marnett LJ (2009) "Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct." Biochemistry, 48, 7079. doi: 10.1021/BI9003588. Non-productive complex of the y-family DNA polymerase dpo4 with dgtp skipping the m1dg adduct to pair with the next template cytosine. SNAP output
2v6e hydrolase X-ray (3.2 Å) Aihara H, Huang WM, Ellenberger T (2007) "An Interlocked Dimer of the Protelomerase Telk Distorts DNA Structure for the Formation of Hairpin Telomeres." Mol.Cell, 27, 901. doi: 10.1016/J.MOLCEL.2007.07.026. Protelomerase telk complexed with substrate DNA. SNAP output
2v9w transferase X-ray (3.0 Å) Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M (2007) "Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene." J.Biol.Chem., 282, 36421. doi: 10.1074/JBC.M707267200. Complex structure of sulfolobus solfataricus dpo4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand. SNAP output
2va2 transferase-DNA X-ray (2.8 Å) Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M (2007) "Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4- Difluorotoluene." J.Biol.Chem., 282, 36421. doi: 10.1074/JBC.M707267200. Complex structure of sulfolobus solfataricus dpo4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand. SNAP output
2va3 transferase X-ray (2.98 Å) Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M (2007) "Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene." J.Biol.Chem., 282, 36421. doi: 10.1074/JBC.M707267200. Complex structure of sulfolobus solfataricus dpo4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand. SNAP output
2vbj hydrolase-DNA X-ray (1.95 Å) Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F, Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) "Molecular Basis of Xeroderma Pigmentosum Group C DNA Recognition by Engineered Meganucleases." Nature, 456, 107. doi: 10.1038/NATURE07343. Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers. SNAP output
2vbl hydrolase X-ray (1.8 Å) Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F, Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) "Molecular Basis of Xeroderma Pigmentosum Group C DNA Recognition by Engineered Meganucleases." Nature, 456, 107. doi: 10.1038/NATURE07343. Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers. SNAP output
2vbn hydrolase X-ray (1.9 Å) Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F, Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) "Molecular Basis of Xeroderma Pigmentosum Group C DNA Recognition by Engineered Meganucleases." Nature, 456, 107. doi: 10.1038/NATURE07343. Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers. SNAP output
2vbo hydrolase X-ray (1.8 Å) Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F, Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) "Molecular Basis of Xeroderma Pigmentosum Group C DNA Recognition by Engineered Meganucleases." Nature, 456, 107. doi: 10.1038/NATURE07343. Molecular basis of human xpc gene recognition and cleavage by engineered homing endonuclease heterodimers. SNAP output
2ve9 transport protein X-ray (1.9 Å) Lowe J, Ellonen A, Allen MD, Atkinson C, Sherratt DJ, Grainge I (2008) "Molecular Mechanism of Sequence-Directed DNA Loading and Translocation by Ftsk." Mol.Cell, 31, 498. doi: 10.1016/J.MOLCEL.2008.05.027. Xray structure of kops bound gamma domain of ftsk (p. aeruginosa). SNAP output
2vhg DNA binding protein X-ray (2.9 Å) Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F (2008) "Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection." Cell(Cambridge,Mass.), 132, 208. doi: 10.1016/J.CELL.2007.12.029. Crystal structure of the ishp608 transposase in complex with right end 31-mer DNA. SNAP output
2vic DNA binding protein X-ray (2.35 Å) Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F (2008) "Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection." Cell(Cambridge,Mass.), 132, 208. doi: 10.1016/J.CELL.2007.12.029. Crystal structure of the ishp608 transposase in complex with left end 26- mer DNA and manganese. SNAP output
2vih DNA binding protein X-ray (2.1 Å) Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F (2008) "Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection." Cell(Cambridge,Mass.), 132, 208. doi: 10.1016/J.CELL.2007.12.029. Crystal structure of the is608 transposase in complex with left end 26-mer DNA. SNAP output
2vju DNA binding protein X-ray (2.4 Å) Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F (2008) "Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection." Cell(Cambridge,Mass.), 132, 208. doi: 10.1016/J.CELL.2007.12.029. Crystal structure of the is608 transposase in complex with the complete right end 35-mer DNA and manganese. SNAP output
2vjv DNA binding protein X-ray (1.9 Å) Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, Chandler M, Dyda F (2008) "Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection." Cell(Cambridge,Mass.), 132, 208. doi: 10.1016/J.CELL.2007.12.029. Crystal structure of the is608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site. SNAP output
2vla hydrolase X-ray (1.3 Å) Sukackaite R, Grazulis S, Bochtler M, Siksnys V (2008) "The Recognition Domain of the Bpuji Restriction Endonuclease in Complex with Cognate DNA at 1.3-A Resolution." J.Mol.Biol., 378, 1084. doi: 10.1016/J.JMB.2008.03.041. Crystal structure of restriction endonuclease bpuji recognition domain in complex with cognate DNA. SNAP output
2voa lyase X-ray (1.7 Å) Schmiedel R, Kuettner EB, Keim A, Strater N, Greiner-Stoffele T (2009) "Structure and Function of the Abasic Site Specificity Pocket of an Ap Endonuclease from Archaeoglobus Fulgidus." DNA Repair, 8, 219. doi: 10.1016/J.DNAREP.2008.10.009. Structure of an ap endonuclease from archaeoglobus fulgidus. SNAP output
2vs7 DNA binding protein X-ray (2.05 Å) Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) "Crystal Structure of I-Dmoi in Complex with its Target DNA Provides New Insights Into Meganuclease Engineering." Proc.Natl.Acad.Sci.USA, 105, 16888. doi: 10.1073/PNAS.0804795105. The crystal structure of i-dmoi in complex with DNA and ca. SNAP output
2vs8 DNA binding protein X-ray (2.1 Å) Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A, Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ, Montoya G (2008) "Crystal Structure of I-Dmoi in Complex with its Target DNA Provides New Insights Into Meganuclease Engineering." Proc.Natl.Acad.Sci.USA, 105, 16888. doi: 10.1073/PNAS.0804795105. The crystal structure of i-dmoi in complex with DNA and mn. SNAP output
2vtb lyase-DNA X-ray (2.01 Å) Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen L-O (2008) "Recognition and Repair of Uv Lesions in Loop Structures of Duplex DNA by Dash-Type Cryptochrome." Proc.Natl.Acad.Sci.USA, 105, 21023. doi: 10.1073/PNAS.0805830106. Structure of cryptochrome 3 - DNA complex. SNAP output
2vum transferase X-ray (3.4 Å) Brueckner F, Cramer P (2008) "Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation." Nat.Struct.Mol.Biol., 15, 811. doi: 10.1038/NSMB.1458. Alpha-amanitin inhibited complete RNA polymerase ii elongation complex. SNAP output
2vw9 DNA binding protein X-ray (2.3 Å) Chan K-W, Lee Y-J, Wang C-H, Huang H, Sun Y-J (2009) "Single-Stranded DNA-Binding Protein Complex from Helicobacter Pylori Suggests an Ssdna-Binding Surface." J.Mol.Biol., 388, 508. doi: 10.1016/J.JMB.2009.03.022. Single stranded DNA binding protein complex from helicobacter pylori. SNAP output
2vwj DNA replication X-ray (2.78 Å) Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA (2008) "Uracil Recognition in Archaeal DNA Polymerases Captured by X-Ray Crystallography." J.Mol.Biol., 381, 529. doi: 10.1016/J.JMB.2008.06.004. Uracil recognition in archaeal DNA polymerases captured by x-ray crystallography.. SNAP output
2vy1 transcription X-ray (2.104 Å) Hames C, Ptchelkine D, Grimm C, Thevenon E, Moyroud E, Gerard F, Martiel JL, Benlloch R, Parcy F, Muller CW (2008) "Structural Basis for Leafy Floral Switch Function and Similarity with Helix-Turn-Helix Proteins." Embo J., 27, 2628. doi: 10.1038/EMBOJ.2008.184. Structure of leafy transcription factor from arabidopsis thaliana in complex with DNA from ap1 promoter. SNAP output
2vy2 transcription X-ray (2.3 Å) Hames C, Ptchelkine D, Grimm C, Thevenon E, Moyroud E, Gerard F, Martiel JL, Benlloch R, Parcy F, Muller CW (2008) "Structural Basis for Leafy Floral Switch Function and Similarity with Helix-Turn-Helix Proteins." Embo J., 27, 2628. doi: 10.1038/EMBOJ.2008.184. Structure of leafy transcription factor from arabidopsis thaliana in complex with DNA from ag-i promoter. SNAP output
2vye hydrolase-DNA X-ray (4.1 Å) Lo YH, Tsai KL, Sun YJ, Chen WT, Huang CY, Hsiao CD (2009) "The Crystal Structure of a Replicative Hexameric Helicase Dnac and its Complex with Single-Stranded DNA." Nucleic Acids Res., 37, 804. doi: 10.1093/NAR/GKN999. Crystal structure of the dnac-ssDNA complex. SNAP output
2vz4 transcription X-ray (2.9 Å) Allan MG, Newberry KJ, Schuman J, Brennan RG, Stetefeld J, Grzesiek S, Schirmer T "Structure of the Transcriptionally Inactive Merr Domain Tipan in Complex with DNA." The n-terminal domain of merr-like protein tipal bound to promoter DNA. SNAP output
2w35 hydrolase X-ray (2.15 Å) Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjoras M (2009) "Structures of Endonuclease V with DNA Reveal Initiation of Deaminated Adenine Repair." Nat.Struct.Mol.Biol., 16, 138. doi: 10.1038/NSMB.1538. Structures of endonuclease v with DNA reveal initiation of deaminated adenine repair. SNAP output
2w36 hydrolase X-ray (2.1 Å) Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjoras M (2009) "Structures of Endonuclease V with DNA Reveal Initiation of Deaminated Adenine Repair." Nat.Struct.Mol.Biol., 16, 138. doi: 10.1038/NSMB.1538. Structures of endonuclease v with DNA reveal initiation of deaminated adenine repair. SNAP output
2w42 protein-DNA complex X-ray (1.9 Å) Parker JS, Parizotto EA, Wang M, Roe SM, Barford D (2009) "Enhancement of the Seed-Target Recognition Step in RNA Silencing by a Piwi-Mid Domain Protein." Mol.Cell, 33, 204. doi: 10.1016/J.MOLCEL.2008.12.012. The structure of a piwi protein from archaeoglobus fulgidus complexed with a 16nt DNA duplex.. SNAP output
2w7n transcription-DNA X-ray (1.85 Å) Koenig B, Mueller JJ, Lanka E, Heinemann U (2009) "Crystal Structure of Kora Bound to Operator DNA: Insight Into Repressor Cooperation in Rp4 Gene Regulation." Nucleic Acids Res., 37, 1915. doi: 10.1093/NAR/GKP044. Crystal structure of kora bound to operator DNA: insight into repressor cooperation in rp4 gene regulation. SNAP output
2w7o DNA binding protein X-ray (3.16 Å) Irimia A, Eoff RL, Guengerich FP, Egli M (2009) "Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine Adduct." J.Biol.Chem., 284, 22467. doi: 10.1074/JBC.M109.003905. Structure and activity of bypass synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxodeoxyguanosine adduct. SNAP output
2w7p DNA binding protein X-ray (3.71 Å) Irimia A, Eoff RL, Guengerich FP, Egli M (2009) "Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine Adduct." J.Biol.Chem., 284, 22467. doi: 10.1074/JBC.M109.003905. Structure and activity of bypass synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxodeoxyguanosine adduct. SNAP output
2w8k transferase-DNA X-ray (3.1 Å) Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) "Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts." J.Biol.Chem., 284, 3563. doi: 10.1074/JBC.M807778200. Y-family DNA polymerase dpo4 bypassing n2-naphthyl-guanine adduct in syn orientation. SNAP output
2w8l transferase-DNA X-ray (3.0 Å) Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) "Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts." J.Biol.Chem., 284, 3563. doi: 10.1074/JBC.M807778200. Y-family DNA polymerase dpo4 bypassing n2-naphthyl-guanine adduct in anti orientation. SNAP output
2w9a transferase-DNA X-ray (2.6 Å) Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) "Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes." J.Biol.Chem., 284, 17687. doi: 10.1074/JBC.M109014274. Ternary complex of dpo4 bound to n2,n2-dimethyl-deoxyguanosine modified DNA with incoming dgtp. SNAP output
2w9b transferase-DNA X-ray (2.28 Å) Zhang H, Eoff RL, Kosekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) "Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes." J.Biol.Chem., 284, 17687. doi: 10.1074/JBC.M109014274. Binary complex of dpo4 bound to n2,n2-dimethyl-deoxyguanosine modified DNA. SNAP output
2w9c transferase-DNA X-ray (2.9 Å) Zhang H, Eoff RL, Kosekov ID, Rizzo CJ, Egli M, Guengerich FP (2009) "Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes." J.Biol.Chem., 284, 17687. doi: 10.1074/JBC.M109014274. Ternary complex of dpo4 bound to n2,n2-dimethyl-deoxyguanosine modified DNA with incoming dttp. SNAP output
2wb2 lyase-DNA X-ray (2.95 Å) Glas AF, Schneider S, Maul MJ, Hennecke U, Carell T (2009) "Crystal Structure of the T(6-4)C Lesion in Complex with a (6-4) DNA Photolyase and Repair of Uv- Induced (6-4) and Dewar Photolesions." Chemistry, 15, 10387. doi: 10.1002/CHEM.200901004. Drosophila melanogaster (6-4) photolyase bound to double stranded DNA containing a t(6-4)c photolesion. SNAP output
2wbs transcription-DNA X-ray (1.7 Å) Schuetz A, Nana D, Rose C, Zocher G, Milanovic M, Koenigsmann J, Blasig R, Heinemann U, Carstanjen D (2011) "The Structure of the Klf4 DNA-Binding Domain Links to Self-Renewal and Macrophage Differentiation." Cell.Mol.Life Sci., 68, 3121. doi: 10.1007/S00018-010-0618-X. Crystal structure of the zinc finger domain of klf4 bound to its target DNA. SNAP output
2wbu transcription-DNA X-ray (2.5 Å) Schuetz A, Nana D, Rose C, Zocher G, Milanovic M, Koenigsmann J, Blasig R, Heinemann U, Carstanjen D (2011) "The Structure of the Klf4 DNA-Binding Domain Links to Self-Renewal and Macrophage Differentiation." Cell.Mol.Life Sci., 68, 3121. doi: 10.1007/S00018-010-0618-X. Crystal structure of the zinc finger domain of klf4 bound to its target DNA. SNAP output
2wcc protein-DNA NMR Fadeev EA, Sam MD, Clubb RT (2009) "NMR Structure of the Amino-Terminal Domain of the Lambda Integrase Protein in Complex with DNA: Immobilization of a Flexible Tail Facilitates Beta- Sheet Recognition of the Major Groove." J.Mol.Biol., 388, 682. doi: 10.1016/J.JMB.2009.03.041. Phage lambda intdbd1-64 complex with p prime 2 DNA. SNAP output
2wiw hydrolase-DNA X-ray (1.8 Å) Carolis C, Koehler C, Sauter C, Basquin J, Suck D, Toeroe I "Crystal Structures of Holliday Junction Resolvases from Archaeoglobus Fulgidus Bound to DNA Substrate." Crystal structures of holliday junction resolvases from archaeoglobus fulgidus bound to DNA substrate. SNAP output
2wiz hydrolase-DNA X-ray (3.3 Å) Carolis C, Koehler C, Sauter C, Basquin J, Suck D, Toeroe I "Crystal Structures of Holliday Junction Resolvases from Archaeoglobus Fulgidus Bound to DNA Substrate." Crystal structures of holliday junction resolvases from archaeoglobus fulgidus bound to DNA substrate. SNAP output
2wj0 hydrolase-DNA X-ray (3.1 Å) Carolis C, Koehler C, Sauter C, Basquin J, Suck D, Toeroe I "Crystal Structures of Holliday Junction Resolvases from Archaeoglobus Fulgidus Bound to DNA Substrate." Crystal structures of holliday junction resolvases from archaeoglobus fulgidus bound to DNA substrate. SNAP output
2wq6 lyase-DNA X-ray (2.3 Å) Glas AF, Kaya E, Schneider S, Heil K, Fazio D, Maul MJ, Carell T (2010) "DNA (6-4) Photolyases Reduce Dewar Isomers for Isomerization Into (6-4) Lesions." J.Am.Chem.Soc., 132, 3254. doi: 10.1021/JA910917F. Structure of the 6-4 photolyase of d. melanogaster in complex with the non-natural n4-methyl t(dewar)c lesion. SNAP output
2wq7 lyase-DNA X-ray (2.0 Å) Glas AF, Kaya E, Schneider S, Heil K, Fazio D, Maul MJ, Carell T (2010) "DNA (6-4) Photolyases Reduce Dewar Isomers for Isomerization Into (6-4) Lesions." J.Am.Chem.Soc., 132, 3254. doi: 10.1021/JA910917F. Structure of the 6-4 photolyase of d. melanogaster in complex with the non-natural n4-methyl t(6-4)c lesion. SNAP output
2wt7 transcription X-ray (2.3 Å) Pogenberg V, Consani Textor L, Vanhille L, Holton SJ, Sieweke MH, Wilmanns M (2014) "Design of a bZIP Transcription Factor with Homo/Heterodimer-Induced DNA-Binding Preference." Structure, 22, 466. doi: 10.1016/J.STR.2013.12.017. Crystal structure of the bzip heterodimeric complex mafb:cfos bound to DNA. SNAP output
2wtf transferase-DNA X-ray (2.5 Å) Reissner T, Schneider S, Schorr S, Carell T (2010) "Crystal Structure of a Cisplatin-(1,3-Gtg) Cross-Link within DNA Polymerase Eta." Angew.Chem.Int.Ed.Engl., 49, 3077. doi: 10.1002/ANIE.201000414. DNA polymerase eta in complex with the cis-diammineplatinum (ii) 1,3- gtg intrastrand cross-link. SNAP output
2wtu DNA binding protein-DNA X-ray (3.4 Å) Lebbink JH, Fish A, Reumer A, Natrajan G, Winterwerp HH, Sixma TK (2010) "Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS." J. Biol. Chem., 285, 13131-13141. doi: 10.1074/jbc.M109.066001. Crystal structure of escherichia coli muts in complex with a 16 basepair oligo containing an a.a mismatch.. SNAP output
2wty transcription X-ray (2.9 Å) Pogenberg V, Consani Textor L, Vanhille L, Holton SJ, Sieweke MH, Wilmanns M (2014) "Design of a bZIP Transcription Factor with Homo/Heterodimer-Induced DNA-Binding Preference." Structure, 22, 466. doi: 10.1016/J.STR.2013.12.017. Crystal structure of the homodimeric mafb in complex with the t-mare binding site. SNAP output
2wwy hydrolase-DNA X-ray (2.9 Å) Pike ACW, Zhang Y, Schnecke C, Chaikuad A, Krojer T, Cooper CDO, von Delft F, Arrowsmith CH, Weigelt J, Edwards A, Bountra C, Gileadi O (2015) "Recq1 Helicase-Driven DNA Unwinding, Annealing, and Branch Migration: Insights from DNA Complex Structures." Proc.Natl.Acad.Sci.USA, 112, 4286. doi: 10.1073/PNAS.1417594112. Structure of human recq-like helicase in complex with a DNA substrate. SNAP output
2x1a transcription-RNA X-ray (2.05 Å) Pancevac C, Goldstone DC, Ramos A, Taylor IA (2010) "Structure of the RNA15 Rrm-RNA Complex Reveals the Molecular Basis of Gu Specificity in Transcriptional 3-End Processing Factors." Nucleic Acids Res., 38, 3119. doi: 10.1093/NAR/GKQ002. Structure of rna15 rrm with RNA bound (g). SNAP output
2x6v transcription-DNA X-ray (2.2 Å) Stirnimann CU, Ptchelkine D, Grimm C, Muller CW (2010) "Structural Basis of Tbx5-DNA Recognition: The T-Box Domain in its DNA-Bound and -Unbound Form." J.Mol.Biol., 400, 71. doi: 10.1016/J.JMB.2010.04.052. Crystal structure of human tbx5 in the DNA-bound and DNA-free form. SNAP output
2xc9 transferase-DNA X-ray (2.2 Å) Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M (2010) "Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus." Acta Crystallogr.,Sect.F, 66, 1013. doi: 10.1107/S1744309110029374. Binary complex of sulfolobus solfataricus dpo4 DNA polymerase and 1, n2-ethenoguanine modified DNA, magnesium form. SNAP output
2xca transferase-DNA X-ray (2.5 Å) Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M (2010) "Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus." Acta Crystallogr.,Sect.F, 66, 1013. doi: 10.1107/S1744309110029374. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, 7,8- dihydro-8-oxodeoxyguanine modified DNA and dgtp - magnesium form. SNAP output
2xcp DNA-transferase X-ray (2.6 Å) Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M (2010) "Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus." Acta Crystallogr.,Sect.F, 66, 1013. doi: 10.1107/S1744309110029374. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, 7,8- dihydro-8-oxodeoxyguanine modified DNA and dctp - magnesium form. SNAP output
2xcr isomerase X-ray (3.5 Å) Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR, Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders MR, Singh O, Spitzfaden C, Shen C, Shillings A, Theobald AF, Wohlkonig A, Pearson ND, Gwynn MN (2010) "Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents." Nature, 466, 935. doi: 10.1038/NATURE09197. The 3.5a crystal structure of the catalytic core (b'a' region) of staphylococcus aureus DNA gyrase complexed with gsk299423 and DNA. SNAP output
2xcs isomerase X-ray (2.1 Å) Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR, Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders MR, Singh O, Spitzfaden C, Shen C, Shillings A, Theobald AF, Wohlkonig A, Pearson ND, Gwynn MN (2010) "Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents." Nature, 466, 935. doi: 10.1038/NATURE09197. The 2.1a crystal structure of s. aureus gyrase complex with gsk299423 and DNA. SNAP output
2xct isomerase-DNA-antibiotic X-ray (3.35 Å) Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR, Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders MR, Singh O, Spitzfaden C, Shen C, Shillings A, Theobald AF, Wohlkonig A, Pearson ND, Gwynn MN (2010) "Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents." Nature, 466, 935. doi: 10.1038/NATURE09197. The twinned 3.35a structure of s. aureus gyrase complex with ciprofloxacin and DNA. SNAP output
2xe0 DNA binding protein-DNA X-ray (2.31 Å) Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, Merino N, Marenchino M, D'Abramo M, Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotine I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano L, Blanco FJ, Montoya G (2011) "Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human Rag1 Locus." Nucleic Acids Res., 39, 729-743. doi: 10.1093/NAR/GKQ801. Molecular basis of engineered meganuclease targeting of the endogenous human rag1 locus. SNAP output
2xgp transferase-DNA X-ray (2.7 Å) Schorr S, Schneider S, Lammens K, Hopfner KP, Carell T (2010) "Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta by Bulky Acetylaminofluorene DNA Adducts." Proc.Natl.Acad.Sci.USA, 107, 20720. doi: 10.1073/PNAS.1008894107. Yeast DNA polymerase eta in complex with c8-2-acetylaminofluorene containing DNA. SNAP output
2xgq transferase-DNA X-ray (2.7 Å) Schorr S, Schneider S, Lammens K, Hopfner KP, Carell T (2010) "Mechanism of Replication Blocking and Bypass of Y-Family Polymerase Eta by Bulky Acetylaminofluorene DNA Adducts." Proc.Natl.Acad.Sci.USA, 107, 20720. doi: 10.1073/PNAS.1008894107. Structure of yeast DNA polymerase eta in complex with c8-n-acetyl-2- aminoanthracene containing DNA. SNAP output
2xhb transferase-DNA X-ray (2.72 Å) Killelea T, Ghosh S, Tan SS, Heslop P, Firbank SJ, Kool ET, Connolly BA (2010) "Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-Ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues." Biochemistry, 49, 5772. doi: 10.1021/BI100421R. Crystal structure of DNA polymerase from thermococcus gorgonarius in complex with hypoxanthine-containing DNA. SNAP output
2xhi lyase-DNA X-ray (1.55 Å) Dalhus B, Forsbring M, Helle IH, Vik ES, Forstrom RJ, Backe PH, Alseth I, Bjoras M (2011) "Separation-of-Function Mutants Unravel the Dual- Reaction Mode of Human 8-Oxoguanine DNA Glycosylase." Structure, 19, 117. doi: 10.1016/J.STR.2010.09.023. Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase. SNAP output
2xkk isomerase-DNA-antibiotic X-ray (3.25 Å) Wohlkonig A, Chan PF, Fosberry AP, Homes P, Huang J, Kranz M, Leydon VR, Miles TJ, Pearson ND, Perera RL, Shillings AJ, Gwynn MN, Bax BD (2010) "Structural Basis of Quinolone Inhibition of Type Iia Topoisomerases and Target-Mediated Resistance." Nat.Struct.Mol.Biol., 17, 1152. doi: 10.1038/NSMB.1892. Crystal structure of moxifloxacin, DNA, and a. baumannii topo iv (pare-parc fusion truncate). SNAP output
2xli hydrolase-RNA X-ray (2.33 Å) Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) "Sequence- and Structure-Specific RNA Processing by a Crispr Endonuclease." Science, 329, 1355. doi: 10.1126/SCIENCE.1192272. Crystal structure of the csy4-crrna complex, monoclinic form. SNAP output
2xlj hydrolase-RNA X-ray (2.6 Å) Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) "Sequence- and Structure-Specific RNA Processing by a Crispr Endonuclease." Science, 329, 1355. doi: 10.1126/SCIENCE.1192272. Crystal structure of the csy4-crrna complex, hexagonal form. SNAP output
2xlk hydrolase-RNA X-ray (1.805 Å) Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) "Sequence- and Structure-Specific RNA Processing by a Crispr Endonuclease." Science, 329, 1355. doi: 10.1126/SCIENCE.1192272. Crystal structure of the csy4-crrna complex, orthorhombic form. SNAP output
2xm3 DNA binding protein-DNA X-ray (2.3 Å) Hickman AB, James JA, Barabas O, Pasternak C, Ton-Hoang B, Chandler M, Sommer S, Dyda F (2010) "DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans." Embo J., 29, 3840. doi: 10.1038/EMBOJ.2010.241. Deinococcus radiodurans isdra2 transposase left end DNA complex. SNAP output
2xma DNA binding protein-DNA X-ray (2.3 Å) Hickman AB, James JA, Barabas O, Pasternak C, Ton-Hoang B, Chandler M, Sommer S, Dyda F (2010) "DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans." Embo J., 29, 3840. doi: 10.1038/EMBOJ.2010.241. Deinococcus radiodurans isdra2 transposase right end DNA complex. SNAP output
2xnr RNA binding protein-RNA X-ray (1.6 Å) Lunde BM, Horner M, Meinhart A (2011) "Structural Insights Into Cis Element Recognition of Non-Polyadenylated Rnas by the Nab3-Rrm." Nucleic Acids Res., 39, 337. doi: 10.1093/NAR/GKQ751. Structural insights into cis element recognition of non- polyadenylated rnas by the nab3-rrm. SNAP output
2xo6 DNA binding protein-DNA X-ray (1.9 Å) Hickman AB, James JA, Barabas O, Pasternak C, Ton-Hoang B, Chandler M, Sommer S, Dyda F (2010) "DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans." Embo J., 29, 3840. doi: 10.1038/EMBOJ.2010.241. Deinococcus radiodurans isdra2 transposase y132f mutant complexed with left end recognition and cleavage site. SNAP output
2xo7 transferase-DNA X-ray (2.85 Å) Muenzel M, Lercher L, Mueller M, Carell T (2010) "Chemical Discrimination between Dc and 5Medc Via Their Hydroxylamine Adducts." Nucleic Acids Res., 38, E192. doi: 10.1093/NAR/GKQ724. Crystal structure of a da:o-allylhydroxylamine-dc basepair in complex with fragment DNA polymerase i from bacillus stearothermophilus. SNAP output
2xqc DNA binding protein-DNA X-ray (1.9 Å) Hickman AB, James JA, Barabas O, Pasternak C, Ton-Hoang B, Chandler M, Sommer S, Dyda F (2010) "DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans." Embo J., 29, 3840. doi: 10.1038/EMBOJ.2010.241. Deinococcus radiodurans isdra2 transposase complexed with left end recognition and cleavage site and zn. SNAP output
2xro DNA-binding protein-DNA X-ray (3.4 Å) Lu D, Fillet S, Meng C, Alguel Y, Kloppsteck P, Bergeron J, Krell T, Gallegos MT, Ramos J, Zhang X (2010) "Crystal Structure of Ttgv in Complex with its DNA Operator Reveals a General Model for Cooperative DNA Binding of Tetrameric Gene Regulators." Genes Dev., 24, 2556. doi: 10.1101/GAD.603510. Crystal structure of ttgv in complex with its DNA operator. SNAP output
2xrz lyase-DNA X-ray (2.2 Å) Kiontke S, Geisselbrecht Y, Pokorny R, Carell T, Batschauer A, Essen LO (2011) "Crystal Structures of an Archaeal Class II DNA Photolyase and its Complex with Uv-Damaged Duplex DNA." Embo J., 30, 4437. doi: 10.1038/EMBOJ.2011.313. X-ray structure of archaeal class ii cpd photolyase from methanosarcina mazei in complex with intact cpd-lesion. SNAP output
2xsd transcription-DNA X-ray (2.049 Å) Jauch R, Choo SH, Ng CKL, Kolatkar PR (2011) "Crystal Structure of the Dimeric Oct6 (POU3F1) POU Domain Bound to Palindromic More DNA." Proteins, 79, 674. doi: 10.1002/PROT.22916. Crystal structure of the dimeric oct-6 (pou3f1) pou domain bound to palindromic more DNA. SNAP output
2xy5 transferase-DNA X-ray (2.22 Å) Kaul C, Mueller M, Wagner M, Schneider S, Carell T (2011) "Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair." Nature Chem., 3, 794. doi: 10.1038/NCHEM.1117. Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase i from bacillus stearothermophilus. SNAP output
2xy6 transferase-DNA X-ray (2.3 Å) Kaul C, Mueller M, Wagner M, Schneider S, Carell T (2011) "Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair." Nature Chem., 3, 794. doi: 10.1038/NCHEM.1117. Crystal structure of a salicylic aldehyde basepair in complex with fragment DNA polymerase i from bacillus stearothermophilus. SNAP output
2xy7 transferase-DNA X-ray (3.05 Å) Kaul C, Mueller M, Wagner M, Schneider S, Carell T (2011) "Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair." Nature Chem., 3, 794. doi: 10.1038/NCHEM.1117. Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase i from bacillus stearothermophilus. SNAP output
2xzf hydrolase-DNA X-ray (1.799 Å) Le Bihan YV, Izquierdo MA, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carrel T, Castaing B (2011) "5-Hydroxy-5-Methylhydantoin DNA Lesion, a Molecular Trap for DNA Glycosylases." Nucleic Acids Res., 39, 6277. doi: 10.1093/NAR/GKR215. Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and an oxidized pyrimidine containing DNA at 293k. SNAP output
2xzu hydrolase-DNA X-ray (1.82 Å) Le Bihan YV, Izquierdo MA, Coste F, Aller P, Culard F, Gehrke TH, Essalhi K, Carrel T, Castaing B (2011) "5-Hydroxy-5-Methylhydantoin DNA Lesion, a Molecular Trap for DNA Glycosylases." Nucleic Acids Res., 39, 6277. doi: 10.1093/NAR/GKR215. Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and an oxidized pyrimidine containing DNA at 310k. SNAP output
2y1i transferase-DNA X-ray (2.78 Å) Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T (2011) "Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion." Chemistry, 17, 9651. doi: 10.1002/CHEM.201100177. Crystal structure of a s-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase i from bacillus stearothermophilus. SNAP output
2y1j transferase-DNA X-ray (2.15 Å) Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T (2011) "Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion." Chemistry, 17, 9651. doi: 10.1002/CHEM.201100177. Crystal structure of a r-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase i from bacillus stearothermophilus. SNAP output
2y35 hydrolase-DNA X-ray (3.2 Å) Jinek M, Coyle SM, Doudna JA (2011) "Coupled 5' Nucleotide Recognition and Processivity in Xrn1-Mediated Mrna Decay." Mol.Cell, 41, 600. doi: 10.1016/J.MOLCEL.2011.02.004. Crystal structure of xrn1-substrate complex. SNAP output
2y7h transferase-DNA cryo-EM (18.0 Å) Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF (2009) "The Structure of M.Ecoki Type I DNA Methyltransferase with a DNA Mimic Antirestriction Protein." Nucleic Acids Res., 37, 762. doi: 10.1093/NAR/GKN988. Atomic model of the DNA-bound methylase complex from the type i restriction-modification enzyme ecoki (m2s1). based on fitting into em map 1534.. SNAP output
2y9h hydrolase-RNA X-ray (2.5 Å) Sashital DG, Jinek M, Doudna JA (2011) "An RNA-Induced Conformational Change Required for Crispr RNA Cleavage by the Endoribonuclease Cse3." Nat.Struct.Mol.Biol., 18, 680. doi: 10.1038/NSMB.2043. Structure a of crispr endoribonuclease cse3 bound to 19 nt RNA. SNAP output
2y9z transcription X-ray (3.601 Å) Yamada K, Frouws TD, Angst B, Fitzgerald DJ, Deluca C, Schimmele K, Sargent DF, Richmond TJ (2011) "Structure and Mechanism of the Chromatin Remodelling Factor Isw1A." Nature, 472, 448. doi: 10.1038/NATURE09947. Chromatin remodeling factor isw1a(del_atpase) in DNA complex. SNAP output
2ypa immune system X-ray (2.8 Å) El Omari K, Hoosdally SJ, Tuladhar K, Karia D, Hall-Ponsele E, Platonova O, Vyas P, Patient R, Porcher C, Mancini EJ (2013) "Structural Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets." Cell Rep., 4, 135. doi: 10.1016/J.CELREP.2013.06.008. Structure of the scl:e47:lmo2:ldb1 complex bound to DNA. SNAP output
2ypb immune system X-ray (2.87 Å) El Omari K, Hoosdally SJ, Tuladhar K, Karia D, Hall-Ponsele E, Platonova O, Vyas P, Patient R, Porcher C, Mancini EJ (2013) "Structural Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets." Cell Rep., 4, 135. doi: 10.1016/J.CELREP.2013.06.008. Structure of the scl:e47 complex bound to DNA. SNAP output
2ypf DNA binding protein-DNA X-ray (2.55 Å) Stella S, Molina R, Yefimenko I, Prieto J, Silva GH, Bertonati C, Juillerat A, Duchateau P, Montoya G (2013) "Structure of the Avrbs3-DNA Complex Provides New Insights Into the Initial Thymine-Recognition Mechanism." Acta Crystallogr.,Sect.D, 69, 1707. doi: 10.1107/S0907444913016429. Structure of the avrbs3-DNA complex provides new insights into the initial thymine-recognition mechanism. SNAP output
2yu9 transcription,transferase-DNA-RNA hybrid X-ray (3.4 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 150 mm mg+2 with utp. SNAP output
2yvh transcription-DNA X-ray (2.5 Å) Itou H, Watanabe N, Yao M, Shirakihara Y, Tanaka I (2010) "Crystal Structures of the Multidrug Binding Repressor Corynebacteriumglutamicum CgmR in Complex with Inducers and with an Operator." J.Mol.Biol., 403, 174-184. doi: 10.1016/j.jmb.2010.07.042. Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor cgmr. SNAP output
2z33 transcription-DNA NMR Yamane T, Okamura H, Ikeguchi M, Nishimura Y, Kidera A (2008) "Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment." Proteins, 71, 1970-1983. doi: 10.1002/prot.21874. Solution structure of the DNA complex of phob DNA-binding-transactivation domain. SNAP output
2z3x DNA binding protein-DNA X-ray (2.1 Å) Lee KS, Bumbaca D, Kosman J, Setlow P, Jedrzejas MJ (2008) "Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species." Proc. Natl. Acad. Sci. U.S.A., 105, 2806-2811. doi: 10.1073/pnas.0708244105. Structure of a protein-DNA complex essential for DNA protection in spore of bacillus species. SNAP output
2z6a transferase-DNA X-ray (2.88 Å) Youngblood B, Shieh FK, Buller F, Bullock T, Reich NO (2007) "S-Adenosyl-l-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation." Biochemistry, 46, 8766-8775. doi: 10.1021/bi7005948. S-adenosyl-l-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation. SNAP output
2z6q transferase-DNA X-ray (2.79 Å) Shieh FK, Youngblood B, Reich NO (2006) "The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI." J.Mol.Biol., 362, 516-527. doi: 10.1016/j.jmb.2006.07.030. Ternary structure of arg165ala m.hhai c5-cytosine DNA methyltransferase with unmodified DNA and adohcy. SNAP output
2z6u transferase-DNA X-ray (2.72 Å) Shieh FK, Reich NO (2007) "AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI." J.Mol.Biol., 373, 1157-1168. doi: 10.1016/j.jmb.2007.08.009. Ternary structure of the glu119ala m.hhai, c5-cytosine DNA methyltransferase, with unmodified DNA and adohcy. SNAP output
2z70 hydrolase X-ray (1.7 Å) Rodriguez SM, Panjikar S, Van Belle K, Wyns L, Messens J, Loris R (2008) "Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli." Protein Sci., 17, 681-690. doi: 10.1110/ps.073420708. E.coli rnase 1 in complex with d(cgcgatcgcg). SNAP output
2z9o replication-DNA X-ray (3.14 Å) Nakamura A, Wada C, Miki K (2007) "Structural basis for regulation of bifunctional roles in replication initiator protein." Proc.Natl.Acad.Sci.Usa, 104, 18484-18489. doi: 10.1073/pnas.0705623104. Crystal structure of the dimeric form of repe in complex with the repe operator DNA. SNAP output
2zcj transferase-DNA X-ray (2.75 Å) Shieh FK, Reich NO (2007) "AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI." J.Mol.Biol., 373, 1157-1168. doi: 10.1016/j.jmb.2007.08.009. Ternary structure of the glu119gln m.hhai, c5-cytosine DNA methyltransferase, with unmodified DNA and adohcy. SNAP output
2zhg transcription-DNA X-ray (2.8 Å) Watanabe S, Kita A, Kobayashi K, Miki K (2008) "Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA." Proc.Natl.Acad.Sci.Usa, 105, 4121-4126. doi: 10.1073/pnas.0709188105. Crystal structure of soxr in complex with DNA. SNAP output
2zkd ligase X-ray (1.6 Å) Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) "Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism." Nature, 455, 818-821. doi: 10.1038/nature07249. Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA. SNAP output
2zke ligase X-ray (2.6 Å) Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) "Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism." Nature, 455, 818-821. doi: 10.1038/nature07249. Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA. SNAP output
2zkf ligase X-ray (2.55 Å) Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) "Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism." Nature, 455, 818-821. doi: 10.1038/nature07249. Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA. SNAP output
2zo0 ligase-DNA X-ray (2.19 Å) Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) "The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix." Nature, 455, 826-829. doi: 10.1038/nature07280. Mouse np95 sra domain DNA specific complex 1. SNAP output
2zo1 ligase-DNA X-ray (1.96 Å) Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) "The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix." Nature, 455, 826-829. doi: 10.1038/nature07280. Mouse np95 sra domain DNA specific complex 2. SNAP output
2zo2 ligase-DNA X-ray (3.09 Å) Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) "The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix." Nature, 455, 826-829. doi: 10.1038/nature07280. Mouse np95 sra domain non-specific DNA complex. SNAP output
316d DNA-antibiotic X-ray (3.0 Å) Takusagawa F, Takusagawa KT, Carlson RG, Weaver RF (1997) "Selectivity of F8-Actinomycin D for RNA:DNA Hybrids and its Anti-Leukemia Activity." Bioorg.Med.Chem., 5, 1197. doi: 10.1016/S0968-0896(97)00062-X. Selectivity of f8-actinomycin d for RNA:DNA hybrids and its anti-leukemia activity. SNAP output
3a01 gene regulation-DNA X-ray (2.7 Å) Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M (2010) "Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless." Embo J., 29, 1613-1623. doi: 10.1038/emboj.2010.53. Crystal structure of aristaless and clawless homeodomains bound to DNA. SNAP output
3a46 hydrolase X-ray (2.2 Å) Imamura K, Wallace SS, Doublie S (2009) "Structural Characterization of a Viral NEIL1 Ortholog Unliganded and Bound to Abasic Site-containing DNA." J.Biol.Chem., 284, 26174-26183. doi: 10.1074/jbc.M109.021907. Crystal structure of mvnei1-thf complex. SNAP output
3a4k hydrolase-DNA X-ray (2.17 Å) Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I (2009) "Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations." Acta Crystallogr.,Sect.D, 65, 1326-1333. doi: 10.1107/S0907444909041134. Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution. SNAP output
3a5t transcription regulator-DNA X-ray (2.8 Å) Kurokawa H, Motohashi H, Sueno S, Kimura M, Takagawa H, Kanno Y, Yamamoto M, Tanaka T (2009) "Structural Basis of Alternative DNA Recognition by Maf Transcription Factors." Mol.Cell.Biol., 29, 6232-6244. doi: 10.1128/MCB.00708-09. Crystal structure of mafg-DNA complex. SNAP output
3a5u DNA binding protein X-ray (2.8 Å) Kaushal PS, Manjunath GP, Sekar K, Muniyappa K, Vijayan M (2009) "Promiscuity and specificity in DNA binding to SSB: Insights from the structure of the Mycobacterium smegmatis SSB-ssDNA complex." Promiscuity and specificity in DNA binding to ssb: insights from the structure of the mycobacterium smegmatis ssb-ssDNA complex. SNAP output
3a6n structural protein-DNA X-ray (2.7 Å) Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H (2010) "Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T." Proc.Natl.Acad.Sci.USA, 107, 10454-10459. doi: 10.1073/pnas.1003064107. The nucleosome containing a testis-specific histone variant, human h3t. SNAP output
3aaf DNA binding protein-DNA X-ray (1.9 Å) Kitano K, Kim SY, Hakoshima T (2010) "Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN." Structure, 18, 177-187. doi: 10.1016/j.str.2009.12.011. Structure of wrn rqc domain bound to double-stranded DNA. SNAP output
3afa structural protein-DNA X-ray (2.5 Å) Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H (2010) "Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T." Proc.Natl.Acad.Sci.USA, 107, 10454-10459. doi: 10.1073/pnas.1003064107. The human nucleosome structure. SNAP output
3an2 structural protein-DNA X-ray (3.6 Å) Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park S-Y, Kimura H, Kurumizaka H (2011) "Crystal structure of the human centromeric nucleosome containing CENP-A." Nature, 476, 232-235. doi: 10.1038/nature10258. The structure of the centromeric nucleosome containing cenp-a. SNAP output
3aoh transcription, transferase-DNA-RNA X-ray (4.1 Å) Tagami S, Sekine SI, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S (2010) "Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein." Nature, 468, 978-982. doi: 10.1038/nature09573. RNA polymerase-gfh1 complex (crystal type 1). SNAP output
3aoi transcription, transferase-DNA-RNA X-ray (4.3 Å) Tagami S, Sekine SI, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S (2010) "Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein." Nature, 468, 978-982. doi: 10.1038/nature09573. RNA polymerase-gfh1 complex (crystal type 2). SNAP output
3au6 transferase-DNA X-ray (3.3 Å) Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R (2012) "The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA." J.Mol.Biol., 417, 179-196. doi: 10.1016/j.jmb.2012.01.025. DNA polymerase x from thermus thermophilus hb8 ternary complex with primer-template DNA and ddgtp. SNAP output
3auo transferase-DNA X-ray (2.7 Å) Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui R (2012) "The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA." J.Mol.Biol., 417, 179-196. doi: 10.1016/j.jmb.2012.01.025. DNA polymerase x from thermus thermophilus hb8 ternary complex with 1-nt gapped DNA and ddgtp. SNAP output
3av1 structural protein-DNA X-ray (2.5 Å) Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H (2011) "Structures of human nucleosomes containing major histone H3 variants." Acta Crystallogr.,Sect.D, 67, 578-583. doi: 10.1107/S0907444911014818. The human nucleosome structure containing the histone variant h3.2. SNAP output
3av2 structural protein-DNA X-ray (2.8 Å) Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H (2011) "Structures of human nucleosomes containing major histone H3 variants." Acta Crystallogr.,Sect.D, 67, 578-583. doi: 10.1107/S0907444911014818. The human nucleosome structure containing the histone variant h3.3. SNAP output
3ayw structural protein-DNA X-ray (2.9 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h3k56q mutation. SNAP output
3aze structural protein-DNA X-ray (3.0 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h3k64q mutation. SNAP output
3azf structural protein-DNA X-ray (2.7 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h3k79q mutation. SNAP output
3azg structural protein-DNA X-ray (2.4 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h3k115q mutation. SNAP output
3azh structural protein-DNA X-ray (3.49 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h3k122q mutation. SNAP output
3azi structural protein-DNA X-ray (2.7 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h4k31q mutation. SNAP output
3azj structural protein-DNA X-ray (2.89 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h4k44q mutation. SNAP output
3azk structural protein-DNA X-ray (3.2 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h4k59q mutation. SNAP output
3azl structural protein-DNA X-ray (2.7 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h4k77q mutation. SNAP output
3azm structural protein-DNA X-ray (2.89 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h4k79q mutation. SNAP output
3azn structural protein-DNA X-ray (3.0 Å) Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T, Kagawa W, Kurumizaka H (2011) "Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (KQ) Substitutions in the H3 and H4 Histone-Fold Domains." Biochemistry, 50, 7822-7832. doi: 10.1021/bi201021h. Crystal structure of human nucleosome core particle containing h4k91q mutation. SNAP output
3b39 transferase-DNA X-ray (2.35 Å) Corn JE, Pelton JG, Berger JM (2008) "Identification of a DNA primase template tracking site redefines the geometry of primer synthesis." Nat.Struct.Mol.Biol., 15, 163-169. doi: 10.1038/nsmb.1373. Structure of the dnag primase catalytic domain bound to ssDNA. SNAP output
3b6f structural protein-DNA X-ray (3.45 Å) Wu B, Droge P, Davey CA (2008) "Site selectivity of platinum anticancer therapeutics." Nat.Chem.Biol., 4, 110-112. doi: 10.1038/nchembio.2007.58. Nucleosome core particle treated with cisplatin. SNAP output
3b6g structural protein-DNA X-ray (3.45 Å) Wu B, Droge P, Davey CA (2008) "Site selectivity of platinum anticancer therapeutics." Nat.Chem.Biol., 4, 110-112. doi: 10.1038/nchembio.2007.58. Nucleosome core particle treated with oxaliplatin. SNAP output
3bam hydrolase-DNA X-ray (1.8 Å) Viadiu H, Aggarwal AK (1998) "The role of metals in catalysis by the restriction endonuclease BamHI." Nat.Struct.Biol., 5, 910-916. doi: 10.1038/2352. Restriction endonuclease bamhi complex with DNA and manganese ions (post-reactive complex). SNAP output
3bbb transferase X-ray (1.3 Å) Dexheimer TS, Carey SS, Zuohe S, Gokhale VM, Hu X, Murata LB, Maes EM, Weichsel A, Sun D, Meuillet EJ, Montfort WR, Hurley LH (2009) "NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1." Mol.Cancer Ther., 8, 1363-1377. doi: 10.1158/1535-7163.MCT-08-1093. Crystal structure of the nm23-h2 transcription factor complex with dinucleotide d(ag). SNAP output
3bbx ribosome cryo-EM (10.0 Å) Jiang L, Schaffitzel C, Bingel-Erlenmeyer R, Ban N, Korber P, Koning RI, de Geus DC, Plaisier JR, Abrahams JP (2009) "Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15." J.Mol.Biol., 386, 1357-1367. doi: 10.1016/j.jmb.2008.10.079. The hsp15 protein fitted into the low resolution cryo-EM map of the 50s.nc-trna.hsp15 complex. SNAP output
3bdn transcription-DNA X-ray (3.909 Å) Stayrook SE, Jaru-Ampornpan P, Ni J, Hochschild A, Lewis M (2008) "Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding." Nature, 452, 1022-1025. doi: 10.1038/nature06831. Crystal structure of the lambda repressor. SNAP output
3bdp transferase-DNA X-ray (1.9 Å) Kiefer JR, Mao C, Braman JC, Beese LS (1998) "Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal." Nature, 391, 304-307. doi: 10.1038/34693. DNA polymerase i-DNA complex. SNAP output
3bep transferase, transcription-DNA X-ray (1.92 Å) Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong X-P, O'Donnell M (2008) "Structure of a sliding clamp on DNA." Cell(Cambridge,Mass.), 132, 43-54. doi: 10.1016/j.cell.2007.11.045. Structure of a sliding clamp on DNA. SNAP output
3bi3 oxidoreductase-DNA X-ray (1.9 Å) Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. X-ray structure of alkb protein bound to dsDNA containing 1mea-a with cofactors. SNAP output
3bie oxidoreductase-DNA X-ray (1.68 Å) Yang C-G, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. X-ray structure of e coli alkb bound to dsDNA containing 1mea-t with mn and 2kg. SNAP output
3bjy transferase-DNA X-ray (2.41 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2008) "Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase." Structure, 16, 239-245. doi: 10.1016/j.str.2007.12.009. Catalytic core of rev1 in complex with DNA (modified template guanine) and incoming nucleotide. SNAP output
3bkz DNA repair,oxidoreductase-DNA X-ray (1.65 Å) Yang C-G, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. X-ray structure of e coli alkb crosslinked to dsDNA in the active site. SNAP output
3bm3 hydrolase-DNA X-ray (1.7 Å) Szczepanowski RH, Carpenter M, Czapinska H, Tamulaitis G, Siksnys V, Bhagwat A, Bochtler M "A direct crystallographic demonstration that Type II restriction endonuclease PspGI flips nucleotides." Restriction endonuclease pspgi-substrate DNA complex. SNAP output
3bq0 transferase-DNA X-ray (2.6 Å) Wilson RC, Pata JD (2008) "Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh." Mol.Cell, 29, 767-779. doi: 10.1016/j.molcel.2008.01.014. Pre-insertion binary complex of dbh DNA polymerase. SNAP output
3bq1 transferase-DNA X-ray (2.7 Å) Wilson RC, Pata JD (2008) "Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh." Mol.Cell, 29, 767-779. doi: 10.1016/j.molcel.2008.01.014. Insertion ternary complex of dbh DNA polymerase. SNAP output
3bq2 transferase-DNA X-ray (2.7 Å) Wilson RC, Pata JD (2008) "Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh." Mol.Cell, 29, 767-779. doi: 10.1016/j.molcel.2008.01.014. Post-insertion binary complex of dbh DNA polymerase. SNAP output
3brd DNA binding protein-DNA X-ray (2.21 Å) Friedmann DR, Wilson JJ, Kovall RA (2008) "RAM-induced Allostery Facilitates Assembly of a Notch Pathway Active Transcription Complex." J.Biol.Chem., 283, 14781-14791. doi: 10.1074/jbc.M709501200. Csl (lag-1) bound to DNA with lin-12 ram peptide, p212121. SNAP output
3brf DNA binding protein-DNA X-ray (2.47 Å) Friedmann DR, Wilson JJ, Kovall RA (2008) "RAM-induced Allostery Facilitates Assembly of a Notch Pathway Active Transcription Complex." J.Biol.Chem., 283, 14781-14791. doi: 10.1074/jbc.M709501200. Csl (lag-1) bound to DNA with lin-12 ram peptide, c2221. SNAP output
3brg DNA binding protein-DNA X-ray (2.2 Å) Friedmann DR, Wilson JJ, Kovall RA (2008) "RAM-induced Allostery Facilitates Assembly of a Notch Pathway Active Transcription Complex." J.Biol.Chem., 283, 14781-14791. doi: 10.1074/jbc.M709501200. Csl (rbp-jk) bound to DNA. SNAP output
3bs1 transcription regulator X-ray (1.6 Å) Sidote DJ, Barbieri CM, Wu T, Stock AM (2008) "Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding." Structure, 16, 727-735. doi: 10.1016/j.str.2008.02.011. Structure of the staphylococcus aureus agra lyttr domain bound to DNA reveals a beta fold with a novel mode of binding. SNAP output
3bsu hydrolase-RNA-DNA X-ray (2.1 Å) Nowotny M, Cerritelli SM, Ghirlando R, Gaidamakov SA, Crouch RJ, Yang W (2008) "Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD." Embo J., 27, 1172-1181. doi: 10.1038/emboj.2008.44. Hybrid-binding domain of human rnase h1 in complex with 12-mer RNA-DNA. SNAP output
3btx oxidoreductase-DNA X-ray (2.0 Å) Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. X-ray structure of human abh2 bound to dsDNA through active site cross-linking. SNAP output
3bty oxidoreductase-DNA X-ray (2.35 Å) Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. Crystal structure of human abh2 bound to dsDNA containing 1mea through cross-linking away from active site. SNAP output
3btz oxidoreductase-DNA X-ray (3.0 Å) Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. Crystal structure of human abh2 cross-linked to dsDNA. SNAP output
3bu0 oxidoreductase-DNA X-ray (2.5 Å) Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. Crystal structure of human abh2 cross-linked to dsDNA with cofactors. SNAP output
3buc oxidoreductase-DNA X-ray (2.59 Å) Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C (2008) "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA." Nature, 452, 961-965. doi: 10.1038/nature06889. X-ray structure of human abh2 bound to dsDNA with mn(ii) and 2kg. SNAP output
3c0w hydrolase-DNA X-ray (2.2 Å) Moure CM, Gimble FS, Quiocho FA (2008) "Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway." Nucleic Acids Res., 36, 3287-3296. doi: 10.1093/nar/gkn178. I-scei in complex with a bottom nicked DNA substrate. SNAP output
3c0x hydrolase-DNA X-ray (2.3 Å) Moure CM, Gimble FS, Quiocho FA (2008) "Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway." Nucleic Acids Res., 36, 3287-3296. doi: 10.1093/nar/gkn178. I-scei in complex with a top nicked DNA substrate. SNAP output
3c1b structural protein-DNA X-ray (2.2 Å) Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K (2008) "The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure." Nat.Struct.Mol.Biol., 15, 1122-1124. doi: 10.1038/nsmb.1489. The effect of h3 k79 dimethylation and h4 k20 trimethylation on nucleosome and chromatin structure. SNAP output
3c1c structural protein-DNA X-ray (3.15 Å) Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K (2008) "The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure." Nat.Struct.Mol.Biol., 15, 1122-1124. doi: 10.1038/nsmb.1489. The effect of h3 k79 dimethylation and h4 k20 trimethylation on nucleosome and chromatin structure. SNAP output
3c25 hydrolase-DNA X-ray (2.5 Å) Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu SY, Stoddard BL (2008) "Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding." Structure, 16, 558-569. doi: 10.1016/j.str.2008.01.017. Crystal structure of noti restriction endonuclease bound to cognate DNA. SNAP output
3c28 recombination-DNA X-ray (2.6 Å) Ghosh K, Van Duyne GD "Detailed study on Synapsis in Cre-loxP recombination reaction." Crystal structure of the product synapse complex. SNAP output
3c29 recombination-DNA X-ray (2.2 Å) Ghosh K, Van Duyne GD "Synapsis study in detail." Cre-loxp synaptic structure. SNAP output
3c2i transcription regulator X-ray (2.5 Å) Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP, Walkinshaw MD (2008) "MeCP2 binding to DNA depends upon hydration at methyl-CpG." Mol.Cell, 29, 525-531. doi: 10.1016/j.molcel.2007.12.028. The crystal structure of methyl-cpg binding domain of human mecp2 in complex with a methylated DNA sequence from bdnf. SNAP output
3c2k transferase-DNA X-ray (2.4 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2008) "Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation." Mol.Cell, 30, 315-324. doi: 10.1016/j.molcel.2008.02.025. DNA polymerase beta with a gapped DNA substrate and dumpnpp with manganese in the active site. SNAP output
3c2l transferase-DNA X-ray (2.6 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2008) "Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation." Mol.Cell, 30, 315-324. doi: 10.1016/j.molcel.2008.02.025. Ternary complex of DNA polymerase beta with a c:dapcpp mismatch in the active site. SNAP output
3c2m transferase, lyase-DNA X-ray (2.15 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2008) "Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation." Mol.Cell, 30, 315-324. doi: 10.1016/j.molcel.2008.02.025. Ternary complex of DNA polymerase beta with a g:dapcpp mismatch in the active site. SNAP output
3c2p transferase-DNA X-ray (2.0 Å) Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS (2008) "Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase." Mol.Cell, 32, 707-717. doi: 10.1016/j.molcel.2008.11.010. X-ray crystal structure of the n4 mini-vrnap p1 promoter complex. SNAP output
3c3l transferase-DNA X-ray (2.4 Å) Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS (2008) "Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase." Mol.Cell, 32, 707-717. doi: 10.1016/j.molcel.2008.11.010. X-ray crystal structure of the n4 mini-vrnap p2 promoter complex. SNAP output
3c46 transferase-DNA X-ray (2.0 Å) Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS (2008) "Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase." Mol.Cell, 32, 707-717. doi: 10.1016/j.molcel.2008.11.010. X-ray crystal structure of the n4 mini-vrnap p2_7a promoter complex soaked with mgcl2. SNAP output
3c58 hydrolase-DNA X-ray (1.9 Å) Coste F, Ober M, Le Bihan YV, Izquierdo MA, Hervouet N, Mueller H, Carell T, Castaing B (2008) "Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode." Chem.Biol., 15, 706-717. doi: 10.1016/j.chembiol.2008.05.014. Crystal structure of a complex between the wild-type lactococcus lactis fpg (mutm) and a n7-benzyl-fapy-dg containing DNA. SNAP output
3c5f transferase, lyase-DNA X-ray (2.25 Å) Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, Kunkel TA (2008) "Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda." Embo Rep., 9, 459-464. doi: 10.1038/embor.2008.33. Structure of a binary complex of the r517a pol lambda mutant. SNAP output
3c5g transferase-DNA, lyase-DNA X-ray (2.2 Å) Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, Kunkel TA (2008) "Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda." Embo Rep., 9, 459-464. doi: 10.1038/embor.2008.33. Structure of a ternary complex of the r517k pol lambda mutant. SNAP output
3cbb transcription-DNA X-ray (2.0 Å) Lu P, Rha GB, Melikishvili M, Wu G, Adkins BC, Fried MG, Chi YI (2008) "Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4alpha. Diabetes gene product." J.Biol.Chem., 283, 33685-33697. doi: 10.1074/jbc.M806213200. Crystal structure of hepatocyte nuclear factor 4alpha in complex with DNA: diabetes gene product. SNAP output
3cfp transferase-DNA X-ray (2.5 Å) Klimenko D, Wang M, Steitz TA, Konigsberg WH, Wang J "Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant." Structure of the replicating complex of a pol alpha family DNA polymerase, ternary complex 1. SNAP output
3cfr transferase-DNA X-ray (2.4 Å) Klimenko D, Wang M, Steitz TA, Konigsberg WH, Wang J "Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant." Structure of the replicating complex of a pol alpha family DNA polymerase, ternary complex 2. SNAP output
3clc transcription regulator-DNA X-ray (2.8 Å) McGeehan JE, Streeter SD, Thresh SJ, Ball N, Ravelli RB, Kneale GG (2008) "Structural analysis of the genetic switch that regulates the expression of restriction-modification genes." Nucleic Acids Res., 36, 4778-4787. doi: 10.1093/nar/gkn448. Crystal structure of the restriction-modification controller protein c.esp1396i tetramer in complex with its natural 35 base-pair operator. SNAP output
3clz ligase X-ray (2.2 Å) Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, Arrowsmith CH, Dhe-Paganon S (2008) "Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1." Nature, 455, 822-825. doi: 10.1038/nature07273. The set and ring associated (sra) domain of uhrf1 bound to methylated DNA. SNAP output
3cmt recombination-DNA X-ray (3.15 Å) Chen Z, Yang H, Pavletich NP (2008) "Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures." Nature, 453, 489-494. doi: 10.1038/nature06971. Mechanism of homologous recombination from the reca-ssDNA-dsDNA structures. SNAP output
3cmu recombination-DNA X-ray (4.2 Å) Chen Z, Yang H, Pavletich NP (2008) "Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures." Nature, 453, 489-494. doi: 10.1038/nature06971. Mechanism of homologous recombination from the reca-ssDNA-dsDNA structures. SNAP output
3cmw recombination-DNA X-ray (2.8 Å) Chen Z, Yang H, Pavletich NP (2008) "Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures." Nature, 453, 489-494. doi: 10.1038/nature06971. Mechanism of homologous recombination from the reca-ssDNA-dsDNA structures. SNAP output
3cmx recombination-DNA X-ray (3.4 Å) Chen Z, Yang H, Pavletich NP (2008) "Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures." Nature, 453, 489-494. doi: 10.1038/nature06971. Mechanism of homologous recombination from the reca-ssDNA-dsDNA structures. SNAP output
3cmy transcription regulator-DNA X-ray (1.95 Å) Birrane G, Soni A, Ladias JA (2009) "Structural Basis for DNA Recognition by the Human PAX3 Homeodomain." Biochemistry, 48, 1148-1155. doi: 10.1021/bi802052y. Structure of a homeodomain in complex with DNA. SNAP output
3co6 transcription-DNA X-ray (2.1 Å) Brent MM, Anand R, Marmorstein R (2008) "Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification." Structure, 16, 1407-1416. doi: 10.1016/j.str.2008.06.013. Crystal structure of foxo1 dbd bound to dbe1 DNA. SNAP output
3co7 transcription-DNA X-ray (2.91 Å) Brent MM, Anand R, Marmorstein R (2008) "Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification." Structure, 16, 1407-1416. doi: 10.1016/j.str.2008.06.013. Crystal structure of foxo1 dbd bound to dbe2 DNA. SNAP output
3coa transcription-DNA X-ray (2.2 Å) Brent MM, Anand R, Marmorstein R (2008) "Structural Basis for DNA Recognition by FoxO1 and Its Regulation by Posttranslational Modification." Structure, 16, 1407-1416. doi: 10.1016/j.str.2008.06.013. Crystal structure of foxo1 dbd bound to ire DNA. SNAP output
3coq transcription-DNA X-ray (2.4 Å) Hong M, Fitzgerald MX, Harper S, Luo C, Speicher DW, Marmorstein R (2008) "Structural basis for dimerization in DNA recognition by gal4." Structure, 16, 1019-1026. doi: 10.1016/j.str.2008.03.015. Structural basis for dimerization in DNA recognition by gal4. SNAP output
3cq8 transferase-DNA X-ray (2.5 Å) Zhong X, Pedersen LC, Kunkel TA (2008) "Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity." Nucleic Acids Res., 36, 3892-3904. doi: 10.1093/nar/gkn312. Ternary complex of the l415f mutant rb69 exo(-)polymerase. SNAP output
3cro transcription-DNA X-ray (2.5 Å) Mondragon A, Harrison SC (1991) "The phage 434 Cro/OR1 complex at 2.5 A resolution." J.Mol.Biol., 219, 321-334. doi: 10.1016/0022-2836(91)90568-Q. The phage 434 cro-or1 complex at 2.5 angstroms resolution. SNAP output
3crx hydrolase, ligase-DNA X-ray (2.5 Å) Gopaul DN, Guo F, Van Duyne GD (1998) "Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination." EMBO J., 17, 4175-4187. doi: 10.1093/emboj/17.14.4175. Cre recombinase-DNA complex intermediate i. SNAP output
3cvs hydrolase-DNA X-ray (2.4 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 8oxoguanine:adenine base pair. SNAP output
3cvt hydrolase-DNA X-ray (2.5 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 8oxoguanine:cytosine base pair. SNAP output
3cvu lyase-DNA X-ray (2.0 Å) Maul MJ, Barends TR, Glas AF, Cryle MJ, Domratcheva T, Schneider S, Schlichting I, Carell T (2008) "Crystal structure and mechanism of a DNA (6-4) photolyase." Angew.Chem.Int.Ed.Engl., 47, 10076-10080. doi: 10.1002/anie.200804268. Drosophila melanogaster (6-4) photolyase bound to ds DNA with a t-t (6-4) photolesion. SNAP output
3cvv lyase-DNA X-ray (2.1 Å) Glas AF, Maul MJ, Cryle M, Barends TR, Schneider S, Kaya E, Schlichting I, Carell T (2009) "The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes." Proc.Natl.Acad.Sci.USA, 106, 11540-11545. doi: 10.1073/pnas.0812665106. Drosophila melanogaster (6-4) photolyase bound to ds DNA with a t-t (6-4) photolesion and f0 cofactor. SNAP output
3cvw lyase-DNA X-ray (3.2 Å) Maul MJ, Barends T, Glas AF, Cryle MJ, Schneider S, Domratcheva T, Schlichting I, Carell T "Structure and mechanism of a cofactor f0 accelerated (6-4) photolyase from the fruit fly." Drosophila melanogaster (6-4) photolyase h365n mutant bound to ds DNA with a t-t (6-4) photolesion and cofactor f0. SNAP output
3cvx lyase-DNA X-ray (3.2 Å) Maul MJ, Barends T, Glas AF, Cryle MJ, Schneider S, Domratcheva T, Schlichting I, Carell T "Structure and mechanism of a coenzyme F0 accelerated (6-4) photolyase from the fruit fly." Drosophila melanogaster (6-4) photolyase h369m mutant bound to ds DNA with a t-t (6-4) photolesion. SNAP output
3cvy lyase-DNA X-ray (2.7 Å) Maul MJ, Barends TR, Glas AF, Cryle MJ, Domratcheva T, Schneider S, Schlichting I, Carell T (2008) "Crystal structure and mechanism of a DNA (6-4) photolyase." Angew.Chem.Int.Ed.Engl., 47, 10076-10080. doi: 10.1002/anie.200804268. Drosophila melanogaster (6-4) photolyase bound to repaired ds DNA. SNAP output
3cw7 hydrolase-DNA X-ray (2.3 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 8oxoguanine:cytosine base pair. SNAP output
3cwa hydrolase-DNA X-ray (2.4 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 8oxoguanine:cytosine base pair. SNAP output
3cws hydrolase-DNA X-ray (2.3 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 2'-fluoro-2'-deoxyinosine:thymine base pair. SNAP output
3cwt hydrolase-DNA X-ray (2.3 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 2'-fluoro-2'-deoxyinosine:adenine base pair. SNAP output
3cwu hydrolase-DNA X-ray (2.8 Å) Bowman BR, Lee S, Wang S, Verdine GL (2008) "Structure of the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA." Structure, 16, 1166-1174. doi: 10.1016/j.str.2008.04.012. Crystal structure of an alka host-guest complex 2'-fluoro-2'-deoxy-1,n6-ethenoadenine:thymine base pair. SNAP output
3d0a transcription-DNA X-ray (1.8 Å) Suad O, Rozenberg H, Brosh R, Diskin-Posner Y, Kessler N, Shimon LJW, Frolow F, Liran A, Rotter V, Shakked Z (2009) "Structural basis of restoring sequence-specific DNA binding and transactivation to mutant p53 by suppressor mutations." J.Mol.Biol., 385, 249-265. doi: 10.1016/j.jmb.2008.10.063. Human p53 core domain with hot spot mutation r249s and second site suppressor mutation h168r in sequence-specific complex with DNA. SNAP output
3d0p hydrolase-DNA X-ray (1.8 Å) Pallan PS, Egli M (2008) "Insights into RNA/DNA hybrid recognition and processing by RNase H from the crystal structure of a non-specific enzyme-dsDNA complex." Cell Cycle, 7, 2562-2569. Insights into RNA-DNA hybrid recognition and processing by rnase h from the crystal structure of a non-specific enzyme-dsDNA complex. SNAP output
3d1n transcription regulator-DNA X-ray (2.51 Å) Pereira JH, Kim SH (2009) "Structure of human Brn-5 transcription factor in complex with CRH gene promoter." J.Struct.Biol., 167, 159-165. doi: 10.1016/j.jsb.2009.05.003. Structure of human brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter. SNAP output
3d2s metal binding protein-RNA X-ray (1.7 Å) Teplova M, Patel DJ (2008) "Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1." Nat.Struct.Mol.Biol., 15, 1343-1351. doi: 10.1038/nsmb.1519. Crystal structure of mbnl1 tandem zinc finger 3 and 4 domain in complex with cgcugu RNA. SNAP output
3d2w DNA-RNA binding protein X-ray (1.65 Å) Kuo PH, Doudeva LG, Wang YT, Shen CK, Yuan HS (2009) "Structural insights into TDP-43 in nucleic-acid binding and domain interactions." Nucleic Acids Res., 37, 1799-1808. doi: 10.1093/nar/gkp013. Crystal structure of mouse tdp-43 rrm2 domain in complex with DNA. SNAP output
3d4v hydrolase-DNA X-ray (2.9 Å) Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL (2008) "Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine." J.Am.Chem.Soc., 130, 11570-11571. doi: 10.1021/ja8025328. Crystal structure of an alka host-guest complex n7methylguanine:cytosine base pair. SNAP output
3d6y transcription regulator-DNA X-ray (2.7 Å) Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N, Neyfakh AA, Brennan RG (2008) "Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion." J.Biol.Chem., 283, 26795-26804. doi: 10.1074/jbc.M804191200. Crystal structure of r275e mutant of bmrr bound to DNA and berberine. SNAP output
3d6z transcription regulator-DNA X-ray (2.6 Å) Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N, Neyfakh AA, Brennan RG (2008) "Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion." J.Biol.Chem., 283, 26795-26804. doi: 10.1074/jbc.M804191200. Crystal structure of r275e mutant of bmrr bound to DNA and rhodamine. SNAP output
3d70 transcription regulator-DNA X-ray (2.8 Å) Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N, Neyfakh AA, Brennan RG (2008) "Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion." J.Biol.Chem., 283, 26795-26804. doi: 10.1074/jbc.M804191200. Crystal structure of e253a mutant of bmrr bound to 22-bp oligonucleotide. SNAP output
3d71 transcription regulator-DNA X-ray (2.8 Å) Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N, Neyfakh AA, Brennan RG (2008) "Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion." J.Biol.Chem., 283, 26795-26804. doi: 10.1074/jbc.M804191200. Crystal structure of e253q bmrr bound to 22 base pair promoter site. SNAP output
3dfv transcription-DNA X-ray (3.1 Å) Bates DL, Chen Y, Kim G, Guo L, Chen L (2008) "Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA." J.Mol.Biol., 381, 1292-1306. doi: 10.1016/j.jmb.2008.06.072. Adjacent gata DNA binding. SNAP output
3dfx transcription-DNA X-ray (2.7 Å) Bates DL, Chen Y, Kim G, Guo L, Chen L (2008) "Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA." J.Mol.Biol., 381, 1292-1306. doi: 10.1016/j.jmb.2008.06.072. Opposite gata DNA binding. SNAP output
3dlb nucleic acid binding protein-DNA X-ray (2.7 Å) Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ (2008) "Structure of the guide-strand-containing argonaute silencing complex." Nature, 456, 209-213. doi: 10.1038/nature07315. Crystal structure of the guide-strand-containing argonaute protein silencing complex. SNAP output
3dlh nucleic acid binding protein-DNA X-ray (3.0 Å) Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ (2008) "Structure of the guide-strand-containing argonaute silencing complex." Nature, 456, 209-213. doi: 10.1038/nature07315. Crystal structure of the guide-strand-containing argonaute protein silencing complex. SNAP output
3dnv transcription-DNA X-ray (2.68 Å) Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG (2009) "Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB." Science, 323, 396-401. doi: 10.1126/science.1163806. Mdt protein. SNAP output
3do7 transcription-DNA X-ray (3.05 Å) Fusco A, Huang DB, Miller D, Vu D, Ghosh G "NF-kapppaB p52:RelB heterodimer uses different binding modes to recognize different kappaB DNA." X-ray structure of a nf-kb p52-relb-DNA complex. SNAP output
3dpg hydrolase-DNA X-ray (1.91 Å) Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC (2008) "The structure of SgrAI bound to DNA; recognition of an 8 base pair target." Nucleic Acids Res., 36, 5405-5416. doi: 10.1093/nar/gkn510. Sgrai with noncognate DNA bound. SNAP output
3dsc hydrolase-DNA X-ray (2.7 Å) Williams RS, Moncalian G, Williams JS, Yamada Y, Limbo O, Shin DS, Groocock LM, Cahill D, Hitomi C, Guenther G, Moiani D, Carney JP, Russell P, Tainer JA (2008) "Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair." Cell(Cambridge,Mass.), 135, 97-109. doi: 10.1016/j.cell.2008.08.017. Crystal structure of p. furiosus mre11 DNA synaptic complex. SNAP output
3dsd hydrolase-DNA X-ray (2.2 Å) Williams RS, Moncalian G, Williams JS, Yamada Y, Limbo O, Shin DS, Groocock LM, Cahill D, Hitomi C, Guenther G, Moiani D, Carney JP, Russell P, Tainer JA (2008) "Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair." Cell(Cambridge,Mass.), 135, 97-109. doi: 10.1016/j.cell.2008.08.017. Crystal structure of p. furiosus mre11-h85s bound to a branched DNA and manganese. SNAP output
3dvo hydrolase-DNA X-ray (1.892 Å) Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC (2008) "The structure of SgrAI bound to DNA; recognition of an 8 base pair target." Nucleic Acids Res., 36, 5405-5416. doi: 10.1093/nar/gkn510. Sgrai with cognate DNA and calcium bound. SNAP output
3dw9 hydrolase-DNA X-ray (2.2 Å) Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC (2008) "The structure of SgrAI bound to DNA; recognition of an 8 base pair target." Nucleic Acids Res., 36, 5405-5416. doi: 10.1093/nar/gkn510. Sgrai with cognate DNA and manganese bound. SNAP output
3dzu transcription-DNA X-ray (3.2 Å) Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F (2008) "Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA." Nature, 456, 350-356. doi: 10.1038/nature07413. Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with bvt.13, 9-cis retinoic acid and ncoa2 peptide. SNAP output
3dzy transcription-DNA X-ray (3.1 Å) Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F (2008) "Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA." Nature, 456, 350-356. doi: 10.1038/nature07413. Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with rosiglitazone, 9-cis retinoic acid and ncoa2 peptide. SNAP output
3e00 transcription-DNA X-ray (3.1 Å) Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y, Burris TP, Rastinejad F (2008) "Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA." Nature, 456, 350-356. doi: 10.1038/nature07413. Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with gw9662, 9-cis retinoic acid and ncoa2 peptide. SNAP output
3e0d transferase-DNA X-ray (4.6 Å) Wing RA, Bailey S, Steitz TA (2008) "Insights into the Replisome from the Structure of a Ternary Complex of the DNA Polymerase III alpha-Subunit." J.Mol.Biol., 382, 859-869. doi: 10.1016/j.jmb.2008.07.058. Insights into the replisome from the crystral structure of the ternary complex of the eubacterial DNA polymerase iii alpha-subunit. SNAP output
3e2e transferase-RNA-DNA X-ray (3.0 Å) Durniak KJ, Bailey S, Steitz TA (2008) "The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation." Science, 322, 553-557. doi: 10.1126/science.1163433. Crystal structure of an intermediate complex of t7 rnap and 7nt of RNA. SNAP output
3e3j transferase-RNA-DNA X-ray (6.7 Å) Durniak KJ, Bailey S, Steitz TA (2008) "The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation." Science, 322, 553-557. doi: 10.1126/science.1163433. Crystal structure of an intermediate complex of t7 rnap and 8nt of RNA. SNAP output
3e3y hydrolase-DNA X-ray (2.13 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to gttaac and cocrystallized with 5 mm ca2+. SNAP output
3e40 hydrolase-DNA X-ray (2.1 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to gttaac and cocrystallized with 5 mm ca2+. SNAP output
3e41 hydrolase-DNA X-ray (2.73 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to gtcgac and 5 mm ca2+. SNAP output
3e42 hydrolase-DNA X-ray (2.68 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to gtcgac and ca2+ (cocrystallized). SNAP output
3e43 hydrolase-DNA X-ray (2.73 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to gttaac and cocrystallized with 2.5 mm mgcl2. SNAP output
3e44 hydrolase-DNA X-ray (2.52 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to cleaved DNA (gtt | aac) and mn2+. SNAP output
3e45 hydrolase-DNA X-ray (2.78 Å) Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC (2008) "DNA distortion and specificity in a sequence-specific endonuclease." J.Mol.Biol., 383, 186-204. doi: 10.1016/j.jmb.2008.08.032. Q138f hincii bound to noncognate DNA (gtgcac) and ca2+. SNAP output
3e54 hydrolase-DNA X-ray (2.5 Å) Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL (2008) "Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases." Nucleic Acids Res., 36, 6988-6998. doi: 10.1093/nar/gkn846. Archaeal intron-encoded homing endonuclease i-vdi141i complexed with DNA. SNAP output
3e6c transcription regulation-DNA X-ray (1.8 Å) Levy C, Pike K, Heyes DJ, Joyce MG, Gabor K, Smidt H, van der Oost J, Leys D (2008) "Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator." Mol.Microbiol., 70, 151-167. doi: 10.1111/j.1365-2958.2008.06399.x. Cprk ocpa DNA complex. SNAP output
3ebc hydrolase-DNA X-ray (2.55 Å) Little EJ, Babic AC, Horton NC (2008) "Early Interrogation and Recognition of DNA Sequence by Indirect Readout." Structure, 16, 1828-1837. Structure of n141a hincii with cognate DNA. SNAP output
3ecp DNA recombination-DNA X-ray (2.5 Å) Klenchin VA, Czyz A, Goryshin IY, Gradman R, Lovell S, Rayment I, Reznikoff WS (2008) "Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif." Nucleic Acids Res., 36, 5855-5862. doi: 10.1093/nar/gkn577. Crystal structure of tn5 transposase complexed with 5' phosphorylated transposon end DNA. SNAP output
3eeo transferase-DNA X-ray (1.94 Å) Porta JC, Christman JK, Borgstahl GEO "M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation." M. hhai co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation.. SNAP output
3eh8 hydrolase-DNA X-ray (2.7 Å) Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL (2009) "Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation." Nucleic Acids Res., 37, 877-890. doi: 10.1093/nar/gkn1007. Crystal structure of y2 i-anii variant (f13y-s111y)-DNA complex with calcium. SNAP output
3ei1 DNA binding protein-DNA X-ray (2.8 Å) Scrima A, Konickova R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP, Thoma NH (2008) "Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex." Cell(Cambridge,Mass.), 135, 1213-1223. doi: 10.1016/j.cell.2008.10.045. Structure of hsddb1-drddb2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex. SNAP output
3ei2 DNA binding protein-DNA X-ray (2.6 Å) Scrima A, Konickova R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP, Thoma NH (2008) "Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex." Cell(Cambridge,Mass.), 135, 1213-1223. doi: 10.1016/j.cell.2008.10.045. Structure of hsddb1-drddb2 bound to a 16 bp abasic site containing DNA-duplex. SNAP output
3epg transferase-DNA X-ray (2.5 Å) Pence MG, Blans P, Zink CN, Hollis T, Fishbein JC, Perrino FW (2009) "Lesion bypass of N2-ethylguanine by human DNA polymerase iota." J.Biol.Chem., 284, 1732-1740. doi: 10.1074/jbc.M807296200. Structure of human DNA polymerase iota complexed with n2-ethylguanine. SNAP output
3epi transferase-DNA X-ray (2.9 Å) Pence MG, Blans P, Zink CN, Hollis T, Fishbein JC, Perrino FW (2009) "Lesion bypass of N2-ethylguanine by human DNA polymerase iota." J.Biol.Chem., 284, 1732-1740. doi: 10.1074/jbc.M807296200. Structure of human DNA polymerase iota complexed with n2-ethylguanine and incoming ttp. SNAP output
3er8 transcription, transferase-DNA, RNA X-ray (3.18 Å) Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL, Gershon PD (2009) "Polymerase Translocation with Respect to Single-Stranded Nucleic Acid: Looping or Wrapping of Primer around a Poly(A) Polymerase." Structure, 17, 680-689. doi: 10.1016/j.str.2009.03.012. Crystal structure of the heterodimeric vaccinia virus mrna polyadenylate polymerase complex with two fragments of RNA. SNAP output
3erc transcription, transferase-DNA, RNA X-ray (3.21 Å) Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL, Gershon PD (2009) "Polymerase Translocation with Respect to Single-Stranded Nucleic Acid: Looping or Wrapping of Primer around a Poly(A) Polymerase." Structure, 17, 680-689. doi: 10.1016/j.str.2009.03.012. Crystal structure of the heterodimeric vaccinia virus mrna polyadenylate polymerase with three fragments of RNA and 3'-deoxy atp. SNAP output
3ere DNA binding protein-DNA X-ray (2.5 Å) Cherney LT, Cherney MM, Garen CR, Lu GJ, James MN (2008) "Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis." J.Mol.Biol., 384, 1330-1340. doi: 10.1016/j.jmb.2008.10.015. Crystal structure of the arginine repressor protein from mycobacterium tuberculosis in complex with the DNA operator. SNAP output
3exj transcription-DNA X-ray (2.0 Å) Malecka KA, Ho WC, Marmorstein R (2009) "Crystal structure of a p53 core tetramer bound to DNA." Oncogene, 28, 325-333. doi: 10.1038/onc.2008.400. Crystal structure of a p53 core tetramer bound to DNA. SNAP output
3exl transcription-DNA X-ray (2.2 Å) Malecka KA, Ho WC, Marmorstein R (2009) "Crystal structure of a p53 core tetramer bound to DNA." Oncogene, 28, 325-333. doi: 10.1038/onc.2008.400. Crystal structure of a p53 core tetramer bound to DNA. SNAP output
3ey1 hydrolase-DNA X-ray (1.6 Å) Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M (2009) "A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution." Chem.Commun.(Camb.), 15, 2017-2019. doi: 10.1039/b822781k. A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. SNAP output
3eyi DNA binding protein-DNA X-ray (1.45 Å) Ha SC, Kim D, Hwang HY, Rich A, Kim YG, Kim KK (2008) "The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA." Proc.Natl.Acad.Sci.USA, 105, 20671-20676. doi: 10.1073/pnas.0810463106. The crystal structure of the second z-DNA binding domain of human dai (zbp1) in complex with z-DNA. SNAP output
3eyz transferase-DNA X-ray (2.1 Å) Golosov AA, Warren JJ, Beese LS, Karplus M (2010) "The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis." Structure, 18, 83-93. doi: 10.1016/j.str.2009.10.014. Cocrystal structure of bacillus fragment DNA polymerase i with duplex DNA (open form). SNAP output
3ez5 transferase-DNA X-ray (1.9 Å) Golosov AA, Warren JJ, Beese LS, Karplus M (2010) "The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis." Structure, 18, 83-93. doi: 10.1016/j.str.2009.10.014. Cocrystal structure of bacillus fragment DNA polymerase i with duplex DNA , dctp, and zinc (closed form).. SNAP output
3f21 hydrolase X-ray (2.2 Å) Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK (2009) "The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ{alpha}ADAR1." Nucleic Acids Res., 37, 629-637. doi: 10.1093/nar/gkn976. Crystal structure of zalpha in complex with d(cacgtg). SNAP output
3f22 hydrolase X-ray (2.5 Å) Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK (2009) "The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ{alpha}ADAR1." Nucleic Acids Res., 37, 629-637. doi: 10.1093/nar/gkn976. Crystal structure of zalpha in complex with d(cgtacg). SNAP output
3f23 hydrolase X-ray (2.7 Å) Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK (2009) "The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ{alpha}ADAR1." Nucleic Acids Res., 37, 629-637. doi: 10.1093/nar/gkn976. Crystal structure of zalpha in complex with d(cggccg). SNAP output
3f27 transcription-DNA X-ray (2.75 Å) Palasingam P, Jauch R, Ng CKL, Kolatkar PR (2009) "The Structure of Sox17 Bound to DNA Reveals a Conserved Bending Topology but Selective Protein Interaction Platforms." J.Mol.Biol., 388, 619-630. doi: 10.1016/j.jmb.2009.03.055. Structure of sox17 bound to DNA. SNAP output
3f2b transferase-DNA X-ray (2.39 Å) Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC (2008) "Structure of PolC reveals unique DNA binding and fidelity determinants." Proc.Natl.Acad.Sci.USA, 105, 20695-20700. doi: 10.1073/pnas.0809989106. DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mg and zn. SNAP output
3f2c transferase-DNA X-ray (2.5 Å) Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC (2008) "Structure of PolC reveals unique DNA binding and fidelity determinants." Proc.Natl.Acad.Sci.USA, 105, 20695-20700. doi: 10.1073/pnas.0809989106. DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp and mn. SNAP output
3f2d transferase-DNA X-ray (2.51 Å) Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC (2008) "Structure of PolC reveals unique DNA binding and fidelity determinants." Proc.Natl.Acad.Sci.USA, 105, 20695-20700. doi: 10.1073/pnas.0809989106. DNA polymerase polc from geobacillus kaustophilus complex with DNA, dgtp, mn and zn. SNAP output
3f73 nucleic acid binding protein-DNA-RNA X-ray (3.0 Å) Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel DJ (2008) "Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex." Nature, 456, 921-926. doi: 10.1038/nature07666. Alignment of guide-target seed duplex within an argonaute silencing complex. SNAP output
3f8i ligase-DNA X-ray (2.29 Å) Hashimoto H, Horton JR, Zhang X, Cheng X (2009) "UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications." Epigenetics, 4, 8-14. Mouse uhrf1 sra domain bound with hemi-methylated cpg, crystal structure in space group p21. SNAP output
3f8j ligase-DNA X-ray (1.99 Å) Hashimoto H, Horton JR, Zhang X, Cheng X (2009) "UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications." Epigenetics, 4, 8-14. Mouse uhrf1 sra domain bound with hemi-methylated cpg, crystal structure in space group c222(1). SNAP output
3fbd hydrolase-DNA X-ray (2.9 Å) Wang YT, Wright JD, Doudeva LG, Jhang HC, Lim C, Yuan HS "Redesign of high-affinity nonspecific nucleases with altered sequence preference." Crystal structure of the nuclease domain of cole7(d493q mutant) in complex with an 18-bp duplex DNA. SNAP output
3fc3 hydrolase-DNA X-ray (1.75 Å) Sokolowska M, Czapinska H, Bochtler M (2009) "Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA." Nucleic Acids Res., 37, 3799-3810. doi: 10.1093/nar/gkp228. Crystal structure of the beta-beta-alpha-me type ii restriction endonuclease hpy99i. SNAP output
3fd2 hydrolase-DNA X-ray (2.69 Å) Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ (2009) "Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins." Nucleic Acids Res., 37, 1650-1662. doi: 10.1093/nar/gkp004. Crystal structure of mmsoi-DNA complex with calcium. SNAP output
3fde ligase X-ray (1.41 Å) Hashimoto H, Horton JR, Zhang X, Cheng X (2009) "UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications." Epigenetics, 4, 8-14. Mouse uhrf1 sra domain bound with hemi-methylated cpg DNA, crystal structure in space group c222(1) at 1.4 Å resolution. SNAP output
3fdq DNA binding protein-DNA X-ray (1.75 Å) Shen A, Higgins DE, Panne D (2009) "Recognition of AT-Rich DNA Binding Sites by the MogR Repressor." Structure, 17, 769-777. doi: 10.1016/j.str.2009.02.018. Recognition of at-rich DNA binding sites by the mogr repressor. SNAP output
3fhz DNA binding protein-DNA X-ray (3.27 Å) Cherney LT, Cherney MM, Garen CR, James MN (2009) "The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine." J.Mol.Biol., 388, 85-97. doi: 10.1016/j.jmb.2009.02.053. Crystal structure of the arginine repressor from mycobacterium tuberculosis bound with its DNA operator and co-repressor, l-arginine. SNAP output
3fmt replication inhibitor-DNA X-ray (2.983 Å) Chung YS, Brendler T, Austin S, Guarne A (2009) "Structural insights into the cooperative binding of SeqA to a tandem GATC repeat." Nucleic Acids Res., 37, 3143-3152. doi: 10.1093/nar/gkp151. Crystal structure of seqa bound to DNA. SNAP output
3foe isomerase-DNA X-ray (4.001 Å) Laponogov I, Sohi MK, Veselkov DA, Pan X-S, Sawhney R, Thompson AW, McAuley KE, Fisher LM, Sanderson MR (2009) "Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases." Nat.Struct.Mol.Biol., 16, 667-669. doi: 10.1038/nsmb.1604. Structural insight into the quinolone-DNA cleavage complex of type iia topoisomerases. SNAP output
3fof isomerase-DNA X-ray (4.0 Å) Laponogov I, Sohi MK, Veselkov DA, Pan X-S, Sawhney R, Thompson AW, McAuley KE, Fisher LM, Sanderson MR (2009) "Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases." Nat.Struct.Mol.Biol., 16, 667-669. doi: 10.1038/nsmb.1604. Structural insight into the quinolone-DNA cleavage complex of type iia topoisomerases. SNAP output
3fsi transferase-DNA X-ray (1.75 Å) Glass LS, Nguyen B, Goodwin KD, Dardonville C, Wilson WD, Long EC, Georgiadis MM (2009) "Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA." Biochemistry, 48, 5943-5952. doi: 10.1021/bi900204w. Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA. SNAP output
3fyl transcription-DNA X-ray (1.63 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:cgt complex. SNAP output
3g00 hydrolase-DNA X-ray (1.74 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 angstrom. SNAP output
3g0q hydrolase-DNA X-ray (2.2 Å) Lee S, Verdine GL (2009) "Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase." Proc.Natl.Acad.Sci.Usa, 106, 18497-18502. doi: 10.1073/pnas.0902908106. Crystal structure of muty bound to its inhibitor DNA. SNAP output
3g0r hydrolase-DNA X-ray (2.4 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Complex of mth0212 and an 8bp dsDNA with distorted ends. SNAP output
3g2c hydrolase-DNA X-ray (2.3 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Mth0212 in complex with a short ssDNA (cgta). SNAP output
3g2d hydrolase-DNA X-ray (2.3 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Complex of mth0212 and a 4 bp dsDNA with 3'-overhang. SNAP output
3g38 hydrolase-DNA X-ray (3.04 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. The catalytically inactive mutant mth0212 (d151n) in complex with an 8 bp dsDNA. SNAP output
3g3c hydrolase-DNA X-ray (3.04 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Mth0212 (wt) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang. SNAP output
3g3y hydrolase-DNA X-ray (2.5 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Mth0212 in complex with ssDNA in space group p32. SNAP output
3g4t hydrolase-DNA X-ray (2.64 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Mth0212 (wt) in complex with a 7bp dsDNA. SNAP output
3g6p transcription-DNA X-ray (1.985 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:fkbp5 complex, 18bp. SNAP output
3g6q transcription-DNA X-ray (2.26 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:fkbp5 binding site complex-9. SNAP output
3g6r transcription-DNA X-ray (2.3 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:fkbp5 complex-52, 18bp. SNAP output
3g6t transcription-DNA X-ray (1.9 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr gamma DNA-binding domain:fkbp5 16bp complex-34. SNAP output
3g6u transcription-DNA X-ray (1.9 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA-binding domain:fkbp5 16bp complex-49. SNAP output
3g6v replication-DNA X-ray (2.2 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota." Structure, 17, 530-537. doi: 10.1016/j.str.2009.02.015. DNA synthesis across an abasic lesion by human DNA polymerase-iota. SNAP output
3g6x replication-DNA X-ray (2.08 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota." Structure, 17, 530-537. doi: 10.1016/j.str.2009.02.015. Ternary complex of DNA polymerase iota:DNA:dgtp with an abasic site at the templating position. SNAP output
3g6y replication-DNA X-ray (2.1 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota." Structure, 17, 530-537. doi: 10.1016/j.str.2009.02.015. Ternary complex of DNA polymerase iota:DNA:dttp with an abasic site at the templating position. SNAP output
3g73 transcription-DNA X-ray (2.21 Å) Littler DR, Alvarez-Fernandez M, Stein A, Hibbert RG, Heidebrecht T, Aloy P, Medema RH, Perrakis A (2010) "Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence." Nucleic Acids Res. doi: 10.1093/nar/gkq194. Structure of the foxm1 DNA binding. SNAP output
3g8u transcription-DNA X-ray (1.9 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. DNA binding domain:gilz 16bp complex-5. SNAP output
3g8x transcription-DNA X-ray (2.05 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:gilz 16bp complex-65. SNAP output
3g97 transcription-DNA X-ray (2.08 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA-binding domain:gilz 16bp complex-9. SNAP output
3g99 transcription-DNA X-ray (1.81 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:pal complex-9. SNAP output
3g9i transcription-DNA X-ray (1.85 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain: pal complex-35. SNAP output
3g9j transcription-DNA X-ray (2.32 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:pal, 18bp complex-36. SNAP output
3g9m transcription-DNA X-ray (1.61 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA-binding domain:sgk 16bp complex-44. SNAP output
3g9o transcription-DNA X-ray (1.65 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA-binding domain:sgk 16bp complex-9. SNAP output
3g9p transcription-DNA X-ray (1.652 Å) Meijsing SH, Pufall MA, So AY, Bates DL, Chen L, Yamamoto KR (2009) "DNA binding site sequence directs glucocorticoid receptor structure and activity." Science, 324, 407-410. doi: 10.1126/science.1164265. Gr DNA binding domain:sgk 16bp complex-7. SNAP output
3ga6 hydrolase-DNA X-ray (1.898 Å) Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R (2010) "Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA." J.Mol.Biol., 399, 604-617. doi: 10.1016/j.jmb.2010.04.044. Mth0212 in complex with two DNA helices. SNAP output
3gat transcription-DNA NMR Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) "Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution." Nat.Struct.Biol., 4, 732-738. doi: 10.1038/nsb0997-732. Solution NMR structure of the c-terminal domain of chicken gata-1 bound to DNA, 34 structures. SNAP output
3gdx transferase-DNA X-ray (2.2 Å) Upton TG, Kashemirov BA, McKenna CE, Goodman MF, Prakash GK, Kultyshev R, Batra VK, Shock DD, Pedersen LC, Beard WA, Wilson SH (2009) "Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function." Org.Lett., 11, 1883-1886. doi: 10.1021/ol701755k. DNA polymerase beta with a gapped dnd substrate and dtmp(cf2)pp. SNAP output
3gfi transcription-DNA X-ray (2.1 Å) Kumarevel T, Tanaka T, Umehara T, Yokoyama S (2009) "ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators." Nucleic Acids Res., 37, 4723-4735. doi: 10.1093/nar/gkp496. Crystal structure of st1710 complexed with its promoter DNA. SNAP output
3gii transferase-DNA X-ray (2.6 Å) Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ (2009) "Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases." Structure, 17, 725-736. doi: 10.1016/j.str.2009.03.011. Dpo4 extension ternary complex with disordered a opposite an oxog in anti conformation. SNAP output
3gij transferase-DNA X-ray (2.4 Å) Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ (2009) "Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases." Structure, 17, 725-736. doi: 10.1016/j.str.2009.03.011. Dpo4 extension ternary complex with oxog(syn)-a(anti) and oxog(anti)-a(syn) pairs. SNAP output
3gik transferase-DNA X-ray (2.9 Å) Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ (2009) "Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases." Structure, 17, 725-736. doi: 10.1016/j.str.2009.03.011. Dpo4 extension ternary complex with the oxog(anti)-c(anti) pair. SNAP output
3gil transferase-DNA X-ray (2.71 Å) Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ (2009) "Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases." Structure, 17, 725-736. doi: 10.1016/j.str.2009.03.011. Dpo4 extension ternary complex with oxog(anti)-t(anti) pair. SNAP output
3gim transferase-DNA X-ray (2.7 Å) Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ (2009) "Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases." Structure, 17, 725-736. doi: 10.1016/j.str.2009.03.011. Dpo4 extension ternary complex with oxog(anti)-g(syn) pair. SNAP output
3glf transferase-DNA X-ray (3.388 Å) Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J (2009) "The mechanism of ATP-dependent primer-template recognition by a clamp loader complex." Cell(Cambridge,Mass.), 137, 659-671. doi: 10.1016/j.cell.2009.03.044. Crystal structure of the ecoli clamp loader bound to primer-template DNA. SNAP output
3glg transferase-DNA X-ray (3.25 Å) Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J (2009) "The mechanism of ATP-dependent primer-template recognition by a clamp loader complex." Cell(Cambridge,Mass.), 137, 659-671. doi: 10.1016/j.cell.2009.03.044. Crystal structure of a mutant (gammat157a) e. coli clamp loader bound to primer-template DNA. SNAP output
3gli transferase-DNA X-ray (3.5 Å) Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J (2009) "The mechanism of ATP-dependent primer-template recognition by a clamp loader complex." Cell(Cambridge,Mass.), 137, 659-671. doi: 10.1016/j.cell.2009.03.044. Crystal structure of the e. coli clamp loader bound to primer-template DNA and psi peptide. SNAP output
3gna recombination X-ray (2.4 Å) Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG (2009) "Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis." Nat.Struct.Mol.Biol., 16, 499-508. doi: 10.1038/nsmb.1593. Crystal structure of the rag1 nonamer-binding domain with DNA. SNAP output
3gnb recombination X-ray (3.0 Å) Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG (2009) "Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis." Nat.Struct.Mol.Biol., 16, 499-508. doi: 10.1038/nsmb.1593. Crystal structure of the rag1 nonamer-binding domain with DNA. SNAP output
3go3 DNA-antibiotic X-ray (1.1 Å) Pfoh R, Cuesta-Seijo JA, Sheldrick GM (2009) "Interaction of an Echinomycin-DNA Complex with Manganese Ion." Acta Crystallogr.,Sect.F, 65, 660. doi: 10.1107/S1744309109019654. Interactions of an echinomycin-DNA complex with manganese(ii) ions. SNAP output
3go8 lyase-DNA X-ray (1.89 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in ec3-loop deletion complex. SNAP output
3gox hydrolase-DNA X-ray (1.5 Å) Sokolowska M, Czapinska H, Bochtler M (2009) "Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA." Nucleic Acids Res., 37, 3799-3810. doi: 10.1093/nar/gkp228. Crystal structure of the beta-beta-alpha-me type ii restriction endonuclease hpy99i in the absence of edta. SNAP output
3gp1 hydrolase-DNA X-ray (2.05 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in ec3-v222p complex. SNAP output
3gp8 hydrolase-DNA X-ray (2.5 Å) Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB (2009) "Mechanistic basis of 5'-3' translocation in SF1B helicases." Cell(Cambridge,Mass.), 137, 849-859. doi: 10.1016/j.cell.2009.03.036. Crystal structure of the binary complex of recd2 with DNA. SNAP output
3gpl hydrolase-DNA X-ray (2.5 Å) Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley DB (2009) "Mechanistic basis of 5'-3' translocation in SF1B helicases." Cell(Cambridge,Mass.), 137, 849-859. doi: 10.1016/j.cell.2009.03.036. Crystal structure of the ternary complex of recd2 with DNA and adpnp. SNAP output
3gpp lyase-DNA X-ray (2.15 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in ec3-t224p complex. SNAP output
3gpu lyase-DNA X-ray (1.62 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in ec4-loop deletion complex. SNAP output
3gpx lyase-DNA X-ray (1.78 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Sequence-matched mutm interrogation complex 4 (ic4). SNAP output
3gpy lyase-DNA X-ray (1.85 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Sequence-matched mutm lesion recognition complex 3 (lrc3). SNAP output
3gq3 lyase-DNA X-ray (1.83 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Mutm encountering an intrahelical 8-oxoguanine (oxog) lesion in ec5-loop deletion complex. SNAP output
3gq4 lyase-DNA X-ray (1.7 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Sequence-matched mutm lesion recognition complex 5 (lrc5). SNAP output
3gq5 lyase-DNA X-ray (1.9 Å) Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme." Nature, 462, 762-766. doi: 10.1038/nature08561. Sequence-matched mutm interrogation complex 5 (ic5). SNAP output
3gqc transferase-DNA X-ray (2.5 Å) Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "Structure of the human Rev1-DNA-dNTP ternary complex." J.Mol.Biol., 390, 699-709. doi: 10.1016/j.jmb.2009.05.026. Structure of human rev1-DNA-dntp ternary complex. SNAP output
3gtg transcription, transferase-DNA-RNA hybrid X-ray (3.78 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex with 12mer RNA. SNAP output
3gtj transcription, transferase-DNA-RNA hybrid X-ray (3.42 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex with 13mer RNA. SNAP output
3gtk transcription, transferase-DNA-RNA hybrid X-ray (3.8 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex with 18mer RNA. SNAP output
3gtl transcription, transferase-DNA-RNA hybrid X-ray (3.38 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex with 13mer with g<>u mismatch. SNAP output
3gtm transcription, transferase-DNA-RNA hybrid X-ray (3.8 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Co-complex of backtracked RNA polymerase ii with tfiis. SNAP output
3gto transcription, transferase-DNA-RNA hybrid X-ray (4.0 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex with 15mer RNA. SNAP output
3gtp transcription, transferase-DNA-RNA hybrid X-ray (3.9 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex with 24mer RNA. SNAP output
3gtq transcription, transferase-DNA-RNA hybrid X-ray (3.8 Å) Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD (2009) "Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution." Science, 324, 1203-1206. doi: 10.1126/science.1168729. Backtracked RNA polymerase ii complex induced by damage. SNAP output
3gut transcription-DNA X-ray (3.59 Å) Stroud JC, Oltman A, Han A, Bates DL, Chen L (2009) "Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR." J.Mol.Biol., 393, 98-112. doi: 10.1016/j.jmb.2009.08.023. Crystal structure of a higher-order complex of p50:rela bound to the hiv-1 ltr. SNAP output
3gv5 transferase-DNA X-ray (2.0 Å) Kirouac KN, Ling H (2009) "Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota." Embo J., 28, 1644-1654. doi: 10.1038/emboj.2009.122. Human DNA polymerase iota in complex with t template DNA and incoming ddadp. SNAP output
3gv7 transferase-DNA X-ray (2.2 Å) Kirouac KN, Ling H (2009) "Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota." Embo J., 28, 1644-1654. doi: 10.1038/emboj.2009.122. Human DNA polymerase iota in complex with t template DNA and incoming dttp. SNAP output
3gv8 transferase-DNA X-ray (2.0 Å) Kirouac KN, Ling H (2009) "Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota." Embo J., 28, 1644-1654. doi: 10.1038/emboj.2009.122. Human DNA polymerase iota in complex with t template DNA and incoming dgtp. SNAP output
3gx4 DNA binding protein-DNA X-ray (2.7 Å) Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ, Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF, Millington C, Arvai AS, Kroeger MD, Peterson LA, Williams DM, Fried MG, Margison GP, Pegg AE, Tainer JA (2009) "Flipping of alkylated DNA damage bridges base and nucleotide excision repair." Nature, 459, 808-813. doi: 10.1038/nature08076. Crystal structure analysis of s. pombe atl in complex with DNA. SNAP output
3gxq DNA binding protein-DNA X-ray (2.35 Å) Ni L, Jensen SO, Ky Tonthat N, Berg T, Kwong SM, Guan FH, Brown MH, Skurray RA, Firth N, Schumacher MA (2009) "The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes." Nucleic Acids Res., 37, 6970-6983. doi: 10.1093/nar/gkp756. Structure of arta and DNA complex. SNAP output
3gyh DNA binding protein-DNA X-ray (2.8 Å) Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ, Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF, Millington C, Arvai AS, Kroeger MD, Peterson LA, Williams DM, Fried MG, Margison GP, Pegg AE, Tainer JA (2009) "Flipping of alkylated DNA damage bridges base and nucleotide excision repair." Nature, 459, 808-813. doi: 10.1038/nature08076. Crystal structure analysis of s. pombe atl in complex with damaged DNA containing pob. SNAP output
3gz6 DNA binding protein-DNA X-ray (2.901 Å) Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, Zhang H (2009) "Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism." Structure, 17, 939-951. doi: 10.1016/j.str.2009.05.012. Crystal structure of shewanella oneidensis nrtr complexed with a 27mer DNA. SNAP output
3h0d transcription-DNA X-ray (2.4 Å) Fuhrmann J, Schmidt A, Spiess S, Lehner A, Turgay K, Mechtler K, Charpentier E, Clausen T (2009) "McsB is a protein arginine kinase that phosphorylates and inhibits the heat-shock regulator CtsR." Science, 324, 1323-1327. doi: 10.1126/science.1170088. Crystal structure of ctsr in complex with a 26bp DNA duplex. SNAP output
3h15 replication-DNA X-ray (2.72 Å) Warren EM, Huang H, Fanning E, Chazin WJ, Eichman BF (2009) "Physical Interactions between Mcm10, DNA, and DNA Polymerase {alpha}." J.Biol.Chem., 284, 24662-24672. doi: 10.1074/jbc.M109.020438. Crystal structure of replication initiation factor mcm10-id bound to ssDNA. SNAP output
3h25 replication-DNA X-ray (2.7 Å) Geibel S, Banchenko S, Engel M, Lanka E, Saenger W (2009) "Structure and function of primase RepB' encoded by broad-host-range plasmid RSF1010 that replicates exclusively in leading-strand mode." Proc.Natl.Acad.Sci.USA, 106, 7810-7815. doi: 10.1073/pnas.0902910106. Crystal structure of the catalytic domain of primase repb' in complex with initiator DNA. SNAP output
3h3v transferase-DNA-RNA X-ray (4.0 Å) Dengl S, Cramer P (2009) "Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro." J.Biol.Chem., 284, 21270-21279. doi: 10.1074/jbc.M109.013847. Yeast rnap ii containing poly(a)-signal sequence in the active site. SNAP output
3h40 replication-DNA X-ray (2.3 Å) Jain R, Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "Replication across template T/U by human DNA polymerase-iota." Structure, 17, 974-980. doi: 10.1016/j.str.2009.04.011. Binary complex of human DNA polymerase iota with template u-t. SNAP output
3h4b replication-DNA X-ray (2.85 Å) Jain R, Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "Replication across template T/U by human DNA polymerase-iota." Structure, 17, 974-980. doi: 10.1016/j.str.2009.04.011. Ternary complex of human DNA polymerase iota with template u-t and incoming datp. SNAP output
3h4d replication-DNA X-ray (2.2 Å) Jain R, Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "Replication across template T/U by human DNA polymerase-iota." Structure, 17, 974-980. doi: 10.1016/j.str.2009.04.011. Ternary complex of human DNA polymerase iota with template u-t and incoming dgtp. SNAP output
3h8o oxidoreductase-DNA X-ray (2.0 Å) Lu L, Yi C, Jian X, Zheng G, He C (2010) "Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system." Nucleic Acids Res., 38, 4415-4425. doi: 10.1093/nar/gkq129. Structure determination of DNA methylation lesions n1-mea and n3-mec in duplex DNA using a cross-linked host-guest system. SNAP output
3h8r oxidoreductase-DNA X-ray (1.77 Å) Lu L, Yi C, Jian X, Zheng G, He C (2010) "Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system." Nucleic Acids Res., 38, 4415-4425. doi: 10.1093/nar/gkq129. Structure determination of DNA methylation lesions n1-mea and n3-mec in duplex DNA using a cross-linked host-guest system. SNAP output
3h8x oxidoreductase-DNA X-ray (1.95 Å) Lu L, Yi C, Jian X, Zheng G, He C (2010) "Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system." Nucleic Acids Res., 38, 4415-4425. doi: 10.1093/nar/gkq129. Structure determination of DNA methylation lesions n1-mea and n3-mec in duplex DNA using a cross-linked host-guest system. SNAP output
3hax isomerase-biosynthetic protein-RNA X-ray (2.11 Å) Duan J, Li L, Lu J, Wang W, Ye K (2009) "Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase." Mol.Cell, 34, 427-439. doi: 10.1016/j.molcel.2009.05.005. Crystal structure of a substrate-bound gar1-minus h-aca rnp from pyrococcus furiosus. SNAP output
3hdd transcription-DNA X-ray (2.2 Å) Fraenkel E, Rould MA, Chambers KA, Pabo CO (1998) "Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures." J.Mol.Biol., 284, 351-361. doi: 10.1006/jmbi.1998.2147. Engrailed homeodomain DNA complex. SNAP output
3hjf nucleic acid binding protein-DNA-RNA X-ray (3.056 Å) Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434. Crystal structure of t. thermophilus argonaute e546 mutant protein complexed with DNA guide strand and 15-nt RNA target strand. SNAP output
3hk2 nucleic acid binding protein-DNA-RNA X-ray (2.8 Å) Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434. Crystal structure of t. thermophilus argonaute n478 mutant protein complexed with DNA guide strand and 19-nt RNA target strand. SNAP output
3hm9 nucleic acid binding protein-DNA-RNA X-ray (3.3 Å) Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434. Crystal structure of t. thermophilus argonaute complexed with DNA guide strand and 19-nt RNA target strand. SNAP output
3ho1 nucleic acid binding protein-DNA-RNA X-ray (2.6 Å) Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434. Crystal structure of t. thermophilus argonaute n546 mutant protein complexed with DNA guide strand and 12-nt RNA target strand. SNAP output
3hos transferase, DNA binding protein-DNA X-ray (3.5 Å) Richardson JM, Colloms SD, Finnegan DJ, Walkinshaw MD (2009) "Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote." Cell(Cambridge,Mass.), 138, 1096-1108. doi: 10.1016/j.cell.2009.07.012. Crystal structure of the mariner mos1 paired end complex with mg. SNAP output
3hot transferase, DNA binding protein-DNA X-ray (3.25 Å) Richardson JM, Colloms SD, Finnegan DJ, Walkinshaw MD (2009) "Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote." Cell(Cambridge,Mass.), 138, 1096-1108. doi: 10.1016/j.cell.2009.07.012. Crystal structure of the mos1 mariner paired end complex with mn. SNAP output
3hou transcription,transferase-DNA-RNA hybrid X-ray (3.2 Å) Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) "Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA." Mol.Cell, 34, 710-721. doi: 10.1016/j.molcel.2009.06.002. Complete RNA polymerase ii elongation complex i with a t-u mismatch. SNAP output
3hov transcription, transferase-DNA-RNA X-ray (3.5 Å) Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) "Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA." Mol.Cell, 34, 710-721. doi: 10.1016/j.molcel.2009.06.002. Complete RNA polymerase ii elongation complex ii. SNAP output
3how transcription,transferase-DNA-RNA hybrid X-ray (3.6 Å) Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) "Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA." Mol.Cell, 34, 710-721. doi: 10.1016/j.molcel.2009.06.002. Complete RNA polymerase ii elongation complex iii with a t-u mismatch and a frayed RNA 3'-uridine. SNAP output
3hox transcription,transferase-DNA-RNA hybrid X-ray (3.65 Å) Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) "Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA." Mol.Cell, 34, 710-721. doi: 10.1016/j.molcel.2009.06.002. Complete RNA polymerase ii elongation complex v. SNAP output
3hoy transcription,transferase-DNA-RNA hybrid X-ray (3.4 Å) Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) "Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA." Mol.Cell, 34, 710-721. doi: 10.1016/j.molcel.2009.06.002. Complete RNA polymerase ii elongation complex vi. SNAP output
3hoz transcription,transferase-DNA-RNA hybrid X-ray (3.65 Å) Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P (2009) "Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA." Mol.Cell, 34, 710-721. doi: 10.1016/j.molcel.2009.06.002. Complete RNA polymerase ii elongation complex iv with a t-u mismatch and a frayed RNA 3'-guanine. SNAP output
3hp6 transferase-DNA X-ray (1.81 Å) Wu EY, Beese LS (2011) "The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism." J.Biol.Chem., 286, 19758-19767. doi: 10.1074/jbc.M110.191130. Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus f710y mutant bound to g:t mismatch. SNAP output
3hpo transferase-DNA X-ray (1.75 Å) Wu EY, Beese LS (2011) "The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism." J.Biol.Chem., 286, 19758-19767. doi: 10.1074/jbc.M110.191130. Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus y714s mutant bound to g:t mismatch. SNAP output
3hqf hydrolase-DNA X-ray (2.51 Å) Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V (2009) "Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII." Nucleic Acids Res., 37, 6613-6624. doi: 10.1093/nar/gkp699. Crystal structure of restriction endonuclease ecorii n-terminal effector-binding domain in complex with cognate DNA. SNAP output
3hqg hydrolase-DNA X-ray (2.6 Å) Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V (2009) "Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII." Nucleic Acids Res., 37, 6613-6624. doi: 10.1093/nar/gkp699. Crystal structure of restriction endonuclease ecorii catalytic c-terminal domain in complex with cognate DNA. SNAP output
3ht3 transferase-DNA X-ray (1.7 Å) Wu EY, Beese LS (2011) "The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism." J.Biol.Chem., 286, 19758-19767. doi: 10.1074/jbc.M110.191130. Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus v713p mutant bound to g:dctp. SNAP output
3hts transcription-DNA X-ray (1.75 Å) Littlefield O, Nelson HC (1999) "A new use for the 'wing' of the 'winged' helix-turn-helix motif in the HSF-DNA cocrystal." Nat.Struct.Biol., 6, 464-470. doi: 10.1038/8269. Heat shock transcription factor-DNA complex. SNAP output
3hvr nucleic acid binding protein-DNA-RNA X-ray (3.211 Å) Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434. Crystal structure of t. thermophilus argonaute complexed with DNA guide strand and 19-nt RNA target strand with two mg2+ at the cleavage site. SNAP output
3hw8 transferase-DNA X-ray (1.95 Å) Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM, Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel TA "Scrunching Durning DNA Repair Synthesis." Ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a c in the scrunch site. SNAP output
3hwt transferase-DNA X-ray (1.95 Å) Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM, Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel TA "Scrunching during DNA repair synthesis." Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched da. SNAP output
3hx0 transferase-DNA X-ray (3.0 Å) Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM, Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel TA "Scrunching During DNA Repair Synthesis." Ternary complex of l277a, h511a, r514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched da. SNAP output
3hxm nucleic acid binding protein-DNA-RNA X-ray (3.1 Å) Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434. Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches.. SNAP output
3hxo blood clotting-blood clotting regulator X-ray (2.4 Å) Huang RH, Fremont DH, Diener JL, Schaub RG, Sadler JE (2009) "A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1." Structure, 17, 1476-1484. doi: 10.1016/j.str.2009.09.011. Crystal structure of von willebrand factor (vwf) a1 domain in complex with DNA aptamer arc1172, an inhibitor of vwf-platelet binding. SNAP output
3hxq blood clotting-blood clotting regulator X-ray (2.694 Å) Huang RH, Fremont DH, Diener JL, Schaub RG, Sadler JE (2009) "A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1." Structure, 17, 1476-1484. doi: 10.1016/j.str.2009.09.011. Crystal structure of von willebrand factor (vwf) a1 domain in complex with DNA aptamer arc1172, an inhibitor of vwf-platelet binding. SNAP output
3hzi transcription-DNA X-ray (2.98 Å) Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG (2009) "Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB." Science, 323, 396-401. doi: 10.1126/science.1163806. Structure of mdt protein. SNAP output
3i0w hydrolase,lyase-DNA X-ray (1.73 Å) Faucher F, Wallace SS, Doublie S (2009) "Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase." Dna Repair, 8, 1283-1289. doi: 10.1016/j.dnarep.2009.08.002. Crystal structure of clostridium acetobutylicum 8-oxoguanine glycosylase-lyase in complex with dsDNA containing cytosine opposite to 8-oxog. SNAP output
3i0x hydrolase,lyase-DNA X-ray (1.8 Å) Faucher F, Wallace SS, Doublie S (2009) "Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase." Dna Repair, 8, 1283-1289. doi: 10.1016/j.dnarep.2009.08.002. Crystal structure of clostridium acetobutylicum 8-oxoguanine glycosylase-lyase in complex with dsDNA containing adenine opposite to 8-oxog. SNAP output
3i2o oxidoreductase-DNA X-ray (1.7 Å) Yu B, Hunt JF (2009) "Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB." Proc.Natl.Acad.Sci.USA, 106, 14315-14320. doi: 10.1073/pnas.0812938106. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate and methylated trinucleotide t-mea-t. SNAP output
3i3m oxidoreductase-DNA X-ray (1.5 Å) Yu B, Hunt JF (2009) "Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB." Proc.Natl.Acad.Sci.USA, 106, 14315-14320. doi: 10.1073/pnas.0812938106. Crystal structure of alkb in complex with mn(ii), 2-oxoglutarate and methylated trinucleotide t-mec-t. SNAP output
3i49 oxidoreductase-DNA X-ray (1.6 Å) Yu B, Hunt JF (2009) "Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB." Proc.Natl.Acad.Sci.USA, 106, 14315-14320. doi: 10.1073/pnas.0812938106. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate and methylated trinucleotide t-mec-t. SNAP output
3i4m transcription,transferase-DNA-RNA hybrid X-ray (3.7 Å) Damsma GE, Cramer P (2009) "Molecular basis of transcriptional mutagenesis at 8-oxoguanine." J.Biol.Chem., 284, 31658-31663. doi: 10.1074/jbc.M109.022764. 8-oxoguanine containing RNA polymerase ii elongation complex d. SNAP output
3i4n transcription,transferase-DNA-RNA hybrid X-ray (3.9 Å) Damsma GE, Cramer P (2009) "Molecular basis of transcriptional mutagenesis at 8-oxoguanine." J.Biol.Chem., 284, 31658-31663. doi: 10.1074/jbc.M109.022764. 8-oxoguanine containing RNA polymerase ii elongation complex e. SNAP output
3i8d hydrolase-DNA X-ray (1.61 Å) Pallan PS, Egli M (2009) "Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography." J.Am.Chem.Soc., 131, 12548-12549. doi: 10.1021/ja905739j. The pairing geometry of the hydrophobic thymine analog 2,4-difluorotoluene in duplex DNA as analyzed by x-ray crystallography. SNAP output
3iag transcription-DNA X-ray (2.0 Å) Friedmann DR, Kovall RA (2010) "Thermodynamic and structural insights into CSL-DNA complexes." Protein Sci., 19, 34-46. doi: 10.1002/pro.280. Csl (rbp-jk) bound to hes-1 nonconsensus site. SNAP output
3iay transferase-DNA X-ray (2.0 Å) Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) "Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta." Nat.Struct.Mol.Biol., 16, 979-986. doi: 10.1038/nsmb.1663. Ternary complex of DNA polymerase delta. SNAP output
3igc isomerase-DNA X-ray (2.1 Å) Perry K, Hwang Y, Bushman FD, Van Duyne GD (2010) "Insights from the Structure of a Smallpox Virus Topoisomerase-DNA Transition State Mimic." Structure, 18, 127-137. doi: 10.1016/j.str.2009.10.020. Smallpox virus topoisomerase-DNA transition state. SNAP output
3igk transcription-DNA X-ray (1.7 Å) Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z (2010) "Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs." Nat.Struct.Mol.Biol., 17, 423-429. doi: 10.1038/nsmb.1800. Diversity in DNA recognition by p53 revealed by crystal structures with hoogsteen base pairs (p53-DNA complex 2). SNAP output
3igl transcription-DNA X-ray (1.8 Å) Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z (2010) "Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs." Nat.Struct.Mol.Biol., 17, 423-429. doi: 10.1038/nsmb.1800. Diversity in DNA recognition by p53 revealed by crystal structures with hoogsteen base pairs (p53-DNA complex 1). SNAP output
3igm transcription-DNA X-ray (2.2 Å) Lindner SE, De Silva EK, Keck JL, Llinas M (2010) "Structural Determinants of DNA Binding by a P. falciparum ApiAP2 Transcriptional Regulator." J.Mol.Biol., 395, 558-567. doi: 10.1016/j.jmb.2009.11.004. A 2.2a crystal structure of the ap2 domain of pf14_0633 from p. falciparum, bound as a domain-swapped dimer to its cognate DNA. SNAP output
3ih7 (hydrolase,lyase)-DNA X-ray (3.1 Å) Crenshaw CM, Oo KS, Kutchukian PS, Verdine GL "A Catalytic Checkpoint in Base Excision by the Human 8-Oxoguanine DNA Glycosylase hOGG1." Crystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA. SNAP output
3iin RNA binding protein-DNA-RNA X-ray (4.18 Å) Antonioli AH, Cochrane JC, Lipchock SV, Strobel SA (2010) "Plasticity of the RNA kink turn structural motif." Rna, 16, 762-768. doi: 10.1261/rna.1883810. Plasticity of the kink turn structural motif. SNAP output
3ikt DNA binding protein-DNA X-ray (2.26 Å) McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D, Soares AS, Paget MS, Kielkopf CL (2010) "Structural basis for NADH/NAD+ redox sensing by a Rex family repressor." Mol.Cell, 38, 563-575. doi: 10.1016/j.molcel.2010.05.006. Crystal structure of a rex-family repressor-DNA-nad+ complex from thermus aquaticus. SNAP output
3il2 DNA binding protein-DNA X-ray (2.49 Å) McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D, Soares AS, Paget MS, Kielkopf CL (2010) "Structural basis for NADH/NAD+ redox sensing by a Rex family repressor." Mol.Cell, 38, 563-575. doi: 10.1016/j.molcel.2010.05.006. Crystal structure of a rex-family repressor r90d mutant-DNA complex from thermus aquaticus. SNAP output
3imb hydrolase-DNA X-ray (1.89 Å) Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Siksnys V, Bochtler M "How BcnI and MvaI distinguish W from S." Alternative binding mode of restriction endonuclease bcni to cognate DNA. SNAP output
3in5 transferase-DNA X-ray (3.2 Å) Vasquez-Del Carpio R, Silverstein TD, Lone S, Swan MK, Choudhury JR, Johnson RE, Prakash S, Prakash L, Aggarwal AK (2009) "Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion." PLOS ONE, 4, e5766. doi: 10.1371/journal.pone.0005766. Structure of human DNA polymerase kappa inserting datp opposite an 8-oxog DNA lesion. SNAP output
3irq hydrolase-DNA X-ray (2.8 Å) de Rosa M, de Sanctis D, Rosario AL, Archer M, Rich A, Athanasiadis A, Carrondo MA (2010) "Crystal structure of a junction between two Z-DNA helices." Proc.Natl.Acad.Sci.USA, 107, 9088-9092. doi: 10.1073/pnas.1003182107. Crystal structure of a z-z junction. SNAP output
3irr hydrolase-DNA X-ray (2.65 Å) de Rosa M, de Sanctis D, Rosario AL, Archer M, Rich A, Athanasiadis A, Carrondo MA (2010) "Crystal structure of a junction between two Z-DNA helices." Proc.Natl.Acad.Sci.USA, 107, 9088-9092. doi: 10.1073/pnas.1003182107. Crystal structure of a z-z junction (with hepes intercalating). SNAP output
3isb transferase-DNA X-ray (2.0 Å) Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson SH (2009) "DNA polymerase beta substrate specificity: side chain modulation of the "A-rule"." J.Biol.Chem., 284, 31680-31689. doi: 10.1074/jbc.M109.029843. Binary complex of human DNA polymerase beta with a gapped DNA. SNAP output
3isc transferase-DNA X-ray (2.0 Å) Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson SH (2009) "DNA polymerase beta substrate specificity: side chain modulation of the "A-rule"." J.Biol.Chem., 284, 31680-31689. doi: 10.1074/jbc.M109.029843. Binary complex of human DNA polymerase beta with an abasic site (thf) in the gapped DNA. SNAP output
3isd transferase-DNA X-ray (2.6 Å) Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson SH (2009) "DNA polymerase beta substrate specificity: side chain modulation of the "A-rule"." J.Biol.Chem., 284, 31680-31689. doi: 10.1074/jbc.M109.029843. Ternary complex of human DNA polymerase beta with an abasic site (thf): dapcpp mismatch. SNAP output
3iv5 DNA binding protein-DNA X-ray (2.9 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp optimal binding sequence f1. SNAP output
3iyd transcription-DNA cryo-EM (19.8 Å) Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL (2009) "Three-dimensional EM structure of an intact activator-dependent transcription initiation complex." Proc.Natl.Acad.Sci.USA, 106, 19830-19835. doi: 10.1073/pnas.0908782106. Three-dimensional em structure of an intact activator-dependent transcription initiation complex. SNAP output
3j9x virus cryo-EM (3.8 Å) DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D, Egelman EH (2015) "A virus that infects a hyperthermophile encapsidates A-form DNA." Science, 348, 914-917. doi: 10.1126/science.aaa4181. A virus that infects a hyperthermophile encapsidates a-form DNA. SNAP output
3jaa transferase-DNA cryo-EM (22.0 Å) Lau WC, Li Y, Zhang Q, Huen MS (2015) "Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA." Sci Rep, 5, 15759. doi: 10.1038/srep15759. Human DNA polymerase eta in complex with normal DNA and inco nucleotide (nrm). SNAP output
3jbw recombination-DNA cryo-EM (4.6 Å) Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H (2015) "Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures." Cell(Cambridge,Mass.), 163, 1138-1152. doi: 10.1016/j.cell.2015.10.055. Cryo-electron microscopy structure of rag paired complex (with nbd, no symmetry). SNAP output
3jbx recombination-DNA cryo-EM (3.4 Å) Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H (2015) "Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures." Cell(Cambridge,Mass.), 163, 1138-1152. doi: 10.1016/j.cell.2015.10.055. Cryo-electron microscopy structure of rag signal end complex (c2 symmetry). SNAP output
3jby recombination-DNA cryo-EM (3.7 Å) Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H (2015) "Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures." Cell(Cambridge,Mass.), 163, 1138-1152. doi: 10.1016/j.cell.2015.10.055. Cryo-electron microscopy structure of rag paired complex (c2 symmetry). SNAP output
3jca viral protein cryo-EM (4.8 Å) Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN (2016) "Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function." Nature, 530, 358-361. doi: 10.1038/nature16955. Core model of the mouse mammary tumor virus intasome. SNAP output
3jpn transferase-DNA X-ray (2.15 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-dichloro methylene triphosphate. SNAP output
3jpo transferase-DNA X-ray (2.0 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochloromethylene triphosphate. SNAP output
3jpp transferase-DNA X-ray (2.1 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monomethyl methylene triphosphate. SNAP output
3jpq transferase-DNA X-ray (1.9 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monobromo methylene triphosphate. SNAP output
3jpr transferase-DNA X-ray (2.1 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-dimethyl methylene triphosphate. SNAP output
3jps transferase-DNA X-ray (2.0 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-fluoro methyl methylene triphosphate. SNAP output
3jpt transferase-DNA X-ray (2.15 Å) Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE (2010) "Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues." J.Am.Chem.Soc., 132, 7617-7625. doi: 10.1021/ja909370k. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-fluoro chloro methylene triphosphate. SNAP output
3jr4 lyase-DNA X-ray (2.601 Å) Qi Y, Spong MC, Nam K, Karplus M, Verdine GL (2010) "Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM." J.Biol.Chem., 285, 1468-1478. doi: 10.1074/jbc.M109.069799. Mutm interrogating an extrahelical g. SNAP output
3jr5 lyase-DNA X-ray (1.704 Å) Qi Y, Spong MC, Nam K, Karplus M, Verdine GL (2010) "Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM." J.Biol.Chem., 285, 1468-1478. doi: 10.1074/jbc.M109.069799. Mutm lesion recognition control complex with n174c crosslinking site. SNAP output
3jr9 DNA binding protein-DNA X-ray (2.9 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp optimal binding sequence f2. SNAP output
3jra DNA binding protein-DNA X-ray (3.11 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27bp non consensus sequence DNA f6. SNAP output
3jrb DNA binding protein-DNA X-ray (3.1 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp DNA f24 containing t-tract at center. SNAP output
3jrc DNA binding protein-DNA X-ray (3.08 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp DNA f29 containing 5 g-cs at center. SNAP output
3jrd DNA binding protein-DNA X-ray (3.1 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp DNA f25 containing t2a3 sequence at center. SNAP output
3jre DNA binding protein-DNA X-ray (3.17 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp DNA f26 containing a-tract at center. SNAP output
3jrf DNA binding protein-DNA X-ray (3.05 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp DNA f27 containing a c-g at center. SNAP output
3jrg DNA binding protein-DNA X-ray (3.11 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp non consensus sequence DNA f18. SNAP output
3jrh DNA binding protein-DNA X-ray (2.88 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp non consensus sequence DNA f21. SNAP output
3jri DNA binding protein-DNA X-ray (3.11 Å) Stella S, Cascio D, Johnson RC (2010) "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis." Genes Dev., 24, 814-826. doi: 10.1101/gad.1900610. Crystal structure of fis bound to 27 bp non consensus sequence DNA f23. SNAP output
3jsm transferase-DNA complex X-ray (3.0 Å) Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG, Tuske S, Tu X, Clark AD, Boyer PL, Hou X, Gaffney BL, Jones RA, Miller MD, Hughes SH, Arnold E (2009) "Structural basis for the role of the K65r mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance." J.Biol.Chem., 284, 35092-35100. doi: 10.1074/jbc.M109.022525. K65r mutant hiv-1 reverse transcriptase cross-linked to ds-DNA and complexed with tenofovir-diphosphate as the incoming nucleotide substrate. SNAP output
3jso hydrolase-DNA X-ray (2.29 Å) Zhang AP, Pigli YZ, Rice PA (2010) "Structure of the LexA-DNA complex and implications for SOS box measurement." Nature, 466, 883-886. doi: 10.1038/nature09200. Classic protein with a new twist: crystal structure of a lexa repressor DNA complex. SNAP output
3jsp hydrolase-DNA X-ray (2.9 Å) Zhang AP, Pigli YZ, Rice PA (2010) "Structure of the LexA-DNA complex and implications for SOS box measurement." Nature, 466, 883-886. doi: 10.1038/nature09200. Classic protein with a new twist: crystal structure of a lexa repressor DNA complex. SNAP output
3jtg transcription X-ray (2.2 Å) Agarkar VB, Babayeva ND, Wilder PJ, Rizzino A, Tahirov TH (2010) "Crystal structure of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-beta receptor promoter DNA." J.Mol.Biol., 397, 278-289. doi: 10.1016/j.jmb.2010.01.017. Crystal structure of mouse elf3 c-terminal DNA-binding domain in complex with type ii tgf-beta receptor promoter DNA. SNAP output
3jx7 hydrolase-DNA X-ray (1.6 Å) Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) "An unprecedented nucleic acid capture mechanism for excision of DNA damage." Nature, 468, 406-411. doi: 10.1038/nature09428. Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog. SNAP output
3jxb transcription regulator X-ray (1.67 Å) Watkins D, Mohan S, Koudelka GB, Williams LD (2010) "Sequence Recognition of DNA by Protein-Induced Conformational Transitions." J.Mol.Biol., 396, 1145-1164. doi: 10.1016/j.jmb.2009.12.050. Crystal structure of the p22 c2 repressor protein in complex with synthetic operator 9c. SNAP output
3jxc transcription regulator X-ray (1.9 Å) Watkins D, Mohan S, Koudelka GB, Williams LD (2010) "Sequence Recognition of DNA by Protein-Induced Conformational Transitions." J.Mol.Biol., 396, 1145-1164. doi: 10.1016/j.jmb.2009.12.050. Crystal structure of the p22 c2 repressor protein in complex with synthetic operator 9t in the presence of tl+. SNAP output
3jxd transcription regulator X-ray (2.1 Å) Watkins D, Mohan S, Koudelka GB, Williams LD (2010) "Sequence Recognition of DNA by Protein-Induced Conformational Transitions." J.Mol.Biol., 396, 1145-1164. doi: 10.1016/j.jmb.2009.12.050. Crystal structure of the p22 c2 repressor protein in complex with synthetic operator 9c in the presence of rb+. SNAP output
3jxy hydrolase-DNA X-ray (1.5 Å) Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) "An unprecedented nucleic acid capture mechanism for excision of DNA damage." Nature, 468, 406-411. doi: 10.1038/nature09428. Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing a gt mismatch. SNAP output
3jxz hydrolase-DNA X-ray (1.75 Å) Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) "An unprecedented nucleic acid capture mechanism for excision of DNA damage." Nature, 468, 406-411. doi: 10.1038/nature09428. Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site (across from t). SNAP output
3jy1 hydrolase-DNA X-ray (1.754 Å) Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF (2010) "An unprecedented nucleic acid capture mechanism for excision of DNA damage." Nature, 468, 406-411. doi: 10.1038/nature09428. Bacillus cereus alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site (across from c). SNAP output
3jyt transferase-DNA complex X-ray (3.3 Å) Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG, Tuske S, Tu X, Clark AD, Boyer PL, Hou X, Gaffney BL, Jones RA, Miller MD, Hughes SH, Arnold E (2009) "Structural basis for the role of the K65r mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance." J.Biol.Chem., 284, 35092-35100. doi: 10.1074/jbc.M109.022525. K65r mutant hiv-1 reverse transcriptase cross-linked to ds-DNA and complexed with datp as the incoming nucleotide substrate. SNAP output
3k0s DNA binding protein-DNA X-ray (2.2 Å) Lebbink JH, Fish A, Reumer A, Natrajan G, Winterwerp HH, Sixma TK (2010) "Magnesium coordination controls the molecular switch function of DNA mismatch repair protein MutS." J.Biol.Chem., 285, 13131-13141. doi: 10.1074/jbc.M109.066001. Crystal structure of e.coli DNA mismatch repair protein muts, d693n mutant, in complex with gt mismatched DNA. SNAP output
3k4x DNA binding protein-DNA X-ray (2.98 Å) McNally R, Bowman GD, Goedken ER, O'Donnell M, Kuriyan J (2010) "Analysis of the role of PCNA-DNA contacts during clamp loading." Bmc Struct.Biol., 10, 3. doi: 10.1186/1472-6807-10-3. Eukaryotic sliding clamp pcna bound to DNA. SNAP output
3k57 transferase-DNA X-ray (2.08 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-normal DNA-datp ternary complex. SNAP output
3k58 transferase-DNA X-ray (2.05 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-normal DNA-dttp ternary complex. SNAP output
3k59 transferase-DNA X-ray (1.92 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-normal DNA-dctp ternary complex. SNAP output
3k5l transferase-DNA X-ray (2.7 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-abasic DNA-datp lt(0, 3) ternary complex. SNAP output
3k5m transferase-DNA X-ray (2.04 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-abasic DNA-ddgtp lt(-2, 2) ternary complex. SNAP output
3k5n transferase-DNA X-ray (3.15 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-abasic DNA binary complex. SNAP output
3k70 hydrolase-DNA X-ray (3.59 Å) Saikrishnan K, Griffiths SP, Cook N, Court R, Wigley DB (2008) "DNA binding to RecD: role of the 1B domain in SF1B helicase activity." Embo J., 27, 2222-2229. Crystal structure of the complete initiation complex of recbcd. SNAP output
3k9f isomerase-DNA X-ray (2.9 Å) Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR (2010) "Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases." Plos One, 5, e11338. doi: 10.1371/journal.pone.0011338. Detailed structural insight into the quinolone-DNA cleavage complex of type iia topoisomerases. SNAP output
3kd1 transferase-DNA X-ray (2.66 Å) Zahn KE, Tchesnokov EP, Gotte M, Doublie S (2011) "Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase." J.Biol.Chem., 286, 25246-25255. doi: 10.1074/jbc.M111.248864. Closed binary complex of an rb69 gp43 fingers domain mutant complexed with an acyclic gmp terminated primer template pair.. SNAP output
3kd5 transferase-DNA X-ray (2.69 Å) Zahn KE, Tchesnokov EP, Gotte M, Doublie S (2011) "Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase." J.Biol.Chem., 286, 25246-25255. doi: 10.1074/jbc.M111.248864. Closed ternary complex of an rb69 gp43 fingers domain mutant complexed with an acyclic gmp terminated primer template pair and phosphonoformic acid.. SNAP output
3kde DNA binding protein-DNA X-ray (1.74 Å) Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC (2010) "THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves." Nat.Struct.Mol.Biol., 17, 117-123. doi: 10.1038/nsmb.1742. Crystal structure of the thap domain from d. melanogaster p-element transposase in complex with its natural DNA binding site. SNAP output
3ket transcription-DNA X-ray (2.4 Å) Franza T, Rogstam A, Thiyagarajan S, Sullivan MJ, Derre-Bobillot A, Bauer MC, Goh KGK, Da Cunha V, Glaser P, Logan DT, Ulett GC, von Wachenfeldt C, Gaudu P (2021) "NAD+ pool depletion as a signal for the Rex regulon involved in Streptococcus agalactiae virulence." Plos Pathog., 17, e1009791. doi: 10.1371/journal.ppat.1009791. Crystal structure of a rex-family transcriptional regulatory protein from streptococcus agalactiae bound to a palindromic operator. SNAP output
3khc oxidoreductase-DNA X-ray (2.2 Å) Holland PJ, Hollis T (2010) "Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching." Plos One, 5, e8680. doi: 10.1371/journal.pone.0008680. Crystal structure of escherichia coli alkb in complex with ssDNA containing a 1-methylguanine lesion. SNAP output
3khg transferase-DNA X-ray (2.96 Å) Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ (2010) "Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4." Nat.Struct.Mol.Biol., 17, 379-388. doi: 10.1038/nsmb.1771. Dpo4 extension ternary complex with misinserted a opposite the 2-aminofluorene-guanine [af]g lesion. SNAP output
3khh transferase-DNA X-ray (2.7 Å) Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ (2010) "Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4." Nat.Struct.Mol.Biol., 17, 379-388. doi: 10.1038/nsmb.1771. Dpo4 extension ternary complex with a c base opposite the 2-aminofluorene-guanine [af]g lesion. SNAP output
3khl transferase-DNA X-ray (2.1 Å) Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ (2010) "Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4." Nat.Struct.Mol.Biol., 17, 379-388. doi: 10.1038/nsmb.1771. Dpo4 post-extension ternary complex with misinserted a opposite the 2-aminofluorene-guanine [af]g lesion. SNAP output
3khr transferase-DNA X-ray (2.01 Å) Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ (2010) "Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4." Nat.Struct.Mol.Biol., 17, 379-388. doi: 10.1038/nsmb.1771. Dpo4 post-extension ternary complex with the correct c opposite the 2-aminofluorene-guanine [af]g lesion. SNAP output
3kjo DNA binding protein-DNA X-ray (1.8 Å) Nandakumar J, Podell ER, Cech TR (2010) "How telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA." Proc.Natl.Acad.Sci.USA, 107, 651-656. doi: 10.1073/pnas.0911099107. Crystal structure of hpot1v2-dtrud(agggttag). SNAP output
3kjp DNA binding protein-DNA X-ray (1.8 Å) Nandakumar J, Podell ER, Cech TR (2010) "How telomeric protein POT1 avoids RNA to achieve specificity for single-stranded DNA." Proc.Natl.Acad.Sci.USA, 107, 651-656. doi: 10.1073/pnas.0911099107. Crystal structure of hpot1v2-ggttagggttag. SNAP output
3kjv transferase-DNA X-ray (3.1 Å) Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S (2010) "Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex." J.Mol.Biol., 397, 967-978. doi: 10.1016/j.jmb.2010.02.019. Hiv-1 reverse transcriptase in complex with DNA. SNAP output
3kk1 transferase-DNA X-ray (2.7 Å) Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S (2010) "Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex." J.Mol.Biol., 397, 967-978. doi: 10.1016/j.jmb.2010.02.019. Hiv-1 reverse transcriptase-DNA complex with nuceotide inhibitor gs-9148-diphosphate bound in nucleotide site. SNAP output
3kk2 transferase-DNA X-ray (2.9 Å) Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S (2010) "Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex." J.Mol.Biol., 397, 967-978. doi: 10.1016/j.jmb.2010.02.019. Hiv-1 reverse transcriptase-DNA complex with datp bound in the nucleotide binding site. SNAP output
3kk3 transferase-DNA X-ray (2.9 Å) Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray AS, McGrath ME, Swaminathan S (2010) "Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex." J.Mol.Biol., 397, 967-978. doi: 10.1016/j.jmb.2010.02.019. Hiv-1 reverse transcriptase-DNA complex with gs-9148 terminated primer. SNAP output
3kle transferase-DNA X-ray (3.2 Å) Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E (2010) "Structural basis of HIV-1 resistance to AZT by excision." Nat.Struct.Mol.Biol., 17, 1202-1209. doi: 10.1038/nsmb.1908. Crystal structure of azt-resistant hiv-1 reverse transcriptase crosslinked to a dsDNA with a bound excision product, aztppppa. SNAP output
3klf transferase-DNA X-ray (3.15 Å) Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E (2010) "Structural basis of HIV-1 resistance to AZT by excision." Nat.Struct.Mol.Biol., 17, 1202-1209. doi: 10.1038/nsmb.1908. Crystal structure of wild-type hiv-1 reverse transcriptase crosslinked to a dsDNA with a bound excision product, aztppppa. SNAP output
3klg transferase-DNA X-ray (3.65 Å) Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E (2010) "Structural basis of HIV-1 resistance to AZT by excision." Nat.Struct.Mol.Biol., 17, 1202-1209. doi: 10.1038/nsmb.1908. Crystal structure of azt-resistant hiv-1 reverse transcriptase crosslinked to pre-translocation aztmp-terminated DNA (complex n). SNAP output
3klh transferase-DNA X-ray (2.9 Å) Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E (2010) "Structural basis of HIV-1 resistance to AZT by excision." Nat.Struct.Mol.Biol., 17, 1202-1209. doi: 10.1038/nsmb.1908. Crystal structure of azt-resistant hiv-1 reverse transcriptase crosslinked to post-translocation aztmp-terminated DNA (complex p). SNAP output
3kmd DNA binding protein-DNA X-ray (2.15 Å) Chen Y, Dey R, Chen L (2010) "Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer." Structure, 18, 246-256. doi: 10.1016/j.str.2009.11.011. Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer. SNAP output
3kmp transcription regulator-DNA X-ray (2.7 Å) BabuRajendran N, Palasingam P, Narasimhan K, Sun W, Prabhakar S, Jauch R, Kolatkar PR (2010) "Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors." Nucleic Acids Res., 38, 3477-3488. doi: 10.1093/nar/gkq046. Crystal structure of smad1-mh1-DNA complex. SNAP output
3knt hydrolase, lyase-DNA X-ray (2.7 Å) Faucher F, Wallace SS, Doublie S (2010) "The C-terminal Lysine of Ogg2 DNA Glycosylases is a Major Molecular Determinant for Guanine/8-Oxoguanine Distinction." J.Mol.Biol., 397, 46-56. doi: 10.1016/j.jmb.2010.01.024. Crystal structure of methanocaldococcus jannaschii 8-oxoguanine glycosylase-lyase in complex with 15mer DNA containing 8-oxoguanine. SNAP output
3ko2 hydrolase-DNA X-ray (2.9 Å) Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D (2010) "Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs." Nucleic Acids Res., 38, 5601-5608. doi: 10.1093/nar/gkq283. I-msoi re-designed for altered DNA cleavage specificity (-7c). SNAP output
3kov transcription-DNA X-ray (2.9 Å) Wu Y, Dey R, Han A, Jayathilaka N, Philips M, Ye J, Chen L (2010) "Structure of the MADS-box/MEF2 Domain of MEF2A Bound to DNA and Its Implication for Myocardin Recruitment." J.Mol.Biol., 397, 520-533. doi: 10.1016/j.jmb.2010.01.067. Structure of mef2a bound to DNA reveals a completely folded mads-box-mef2 domain that recognizes DNA and recruits transcription co-factors. SNAP output
3kqh hydrolase-DNA X-ray (2.4 Å) Gu M, Rice CM (2010) "Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism." Proc.Natl.Acad.Sci.USA, 107, 521-528. doi: 10.1073/pnas.0913380107. Three conformational snapshots of the hepatitis c virus ns3 helicase reveal a ratchet translocation mechanism. SNAP output
3kqk hydrolase-DNA X-ray (2.8 Å) Gu M, Rice CM (2010) "Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism." Proc.Natl.Acad.Sci.USA, 107, 521-528. doi: 10.1073/pnas.0913380107. Three conformational snapshots of the hepatitis c virus ns3 helicase reveal a ratchet translocation mechanism. SNAP output
3kql hydrolase-DNA X-ray (2.5 Å) Gu M, Rice CM (2010) "Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism." Proc.Natl.Acad.Sci.USA, 107, 521-528. doi: 10.1073/pnas.0913380107. Three conformational snapshots of the hepatitis c virus ns3 helicase reveal a ratchet translocation mechanism. SNAP output
3kqn hydrolase-DNA X-ray (2.05 Å) Gu M, Rice CM (2010) "Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism." Proc.Natl.Acad.Sci.USA, 107, 521-528. doi: 10.1073/pnas.0913380107. Three conformational snapshots of the hepatitis c virus ns3 helicase reveal a ratchet translocation mechanism. SNAP output
3kqu hydrolase-DNA X-ray (2.4 Å) Gu M, Rice CM (2010) "Inaugural Article: Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism." Proc.Natl.Acad.Sci.USA, 107, 521-528. doi: 10.1073/pnas.0913380107. Three conformational snapshots of the hepatitis c virus ns3 helicase reveal a ratchet translocation mechanism. SNAP output
3ksa isomerase-DNA X-ray (3.3 Å) Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR (2010) "Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases." Plos One, 5, e11338. doi: 10.1371/journal.pone.0011338. Detailed structural insight into the DNA cleavage complex of type iia topoisomerases (cleaved form). SNAP output
3ksb isomerase-DNA X-ray (3.5 Å) Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR (2010) "Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases." Plos One, 5, e11338. doi: 10.1371/journal.pone.0011338. Detailed structural insight into the DNA cleavage complex of type iia topoisomerases (re-sealed form). SNAP output
3ktq transferase-DNA X-ray (2.3 Å) Li Y, Korolev S, Waksman G (1998) "Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation." EMBO J., 17, 7514-7525. doi: 10.1093/emboj/17.24.7514. Crystal structure of an active ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
3ktu hydrolase,lyase-DNA X-ray (2.3 Å) Verdine GL, Lee SM "Structural investigation of hOGG1 bound to a fluorinated oxoG analog." Structure of human 8-oxoguanine glycosylase 1 bound to fluorninated oxog-containing DNA. SNAP output
3kuy structural protein-DNA X-ray (2.9 Å) Davey GE, Wu B, Dong Y, Surana U, Davey CA (2010) "DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent." Nucleic Acids Res., 38, 2081-2088. doi: 10.1093/nar/gkp1174. DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumor agent. SNAP output
3kwq structural protein-DNA X-ray (3.5 Å) Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen JC, Peterson C, Luger K "Structural characterization of H3K56Q nucleosomes and nucleosomal arrays." Biochim.Biophys.Acta, 1799, 480-486. doi: 10.1016/j.bbagrm.2010.01.009. Structural characterization of h3k56q nucleosomes and nucleosomal arrays. SNAP output
3kxb transcription-DNA X-ray (3.2 Å) Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen JC, Peterson C, Luger K (2010) "Structural characterization of H3K56Q nucleosomes and nucleosomal arrays." Biochim.Biophys.Acta, 1799, 480-486. doi: 10.1016/j.bbagrm.2010.01.009. Structural characterization of h3k56q nucleosomes and nucleosomal arrays. SNAP output
3kxt DNA binding protein-DNA X-ray (1.602 Å) Feng Y, Yao H, Wang J (2010) "Crystal structure of the crenarchaeal conserved chromatin protein Cren7 and double-stranded DNA complex." Protein Sci., 19, 1253-1257. doi: 10.1002/pro.385. Crystal structure of sulfolobus cren7-dsDNA complex. SNAP output
3kyl nucleic acid binding protein-DNA-RNA X-ray (2.7 Å) Mitchell M, Gillis A, Futahashi M, Fujiwara H, Skordalakes E (2010) "Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA." Nat.Struct.Mol.Biol., 17, 513-518. doi: 10.1038/nsmb.1777. Structure of the catalytic subunit of telomerase bound to its RNA template and telomeric DNA. SNAP output
3kz8 transcription-DNA X-ray (1.91 Å) Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z (2010) "Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs." Nat.Struct.Mol.Biol., 17, 423-429. doi: 10.1038/nsmb.1800. Diversity in DNA recognition by p53 revealed by crystal structures with hoogsteen base pairs (p53-DNA complex 3). SNAP output
3l1p transcription-DNA X-ray (2.8 Å) Esch D, Vahokoski J, Groves MR, Pogenberg V, Cojocaru V, Vom Bruch H, Han D, Drexler HCA, Arauzo-Bravo MJ, Ng CKL, Jauch R, Wilmanns M, Scholer HR (2013) "A unique Oct4 interface is crucial for reprogramming to pluripotency." Nat.Cell Biol., 15, 295-301. doi: 10.1038/ncb2680. Pou protein:DNA complex. SNAP output
3l2c transcription-DNA X-ray (1.868 Å) Boura E, Rezabkova L, Brynda J, Obsilova V, Obsil T (2010) "Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA." Acta Crystallogr.,Sect.D, 66, 1351-1357. doi: 10.1107/S0907444910042228. Crystal structure of the DNA binding domain of foxo4 bound to DNA. SNAP output
3l2p ligase-DNA X-ray (3.0 Å) Cotner-Gohara E, Kim IK, Hammel M, Tainer JA, Tomkinson AE, Ellenberger T (2010) "Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States." Biochemistry, 49, 6165-6176. doi: 10.1021/bi100503w. Human DNA ligase iii recognizes DNA ends by dynamic switching between two DNA bound states. SNAP output
3l2q recombination-DNA X-ray (3.25 Å) Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) "Retroviral intasome assembly and inhibition of DNA strand transfer." Nature, 464, 232-236. doi: 10.1038/nature08784. Crystal structure of the prototype foamy virus (pfv) intasome in apo form. SNAP output
3l2r recombination-DNA X-ray (2.88 Å) Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) "Retroviral intasome assembly and inhibition of DNA strand transfer." Nature, 464, 232-236. doi: 10.1038/nature08784. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium. SNAP output
3l2u recombination-DNA X-ray (3.15 Å) Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) "Retroviral intasome assembly and inhibition of DNA strand transfer." Nature, 464, 232-236. doi: 10.1038/nature08784. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and gs9137 (elvitegravir). SNAP output
3l2v recombination-DNA X-ray (3.2 Å) Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) "Retroviral intasome assembly and inhibition of DNA strand transfer." Nature, 464, 232-236. doi: 10.1038/nature08784. Crystal structure of the prototype foamy virus (pfv) intasome in complex with manganese and mk0518 (raltegravir). SNAP output
3l2w recombination-DNA X-ray (3.2 Å) Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) "Retroviral intasome assembly and inhibition of DNA strand transfer." Nature, 464, 232-236. doi: 10.1038/nature08784. Crystal structure of the prototype foamy virus (pfv) intasome in complex with manganese and gs9137 (elvitegravir). SNAP output
3l4j isomerase-DNA X-ray (2.48 Å) Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM (2010) "A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases." Nature, 465, 641-644. doi: 10.1038/nature08974. Topoisomerase ii-DNA cleavage complex, apo. SNAP output
3l4k isomerase-DNA X-ray (2.98 Å) Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM (2010) "A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases." Nature, 465, 641-644. doi: 10.1038/nature08974. Topoisomerase ii-DNA cleavage complex, metal-bound. SNAP output
3l8b transferase-DNA X-ray (2.15 Å) Aller P, Ye Y, Wallace SS, Burrows CJ, Doublie S (2010) "Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin." Biochemistry, 49, 2502-2509. doi: 10.1021/bi902195p. Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin. SNAP output
3laj transcription regulator X-ray (2.306 Å) Cherney LT, Cherney MM, Garen CR, James MN (2010) "crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression." J.Mol.Biol., 399, 240-254. doi: 10.1016/j.jmb.2010.03.065. The structure of the intermediate complex of the arginine repressor from mycobacterium tuberculosis bound to its DNA operator and l-arginine.. SNAP output
3lap transcription regulator-DNA X-ray (2.15 Å) Cherney LT, Cherney MM, Garen CR, James MN (2010) "crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression." J.Mol.Biol., 399, 240-254. doi: 10.1016/j.jmb.2010.03.065. The structure of the intermediate complex of the arginine repressor from mycobacterium tuberculosis bound to its DNA operator and l-canavanine.. SNAP output
3lds transferase-DNA X-ray (3.0 Å) Hogg M, Rudnicki J, Midkiff J, Reha-Krantz L, Doublie S, Wallace SS (2010) "Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69." Biochemistry, 49, 2317-2325. doi: 10.1021/bi901488d. Crystal structure of rb69 gp43 with DNA and datp opposite 8-oxog. SNAP output
3ldy hydrolase-DNA X-ray (1.97 Å) Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan RD, Wilson GG, Stoddard BL (2010) "Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI." Structure, 18, 734-743. doi: 10.1016/j.str.2010.03.009. An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting hnh restriction endonuclease paci. SNAP output
3lel structural protein-DNA X-ray (2.95 Å) Wu B, Mohideen K, Vasudevan D, Davey CA (2010) "Structural insight into the sequence dependence of nucleosome positioning." Structure, 18, 528-536. doi: 10.1016/j.str.2010.01.015. Structural insight into the sequence-dependence of nucleosome positioning. SNAP output
3lja structural protein-DNA X-ray (2.75 Å) Wu B, Davey CA (2010) "Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome." J.Mol.Biol., 398, 633-640. doi: 10.1016/j.jmb.2010.03.038. Using soft x-rays for a detailed picture of divalent metal binding in the nucleosome. SNAP output
3lk9 lyase,transferase-DNA X-ray (2.5 Å) Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA (2010) "Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid." Proc.Natl.Acad.Sci.USA, 107, 15693-15698. doi: 10.1073/pnas.1007430107. DNA polymerase beta with a gapped DNA substrate and dtmp(cf2)p(cf2)p. SNAP output
3lnq gene regulation-DNA X-ray (2.25 Å) Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M (2010) "Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless." Embo J., 29, 1613-1623. doi: 10.1038/emboj.2010.53. Structure of aristaless homeodomain in complex with DNA. SNAP output
3lsp transcription-DNA X-ray (2.66 Å) Miller DJ, Zhang YM, Subramanian C, Rock CO, White SW (2010) "Structural basis for the transcriptional regulation of membrane lipid homeostasis." Nat.Struct.Mol.Biol., 17, 971-975. doi: 10.1038/nsmb.1847. Crystal structure of dest bound to descb promoter and oleoyl-coa. SNAP output
3lsr transcription-DNA X-ray (2.55 Å) Miller DJ, Zhang YM, Subramanian C, Rock CO, White SW (2010) "Structural basis for the transcriptional regulation of membrane lipid homeostasis." Nat.Struct.Mol.Biol., 17, 971-975. doi: 10.1038/nsmb.1847. Crystal structure of dest in complex with duplex DNA. SNAP output
3ltn isomerase-DNA X-ray (3.1 Å) Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR (2010) "Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases." Plos One, 5, e11338. doi: 10.1371/journal.pone.0011338. Inhibitor-stabilized topoisomerase iv-DNA cleavage complex (s. pneumoniae). SNAP output
3lwh DNA binding protein-DNA X-ray (1.9 Å) Zhang ZF, Gong Y, Guo L, Jiang T, Huang L (2010) "Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA." Mol.Microbiol., 76, 749-759. doi: 10.1111/j.1365-2958.2010.07136.x. Crystal structure of cren7-dsDNA complex. SNAP output
3lwi DNA binding protein-DNA X-ray (2.3 Å) Zhang ZF, Gong Y, Guo L, Jiang T, Huang L (2010) "Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA." Mol.Microbiol., 76, 749-759. doi: 10.1111/j.1365-2958.2010.07136.x. Crystal structure of cren7-dsDNA complex. SNAP output
3lwl transferase-DNA X-ray (2.25 Å) Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs K, Welte W, Marx A (2010) "Replication through an abasic DNA lesion: structural basis for adenine selectivity." Embo J., 29, 1738-1747. doi: 10.1038/emboj.2010.64. Structure of klenow fragment of taq polymerase in complex with an abasic site. SNAP output
3lwm transferase-DNA X-ray (2.186 Å) Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs K, Welte W, Marx A (2010) "Replication through an abasic DNA lesion: structural basis for adenine selectivity." Embo J., 29, 1738-1747. doi: 10.1038/emboj.2010.64. Structure of the large fragment of thermus aquaticus DNA polymerase i in complex with a blunt-ended DNA and ddatp. SNAP output
3lz0 structural protein-DNA X-ray (2.5 Å) Vasudevan D, Chua EY, Davey CA (2010) "Crystal structures of nucleosome core particles containing the '601' strong positioning sequence." J.Mol.Biol., 403, 1-10. doi: 10.1016/j.jmb.2010.08.039. Crystal structure of nucleosome core particle composed of the widom 601 DNA sequence (orientation 1). SNAP output
3lz1 structural protein-DNA X-ray (2.5 Å) Vasudevan D, Chua EY, Davey CA (2010) "Crystal structures of nucleosome core particles containing the '601' strong positioning sequence." J.Mol.Biol., 403, 1-10. doi: 10.1016/j.jmb.2010.08.039. Crystal structure of nucleosome core particle composed of the widom 601 DNA sequence (orientation 2). SNAP output
3lzi transferase-DNA X-ray (2.3 Å) Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH (2010) "Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine ." Biochemistry, 49, 4116-4125. doi: 10.1021/bi100102s. Rb69 DNA polymerase (y567a) ternary complex with datp opposite 7,8-dihydro-8-oxoguanine. SNAP output
3lzj transferase-DNA X-ray (2.05 Å) Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH (2010) "Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine ." Biochemistry, 49, 4116-4125. doi: 10.1021/bi100102s. Rb69 DNA polymerase (y567a) ternary complex with dctp opposite 7,8-dihydro-8-oxoguanine. SNAP output
3m3y transferase-DNA-RNA hybrid X-ray (3.18 Å) Wang D, Zhu G, Huang X, Lippard SJ (2010) "X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct." Proc.Natl.Acad.Sci.USA, 107, 9584-9589. doi: 10.1073/pnas.1002565107. RNA polymerase ii elongation complex c. SNAP output
3m4a isomerase-DNA X-ray (1.65 Å) Patel A, Yakovleva L, Shuman S, Mondragon A (2010) "Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site." Structure, 18, 725-733. doi: 10.1016/j.str.2010.03.007. Crystal structure of a bacterial topoisomerase ib in complex with DNA reveals a secondary DNA binding site. SNAP output
3m4o transferase-DNA-RNA hybrid X-ray (3.57 Å) Wang D, Zhu G, Huang X, Lippard SJ (2010) "X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct." Proc.Natl.Acad.Sci.USA, 107, 9584-9589. doi: 10.1073/pnas.1002565107. RNA polymerase ii elongation complex b. SNAP output
3m7k hydrolase-DNA X-ray (1.92 Å) Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan RD, Wilson GG, Stoddard BL (2010) "Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI." Structure, 18, 734-743. doi: 10.1016/j.str.2010.03.009. Crystal structure of paci-DNA enzyme product complex. SNAP output
3m8r transferase-DNA X-ray (2.0 Å) Betz K, Streckenbach F, Schnur A, Exner T, Welte W, Diederichs K, Marx A (2010) "Structures of DNA polymerases caught processing size-augmented nucleotide probes." Angew.Chem.Int.Ed.Engl., 49, 5181-5184. doi: 10.1002/anie.200905724. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with trapped 4'-ethylated dttp. SNAP output
3m8s transferase-DNA X-ray (2.2 Å) Betz K, Streckenbach F, Schnur A, Exner T, Welte W, Diederichs K, Marx A (2010) "Structures of DNA polymerases caught processing size-augmented nucleotide probes." Angew.Chem.Int.Ed.Engl., 49, 5181-5184. doi: 10.1002/anie.200905724. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with trapped 4'-methylated dttp. SNAP output
3m9e transcription-DNA X-ray (2.406 Å) Chen Y, Young MA (2010) "Structure of a thyroid hormone receptor DNA-binding domain homodimer bound to an inverted palindrome DNA response element." Mol.Endocrinol., 24, 1650-1664. doi: 10.1210/me.2010-0129. Thyroid hormone beta DNA binding domain homodimer with inverted palindrome tre. SNAP output
3m9m transferase-DNA X-ray (2.9 Å) Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling H (2010) "Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4." Embo J., 29, 2059-2069. doi: 10.1038/emboj.2010.101. Crystal structure of dpo4 in complex with DNA containing the major cisplatin lesion. SNAP output
3m9n transferase-DNA X-ray (1.93 Å) Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling H (2010) "Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4." Embo J., 29, 2059-2069. doi: 10.1038/emboj.2010.101. Crystal structure of dpo4 in complex with DNA containing the major cisplatin lesion. SNAP output
3m9o transferase-DNA X-ray (2.0 Å) Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling H (2010) "Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4." Embo J., 29, 2059-2069. doi: 10.1038/emboj.2010.101. Crystal structure of dpo4 in complex with DNA containing the major cisplatin lesion. SNAP output
3maq transferase-DNA X-ray (2.4 Å) Wang F, Yang W (2009) "Structural insight into translesion synthesis by DNA Pol II." Cell(Cambridge,Mass.), 139, 1279-1289. doi: 10.1016/j.cell.2009.11.043. Crystal structure of e.coli pol ii-normal DNA-dgtp ternary complex. SNAP output
3mby transferase, lyase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Hou EW, Pedersen LC, Prasad R, Wilson SH (2010) "Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site." Nat.Struct.Mol.Biol., 17, 889-890. doi: 10.1038/nsmb.1852. Ternary complex of DNA polymerase beta with template base a and 8oxodgtp in the active site with a dideoxy terminated primer. SNAP output
3mda lyase,transferase-DNA X-ray (2.031 Å) Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM (2010) "Interaction between DNA Polymerase lambda and anticancer nucleoside analogs." J.Biol.Chem., 285, 16874-16879. doi: 10.1074/jbc.M109.094391. DNA polymerase lambda in complex with arac. SNAP output
3mdc lyase,transferase-DNA X-ray (1.999 Å) Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM (2010) "Interaction between DNA Polymerase lambda and anticancer nucleoside analogs." J.Biol.Chem., 285, 16874-16879. doi: 10.1074/jbc.M109.094391. DNA polymerase lambda in complex with dfdctp. SNAP output
3mfh transferase-DNA X-ray (2.0 Å) Silverstein TD, Johnson RE, Jain R, Prakash L, Prakash S, Aggarwal AK (2010) "Structural basis for the suppression of skin cancers by DNA polymerase eta." Nature, 465, 1039-1043. doi: 10.1038/nature09104. DNA polymerase eta in complex with undamaged DNA. SNAP output
3mfi transferase-DNA X-ray (1.76 Å) Silverstein TD, Johnson RE, Jain R, Prakash L, Prakash S, Aggarwal AK (2010) "Structural basis for the suppression of skin cancers by DNA polymerase eta." Nature, 465, 1039-1043. doi: 10.1038/nature09104. DNA polymerase eta in complex with a cis-syn thymidine dimer. SNAP output
3mfk transcription-DNA X-ray (3.0 Å) Babayeva ND, Wilder PJ, Shiina M, Mino K, Desler M, Ogata K, Rizzino A, Tahirov TH (2010) "Structural basis of Ets1 cooperative binding to palindromic sequences on stromelysin-1 promoter DNA." Cell Cycle, 9, 3054-3062. Ets1 complex with stromelysin-1 promoter DNA. SNAP output
3mgh lyase,transferase-DNA X-ray (2.4 Å) Bebenek K, Garcia-Diaz M, Zhou RZ, Povirk LF, Kunkel TA (2010) "Loop 1 modulates the fidelity of DNA polymerase lambda." Nucleic Acids Res., 38, 5419-5431. doi: 10.1093/nar/gkq261. Binary complex of a DNA polymerase lambda loop mutant. SNAP output
3mgi lyase,transferase-DNA X-ray (2.603 Å) Bebenek K, Garcia-Diaz M, Zhou RZ, Povirk LF, Kunkel TA (2010) "Loop 1 modulates the fidelity of DNA polymerase lambda." Nucleic Acids Res., 38, 5419-5431. doi: 10.1093/nar/gkq261. Ternary complex of a DNA polymerase lambda loop mutant. SNAP output
3mgp structural protein-DNA X-ray (2.44 Å) Mohideen K, Muhammad R, Davey CA (2010) "Perturbations in nucleosome structure from heavy metal association." Nucleic Acids Res., 38, 6301-6311. doi: 10.1093/nar/gkq420. Binding of cobalt ions to the nucleosome core particle. SNAP output
3mgq structural protein-DNA X-ray (2.65 Å) Mohideen K, Muhammad R, Davey CA (2010) "Perturbations in nucleosome structure from heavy metal association." Nucleic Acids Res., 38, 6301-6311. doi: 10.1093/nar/gkq420. Binding of nickel ions to the nucleosome core particle. SNAP output
3mgr structural protein-DNA X-ray (2.3 Å) Mohideen K, Muhammad R, Davey CA (2010) "Perturbations in nucleosome structure from heavy metal association." Nucleic Acids Res., 38, 6301-6311. doi: 10.1093/nar/gkq420. Binding of rubidium ions to the nucleosome core particle. SNAP output
3mgs structural protein-DNA X-ray (3.15 Å) Mohideen K, Muhammad R, Davey CA (2010) "Perturbations in nucleosome structure from heavy metal association." Nucleic Acids Res. doi: 10.1093/nar/gkq420. Binding of cesium ions to the nucleosome core particle. SNAP output
3mgv isomerase-DNA X-ray (2.29 Å) Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne GD (2010) "Requirements for catalysis in the Cre recombinase active site." Nucleic Acids Res., 38, 5817-5832. doi: 10.1093/nar/gkq384. Cre recombinase-DNA transition state. SNAP output
3mht transferase-DNA X-ray (2.7 Å) O'Gara M, Klimasauskas S, Roberts RJ, Cheng X (1996) "Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes." J.Mol.Biol., 261, 634-645. doi: 10.1006/jmbi.1996.0489. Ternary structure of hhai methyltransferase with unmodified DNA and adohcy. SNAP output
3mip de novo protein-DNA X-ray (2.4 Å) Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D (2010) "Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs." Nucleic Acids Res., 38, 5601-5608. doi: 10.1093/nar/gkq283. I-msoi re-designed for altered DNA cleavage specificity (-8gcg). SNAP output
3mis de novo protein-DNA X-ray (2.3 Å) Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D (2010) "Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs." Nucleic Acids Res., 38, 5601-5608. doi: 10.1093/nar/gkq283. I-msoi re-designed for altered DNA cleavage specificity (-8g). SNAP output
3mkw DNA binding protein-DNA X-ray (2.99 Å) Schumacher MA, Piro KM, Xu W (2010) "Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes." Nucleic Acids Res., 38, 4514-4526. doi: 10.1093/nar/gkq161. Structure of sopb(155-272)-18mer complex, i23 form. SNAP output
3mky DNA binding protein-DNA X-ray (2.86 Å) Schumacher MA, Piro KM, Xu W (2010) "Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes." Nucleic Acids Res., 38, 4514-4526. doi: 10.1093/nar/gkq161. Structure of sopb(155-323)-18mer DNA complex, i23 form. SNAP output
3mkz DNA-binding protein-DNA X-ray (2.98 Å) Schumacher MA, Piro KM, Xu W (2010) "Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes." Nucleic Acids Res., 38, 4514-4526. doi: 10.1093/nar/gkq161. Structure of sopb(155-272)-18mer complex, p21 form. SNAP output
3mln transcription-DNA X-ray (2.4 Å) Treiber N, Treiber T, Zocher G, Grosschedl R (2010) "Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins." Genes Dev., 24, 2270-2275. doi: 10.1101/gad.1976610. DNA binding domain of early b-cell factor 1 (ebf1) bound to DNA (crystal form ii). SNAP output
3mlo transcription-DNA X-ray (3.01 Å) Treiber N, Treiber T, Zocher G, Grosschedl R (2010) "Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins." Genes Dev., 24, 2270-2275. doi: 10.1101/gad.1976610. DNA binding domain of early b-cell factor 1 (ebf1) bound to DNA (crystal form i). SNAP output
3mlp transcription-DNA X-ray (2.8 Å) Treiber N, Treiber T, Zocher G, Grosschedl R (2010) "Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins." Genes Dev., 24, 2270-2275. doi: 10.1101/gad.1976610. Early b-cell factor 1 (ebf1) bound to DNA. SNAP output
3mnn structural protein-DNA X-ray (2.5 Å) Wu B, Ong MS, Groessl M, Adhireksan Z, Hartinger CG, Dyson PJ, Davey CA (2011) "A ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core." Chemistry, 17, 3562-3566. doi: 10.1002/chem.201100298. A ruthenium antitumour agent forms specific histone protein adducts in the nucleosome core. SNAP output
3mq6 hydrolase-DNA X-ray (2.0 Å) Park CK, Joshi HK, Agrawal A, Ghare MI, Little EJ, Dunten PW, Bitinaite J, Horton NC (2010) "Domain swapping in allosteric modulation of DNA specificity." Plos Biol., 8, e1000554. doi: 10.1371/journal.pbio.1000554. Domain swapped sgrai with DNA and calcium bound. SNAP output
3mqy hydrolase-DNA X-ray (2.0 Å) Little EJ, Dunten PW, Bitinaite J, Horton NC (2011) "New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA." Acta Crystallogr.,Sect.D, 67, 67-74. doi: 10.1107/S0907444910047785. Sgrai with cleaved DNA and magnesium bound. SNAP output
3mr2 transferase-DNA X-ray (1.83 Å) Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W (2010) "Structure and mechanism of human DNA polymerase eta." Nature, 465, 1044-1048. doi: 10.1038/nature09196. Human DNA polymerase eta in complex with normal DNA and incoming nucleotide (nrm). SNAP output
3mr3 transferase-DNA X-ray (1.75 Å) Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W (2010) "Structure and mechanism of human DNA polymerase eta." Nature, 465, 1044-1048. doi: 10.1038/nature09196. Human DNA polymerase eta - DNA ternary complex with the 3't of a cpd in the active site (tt1). SNAP output
3mr5 transferase-DNA X-ray (1.8 Å) Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W (2010) "Structure and mechanism of human DNA polymerase eta." Nature, 465, 1044-1048. doi: 10.1038/nature09196. Human DNA polymerase eta - DNA ternary complex with a cpd 1bp upstream of the active site (tt3). SNAP output
3mr6 transferase-DNA X-ray (1.9 Å) Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W (2010) "Structure and mechanism of human DNA polymerase eta." Nature, 465, 1044-1048. doi: 10.1038/nature09196. Human DNA polymerase eta - DNA ternary complex with a cpd 2bp upstream of the active site (tt4). SNAP output
3mu6 DNA binding protein-DNA X-ray (2.434 Å) Jayathilaka N, Han A, Gaffney KJ, Dey R, Jarusiewicz JA, Noridomi K, Philips MA, Lei X, He J, Ye J, Gao T, Petasis NA, Chen L (2012) "Inhibition of the function of class IIa HDACs by blocking their interaction with MEF2." Nucleic Acids Res., 40, 5378-5388. doi: 10.1093/nar/gks189. Inhibiting the binding of class iia histone deacetylases to myocyte enhancer factor-2 by small molecules. SNAP output
3mva transcription-DNA X-ray (2.2 Å) Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E, Garcia-Diaz M (2010) "Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription." Cell(Cambridge,Mass.), 141, 982-993. doi: 10.1016/j.cell.2010.05.018. Crystal structure of human mterf1 bound to the termination sequence. SNAP output
3mvb transcription-DNA X-ray (2.786 Å) Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E, Garcia-Diaz M (2010) "Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription." Cell(Cambridge,Mass.), 141, 982-993. doi: 10.1016/j.cell.2010.05.018. Crystal structure of a triple rfy mutant of human mterf1 bound to the termination sequence. SNAP output
3mvd signaling protein-structural protein-DNA X-ray (2.9 Å) Makde RD, England JR, Yennawar HP, Tan S (2010) "Structure of RCC1 chromatin factor bound to the nucleosome core particle." Nature, 467, 562-566. doi: 10.1038/nature09321. Crystal structure of the chromatin factor rcc1 in complex with the nucleosome core particle. SNAP output
3mx4 hydrolase-DNA X-ray (2.5 Å) Mak AN, Lambert AR, Stoddard BL (2010) "Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI." Structure, 18, 1321-1331. doi: 10.1016/j.str.2010.07.006. DNA binding and cleavage by the giy-yig endonuclease r.eco29ki inactive variant e142q. SNAP output
3mx9 hydrolase-DNA X-ray (2.6 Å) Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, Merino N, Marenchino M, D'Abramo M, Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano L, Blanco FJ, Montoya G (2011) "Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus." Nucleic Acids Res., 39, 729-743. doi: 10.1093/nar/gkq801. Molecular basis of engineered meganuclease targeting of the endogenous human rag1 locus. SNAP output
3mxa hydrolase-DNA X-ray (2.3 Å) Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, Merino N, Marenchino M, D'Abramo M, Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano L, Blanco FJ, Montoya G (2011) "Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus." Nucleic Acids Res., 39, 729-743. doi: 10.1093/nar/gkq801. Molecular basis of engineered meganuclease targeting of the endogenous human rag1 locus. SNAP output
3mxb hydrolase-DNA X-ray (2.3 Å) Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, Merino N, Marenchino M, D'Abramo M, Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano L, Blanco FJ, Montoya G (2011) "Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus." Nucleic Acids Res., 39, 729-743. doi: 10.1093/nar/gkq801. Molecular basis of engineered meganuclease targeting of the endogenous human rag1 locus. SNAP output
3mxi hydrolase-DNA X-ray (2.55 Å) Bailey SL, Harvey S, Perrino FW, Hollis T "X-ray Crystal Structures of TREX1 3' Exonuclease Autoimmune Disease Mutants." Trex1 3' exonuclease d18n familial chilblain lupus mutant. SNAP output
3mxm hydrolase-DNA X-ray (1.75 Å) Bailey SL, Harvey S, Perrino FW, Hollis T "X-ray Crystal Structures of TREX1 3' Exonuclease Autoimmune Disease Mutants." Trex1 3' exonuclease v201d aicardi-goutieres syndrome mutant. SNAP output
3mzh transcription-DNA X-ray (2.9 Å) Akhter Y, Pogenberg V, Hasnain SE, Wilmanns M "Crystal Structure of Camp Receptor Protein from Mycobacterium Tuberculosis in Complex with DNA and cAMP." Crystal structure of camp receptor protein from mycobacterium tuberculosis in complex with camp and its DNA binding element. SNAP output
3n1i DNA binding protein-DNA X-ray (2.2 Å) Cappadocia L, Marechal A, Parent JS, Lepage E, Sygusch J, Brisson N (2010) "Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair." Plant Cell, 22, 1849-1867. doi: 10.1105/tpc.109.071399. Crystal structure of a stwhy2-ere32 complex. SNAP output
3n1j DNA binding protein-DNA X-ray (2.65 Å) Cappadocia L, Marechal A, Parent JS, Lepage E, Sygusch J, Brisson N (2010) "Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair." Plant Cell, 22, 1849-1867. doi: 10.1105/tpc.109.071399. Crystal structure of a stwhy2-dt32 complex. SNAP output
3n1k DNA binding protein-DNA X-ray (2.702 Å) Cappadocia L, Marechal A, Parent JS, Lepage E, Sygusch J, Brisson N (2010) "Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair." Plant Cell, 22, 1849-1867. doi: 10.1105/tpc.109.071399. Crystal structure of a stwhy2-cere32 complex. SNAP output
3n1l DNA binding protein-DNA X-ray (2.35 Å) Cappadocia L, Marechal A, Parent JS, Lepage E, Sygusch J, Brisson N (2010) "Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair." Plant Cell, 22, 1849-1867. doi: 10.1105/tpc.109.071399. Crystal structure of a stwhy2-rcere32 complex. SNAP output
3n4m gene regulation-DNA X-ray (2.987 Å) Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL (2020) "The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element." Biochemistry, 59, 4523-4532. doi: 10.1021/acs.biochem.0c00571. E. coli RNA polymerase alpha subunit c-terminal domain in complex with cap and DNA. SNAP output
3n6s transcription, replication-DNA X-ray (3.1 Å) Jimenez-Menendez N, Fernandez-Millan P, Rubio-Cosials A, Arnan C, Montoya J, Jacobs HT, Bernado P, Coll M, Uson I, Sola M (2010) "Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat." Nat.Struct.Mol.Biol., 17, 891-893. doi: 10.1038/nsmb.1859. Crystal structure of human mitochondrial mterf in complex with a 15-mer DNA encompassing the trnaleu(uur) binding sequence. SNAP output
3n78 hydrolase-DNA X-ray (2.95 Å) Little EJ, Dunten PW, Bitinaite J, Horton NC (2011) "New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA." Acta Crystallogr.,Sect.D, 67, 67-74. doi: 10.1107/S0907444910047785. Sgrai bound to secondary site DNA and mg(ii). SNAP output
3n7b hydrolase-DNA X-ray (2.65 Å) Little EJ, Dunten PW, Bitinaite J, Horton NC (2011) "New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA." Acta Crystallogr.,Sect.D, 67, 67-74. doi: 10.1107/S0907444910047785. Sgrai bound to secondary site DNA and ca(ii). SNAP output
3n7q transcription, replication-DNA X-ray (2.4 Å) Jimenez-Menendez N, Fernandez-Millan P, Rubio-Cosials A, Arnan C, Montoya J, Jacobs HT, Bernado P, Coll M, Uson I, Sola M (2010) "Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat." Nat.Struct.Mol.Biol., 17, 891-893. doi: 10.1038/nsmb.1859. Crystal structure of human mitochondrial mterf fragment (aa 99-399) in complex with a 12-mer DNA encompassing the trnaleu(uur) binding sequence. SNAP output
3n97 gene regulation-DNA X-ray (3.252 Å) Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL (2020) "The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element." Biochemistry, 59, 4523-4532. doi: 10.1021/acs.biochem.0c00571. RNA polymerase alpha c-terminal domain (e. coli) and sigma region 4 (t. aq. mutant) bound to (up,-35 element) DNA. SNAP output
3nae transferase-DNA X-ray (2.003 Å) Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH (2010) "Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP and dGMP To Be Inserted opposite Guanidinohydantoin ." Biochemistry, 49, 8554-8563. doi: 10.1021/bi100913v. Rb69 DNA polymerase (y567a) ternary complex with datp opposite guanidinohydantoin. SNAP output
3nbn transcription-DNA X-ray (3.45 Å) Arnett KL, Hass M, McArthur DG, Ilagan MX, Aster JC, Kopan R, Blacklow SC (2010) "Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes." Nat.Struct.Mol.Biol., 17, 1312-1317. doi: 10.1038/nsmb.1938. Crystal structure of a dimer of notch transcription complex trimers on hes1 DNA. SNAP output
3nci transferase-DNA X-ray (1.79 Å) Wang M, Xia S, Blaha G, Steitz TA, Konigsberg WH, Wang J (2011) "Insights into base selectivity from the 1.8 A resolution structure of an RB69 DNA polymerase ternary complex." Biochemistry, 50, 581-590. doi: 10.1021/bi101192f. Rb69 DNA polymerase ternary complex with dctp opposite dg at 1.8 angstrom resolution. SNAP output
3ndh hydrolase-DNA X-ray (1.3 Å) Firczuk M, Wojciechowski M, Czapinska H, Bochtler M (2011) "DNA intercalation without flipping in the specific ThaI-DNA complex." Nucleic Acids Res., 39, 744-754. doi: 10.1093/nar/gkq834. Restriction endonuclease in complex with substrate DNA. SNAP output
3ndk transferase-DNA X-ray (2.0 Å) Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W (2011) "Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures." J.Mol.Biol., 406, 558-570. doi: 10.1016/j.jmb.2010.12.033. Rb69 DNA polymerase (y567a) ternary complex with dctp opposite dg. SNAP output
3ne6 transferase-DNA X-ray (2.001 Å) Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W (2011) "Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures." J.Mol.Biol., 406, 558-570. doi: 10.1016/j.jmb.2010.12.033. Rb69 DNA polymerase (s565g-y567a) ternary complex with dctp opposite dg. SNAP output
3ngd transferase-DNA X-ray (2.8 Å) Pence MG, Choi JY, Egli M, Guengerich FP (2010) "Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase {iota}." J.Biol.Chem., 285, 40666-40672. doi: 10.1074/jbc.M110.183665. Structural basis for proficient incorporation of dttp opposite o6-methylguanine by human DNA polymerase iota. SNAP output
3ngi transferase-DNA X-ray (1.886 Å) Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W (2011) "Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures." J.Mol.Biol., 406, 558-570. doi: 10.1016/j.jmb.2010.12.033. Rb69 DNA polymerase (y567a) ternary complex with dttp opposite dg. SNAP output
3ngo hydrolase-DNA X-ray (2.2 Å) Wang H, Morita M, Yang X, Suzuki T, Yang W, Wang J, Ito K, Wang Q, Zhao C, Bartlam M, Yamamoto T, Rao Z (2010) "Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity." Embo J. doi: 10.1038/emboj.2010.152. Crystal structure of the human cnot6l nuclease domain in complex with poly(a) DNA. SNAP output
3ngz hydrolase-DNA X-ray (2.1 Å) Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan HS (2011) "Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation." Nat.Chem.Biol., 7, 236-243. doi: 10.1038/nchembio.524. Crystal structure of rnase t in complex with a non-preferred ssDNA (gc) with one mg in the active site. SNAP output
3nh0 hydrolase-DNA X-ray (2.3 Å) Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan HS (2011) "Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation." Nat.Chem.Biol., 7, 236-243. doi: 10.1038/nchembio.524. Crystal structure of rnase t in complex with a non-preferred ssDNA (aac). SNAP output
3nh1 hydrolase-DNA X-ray (2.107 Å) Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan HS (2011) "Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation." Nat.Chem.Biol., 7, 236-243. doi: 10.1038/nchembio.524. Crystal structure of rnase t in complex with a preferred ssDNA (tagg) with two mg in the active site. SNAP output
3nh2 hydrolase-DNA X-ray (2.3 Å) Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan HS (2011) "Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation." Nat.Chem.Biol., 7, 236-243. doi: 10.1038/nchembio.524. Crystal structure of rnase t in complex with a stem DNA with a 3' overhang. SNAP output
3nhg transferase-DNA X-ray (2.5 Å) Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W (2011) "Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures." J.Mol.Biol., 406, 558-570. doi: 10.1016/j.jmb.2010.12.033. Rb69 DNA polymerase (s565g-y567a) ternary complex with dttp opposite dg. SNAP output
3nic hydrolase-DNA X-ray (2.8 Å) Mak AN, Lambert AR, Stoddard BL (2010) "Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI." Structure, 18, 1321-1331. doi: 10.1016/j.str.2010.07.006. DNA binding and cleavage by the giy-yig endonuclease r.eco29ki inactive variant y49f. SNAP output
3nm9 gene regulation-DNA X-ray (2.85 Å) Churchill ME, Klass J, Zoetewey DL (2010) "Structural analysis of HMGD-DNA complexes reveals influence of intercalation on sequence selectivity and DNA bending." J.Mol.Biol., 403, 88-102. doi: 10.1016/j.jmb.2010.08.031. Hmgd(m13a)-DNA complex. SNAP output
3o1m oxidoreductase X-ray (1.75 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1o oxidoreductase X-ray (1.92 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang C-G, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1p oxidoreductase X-ray (1.51 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1r oxidoreductase X-ray (1.77 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1s oxidoreductase X-ray (1.58 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1t oxidoreductase X-ray (1.48 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1u oxidoreductase X-ray (1.54 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o1v oxidoreductase X-ray (1.9 Å) Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase." Nature, 468, 330-333. doi: 10.1038/nature09497. Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase. SNAP output
3o3f hydrolase-DNA-RNA hybrid X-ray (2.0 Å) Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M (2010) "Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage." Mol.Cell, 40, 658-670. doi: 10.1016/j.molcel.2010.11.001. T. maritima rnase h2 d107n in complex with nucleic acid substrate and magnesium ions. SNAP output
3o3g hydrolase-DNA-RNA hybrid X-ray (2.1 Å) Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M (2010) "Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage." Mol.Cell, 40, 658-670. doi: 10.1016/j.molcel.2010.11.001. T. maritima rnase h2 in complex with nucleic acid substrate and calcium ions. SNAP output
3o3h hydrolase-DNA-RNA hybrid X-ray (2.8 Å) Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch RJ, Nowotny M (2010) "Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage." Mol.Cell, 40, 658-670. doi: 10.1016/j.molcel.2010.11.001. T. maritima rnase h2 d107n in complex with nucleic acid substrate and manganese ions. SNAP output
3o62 structural protein-DNA X-ray (3.216 Å) Todd RC, Lippard SJ (2010) "Consequences of Cisplatin binding on nucleosome structure and dynamics." Chem.Biol., 17, 1334-1343. doi: 10.1016/j.chembiol.2010.10.018. Nucleosome core particle modified with a cisplatin 1,3-cis-{pt(nh3)2}2+-d(gptpg) intrastrand cross-link. SNAP output
3o9x transcription regulator-DNA X-ray (2.1 Å) Brown BL, Wood TK, Peti W, Page R (2011) "Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation." J.Biol.Chem., 286, 2285-2296. doi: 10.1074/jbc.M110.172643. Structure of the e. coli antitoxin mqsa (ygit-b3021) in complex with its gene promoter. SNAP output
3oa6 DNA binding protein-DNA X-ray (2.35 Å) Kim D, Blus BJ, Chandra V, Huang P, Rastinejad F, Khorasanizadeh S (2010) "Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain." Nat.Struct.Mol.Biol., 17, 1027-1029. doi: 10.1038/nsmb.1856. Human msl3 chromodomain bound to DNA and h4k20me1 peptide. SNAP output
3od8 DNA binding protein-DNA X-ray (2.4 Å) Langelier MF, Planck JL, Roy S, Pascal JM (2011) "Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY." J.Biol.Chem., 286, 10690-10701. doi: 10.1074/jbc.M110.202507. Human parp-1 zinc finger 1 (zn1) bound to DNA. SNAP output
3oda DNA binding protein-DNA X-ray (2.64 Å) Langelier MF, Planck JL, Roy S, Pascal JM (2011) "Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY." J.Biol.Chem., 286, 10690-10701. doi: 10.1074/jbc.M110.202507. Human parp-1 zinc finger 1 (zn1) bound to DNA. SNAP output
3odc DNA binding protein-DNA X-ray (2.8 Å) Langelier MF, Planck JL, Roy S, Pascal JM (2011) "Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY." J.Biol.Chem., 286, 10690-10701. doi: 10.1074/jbc.M110.202507. Human parp-1 zinc finger 2 (zn2) bound to DNA. SNAP output
3ode DNA binding protein-DNA X-ray (2.95 Å) Langelier MF, Planck JL, Roy S, Pascal JM (2011) "Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY." J.Biol.Chem., 286, 10690-10701. doi: 10.1074/jbc.M110.202507. Human parp-1 zinc finger 2 (zn2) bound to DNA. SNAP output
3odh hydrolase-DNA X-ray (2.3 Å) Vanamee ES, Viadiu H, Chan SH, Ummat A, Hartline AM, Xu SY, Aggarwal AK (2011) "Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI." Nucleic Acids Res., 39, 712-719. doi: 10.1093/nar/gkq779. Structure of okrai-DNA complex. SNAP output
3ogd hydrolase-DNA X-ray (2.8 Å) Bowman BR, Lee S, Wang S, Verdine GL (2010) "Structure of Escherichia coli AlkA in Complex with Undamaged DNA." J.Biol.Chem., 285, 35783-35791. doi: 10.1074/jbc.M110.155663. Alka undamaged DNA complex: interrogation of a g*:c base pair. SNAP output
3ogu transferase-DNA X-ray (1.845 Å) Gieseking S, Bergen K, Di Pasquale F, Diederichs K, Welte W, Marx A (2011) "Human DNA polymerase beta mutations allowing efficient abasic site bypass." J.Biol.Chem., 286, 4011-4020. doi: 10.1074/jbc.M110.176826. DNA polymerase beta mutant 5p20 complexed with 6bp of DNA. SNAP output
3oh6 hydrolase-DNA X-ray (2.894 Å) Bowman BR, Lee S, Wang S, Verdine GL (2010) "Structure of Escherichia coli AlkA in Complex with Undamaged DNA." J.Biol.Chem., 285, 35783-35791. doi: 10.1074/jbc.M110.155663. Alka undamaged DNA complex: interrogation of a c:g base pair. SNAP output
3oh9 hydrolase-DNA X-ray (2.802 Å) Bowman BR, Lee S, Wang S, Verdine GL (2010) "Structure of Escherichia coli AlkA in Complex with Undamaged DNA." J.Biol.Chem., 285, 35783-35791. doi: 10.1074/jbc.M110.155663. Alka undamaged DNA complex: interrogation of a t:a base pair. SNAP output
3oha transferase-DNA X-ray (2.0 Å) Silverstein TD, Jain R, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2010) "Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta." Structure, 18, 1463-1470. doi: 10.1016/j.str.2010.08.019. Yeast DNA polymerase eta inserting dctp opposite an 8oxog lesion. SNAP output
3ohb transferase-DNA X-ray (2.0 Å) Silverstein TD, Jain R, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2010) "Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta." Structure, 18, 1463-1470. doi: 10.1016/j.str.2010.08.019. Yeast DNA polymerase eta extending from an 8-oxog lesion. SNAP output
3ojs transferase-DNA X-ray (1.9 Å) Obeid S, Baccaro A, Welte W, Diederichs K, Marx A (2010) "Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 21327-21331. doi: 10.1073/pnas.1013804107. Snapshots of the large fragment of DNA polymerase i from thermus aquaticus processing c5 modified thymidines. SNAP output
3oju transferase-DNA X-ray (2.0 Å) Obeid S, Baccaro A, Welte W, Diederichs K, Marx A (2010) "Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 21327-21331. doi: 10.1073/pnas.1013804107. Snapshot of the large fragment of DNA polymerase i from thermus aquaticus processing c5 modified thymidies. SNAP output
3on0 DNA binding protein-DNA X-ray (2.874 Å) Wong JJ, Lu J, Edwards RA, Frost LS, Glover JN (2011) "Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM." Nucleic Acids Res., 39, 6775-6788. doi: 10.1093/nar/gkr296. Crystal structure of the ped208 tram-sbma complex. SNAP output
3ool hydrolase-DNA X-ray (2.3 Å) Joshi R, Ho KK, Tenney K, Chen JH, Golden BL, Gimble FS (2011) "Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity." J.Mol.Biol., 405, 185-200. doi: 10.1016/j.jmb.2010.10.029. I-scei complexed with c-g+4 DNA substrate. SNAP output
3oor hydrolase-DNA X-ray (2.5 Å) Joshi R, Ho KK, Tenney K, Chen JH, Golden BL, Gimble FS (2011) "Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity." J.Mol.Biol., 405, 185-200. doi: 10.1016/j.jmb.2010.10.029. I-scei mutant (k86r-g100t)complexed with c-g+4 DNA substrate. SNAP output
3oqg hydrolase-DNA X-ray (1.75 Å) Sokolowska M, Czapinska H, Bochtler M (2011) "Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis." Nucleic Acids Res., 39, 1554-1564. doi: 10.1093/nar/gkq821. Restriction endonuclease hpy188i in complex with substrate DNA. SNAP output
3oqm transcription-transferase-DNA X-ray (2.96 Å) Schumacher MA, Sprehe M, Bartholomae M, Hillen W, Brennan RG (2011) "Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators." Nucleic Acids Res., 39, 2931-2942. doi: 10.1093/nar/gkq1177. Structure of ccpa-hpr-ser46p-acka2 complex. SNAP output
3oqn transcription-transferase-DNA X-ray (3.3 Å) Schumacher MA, Sprehe M, Bartholomae M, Hillen W, Brennan RG (2011) "Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators." Nucleic Acids Res., 39, 2931-2942. doi: 10.1093/nar/gkq1177. Structure of ccpa-hpr-ser46-p-gntr-down cre. SNAP output
3oqo transcription-transferase-DNA X-ray (2.97 Å) Schumacher MA, Sprehe M, Bartholomae M, Hillen W, Brennan RG (2011) "Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators." Nucleic Acids Res., 39, 2931-2942. doi: 10.1093/nar/gkq1177. Ccpa-hpr-ser46p-syn cre. SNAP output
3or3 hydrolase-DNA X-ray (1.95 Å) Sokolowska M, Czapinska H, Bochtler M (2011) "Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis." Nucleic Acids Res., 39, 1554-1564. doi: 10.1093/nar/gkq821. Restriction endonuclease hpy188i in complex with product DNA. SNAP output
3orc gene regulation-DNA X-ray (3.0 Å) Albright RA, Mossing MC, Matthews BW (1998) "Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein." Protein Sci., 7, 1485-1494. Crystal structure of an engineered cro monomer bound nonspecifically to DNA. SNAP output
3os0 recombination-DNA X-ray (2.81 Å) Maertens GN, Hare S, Cherepanov P (2010) "The mechanism of retroviral integration from X-ray structures of its key intermediates." Nature, 468, 326-329. doi: 10.1038/nature09517. Pfv strand transfer complex (stc) at 2.81 Å resolution. SNAP output
3os1 recombination-DNA X-ray (2.97 Å) Maertens GN, Hare S, Cherepanov P (2010) "The mechanism of retroviral integration from X-ray structures of its key intermediates." Nature, 468, 326-329. doi: 10.1038/nature09517. Pfv target capture complex (tcc) at 2.97 Å resolution. SNAP output
3os2 recombination-DNA X-ray (3.32 Å) Maertens GN, Hare S, Cherepanov P (2010) "The mechanism of retroviral integration from X-ray structures of its key intermediates." Nature, 468, 326-329. doi: 10.1038/nature09517. Pfv target capture complex (tcc) at 3.32 Å resolution. SNAP output
3osf transcription-DNA X-ray (2.032 Å) Jiang I, Tsai CK, Chen SC, Wang SH, Amiraslanov I, Chang CF, Wu WJ, Tai JH, Liaw YC, Huang TH (2011) "Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis." Nucleic Acids Res., 39, 8992-9008. doi: 10.1093/nar/gkr558. The structure of protozoan parasite trichomonas vaginalis myb2 in complex with mre-2f-13 DNA. SNAP output
3osg transcription-DNA X-ray (1.997 Å) Jiang I, Tsai CK, Chen SC, Wang SH, Amiraslanov I, Chang CF, Wu WJ, Tai JH, Liaw YC, Huang TH (2011) "Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis." Nucleic Acids Res., 39, 8992-9008. doi: 10.1093/nar/gkr558. The structure of protozoan parasite trichomonas vaginalis myb2 in complex with mre-1-12 DNA. SNAP output
3osn transferase-DNA X-ray (1.9 Å) Pence MG, Choi JY, Egli M, Guengerich FP (2010) "Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase {iota}." J.Biol.Chem., 285, 40666-40672. doi: 10.1074/jbc.M110.183665. Structural basis for proficient incorporation of dttp opposite o6-methylguanine by human DNA polymerase iota. SNAP output
3osp transferase-DNA X-ray (2.5 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2011) "DNA synthesis across an abasic lesion by yeast REV1 DNA polymerase." J.Mol.Biol., 406, 18-28. doi: 10.1016/j.jmb.2010.12.016. Structure of rev1. SNAP output
3oy9 recombination,viral protein-DNA X-ray (2.55 Å) Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P (2010) "Retroviral intasome assembly and inhibition of DNA strand transfer." Nature, 464, 232-236. doi: 10.1038/nature08784. Crystal structure of the prototype foamy virus (pfv) intasome in complex with manganese at 2.55 resolution. SNAP output
3oya recombination,viral protein-DNA X-ray (2.65 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and raltegravir at 2.65 resolution. SNAP output
3oyb recombination,viral protein-DNA X-ray (2.54 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti mk2048. SNAP output
3oyc recombination,viral protein-DNA X-ray (2.66 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti pica. SNAP output
3oyd recombination,viral protein-DNA X-ray (2.54 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti gs9160. SNAP output
3oye recombination,viral protein-DNA X-ray (2.74 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti compound2. SNAP output
3oyf recombination,viral protein-DNA X-ray (2.51 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti l-870,810. SNAP output
3oyg recombination,viral protein-DNA X-ray (2.56 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti compound1 (compoundg). SNAP output
3oyh recombination,viral protein-DNA X-ray (2.74 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti mk0536. SNAP output
3oyi recombination,viral protein-DNA X-ray (2.72 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the pfv s217q mutant intasome in complex with manganese. SNAP output
3oyj recombination,viral protein-DNA X-ray (2.68 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the pfv s217q mutant intasome in complex with magnesium and the insti mk2048. SNAP output
3oyk recombination,viral protein-DNA X-ray (2.72 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the pfv s217h mutant intasome bound to manganese. SNAP output
3oyl recombination,viral protein-DNA X-ray (2.54 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the pfv s217h mutant intasome bound to magnesium and the insti mk2048. SNAP output
3oym recombination,viral protein-DNA X-ray (2.02 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the pfv n224h mutant intasome bound to manganese. SNAP output
3oyn recombination,viral protein-DNA X-ray (2.68 Å) Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P (2010) "Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance." Proc.Natl.Acad.Sci.USA, 107, 20057-20062. doi: 10.1073/pnas.1010246107. Crystal structure of the pfv n224h mutant intasome bound to magnesium and the insti mk2048. SNAP output
3p57 transferase-transcription activator-DNA X-ray (2.19 Å) He J, Ye J, Cai Y, Riquelme C, Liu JO, Liu X, Han A, Chen L (2011) "Structure of p300 bound to MEF2 on DNA reveals a mechanism of enhanceosome assembly." Nucleic Acids Res., 39, 4464-4474. doi: 10.1093/nar/gkr030. Crystal structure of the p300 taz2 domain bound to mef2 on DNA. SNAP output
3p6y RNA binding protein-RNA X-ray (2.9 Å) Li H, Tong S, Li X, Shi H, Gao Y, Ge H, Niu L, Teng M "Structural basis of pre-mRNA recognition by the human cleavage factor Im complex." Cf im25-cf im68-uguaa complex. SNAP output
3pih hydrolase-DNA X-ray (2.9 Å) Jaciuk M, Nowak E, Skowronek K, Tanska A, Nowotny M (2011) "Structure of UvrA nucleotide excision repair protein in complex with modified DNA." Nat.Struct.Mol.Biol., 18, 191-197. doi: 10.1038/nsmb.1973. T. maritima uvra in complex with fluorescein-modified DNA. SNAP output
3pjr hydrolase-DNA X-ray (3.3 Å) Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB (1999) "Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism." Cell(Cambridge,Mass.), 97, 75-98. doi: 10.1016/S0092-8674(00)80716-3. Helicase substrate complex. SNAP output
3pky transferase-DNA X-ray (3.1 Å) Brissett NC, Martin MJ, Pitcher RS, Bianchi J, Juarez R, Green AJ, Fox GC, Blanco L, Doherty AJ (2011) "Structure of a Preternary Complex Involving a Prokaryotic NHEJ DNA Polymerase." Mol.Cell, 41, 221-231. doi: 10.1016/j.molcel.2010.12.026. Polymerase domain from mycobacterium tuberculosis ligase d in complex with DNA, utp and manganese.. SNAP output
3pml lyase,transferase-DNA X-ray (2.6 Å) Bebenek K, Pedersen LC, Kunkel TA (2011) "Replication infidelity via a mismatch with Watson-Crick geometry." Proc.Natl.Acad.Sci.USA, 108, 1862-1867. doi: 10.1073/pnas.1012825108. Crystal structure of a polymerase lambda variant with a dgtp analog opposite a templating t. SNAP output
3pmn lyase,transferase-DNA X-ray (2.2 Å) Bebenek K, Pedersen LC, Kunkel TA (2011) "Replication infidelity via a mismatch with Watson-Crick geometry." Proc.Natl.Acad.Sci.USA, 108, 1862-1867. doi: 10.1073/pnas.1012825108. Ternary crystal structure of polymerase lambda variant with a gt mispair at the primer terminus with mn2+ in the active site. SNAP output
3pnc lyase,transferase-DNA X-ray (2.0 Å) Bebenek K, Pedersen LC, Kunkel TA (2011) "Replication infidelity via a mismatch with Watson-Crick geometry." Proc.Natl.Acad.Sci.USA, 108, 1862-1867. doi: 10.1073/pnas.1012825108. Ternary crystal structure of a polymerase lambda variant with a gt mispair at the primer terminus and sodium at catalytic metal site. SNAP output
3po2 transferase-DNA-RNA X-ray (3.3 Å) Cheung AC, Cramer P (2011) "Structural basis of RNA polymerase II backtracking, arrest and reactivation." Nature, 471, 249-253. doi: 10.1038/nature09785. Arrested RNA polymerase ii elongation complex. SNAP output
3po3 transferase-DNA-RNA X-ray (3.3 Å) Cheung AC, Cramer P (2011) "Structural basis of RNA polymerase II backtracking, arrest and reactivation." Nature, 471, 249-253. doi: 10.1038/nature09785. Arrested RNA polymerase ii reactivation intermediate. SNAP output
3po4 transferase-DNA X-ray (1.8 Å) Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A (2011) "Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity." Chembiochem, 12, 1574-1580. doi: 10.1002/cbic.201000783. Structure of a mutant of the large fragment of DNA polymerase i from thermus aquaticus in complex with a blunt-ended DNA and ddatp. SNAP output
3po5 transferase-DNA X-ray (2.39 Å) Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A (2011) "Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity." Chembiochem, 12, 1574-1580. doi: 10.1002/cbic.201000783. Structure of a mutant of the large fragment of DNA polymerase i from thermus auqaticus in complex with an abasic site and ddatp. SNAP output
3pov DNA binding protein-DNA X-ray (2.5 Å) Bagneris C, Briggs LC, Savva R, Ebrahimi B, Barrett TE (2011) "Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff." Nucleic Acids Res., 39, 5744-5756. doi: 10.1093/nar/gkr111. Crystal structure of a sox-DNA complex. SNAP output
3pr4 transferase-DNA X-ray (2.65 Å) Kirouac KN, Suo Z, Ling H (2011) "Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase." J.Mol.Biol., 407, 382-390. doi: 10.1016/j.jmb.2011.01.037. Dpo4 y12a mutant incorporating dadp opposite template dt. SNAP output
3pr5 transferase-DNA X-ray (2.4 Å) Kirouac KN, Suo Z, Ling H (2011) "Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase." J.Mol.Biol., 407, 382-390. doi: 10.1016/j.jmb.2011.01.037. Dpo4 y12a mutant incorporating adp opposite template dt. SNAP output
3pt6 transferase-DNA X-ray (3.0 Å) Song J, Rechkoblit O, Bestor TH, Patel DJ (2011) "Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation." Science, 331, 1036-1040. doi: 10.1126/science.1195380. Crystal structure of mouse dnmt1(650-1602) in complex with DNA. SNAP output
3pta transferase-DNA X-ray (3.6 Å) Song J, Rechkoblit O, Bestor TH, Patel DJ (2011) "Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation." Science, 331, 1036-1040. doi: 10.1126/science.1195380. Crystal structure of human dnmt1(646-1600) in complex with DNA. SNAP output
3pv8 transferase-DNA X-ray (1.52 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and ddttp-da in closed conformation. SNAP output
3pvi hydrolase-DNA X-ray (1.59 Å) Horton JR, Nastri HG, Riggs PD, Cheng X (1998) "Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis." J.Mol.Biol., 284, 1491-1504. doi: 10.1006/jmbi.1998.2269. D34g mutant of pvuii endonuclease complexed with cognate DNA shows that asp34 is directly involved in DNA recognition and indirectly involved in catalysis. SNAP output
3pvp DNA binding protein-DNA X-ray (2.3 Å) Tsodikov OV, Biswas T (2011) "Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA." J.Mol.Biol., 410, 461-476. doi: 10.1016/j.jmb.2011.05.007. Structure of mycobacterium tuberculosis dnaa-dbd in complex with box2 DNA. SNAP output
3pvv DNA binding protein-DNA X-ray (2.0 Å) Tsodikov OV, Biswas T (2011) "Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA." J.Mol.Biol., 410, 461-476. doi: 10.1016/j.jmb.2011.05.007. Structure of mycobacterium tuberculosis dnaa-dbd in complex with box1 DNA. SNAP output
3pvx transferase-DNA X-ray (3.03 Å) Banerjee S, Brown KL, Egli M, Stone MP (2011) "Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV." J.Am.Chem.Soc., 133, 12556-12568. doi: 10.1021/ja2015668. Binary complex of aflatoxin b1 adduct modified DNA (afb1-fapy) with DNA polymerase iv. SNAP output
3pw0 transferase-DNA X-ray (2.91 Å) Banerjee S, Brown KL, Egli M, Stone MP (2011) "Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV." J.Am.Chem.Soc., 133, 12556-12568. doi: 10.1021/ja2015668. Ternary complex of aflatoxin b1 adduct modified DNA (afb1-fapy) with DNA polymerase iv and incoming datp. SNAP output
3pw2 transferase-DNA X-ray (2.74 Å) Banerjee S, Brown KL, Egli M, Stone MP (2011) "Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV." J.Am.Chem.Soc., 133, 12556-12568. doi: 10.1021/ja2015668. Ternary complex of aflatoxin b1 adduct modified DNA (afb1-fapy) with DNA polymerase iv and incoming dttp. SNAP output
3pw4 transferase-DNA X-ray (2.9 Å) Banerjee S, Brown KL, Egli M, Stone MP (2011) "Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV." J.Am.Chem.Soc., 133, 12556-12568. doi: 10.1021/ja2015668. Ternary complex of aflatoxin b1 adduct modified DNA (afb1-n7-gua) with DNA polymerase iv and incoming datp. SNAP output
3pw5 transferase-DNA X-ray (3.0 Å) Banerjee S, Brown KL, Egli M, Stone MP (2011) "Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV." J.Am.Chem.Soc., 133, 12556-12568. doi: 10.1021/ja2015668. Ternary complex of aflatoxin b1 adduct modified DNA (afb1-n7-gua) with DNA polymerase iv and incoming dttp. SNAP output
3pw7 transferase-DNA X-ray (2.9 Å) Banerjee S, Brown KL, Egli M, Stone MP (2011) "Bypass of Aflatoxin B(1) Adducts by the Sulfolobus solfataricus DNA Polymerase IV." J.Am.Chem.Soc., 133, 12556-12568. doi: 10.1021/ja2015668. Ternary complex of aflatoxin b1 adduct modified DNA (afb1-n7-gua) with DNA polymerase iv and incoming dctp. SNAP output
3px0 transferase-DNA X-ray (1.73 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and dctp-da mismatch (tautomer) in closed conformation. SNAP output
3px4 transferase-DNA X-ray (1.582 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and ddctp-da mismatch (wobble) in ajar conformation. SNAP output
3px6 transferase-DNA X-ray (1.59 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and ddctp-da mismatch (tautomer) in closed conformation. SNAP output
3px7 isomerase-DNA X-ray (2.3 Å) Tse-Dinh YC, Zhang Z, Cheng B "Structure of E. coli Topoisomerase I Trapped as Covalent Complex Intermediate with Cleaved DNA." Crystal structure of covalent complex of topoisomerase 1a with substrate. SNAP output
3py8 transferase-DNA X-ray (1.74 Å) Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W, Diederichs K, Marx A (2011) "Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity." Chembiochem, 12, 1574-1580. doi: 10.1002/cbic.201000783. Crystal structure of a mutant of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with DNA and ddctp. SNAP output
3pzp transferase-DNA X-ray (3.336 Å) Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2011) "Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer." J.Mol.Biol., 408, 252-261. doi: 10.1016/j.jmb.2011.02.042. Human DNA polymerase kappa extending opposite a cis-syn thymine dimer. SNAP output
3q05 antitumor protein-DNA X-ray (2.4 Å) Petty TJ, Emamzadah S, Costantino L, Petkova I, Stavridi ES, Saven JG, Vauthey E, Halazonetis TD (2011) "An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity." Embo J., 30, 2167-2176. doi: 10.1038/emboj.2011.127. An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity. SNAP output
3q06 cell cycle-DNA X-ray (3.2 Å) Petty TJ, Emamzadah S, Costantino L, Petkova I, Stavridi ES, Saven JG, Vauthey E, Halazonetis TD (2011) "An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity." Embo J., 30, 2167-2176. doi: 10.1038/emboj.2011.127. An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity. SNAP output
3q0a transcription-DNA X-ray (2.69 Å) Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS (2011) "X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides." Proc.Natl.Acad.Sci.USA, 108, 3566-3571. doi: 10.1073/pnas.1016691108. X-ray crystal structure of the transcription initiation complex of the n4 mini-vrnap with p2 promoter: mismatch complex. SNAP output
3q0b transferase-DNA X-ray (2.2 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra- fully methylated cg DNA complex in space group p42212. SNAP output
3q0c transferase-DNA X-ray (2.66 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra-fully methylated cg DNA complex in space group p6122. SNAP output
3q0d transferase-DNA X-ray (2.37 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra- hemi methylated cg DNA complex. SNAP output
3q0f transferase-DNA X-ray (2.75 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra- methylated chh DNA complex. SNAP output
3q1m transcription-DNA X-ray (3.2 Å) Bachas S, Eginton C, Gunio D, Wade H (2011) "Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR." Proc.Natl.Acad.Sci.USA, 108, 11046-11051. doi: 10.1073/pnas.1104850108. Crystal structure of bmrr dimer bound to DNA and the ligand 4-amino-quinaldine. SNAP output
3q1q hydrolase-RNA X-ray (3.8 Å) Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A (2010) "Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA." Nature, 468, 784-789. doi: 10.1038/NATURE09516. Structure of a bacterial ribonuclease p holoenzyme in complex with trna. SNAP output
3q1r hydrolase-RNA X-ray (4.21 Å) Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A (2010) "Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA." Nature, 468, 784-789. doi: 10.1038/NATURE09516. Crystal structure of a bacterial rnase p holoenzyme in complex with trna and in the presence of 5' leader. SNAP output
3q22 transferase-DNA X-ray (2.11 Å) Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS (2011) "X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides." Proc.Natl.Acad.Sci.USA, 108, 3566-3571. doi: 10.1073/pnas.1016691108. X-ray crystal structure of the n4 mini-vrnap and p2_7a promoter transcription initiation complex with gtp and magnesium: substrate complex i. SNAP output
3q23 transferase-DNA X-ray (1.8 Å) Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS (2011) "X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides." Proc.Natl.Acad.Sci.USA, 108, 3566-3571. doi: 10.1073/pnas.1016691108. X-ray crystal structure of the n4 mini-vrnap and p2_7a promoter transcription initiation complex with gmpcpp and manganese: sustrate complex ii. SNAP output
3q24 transferase-DNA-RNA X-ray (1.81 Å) Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS (2011) "X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides." Proc.Natl.Acad.Sci.USA, 108, 3566-3571. doi: 10.1073/pnas.1016691108. X-ray crystal structure of the n4 mini-vrnap and p2_7a promoter transcription initiation complex with pppgpg and pyrophosphate: product complex. SNAP output
3q2y transcription-DNA X-ray (2.95 Å) Bachas S, Eginton C, Gunio D, Wade H (2011) "Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR." Proc.Natl.Acad.Sci.USA, 108, 11046-11051. doi: 10.1073/pnas.1104850108. Crystal structure of bmrr bound to ethidium. SNAP output
3q3d transcription regulator-DNA-antibiotic X-ray (2.79 Å) Bachas S, Eginton C, Gunio D, Wade H (2011) "Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR." Proc.Natl.Acad.Sci.USA, 108, 11046-11051. doi: 10.1073/pnas.1104850108. Crystal structure of bmrr bound to puromycin. SNAP output
3q5f transcription-DNA X-ray (2.96 Å) Dolan KT, Duguid EM, He C (2011) "Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States." J.Biol.Chem., 286, 22178-22185. doi: 10.1074/jbc.M111.245258. Crystal structure of the salmonella transcriptional regulator slya in complex with DNA. SNAP output
3q5p transcription-DNA-antibiotic X-ray (2.942 Å) Bachas S, Eginton C, Gunio D, Wade H (2011) "Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR." Proc.Natl.Acad.Sci.USA, 108, 11046-11051. doi: 10.1073/pnas.1104850108. Crystal structure of bmrr bound to tetracycline. SNAP output
3q5r transcription-RNA-antibiotic X-ray (3.05 Å) Bachas S, Eginton C, Gunio D, Wade H (2011) "Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR." Proc.Natl.Acad.Sci.USA, 108, 11046-11051. doi: 10.1073/pnas.1104850108. Crystal structure of bmrr bound to kanamycin. SNAP output
3q5s transcription-DNA X-ray (3.1 Å) Bachas S, Eginton C, Gunio D, Wade H (2011) "Structural contributions to multidrug recognition in the multidrug resistance (MDR) gene regulator, BmrR." Proc.Natl.Acad.Sci.USA, 108, 11046-11051. doi: 10.1073/pnas.1104850108. Crystal structure of bmrr bound to acetylcholine. SNAP output
3q8k hydrolase-DNA X-ray (2.2 Å) Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, Tainer JA (2011) "Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily." Cell(Cambridge,Mass.), 145, 198-211. doi: 10.1016/j.cell.2011.03.004. Crystal structure of human flap endonuclease fen1 (wt) in complex with product 5'-flap DNA, sm3+, and k+. SNAP output
3q8l hydrolase-DNA X-ray (2.319 Å) Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, Tainer JA (2011) "Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily." Cell(Cambridge,Mass.), 145, 198-211. doi: 10.1016/j.cell.2011.03.004. Crystal structure of human flap endonuclease fen1 (wt) in complex with substrate 5'-flap DNA, sm3+, and k+. SNAP output
3q8m hydrolase-DNA X-ray (2.6 Å) Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, Tainer JA (2011) "Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily." Cell(Cambridge,Mass.), 145, 198-211. doi: 10.1016/j.cell.2011.03.004. Crystal structure of human flap endonuclease fen1 (d181a) in complex with substrate 5'-flap DNA and k+. SNAP output
3q8p transferase-DNA X-ray (1.95 Å) Kirouac KN, Ling H (2011) "Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota." Proc.Natl.Acad.Sci.USA, 108, 3210-3215. doi: 10.1073/pnas.1013909108. Human DNA polymerase iota incorporating dctp opposite 8-oxo-guanine. SNAP output
3q8q transferase-DNA X-ray (2.031 Å) Kirouac KN, Ling H (2011) "Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota." Proc.Natl.Acad.Sci.USA, 108, 3210-3215. doi: 10.1073/pnas.1013909108. Human DNA polymerase iota incorporating datp opposite 8-oxo-guanine. SNAP output
3q8r transferase-DNA X-ray (2.45 Å) Kirouac KN, Ling H (2011) "Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota." Proc.Natl.Acad.Sci.USA, 108, 3210-3215. doi: 10.1073/pnas.1013909108. Human DNA polymerase iota incorporating dgtp opposite 8-oxo-guanine. SNAP output
3q8s transferase-DNA X-ray (2.09 Å) Kirouac KN, Ling H "Human DNA polymerase iota incorporating dTTP opposite 8-oxo-guanine." Human DNA polymerase iota incorporating dttp opposite 8-oxo-guanine. SNAP output
3qe9 hydrolase-DNA X-ray (2.51 Å) Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS (2011) "Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family." Cell(Cambridge,Mass.), 145, 212-223. doi: 10.1016/j.cell.2011.03.005. Crystal structure of human exonuclease 1 exo1 (d173a) in complex with DNA (complex i). SNAP output
3qea hydrolase-DNA X-ray (3.1 Å) Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS (2011) "Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family." Cell(Cambridge,Mass.), 145, 212-223. doi: 10.1016/j.cell.2011.03.005. Crystal structure of human exonuclease 1 exo1 (wt) in complex with DNA (complex ii). SNAP output
3qeb hydrolase-DNA X-ray (3.0 Å) Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS (2011) "Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family." Cell(Cambridge,Mass.), 145, 212-223. doi: 10.1016/j.cell.2011.03.005. Crystal structure of human exonuclease 1 exo1 (wt) in complex with DNA and mn2+ (complex iii). SNAP output
3qei transferase-DNA X-ray (2.178 Å) Xia S, Eom SH, Konigsberg WH, Wang J (2012) "Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue." Biochemistry, 51, 1476-1485. doi: 10.1021/bi2016487. Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dctp opposite difluorotoluene nucleoside. SNAP output
3qep transferase-DNA X-ray (1.8 Å) Xia S, Konigsberg WH, Wang J (2011) "Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex." J.Am.Chem.Soc., 133, 10003-10005. doi: 10.1021/ja2021735. Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dttp opposite difluorotoluene nucleoside. SNAP output
3qer transferase-DNA X-ray (1.96 Å) Xia S, Eom SH, Konigsberg WH, Wang J (2012) "Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue." Biochemistry, 51, 1476-1485. doi: 10.1021/bi2016487. Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with datp opposite difluorotoluene nucleoside. SNAP output
3qes transferase-DNA X-ray (1.98 Å) Xia S, Eom SH, Konigsberg WH, Wang J (2012) "Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue." Biochemistry, 51, 1476-1485. doi: 10.1021/bi2016487. Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dgtp opposite difluorotoluene nucleoside. SNAP output
3qet transferase-DNA X-ray (2.08 Å) Xia S, Konigsberg WH, Wang J "Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes." Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dttp opposite dt. SNAP output
3qev transferase-DNA X-ray (1.77 Å) Xia S, Konigsberg WH, Wang J "Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes." Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dctp opposite dt. SNAP output
3qew transferase-DNA X-ray (1.84 Å) Xia S, Konigsberg WH, Wang J "Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes." Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with ddtp opposite dt. SNAP output
3qex transferase-DNA X-ray (1.73 Å) Xia S, Konigsberg WH, Wang J "Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes." Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dgtp opposite dt. SNAP output
3qfq DNA binding protein-DNA X-ray (2.9 Å) Harrison CJ, Meinke G, Kwun HJ, Rogalin H, Phelan PJ, Bullock PA, Chang Y, Moore PS, Bohm A (2011) "Asymmetric assembly of merkel cell polyomavirus large T-antigen origin binding domains at the viral origin." J.Mol.Biol., 409, 529-542. doi: 10.1016/j.jmb.2011.03.051. Asymmetric assembly of merkel cell polyomavirus large t-antigen origin binding domains at the viral origin. SNAP output
3qi5 hydrolase-DNA X-ray (2.2 Å) Lingaraju GM, Davis CA, Setser JW, Samson LD, Drennan CL (2011) "Structural Basis for the Inhibition of Human Alkyladenine DNA Glycosylase (AAG) by 3,N4-Ethenocytosine-containing DNA." J.Biol.Chem., 286, 13205-13213. doi: 10.1074/jbc.M110.192435. Crystal structure of human alkyladenine DNA glycosylase in complex with 3,n4-ethenocystosine containing duplex DNA. SNAP output
3qlp hydrolase-hydrolase inhibitor-DNA X-ray (2.14 Å) Russo Krauss I, Merlino A, Giancola C, Randazzo A, Mazzarella L, Sica F (2011) "Thrombin-aptamer recognition: a revealed ambiguity." Nucleic Acids Res., 39, 7858-7867. doi: 10.1093/nar/gkr522. X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mtba). SNAP output
3qmb DNA binding protein-DNA X-ray (2.06 Å) Xu C, Bian C, Lam R, Dong A, Min J (2011) "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain." Nat Commun, 2, 227. doi: 10.1038/ncomms1237. Structural basis of selective binding of nonmethylated cpg islands by the cxxc domain of cfp1. SNAP output
3qmc DNA binding protein-DNA X-ray (2.1 Å) Xu C, Bian C, Lam R, Dong A, Min J (2011) "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain." Nat Commun, 2, 227. doi: 10.1038/ncomms1237. Structural basis of selective binding of nonmethylated cpg islands by the cxxc domain of cfp1. SNAP output
3qmd DNA binding protein-DNA X-ray (1.9 Å) Xu C, Bian C, Lam R, Dong A, Min J (2011) "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain." Nat Commun, 2, 227. doi: 10.1038/ncomms1237. Structural basis of selective binding of nonmethylated cpg islands by the cxxc domain of cfp1. SNAP output
3qmg DNA binding protein-DNA X-ray (2.3 Å) Xu C, Bian C, Lam R, Dong A, Min J (2011) "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain." Nat Commun, 2, 227. doi: 10.1038/ncomms1237. Structural basis of selective binding of non-methylated cpg islands by the cxxc domain of cfp1. SNAP output
3qmh DNA binding protein-DNA X-ray (2.5 Å) Xu C, Bian C, Lam R, Dong A, Min J (2011) "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain." Nat Commun, 2, 227. doi: 10.1038/ncomms1237. Structural basis of selective binding of non-methylated cpg islands (DNA-tcga) by the cxxc domain of cfp1. SNAP output
3qmi DNA binding protein-DNA X-ray (2.1 Å) Xu C, Bian C, Lam R, Dong A, Min J (2011) "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain." Nat Commun, 2, 227. doi: 10.1038/ncomms1237. Structural basis of selective binding of non-methylated cpg islands (DNA-acgt) by the cxxc domain of cfp1. SNAP output
3qnn transferase-DNA X-ray (1.92 Å) Xia S, Beckman J, Wang J, Konigsberg WH (2012) "Using a Fluorescent Cytosine Analogue tC(o) To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase." Biochemistry, 51, 4609-4617. doi: 10.1021/bi300241m. Rb69 DNA polymerase (y567a) ternary complex with dgt opposite 3tco. SNAP output
3qno transferase-DNA X-ray (1.88 Å) Xia S, Beckman J, Wang J, Konigsberg WH (2012) "Using a Fluorescent Cytosine Analogue tC(o) To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase." Biochemistry, 51, 4609-4617. doi: 10.1021/bi300241m. Rb69 DNA polymerase (y567a) ternary complex with datp opposite 3tco. SNAP output
3qoq transcription-DNA X-ray (3.1 Å) Pryor Jr EE, Waligora EA, Xu B, Dellos-Nolan S, Wozniak DJ, Hollis T (2012) "The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes." Plos Pathog., 8, e1002648. doi: 10.1371/journal.ppat.1002648. Crystal structure of the transcription factor amrz in complex with the 18 base pair amrz1 binding site. SNAP output
3qqy hydrolase-DNA X-ray (2.401 Å) Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL (2011) "Tapping natural reservoirs of homing endonucleases for targeted gene modification." Proc.Natl.Acad.Sci.USA, 108, 13077-13082. doi: 10.1073/pnas.1107719108. Crystal structure of a novel laglidadg homing endonuclease, i-onui (from ophiostoma novo-ulmi subsp. americana). SNAP output
3qrf DNA binding protein-DNA X-ray (2.8 Å) Bandukwala HS, Wu Y, Feuerer M, Chen Y, Barboza B, Ghosh S, Stroud JC, Benoist C, Mathis D, Rao A, Chen L (2011) "Structure of a Domain-Swapped FOXP3 Dimer on DNA and Its Function in Regulatory T Cells." Immunity, 34, 479-491. doi: 10.1016/j.immuni.2011.02.017. Structure of a domain-swapped foxp3 dimer. SNAP output
3qsv transcription-DNA X-ray (2.708 Å) Baburajendran N, Jauch R, Zhen CTY, Kolatkar PR "Structural basis for DNA recognition by constitutive Smad4 MH1 dimers." Structural basis for DNA recognition by constitutive smad4 mh1 dimers. SNAP output
3qx3 isomerase-DNA-isomerase inhibitor X-ray (2.162 Å) Wu CC, Li TK, Farh L, Lin LY, Lin TS, Yu YJ, Yen TJ, Chiang CW, Chan NL (2011) "Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide." Science, 333, 459-462. doi: 10.1126/science.1204117. Human topoisomerase iibeta in complex with DNA and etoposide. SNAP output
3qym transcription activator-DNA X-ray (3.2 Å) Chen C, Gorlatova N, Kelman Z, Herzberg O (2011) "Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements." Proc.Natl.Acad.Sci.USA, 108, 6456-6461. doi: 10.1073/pnas.1013657108. Structure of p63 DNA binding domain in complex with a 10 base pair a-t rich response element half site. SNAP output
3qyn transcription activator-DNA X-ray (2.5 Å) Chen C, Gorlatova N, Kelman Z, Herzberg O (2011) "Structures of p63 DNA binding domain in complexes with half-site and with spacer-containing full response elements." Proc.Natl.Acad.Sci.USA, 108, 6456-6461. doi: 10.1073/pnas.1013657108. Structure of p63 DNA binding domain in complex with a 22 base pair a-t rich response element containing 2 base pair spacer between half sites. SNAP output
3qyx transcription-DNA X-ray (3.75 Å) Blasco B, Stenta M, Alonso-Sarduy L, Dietler G, Peraro MD, Cole ST, Pojer F (2011) "Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis." Mol.Microbiol., 82, 251-264. doi: 10.1111/j.1365-2958.2011.07813.x. Crystal structure of mycobacterium tuberculosis espr in complex with a small DNA fragment. SNAP output
3qz7 transferase-DNA X-ray (1.998 Å) Wu Y, Wilson RC, Pata JD (2011) "The y-family DNA polymerase dpo4 uses a template slippage mechanism to create single-base deletions." J.Bacteriol., 193, 2630-2636. doi: 10.1128/JB.00012-11. T-3 ternary complex of dpo4. SNAP output
3qz8 transferase-DNA X-ray (1.999 Å) Wu Y, Wilson RC, Pata JD (2011) "The y-family DNA polymerase dpo4 uses a template slippage mechanism to create single-base deletions." J.Bacteriol., 193, 2630-2636. doi: 10.1128/JB.00012-11. Tt-4 ternary complex of dpo4. SNAP output
3r7p hydrolase-DNA X-ray (2.704 Å) Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL (2011) "Tapping natural reservoirs of homing endonucleases for targeted gene modification." Proc.Natl.Acad.Sci.USA, 108, 13077-13082. doi: 10.1073/pnas.1107719108. The crystal structure of i-ltri. SNAP output
3r8f replication activator-DNA X-ray (3.366 Å) Duderstadt KE, Chuang K, Berger JM (2011) "DNA stretching by bacterial initiators promotes replication origin opening." Nature, 478, 209-213. doi: 10.1038/nature10455. Replication initiator dnaa bound to amppcp and single-stranded DNA. SNAP output
3ra0 DNA binding protein-DNA X-ray (2.451 Å) Cappadocia L, Parent JS, Zampini E, Lepage E, Sygusch J, Brisson N (2012) "A conserved lysine residue of plant Whirly proteins is necessary for higher order protein assembly and protection against DNA damage." Nucleic Acids Res., 40, 258-269. doi: 10.1093/nar/gkr740. Crystal structure of a stwhy2 k67a-dt32 complex. SNAP output
3ra4 virus X-ray (2.7 Å) Nam HJ, Gurda BL, McKenna R, Potter M, Byrne B, Salganik M, Muzyczka N, Agbandje-McKenna M (2011) "Structural studies of adeno-associated virus serotype 8 capsid transitions associated with endosomal trafficking." J.Virol., 85, 11791-11799. doi: 10.1128/JVI.05305-11. Structural studies of aav8 capsid transitions associated with endosomal trafficking. SNAP output
3ra9 virus X-ray (2.7 Å) Nam HJ, Gurda BL, McKenna R, Potter M, Byrne B, Salganik M, Muzyczka N, Agbandje-McKenna M (2011) "Structural studies of adeno-associated virus serotype 8 capsid transitions associated with endosomal trafficking." J.Virol., 85, 11791-11799. doi: 10.1128/JVI.05305-11. Structural studies of aav8 capsid transitions associated with endosomal trafficking. SNAP output
3rad isomerase-DNA-antibiotic X-ray (3.35 Å) Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR (2016) "Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones." Open Biol, 6. doi: 10.1098/rsob.160157. Quinolone(clinafloxacin)-DNA cleavage complex of type iv topoisomerase from s. pneumoniae. SNAP output
3rae isomerase-DNA-antibiotic X-ray (2.9 Å) Veselkov DA, Laponogov I, Pan XS, Selvarajah J, Skamrova GB, Branstrom A, Narasimhan J, Prasad JV, Fisher LM, Sanderson MR (2016) "Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex." Acta Crystallogr.,Sect.D, 72, 488-496. doi: 10.1107/S2059798316001212. Quinolone(levofloxacin)-DNA cleavage complex of type iv topoisomerase from s. pneumoniae. SNAP output
3raf isomerase-DNA-antibiotic X-ray (3.24 Å) Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher LM, Sanderson MR "Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions." Quinazolinedione-DNA cleavage complex of type iv topoisomerase from s. pneumoniae. SNAP output
3raq transferase-DNA X-ray (2.25 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer c base opposite the 1-methylguanine (mg1) lesion. SNAP output
3rax transferase-DNA X-ray (1.891 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer t base opposite the 1-methylguanine (m1g) lesion. SNAP output
3rb0 transferase-DNA X-ray (3.225 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer g base opposite the 1-methylguanine (m1g) lesion. SNAP output
3rb3 transferase-DNA X-ray (2.8 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer a base opposite the 1-methylguanine (m1g) lesion. SNAP output
3rb4 transferase-DNA X-ray (2.805 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer g base opposite the 3-methylcytosine (m3c) lesion. SNAP output
3rb6 transferase-DNA X-ray (2.7 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer a base opposite the 3-methylcytosine (m3c) lesion. SNAP output
3rbd transferase-DNA X-ray (2.502 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer c base opposite the 3-methylcytosine (m3c) lesion. SNAP output
3rbe transferase-DNA X-ray (2.8 Å) Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ (2011) "Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions." Structure, 19, 821-832. doi: 10.1016/j.str.2011.03.020. Dpo4 extension ternary complex with 3'-terminal primer t base opposite the 3-methylcytosine (m3c) lesion. SNAP output
3reh structural protein-DNA X-ray (2.5 Å) Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA (2011) "Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation." Nucleic Acids Res., 39, 8200-8212. doi: 10.1093/nar/gkr491. 2.5 angstrom crystal structure of the nucleosome core particle assembled with a 145 bp alpha-satellite DNA (ncp145). SNAP output
3rei structural protein-DNA X-ray (2.65 Å) Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA (2011) "Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation." Nucleic Acids Res., 39, 8200-8212. doi: 10.1093/nar/gkr491. 2.65 angstrom crystal structure of the nucleosome core particle assembled with a 145 bp alpha-satellite DNA (ncp145) derivatized with triamminechloroplatinum(ii) chloride. SNAP output
3rej structural protein-DNA X-ray (2.55 Å) Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA (2011) "Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation." Nucleic Acids Res., 39, 8200-8212. doi: 10.1093/nar/gkr491. 2.55 angstrom crystal structure of the nucleosome core particle assembled with a 146 bp alpha-satellite DNA (ncp146b). SNAP output
3rek structural protein-DNA X-ray (2.6 Å) Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA (2011) "Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation." Nucleic Acids Res., 39, 8200-8212. doi: 10.1093/nar/gkr491. 2.6 angstrom crystal structure of the nucleosome core particle assembled with a 146 bp alpha-satellite DNA (ncp146b) derivatized with oxaliplatin. SNAP output
3rel structural protein-DNA X-ray (2.7 Å) Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA (2011) "Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation." Nucleic Acids Res., 39, 8200-8212. doi: 10.1093/nar/gkr491. 2.7 angstrom crystal structure of the nucleosome core particle assembled with a 146 bp alpha-satellite DNA (ncp146b) derivatized with triamminechloroplatinum(ii) chloride. SNAP output
3rh4 transferase-DNA X-ray (1.918 Å) Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH (2011) "Molecular insights into DNA polymerase deterrents for ribonucleotide insertion." J.Biol.Chem., 286, 31650-31660. doi: 10.1074/jbc.M111.253401. DNA polymerase beta with a dideoxy-terminated primer with an incoming ribonucleotide (rctp). SNAP output
3rh5 transferase-DNA X-ray (2.096 Å) Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH (2011) "Molecular insights into DNA polymerase deterrents for ribonucleotide insertion." J.Biol.Chem., 286, 31650-31660. doi: 10.1074/jbc.M111.253401. DNA polymerase beta mutant (y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dctp). SNAP output
3rh6 transferase-DNA X-ray (2.048 Å) Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH (2011) "Molecular insights into DNA polymerase deterrents for ribonucleotide insertion." J.Biol.Chem., 286, 31650-31660. doi: 10.1074/jbc.M111.253401. DNA polymerase beta mutant (y271) with a dideoxy-terminated primer with an incoming ribonucleotide (rctp). SNAP output
3ri4 transcription-DNA X-ray (3.0 Å) Babayeva ND, Baranovskaya OI, Tahirov TH (2012) "Structural basis of ets1 cooperative binding to widely separated sites on promoter DNA." Plos One, 7, e33698. doi: 10.1371/journal.pone.0033698. Ets1 cooperative binding to widely separated sites on promoter DNA. SNAP output
3rje transferase, lyase-DNA X-ray (2.1 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Ternary complex of DNA polymerase beta with a gapped DNA containing 8odg at template position. SNAP output
3rjf transferase, lyase-DNA X-ray (2.3 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Ternary complex of DNA polymerase beta with a gapped DNA containing (syn)8odg at template position paired with non-hydrolyzable datp analog (dapcpp). SNAP output
3rjg transferase, lyase-DNA X-ray (2.0 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Binary complex of DNA polymerase beta with a gapped DNA containing 8odg:da base-pair at primer terminus. SNAP output
3rjh transferase, lyase-DNA X-ray (2.2 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Ternary complex of DNA polymerase beta with a gapped DNA containing (syn)8odg:da at primer terminus and dg:dcmp(cf2)ppin the active site. SNAP output
3rji transferase, lyase-DNA X-ray (2.3 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Ternary complex of DNA polymerase beta with a gapped DNA containing 8odg at template position paired with non-hydrolyzable dctp analog (dcmp(cf2)pp). SNAP output
3rjj transferase, lyase-DNA X-ray (2.0 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Ternary complex crystal structure of DNA polymerase beta with template 8odg provides insight into mutagenic lesion bypass. SNAP output
3rjk transferase, lyase-DNA X-ray (2.1 Å) Batra VK, Shock DD, Beard WA, McKenna CE, Wilson SH (2012) "Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion." Proc.Natl.Acad.Sci.USA, 109, 113-118. doi: 10.1073/pnas.1112235108. Ternary complex of DNA polymerase beta with a gapped DNA containing 8odg:dc base pair at primer terminus and dg:dcmp(cf2)pp in the active site. SNAP output
3rkq transcription-DNA X-ray (1.7 Å) Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ (2012) "Crystal structure of the human NKX2.5 homeodomain in complex with DNA target." Biochemistry, 51, 6312-6319. doi: 10.1021/bi300849c. Nkx2.5 homeodomain dimer bound to anf-242 DNA. SNAP output
3rma transferase-DNA X-ray (2.84 Å) Aller P, Duclos S, Wallace SS, Doublie S (2011) "A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex." J.Mol.Biol., 412, 22-34. doi: 10.1016/j.jmb.2011.07.007. Crystal structure of a replicative DNA polymerase bound to DNA containing thymine glycol. SNAP output
3rmb transferase-DNA X-ray (2.65 Å) Aller P, Duclos S, Wallace SS, Doublie S (2011) "A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex." J.Mol.Biol., 412, 22-34. doi: 10.1016/j.jmb.2011.07.007. Crystal structure of a replicative DNA polymerase bound to DNA containing thymine glycol. SNAP output
3rmc transferase-DNA X-ray (3.0 Å) Aller P, Duclos S, Wallace SS, Doublie S (2011) "A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex." J.Mol.Biol., 412, 22-34. doi: 10.1016/j.jmb.2011.07.007. Crystal structure of a replicative DNA polymerase bound to DNA containing thymine glycol. SNAP output
3rmd transferase-DNA X-ray (2.98 Å) Aller P, Duclos S, Wallace SS, Doublie S (2011) "A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex." J.Mol.Biol., 412, 22-34. doi: 10.1016/j.jmb.2011.07.007. Crystal structure of a replicative DNA polymerase bound to DNA containing thymine glycol. SNAP output
3rmp DNA binding protein-DNA X-ray (2.21 Å) Szwagierczak A, Popowicz GM, Holak TA, Rakin A, Antonenka U "Structural basis for the recognition of attP substrates by P4-like integrases." Structural basis for the recognition of attp substrates by p4-like integrases. SNAP output
3rn2 immune system-DNA X-ray (2.55 Å) Jin T, Perry A, Jiang J, Smith P, Curry JA, Unterholzner L, Jiang Z, Horvath G, Rathinam VA, Johnstone RW, Hornung V, Latz E, Bowie AG, Fitzgerald KA, Xiao TS (2012) "Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor." Immunity, 36, 561-571. doi: 10.1016/j.immuni.2012.02.014. Structural basis of cytosolic DNA recognition by innate immune receptors. SNAP output
3rn5 immune system-DNA X-ray (2.5 Å) Jin T, Perry A, Jiang J, Smith P, Curry JA, Unterholzner L, Jiang Z, Horvath G, Rathinam VA, Johnstone RW, Hornung V, Latz E, Bowie AG, Fitzgerald KA, Xiao TS (2012) "Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor." Immunity, 36, 561-571. doi: 10.1016/j.immuni.2012.02.014. Structural basis of cytosolic DNA recognition by innate immune receptors. SNAP output
3rnu transcription activator-DNA X-ray (2.502 Å) Jin T, Perry A, Jiang J, Smith P, Curry JA, Unterholzner L, Jiang Z, Horvath G, Rathinam VA, Johnstone RW, Hornung V, Latz E, Bowie AG, Fitzgerald KA, Xiao TS (2012) "Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor." Immunity, 36, 561-571. doi: 10.1016/j.immuni.2012.02.014. Structural basis of cytosolic DNA sensing by innate immune receptors. SNAP output
3rr7 transferase-DNA X-ray (1.95 Å) Obeid S, Welte W, Diederichs K, Marx A (2012) "Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase." J.Biol.Chem., 287, 14099-14108. doi: 10.1074/jbc.M111.334904. Binary structure of the large fragment of taq DNA polymerase bound to an abasic site. SNAP output
3rr8 transferase-DNA X-ray (2.4 Å) Obeid S, Welte W, Diederichs K, Marx A (2012) "Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase." J.Biol.Chem., 287, 14099-14108. doi: 10.1074/jbc.M111.334904. Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and a ddgtp. SNAP output
3rrg transferase-DNA X-ray (2.3 Å) Obeid S, Welte W, Diederichs K, Marx A (2012) "Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase." J.Biol.Chem., 287, 14099-14108. doi: 10.1074/jbc.M111.334904. Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and a ddgtp. SNAP output
3rrh transferase-DNA X-ray (1.8 Å) Obeid S, Welte W, Diederichs K, Marx A (2012) "Amino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase." J.Biol.Chem., 287, 14099-14108. doi: 10.1074/jbc.M111.334904. Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and a ddttp. SNAP output
3rtv transferase-DNA X-ray (1.9 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012) "KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry." Nat.Chem.Biol., 8, 612-614. doi: 10.1038/nchembio.966. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with natural primer-template DNA. SNAP output
3rwu transferase-DNA X-ray (2.33 Å) Xia S, Konigsberg WH, Wang J (2011) "Hydrogen-Bonding Capability of a Templating Difluorotoluene Nucleotide Residue in an RB69 DNA Polymerase Ternary Complex." J.Am.Chem.Soc., 133, 10003-10005. doi: 10.1021/ja2021735. Rb69 DNA polymerase (y567a) ternary complex with datp opposite difluorotoluene nucleoside. SNAP output
3rzd transcription-RNA-DNA X-ray (3.3 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 5-nt RNA. SNAP output
3rzg oxidoreductase-DNA X-ray (1.62 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Duplex interrogation by a direct DNA repair protein in the search of damage. SNAP output
3rzh oxidoreductase-DNA X-ray (2.25 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Duplex interrogation by a direct DNA repair protein in the search of damage. SNAP output
3rzj oxidoreductase-DNA X-ray (2.5 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Duplex interrogation by a direct DNA repair protein in the search of damage. SNAP output
3rzk oxidoreductase-DNA X-ray (2.78 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Duplex interrogation by a direct DNA repair protein in the search of damage. SNAP output
3rzl oxidoreductase-DNA X-ray (2.6 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Duplex interrogation by a direct DNA repair protein in the search of damage. SNAP output
3rzm oxidoreductase-DNA X-ray (3.06 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Duplex interrogation by a direct DNA repair protein in the search of damage. SNAP output
3rzo transcription-RNA-DNA X-ray (3.0 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 4-nt RNA. SNAP output
3s14 transcription-RNA-DNA X-ray (2.85 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 6-nt RNA. SNAP output
3s15 transcription-RNA-DNA X-ray (3.3 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 7-nt RNA. SNAP output
3s16 transcription-RNA-DNA X-ray (3.241 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with an 8-nt RNA. SNAP output
3s17 transcription-RNA-DNA X-ray (3.2 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 9-nt RNA. SNAP output
3s1m transcription-RNA-DNA X-ray (3.13 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 5-nt RNA (variant 1). SNAP output
3s1n transcription-RNA-DNA X-ray (3.1 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 5-nt RNA (variant 2). SNAP output
3s1q transcription-RNA-DNA X-ray (3.3 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 5-nt 3'-deoxy RNA soaked with atp. SNAP output
3s1r transcription-RNA-DNA X-ray (3.2 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 5-nt 3'-deoxy RNA soaked with gtp. SNAP output
3s2d transcription-RNA-DNA X-ray (3.2 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 5-nt RNA containing a 5br-u. SNAP output
3s2h transcription-RNA-DNA X-ray (3.3 Å) Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD (2011) "Initiation complex structure and promoter proofreading." Science, 333, 633-637. doi: 10.1126/science.1206629. RNA polymerase ii initiation complex with a 6-nt RNA containing a 2[prime]-iodo atp. SNAP output
3s3m recombination-inhibitor-DNA X-ray (2.49 Å) Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P (2011) "Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572)." Mol.Pharmacol., 80, 565-572. doi: 10.1124/mol.111.073189. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and dolutegravir (s-gsk1349572). SNAP output
3s3n transferase-inhibitor-DNA X-ray (2.49 Å) Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P (2011) "Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572)." Mol.Pharmacol., 80, 565-572. doi: 10.1124/mol.111.073189. Crystal structure of the prototype foamy virus (pfv) s217h mutant intasome in complex with magnesium and dolutegravir (s-gsk1349572). SNAP output
3s3o recombination-inhibitor-DNA X-ray (2.55 Å) Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P (2011) "Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572)." Mol.Pharmacol., 80, 565-572. doi: 10.1124/mol.111.073189. Crystal structure of the prototype foamy virus (pfv) n224h mutant intasome in complex with magnesium and dolutegravir (s-gsk1349572). SNAP output
3s57 oxidoreductase-DNA X-ray (1.6 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Abh2 cross-linked with undamaged dsDNA-1 containing cofactors. SNAP output
3s5a oxidoreductase-DNA X-ray (1.7 Å) Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C (2012) "Duplex interrogation by a direct DNA repair protein in search of base damage." Nat.Struct.Mol.Biol., 19, 671-676. doi: 10.1038/nsmb.2320. Abh2 cross-linked to undamaged dsDNA-2 with cofactors. SNAP output
3s6i hydrolase-DNA X-ray (2.28 Å) Adhikary S, Eichman BF (2011) "Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase." Embo Rep., 12, 1286-1292. doi: 10.1038/embor.2011.189. Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (mag1) in complex with abasic-DNA.. SNAP output
3s8q protein binding-DNA X-ray (2.1 Å) McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG (2012) "Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex." Nucleic Acids Res., 40, 4158-4167. doi: 10.1093/nar/gkr1250. Crystal structure of the r-m controller protein c.esp1396i ol operator complex. SNAP output
3s9h transferase-DNA X-ray (1.95 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase triple mutant(l561a-s565g-y567a) ternary complex with dupnpp and a dideoxy-terminated primer in the presence of ca2+. SNAP output
3sar hydrolase-DNA X-ray (1.95 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm slanted complex 1. SNAP output
3sas hydrolase-DNA X-ray (2.05 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm slanted complex 4 with r112a mutation. SNAP output
3sat hydrolase-DNA X-ray (2.15 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm slanted complex 6 with r112a mutation. SNAP output
3sau hydrolase-DNA X-ray (1.65 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm interrogation complex 6. SNAP output
3sav hydrolase-DNA X-ray (2.125 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm slanted complex 8. SNAP output
3saw hydrolase-DNA X-ray (2.35 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm slanted complex 8 with r112a mutation. SNAP output
3sbj hydrolase-DNA X-ray (2.1 Å) Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M, Karplus M, Verdine GL (2012) "Strandwise translocation of a DNA glycosylase on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 1086-1091. doi: 10.1073/pnas.1111237108. Mutm slanted complex 7. SNAP output
3scx transferase-DNA X-ray (2.35 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase triple mutant(l561a-s565g-y567a) ternary complex with dupnpp and a deoxy-terminated primer in the presence of ca2+. SNAP output
3si6 transferase-DNA X-ray (1.85 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase triple mutant (l561a-s565g-y567a) ternary complex with dupnpp and a deoxy-terminated primer in the presence of mg2+. SNAP output
3si8 transferase-DNA X-ray (2.15 Å) Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W (2010) "Structure and mechanism of human DNA polymerase eta." Nature, 465, 1044-1048. doi: 10.1038/nature09196. Human DNA polymerase eta - DNA ternary complex with the 5't of a cpd in the active site (tt2). SNAP output
3sjj transferase-DNA X-ray (2.38 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase triple mutant (l561a-s565g-y567a) ternary complex with dupnpp and a deoxy-terminated primer in the presence of mn2+. SNAP output
3sjm DNA-DNA binding protein X-ray (1.35 Å) Nair SK, Sliverman SK, Chen JH, Xiao Y "Crystal Structure Analysis of TRF2-Dbd-DNA complex." Crystal structure analysis of trf2-dbd-DNA complex. SNAP output
3slp hydrolase-DNA X-ray (2.3 Å) Zhang J, McCabe KA, Bell CE (2011) "Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity." Proc.Natl.Acad.Sci.USA, 108, 11872-11877. doi: 10.1073/pnas.1103467108. Crystal structure of lambda exonuclease in complex with a 12 bp symmetric DNA duplex. SNAP output
3sm4 hydrolase-DNA X-ray (1.88 Å) Zhang J, McCabe KA, Bell CE (2011) "Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity." Proc.Natl.Acad.Sci.USA, 108, 11872-11877. doi: 10.1073/pnas.1103467108. Crystal structure of the k131a mutant of lambda exonuclease in complex with a 5'-phosphorylated 14-mer-12-mer duplex and magnesium. SNAP output
3snn transferase-DNA X-ray (2.0 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex with dctp opposite dg in the presence of mg2+. SNAP output
3spd hydrolase-DNA X-ray (1.912 Å) Gong Y, Zhu D, Ding J, Dou C, Ren X, Gu L, Jiang T, Wang D (2011) "Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA." Nat.Struct.Mol.Biol., 18, 1297-1299. doi: 10.1038/nsmb.2145. Crystal structure of aprataxin ortholog hnt3 in complex with DNA. SNAP output
3spl hydrolase-DNA X-ray (2.101 Å) Gong Y, Zhu D, Ding J, Dou C, Ren X, Gu L, Jiang T, Wang D (2011) "Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA." Nat.Struct.Mol.Biol., 18, 1297-1299. doi: 10.1038/nsmb.2145. Crystal structure of aprataxin ortholog hnt3 in complex with DNA and amp. SNAP output
3spy transferase-DNA X-ray (2.14 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase(l415a-l561a-s565g-y567a) ternary complex with dupcpp opposite da. SNAP output
3spz transferase-DNA X-ray (2.43 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. DNA polymerase(l415a-l561a-s565g-y567a) ternary complex with dupcpp opposite da (ca2+). SNAP output
3sq0 transferase-DNA X-ray (2.0 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. DNA polymerase(l561a-s565g-y567a) ternary complex with dupnpp opposite da (mn2+). SNAP output
3sq1 transferase-DNA X-ray (1.82 Å) Xia S, Wang M, Blaha G, Konigsberg WH, Wang J (2011) "Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase." Biochemistry, 50, 9114-9124. doi: 10.1021/bi201260h. Rb69 DNA polymerase ternary complex with dupcpp opposite da. SNAP output
3sq2 transferase-DNA X-ray (2.1 Å) Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W (2011) "Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase." Biochemistry, 50, 10136-10149. doi: 10.1021/bi2014618. Rb69 DNA polymerase ternary complex with dttp opposite 2ap (at rich sequence). SNAP output
3sq4 transferase-DNA X-ray (2.23 Å) Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W (2011) "Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase." Biochemistry, 50, 10136-10149. doi: 10.1021/bi2014618. Rb69 DNA polymerase ternary complex with dttp opposite 2ap (gc rich sequence). SNAP output
3sqi DNA binding protein-DNA X-ray (2.82 Å) Cho US, Harrison SC (2011) "Ndc10 is a platform for inner kinetochore assembly in budding yeast." Nat.Struct.Mol.Biol., 19, 48-55. doi: 10.1038/nsmb.2178. DNA binding domain of ndc10. SNAP output
3sqx hydrolase-RNA X-ray (2.112 Å) Mohr G, Del Campo M, Turner KG, Gilman B, Wolf RZ, Lambowitz AM (2011) "High-Throughput Genetic Identification of Functionally Important Regions of the Yeast DEAD-Box Protein Mss116p." J.Mol.Biol., 413, 952-972. doi: 10.1016/j.jmb.2011.09.015. Structure of mss116p (nte and c-tail double deletion) bound to ssrna and amp-pnp. SNAP output
3ssc DNA binding protein-DNA X-ray (2.1 Å) Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V (2012) "The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine." Nucleic Acids Res., 40, 7552-7562. doi: 10.1093/nar/gks332. DNA binding domain of restriction endonuclease bound to DNA. SNAP output
3ssd DNA binding protein-DNA X-ray (2.2 Å) Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V (2012) "The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine." Nucleic Acids Res., 40, 7552-7562. doi: 10.1093/nar/gks332. DNA binding domain of restriction endonuclease bound to DNA. SNAP output
3sse DNA binding protein-DNA X-ray (2.7 Å) Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V (2012) "The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine." Nucleic Acids Res., 40, 7552-7562. doi: 10.1093/nar/gks332. DNA binding domain of restriction endonuclease bound to DNA. SNAP output
3sun transferase-DNA X-ray (2.42 Å) Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W (2011) "Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase." Biochemistry, 50, 10136-10149. doi: 10.1021/bi2014618. Rb69 DNA polymerase (y567a) ternary complex with dttp opposite 2ap (at rich sequence). SNAP output
3suo transferase-DNA X-ray (2.23 Å) Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W (2011) "Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase." Biochemistry, 50, 10136-10149. doi: 10.1021/bi2014618. Rb69 DNA polymerase (y567a) ternary complex with dttp opposite 2ap (gc rich sequence). SNAP output
3sup transferase-DNA X-ray (2.32 Å) Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W (2011) "Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase." Biochemistry, 50, 10136-10149. doi: 10.1021/bi2014618. Rb69 DNA polymerase (y567a) ternary complex with dctp opposite 2ap (gc rich sequence). SNAP output
3suq transferase-DNA X-ray (3.15 Å) Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W (2011) "Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase." Biochemistry, 50, 10136-10149. doi: 10.1021/bi2014618. Rb69 DNA polymerase (y567a) ternary complex with dctp opposite 2ap (at rich sequence). SNAP output
3sv3 transferase-DNA X-ray (2.1 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012) "KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry." Nat.Chem.Biol., 8, 612-614. doi: 10.1038/nchembio.966. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with the artificial base pair dnam-d5sicstp. SNAP output
3sv4 transferase-DNA X-ray (1.99 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012) "KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry." Nat.Chem.Biol., 8, 612-614. doi: 10.1038/nchembio.966. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in an open binary complex with dt as templating nucleobase. SNAP output
3swm transcription-DNA X-ray (4.25 Å) Welner DH, Lindemose S, Grossmann JG, Mollegaard NE, Olsen AN, Helgstrand C, Skriver K, Lo Leggio L (2012) "DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors." Biochem.J., 444, 395-404. doi: 10.1042/BJ20111742. The nac domain of anac019 in complex with DNA, gold derivative. SNAP output
3swp transcription-DNA X-ray (4.113 Å) Welner DH, Lindemose S, Grossmann JG, Mollegaard NE, Olsen AN, Helgstrand C, Skriver K, Lo Leggio L (2012) "DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors." Biochem.J., 444, 395-404. doi: 10.1042/BJ20111742. Anac019 nac domain in complex with DNA. SNAP output
3syz transferase-DNA X-ray (1.952 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012) "KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry." Nat.Chem.Biol., 8, 612-614. doi: 10.1038/nchembio.966. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in an open binary complex with dnam as templating nucleobase. SNAP output
3sz2 transferase-DNA X-ray (2.15 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A (2012) "KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry." Nat.Chem.Biol., 8, 612-614. doi: 10.1038/nchembio.966. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in an open binary complex with dg as templating nucleobase. SNAP output
3sz5 hydrolase-DNA X-ray (2.8 Å) Yang W, Chen WY, Wang H, Ho JW, Huang JD, Woo PC, Lau SK, Yuen KY, Zhang Q, Zhou W, Bartlam M, Watt RM, Rao Z (2011) "Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis." Nucleic Acids Res., 39, 9803-9819. doi: 10.1093/nar/gkr660. Crystal structure of lhk-exo in complex with 5-phosphorylated oligothymidine (dt)4. SNAP output
3szq hydrolase-DNA X-ray (2.353 Å) Tumbale P, Appel CD, Kraehenbuehl R, Robertson PD, Williams JS, Krahn J, Ahel I, Williams RS (2011) "Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease." Nat.Struct.Mol.Biol., 18, 1189-1195. doi: 10.1038/nsmb.2146. Structure of an s. pombe aptx-DNA-amp-zn complex. SNAP output
3t3f transferase-DNA X-ray (1.9 Å) Obeid S, Welte W, Diederichs K, Marx A (2012) "Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase." J.Biol.Chem., 287, 14099-14108. doi: 10.1074/jbc.M111.334904. Ternary structure of the large fragment of taq DNA polymerase bound to an abasic site and dnitp. SNAP output
3t5h DNA-transferase X-ray (2.35 Å) Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP (2012) "Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV." Chem.Res.Toxicol., 25, 422-435. doi: 10.1021/tx200460j. Ternary complex of hne adduct modified DNA (5'-cxg-3' vs 13-mer) with dpo4 and incoming ddgt. SNAP output
3t5j DNA-transferase X-ray (2.4 Å) Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP (2012) "Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV." Chem.Res.Toxicol., 25, 422-435. doi: 10.1021/tx200460j. Ternary complex of hne adduct modified DNA (5'-txg-3' vs 13-mer) with dpo4 and incoming ddtp. SNAP output
3t5k DNA-transferase X-ray (2.9 Å) Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP (2012) "Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV." Chem.Res.Toxicol., 25, 422-435. doi: 10.1021/tx200460j. Ternary complex of hne adduct modified DNA (5'-txg-3' vs 14-mer) with dpo4 and incoming ddtp. SNAP output
3t5l DNA-transferase X-ray (2.9 Å) Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli M, Stone MP (2012) "Replication bypass of the trans-4-Hydroxynonenal-derived (6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the sulfolobus solfataricus DNA polymerase IV." Chem.Res.Toxicol., 25, 422-435. doi: 10.1021/tx200460j. Ternary complex of hne adduct modified DNA (5'-cxg-3' vs 14-mer) with dpo4 and incoming ddgt. SNAP output
3t79 DNA binding protein-DNA X-ray (3.61 Å) Cho US, Harrison SC (2011) "Ndc10 is a platform for inner kinetochore assembly in budding yeast." Nat.Struct.Mol.Biol., 19, 48-55. doi: 10.1038/nsmb.2178. Ndc10: a platform for inner kinetochore assembly in budding yeast. SNAP output
3tab transferase-DNA X-ray (2.8 Å) Zahn KE, Averill A, Wallace SS, Doublie S (2011) "The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site." Biochemistry, 50, 10350-10358. doi: 10.1021/bi201219s. 5-hydroxycytosine paired with dgmp in rb69 gp43. SNAP output
3tae transferase-DNA X-ray (2.71 Å) Zahn KE, Averill A, Wallace SS, Doublie S (2011) "The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site." Biochemistry, 50, 10350-10358. doi: 10.1021/bi201219s. 5-hydroxycytosine paired with damp in rb69 gp43. SNAP output
3taf transferase-DNA X-ray (3.0 Å) Zahn KE, Averill A, Wallace SS, Doublie S (2011) "The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site." Biochemistry, 50, 10350-10358. doi: 10.1021/bi201219s. 5-fluorocytosine paired with ddgmp in rb69 gp43. SNAP output
3tag transferase-DNA X-ray (2.95 Å) Zahn KE, Averill A, Wallace SS, Doublie S (2011) "The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site." Biochemistry, 50, 10350-10358. doi: 10.1021/bi201219s. 5-fluorocytosine paired with damp in rb69 gp43. SNAP output
3tan transferase-DNA X-ray (1.53 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to duplex DNA with cytosine-adenine mismatch at (n-1) position. SNAP output
3tap transferase-DNA X-ray (1.655 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to duplex DNA with cytosine-adenine mismatch at (n-3) position. SNAP output
3taq transferase-DNA X-ray (1.65 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to duplex DNA with cytosine-adenine mismatch at (n-4) position. SNAP output
3tar transferase-DNA X-ray (1.6 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to duplex DNA with cytosine-adenine mismatch at (n-6) position. SNAP output
3ted DNA binding protein-DNA X-ray (2.0 Å) Sharma A, Jenkins KR, Heroux A, Bowman GD (2011) "DNA-binding domain of Chd1 in complex with a DNA duplex." J.Biol.Chem. Crystal structure of the chd1 DNA-binding domain in complex with a DNA duplex. SNAP output
3tfr transferase-DNA X-ray (2.0 Å) Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2012) "Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta." Chembiochem, 13, 528-530. doi: 10.1002/cbic.201100738. Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b damp(cf2)pp in the active site. SNAP output
3tfs transferase-DNA X-ray (2.0 Å) Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2012) "Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta." Chembiochem, 13, 528-530. doi: 10.1002/cbic.201100738. Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b damp(cfh)pp in the active site: stereoselective binding of (s) isomer. SNAP output
3thv transferase-DNA X-ray (1.611 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and ddatp-dt in closed conformation. SNAP output
3thw DNA binding protein-DNA X-ray (3.09 Å) Gupta S, Gellert M, Yang W (2012) "Mechanism of mismatch recognition revealed by human MutSbeta bound to unpaired DNA loops." Nat.Struct.Mol.Biol., 19, 72-78. doi: 10.1038/nsmb.2175. Human mutsbeta complexed with an idl of 4 bases (loop4) and adp. SNAP output
3thx DNA binding protein-DNA X-ray (2.7 Å) Gupta S, Gellert M, Yang W (2012) "Mechanism of mismatch recognition revealed by human MutSbeta bound to unpaired DNA loops." Nat.Struct.Mol.Biol., 19, 72-78. doi: 10.1038/nsmb.2175. Human mutsbeta complexed with an idl of 3 bases (loop3) and adp. SNAP output
3thy DNA binding protein-DNA X-ray (2.894 Å) Gupta S, Gellert M, Yang W (2012) "Mechanism of mismatch repair revealed by human MutSbeta bound to unpaired DNA loops." Nat.Struct.Mol.Biol., 19, 72-78. doi: 10.1038/nsmb.2175. Human mutsbeta complexed with an idl of 2 bases (loop2) and adp. SNAP output
3thz DNA binding protein-DNA X-ray (4.3 Å) Gupta S, Gellert M, Yang W (2012) "Mechanism of mismatch repair revealed by human MutS bound to unpaired DNA loops." Nat.Struct.Mol.Biol., 19, 72-78. doi: 10.1038/nsmb.2175. Human mutsbeta complexed with an idl of 6 bases (loop6) and adp. SNAP output
3ti0 transferase-DNA X-ray (1.62 Å) Wang W, Hellinga HW, Beese LS (2011) "Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis." Proc.Natl.Acad.Sci.USA, 108, 17644-17648. doi: 10.1073/pnas.1114496108. Crystal structure of bacillus DNA polymerase i large fragment bound to DNA and ddgtp-dc in closed conformation. SNAP output
3tmm transcription-DNA X-ray (2.5 Å) Ngo HB, Kaiser JT, Chan DC (2011) "The mitochondrial transcription and packaging factor Tfam imposes a U-turn on mitochondrial DNA." Nat.Struct.Mol.Biol., 18, 1290-1296. doi: 10.1038/nsmb.2159. Tfam imposes a u-turn on mitochondrial DNA. SNAP output
3tq1 transferase-DNA X-ray (2.556 Å) Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2012) "Human DNA Polymerase Eta Is Pre-Aligned for dNTP Binding and Catalysis." J.Mol.Biol., 415, 627-634. doi: 10.1016/j.jmb.2011.11.038. Human DNA polymerase eta in binary complex with DNA. SNAP output
3tq6 transcription-DNA X-ray (2.45 Å) Rubio-Cosials A, Sidow JF, Jimenez-Menendez N, Fernandez-Millan P, Montoya J, Jacobs HT, Coll M, Bernado P, Sola M (2011) "Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter." Nat.Struct.Mol.Biol., 18, 1281-1289. doi: 10.1038/nsmb.2160. Crystal structure of human mitochondrial transcription factor a, tfam or mttfa, bound to the light strand promoter lsp. SNAP output
3ts8 antitumor protein-DNA X-ray (2.8 Å) Emamzadah S, Tropia L, Halazonetis TD (2011) "Crystal Structure of a Multidomain Human p53 Tetramer Bound to the Natural CDKN1A (p21) p53-Response Element." Mol Cancer Res, 9, 1493-1499. doi: 10.1158/1541-7786.MCR-11-0351. Crystal structure of a multidomain human p53 tetramer bound to the natural cdkn1a(p21) p53-response element. SNAP output
3tu4 signaling protein-structural protein-DNA X-ray (3.0 Å) Armache KJ, Garlick JD, Canzio D, Narlikar GJ, Kingston RE (2011) "Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution." Science, 334, 977-982. doi: 10.1126/science.1210915. Crystal structure of the sir3 bah domain in complex with a nucleosome core particle.. SNAP output
3twh hydrolase-RNA-DNA X-ray (1.79 Å) Abdur R, Gerlits OO, Gan J, Jiang J, Salon J, Kovalevsky AY, Chumanevich AA, Weber IT, Huang Z (2014) "Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides." Acta Crystallogr.,Sect.D, 70, 354-361. doi: 10.1107/S1399004713027922. Selenium derivatized RNA-DNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
3twm hydrolase-DNA X-ray (2.8 Å) Duclos S, Aller P, Jaruga P, Dizdaroglu M, Wallace SS, Doublie S (2012) "Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine." Dna Repair, 11, 714-725. doi: 10.1016/j.dnarep.2012.06.004. Crystal structure of arabidopsis thaliana fpg. SNAP output
3u2b transcription-DNA X-ray (2.402 Å) Jauch R, Ng CKL, Narasimhan K, Kolatkar PR (2012) "The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition." Biochem.J., 443, 39-47. doi: 10.1042/BJ20111768. Structure of the sox4 hmg domain bound to DNA. SNAP output
3u3w transcription activator-DNA X-ray (2.4 Å) Grenha R, Slamti L, Nicaise M, Refes Y, Lereclus D, Nessler S (2013) "Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR." Proc.Natl.Acad.Sci.USA, 110, 1047-1052. doi: 10.1073/pnas.1213770110. Crystal structure of bacillus thuringiensis plcr in complex with the peptide papr7 and DNA. SNAP output
3u3y hydrolase-DNA X-ray (2.28 Å) Bailey SL, Harvey S, Perrino FW, Hollis T (2012) "Defects in DNA degradation revealed in crystal structures of TREX1 exonuclease mutations linked to autoimmune disease." Dna Repair, 11, 65-73. doi: 10.1016/j.dnarep.2011.10.007. Mouse trex1 d200h mutant. SNAP output
3u44 hydrolase-DNA X-ray (3.201 Å) Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW, Dillingham MS, Wigley DB (2012) "Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex." Embo J., 31, 1568-1578. doi: 10.1038/emboj.2012.9. Crystal structure of addab-DNA complex. SNAP output
3u4q hydrolase-DNA X-ray (2.8 Å) Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW, Dillingham MS, Wigley DB (2012) "Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex." Embo J., 31, 1568-1578. doi: 10.1038/emboj.2012.9. Structure of addab-DNA complex at 2.8 angstroms. SNAP output
3u58 DNA binding protein-DNA X-ray (2.613 Å) Zeng Z, Min B, Huang J, Hong K, Yang Y, Collins K, Lei M (2011) "Structural basis for Tetrahymena telomerase processivity factor Teb1 binding to single-stranded telomeric-repeat DNA." Proc.Natl.Acad.Sci.USA, 108, 20357-20361. doi: 10.1073/pnas.1113624108. Crystal structure of the tetrahymena telomerase processivity factor teb1 ab. SNAP output
3u5z DNA binding protein-DNA X-ray (3.5 Å) Kelch BA, Makino DL, O'Donnell M, Kuriyan J (2011) "How a DNA polymerase clamp loader opens a sliding clamp." Science, 334, 1675-1680. doi: 10.1126/science.1211884. Structure of t4 bacteriophage clamp loader bound to the t4 clamp, primer-template DNA, and atp analog. SNAP output
3u60 DNA binding protein-DNA X-ray (3.34 Å) Kelch BA, Makino DL, O'Donnell M, Kuriyan J (2011) "How a DNA polymerase clamp loader opens a sliding clamp." Science, 334, 1675-1680. doi: 10.1126/science.1211884. Structure of t4 bacteriophage clamp loader bound to open clamp, DNA and atp analog. SNAP output
3u61 DNA binding protein-DNA X-ray (3.2 Å) Kelch BA, Makino DL, O'Donnell M, Kuriyan J (2011) "How a DNA polymerase clamp loader opens a sliding clamp." Science, 334, 1675-1680. doi: 10.1126/science.1211884. Structure of t4 bacteriophage clamp loader bound to closed clamp, DNA and atp analog and adp. SNAP output
3u6c hydrolase-DNA X-ray (1.8 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 1 apgo. SNAP output
3u6d hydrolase-DNA X-ray (1.87 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 1 gpgo. SNAP output
3u6e hydrolase-DNA X-ray (1.7 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 1 tpgo. SNAP output
3u6f hydrolase-DNA X-ray (2.3 Å) Bailey SL, Harvey S, Perrino FW, Hollis T (2012) "Defects in DNA degradation revealed in crystal structures of TREX1 exonuclease mutations linked to autoimmune disease." Dna Repair, 11, 65-73. doi: 10.1016/j.dnarep.2011.10.007. Mouse trex1 d200n mutant. SNAP output
3u6l hydrolase-DNA X-ray (1.97 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 2 cpgo. SNAP output
3u6m hydrolase-DNA X-ray (2.1 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Structural effects of sequence context on lesion recognition by mutm. SNAP output
3u6o hydrolase-DNA X-ray (1.9 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 1 apg. SNAP output
3u6p hydrolase-DNA X-ray (1.6 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 1 gpg. SNAP output
3u6q hydrolase-DNA X-ray (1.981 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 2 apgo. SNAP output
3u6s hydrolase-DNA X-ray (1.77 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2012) "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM." J.Biol.Chem., 287, 18044-18054. doi: 10.1074/jbc.M111.313635. Mutm set 1 tpg. SNAP output
3u6y DNA binding protein-DNA X-ray (2.0 Å) Tanaka T, Padavattan S, Kumarevel T (2012) "Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1." J.Biol.Chem., 287, 10394-10402. doi: 10.1074/jbc.M112.343210. Crystal structure of alba2-DNA complex. SNAP output
3u7f hydrolase,transferase-DNA X-ray (1.8 Å) Coquelle N, Havali-Shahriari Z, Bernstein N, Green R, Glover JN (2011) "Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates." Proc.Natl.Acad.Sci.USA, 108, 21022-21027. doi: 10.1073/pnas.1112036108. Crystal structure of mpnkp catalytic fragment (d170a) bound to single-stranded DNA (tcctcp). SNAP output
3u7g hydrolase,transferase-DNA X-ray (2.1 Å) Coquelle N, Havali-Shahriari Z, Bernstein N, Green R, Glover JN (2011) "Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates." Proc.Natl.Acad.Sci.USA, 108, 21022-21027. doi: 10.1073/pnas.1112036108. Crystal structure of mpnkp catalytic fragment (d170a) bound to single-stranded DNA (tcctap). SNAP output
3u7h hydrolase,transferase-DNA X-ray (2.0 Å) Coquelle N, Havali-Shahriari Z, Bernstein N, Green R, Glover JN (2011) "Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates." Proc.Natl.Acad.Sci.USA, 108, 21022-21027. doi: 10.1073/pnas.1112036108. Crystal structure of mpnkp catalytic fragment (d170a) bound to single-stranded DNA (tccttp). SNAP output
3ubt transferase-DNA X-ray (2.502 Å) Didovyk A, Verdine GL (2012) "Structural origins of DNA target selection and nucleobase extrusion by a DNA Cytosine methyltransferase." J.Biol.Chem., 287, 40099-40105. doi: 10.1074/jbc.M112.413054. Crystal structure of c71s mutant of DNA cytosine-5 methyltransferase m.haeiii bound to DNA. SNAP output
3uby hydrolase-DNA X-ray (2.0 Å) Setser JW, Lingaraju GM, Davis CA, Samson LD, Drennan CL (2012) "Searching for DNA lesions: structural evidence for lower- and higher-affinity DNA binding conformations of human alkyladenine DNA glycosylase." Biochemistry, 51, 382-390. doi: 10.1021/bi201484k. Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA. SNAP output
3udg DNA binding protein-DNA X-ray (2.4 Å) George NP, Ngo KV, Chitteni-Pattu S, Norais CA, Battista JR, Cox MM, Keck JL (2012) "Structure and Cellular Dynamics of Deinococcus radiodurans Single-stranded DNA (ssDNA)-binding Protein (SSB)-DNA Complexes." J.Biol.Chem., 287, 22123-22132. doi: 10.1074/jbc.M112.367573. Structure of deinococcus radiodurans ssb bound to ssDNA. SNAP output
3ufd DNA binding protein-DNA X-ray (2.8 Å) Ball NJ, McGeehan JE, Streeter SD, Thresh SJ, Kneale GG (2012) "The structural basis of differential DNA sequence recognition by restriction-modification controller proteins." Nucleic Acids Res., 40, 10532-10542. doi: 10.1093/nar/gks718. C.esp1396i bound to its highest affinity operator site om. SNAP output
3ufj hydrolase-DNA X-ray (2.967 Å) Maiti A, Noon MS, Mackerell AD, Pozharski E, Drohat AC (2012) "Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA." Proc.Natl.Acad.Sci.USA, 109, 8091-8096. doi: 10.1073/pnas.1201010109. Human thymine DNA glycosylase bound to substrate analog 2'-fluoro-2'-deoxyuridine. SNAP output
3ugm transcription-DNA X-ray (3.0 Å) Mak AN, Bradley P, Cernadas RA, Bogdanove AJ, Stoddard BL (2012) "The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target." Science, 335, 716-719. doi: 10.1126/science.1216211. Structure of tal effector pthxo1 bound to its DNA target. SNAP output
3ugo transcription-DNA X-ray (2.096 Å) Feklistov A, Darst SA (2011) "Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit." Cell(Cambridge,Mass.), 147, 1257-1269. doi: 10.1016/j.cell.2011.10.041. Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (tacaat). SNAP output
3ugp transcription-DNA X-ray (2.697 Å) Feklistov A, Darst SA (2011) "Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit." Cell(Cambridge,Mass.), 147, 1257-1269. doi: 10.1016/j.cell.2011.10.041. Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (tataat). SNAP output
3uiq transferase-DNA X-ray (1.879 Å) Xia S, Eom SH, Konigsberg WH, Wang J (2012) "Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase." Protein Sci., 21, 447-451. doi: 10.1002/pro.2026. Rb69 DNA polymerase ternary complex containing dupnpp. SNAP output
3uk3 DNA-metal binding protein X-ray (2.1 Å) Vandevenne MS, Jacques DA, Guss JM, Mackay JP "Rediscovering DNA recognition by classical Zinc Fingers." Crystal structure of znf217 bound to DNA. SNAP output
3ukg DNA binding protein-DNA X-ray (2.95 Å) Matot B, Le Bihan YV, Lescasse R, Perez J, Miron S, David G, Castaing B, Weber P, Raynal B, Zinn-Justin S, Gasparini S, Le Du MH (2012) "The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA." Nucleic Acids Res., 40, 3197-3207. doi: 10.1093/nar/gkr1166. Crystal structure of rap1-DNA complex. SNAP output
3uld hydrolase-RNA-DNA X-ray (1.6 Å) Gan JH, Abdur R, Huang Z "RNA/DNA hybrid in complex with RNase H catalytic domain mutant D132N." High resolution structure of DNA-RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
3ulp DNA binding protein-DNA X-ray (2.1 Å) Antony E, Weiland EA, Korolev S, Lohman TM (2012) "Plasmodium falciparum SSB Tetramer Wraps Single-Stranded DNA with Similar Topology but Opposite Polarity to E. coli SSB." J.Mol.Biol., 420, 269-283. doi: 10.1016/j.jmb.2012.04.021. Plasmodium falciparum ssb complex with ssDNA. SNAP output
3uo7 hydrolase-DNA X-ray (3.002 Å) Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C, Jiang H, He C (2012) "Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA." Nat.Chem.Biol., 8, 328-330. doi: 10.1038/nchembio.914. Crystal structure of human thymine DNA glycosylase bound to substrate 5-carboxylcytosine. SNAP output
3uob hydrolase-DNA X-ray (3.011 Å) Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C, Jiang H, He C (2012) "Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA." Nat.Chem.Biol., 8, 328-330. doi: 10.1038/nchembio.914. Crystal structure of human thymine DNA glycosylase bound to substrate analog 2'-deoxy-2'-beta-fluoro-cytidine. SNAP output
3upq transferase, lyase-DNA X-ray (1.95 Å) Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K (2012) "The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda." Nucleic Acids Res., 40, 7518-7527. doi: 10.1093/nar/gks413. Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an ratp analog opposite a templating t.. SNAP output
3upu hydrolase-DNA X-ray (3.299 Å) He X, Byrd AK, Yun MK, Pemble CW, Harrison D, Yeruva L, Dahl C, Kreuzer KN, Raney KD, White SW (2012) "The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation." Structure, 20, 1189-1200. doi: 10.1016/j.str.2012.04.013. Crystal structure of the t4 phage sf1b helicase dda. SNAP output
3uq0 transferase, lyase-DNA X-ray (2.14 Å) Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K (2012) "The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda." Nucleic Acids Res., 40, 7518-7527. doi: 10.1093/nar/gks413. Crystal structure of the post-catalytic product complex of polymerase lambda with an ramp at the primer terminus.. SNAP output
3uq2 transferase, lyase-DNA X-ray (2.25 Å) Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K (2012) "The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda." Nucleic Acids Res., 40, 7518-7527. doi: 10.1093/nar/gks413. Crystal structure of the post-catalytic product complex of polymerase lambda with an rcmp inserted opposite a templating g and damp inserted opposite a templating t at the primer terminus.. SNAP output
3us0 transcription activator-DNA X-ray (2.5 Å) Chen C, Gorlatova N, Herzberg O (2012) "Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63." J.Biol.Chem., 287, 7477-7486. doi: 10.1074/jbc.M111.315820. Structure of p63 DNA binding domain in complex with a 22 base pair a-t rich response element containing a two base pair "at" spacer between half sites. SNAP output
3us1 transcription activator-DNA X-ray (2.8 Å) Chen C, Gorlatova N, Herzberg O (2012) "Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63." J.Biol.Chem., 287, 7477-7486. doi: 10.1074/jbc.M111.315820. Structure of p63 DNA binding domain in complex with a 22 base pair response element containing a two base pair "gc" spacer between half sites. SNAP output
3us2 transcription activator-DNA X-ray (4.2 Å) Chen C, Gorlatova N, Herzberg O (2012) "Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63." J.Biol.Chem., 287, 7477-7486. doi: 10.1074/jbc.M111.315820. Structure of p63 DNA binding domain in complex with a 19 base pair a-t rich response element containing two half sites with a single base pair overlap. SNAP output
3ut9 structural protein-DNA X-ray (2.2 Å) Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA (2012) "The mechanics behind DNA sequence-dependent properties of the nucleosome." Nucleic Acids Res., 40, 6338-6352. doi: 10.1093/nar/gks261. Crystal structure of nucleosome core particle assembled with a palindromic widom '601' derivative (ncp-601l). SNAP output
3uta structural protein-DNA X-ray (2.07 Å) Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA (2012) "The mechanics behind DNA sequence-dependent properties of the nucleosome." Nucleic Acids Res., 40, 6338-6352. doi: 10.1093/nar/gks261. Crystal structure of nucleosome core particle assembled with an alpha-satellite sequence containing two ttaaa elements (ncp-ta2). SNAP output
3utb structural protein-DNA X-ray (2.2 Å) Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA (2012) "The mechanics behind DNA sequence-dependent properties of the nucleosome." Nucleic Acids Res., 40, 6338-6352. doi: 10.1093/nar/gks261. Crystal structure of nucleosome core particle assembled with the 146b alpha-satellite sequence (ncp146b). SNAP output
3uvf hydrolase-DNA X-ray (3.0 Å) Jacoby K, Metzger M, Shen BW, Certo MT, Jarjour J, Stoddard BL, Scharenberg AM (2012) "Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space." Nucleic Acids Res., 40, 4954-4964. doi: 10.1093/nar/gkr1303. Expanding lagalidadg endonuclease scaffold diversity by rapidly surveying evolutionary sequence space. SNAP output
3uxp transferase, lyase-DNA X-ray (2.723 Å) Gridley CL, Rangarajan S, Firbank S, Dalal S, Sweasy JB, Jaeger J (2013) "Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta." Biochemistry, 52, 4422-4432. doi: 10.1021/bi301368f. Co-crystal structure of rat DNA polymerase beta mutator i260q: enzyme-DNA-ddttp. SNAP output
3uxw DNA-peptide X-ray (2.27 Å) Fonfria-Subiros E, Acosta-Reyes F, Saperas N, Pous J, Subirana JA, Campos JL (2012) "Crystal structure of a complex of DNA with one AT-hook of HMGA1." Plos One, 7, e37120. doi: 10.1371/journal.pone.0037120. Crystal structures of an a-t-hook-DNA complex. SNAP output
3v1z hydrolase-DNA X-ray (2.2 Å) Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V (2012) "Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease." Nucleic Acids Res., 40, 6741-6751. doi: 10.1093/nar/gks300. Crystal structure of type iif restriction endonuclease bse634i with cognate DNA. SNAP output
3v20 DNA binding protein, hydrolase-DNA X-ray (2.35 Å) Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V (2012) "Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease." Nucleic Acids Res., 40, 6741-6751. doi: 10.1093/nar/gks300. Crystal structure of type iif restriction endonuclease bse634i with cognate DNA. SNAP output
3v21 DNA binding protein, hydrolase-DNA X-ray (2.7 Å) Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V (2012) "Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease." Nucleic Acids Res., 40, 6741-6751. doi: 10.1093/nar/gks300. Crystal structure of type iif restriction endonuclease bse634i with cognate DNA. SNAP output
3v4i transferase-DNA X-ray (2.8 Å) Das K, Martinez SE, Bauman JD, Arnold E (2012) "HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism." Nat.Struct.Mol.Biol., 19, 253-259. doi: 10.1038/nsmb.2223. Crystal structure of hiv-1 reverse transcriptase (rt) with DNA and azttp. SNAP output
3v4r hydrolase-DNA X-ray (3.25 Å) Webster MP, Jukes R, Zamfir VS, Kay CW, Bagneris C, Barrett T (2012) "Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes." Nucleic Acids Res., 40, 8743-8758. doi: 10.1093/nar/gks633. Crystal structure of a uvrb dimer-DNA complex. SNAP output
3v6d transferase-DNA X-ray (2.7 Å) Das K, Martinez SE, Bauman JD, Arnold E (2012) "HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism." Nat.Struct.Mol.Biol., 19, 253-259. doi: 10.1038/nsmb.2223. Crystal structure of hiv-1 reverse transcriptase (rt) cross-linked with azt-terminated DNA. SNAP output
3v6h transferase-DNA X-ray (2.3 Å) Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP (2012) "Replication of n(2) ,3-ethenoguanine by DNA polymerases." Angew.Chem.Int.Ed.Engl., 51, 5466-5469. doi: 10.1002/anie.201109004. Replication of n2,3-ethenoguanine by DNA polymerases. SNAP output
3v6j transferase-DNA X-ray (2.3 Å) Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP (2012) "Replication of n(2) ,3-ethenoguanine by DNA polymerases." Angew.Chem.Int.Ed.Engl., 51, 5466-5469. doi: 10.1002/anie.201109004. Replication of n2,3-ethenoguanine by DNA polymerases. SNAP output
3v6k transferase-DNA X-ray (3.6 Å) Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS, Rizzo CJ, Egli M, Guengerich FP (2012) "Replication of n(2) ,3-ethenoguanine by DNA polymerases." Angew.Chem.Int.Ed.Engl., 51, 5466-5469. doi: 10.1002/anie.201109004. Replication of n2,3-ethenoguanine by DNA polymerases. SNAP output
3v6t DNA binding protein-DNA X-ray (1.85 Å) Deng D, Yan CY, Pan XJ, Mahfouz M, Wang JW, Zhu JK, Shi YG, Yan N (2012) "Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors." Science. doi: 10.1126/science.1215670. Crystal structure of the DNA-bound dhax3, a tal effector, at 1.85 angstrom. SNAP output
3v72 DNA binding protein-DNA X-ray (2.49 Å) Li Y, Gridley CL, Jaeger J, Sweasy JB, Schlick T (2012) "Unfavorable Electrostatic and Steric Interactions in DNA Polymerase beta E295K Mutant Interfere with the Enzyme s Pathway." J.Am.Chem.Soc., 134, 9999-10010. doi: 10.1021/ja300361r. Crystal structure of rat DNA polymerase beta mutator e295k: enzyme-dsDNA. SNAP output
3v79 transcription-DNA X-ray (3.85 Å) Choi SH, Wales TE, Nam Y, O'Donovan DJ, Sliz P, Engen JR, Blacklow SC (2012) "Conformational Locking upon Cooperative Assembly of Notch Transcription Complexes." Structure, 20, 340-349. doi: 10.1016/j.str.2011.12.011. Structure of human notch1 transcription complex including csl, ram, ank, and maml-1 on hes-1 promoter DNA sequence. SNAP output
3v7j transferase-DNA X-ray (2.25 Å) Rangarajan S, Gridley CL, Firbank S, Dalal S, Sweasy JB, Jaeger J "Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain." Co-crystal structure of wild type rat polymerase beta: enzyme-DNA binary complex. SNAP output
3v7k transferase-DNA X-ray (2.271 Å) Rangarajan S, Gridley CL, Firbank S, Dalal S, Sweasy JB, Jaeger J "Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain." Co-crystal structure of k72e variant of rat polymerase beta: enzyme-DNA binary complex. SNAP output
3v81 transferase-DNA X-ray (2.85 Å) Das K, Martinez SE, Bauman JD, Arnold E (2012) "HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism." Nat.Struct.Mol.Biol., 19, 253-259. doi: 10.1038/nsmb.2223. Crystal structure of hiv-1 reverse transcriptase (rt) with DNA and the nonnucleoside inhibitor nevirapine. SNAP output
3v9s hydrolase-DNA X-ray (2.1 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a product ssDNA (aac) with one mg in the active site. SNAP output
3v9u hydrolase-DNA X-ray (2.298 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a preferred ssDNA (aat) with two mg in the active site. SNAP output
3v9w hydrolase-DNA X-ray (1.702 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a preferred ssDNA (tta) with two mg in the active site. SNAP output
3v9x hydrolase-DNA X-ray (1.9 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a preferred ssDNA (aaa) with two mg in the active site. SNAP output
3v9z hydrolase-DNA X-ray (1.8 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a product ssDNA (acc) with one mg in the active site. SNAP output
3va0 hydrolase-DNA X-ray (2.201 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a di-nucleotide product (gg) with one mg in the active site. SNAP output
3va3 hydrolase-DNA X-ray (2.714 Å) Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS (2012) "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes." Nucleic Acids Res., 40, 8144-8154. doi: 10.1093/nar/gks548. Crystal structure of rnase t in complex with a duplex DNA product (stem loop DNA with 2 nucleotide 3' overhang). SNAP output
3vaf RNA binding protein-DNA X-ray (2.49 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru3 DNA. SNAP output
3vag RNA binding protein-DNA X-ray (2.19 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru3c2 DNA. SNAP output
3vah RNA binding protein-DNA X-ray (2.5 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru3c4 DNA. SNAP output
3vai RNA binding protein-DNA X-ray (2.2 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru3c5 DNA. SNAP output
3vaj RNA binding protein-DNA X-ray (1.9 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru5c6 DNA. SNAP output
3vak RNA binding protein-DNA X-ray (2.17 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru5 DNA. SNAP output
3val RNA binding protein-DNA X-ray (2.5 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru5c1 DNA. SNAP output
3vam RNA binding protein-DNA X-ray (2.4 Å) Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf CL (2013) "U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs." Nucleic Acids Res., 41, 3859-3873. doi: 10.1093/nar/gkt046. Structure of u2af65 variant with bru5c2 DNA. SNAP output
3vd0 antitumor protein-DNA X-ray (2.95 Å) Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A, Fronza G, Viadiu H (2012) "Structure of p73 DNA-binding domain tetramer modulates p73 transactivation." Proc.Natl.Acad.Sci.USA, 109, 6066-6071. doi: 10.1073/pnas.1115463109. Structure of p73 DNA binding domain tetramer modulates p73 transactivation. SNAP output
3vd1 antitumor protein-DNA X-ray (2.95 Å) Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A, Fronza G, Viadiu H (2012) "Structure of p73 DNA-binding domain tetramer modulates p73 transactivation." Proc.Natl.Acad.Sci.USA, 109, 6066-6071. doi: 10.1073/pnas.1115463109. Structure of p73 DNA binding domain tetramer modulates p73 transactivation. SNAP output
3vd2 antitumor protein-DNA X-ray (4.0 Å) Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A, Fronza G, Viadiu H (2012) "Structure of p73 DNA-binding domain tetramer modulates p73 transactivation." Proc.Natl.Acad.Sci.USA, 109, 6066-6071. doi: 10.1073/pnas.1115463109. Structure of p73 DNA binding domain tetramer modulates p73 transactivation. SNAP output
3vd6 transcription-DNA X-ray (1.98 Å) Wilkinson-White L, Lester KL, Ripin N, Jacques DA, Mitchell Guss J, Matthews JM (2015) "GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA." Protein Sci., 24, 1649-1659. doi: 10.1002/pro.2760. Both zn fingers of gata1 bound to palindromic DNA recognition site, p21 crystal form. SNAP output
3vdy DNA binding protein-DNA X-ray (2.8 Å) Yadav T, Carrasco B, Myers AR, George NP, Keck JL, Alonso JC (2012) "Genetic recombination in Bacillus subtilis: a division of labor between two single-strand DNA-binding proteins." Nucleic Acids Res., 40, 5546-5559. doi: 10.1093/nar/gks173. B. subtilis ssbb-ssDNA. SNAP output
3vea DNA binding protein-DNA X-ray (2.55 Å) Dupaigne P, Tonthat NK, Espeli O, Whitfill T, Boccard F, Schumacher MA (2012) "Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome." Mol.Cell, 48, 560-571. doi: 10.1016/j.molcel.2012.09.009. Crystal structure of matp-mats23mer. SNAP output
3veb DNA binding protein-DNA X-ray (2.8 Å) Dupaigne P, Tonthat NK, Espeli O, Whitfill T, Boccard F, Schumacher MA (2012) "Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome." Mol.Cell, 48, 560-571. doi: 10.1016/j.molcel.2012.09.009. Crystal structure of matp-mats. SNAP output
3vek transcription-DNA X-ray (2.63 Å) Wilkinson-White L, Lester KL, Ripin N, Jacques DA, Mitchell Guss J, Matthews JM (2015) "GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA." Protein Sci., 24, 1649-1659. doi: 10.1002/pro.2760. Both zn fingers of gata1 bound to palindromic DNA recognition site, p1 crystal form. SNAP output
3vh0 protein binding-DNA X-ray (2.9 Å) Kagawa W, Sagawa T, Niki H, Kurumizaka H (2011) "Structural basis for the DNA-binding activity of the bacterial beta-propeller protein YncE." Acta Crystallogr.,Sect.D, 67, 1045-1053. doi: 10.1107/S0907444911045033. Crystal structure of e. coli ynce complexed with DNA. SNAP output
3vk7 hydrolase-DNA X-ray (2.1 Å) Imamura K, Averill A, Wallace SS, Doublie S (2012) "Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA." J.Biol.Chem., 287, 4288-4298. doi: 10.1074/jbc.M111.315309. Crystal structure of DNA-glycosylase bound to DNA containing 5-hydroxyuracil. SNAP output
3vk8 hydrolase-DNA X-ray (2.0 Å) Imamura K, Averill A, Wallace SS, Doublie S (2012) "Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA." J.Biol.Chem., 287, 4288-4298. doi: 10.1074/jbc.M111.315309. Crystal structure of DNA-glycosylase bound to DNA containing thymine glycol. SNAP output
3vke DNA binding protein-DNA X-ray (1.77 Å) Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR, Barker A, Leedman PJ, Wilce JA, Wilce MCJ (2012) "Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides." Nucleic Acids Res., 40, 5101-5114. doi: 10.1093/nar/gks058. Contribution of the first k-homology domain of poly(c)-binding protein 1 to its affinity and specificity for c-rich oligonucleotides. SNAP output
3vok transcription-DNA X-ray (2.0 Å) Sawai H, Yamanaka M, Sugimoto H, Shiro Y, Aono S (2012) "Structural Basis for the Transcriptional Regulation of Heme Homeostasis in Lactococcus lactis." J.Biol.Chem., 287, 30755-30768. doi: 10.1074/jbc.M112.370916. X-ray crystal structure of wild type hrtr in the apo form with the target DNA.. SNAP output
3vw3 immune system-DNA X-ray (2.5 Å) Yokoyama H, Mizutani R, Satow Y (2013) "Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab." Acta Crystallogr.,Sect.D, 69, 504-512. doi: 10.1107/S0907444912050007. Antibody 64m-5 fab in complex with a double-stranded DNA (6-4) photoproduct. SNAP output
3vw4 DNA binding protein-DNA X-ray (2.7 Å) Itou H, Yagura M, Shirakihara Y, Itoh T (2015) "Structural Basis for Replication Origin Unwinding by An Initiator-Primase of Plasmid ColE2-P9: Duplex DNA Unwinding by A Single Protein." J.Biol.Chem., 290, 3601-3611. doi: 10.1074/jbc.M114.595645. Crystal structure of the DNA-binding domain of cole2-p9 rep in complex with the replication origin. SNAP output
3vwb transcription-DNA X-ray (2.416 Å) Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger S, Wang MT, Cui S, Jin Q (2013) "Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes." Nucleic Acids Res., 41, 10529-10541. doi: 10.1093/nar/gkt748. Crystal structure of virb core domain (se-met derivative) complexed with the cis-acting site (5-bru modifications) upstream icsb promoter. SNAP output
3vxv hydrolase-DNA X-ray (2.0 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of methyl cpg binding domain of mbd4 in complex with the 5mcg-tg sequence. SNAP output
3vxx hydrolase-DNA X-ray (2.204 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of methyl cpg binding domain of mbd4 in complex with the 5mcg-5mcg sequence. SNAP output
3vyb hydrolase-DNA X-ray (2.4 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of methyl cpg binding domain of mbd4 in complex with the 5mcg-hmcg sequence. SNAP output
3vyq hydrolase-DNA X-ray (2.525 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of the methyl cpg binding domain of mbd4 in complex with the 5mcg-tg sequence in space group p1. SNAP output
3w2a transcription-DNA X-ray (2.775 Å) Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger S, Wang MT, Cui S, Jin Q (2013) "Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes." Nucleic Acids Res., 41, 10529-10541. doi: 10.1093/nar/gkt748. Crystal structure of virb core domain complexed with the cis-acting site upstream icsp promoter. SNAP output
3w3c transcription-DNA X-ray (2.431 Å) Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger S, Wang MT, Cui S, Jin Q (2013) "Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes." Nucleic Acids Res., 41, 10529-10541. doi: 10.1093/nar/gkt748. Crystal structure of virb core domain complexed with the cis-acting site upstream icsb promoter. SNAP output
3w6v transcription activator-DNA X-ray (2.95 Å) Yao MD, Ohtsuka J, Nagata K, Miyazono K, Zhi Y, Ohnishi Y, Tanokura M (2013) "Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity." J.Biol.Chem., 288, 31019-31029. doi: 10.1074/jbc.M113.473611. Crystal structure of the DNA-binding domain of adpa, the global transcriptional factor, in complex with a target DNA. SNAP output
3w96 structural protein-DNA X-ray (3.0 Å) Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H (2013) "Contribution of histone N-terminal tails to the structure and stability of nucleosomes." FEBS Open Bio, 3, 363-369. doi: 10.1016/j.fob.2013.08.007. Crystal structure of human nucleosome core particle lacking h2a n-terminal region. SNAP output
3w97 structural protein-DNA X-ray (3.2 Å) Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H (2013) "Contribution of histone N-terminal tails to the structure and stability of nucleosomes." FEBS Open Bio, 3, 363-369. doi: 10.1016/j.fob.2013.08.007. Crystal structure of human nucleosome core particle lacking h2b n-terminal region. SNAP output
3w98 structural protein-DNA X-ray (3.42 Å) Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H (2013) "Contribution of histone N-terminal tails to the structure and stability of nucleosomes." FEBS Open Bio, 3, 363-369. doi: 10.1016/j.fob.2013.08.007. Crystal structure of human nucleosome core particle lacking h3.1 n-terminal region. SNAP output
3w99 structural protein-DNA X-ray (3.0 Å) Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H (2013) "Contribution of histone N-terminal tails to the structure and stability of nucleosomes." FEBS Open Bio, 3, 363-369. doi: 10.1016/j.fob.2013.08.007. Crystal structure of human nucleosome core particle lacking h4 n-terminal region. SNAP output
3wa9 structural protein-DNA X-ray (3.07 Å) Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H (2013) "Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2." Acta Crystallogr.,Sect.D, 69, 2431-2439. doi: 10.1107/S090744491302252X. The nucleosome containing human h2a.z.1. SNAP output
3waa structural protein-DNA X-ray (3.2 Å) Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A, Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W, Harata M, Kimura H, Kurumizaka H (2013) "Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2." Acta Crystallogr.,Sect.D, 69, 2431-2439. doi: 10.1107/S090744491302252X. The nucleosome containing human h2a.z.2. SNAP output
3waz hydrolase-DNA X-ray (3.0 Å) Miyazono K, Furuta Y, Watanabe-Matsui M, Miyakawa T, Ito T, Kobayashi I, Tanokura M (2014) "A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi." Nat Commun, 5, 3178. doi: 10.1038/ncomms4178. Crystal structure of a restriction enzyme pabi in complex with DNA. SNAP output
3wgi transcription-DNA X-ray (3.25 Å) Zheng Y, Ko T-P, Sun H, Huang C-H, Pei J, Qiu R, Wang AH-J, Wiegel J, Shao W, Guo R-T (2014) "Distinct structural features of Rex-family repressors to sense redox levels in anaerobes and aerobes." J.Struct.Biol., 188, 195-204. doi: 10.1016/j.jsb.2014.11.001. Crystal structure of rsp in complex with beta-nad+ and operator DNA. SNAP output
3wkj structural protein-DNA X-ray (2.8 Å) Urahama T, Horikoshi N, Osakabe A, Tachiwana H, Kurumizaka H (2014) "Structure of human nucleosome containing the testis-specific histone variant TSH2B." Acta Crystallogr.,Sect.F, 70, 444-449. doi: 10.1107/S2053230X14004695. The nucleosome containing human tsh2b. SNAP output
3wpc DNA binding protein-DNA X-ray (1.6 Å) Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T (2015) "Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9." Nature, 520, 702-705. doi: 10.1038/nature14138. Crystal structure of horse tlr9 in complex with agonistic dna1668_12mer. SNAP output
3wpd DNA binding protein-DNA X-ray (2.75 Å) Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T (2015) "Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9." Nature, 520, 702-705. doi: 10.1038/nature14138. Crystal structure of horse tlr9 in complex with inhibitory dna4084. SNAP output
3wpe DNA binding protein-DNA X-ray (2.38 Å) Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T (2015) "Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9." Nature, 520, 702-705. doi: 10.1038/nature14138. Crystal structure of bovine tlr9 in complex with agonistic dna1668_12mer. SNAP output
3wpg DNA binding protein-DNA X-ray (2.246 Å) Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T (2015) "Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9." Nature, 520, 702-705. doi: 10.1038/nature14138. Crystal structure of mouse tlr9 in complex with inhibitory dna4084 (form 1). SNAP output
3wph DNA binding protein-DNA X-ray (2.327 Å) Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T (2015) "Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9." Nature, 520, 702-705. doi: 10.1038/nature14138. Crystal structure of mouse tlr9 in complex with inhibitory dna4084 (form 2). SNAP output
3wpi DNA binding protein-DNA X-ray (2.246 Å) Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E, Uchiyama S, Miyake K, Shimizu T (2015) "Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9." Nature, 520, 702-705. doi: 10.1038/nature14138. Crystal structure of mouse tlr9 in complex with inhibitory dna_super. SNAP output
3wtp DNA binding protein-DNA X-ray (2.67 Å) Arimura Y, Shirayama K, Horikoshi N, Fujita R, Taguchi H, Kagawa W, Fukagawa T, Almouzni G, Kurumizaka H (2014) "Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3." Sci Rep, 4, 7115. doi: 10.1038/srep07115. Crystal structure of the heterotypic nucleosome containing human cenp-a and h3.3. SNAP output
3wts transcription-DNA X-ray (2.35 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of ets1, runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wtt transcription-DNA X-ray (2.35 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of phosphorylated ets1, runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wtu transcription-DNA X-ray (2.7 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of ets1 (v170a), runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wtv transcription-DNA X-ray (2.7 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of ets1(v170g), runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wtw transcription-DNA X-ray (2.9 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of ets1(k167a), runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wtx transcription-DNA X-ray (2.8 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of ets1(y329a), runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wty transcription-DNA X-ray (2.7 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the complex comprised of ets1(g333p), runx1, cbfbeta, and the tcralpha gene enhancer DNA. SNAP output
3wu1 transcription-DNA X-ray (2.4 Å) Shiina M, Hamada K, Inoue-Bungo T, Shimamura M, Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K (2015) "A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions." J.Mol.Biol., 427, 1655-1669. doi: 10.1016/j.jmb.2014.07.020. Crystal structure of the ets1-runx1-DNA ternary complex. SNAP output
3wvg hydrolase-DNA X-ray (2.25 Å) Kawamura T, Kobayashi T, Watanabe N (2015) "Analysis of the HindIII-catalyzed reaction by time-resolved crystallography." Acta Crystallogr.,Sect.D, 71, 256-265. doi: 10.1107/S1399004714025188. Time-resolved crystal structure of hindiii with 0sec soaking. SNAP output
3wvh hydrolase-DNA X-ray (2.54 Å) Kawamura T, Kobayashi T, Watanabe N (2015) "Analysis of the HindIII-catalyzed reaction by time-resolved crystallography." Acta Crystallogr.,Sect.D, 71, 256-265. doi: 10.1107/S1399004714025188. Time-resolved crystal structure of hindiii with 25sec soaking. SNAP output
3wvi hydrolase-DNA X-ray (2.55 Å) Kawamura T, Kobayashi T, Watanabe N (2015) "Analysis of the HindIII-catalyzed reaction by time-resolved crystallography." Acta Crystallogr.,Sect.D, 71, 256-265. doi: 10.1107/S1399004714025188. Time-resolved crystal structure of hindiii with 40 sec soaking. SNAP output
3wvk hydrolase-DNA X-ray (2.0 Å) Kawamura T, Kobayashi T, Watanabe N (2015) "Analysis of the HindIII-catalyzed reaction by time-resolved crystallography." Acta Crystallogr.,Sect.D, 71, 256-265. doi: 10.1107/S1399004714025188. Time-resolved crystal structure of hindiii with 230sec soaking. SNAP output
3wvp hydrolase-DNA X-ray (2.3 Å) Kawamura T, Kobayashi T, Watanabe N (2015) "Analysis of the HindIII-catalyzed reaction by time-resolved crystallography." Acta Crystallogr.,Sect.D, 71, 256-265. doi: 10.1107/S1399004714025188. Time-resolved crystal structure of hindiii with 60sec soaking. SNAP output
3x1l RNA binding protein-RNA-DNA X-ray (2.096 Å) Osawa T, Inanaga H, Sato C, Numata T (2015) "Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog." Mol.Cell, 58, 418-430. doi: 10.1016/j.molcel.2015.03.018. Crystal structure of the crispr-cas RNA silencing cmr complex bound to a target analog. SNAP output
3x1s structural protein-DNA X-ray (2.805 Å) Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2015) "Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming." Biochem.Biophys.Res.Commun., 464, 929-935. doi: 10.1016/j.bbrc.2015.07.070. Crystal structure of the nucleosome core particle. SNAP output
3x1t structural protein-DNA X-ray (2.808 Å) Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2015) "Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming." Biochem.Biophys.Res.Commun., 464, 929-935. doi: 10.1016/j.bbrc.2015.07.070. Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants h2aa and h2ba. SNAP output
3x1u structural protein-DNA X-ray (3.25 Å) Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2015) "Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming." Biochem.Biophys.Res.Commun., 464, 929-935. doi: 10.1016/j.bbrc.2015.07.070. Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming. SNAP output
3x1v structural protein-DNA X-ray (2.921 Å) Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2015) "Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming." Biochem.Biophys.Res.Commun., 464, 929-935. doi: 10.1016/j.bbrc.2015.07.070. Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming. SNAP output
3zda hydrolase-DNA X-ray (1.5 Å) Anstey-Gilbert CS, Hemsworth GR, Flemming CS, Hodskinson MRG, Zhang J, Sedelnikova SE, Stillman TJ, Sayers JR, Artymiuk PJ (2013) "The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases." Nucleic Acids Res., 41, 8357. doi: 10.1093/NAR/GKT591. Structure of e. coli exoix in complex with a fragment of the flap1 DNA oligonucleotide, potassium and magnesium. SNAP output
3zdb hydrolase-DNA X-ray (1.47 Å) Anstey-Gilbert CS, Hemsworth GR, Flemming CS, Hodskinson MRG, Zhang J, Sedelnikova SE, Stillman TJ, Sayers JR, Artymiuk PJ (2013) "The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases." Nucleic Acids Res., 41, 8357. doi: 10.1093/NAR/GKT591. Structure of e. coli exoix in complex with the palindromic 5ov4 DNA oligonucleotide, di-magnesium and potassium. SNAP output
3zdc hydrolase X-ray (1.53 Å) Anstey-Gilbert CS, Hemsworth GR, Flemming CS, Hodskinson MRG, Zhang J, Sedelnikova SE, Stillman TJ, Sayers JR, Artymiuk PJ (2013) "The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases." Nucleic Acids Res., 41, 8357. doi: 10.1093/NAR/GKT591. Structure of e. coli exoix in complex with the palindromic 5ov4 DNA oligonucleotide, potassium and calcium. SNAP output
3zdd hydrolase-DNA X-ray (1.5 Å) Anstey-Gilbert CS, Hemsworth GR, Flemming CS, Hodskinson MR, Zhang J, Sedelnikova SE, Stillman TJ, Sayers JR, Artymiuk PJ (2013) "The structure of Escherichia coli ExoIX--implications for DNA binding and catalysis in flap endonucleases." Nucleic Acids Res., 41, 8357-8367. doi: 10.1093/nar/gkt591. Structure of e. coli exoix in complex with the palindromic 5ov6 oligonucleotide and potassium. SNAP output
3zgz ligase-RNA X-ray (2.4 Å) Chopra S, Palencia A, Virus C, Tripathy A, Temple BR, Velazquez-Campoy A, Cusack S, Reader JS (2013) "Plant Tumour Biocontrol Agent Employs a tRNA-Dependent Mechanism to Inhibit Leucyl-tRNA Synthetase." Nat.Commun., 4, 1417. doi: 10.1038/NCOMMS2421. Ternary complex of e. coli leucyl-trna synthetase, trna(leu) and toxic moiety from agrocin 84 (tm84) in aminoacylation-like conformation. SNAP output
3zh2 oxidoreductase X-ray (2.1 Å) Cheung YW, Kwok J, Law AWL, Watt RM, Kotaka M, Tanner JA (2013) "Structural Basis for Discriminatory Recognition of Plasmodium Lactate Dehydrogenase by a DNA Aptamer." Proc.Natl.Acad.Sci.USA, 110, 15967. doi: 10.1073/PNAS.1309538110. Structure of plasmodium falciparum lactate dehydrogenase in complex with a DNA aptamer. SNAP output
3zhm transcription X-ray (2.6 Å) Frandsen KH, Rasmussen KK, Jensen MR, Hammer K, Pedersen M, Poulsen JN, Arleth L, Lo Leggio L (2013) "Binding of the N-Terminal Domain of the Lactococcal Bacteriophage Tp901-1 Ci Repressor to its Target DNA: A Crystallography, Small Angle Scattering, and Nuclear Magnetic Resonance Study." Biochemistry, 52, 6892. doi: 10.1021/BI400439Y. N-terminal domain of the ci repressor from bacteriophage tp901-1 in complex with the ol2 operator half-site. SNAP output
3zi5 hydrolase-DNA X-ray (3.2 Å) Golovenko D, Grazulis S, Manakova E, Sasnauskas G, Siksnys V, Zakrys L, Zaremba M (2014) "Structural Insight Into the Specificity of the B3 DNA-Binding Domains Provided by the Co-Crystal Structure of the C-Terminal Fragment of Bfii Restriction Enzyme." Nucleic Acids Res., 42, 4113. doi: 10.1093/NAR/GKT1368. Crystal structure of restriction endonuclease bfii c-terminal recognition domain in complex with cognate DNA. SNAP output
3zkc transcription-DNA X-ray (3.0 Å) Newman JA, Rodrigues C, Lewis RJ (2013) "Molecular Basis of the Activity of Sinr, the Master Regulator of Biofilm Formation in Bacillus Subtilis." J.Biol.Chem., 288, 10766. doi: 10.1074/JBC.M113.455592. Crystal structure of the master regulator for biofilm formation sinr in complex with DNA.. SNAP output
3zlj DNA binding protein-DNA X-ray (3.1 Å) Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HHK, Marinus MG, Lebbink JHG, Svergun DI, Friedhoff P, Sixma TK (2013) "Using Stable Muts Dimers and Tetramers to Quantitatively Analyze DNA Mismatch Recognition and Sliding Clamp Formation." Nucleic Acids Res., 41, 8166. doi: 10.1093/NAR/GKT582. Crystal structure of full-length e.coli DNA mismatch repair protein muts d835r mutant in complex with gt mismatched DNA. SNAP output
3zp5 transcription-DNA X-ray (2.0 Å) Cooper CDO, Newman JA, Aitkenhead H, Allerston CK, Gileadi O (2015) "Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation." J.Biol.Chem., 290, 13692. doi: 10.1074/JBC.M115.646737. Crystal structure of the DNA binding ets domain of the human protein fev in complex with DNA. SNAP output
3zpl transcription-DNA X-ray (2.8 Å) Stevenson CEM, Assaad A, Chandra G, Le TBK, Greive SJ, Bibb MJ, Lawson DM (2013) "Investigation of DNA Sequence Recognition by a Streptomycete Marr Family Transcriptional Regulator Through Surface Plasmon Resonance and X-Ray Crystallography." Nucleic Acids Res., 41, 7009. doi: 10.1093/NAR/GKT523. Crystal structure of sco3205, a marr family transcriptional regulator from streptomyces coelicolor, in complex with DNA. SNAP output
3zqc transcription-DNA X-ray (2.9 Å) Wei S-Y, Lou Y-C, Tsai J-Y, Ho MR, Chou CC, Rajasekaran M, Hsu H-M, Tai J-H, Hsiao C-D, Chen C (2012) "Structure of the Trichomonas Vaginalis Myb3 DNA-Binding Domain Bound to a Promoter Sequence Reveals a Unique C-Terminal Beta-Hairpin Conformation." Nucleic Acids Res., 40, 449. doi: 10.1093/NAR/GKR707. Structure of the trichomonas vaginalis myb3 DNA-binding domain bound to a promoter sequence reveals a unique c-terminal beta-hairpin conformation. SNAP output
3zql protein-DNA complex X-ray (2.99 Å) Le TBK, Schumacher MA, Lawson DM, Brennan RG, Buttner MJ (2011) "The Crystal Structure of the Tetr Family Transcriptional Repressor Simr Bound to DNA and the Role of a Flexible N-Terminal Extension in Minor Groove Binding." Nucleic Acids Res., 39, 9433. doi: 10.1093/NAR/GKR640. DNA-bound form of tetr-like repressor simr. SNAP output
3zvk antitoxin-toxin-DNA X-ray (2.5 Å) Mate MJ, Vincentelli R, Foos N, Raoult D, Cambillau C, Ortiz-Lombardia M (2012) "Crystal Structure of the DNA-Bound Vapbc2 Antitoxin/Toxin Pair from Rickettsia Felis." Nucleic Acids Res., 40, 3245. doi: 10.1093/NAR/GKR1167. Crystal structure of vapbc2 from rickettsia felis bound to a DNA fragment from their promoter. SNAP output
3zvm hydrolase-transferase-DNA X-ray (1.997 Å) Garces F, Pearl LH, Oliver AW (2011) "The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase." Mol. Cell, 44, 385-396. doi: 10.1016/j.molcel.2011.08.036. The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase. SNAP output
3zvn hydrolase-transferase-DNA X-ray (2.15 Å) Garces F, Pearl LH, Oliver AW (2011) "The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase." Mol. Cell, 44, 385-396. doi: 10.1016/j.molcel.2011.08.036. The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase. SNAP output
4a04 transcription X-ray (2.58 Å) El Omari K, De Mesmaeker J, Karia D, Ginn H, Bhattacharya S, Mancini EJ (2012) "Structure of the DNA-Bound T-Box Domain of Human Tbx1, a Transcription Factor Associated with the Digeorge Syndrome." Proteins, 80, 655. doi: 10.1002/PROT.23208. Structure of the DNA-bound t-box domain of human tbx1, a transcription factor associated with the digeorge syndrome. SNAP output
4a08 DNA-binding protein-DNA X-ray (3.0 Å) Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH (2011) "The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation." Cell(Cambridge,Mass.), 147, 1024. doi: 10.1016/J.CELL.2011.10.035. Structure of hsddb1-drddb2 bound to a 13 bp cpd-duplex (purine at d-1 position) at 3.0 Å resolution (cpd 1). SNAP output
4a09 DNA-binding protein-DNA X-ray (3.1 Å) Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH (2011) "The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation." Cell(Cambridge,Mass.), 147, 1024. doi: 10.1016/J.CELL.2011.10.035. Structure of hsddb1-drddb2 bound to a 15 bp cpd-duplex (purine at d-1 position) at 3.1 Å resolution (cpd 2). SNAP output
4a0a DNA binding protein-DNA X-ray (3.6 Å) Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH (2011) "The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation." Cell(Cambridge,Mass.), 147, 1024. doi: 10.1016/J.CELL.2011.10.035. Structure of hsddb1-drddb2 bound to a 16 bp cpd-duplex (pyrimidine at d-1 position) at 3.6 Å resolution (cpd 3). SNAP output
4a0b DNA binding protein-DNA X-ray (3.8 Å) Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH (2011) "The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation." Cell(Cambridge,Mass.), 147, 1024. doi: 10.1016/J.CELL.2011.10.035. Structure of hsddb1-drddb2 bound to a 16 bp cpd-duplex (pyrimidine at d-1 position) at 3.8 Å resolution (cpd 4). SNAP output
4a0k ligase-DNA-binding protein-DNA X-ray (5.93 Å) Fischer ES, Scrima A, Bohm K, Matsumoto S, Lingaraju GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F, Iwai S, Gut H, Sugasawa K, Thoma NH (2011) "The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation." Cell(Cambridge,Mass.), 147, 1024. doi: 10.1016/J.CELL.2011.10.035. Structure of ddb1-ddb2-cul4a-rbx1 bound to a 12 bp abasic site containing DNA-duplex. SNAP output
4a0l ligase-DNA-binding protein-DNA X-ray (7.4 Å) Fischer ES, Scrima A, Bohm K, Matsumoto S, Lingaraju GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F, Iwai S, Gut H, Sugasawa K, Thoma NH (2011) "The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation." Cell(Cambridge,Mass.), 147, 1024. doi: 10.1016/J.CELL.2011.10.035. Structure of ddb1-ddb2-cul4b-rbx1 bound to a 12 bp abasic site containing DNA-duplex. SNAP output
4a12 transcription X-ray (3.15 Å) Albanesi D, Reh G, Guerin ME, Schaeffer F, Debarbouille M, Buschiazzo A, Schujman GE, De Mendoza D, Alzari PM (2013) "Structural Basis for Feed-Forward Transcriptional Regulation of Membrane Lipid Homeostasis in Staphylococcus Aureus." Plos Pathog., 9, 3108. doi: 10.1371/JOURNAL.PPAT.1003108. Structure of the global transcription regulator fapr from staphylococcus aureus in complex with DNA operator. SNAP output
4a15 hydrolase X-ray (2.2 Å) Kuper J, Wolski SC, Michels G, Kisker C (2011) "Functional and Structural Studies of the Nucleotide Excision Repair Helicase Xpd Suggest a Polarity for DNA Translocation." Embo J., 31, 494. doi: 10.1038/EMBOJ.2011.374. Crystal structure of an xpd DNA complex. SNAP output
4a3b transcription X-ray (3.5 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid. SNAP output
4a3c transcription X-ray (3.5 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 5nt DNA-RNA hybrid. SNAP output
4a3d transcription X-ray (3.4 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 6nt DNA-RNA hybrid. SNAP output
4a3e transcription X-ray (3.4 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with ampcpp. SNAP output
4a3f transcription X-ray (3.5 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 6nt DNA-RNA hybrid and soaked with ampcpp. SNAP output
4a3g transcription X-ray (3.5 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid. SNAP output
4a3i transcription X-ray (3.8 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii binary complex with DNA. SNAP output
4a3j transcription X-ray (3.7 Å) Cheung ACM, Sainsbury S, Cramer P (2011) "Structural Basis of Initial RNA Polymerase II Transcription." Embo J., 30, 4755. doi: 10.1038/EMBOJ.2011.396. RNA polymerase ii initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with gmpcpp. SNAP output
4a3k transcription X-ray (3.5 Å) Cheung ACM, Sainsbury S, Cramer P (2011) "Structural Basis of Initial RNA Polymerase II Transcription." Embo J., 30, 4755. doi: 10.1038/EMBOJ.2011.396. RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid. SNAP output
4a3l transcription X-ray (3.5 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with ampcpp. SNAP output
4a3m transcription X-ray (3.9 Å) Cheung AC, Sainsbury S, Cramer P (2011) "Structural basis of initial RNA polymerase II transcription." EMBO J., 30, 4755-4763. doi: 10.1038/emboj.2011.396. RNA polymerase ii initial transcribing complex with a 4nt DNA-RNA hybrid and soaked with ampcpp. SNAP output
4a75 chaperone-DNA X-ray (1.75 Å) Mayr F, Schutz A, Doge N, Heinemann U (2012) "The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna." Nucleic Acids Res., 40, 7492. doi: 10.1093/NAR/GKS355. The lin28b cold shock domain in complex with hexathymidine.. SNAP output
4a76 chaperone-DNA X-ray (1.92 Å) Mayr F, Schutz A, Doge N, Heinemann U (2012) "The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna." Nucleic Acids Res., 40, 7492. doi: 10.1093/NAR/GKS355. The lin28b cold shock domain in complex with heptathymidine. SNAP output
4a8f transferase X-ray (3.3 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a8k transferase-DNA X-ray (3.5 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a8m transferase-DNA X-ray (2.92 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a8q transferase-DNA X-ray (3.06 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a8s transferase-DNA X-ray (2.9 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a8w transferase-DNA X-ray (3.04 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a8y transferase-DNA X-ray (3.41 Å) Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM (2012) "Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation to Elongation." J.Virol., 86, 2837. doi: 10.1128/JVI.05168-11. Non-catalytic ions direct the RNA-dependent RNA polymerase of bacterial dsrna virus phi6 from de novo initiation to elongation. SNAP output
4a93 transcription X-ray (3.4 Å) Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C, Gotte D, Strathern JN, Carell T, Cramer P, Kashlev M (2012) "Mechanism of Translesion Transcription by RNA Polymerase II and its Role in Cellular Resistance to DNA Damage." Mol.Cell, 46, 18. doi: 10.1016/J.MOLCEL.2012.02.006. RNA polymerase ii elongation complex containing a cpd lesion. SNAP output
4aa6 transcription-DNA X-ray (2.6 Å) Schwabe JW, Chapman L, Rhodes D (1995) "The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation." Structure, 3, 201-213. doi: 10.1016/s0969-2126(01)00150-2. The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation. SNAP output
4aab hydrolase-DNA X-ray (2.5 Å) Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2012) "Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage." Nucleic Acids Res., 40, 6936-6945. doi: 10.1093/NAR/GKS320. Crystal structure of the mutant d75n i-crei in complex with its wild- type target (the four central bases, 2nn region, are composed by gtac from 5' to 3'). SNAP output
4aad hydrolase-DNA X-ray (3.1 Å) Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2012) "Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage." Nucleic Acids Res., 40, 6936-6945. doi: 10.1093/NAR/GKS320. Crystal structure of the mutant d75n i-crei in complex with its wild- type target in absence of metal ions at the active site (the four central bases, 2nn region, are composed by gtac from 5' to 3'). SNAP output
4aae hydrolase-DNA X-ray (2.6 Å) Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2012) "Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage." Nucleic Acids Res., 40, 6936-6945. doi: 10.1093/NAR/GKS320. Crystal structure of the mutant d75n i-crei in complex with an altered target (the four central bases, 2nn region, are composed by agcg from 5' to 3'). SNAP output
4aaf hydrolase-DNA X-ray (2.5 Å) Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2012) "Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage." Nucleic Acids Res., 40, 6936. doi: 10.1093/NAR/GKS320. Crystal structure of the mutant d75n i-crei in complex with an altered target (the four central bases, 2nn region, are composed by tgca from 5' to 3'). SNAP output
4aag hydrolase-DNA X-ray (2.8 Å) Molina R, Redondo P, Stella S, Marenchino M, D'Abramo M, Gervasio FL, Charles Epinat J, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2012) "Non-Specific Protein-DNA Interactions Control I-Crei Target Binding and Cleavage." Nucleic Acids Res., 40, 6936. doi: 10.1093/NAR/GKS320. Crystal structure of the mutant d75n i-crei in complex with its wild- type target in presence of ca at the active site (the four central bases, 2nn region, are composed by gtac from 5' to 3'). SNAP output
4abt hydrolase-DNA X-ray (2.22 Å) Manakova EN, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V "Structure of Type Iif Restriction Endonuclease Ngomiv with Cognate Uncleaved DNA." Crystal structure of type iif restriction endonuclease ngomiv with cognate uncleaved DNA. SNAP output
4aij transcription X-ray (2.05 Å) Quade N, Mendonca C, Herbst K, Heroven AK, Ritter C, Heinz DW, Dersch P (2012) "Structural Basis for Intrinsic Thermosensing by the Master Virulence Regulator Rova of Yersinia." J.Biol.Chem., 287, 35796. doi: 10.1074/JBC.M112.379156. Crystal structure of rova from yersinia in complex with a rova promoter fragment. SNAP output
4aik transcription X-ray (1.85 Å) Quade N, Mendonca C, Herbst K, Heroven AK, Ritter C, Heinz DW, Dersch P (2012) "Structural Basis for Intrinsic Thermosensing by the Master Virulence Regulator Rova of Yersinia." J.Biol.Chem., 287, 35796. doi: 10.1074/JBC.M112.379156. Crystal structure of rova from yersinia in complex with an invasin promoter fragment. SNAP output
4ail transferase X-ray (2.9 Å) Wynne SA, Pinheiro VB, Holliger P, Leslie AG (2013) "Structures of an Apo and a Binary Complex of an Evolved Archeal B Family DNA Polymerase Capable of Synthesising Highly Cy-Dye Labelled DNA." Plos One, 8, 70892. doi: 10.1371/JOURNAL.PONE.0070892. Crystal structure of an evolved replicating DNA polymerase. SNAP output
4al5 hydrolase-RNA X-ray (2.0 Å) Haurwitz RE, Sternberg SH, Doudna JA (2012) "Csy4 Relies on an Unusual Catalytic Dyad to Position and Cleave Crispr RNA." Embo J., 31, 2824. doi: 10.1038/EMBOJ.2012.107. Crystal structure of the csy4-crrna product complex. SNAP output
4am3 transferase-RNA X-ray (3.0 Å) Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF (2012) "Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly." Open Biol., 2, 20028. doi: 10.1098/RSOB.120028. Crystal structure of c. crescentus pnpase bound to RNA. SNAP output
4aqu hydrolase X-ray (2.3 Å) Valton J, Daboussi F, Leduc S, Molina R, Redondo P, Macmaster R, Montoya G, Duchateau P (2012) "5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases." J.Biol.Chem., 287, 30139. doi: 10.1074/JBC.M112.379966. Crystal structure of i-crei complexed with its target methylated at position plus 2 (in the b strand) in the presence of calcium. SNAP output
4aqx hydrolase X-ray (2.2 Å) Valton J, Daboussi F, Leduc S, Molina R, Redondo P, Macmaster R, Montoya G, Duchateau P (2012) "5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases." J.Biol.Chem., 287, 30139. doi: 10.1074/JBC.M112.379966. Crystal structure of i-crei complexed with its target methylated at position plus 2 (in the b strand) in the presence of magnesium. SNAP output
4aso structural protein-DNA X-ray (7.0 Å) Aylett CHS, Lowe J (2012) "Superstructure of the Centromeric Complex of Tubzrc Plasmid Partitioning Systems." Proc.Natl.Acad.Sci.USA, 109, 16522. doi: 10.1073/PNAS.1210899109. Tubr bound to 24 bp of tubc from bacillus thuringiensis serovar israelensis pbtoxis. SNAP output
4ass structural protein-DNA X-ray (7.0 Å) Aylett CHS, Lowe J (2012) "Superstructure of the Centromeric Complex of Tubzrc Plasmid Partitioning Systems." Proc.Natl.Acad.Sci.USA, 109, 16522. doi: 10.1073/PNAS.1210899109. Tubr bound to tubc - 26 bp - from bacillus thuringiensis serovar israelensis pbtoxis. SNAP output
4ati DNA-binding protein-DNA X-ray (2.6 Å) Pogenberg V, Hogmundsdottir M, Bergsteinsdottir K, Schepsky A, Phung B, Deineko V, Milewski M, Steingrimsson E, Wilmanns M (2012) "Restricted Leucine Zipper Dimerization and Specificity of DNA Recognition of the Melanocyte Master Regulator Mitf." Genes Dev., 26, 2647. doi: 10.1101/GAD.198192.112. Mitf:m-box complex. SNAP output
4atk DNA binding protein-DNA X-ray (2.95 Å) Pogenberg V, Hogmundsdottir M, Bergsteinsdottir K, Schepsky A, Phung B, Deineko V, Milewski M, Steingrimsson E, Wilmanns M (2012) "Restricted Leucine Zipper Dimerization and Specificity of DNA Recognition of the Melanocyte Master Regulator Mitf." Genes Dev., 26, 2647. doi: 10.1101/GAD.198192.112. Mitf:e-box complex. SNAP output
4auw transcription X-ray (2.9 Å) Textor LC, Wilmanns M, Holton SJ (2007) "Expression, purification, crystallization and preliminary crystallographic analysis of the mouse transcription factor MafB in complex with its DNA-recognition motif Cmare." Acta Crystallogr Sect F Struct Biol Cryst Commun., 63, 657-661. doi: 10.1107/S1744309107031260. Crystal structure of the bzip homodimeric mafb in complex with the c- mare binding site. SNAP output
4av1 transferase X-ray (3.1 Å) Ali AAE, Timinszky G, Arribas-Bosacoma R, Kozlowski M, Hassa PO, Hassler M, Ladurner AG, Pearl LH, Oliver AW (2012) "The Zinc-Finger Domains of Parp1 Cooperate to Recognise DNA Strand-Breaks." Nat.Struct.Mol.Biol., 19, 685. doi: 10.1038/NSMB.2335. Crystal structure of the human parp-1 DNA binding domain in complex with DNA. SNAP output
4awl transcription-DNA X-ray (3.08 Å) Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M, Mantovani R (2013) "Sequence-Specific Transcription Factor NF-Y Displays Histone-Like DNA Binding and H2B-Like Ubiquitination." Cell(Cambridge,Mass.), 152, 132. doi: 10.1016/J.CELL.2012.11.047. The nf-y transcription factor is structurally and functionally a sequence specific histone. SNAP output
4b20 hydrolase X-ray (2.75 Å) Rosnes I, Rowe AD, Vik ES, Forstrom RJ, Alseth I, Bjoras M, Dalhus B (2013) "Structural Basis of DNA Loop Recognition by Endonuclease V." Structure, 21, 257. doi: 10.1016/J.STR.2012.12.007. Structural basis of DNA loop recognition by endonuclease v. SNAP output
4b21 hydrolase-DNA X-ray (1.45 Å) Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M (2013) "Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2." Structure, 21, 154. doi: 10.1016/J.STR.2012.11.004. Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. SNAP output
4b22 hydrolase X-ray (1.9 Å) Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M (2013) "Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2." Structure, 21, 154. doi: 10.1016/J.STR.2012.11.004. Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. SNAP output
4b23 hydrolase-DNA X-ray (2.0 Å) Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M (2013) "Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2." Structure, 21, 154. doi: 10.1016/J.STR.2012.11.004. Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. SNAP output
4b24 hydrolase-DNA X-ray (2.3 Å) Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M (2013) "Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2." Structure, 21, 154. doi: 10.1016/J.STR.2012.11.004. Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. SNAP output
4b3o hydrolase-DNA-RNA X-ray (3.3 Å) Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang W (2013) "Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation." Nat.Struct.Mol.Biol., 20, 230. doi: 10.1038/NSMB.2485. Structures of hiv-1 rt and RNA-DNA complex reveal a unique rt conformation and substrate interface. SNAP output
4b3p hydrolase-RNA-DNA X-ray (4.839 Å) Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang W (2013) "Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation." Nat.Struct.Mol.Biol., 20, 230. doi: 10.1038/NSMB.2485. Structures of hiv-1 rt and RNA-DNA complex reveal a unique rt conformation and substrate interface. SNAP output
4b3q hydrolase-DNA-RNA X-ray (5.0 Å) Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang W (2013) "Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation." Nat.Struct.Mol.Biol., 20, 230. doi: 10.1038/NSMB.2485. Structures of hiv-1 rt and RNA-DNA complex reveal a unique rt conformation and substrate interface. SNAP output
4b5f hydrolase-DNA X-ray (2.005 Å) Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS (2012) "Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis." Proc. Natl. Acad. Sci. U.S.A., 109, 16852-16857. doi: 10.1073/pnas.1206563109. Substrate bound neisseria ap endonuclease in absence of metal ions (crystal form 1). SNAP output
4b5g hydrolase-DNA X-ray (2.75 Å) Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS (2012) "Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis." Proc. Natl. Acad. Sci. U.S.A., 109, 16852-16857. doi: 10.1073/pnas.1206563109. Substrate bound neisseria ap endonuclease in absence of metal ions (crystal form 2). SNAP output
4b5h hydrolase-DNA X-ray (3.05 Å) Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS (2012) "Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis." Proc. Natl. Acad. Sci. U.S.A., 109, 16852-16857. doi: 10.1073/pnas.1206563109. Substate bound inactive mutant of neisseria ap endonuclease in presence of metal ions. SNAP output
4b5i hydrolase-DNA X-ray (2.555 Å) Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS (2012) "Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis." Proc. Natl. Acad. Sci. U.S.A., 109, 16852-16857. doi: 10.1073/pnas.1206563109. Product complex of neisseria ap endonuclease in presence of metal ions. SNAP output
4b5j hydrolase-DNA X-ray (2.1 Å) Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS (2012) "Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis." Proc. Natl. Acad. Sci. U.S.A., 109, 16852-16857. doi: 10.1073/pnas.1206563109. Neisseria ap endonuclease bound to the substrate with an orphan adenine base. SNAP output
4b5m hydrolase-DNA X-ray (2.758 Å) Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K, Tang CM, Baldwin GS, Freemont PS (2012) "Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis." Proc. Natl. Acad. Sci. U.S.A., 109, 16852-16857. doi: 10.1073/pnas.1206563109. Neisseria ap endonuclease bound to the substrate with a cytosine orphan base. SNAP output
4b9l transferase-DNA X-ray (2.05 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i with the oxidative formamidopyrimidine-da DNA lesion in the pre-insertion site.. SNAP output
4b9m transferase-DNA X-ray (2.05 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i with an oxidative formamidopyrimidine-da DNA lesion -thymine basepair in the post- insertion site.. SNAP output
4b9n transferase-DNA X-ray (2.2 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i correctly bypassing the oxidative formamidopyrimidine-da DNA lesion.. SNAP output
4b9s transferase-DNA X-ray (1.73 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i with an oxidative formamidopyrimidine-dg DNA lesion outside of the pre-insertion site.. SNAP output
4b9t transferase-DNA X-ray (2.65 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i with an oxidative formamidopyrimidine-dg DNA lesion -dc basepair in the post-insertion site.. SNAP output
4b9u transferase-DNA X-ray (2.1 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i with an oxidative formamidopyrimidine-dg DNA lesion -da basepair in the post-insertion site.. SNAP output
4b9v transferase-DNA X-ray (2.0 Å) Gehrke TH, Lischke U, Gasteiger KL, Schneider S, Arnold S, Muller HC, Stephenson DS, Zipse H, Carell T (2013) "Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions." Nat.Chem.Biol., 9, 455. doi: 10.1038/NCHEMBIO.1254. Structure of the high fidelity DNA polymerase i with extending from an oxidative formamidopyrimidine-dg DNA lesion -da basepair.. SNAP output
4bac transferase-DNA X-ray (3.263 Å) Yin Z, Lapkouski M, Yang W, Craigie R (2012) "Assembly of Prototype Foamy Virus Strand Transfer Complexes on Product DNA Bypassing Catalysis of Integration." Protein Sci., 21, 1849. doi: 10.1002/PRO.2166. Prototype foamy virus strand transfer complexes on product DNA. SNAP output
4bbs transcription X-ray (3.6 Å) Sainsbury S, Niesser J, Cramer P (2013) "Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex." Nature, 493, 437. doi: 10.1038/NATURE11715. Structure of an initially transcribing RNA polymerase ii-tfiib complex. SNAP output
4bdp transferase-DNA X-ray (1.8 Å) Kiefer JR, Mao C, Braman JC, Beese LS (1998) "Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal." Nature, 391, 304-307. doi: 10.1038/34693. Crystal structure of bacillus DNA polymerase i fragment complexed to 11 base pairs of duplex DNA after addition of two datp residues. SNAP output
4bdy transferase-DNA X-ray (2.52 Å) Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y (2013) "Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase." Acs Chem.Biol., 8, 209. doi: 10.1021/CB300471N. Pfv intasome with inhibitor xz-89. SNAP output
4bdz transferase-DNA X-ray (2.85 Å) Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y (2013) "Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase." Acs Chem.Biol., 8, 209. doi: 10.1021/CB300471N. Pfv intasome with inhibitor xz-90. SNAP output
4be0 transferase-DNA X-ray (2.68 Å) Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y (2013) "Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase." Acs Chem.Biol., 8, 209. doi: 10.1021/CB300471N. Pfv intasome with inhibitor xz-115. SNAP output
4be1 transferase-DNA X-ray (2.71 Å) Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y (2013) "Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase." Acs Chem.Biol., 8, 209. doi: 10.1021/CB300471N. Pfv intasome with inhibitor xz-116. SNAP output
4be2 transferase-DNA X-ray (2.38 Å) Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y (2013) "Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase." Acs Chem.Biol., 8, 209. doi: 10.1021/CB300471N. Pfv intasome with inhibitor xz-259. SNAP output
4bhk transcription-DNA X-ray (2.32 Å) Sayou C, Monniaux M, Nanao MH, Moyroud E, Brockington SF, Thevenon E, Chahtane H, Warthmann N, Melkonian M, Zhang Y, Wong GK, Weigel D, Parcy F, Dumas R (2014) "A Promiscuous Intermediate Underlies the Evolution of Leafy DNA Binding Specificity." Science, 343, 645. doi: 10.1126/SCIENCE.1248229. Crystal structure of moss leafy bound to DNA. SNAP output
4bhm transcription-DNA X-ray (2.7 Å) Huang J, Zhao Y, Liu H, Huang D, Cheng X, Zhao W, Taylor IA, Liu J, Peng YL (2015) "Substitution of Tryptophan 89 with Tyrosine Switches the DNA Binding Mode of Pc4." Sci.Rep., 5, 8789. doi: 10.1038/SREP08789. The crystal structure of mosub1-DNA complex reveals a novel DNA binding mode. SNAP output
4bnc DNA binding protein X-ray (2.9 Å) Cooper CDO, Newman JA, Aitkenhead H, Allerston CK, Gileadi O (2015) "Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation." J.Biol.Chem., 290, 13692. doi: 10.1074/JBC.M115.646737. Crystal structure of the DNA-binding domain of human etv1 complexed with DNA. SNAP output
4boc transcription X-ray (2.65 Å) Schwinghammer K, Cheung ACM, Morozov YI, Agaronyan K, Temiakov D, Cramer P (2013) "Structure of Human Mitochondrial RNA Polymerase Elongation Complex." Nat.Struct.Mol.Biol., 20, 1298. doi: 10.1038/NSMB.2683. Structure of mitochondrial RNA polymerase elongation complex. SNAP output
4bqa transcription X-ray (2.5 Å) Newman JA, Cooper CDO, Aitkenhead H, Gileadi O (2015) "Structural Insights Into the Autoregulation and Cooperativity of the Human Transcription Factor Ets-2." J.Biol.Chem., 290, 8539. doi: 10.1074/JBC.M114.619270. Crystal structure of the ets domain of human ets2 in complex with DNA. SNAP output
4bul isomerase X-ray (2.6 Å) Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS, Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken JM, Giordano I, Hoover JL, Huang J, Jones GE, Kusalakumari Sukmar SK, Spitzfaden C, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN, Pearson ND (2013) "Novel Hydroxyl Tricyclics (E.G., Gsk966587) as Potent Inhibitors of Bacterial Type Iia Topoisomerases." Bioorg.Med.Chem.Lett., 23, 5437. doi: 10.1016/J.BMCL.2013.07.013. Novel hydroxyl tricyclics (e.g. gsk966587) as potent inhibitors of bacterial type iia topoisomerases. SNAP output
4bwj transferase-DNA X-ray (1.55 Å) Blatter N, Bergen K, Nolte O, Welte W, Diederichs K, Mayer J, Wieland M, Marx A (2013) "Structure and Function of an RNA-Reading Thermostable DNA Polymerase." Angew.Chem.Int.Ed.Engl., 52, 11935. doi: 10.1002/ANIE.201306655. Klentaq mutant in complex with DNA and ddctp. SNAP output
4bwm transferase-DNA-RNA X-ray (1.749 Å) Blatter N, Bergen K, Nolte O, Welte W, Diederichs K, Mayer J, Wieland M, Marx A (2013) "Structure and Function of an RNA-Reading Thermostable DNA Polymerase." Angew.Chem.Int.Ed.Engl., 52, 11935. doi: 10.1002/ANIE.201306655. Klentaq mutant in complex with a RNA-DNA hybrid. SNAP output
4bxo hydrolase-DNA X-ray (2.15 Å) Coulthard R, Deans AJ, Swuec P, Bowles M, Costa A, West SC, Mcdonald NQ (2013) "Architecture and DNA Recognition Elements of the Fanconi Anemia Fancm-Faap24 Complex." Structure, 21, 1648. doi: 10.1016/J.STR.2013.07.006. Architecture and DNA recognition elements of the fanconi anemia fancm- faap24 complex. SNAP output
4bxx transcription X-ray (3.28 Å) Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M, Strahl BD, Cramer P (2013) "Structures of RNA Polymerase II Complexes with Bye1, a Chromatin-Binding Phf3/Dido1 Homologue." Proc.Natl.Acad.Sci.USA, 110, 15277. doi: 10.1073/PNAS.1311010110. Arrested RNA polymerase ii-bye1 complex. SNAP output
4by1 transcription X-ray (3.6 Å) Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M, Strahl BD, Cramer P (2013) "Structures of RNA Polymerase II Complexes with Bye1, a Chromatin-Binding Phf3/Dido1 Homologue." Proc.Natl.Acad.Sci.USA, 110, 15277. doi: 10.1073/PNAS.1311010110. Elongating RNA polymerase ii-bye1 tld complex soaked with ampcpp. SNAP output
4by7 transcription X-ray (3.15 Å) Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M, Strahl BD, Cramer P (2013) "Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue." Proc. Natl. Acad. Sci. U.S.A., 110, 15277-15282. doi: 10.1073/pnas.1311010110. Elongating RNA polymerase ii-bye1 tld complex. SNAP output
4c2t hydrolase-DNA X-ray (3.997 Å) Stelter M, Acajjaoui S, Mcsweeney S, Timmins J (2013) "Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd." Plos One, 8, 77364. doi: 10.1371/JOURNAL.PONE.0077364. Crystal structure of full length deinococcus radiodurans uvrd in complex with DNA. SNAP output
4c2u hydrolase-DNA X-ray (2.55 Å) Stelter M, Acajjaoui S, Mcsweeney S, Timmins J (2013) "Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd." Plos One, 8, 77364. doi: 10.1371/JOURNAL.PONE.0077364. Crystal structure of deinococcus radiodurans uvrd in complex with DNA, form 1. SNAP output
4c30 hydrolase-DNA X-ray (3.0 Å) Stelter M, Acajjaoui S, Mcsweeney S, Timmins J (2013) "Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd." Plos One, 8, 77364. doi: 10.1371/JOURNAL.PONE.0077364. Crystal structure of deinococcus radiodurans uvrd in complex with DNA, form 2. SNAP output
4c8k transferase-DNA X-ray (2.17 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A (2013) "Structural Insights Into DNA Replication without Hydrogen Bonds." J.Am.Chem.Soc., 135, 18637. doi: 10.1021/JA409609J. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a partially closed complex with the artificial base pair d5sics-dnamtp. SNAP output
4c8l transferase-DNA X-ray (1.7 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A (2013) "Structural Insights Into DNA Replication without Hydrogen Bonds." J.Am.Chem.Soc., 135, 18637. doi: 10.1021/JA409609J. Binary complex of the large fragment of DNA polymerase i from thermus aquaticus with the artificial base pair dnam-d5sics at the postinsertion site (sequence context 1). SNAP output
4c8m transferase-DNA X-ray (1.568 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A (2013) "Structural Insights Into DNA Replication without Hydrogen Bonds." J.Am.Chem.Soc., 135, 18637. doi: 10.1021/JA409609J. Binary complex of the large fragment of DNA polymerase i from thermus aquaticus with the aritificial base pair d5sics-dnam at the postinsertion site (sequence context 2). SNAP output
4c8n transferase-DNA X-ray (1.88 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A (2013) "Structural Insights Into DNA Replication without Hydrogen Bonds." J.Am.Chem.Soc., 135, 18637. doi: 10.1021/JA409609J. Binary complex of the large fragment of DNA polymerase i from thermus aquaticus with the aritificial base pair dnam-d5sics at the postinsertion site (sequence context 3). SNAP output
4c8o transferase-DNA X-ray (1.75 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A (2013) "Structural Insights Into DNA Replication without Hydrogen Bonds." J.Am.Chem.Soc., 135, 18637. doi: 10.1021/JA409609J. Binary complex of the large fragment of DNA polymerase i from thermus aquaticus with the aritificial base pair dnam-d5sics at the postinsertion site (sequence context 2). SNAP output
4c8y RNA binding protein-RNA X-ray (1.8 Å) Niewoehner O, Jinek M, Doudna JA (2014) "Evolution of Crispr RNA Recognition and Processing by Cas6 Endonucleases." Nucleic Acids Res., 42, 1341. doi: 10.1093/NAR/GKT922. Cas6 (ttha0078) substrate mimic complex. SNAP output
4cch transferase-DNA X-ray (2.55 Å) Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A (2013) "Structural Insights Into DNA Replication without Hydrogen Bonds." J.Am.Chem.Soc., 135, 18637. doi: 10.1021/JA409609J. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in an open binary complex with d5sics as templating nucleotide. SNAP output
4ceh hydrolase-DNA X-ray (3.24 Å) Krajewski WW, Fu X, Wilkinson M, Cronin NB, Dillingham MS, Wigley DB (2014) "Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites." Nature, 508, 416. doi: 10.1038/NATURE13037. Crystal structure of addab with a forked DNA substrate. SNAP output
4cei hydrolase-DNA X-ray (2.8 Å) Krajewski WW, Fu X, Wilkinson M, Cronin NB, Dillingham MS, Wigley DB (2014) "Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites." Nature, 508, 416. doi: 10.1038/NATURE13037. Crystal structure of adpnp-bound addab with a forked DNA substrate. SNAP output
4cej hydrolase-DNA X-ray (3.0 Å) Krajewski WW, Fu X, Wilkinson M, Cronin NB, Dillingham MS, Wigley DB (2014) "Structural Basis for Translocation by Addab Helicase-Nuclease and its Arrest at Chi Sites." Nature, 508, 416. doi: 10.1038/NATURE13037. Crystal structure of addab-DNA-adpnp complex at 3 angstrom resolution. SNAP output
4cgz hydrolase-DNA X-ray (3.2 Å) Newman JA, Savitsky P, Allerston CK, Bizard AH, Ozer O, Sarlos K, Liu Y, Pardon E, Steyaert J, Hickson ID, Gileadi O (2015) "Crystal Structure of the Bloom'S Syndrome Helicase Indicates a Role for the Hrdc Domain in Conformational Changes." Nucleic Acids Res., 43, 5221. doi: 10.1093/NAR/GKV373. Crystal structure of the bloom's syndrome helicase blm in complex with DNA. SNAP output
4ch1 transcription-DNA NMR Amrane S, Rebora K, Zniber I, Dupuy D, Mackereth CD (2014) "Backbone-Independent Nucleic Acid Binding by Splicing Factor Sup-12 Reveals Key Aspects of Molecular Recognition." Nat.Commun., 5, 4595. doi: 10.1038/NCOMMS5595. Rrm domain from c. elegans sup-12 bound to ggtgtgc DNA. SNAP output
4chu transcription X-ray (2.489 Å) Santos JA, Alonso-Garcia N, Macedo-Ribeiro S, Pereira PJB (2014) "The Unique Regulation of Iron-Sulfur Cluster Biogenesis in a Gram-Positive Bacterium." Proc.Natl.Acad.Sci.USA, 111, E2251. doi: 10.1073/PNAS.1322728111. E. coli iscr-DNA complex. SNAP output
4cis hydrolase X-ray (2.05 Å) Sadeghian K, Flaig D, Blank ID, Schneider S, Strasser R, Stathis D, Winnacker M, Carell T, Ochsenfeld C (2014) "Ribose-protonated DNA base excision repair: a combined theoretical and experimental study." Angew. Chem. Int. Ed. Engl., 53, 10044-10048. doi: 10.1002/anie.201403334. Structure of mutm in complex with carbocyclic 8-oxo-g containing DNA. SNAP output
4cja transcription X-ray (2.651 Å) Stella S, Molina R, Lopez-Mendez B, Juillerat A, Bertonati C, Daboussi F, Campos-Olivas R, Duchateau P, Montoya G (2014) "Bud, a Helix-Loop-Helix DNA-Binding Domain for Genome Modification." Acta Crystallogr.,Sect.D, 70, 2042. doi: 10.1107/S1399004714011183. Burrh DNA-binding protein from burkholderia rhizoxinica in complex with its target DNA. SNAP output
4cn2 transcription-DNA X-ray (2.069 Å) Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E, Birck C, Davidson I, Moras D, Rochel N (2015) "Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor." Sci.Rep., 5, 8216. doi: 10.1038/SREP08216. Crystal structure of the human retinoid x receptor DNA-binding domain bound to the human ramp2 response element. SNAP output
4cn3 transcription-DNA X-ray (2.35 Å) Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E, Birck C, Davidson I, Moras D, Rochel N (2015) "Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor." Sci.Rep., 5, 8216. doi: 10.1038/SREP08216. Crystal structure of the human retinoid x receptor DNA-binding domain bound to the human gde1spa response element. SNAP output
4cn5 transcription-DNA X-ray (2.0 Å) Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E, Birck C, Davidson I, Moras D, Rochel N (2015) "Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor." Sci.Rep., 5, 8216. doi: 10.1038/SREP08216. Crystal structure of the human retinoid x receptor DNA-binding domain bound to the human nr1d1 response element. SNAP output
4cn7 transcription-DNA X-ray (2.34 Å) Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E, Birck C, Davidson I, Moras D, Rochel N (2015) "Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor." Sci.Rep., 5, 8216. doi: 10.1038/SREP08216. Crystal structure of the human retinoid x receptor DNA-binding domain bound to an idealized dr1 response element. SNAP output
4crx protein-DNA X-ray (2.2 Å) Guo F, Gopaul DN, Van Duyne GD (1999) "Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse." Proc.Natl.Acad.Sci.USA, 96, 7143-7148. doi: 10.1073/pnas.96.13.7143. Asymmetric DNA-bending in the cre-loxp site-specific recombination synapse. SNAP output
4csa viral protein-DNA X-ray (2.28 Å) Leyrat C, Renner M, Harlos K, Huiskonen JT, Grimes JM (2014) "Drastic Changes in Conformational Dynamics of the Antiterminator M2-1 Regulate Transcription Efficiency in Pneumovirinae." Elife, 3, 02674. doi: 10.7554/ELIFE.02674. Crystal structure of the asymmetric human metapneumovirus m2-1 tetramer bound to a DNA 4-mer. SNAP output
4cyc transcription X-ray (2.36 Å) Foos N, Maurel-Zaffran C, Mate MJ, Vincentelli R, Hainaut M, Berenger H, Pradel J, Saurin AJ, Ortiz-Lombardia M, Graba Y (2015) "A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode." Structure, 23, 270. doi: 10.1016/J.STR.2014.12.011. Crystal structure of a ubx-exd-DNA complex including the hexapeptide and ubda motifs. SNAP output
4d1q protein-DNA complex X-ray (3.4 Å) Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss A, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F (2014) "Structural Basis of Hat Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca Domestica." Cell(Cambridge,Mass.), 158, 353. doi: 10.1016/J.CELL.2014.05.037. Hermes transposase bound to its terminal inverted repeat. SNAP output
4d6n hydrolase-DNA X-ray (2.35 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 10 days incubation in 5mm mg (state 7). SNAP output
4d6o hydrolase-DNA X-ray (2.2 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 1h incubation in 5mm mg (state 2). SNAP output
4d8j DNA binding protein X-ray (3.55 Å) Dupaigne P, Tonthat NK, Espeli O, Whitfill T, Boccard F, Schumacher MA (2012) "Molecular basis for a protein-mediated DNA-bridging mechanism that functions in condensation of the E. coli chromosome." Mol.Cell, 48, 560-571. doi: 10.1016/j.molcel.2012.09.009. Structure of e. coli matp-mats complex. SNAP output
4da4 transferase-DNA X-ray (2.6 Å) Song J, Teplova M, Ishibe-Murakami S, Patel DJ (2012) "Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation." Science, 335, 709-712. doi: 10.1126/science.1214453. Structure of mouse dnmt1 (731-1602) bound to hemimethylated cpg DNA. SNAP output
4dav hydrolase-DNA X-ray (2.2 Å) Allen FL, Akerboom J, Bliss SJ, Blombach F, Sedelnikova SE, van der Oost J, Baker PJ "The structure of SfsA and its DNA complex; A DNA/RNA nuclease with a novel domain combination." The structure of pyrococcus furiosus sfsa in complex with DNA. SNAP output
4db4 RNA-binding protein-DNA,RNA X-ray (3.599 Å) Mallam AL, Del Campo M, Gilman B, Sidote DJ, Lambowitz AM (2012) "Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p." Nature, 490, 121-125. doi: 10.1038/nature11402. Mss116p dead-box helicase domain 2 bound to a chimaeric RNA-DNA duplex. SNAP output
4df4 transferase-DNA X-ray (2.2 Å) Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A (2012) "Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates." J.Am.Chem.Soc., 134, 11840-11843. doi: 10.1021/ja3017889. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with 7-(n-(10-hydroxydecanoyl)-aminopentinyl)-7-deaza-2 -datp. SNAP output
4df8 transferase-DNA X-ray (2.0 Å) Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A (2012) "Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates." J.Am.Chem.Soc., 134, 11840-11843. doi: 10.1021/ja3017889. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-datp. SNAP output
4dfj transferase-DNA X-ray (1.9 Å) Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A (2012) "Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates." J.Am.Chem.Soc., 134, 11840-11843. doi: 10.1021/ja3017889. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dttp. SNAP output
4dfk transferase-DNA X-ray (1.647 Å) Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A (2012) "Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates." J.Am.Chem.Soc., 134, 11840-11843. doi: 10.1021/ja3017889. Large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with 5-(n-(10-hydroxydecanoyl)-aminopentinyl)-2-dutp. SNAP output
4dfm transferase-DNA X-ray (1.886 Å) Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A (2012) "Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates." J.Am.Chem.Soc., 134, 11840-11843. doi: 10.1021/ja3017889. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dctp. SNAP output
4dfp transferase-DNA X-ray (2.0 Å) Bergen K, Steck AL, Strutt S, Baccaro A, Welte W, Diederichs K, Marx A (2012) "Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates." J.Am.Chem.Soc., 134, 11840-11843. doi: 10.1021/ja3017889. Crystal structure of the large fragment of DNA polymerase i from thermus aqauticus in a ternary complex with 7-(aminopentinyl)-7-deaza-dgtp. SNAP output
4dih hydrolase-hydrolase inhibitor-DNA X-ray (1.8 Å) Russo Krauss I, Merlino A, Randazzo A, Novellino E, Mazzarella L, Sica F (2012) "High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity." Nucleic Acids Res., 40, 8119-8128. doi: 10.1093/nar/gks512. X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions. SNAP output
4dii hydrolase-hydrolase inhibitor-DNA X-ray (2.05 Å) Russo Krauss I, Merlino A, Randazzo A, Novellino E, Mazzarella L, Sica F (2012) "High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity." Nucleic Acids Res., 40, 8119-8128. doi: 10.1093/nar/gks512. X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions. SNAP output
4dk9 hydrolase-DNA X-ray (2.76 Å) Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat AC (2012) "Crystal Structure of Human Methyl-Binding Domain IV Glycosylase Bound to Abasic DNA." J.Mol.Biol., 420, 164-175. doi: 10.1016/j.jmb.2012.04.028. Crystal structure of mbd4 catalytic domain bound to abasic DNA. SNAP output
4dkj transferase-DNA X-ray (2.15 Å) Wojciechowski M, Czapinska H, Bochtler M (2013) "CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI." Proc.Natl.Acad.Sci.USA, 110, 105-110. doi: 10.1073/pnas.1207986110. Cpg specific methyltransferase in complex with target DNA. SNAP output
4dl2 transferase-DNA-inhibitor X-ray (2.15 Å) Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W (2012) "Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta." Proc.Natl.Acad.Sci.USA, 109, 7269-7274. doi: 10.1073/pnas.1202681109. Human DNA polymerase eta inserting dcmpnpp opposite cg template (gg0a). SNAP output
4dl3 transferase-DNA-inhibitor X-ray (2.1 Å) Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W (2012) "Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta." Proc.Natl.Acad.Sci.USA, 109, 7269-7274. doi: 10.1073/pnas.1202681109. Human DNA polymerase eta inserting dcmpnpp opposite gg template (gg0b).. SNAP output
4dl4 transferase-DNA-inhibitor X-ray (2.0 Å) Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W (2012) "Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta." Proc.Natl.Acad.Sci.USA, 109, 7269-7274. doi: 10.1073/pnas.1202681109. Human DNA polymerase eta inserting dcmpnpp opposite the 3'g of cisplatin crosslinked gs (pt-gg1).. SNAP output
4dl5 transferase-DNA-inhibitor X-ray (2.92 Å) Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W (2012) "Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta." Proc.Natl.Acad.Sci.USA, 109, 7269-7274. doi: 10.1073/pnas.1202681109. Human DNA polymerase eta inserting dcmpnpp opposite the 5'g of cisplatin crosslinked gs (pt-gg2).. SNAP output
4dl6 transferase-DNA-inhibitor X-ray (2.5 Å) Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W (2012) "Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta." Proc.Natl.Acad.Sci.USA, 109, 7269-7274. doi: 10.1073/pnas.1202681109. Human DNA polymerase eta extending primer immediately after cisplatin crosslink (pt-gg3).. SNAP output
4dl7 transferase-DNA-inhibitor X-ray (1.97 Å) Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W (2012) "Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta." Proc.Natl.Acad.Sci.USA, 109, 7269-7274. doi: 10.1073/pnas.1202681109. Human DNA polymerase eta fails to extend primer 2 nucleotide after cisplatin crosslink (pt-gg4).. SNAP output
4dle transferase-DNA X-ray (2.44 Å) Holzberger B, Obeid S, Welte W, Diederichs K, Marx A (2012) "Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of protein." Chem Sci, 3, 2924-2931. doi: 10.1039/C2SC20545A. Ternary structure of the large fragment of taq DNA polymerase: 4-fluoroproline variant. SNAP output
4dlg transferase-DNA X-ray (1.89 Å) Holzberger B, Obeid S, Welte W, Diederichs K, Marx A (2012) "Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of protein." Chem Sci, 3, 2924-2931. doi: 10.1039/C2SC20545A. Ternary structure of the large fragment of taq DNA polymerase. SNAP output
4dm0 hydrolase-DNA X-ray (2.5 Å) Lovell S, Goryshin IY, Reznikoff WR, Rayment I (2002) "Two-metal active site binding of a TN5 transposase synaptic complex." Nat.Struct.Biol., 9, 278-281. Tn5 transposase: 20mer outside end 2 mn complex. SNAP output
4do9 transferase-DNA X-ray (2.05 Å) Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE (2012) "Beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases." J.Am.Chem.Soc., 134, 8734-8737. doi: 10.1021/ja300218x. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: stereoselective binding of r-isomer. SNAP output
4doa transferase-DNA X-ray (2.051 Å) Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE (2012) "Beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases." J.Am.Chem.Soc., 134, 8734-8737. doi: 10.1021/ja300218x. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: non-interactive binding of s-isomer. SNAP output
4dob transferase-DNA X-ray (2.05 Å) Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE (2012) "Beta,Gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases." J.Am.Chem.Soc., 134, 8734-8737. doi: 10.1021/ja300218x. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate: stereoselective binding of r-isomer. SNAP output
4doc transferase-DNA X-ray (1.949 Å) Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE (2012) "Beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases." J.Am.Chem.Soc., 134, 8734-8737. doi: 10.1021/ja300218x. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of s-isomer. SNAP output
4dpv virus-DNA X-ray (2.9 Å) Xie Q, Chapman MS (1996) "Canine parvovirus capsid structure, analyzed at 2.9 A resolution." J.Mol.Biol., 264, 497-520. doi: 10.1006/jmbi.1996.0657. Parvovirus-DNA complex. SNAP output
4dqi transferase-DNA X-ray (1.69 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment, DNA duplex, and dctp (paired with dg of template). SNAP output
4dqp transferase-DNA X-ray (1.74 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment, DNA duplex, and ddctp (paired with dg of template). SNAP output
4dqq transferase-DNA X-ray (1.595 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment e658a, DNA duplex, and rctp (paired with dg of template) in presence of mg2+. SNAP output
4dqr transferase-DNA X-ray (1.95 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment e658a, DNA duplex, and rctp (paired with dg of template) in presence of mn2+. SNAP output
4dqs transferase-DNA X-ray (1.66 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Binary complex of bacillus DNA polymerase i large fragment and duplex DNA with rc in primer terminus paired with dg of template. SNAP output
4dqy transferase-DNA X-ray (3.25 Å) Langelier MF, Planck JL, Roy S, Pascal JM (2012) "Structural basis for DNA damage-dependent poly(ADP-ribosyl)ation by human PARP-1." Science, 336, 728-732. doi: 10.1126/science.1216338. Structure of human parp-1 bound to a DNA double strand break. SNAP output
4ds4 transferase-DNA X-ray (1.681 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment, DNA duplex, and rctp in presence of mn2+. SNAP output
4ds5 transferase-DNA X-ray (1.68 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment, DNA duplex, and rctp in presence of mg2+. SNAP output
4dse transferase-DNA X-ray (1.67 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment f710y, DNA duplex, and rctp (paired with dg of template) in presence of mg2+. SNAP output
4dsf transferase-DNA X-ray (1.661 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Ternary complex of bacillus DNA polymerase i large fragment f710y, DNA duplex, and rctp (paired with dg of template) in presence of mn2+. SNAP output
4dsi transferase-DNA X-ray (2.05 Å) Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J, Soares AS, Huang Z "Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase." Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus with duplex DNA, se-dgtp and calcium. SNAP output
4dsj transferase-DNA X-ray (2.86 Å) Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J, Soares AS, Huang Z "Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase." Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus with duplex DNA, dgtp and calcium. SNAP output
4dsk transferase-DNA X-ray (2.18 Å) Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J, Soares AS, Huang Z "Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase." Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus with duplex DNA, ppi and calcium. SNAP output
4dsl transferase-DNA X-ray (2.45 Å) Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J, Soares AS, Huang Z "Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase." Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus with duplex DNA and calcium. SNAP output
4dtj transferase-DNA X-ray (1.9 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dttp opposite an abasic site and ddt-da as the penultimate base-pair. SNAP output
4dtm transferase-DNA X-ray (1.95 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dctp opposite an abasic site and ddg-dc as the penultimate base-pair. SNAP output
4dtn transferase-DNA X-ray (1.96 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with datp opposite an abasic site and dda-dt as the penultimate base-pair. SNAP output
4dto transferase-DNA X-ray (2.05 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dctp opposite an abasic site and dda-dt as the penultimate base-pair. SNAP output
4dtp transferase-DNA X-ray (2.05 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dgtp opposite an abasic site and dda-dt as the penultimate base-pair. SNAP output
4dtr transferase-DNA X-ray (2.04 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with datp opposite an abasic site and ddc-dg as the penultimate base-pair. SNAP output
4dts transferase-DNA X-ray (1.96 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dctp opposite an abasic site and ddc-dg as the penultimate base-pair. SNAP output
4dtu transferase-DNA X-ray (1.86 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dgtp opposite an abasic site and ddc-dg as the penultimate base-pair. SNAP output
4dtx transferase-DNA X-ray (1.84 Å) Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH (2012) "Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA." Biochemistry, 51, 4922-4931. doi: 10.1021/bi300296q. Rb69 DNA polymerase ternary complex with dttp opposite an abasic site and ddc-dg as the penultimate base-pair. SNAP output
4du1 transferase-DNA X-ray (2.15 Å) Xia S, Christian TD, Wang J, Konigsberg WH (2012) "Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA." Biochemistry, 51, 4343-4353. doi: 10.1021/bi300416z. Rb69 DNA polymerase ternary complex with datp opposite dt. SNAP output
4du3 transferase-DNA X-ray (2.02 Å) Xia S, Christian TD, Wang J, Konigsberg WH (2012) "Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA." Biochemistry, 51, 4343-4353. doi: 10.1021/bi300416z. Rb69 DNA polymerase ternary complex with ddtp opposite dt with 3-deaza-adenine at the n-1 position of template strand. SNAP output
4du4 transferase-DNA X-ray (2.28 Å) Xia S, Christian TD, Wang J, Konigsberg WH (2012) "Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA." Biochemistry, 51, 4343-4353. doi: 10.1021/bi300416z. Rb69 DNA polymerase ternary complex with datp opposite dt with 3-deaza-adenine at the n-3 position of primer strand. SNAP output
4dwi transferase-DNA X-ray (1.85 Å) Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J, Soares AS, Huang Z "Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase." Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus with self complementary DNA, se-dgtp and calcium. SNAP output
4dwp DNA binding protein-DNA X-ray (2.35 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Semet protelomerase tela covalently complexed with substrate DNA. SNAP output
4e0d transferase-DNA X-ray (1.58 Å) Wang W, Wu EY, Hellinga HW, Beese LS (2012) "Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides." J.Biol.Chem., 287, 28215-28226. doi: 10.1074/jbc.M112.366609. Binary complex of bacillus DNA polymerase i large fragment e658a and duplex DNA. SNAP output
4e0g DNA binding protein-DNA X-ray (2.2 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Protelomerase tela-DNA hairpin product-vanadate complex. SNAP output
4e0j DNA binding protein-DNA X-ray (2.3 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Protelomerase tela r255a mutant complexed with DNA hairpin product. SNAP output
4e0p DNA binding protein-DNA X-ray (2.2 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Protelomerase tela covalently complexed with substrate DNA. SNAP output
4e0y DNA binding protein-DNA X-ray (2.4 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Protelomerase tela covalently complexed with mutated substrate DNA. SNAP output
4e0z DNA binding protein-DNA X-ray (2.42 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Protelomerase tela r205a covalently complexed with substrate DNA. SNAP output
4e10 DNA binding protein-DNA X-ray (2.506 Å) Shi K, Huang WM, Aihara H (2013) "An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation." Plos Biol., 11, e1001472. doi: 10.1371/journal.pbio.1001472. Protelomerase tela y201a covalently complexed with substrate DNA. SNAP output
4e3s transferase-DNA X-ray (2.04 Å) Xia S, Christian TD, Wang J, Konigsberg WH (2012) "Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA." Biochemistry, 51, 4343-4353. doi: 10.1021/bi300416z. Rb69 DNA polymerase ternary complex with dqtp opposite dt. SNAP output
4e54 DNA binding protein-DNA X-ray (2.85 Å) Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H, Shi H, Hsieh CL, Conway JF, Van Houten B, Rapic-Otrin V (2012) "Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair." Proc.Natl.Acad.Sci.USA, 109, E2737-E2746. doi: 10.1073/pnas.1110067109. Damaged DNA induced uv-damaged DNA-binding protein (uv-ddb) dimerization and its roles in chromatinized DNA repair. SNAP output
4e5z DNA binding protein-DNA X-ray (3.22 Å) Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H, Shi H, Hsieh CL, Conway JF, Van Houten B, Rapic-Otrin V (2012) "Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair." Proc.Natl.Acad.Sci.USA, 109, E2737-E2746. doi: 10.1073/pnas.1110067109. Damaged DNA induced uv-damaged DNA-binding protein (uv-ddb) dimerization and its roles in chromatinized DNA repair. SNAP output
4e68 transcription-DNA X-ray (2.585 Å) Nkansah E, Shah R, Collie GW, Parkinson GN, Palmer J, Rahman KM, Bui TT, Drake AF, Husby J, Neidle S, Zinzalla G, Thurston DE, Wilderspin AF (2013) "Observation of unphosphorylated STAT3 core protein binding to target dsDNA by PEMSA and X-ray crystallography." Febs Lett., 587, 833-839. doi: 10.1016/j.febslet.2013.01.065. Unphosphorylated stat3b core protein binding to dsDNA. SNAP output
4e7h recombination-DNA X-ray (2.57 Å) Hare S, Maertens GN, Cherepanov P (2012) "3'-Processing and strand transfer catalysed by retroviral integrase in crystallo." Embo J., 31, 3020-3028. doi: 10.1038/emboj.2012.118. Pfv intasome prior to 3'-processing, apo form (ui-apo). SNAP output
4e7i recombination-DNA X-ray (2.53 Å) Hare S, Maertens GN, Cherepanov P (2012) "3'-Processing and strand transfer catalysed by retroviral integrase in crystallo." Embo J., 31, 3020-3028. doi: 10.1038/emboj.2012.118. Pfv intasome freeze-trapped prior to 3'-processing, mn-bound form (ui-mn). SNAP output
4e7j recombination-DNA X-ray (3.15 Å) Hare S, Maertens GN, Cherepanov P (2012) "3'-Processing and strand transfer catalysed by retroviral integrase in crystallo." Embo J., 468, 326-329. doi: 10.1038/emboj.2012.118. Pfv integrase target capture complex, apo form (tcc-apo), at 3.15 Å resolution. SNAP output
4e7k recombination-DNA X-ray (3.02 Å) Hare S, Maertens GN, Cherepanov P (2012) "3'-Processing and strand transfer catalysed by retroviral integrase in crystallo." Embo J., 31, 3020-3028. doi: 10.1038/emboj.2012.118. Pfv integrase target capture complex (tcc-mn), freeze-trapped prior to strand transfer, at 3.0 Å resolution. SNAP output
4e7l recombination-DNA X-ray (3.0 Å) Hare S, Maertens GN, Cherepanov P (2012) "3'-Processing and strand transfer catalysed by retroviral integrase in crystallo." Embo J., 31, 3020-3028. doi: 10.1038/emboj.2012.118. Pfv integrase strand transfer complex (stc-mn*) following reaction in crystallo, at 3.0 Å resolution.. SNAP output
4e9f hydrolase-DNA X-ray (1.79 Å) Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA (2012) "Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA." Nucleic Acids Res., 40, 9917-9926. doi: 10.1093/nar/gks714. Structure of the glycosylase domain of mbd4 bound to ap site containing DNA. SNAP output
4e9g hydrolase-DNA X-ray (2.35 Å) Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA (2012) "Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA." Nucleic Acids Res., 40, 9917-9926. doi: 10.1093/nar/gks714. Structure of the glycosylase domain of mbd4 bound to thymine containing DNA. SNAP output
4e9h hydrolase-DNA X-ray (3.0 Å) Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA (2012) "Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA." Nucleic Acids Res., 40, 9917-9926. doi: 10.1093/nar/gks714. Structure of glycosylase domain of mbd4 bound to 5hmu containing DNA. SNAP output
4ea4 hydrolase-DNA X-ray (2.0 Å) Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA (2012) "Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA." Nucleic Acids Res., 40, 9917-9926. doi: 10.1093/nar/gks714. Structure of the glycosylase domain of mbd4 bound to 5hmu-containing DNA. SNAP output
4ea5 hydrolase-DNA X-ray (2.14 Å) Morera S, Grin I, Vigouroux A, Couve S, Henriot V, Saparbaev M, Ishchenko AA (2012) "Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA." Nucleic Acids Res., 40, 9917-9926. doi: 10.1093/nar/gks714. Structure of the glycoslyase domain of mbd4 bound to a 5hmu containing DNA. SNAP output
4ebc transferase-DNA X-ray (2.901 Å) Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL (2012) "A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota." J.Am.Chem.Soc., 134, 10698-10705. doi: 10.1021/ja304176q. Conformationally restrained north-methanocarba-2'-deoxyadenosine corrects the error-prone nature of human DNA polymerase iota. SNAP output
4ebd transferase-DNA X-ray (2.571 Å) Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL (2012) "A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota." J.Am.Chem.Soc., 134, 10698-10705. doi: 10.1021/ja304176q. Conformationally restrained north-methanocarba-2'-deoxyadenosine corrects the error-prone nature of human DNA polymerase iota. SNAP output
4ebe transferase-DNA X-ray (2.1 Å) Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL (2012) "A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota." J.Am.Chem.Soc., 134, 10698-10705. doi: 10.1021/ja304176q. Conformationally restrained north-methanocarba-2'-deoxyadenosine corrects the error-prone nature of human DNA polymerase iota. SNAP output
4ecq transferase-DNA X-ray (1.5 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta- DNA ternary complex: at crystal at ph6.8(k+ mes) with 1 ca2+ ion. SNAP output
4ecr transferase-DNA X-ray (1.892 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 40 sec. SNAP output
4ecs transferase-DNA X-ray (1.951 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 80 sec. SNAP output
4ect transferase-DNA X-ray (1.795 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 140 sec. SNAP output
4ecu transferase-DNA X-ray (1.949 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 200 sec. SNAP output
4ecv transferase-DNA X-ray (1.521 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 230 sec. SNAP output
4ecw transferase-DNA X-ray (1.896 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 250 sec. SNAP output
4ecx transferase-DNA X-ray (1.744 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 7.0 for 300 sec. SNAP output
4ecy transferase-DNA X-ray (1.943 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: at crystal at ph 6.0 (na+ mes) with 1 ca2+ ion. SNAP output
4ecz transferase-DNA X-ray (1.834 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: at crystal at ph 6.5 (na+ mes) with 1 ca2+ ion. SNAP output
4ed0 transferase-DNA X-ray (1.653 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: at crystal at ph 6.8 (na+ mes) with 1 ca2+ ion. SNAP output
4ed1 transferase-DNA X-ray (1.806 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: at crystal at ph 7.0 (na+ mes) with 1 ca2+ ion. SNAP output
4ed2 transferase-DNA X-ray (1.711 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: at crystal at ph 7.2 (na+ hepes) with 1 ca2+ ion. SNAP output
4ed3 transferase-DNA X-ray (1.791 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: at crystal at ph 7.5 (na+ hepes) with 1 ca2+ ion. SNAP output
4ed5 RNA binding protein-RNA X-ray (2.0 Å) Wang H, Zeng F, Liu Q, Liu H, Liu Z, Niu L, Teng M, Li X (2013) "The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding." Acta Crystallogr.,Sect.D, 69, 373-380. doi: 10.1107/S0907444912047828. Crystal structure of the two n-terminal rrm domains of hur complexed with RNA. SNAP output
4ed6 transferase-DNA X-ray (2.211 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the at crystal at ph 6.7 for 15 hr, sideway translocation. SNAP output
4ed7 transferase-DNA X-ray (1.717 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: tg crystal at ph 7.0 (k+ mes) with 1 ca2+ ion. SNAP output
4ed8 transferase-DNA X-ray (1.521 Å) Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W (2012) "Watching DNA polymerase eta make a phosphodiester bond." Nature, 487, 196-201. doi: 10.1038/nature11181. Human DNA polymerase eta - DNA ternary complex: reaction in the tg crystal at ph 7.0, normal translocation. SNAP output
4eey transferase-DNA X-ray (2.32 Å) Ummat A, Rechkoblit O, Jain R, Roy Choudhury J, Johnson RE, Silverstein TD, Buku A, Lone S, Prakash L, Prakash S, Aggarwal AK (2012) "Structural basis for cisplatin DNA damage tolerance by human polymerase {eta} during cancer chemotherapy." Nat.Struct.Mol.Biol., 19, 628-632. doi: 10.1038/nsmb.2295. Crystal structure of human DNA polymerase eta in ternary complex with a cisplatin DNA adduct. SNAP output
4efj hydrolase-DNA X-ray (2.8 Å) Kulshina N "Crystal structure of I-GzeMII LAGLIDADG homing endonuclease in complex with DNA target site." Crystal structure of i-gzeii laglidadg homing endonuclease in complex with DNA target site. SNAP output
4egy transcription-DNA X-ray (2.301 Å) Jain D, Nair DT (2013) "Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators." Nucleic Acids Res., 41, 639-647. doi: 10.1093/nar/gks962. Crystal structure of arar(dbd) in complex with operator ora1. SNAP output
4egz transcription-DNA X-ray (2.3 Å) Jain D, Nair DT (2013) "Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators." Nucleic Acids Res., 41, 639-647. doi: 10.1093/nar/gks962. Crystal structure of arar(dbd) in complex with operator orr3. SNAP output
4ejy hydrolase-DNA X-ray (2.0 Å) Yu HJ, Yang MZ, Zhang XE, Bi LJ, Jiang T (2013) "Crystal structures of MBOgg1 in complex with two abasic DNA ligands." J.Struct.Biol., 181, 252-263. doi: 10.1016/j.jsb.2012.12.003. Structure of mbogg1 in complex with high affinity DNA ligand. SNAP output
4ejz hydrolase-DNA X-ray (3.05 Å) Yu HJ, Yang MZ, Zhang XE, Bi LJ, Jiang T (2013) "Crystal structures of MBOgg1 in complex with two abasic DNA ligands." J.Struct.Biol., 181, 252-263. doi: 10.1016/j.jsb.2012.12.003. Structure of mbogg1 in complex with low affinity DNA ligand. SNAP output
4elt transferase-DNA X-ray (2.2 Å) Obeid S, Busskamp H, Welte W, Diederichs K, Marx A (2012) "Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site." Chem.Commun.(Camb.), 48, 8320-8322. doi: 10.1039/c2cc34181f. Snapshot of the large fragment of DNA polymerase i from thermus aquaticus processing modified pyrimidines. SNAP output
4elu transferase-DNA X-ray (1.8 Å) Obeid S, Busskamp H, Welte W, Diederichs K, Marx A (2012) "Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site." Chem.Commun.(Camb.), 48, 8320-8322. doi: 10.1039/c2cc34181f. Snapshot of the large fragment of DNA polymerase i from thermus aquaticus processing modified pyrimidines. SNAP output
4elv transferase-DNA X-ray (1.9 Å) Obeid S, Bu kamp H, Welte W, Diederichs K, Marx A "Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines." Snapshot of the large fragment of DNA polymerase i from thermus aquaticus processing modified pyrimidines. SNAP output
4enj DNA binding protein-DNA X-ray (3.1 Å) Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai AS, Millington CL, Povey AC, Williams DM, Santibanez-Koref MF, Tainer JA, Margison GP (2012) "Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines." Mol.Cell, 47, 50-60. doi: 10.1016/j.molcel.2012.04.028. Crystal structure of s. pombe atl1 in complex with damaged DNA containing o6-hydroxyethylguanine. SNAP output
4enk DNA binding protein-DNA X-ray (3.04 Å) Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai AS, Millington CL, Povey AC, Williams DM, Santibanez-Koref MF, Tainer JA, Margison GP (2012) "Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines." Mol.Cell, 47, 50-60. doi: 10.1016/j.molcel.2012.04.028. Crystal structure of s. pombe atl1 in complex with damaged DNA containing o6-propylguanine. SNAP output
4enm DNA binding protein-DNA X-ray (2.84 Å) Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai AS, Millington CL, Povey AC, Williams DM, Santibanez-Koref MF, Tainer JA, Margison GP (2012) "Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines." Mol.Cell, 47, 50-60. doi: 10.1016/j.molcel.2012.04.028. Crystal structure of s. pombe atl1 in complex with damaged DNA containing o6-benzylguanine. SNAP output
4enn DNA binding protein-DNA X-ray (2.84 Å) Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai AS, Millington CL, Povey AC, Williams DM, Santibanez-Koref MF, Tainer JA, Margison GP (2012) "Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines." Mol.Cell, 47, 50-60. doi: 10.1016/j.molcel.2012.04.028. Crystal structure of s. pombe atl1 in complex with damaged DNA containing o6-carboxymethylguanine. SNAP output
4eot transcription-DNA X-ray (2.855 Å) Lu X, Guanga GP, Wan C, Rose RB (2012) "A Novel DNA Binding Mechanism for maf Basic Region-Leucine Zipper Factors Inferred from a MafA-DNA Complex Structure and Binding Specificities." Biochemistry, 51, 9706-9717. doi: 10.1021/bi301248j. Crystal structure of the mafa homodimer bound to the consensus mare. SNAP output
4er8 DNA binding protein-DNA X-ray (2.6 Å) Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ, Peaslee GF, Ghirlando R, Chandler M, Dyda F (2012) "The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease." Nucleic Acids Res., 40, 9964-9979. doi: 10.1093/nar/gks741. Structure of the rep associates tyrosine transposase bound to a rep hairpin. SNAP output
4esj hydrolase-DNA X-ray (2.05 Å) Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K (2012) "Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI." Nucleic Acids Res., 40, 7563-7572. doi: 10.1093/nar/gks428. Restriction endonuclease dpni in complex with target DNA. SNAP output
4esv hydrolase-DNA X-ray (3.2 Å) Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA (2012) "The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation." Cell(Cambridge,Mass.), 151, 267-277. doi: 10.1016/j.cell.2012.09.014. A new twist on the translocation mechanism of helicases from the structure of dnab with its substrates. SNAP output
4euw transcription-DNA X-ray (2.77 Å) Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology "Crystal structure of a HMG domain of transcription factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens at 2.77 A resolution." Crystal structure of a hmg domain of transcription factor sox-9 bound to DNA (sox-9-DNA) from homo sapiens at 2.77 Å resolution. SNAP output
4evv hydrolase-DNA X-ray (2.39 Å) Hashimoto H, Zhang X, Cheng X (2012) "Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation." Nucleic Acids Res., 40, 8276-8284. doi: 10.1093/nar/gks628. Mouse mbd4 glycosylase domain in complex with a g:t mismatch. SNAP output
4ew0 hydrolase-DNA X-ray (2.39 Å) Hashimoto H, Zhang X, Cheng X (2012) "Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation." Nucleic Acids Res., 40, 8276-8284. doi: 10.1093/nar/gks628. Mouse mbd4 glycosylase domain in complex with a g:5hmu (5-hydroxymethyluracil) mismatch. SNAP output
4ew4 hydrolase-DNA X-ray (2.791 Å) Hashimoto H, Zhang X, Cheng X (2012) "Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation." Nucleic Acids Res., 40, 8276-8284. doi: 10.1093/nar/gks628. Mouse mbd4 glycosylase domain in complex with DNA containing a ribose sugar. SNAP output
4eyh transferase-DNA X-ray (2.9 Å) Kirouac KN, Basu AK, Ling H (2013) "Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase." Nucleic Acids Res., 41, 2060-2071. doi: 10.1093/nar/gks1296. Human DNA polymerase iota incorporating dctp opposite n-(deoxyguanosin-8-yl)-1-aminopyrene lesion. SNAP output
4eyi transferase-DNA X-ray (2.9 Å) Kirouac KN, Basu AK, Ling H (2013) "Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase." Nucleic Acids Res., 41, 2060-2071. doi: 10.1093/nar/gks1296. Human DNA polymerase iota incorporating datp opposite n-(deoxyguanosin-8-yl)-1-aminopyrene lesion. SNAP output
4ez6 transferase-DNA X-ray (1.64 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." Bacillus DNA polymerase i large fragment complex 1. SNAP output
4ez9 transferase-DNA X-ray (1.64 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." Bacillus DNA polymerase i large fragment complex 2. SNAP output
4f1h hydrolase-DNA X-ray (1.662 Å) Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H (2012) "Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2." Nat.Struct.Mol.Biol., 19, 1372-1377. doi: 10.1038/nsmb.2423. Crystal structure of tdp2 from danio rerio complexed with a single strand DNA. SNAP output
4f2j metal binding protein-DNA X-ray (2.64 Å) Vandevenne MS, Jacques DA, Artuz C, Nguyen CD, Kwan AH, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay JP (2013) "New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217." J.Biol.Chem., 288, 10616-10627. doi: 10.1074/jbc.M112.441451. Crystal structure of znf217 bound to DNA, p6522 crystal form. SNAP output
4f2r transferase-DNA X-ray (1.63 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." DNA polymerase i large fragment complex 3. SNAP output
4f2s transferase-DNA X-ray (1.651 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." DNA polymerase i large fragment complex 4. SNAP output
4f3o transferase-DNA X-ray (1.57 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." DNA polymerase i large fragment complex 5. SNAP output
4f41 recombination-DNA X-ray (2.5 Å) Huang WM, Dagloria J, Fox H, Ruan Q, Tillou J, Shi K, Aihara H, Aron J, Casjens S (2012) "Linear Chromosome-generating System of Agrobacterium tumefaciens C58: PROTELOMERASE GENERATES AND PROTECTS HAIRPIN ENDS." J.Biol.Chem., 287, 25551-25563. doi: 10.1074/jbc.M112.369488. Protelomerase tela mutant r255a complexed with cttg hairpin DNA. SNAP output
4f43 recombination-DNA X-ray (2.354 Å) Huang WM, Dagloria J, Fox H, Ruan Q, Tillou J, Shi K, Aihara H, Aron J, Casjens S (2012) "Linear Chromosome-generating System of Agrobacterium tumefaciens C58: PROTELOMERASE GENERATES AND PROTECTS HAIRPIN ENDS." J.Biol.Chem., 287, 25551-25563. doi: 10.1074/jbc.M112.369488. Protelomerase tela mutant r255a complexed with caag hairpin DNA. SNAP output
4f4k transferase-DNA X-ray (1.6 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." DNA polymerase i large fragment complex 6. SNAP output
4f4w transferase-DNA X-ray (1.898 Å) Wilson RC, Jackson MA, Pata JD (2013) "Y-family polymerase conformation is a major determinant of fidelity and translesion specificity." Structure, 21, 20-31. doi: 10.1016/j.str.2012.11.005. Y-family DNA polymerase chimera dbh-dpo4-dpo4 #1. SNAP output
4f4x transferase-DNA X-ray (2.049 Å) Wilson RC, Jackson MA, Pata JD (2013) "Y-family polymerase conformation is a major determinant of fidelity and translesion specificity." Structure, 21, 20-31. doi: 10.1016/j.str.2012.11.005. Y-family DNA polymerase chimera dbh-dpo4-dpo4 #2. SNAP output
4f4y transferase-DNA X-ray (2.338 Å) Wilson RC, Jackson MA, Pata JD (2013) "Y-family polymerase conformation is a major determinant of fidelity and translesion specificity." Structure, 21, 20-31. doi: 10.1016/j.str.2012.11.005. Y-family DNA polymerase chimera dbh-dpo4-dbh. SNAP output
4f4z transferase-DNA X-ray (2.305 Å) Wilson RC, Jackson MA, Pata JD (2013) "Y-family polymerase conformation is a major determinant of fidelity and translesion specificity." Structure, 21, 20-31. doi: 10.1016/j.str.2012.11.005. Y-family DNA polymerase chimera dpo4-dpo4-dbh. SNAP output
4f50 transferase-DNA X-ray (2.215 Å) Wilson RC, Jackson MA, Pata JD (2013) "Y-family polymerase conformation is a major determinant of fidelity and translesion specificity." Structure, 21, 20-31. doi: 10.1016/j.str.2012.11.005. Y-family DNA polymerase chimera dbh-dbh-dpo4. SNAP output
4f5n transferase, lyase-DNA X-ray (1.8 Å) Freudenthal BD, Beard WA, Wilson SH (2012) "Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly." Structure, 20, 1829-1837. doi: 10.1016/j.str.2012.08.008. Open ternary complex of r283k DNA polymerase beta with a metal free dctp analog. SNAP output
4f5o transferase, lyase-DNA X-ray (2.0 Å) Freudenthal BD, Beard WA, Wilson SH (2012) "Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly." Structure, 20, 1829-1837. doi: 10.1016/j.str.2012.08.008. Open ternary complex of r283k DNA polymerase beta with a one metal bound dctp analog. SNAP output
4f5p transferase, lyase-DNA X-ray (1.85 Å) Freudenthal BD, Beard WA, Wilson SH (2012) "Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly." Structure, 20, 1829-1837. doi: 10.1016/j.str.2012.08.008. Open ternary mismatch complex of r283k DNA polymerase beta with a datp analog. SNAP output
4f5q transferase, lyase-DNA X-ray (2.25 Å) Freudenthal BD, Beard WA, Wilson SH (2012) "Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly." Structure, 20, 1829-1837. doi: 10.1016/j.str.2012.08.008. Closed ternary complex of r283k DNA polymerase beta. SNAP output
4f5r transferase, lyase-DNA X-ray (2.2 Å) Freudenthal BD, Beard WA, Wilson SH (2012) "Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly." Structure, 20, 1829-1837. doi: 10.1016/j.str.2012.08.008. Open and closed ternary complex of r283k DNA polymerase beta with a dctp analog in the same asymmetric unit. SNAP output
4f6m DNA binding protein-DNA X-ray (2.4 Å) Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE (2012) "Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso." Proc.Natl.Acad.Sci.USA, 109, 15229-15234. doi: 10.1073/pnas.1213726109. Crystal structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA. SNAP output
4f6n DNA binding protein-DNA X-ray (2.8 Å) Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE (2012) "Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso." Proc.Natl.Acad.Sci.USA, 109, 15229-15234. doi: 10.1073/pnas.1213726109. Crystal structure of kaiso zinc finger DNA binding protein in complex with methylated cpg site DNA. SNAP output
4f8r transferase-DNA X-ray (1.64 Å) Wang W, Hellinga HW, Beese LS "Structures of a High-fidelity DNA Polymerase." Bacillus DNA polymerase i large fragment complex 7. SNAP output
4fb3 DNA binding protein-DNA X-ray (3.79 Å) Harrison C, Jiang T, Banerjee P, Meinke G, D'Abramo CM, Schaffhausen B, Bohm A (2013) "Polyomavirus large T antigen binds symmetrical repeats at the viral origin in an asymmetrical manner." J.Virol., 87, 13751-13759. doi: 10.1128/JVI.01740-13. Polyomavirus t-ag binds symmetrical repeats at the viral origin in an asymmetrical manner. SNAP output
4fbt transferase-DNA X-ray (2.0 Å) Kirouac KN, Basu AK, Ling H (2013) "Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase." J.Mol.Biol., 425, 4167-4176. doi: 10.1016/j.jmb.2013.07.020. Dpo4 post-insertion complex with the n-(deoxyguanosin-8-yl)-1-aminopyrene lesion. SNAP output
4fbu transferase-DNA X-ray (2.6 Å) Kirouac KN, Basu AK, Ling H (2013) "Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase." J.Mol.Biol., 425, 4167-4176. doi: 10.1016/j.jmb.2013.07.020. Dpo4 polymerase pre-insertion binary complex with the n-(deoxyguanosin-8-yl)-1-aminopyrene lesion. SNAP output
4fcy DNA binding protein-DNA X-ray (3.706 Å) Montano SP, Pigli YZ, Rice PA (2012) "The Mu transpososome structure sheds light on DDE recombinase evolution." Nature, 491, 413-417. doi: 10.1038/nature11602. Crystal structure of the bacteriophage mu transpososome. SNAP output
4ff1 transferase-DNA X-ray (2.47 Å) Basu RS, Murakami KS (2013) "Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography." J.Biol.Chem., 288, 3305-3311. doi: 10.1074/jbc.M112.387712. N4 mini-vrnap transcription initiation complex, 1 min after soaking gtp, atp and mn. SNAP output
4ff2 transferase-DNA X-ray (2.0 Å) Basu RS, Murakami KS (2013) "Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography." J.Biol.Chem., 288, 3305-3311. doi: 10.1074/jbc.M112.387712. N4 mini-vrnap transcription initiation complex, 2 min after soaking gtp, atp and mn. SNAP output
4ff3 transferase-DNA X-ray (1.997 Å) Basu RS, Murakami KS (2013) "Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography." J.Biol.Chem., 288, 3305-3311. doi: 10.1074/jbc.M112.387712. N4 mini-vrnap transcription initiation complex, 3 min after soaking gtp, atp and mn. SNAP output
4ff4 transferase-DNA X-ray (2.026 Å) Basu RS, Murakami KS (2013) "Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography." J.Biol.Chem., 288, 3305-3311. doi: 10.1074/jbc.M112.387712. N4 mini-vrnap transcription initiation complex, 4 min after soaking gtp, atp and mn. SNAP output
4fgn DNA binding protein-DNA X-ray (3.2 Å) Meinke G, Phelan PJ, Harrison CJ, Bullock PA (2013) "Analysis of the Costructure of the Simian Virus 40 T-Antigen Origin Binding Domain with Site I Reveals a Correlation between GAGGC Spacing and Spiral Assembly." J.Virol., 87, 2923-2934. doi: 10.1128/JVI.02549-12. Crystal structure of the sv40 large t-antigen origin bining domain bound to site i DNA. SNAP output
4fj5 transferase-DNA X-ray (2.05 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with datp-dt. SNAP output
4fj7 transferase-DNA X-ray (1.9 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dgtp-dt. SNAP output
4fj8 transferase-DNA X-ray (2.19 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dctp-dt. SNAP output
4fj9 transferase-DNA X-ray (1.97 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dttp-dt. SNAP output
4fjg transferase-DNA X-ray (2.02 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with datp-dc. SNAP output
4fjh transferase-DNA X-ray (2.11 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dgtp-dc. SNAP output
4fji transferase-DNA X-ray (2.2 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dctp-dc. SNAP output
4fjj transferase-DNA X-ray (1.99 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dttp-dc. SNAP output
4fjk transferase-DNA X-ray (2.0 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with datp-da. SNAP output
4fjl transferase-DNA X-ray (1.87 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dgtp-da. SNAP output
4fjm transferase-DNA X-ray (2.02 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dctp-da. SNAP output
4fjn transferase-DNA X-ray (1.98 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dttp-da. SNAP output
4fjx transferase-DNA X-ray (2.11 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with datp-dg. SNAP output
4fk0 transferase-DNA X-ray (2.18 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dctp-dg. SNAP output
4fk2 transferase-DNA X-ray (1.98 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dttp-dg. SNAP output
4fk4 transferase-DNA X-ray (1.9 Å) Xia S, Wang J, Konigsberg WH (2013) "DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase." J.Am.Chem.Soc., 135, 193-202. doi: 10.1021/ja3079048. Rb69 DNA polymerase ternary complex with dgtp-dg. SNAP output
4flt transferase-DNA X-ray (2.9 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4flu transferase-DNA X-ray (3.1 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4flv transferase-DNA X-ray (2.7 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4flw transferase-DNA X-ray (2.15 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4flx transferase-DNA X-ray (2.9 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4fly transferase-DNA X-ray (2.3 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4flz transferase-DNA X-ray (3.2 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4fm0 transferase-DNA X-ray (3.12 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4fm1 transferase-DNA X-ray (3.0 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase bound to a dsDNA, in edition mode. SNAP output
4fm2 transferase-DNA X-ray (2.9 Å) Gouge J, Ralec C, Henneke G, Delarue M (2012) "Molecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase." J.Mol.Biol., 423, 315-336. doi: 10.1016/j.jmb.2012.07.025. Pyrococcus abyssi b family DNA polymerase (triple mutant) bound to a dsDNA, in edition mode. SNAP output
4fm9 isomerase-DNA X-ray (2.901 Å) Wendorff TJ, Schmidt BH, Heslop P, Austin CA, Berger JM (2012) "The Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage." J.Mol.Biol., 424, 109-124. doi: 10.1016/j.jmb.2012.07.014. Human topoisomerase ii alpha bound to DNA. SNAP output
4fnc hydrolase-DNA X-ray (2.493 Å) Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng X (2012) "Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation." Nucleic Acids Res., 40, 10203-10214. doi: 10.1093/nar/gks845. Human tdg in a post-reactive complex with 5-hydroxymethyluracil (5hmu). SNAP output
4fo6 transferase, lyase-DNA X-ray (2.007 Å) Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek K (2012) "The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda." Nucleic Acids Res., 40, 1-10. doi: 10.1093/nar/gks413. Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a datp analog opposite a templating t and an rcmp at the primer terminus.. SNAP output
4fpv hydrolase-DNA X-ray (1.73 Å) Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H (2012) "Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2." Nat.Struct.Mol.Biol., 19, 1372-1377. doi: 10.1038/nsmb.2423. Crystal structure of d. rerio tdp2 complexed with single strand DNA product. SNAP output
4fs1 transferase-DNA X-ray (2.5 Å) Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY, Rizzo CJ, Egli M, Guengerich FP (2012) "Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases." J.Biol.Chem., 287, 35516-35526. doi: 10.1074/jbc.M112.403253. Base pairing mechanism of n2,3-ethenoguanine with dttp by human polymerase iota. SNAP output
4fs2 transferase-DNA X-ray (2.05 Å) Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY, Rizzo CJ, Egli M, Guengerich FP (2012) "Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases." J.Biol.Chem., 287, 35516-35526. doi: 10.1074/jbc.M112.403253. Base pairing mechanism of n2,3-ethenoguanine with dctp by human polymerase iota. SNAP output
4fth transcription regulator-DNA X-ray (3.004 Å) Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y, Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE (2014) "DNA Recognition by a sigma (54) Transcriptional Activator from Aquifex aeolicus." J.Mol.Biol., 426, 3553-3568. doi: 10.1016/j.jmb.2014.08.009. Crystal structure of ntrc4 DNA-binding domain bound to double-stranded DNA. SNAP output
4fx4 transcription regulator-DNA X-ray (3.1 Å) Brugarolas P, Movahedzadeh F, Wang Y, Zhang N, Bartek IL, Gao YN, Voskuil MI, Franzblau SG, He C (2012) "The Oxidation-sensing Regulator (MosR) Is a New Redox-dependent Transcription Factor in Mycobacterium tuberculosis." J.Biol.Chem., 287, 37703-37712. doi: 10.1074/jbc.M112.388611. Crystal structure of m. tuberculosis transcriptional regulator mosr (rv1049) in compex with DNA. SNAP output
4fxd transferase-DNA-RNA X-ray (3.0 Å) Perera RL, Torella R, Klinge S, Kilkenny ML, Maman JD, Pellegrini L (2013) "Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha." eLife, 2, e00482. doi: 10.7554/eLife.00482. Crystal structure of yeast DNA polymerase alpha bound to DNA-RNA. SNAP output
4fyd transferase-DNA X-ray (3.1 Å) Perera RL, Torella R, Klinge S, Kilkenny ML, Maman JD, Pellegrini L (2013) "Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha." eLife, 2, e00482. doi: 10.7554/eLife.00482. Crystal structure of yeast DNA polymerase alpha bound to DNA-RNA and dgtp. SNAP output
4fzx hydrolase-DNA X-ray (2.3 Å) Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T (2013) "Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease." Nucleic Acids Res., 41, 7556-7565. doi: 10.1093/nar/gkt495. Exonuclease x in complex with 3' overhanging duplex DNA. SNAP output
4fzy hydrolase-DNA X-ray (2.5 Å) Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T (2013) "Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease." Nucleic Acids Res., 41, 7556-7565. doi: 10.1093/nar/gkt495. Exonuclease x in complex with 12bp blunt-ended dsDNA. SNAP output
4fzz hydrolase-DNA X-ray (2.8 Å) Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T (2013) "Recognition and processing of double-stranded DNA by ExoX, a distributive 3'-5' exonuclease." Nucleic Acids Res., 41, 7556-7565. doi: 10.1093/nar/gkt495. Exonuclease x in complex with 5' overhanging duplex DNA. SNAP output
4g0r virus-DNA X-ray (2.7 Å) Halder S, Nam HJ, Govindasamy L, Vogel M, Dinsart C, Salome N, McKenna R, Agbandje-McKenna M (2013) "Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids." J.Virol., 87, 5128-5140. doi: 10.1128/JVI.03416-12. Structural characterization of h-1 parvovirus: comparison of infectious virions to replication defective particles. SNAP output
4g0u isomerase-DNA-isomerase inhibitor X-ray (2.7 Å) Wu CC, Li YC, Wang YR, Li TK, Chan NL (2013) "On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs." Nucleic Acids Res., 41, 10630-10640. doi: 10.1093/nar/gkt828. Human topoisomerase iibeta in complex with DNA and amsacrine. SNAP output
4g0v isomerase-DNA-isomerase inhibitor X-ray (2.548 Å) Wu CC, Li YC, Wang YR, Li TK, Chan NL (2013) "On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs." Nucleic Acids Res., 41, 10630-10640. doi: 10.1093/nar/gkt828. Human topoisomerase iibeta in complex with DNA and mitoxantrone. SNAP output
4g0w isomerase-DNA-isomerase inhibitor X-ray (2.696 Å) Wu CC, Li YC, Wang YR, Li TK, Chan NL (2013) "On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs." Nucleic Acids Res., 41, 10630-10640. doi: 10.1093/nar/gkt828. Human topoisomerase iibeta in complex with DNA and ametantrone. SNAP output
4g3i transferase-DNA X-ray (2.5 Å) Yan YY, Gan JH, Huang Z "Crystal structure of Dpo4 in complex with DNA duplex." Crystal structure of dpo4 in complex with DNA duplex. SNAP output
4g4n hydrolase-DNA X-ray (1.85 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2013) "Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM." J.Biol.Chem., 288, 10012-10023. doi: 10.1074/jbc.M112.415612. Mutm containing m77a mutation bound to undamaged DNA. SNAP output
4g4o hydrolase-DNA X-ray (1.95 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2013) "Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM." J.Biol.Chem., 288, 10012-10023. doi: 10.1074/jbc.M112.415612. Mutm containing m77a mutation bound to oxog-containing DNA. SNAP output
4g4q hydrolase-DNA X-ray (1.86 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2013) "Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM." J.Biol.Chem., 288, 10012-10023. doi: 10.1074/jbc.M112.415612. Mutm containing f114a mutation bound to undamaged DNA. SNAP output
4g4r hydrolase-DNA X-ray (1.95 Å) Sung RJ, Zhang M, Qi Y, Verdine GL (2013) "Structural and Biochemical Analysis of DNA Helix Invasion by the Bacterial 8-Oxoguanine DNA Glycosylase MutM." J.Biol.Chem., 288, 10012-10023. doi: 10.1074/jbc.M112.415612. Mutm containing f114a mutation bound to oxog-containing DNA. SNAP output
4g7h transcription, transferase-DNA X-ray (2.9 Å) Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH (2012) "Structural basis of transcription initiation." Science, 338, 1076-1080. doi: 10.1126/science.1227786. Crystal structure of thermus thermophilus transcription initiation complex. SNAP output
4g7o transcription, transferase-DNA X-ray (2.993 Å) Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH (2012) "Structural basis of transcription initiation." Science, 338, 1076-1080. doi: 10.1126/science.1227786. Crystal structure of thermus thermophilus transcription initiation complex containing 2 nt of RNA. SNAP output
4g7z transcription, transferase-DNA X-ray (3.815 Å) Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold E, Ebright RH (2012) "Structural basis of transcription initiation." Science, 338, 1076-1080. doi: 10.1126/science.1227786. Crystal structure of thermus thermophilus transcription initiation complex containing 5-bru at template-strand position +1. SNAP output
4g82 DNA binding protein-DNA X-ray (3.1 Å) Ethayathulla AS, Viadiu H (2013) "Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element." J.Biol.Chem. Crystal structure of p73 DNA-binding domain tetramer bound to a full response-element. SNAP output
4g83 DNA binding protein-DNA X-ray (4.0 Å) Ethayathulla AS, Viadiu H (2013) "Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element." J.Biol.Chem. Crystal structure of p73 DNA-binding domain tetramer bound to a full response-element. SNAP output
4g92 transcription-DNA X-ray (1.8 Å) Huber EM, Scharf DH, Hortschansky P, Groll M, Brakhage AA (2012) "DNA Minor Groove Sensing and Widening by the CCAAT-Binding Complex." Structure, 20, 1757-1768. doi: 10.1016/j.str.2012.07.012. Ccaat-binding complex from aspergillus nidulans with DNA. SNAP output
4gat transcription-DNA NMR Starich MR, Wikstrom M, Arst Jr HN, Clore GM, Gronenborn AM (1998) "The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors." J.Mol.Biol., 277, 605-620. doi: 10.1006/jmbi.1998.1625. Solution NMR structure of the wild type DNA binding domain of area complexed to a 13bp DNA containing a cgata site, regularized mean structure. SNAP output
4gc6 transferase-DNA X-ray (2.895 Å) Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL (2012) "Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues." Biochemistry, 51, 9234-9244. doi: 10.1021/bi301043k. Crystal structure of dpo4 in complex with n-mc-damp opposite dt. SNAP output
4gc7 transferase-RNA X-ray (2.89 Å) Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL (2012) "Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues." Biochemistry, 51, 9234-9244. doi: 10.1021/bi301043k. Crystal structure of dpo4 in complex with s-mc-dadp opposite dt. SNAP output
4gck DNA binding protein-DNA X-ray (2.05 Å) Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin W, Schumacher MA (2013) "SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid." Proc.Natl.Acad.Sci.USA, 110, 10586-10591. doi: 10.1073/pnas.1221036110. Structure of no-DNA complex. SNAP output
4gcl DNA binding protein-DNA X-ray (2.65 Å) Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin W, Schumacher MA (2013) "SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid." Proc.Natl.Acad.Sci.USA, 110, 10586-10591. doi: 10.1073/pnas.1221036110. Structure of no-DNA factor. SNAP output
4gct DNA binding protein-DNA X-ray (2.45 Å) Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin W, Schumacher MA (2013) "SlmA forms a higher-order structure on DNA that inhibits cytokinetic Z-ring formation over the nucleoid." Proc.Natl.Acad.Sci.USA, 110, 10586-10591. doi: 10.1073/pnas.1221036110. Structure of no factor protein-DNA complex. SNAP output
4gdf hydrolase-DNA X-ray (2.8 Å) Chang YP, Xu M, Machado AC, Yu XJ, Rohs R, Chen XS (2013) "Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen." Cell Rep, 3, 1117-1127. doi: 10.1016/j.celrep.2013.03.002. A crystal structure of sv40 large t antigen. SNAP output
4gfb transcription-DNA X-ray (2.99 Å) Le Bihan YV, Matot B, Pietrement O, Giraud-Panis MJ, Gasparini S, Le Cam E, Gilson E, Sclavi B, Miron S, Le Du MH (2013) "Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity." Acta Crystallogr.,Sect.D, 69, 409-419. doi: 10.1107/S0907444912049311. Rap1-DNA complex. SNAP output
4gfh isomerase-DNA X-ray (4.408 Å) Schmidt BH, Osheroff N, Berger JM (2012) "Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity." Nat.Struct.Mol.Biol., 19, 1147-1154. doi: 10.1038/nsmb.2388. Topoisomerase ii-DNA-amppnp complex. SNAP output
4gg4 DNA binding protein-DNA-RNA X-ray (2.501 Å) Yin P, Deng D, Yan C, Pan XJ, Xi JJ, Yan N, Shi Y (2012) "Specific DNA-RNA hybrid recognition by TAL effectors." Cell Rep, 2, 707-713. doi: 10.1016/j.celrep.2012.09.001. Crystal structure of the tal effector dhax3 bound to specific DNA-RNA hybrid. SNAP output
4gjp transcription-DNA X-ray (1.94 Å) Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG "Crystal structure of a protein complex." Crystal structure of the tal effector dhax3 bound to dsDNA containing repetitive methyl-cpg. SNAP output
4gjr transcription-DNA X-ray (1.85 Å) Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG "Crystal structure of a protein complex." Crystal structure of the tal effector dhax3 bound to methylated dsDNA. SNAP output
4gle hydrolase-DNA X-ray (2.7 Å) Meulenbroek EM, Peron Cane C, Jala I, Iwai S, Moolenaar GF, Goosen N, Pannu NS (2013) "UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions." Nucleic Acids Res., 41, 1363-1371. doi: 10.1093/nar/gks1127. Sacuvde in complex with 6-4pp-containing DNA. SNAP output
4glx ligase-ligase inhibitor-DNA X-ray (1.9 Å) Surivet JP, Lange R, Hubschwerlen C, Keck W, Specklin JL, Ritz D, Bur D, Locher H, Seiler P, Strasser DS, Prade L, Kohl C, Schmitt C, Chapoux G, Ilhan E, Ekambaram N, Athanasiou A, Knezevic A, Sabato D, Chambovey A, Gaertner M, Enderlin M, Boehme M, Sippel V, Wyss P (2012) "Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity." Bioorg.Med.Chem.Lett., 22, 6705-6711. doi: 10.1016/j.bmcl.2012.08.094. DNA ligase a in complex with inhibitor. SNAP output
4gnx DNA binding protein-DNA X-ray (2.8 Å) Pavletich NP, Fan J "Structure of." Structure of u. maydis replication protein a bound to ssDNA. SNAP output
4gop DNA binding protein-DNA X-ray (3.1 Å) Fan J, Pavletich NP (2012) "Structure and conformational change of a replication protein A heterotrimer bound to ssDNA." Genes Dev., 26, 2337-2347. doi: 10.1101/gad.194787.112. Structure and conformational change of a replication protein a heterotrimer bound to ssDNA. SNAP output
4guo transcription-DNA X-ray (3.19 Å) S Ethayathulla A, Viadiu H "structure of p73 DNA binding domain complex with 12 bp DNA." Structure of p73 DNA binding domain complex with 12 bp DNA. SNAP output
4guq transcription-DNA X-ray (3.7 Å) Ciribilli Y, Monti P, Bisio A, Nguyen HT, Ethayathulla AS, Ramos A, Foggetti G, Menichini P, Menendez D, Resnick MA, Viadiu H, Fronza G, Inga A (2013) "Transactivation specificity is conserved among p53 family proteins and depends on a response element sequence code." Nucleic Acids Res., 41, 8637-8653. doi: 10.1093/nar/gkt657. Structure of muts139f p73 DNA binding domain complexed with 20bp DNA response element. SNAP output
4gxi transferase-DNA X-ray (1.949 Å) Freudenthal BD, Beard WA, Wilson SH (2013) "DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion." Nucleic Acids Res., 41, 1848-1858. doi: 10.1093/nar/gks1276. R283k DNA polymerase beta binary complex with a templating 8og. SNAP output
4gxj transferase-DNA X-ray (2.2 Å) Freudenthal BD, Beard WA, Wilson SH (2013) "DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion." Nucleic Acids Res., 41, 1848-1858. doi: 10.1093/nar/gks1276. R283k DNA polymerase beta ternary complex with a templating 8og and incoming dctp analog. SNAP output
4gxk transferase-DNA X-ray (1.998 Å) Freudenthal BD, Beard WA, Wilson SH (2013) "DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion." Nucleic Acids Res., 41, 1848-1858. doi: 10.1093/nar/gks1276. R283k DNA polymerase beta ternary complex with a templating 8og and incoming datp analog. SNAP output
4gz0 hydrolase-DNA X-ray (2.113 Å) Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS (2012) "Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2." Nat.Struct.Mol.Biol., 19, 1363-1371. doi: 10.1038/nsmb.2418. Mus musculus tdp2-DNA substrate analog (5'-6-aminohexanol) complex. SNAP output
4gz1 hydrolase-DNA X-ray (1.5 Å) Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS (2012) "Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2." Nat.Struct.Mol.Biol., 19, 1363-1371. doi: 10.1038/nsmb.2418. Mus musculus tdp2 reaction product (5'-phosphorylated DNA)-mg2+ complex at 1.5 angstroms resolution. SNAP output
4gz2 hydrolase-DNA X-ray (1.85 Å) Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS (2012) "Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2." Nat.Struct.Mol.Biol., 19, 1363-1371. doi: 10.1038/nsmb.2418. Mus musculus tdp2 excluded ssDNA complex. SNAP output
4gzn transcription-DNA X-ray (0.99 Å) Liu Y, Toh H, Sasaki H, Zhang X, Cheng X (2012) "An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence." Genes Dev., 26, 2374-2379. doi: 10.1101/gad.202200.112. Mouse zfp57 zinc fingers in complex with methylated DNA. SNAP output
4gzy transcription-DNA-RNA X-ray (3.51 Å) Weixlbaumer A, Leon K, Landick R, Darst SA (2013) "Structural basis of transcriptional pausing in bacteria." Cell(Cambridge,Mass.), 152, 431-441. doi: 10.1016/j.cell.2012.12.020. Crystal structures of bacterial RNA polymerase paused elongation complexes. SNAP output
4gzz transcription-DNA-RNA hybrid X-ray (4.29 Å) Weixlbaumer A, Leon K, Landick R, Darst SA (2013) "Structural basis of transcriptional pausing in bacteria." Cell(Cambridge,Mass.), 152, 431-441. doi: 10.1016/j.cell.2012.12.020. Crystal structures of bacterial RNA polymerase paused elongation complexes. SNAP output
4h0e transcription-DNA X-ray (1.973 Å) Jain D, Nair DT (2013) "Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators." Nucleic Acids Res., 41, 639-647. doi: 10.1093/nar/gks962. Crystal structure of mutant orr3 in complex with ntd of arar. SNAP output
4h10 transcription-DNA X-ray (2.402 Å) Wang Z, Wu Y, Li L, Su XD (2013) "Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA." Cell Res., 23, 213-224. doi: 10.1038/cr.2012.170. Intermolecular recognition revealed by the complex structure of human clock-bmal1 basic helix-loop-helix domains with e-box DNA. SNAP output
4h5q viral protein-DNA X-ray (2.7 Å) Raymond DD, Piper ME, Gerrard SR, Skiniotis G, Smith JL (2012) "Phleboviruses encapsidate their genomes by sequestering RNA bases." Proc.Natl.Acad.Sci.USA, 109, 19208-19213. doi: 10.1073/pnas.1213553109. Crystal structure of rift valley fever virus nucleocapsid protein hexamer bound to single-stranded DNA. SNAP output
4h8k hydrolase-DNA-RNA X-ray (2.3 Å) Nguyen TN, You DJ, Matsumoto H, Kanaya E, Koga Y, Kanaya S (2013) "Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid." J.Struct.Biol., 182, 144-154. doi: 10.1016/j.jsb.2013.02.018. Crystal structure of lc11-rnase h1 in complex with RNA-DNA hybrid. SNAP output
4hc7 transcription-DNA X-ray (2.65 Å) Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L (2012) "DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation." Cell Rep, 2, 1197-1206. doi: 10.1016/j.celrep.2012.10.012. Crystal structure of the full DNA binding domain of gata3-complex 2. SNAP output
4hc9 transcription-DNA X-ray (1.6 Å) Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L (2012) "DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation." Cell Rep, 2, 1197-1206. doi: 10.1016/j.celrep.2012.10.012. DNA binding by gata transcription factor-complex 3. SNAP output
4hca transcription-DNA X-ray (2.8 Å) Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L (2012) "DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation." Cell Rep, 2, 1197-1206. doi: 10.1016/j.celrep.2012.10.012. DNA binding by gata transcription factor-complex 1. SNAP output
4hcb hydrolase-DNA X-ray (2.0 Å) Qiu R, Lou T, Wei J, Liu M, Gu S, Tang R, Ji C, Gong W "The structures of Escherichia coli exonuclease I in complex with the single strand DNA." The metal-free form of crystal structure of e.coli exoi-ssDNA complex. SNAP output
4hcc hydrolase-DNA X-ray (2.96 Å) Qiu R, Lou T, Wei J, Liu M, Gu S, Tang R, Ji C, Gong W "The structures of Escherichia coli exonuclease I in complex with the single strand DNA." The zinc ion bound form of crystal structure of e.coli exoi-ssDNA complex. SNAP output
4hdu DNA binding protein-DNA X-ray (2.848 Å) Wilkinson OJ, Latypov V, Tubbs JL, Millington CL, Morita R, Blackburn H, Marriott A, McGown G, Thorncroft M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA, Tainer JA, Margison GP, Williams DM (2012) "Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-{pi} interactions." Proc.Natl.Acad.Sci.USA, 109, 18755-18760. doi: 10.1073/pnas.1209451109. Crystal structure of s. pombe atl1 in complex with damaged DNA containing 2-aminopurine. SNAP output
4hdv DNA binding protein-DNA X-ray (2.702 Å) Wilkinson OJ, Latypov V, Tubbs JL, Millington CL, Morita R, Blackburn H, Marriott A, McGown G, Thorncroft M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA, Tainer JA, Margison GP, Williams DM (2012) "Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-{pi} interactions." Proc.Natl.Acad.Sci.USA, 109, 18755-18760. doi: 10.1073/pnas.1209451109. Crystal structure of s. pombe atl1 in complex with damaged DNA containing 2,6-diaminopurine. SNAP output
4hf1 transcription-DNA X-ray (2.222 Å) Rajagopalan S, Teter SJ, Zwart PH, Brennan RG, Phillips KJ, Kiley PJ (2013) "Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity." Nat.Struct.Mol.Biol., 20, 740-747. doi: 10.1038/nsmb.2568. Crystal structure of iscr bound to its promoter. SNAP output
4hf2 transcription-DNA X-ray (2.99 Å) Rajagopalan S, Teter SJ, Zwart PH, Brennan RG, Phillips KJ, Kiley PJ (2013) "Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity." Nat.Struct.Mol.Biol., 20, 740-747. doi: 10.1038/nsmb.2568. Crystal structure of e43a iscr mutant bound to its promoter. SNAP output
4hht hydrolase-DNA X-ray (3.1 Å) Chon H, Sparks JL, Rychlik M, Nowotny M, Burgers PM, Crouch RJ, Cerritelli SM (2013) "RNase H2 roles in genome integrity revealed by unlinking its activities." Nucleic Acids Res., 41, 3130-3143. doi: 10.1093/nar/gkt027. T. maritima rnase h2 g21s in complex with nucleic acid substrate and calcium ions. SNAP output
4hid DNA binding protein X-ray (1.822 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (gcttacggt). SNAP output
4hik DNA binding protein X-ray (1.636 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (ggttacggt). SNAP output
4him DNA binding protein X-ray (1.75 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (ggatacggt). SNAP output
4hio DNA binding protein X-ray (1.753 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (ggtaacggt). SNAP output
4hiv DNA-antibiotic X-ray (2.6 Å) Lo YS, Tseng WH, Chuang CY, Hou MH (2013) "The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats." Nucleic Acids Res., 41, 4284-4294. doi: 10.1093/nar/gkt084. Structure of actinomycin d d(atgcggcat) complex. SNAP output
4hj5 DNA binding protein X-ray (2.04 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (ggtttcggt). SNAP output
4hj7 DNA binding protein X-ray (1.783 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (ggttagggt). SNAP output
4hj8 DNA binding protein X-ray (2.043 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (ggttacgct). SNAP output
4hj9 DNA binding protein X-ray (1.85 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (cggttacggt). SNAP output
4hja DNA binding protein X-ray (2.1 Å) Dickey TH, McKercher MA, Wuttke DS (2013) "Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes." Structure, 21, 121-132. doi: 10.1016/j.str.2012.10.015. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssDNA (acggttacggt). SNAP output
4hje transcription-DNA X-ray (1.907 Å) Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L (2013) "Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion." Nucleic Acids Res., 41, 8368-8376. doi: 10.1093/nar/gkt584. Crystal structure of p53 core domain in complex with DNA. SNAP output
4hkq transcription-RNA-DNA X-ray (3.04 Å) Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M (2013) "Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid." Nucleic Acids Res., 41, 3874-3887. doi: 10.1093/nar/gkt053. Xmrv reverse transcriptase in complex with RNA-DNA hybrid. SNAP output
4hly DNA binding protein-DNA X-ray (1.48 Å) Hew K, Dahlroth SL, Venkatachalam R, Nasertorabi F, Lim BT, Cornvik T, Nordlund P (2013) "The crystal structure of the DNA-binding domain of vIRF-1 from the oncogenic KSHV reveals a conserved fold for DNA binding and reinforces its role as a transcription factor." Nucleic Acids Res., 41, 4295-4306. doi: 10.1093/nar/gkt082. The complex crystal structure of the DNA binding domain of virf-1 from the oncogenic kshv with DNA. SNAP output
4hn5 transcription-DNA X-ray (1.902 Å) Hudson WH, Youn C, Ortlund EA (2013) "The structural basis of direct glucocorticoid-mediated transrepression." Nat.Struct.Mol.Biol., 20, 53-58. doi: 10.1038/nsmb.2456. Gr DNA binding domain - tslp ngre complex. SNAP output
4hn6 transcription-DNA X-ray (2.549 Å) Hudson WH, Youn C, Ortlund EA (2013) "The structural basis of direct glucocorticoid-mediated transrepression." Nat.Struct.Mol.Biol., 20, 53-58. doi: 10.1038/nsmb.2456. Gr DNA binding domain r460d-d462r - tslp ngre complex. SNAP output
4hp1 DNA binding protein-DNA X-ray (2.25 Å) Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG (2012) "Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development." Cell(Cambridge,Mass.), 151, 1200-1213. doi: 10.1016/j.cell.2012.11.014. Crystal structure of tet3 in complex with a non-cpg dsDNA. SNAP output
4hp3 DNA binding protein-DNA X-ray (2.05 Å) Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG (2012) "Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development." Cell(Cambridge,Mass.), 151, 1200-1213. doi: 10.1016/j.cell.2012.11.014. Crystal structure of tet3 in complex with a cpg dsDNA. SNAP output
4hqb DNA binding protein-DNA X-ray (2.301 Å) Sugiman-Marangos SN, Peel JK, Weiss YM, Ghirlando R, Junop MS (2013) "Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states." Nucleic Acids Res., 41, 9934-9944. doi: 10.1093/nar/gkt759. Crystal structure of ddrb from deinococcus radiodurans bound to ssDNA. SNAP output
4hqe transcription-DNA X-ray (2.299 Å) Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, Cho H, Brugarolas P, Gao YN, Peterson SN, Lan L, Bae T, He C (2013) "Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR." Proc.Natl.Acad.Sci.USA, 110, 5010-5015. doi: 10.1073/pnas.1219446110. The crystal structure of qsrr-DNA complex. SNAP output
4hqu hormone-DNA X-ray (2.2 Å) Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC (2012) "Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets." Proc.Natl.Acad.Sci.USA, 109, 19971-19976. doi: 10.1073/pnas.1213933109. Crystal structure of human pdgf-bb in complex with a modified nucleotide aptamer (somamer sl5). SNAP output
4hqx hormone-DNA X-ray (2.3 Å) Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC (2012) "Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets." Proc.Natl.Acad.Sci.USA, 109, 19971-19976. doi: 10.1073/pnas.1213933109. Crystal structure of human pdgf-bb in complex with a modified nucleotide aptamer (somamer sl4). SNAP output
4hri transcription-DNA X-ray (2.954 Å) Hu HX, Jiang YL, Zhao MX, Zhu PF, Yang XY, Wen B, Zhang Z, Wu Q, Chen Y, Zhang CC, Zhou CZ "Structural and biochemical analyses of Anabaena HetR reveal insights into its binding to DNA targets and the inhibitory hexapeptide ERGSGR." Crystal structure of hetr in complex with a 21-bp palindromic DNA at the upstream of the hetp promoter from anabaena. SNAP output
4hsb hydrolase-DNA X-ray (1.9 Å) Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF (2013) "Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe." Dna Repair, 12, 196-204. doi: 10.1016/j.dnarep.2012.12.001. S. pombe 3-methyladenine DNA glycosylase-like protein mag2 bound to damaged DNA. SNAP output
4ht4 hydrolase-DNA X-ray (2.907 Å) Edwards JS, Betts L, Frazier ML, Pollet RM, Kwong SM, Walton WG, Ballentine WK, Huang JJ, Habibi S, Del Campo M, Meier JL, Dervan PB, Firth N, Redinbo MR (2013) "Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus." Proc.Natl.Acad.Sci.USA, 110, 2804-2809. doi: 10.1073/pnas.1219701110. Molecular basis of vancomycin resistance transfer in staphylococcus aureus. SNAP output
4htu hydrolase-DNA X-ray (1.489 Å) Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M (2013) "Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs." Nucleic Acids Res., 41, 2689-2697. doi: 10.1093/nar/gks1316. Structure of 5-chlorouracil modified a:u base pair. SNAP output
4hue hydrolase-DNA X-ray (1.561 Å) Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M (2013) "Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs." Nucleic Acids Res., 41, 2689-2697. doi: 10.1093/nar/gks1316. Structure of 5-chlorouracil modified g:u base pair. SNAP output
4huf hydrolase-DNA X-ray (1.69 Å) Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M (2013) "Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs." Nucleic Acids Res., 41, 2689-2697. doi: 10.1093/nar/gks1316. Structure of 5-chlorouracil modified a:u base pair. SNAP output
4hug hydrolase-DNA X-ray (1.64 Å) Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M (2013) "Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs." Nucleic Acids Res., 41, 2689-2697. doi: 10.1093/nar/gks1316. Structure of 5-chlorouracil modified a:u base pairs. SNAP output
4hyk transferase-DNA X-ray (2.802 Å) Wilson RC, Jackson MA, Pata JD (2013) "Y-family polymerase conformation is a major determinant of fidelity and translesion specificity." Structure, 21, 20-31. doi: 10.1016/j.str.2012.11.005. Dbh ternary complex (substrates partially disordered). SNAP output
4i27 transferase-DNA X-ray (2.6 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Ternary complex of mouse tdt with ssDNA and incoming nucleotide. SNAP output
4i28 transferase-DNA X-ray (2.15 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Binary complex of mouse tdt with ssDNA and zn++. SNAP output
4i29 transferase-DNA X-ray (2.2 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Binary complex of mouse tdt with ssDNA and mn++. SNAP output
4i2a transferase-DNA X-ray (1.9 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Binary complex of mouse tdt with ssDNA in absence of divalent transition metal ion. SNAP output
4i2b transferase-DNA X-ray (2.2 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Ternary complex of mouse tdt with ssDNA and ampcpp. SNAP output
4i2c transferase-DNA X-ray (2.1 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Ternary complex of mouse tdt with ssDNA and ampcpp. SNAP output
4i2e transferase-DNA X-ray (2.0 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Ternary complex of mouse tdt with ssDNA and ampcpp. SNAP output
4i2f transferase-DNA X-ray (2.1 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Binary complex of mouse tdt with ssDNA. SNAP output
4i2g transferase-DNA X-ray (2.5 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Binary complex of mouse tdt with ssDNA. SNAP output
4i2h transferase-DNA X-ray (2.75 Å) Gouge J, Rosario S, Romain F, Beguin P, Delarue M (2013) "Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism." J.Mol.Biol., 425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009. Ternary complex of mouse tdt with ssDNA and ampcpp. SNAP output
4i2o transcription regulator-DNA X-ray (1.77 Å) Bonnet M, Kurz M, Mesa S, Briand C, Hennecke H, Grutter MG (2013) "The Structure of Bradyrhizobium japonicum Transcription Factor FixK2 Unveils Sites of DNA Binding and Oxidation." J.Biol.Chem., 288, 14238-14246. doi: 10.1074/jbc.M113.465484. The structure of fixk2 from bradyrhizobium japonicum. SNAP output
4i3h isomerase-DNA X-ray (3.7 Å) Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR (2013) "Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport." Nucleic Acids Res., 41, 9911-9923. doi: 10.1093/nar/gkt749. A three-gate structure of topoisomerase iv from streptococcus pneumoniae. SNAP output
4i6z transcription regulator-DNA X-ray (3.2 Å) Koclega KD, Chruszcz M, Cooper DR, Petkowski JJ, Tkaczuk KL, Joachimiak A, Minor W "Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide." Crystal structure of the transcriptional regulator tm1030 with 24bp DNA oligonucleotide. SNAP output
4i7y hydrolase-hydrolase inhibitor-DNA X-ray (2.4 Å) Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F (2013) "Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer." Acta Crystallogr.,Sect.D, 69, 2403-2411. doi: 10.1107/S0907444913022269. Crystal structure of human alpha thrombin in complex with a 27-mer aptamer bound to exosite ii. SNAP output
4i8t transcription-DNA X-ray (3.0 Å) Martin RN, McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG (2013) "Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I." Acta Crystallogr.,Sect.F, 69, 962-966. doi: 10.1107/S174430911302126X. C.esp1396i bound to a 19 base pair DNA duplex. SNAP output
4i9q transferase-DNA X-ray (2.3 Å) Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M (2013) "A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site." Plos One, 8, e76700. doi: 10.1371/journal.pone.0076700. Crystal structure of the ternary complex of the d714a mutant of rb69 DNA polymerase. SNAP output
4ibu DNA binding protein-DNA X-ray (1.7 Å) Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z (2013) "Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions." Nucleic Acids Res., 41, 8748-8759. doi: 10.1093/nar/gkt630. Human p53 core domain with hot spot mutation r273c and second-site suppressor mutation t284r in sequence-specific complex with DNA. SNAP output
4ibv DNA binding protein-DNA X-ray (2.1 Å) Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z (2013) "Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions." Nucleic Acids Res., 41, 8748-8759. doi: 10.1093/nar/gkt630. Human p53 core domain with hot spot mutation r273c and second-site suppressor mutation s240r in sequence-specific complex with DNA. SNAP output
4ibw DNA binding protein-DNA X-ray (1.791 Å) Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R, Shakked Z (2013) "Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions." Nucleic Acids Res., 41, 8748-8759. doi: 10.1093/nar/gkt630. Human p53 core domain with hot spot mutation r273h and second-site suppressor mutation t284r in sequence-specific complex with DNA. SNAP output
4iem hydrolase, lyase-DNA X-ray (2.39 Å) Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, Tainer JA (2013) "Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes." J.Biol.Chem., 288, 8445-8455. doi: 10.1074/jbc.M112.422774. Human apurinic-apyrimidinic endonuclease (ape1) with product DNA and mg2+. SNAP output
4ihs transcription-DNA X-ray (3.1 Å) Alanazi AM, Neidle EL, Momany C (2013) "The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators." Acta Crystallogr.,Sect.D, 69, 1995-2007. doi: 10.1107/S0907444913017320. Crystal structure of benm_dbd-catb site 1 DNA complex. SNAP output
4iht transcription-DNA X-ray (3.0 Å) Alanazi AM, Neidle EL, Momany C (2013) "The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators." Acta Crystallogr.,Sect.D, 69, 1995-2007. doi: 10.1107/S0907444913017320. Crystal structure of benm_dbd-bena site 1 DNA complex. SNAP output
4ihv transcription-DNA X-ray (2.716 Å) Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC (2013) "Control of DNA minor groove width and Fis protein binding by the purine 2-amino group." Nucleic Acids Res., 41, 6750-6760. doi: 10.1093/nar/gkt357. Crystal structure of fis bound to 27 bp sequence DNA f28 (aaatttgtttgagcgttgagcaaattt). SNAP output
4ihw transcription-DNA X-ray (2.7 Å) Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC (2013) "Control of DNA minor groove width and Fis protein binding by the purine 2-amino group." Nucleic Acids Res., 41, 6750-6760. doi: 10.1093/nar/gkt357. Crystal structure of fis bound to 27 bp inosine substituted DNA f28-di (aaatttgtttgaicittgagcaaattt). SNAP output
4ihx transcription-DNA X-ray (2.8 Å) Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC (2013) "Control of DNA minor groove width and Fis protein binding by the purine 2-amino group." Nucleic Acids Res., 41, 6750-6760. doi: 10.1093/nar/gkt357. Crystal structure of fis bound to 27 bp 2-aminopurine substituted DNA f28-2ap (aaatttgtttga2t2ttgagcaaattt). SNAP output
4ihy transcription-DNA X-ray (2.9 Å) Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC (2013) "Control of DNA minor groove width and Fis protein binding by the purine 2-amino group." Nucleic Acids Res., 41, 6750-6760. doi: 10.1093/nar/gkt357. Crystal structure of fis bound to 27bp inosine substituted DNA f29-di (aaatttgtttgiicictgagcaaattt). SNAP output
4ikf viral protein-DNA-inhibitor X-ray (3.4 Å) Desimmie BA, Demeulemeester J, Suchaud V, Taltynov O, Billamboz M, Lion C, Bailly F, Strelkov SV, Debyser Z, Cotelle P, Christ F (2013) "2-Hydroxyisoquinoline-1,3(2H,4H)-diones (HIDs), novel inhibitors of HIV integrase with a high barrier to resistance." Acs Chem.Biol., 8, 1187-1194. doi: 10.1021/cb4000426. Pfv intasome with inhibitor mb-76. SNAP output
4iqj transferase-DNA X-ray (3.2 Å) Liu B, Lin J, Steitz TA (2013) "Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome." Structure, 21, 658-664. doi: 10.1016/j.str.2013.02.002. Structure of poliiialpha-tauc-DNA complex suggests an atomic model of the replisome. SNAP output
4iqr transcription-DNA X-ray (2.9 Å) Chandra V, Huang P, Potluri N, Wu D, Kim Y, Rastinejad F (2013) "Multidomain integration in the structure of the HNF-4 alpha nuclear receptor complex." Nature, 495, 394-398. doi: 10.1038/nature11966. Multi-domain organization of the hnf4alpha nuclear receptor complex on DNA. SNAP output
4iqv transferase-transferase inhibitor-DNA X-ray (2.9 Å) Costi R, Cuzzucoli Crucitti G, Pescatori L, Messore A, Scipione L, Tortorella S, Amoroso A, Crespan E, Campiglia P, Maresca B, Porta A, Granata I, Novellino E, Gouge J, Delarue M, Maga G, Di Santo R (2013) "New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target." J.Med.Chem., 56, 7431-7441. doi: 10.1021/jm4010187. Tdt core in complex with inhibitor 6-[4-(3-fluorobenzoyl)-1h-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssDNA. SNAP output
4iqw transferase-transferase inhibitor-DNA X-ray (2.6 Å) Costi R, Cuzzucoli Crucitti G, Pescatori L, Messore A, Scipione L, Tortorella S, Amoroso A, Crespan E, Campiglia P, Maresca B, Porta A, Granata I, Novellino E, Gouge J, Delarue M, Maga G, Di Santo R (2013) "New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target." J.Med.Chem., 56, 7431-7441. doi: 10.1021/jm4010187. Tdt core in complex with inhibitor (2z,5e)-6-[4-(4-fluorobenzoyl)-1h-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssDNA. SNAP output
4ir1 transferase-DNA X-ray (2.38 Å) Sharma A, Kottur J, Narayanan N, Nair DT (2013) "A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli." Nucleic Acids Res., 41, 5104-5114. doi: 10.1093/nar/gkt146. Polymerase-DNA complex. SNAP output
4ir9 transferase-DNA X-ray (2.33 Å) Sharma A, Kottur J, Narayanan N, Nair DT (2013) "A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli." Nucleic Acids Res., 41, 5104-5114. doi: 10.1093/nar/gkt146. Polymerase-DNA complex. SNAP output
4irc transferase-DNA X-ray (2.67 Å) Sharma A, Kottur J, Narayanan N, Nair DT (2013) "A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli." Nucleic Acids Res., 41, 5104-5114. doi: 10.1093/nar/gkt146. Polymerase-DNA complex. SNAP output
4ird transferase-DNA X-ray (2.48 Å) Sharma A, Kottur J, Narayanan N, Nair DT (2013) "A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli." Nucleic Acids Res., 41, 5104-5114. doi: 10.1093/nar/gkt146. Structure of polymerase-DNA complex. SNAP output
4iri DNA binding protein-DNA X-ray (2.77 Å) Regan MC, Horanyi PS, Pryor EE, Sarver JL, Cafiso DS, Bushweller JH (2013) "Structural and dynamic studies of the transcription factor ERG reveal DNA binding is allosterically autoinhibited." Proc.Natl.Acad.Sci.USA, 110, 13374-13379. doi: 10.1073/pnas.1301726110. Auto-inhibited erg ets domain-DNA complex. SNAP output
4irk transferase-DNA X-ray (2.32 Å) Sharma A, Kottur J, Narayanan N, Nair DT (2013) "A strategically located serine residue is critical for the mutator activity of DNA polymerase IV from Escherichia coli." Nucleic Acids Res., 41, 5104-5114. doi: 10.1093/nar/gkt146. Structure of polymerase-DNA complex, DNA. SNAP output
4is1 metal binding protein-DNA X-ray (2.1 Å) Vandevenne M, Jacques DA, Artuz C, Nguyen CD, Kwan AH, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay JP (2013) "New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217." J.Biol.Chem., 288, 10616-10627. doi: 10.1074/jbc.M112.441451. Crystal structure of znf217 bound to DNA. SNAP output
4itq gene regulation, structural protein-DNA X-ray (2.7 Å) Swiercz JP, Nanji T, Gloyd M, Guarne A, Elliot MA (2013) "A novel nucleoid-associated protein specific to the actinobacteria." Nucleic Acids Res., 41, 4171-4184. doi: 10.1093/nar/gkt095. Crystal structure of hypothetical protein sco1480 bound to DNA. SNAP output
4iuf transcription regulator-DNA X-ray (2.752 Å) Kuo PH, Chiang CH, Wang YT, Doudeva LG, Yuan HS (2014) "The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids." Nucleic Acids Res., 42, 4712-4722. doi: 10.1093/nar/gkt1407. Crystal structure of human tdp-43 rrm1 domain in complex with a single-stranded DNA. SNAP output
4ivz transcription-DNA X-ray (3.1 Å) Martin RN, McGeehan JE, Kneale G (2014) "Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I." Plos One, 9, e98365. doi: 10.1371/journal.pone.0098365. A y37f mutant of c.esp1396i bound to its highest affinity operator site om. SNAP output
4iwr transcription-DNA X-ray (2.4 Å) Martin RN, McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale GG (2013) "Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I." Acta Crystallogr.,Sect.F, 69, 962-966. doi: 10.1107/S174430911302126X. C.esp1396i bound to a 25 base pair operator site. SNAP output
4ix7 DNA binding protein-DNA X-ray (1.581 Å) Dai Q, Ren A, Westholm JO, Serganov AA, Patel DJ, Lai EC (2013) "The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors." Genes Dev., 27, 602-614. doi: 10.1101/gad.213314.113. Crystal structure of the insv-ben domain complexed to its DNA target site. SNAP output
4izz transcription-DNA X-ray (2.502 Å) Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K, Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak A (2013) "Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets." Proc.Natl.Acad.Sci.USA, 110, E1716-E1723. doi: 10.1073/pnas.1305971110. Crystal structure of fischerella transcription factor hetr complexed with 21mer DNA target. SNAP output
4j00 transcription-DNA X-ray (3.004 Å) Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K, Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak A (2013) "Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets." Proc.Natl.Acad.Sci.USA, 110, E1716-E1723. doi: 10.1073/pnas.1305971110. Crystal structure of fischerella transcription factor hetr complexed with 24mer DNA target. SNAP output
4j01 transcription-DNA X-ray (3.246 Å) Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K, Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak A (2013) "Structures of complexes comprised of Fischerella transcription factor HetR with Anabaena DNA targets." Proc.Natl.Acad.Sci.USA, 110, E1716-E1723. doi: 10.1073/pnas.1305971110. Crystal structure of fischerella transcription factor hetr complexed with 29mer DNA target. SNAP output
4j19 transcription-DNA X-ray (2.9 Å) Kappei D, Butter F, Benda C, Scheibe M, Draskovic I, Stevense M, Novo CL, Basquin C, Araki M, Araki K, Krastev DB, Kittler R, Jessberger R, Londono-Vallejo JA, Mann M, Buchholz F (2013) "HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment." Embo J., 32, 1681-1701. doi: 10.1038/emboj.2013.105. Structure of a novel telomere repeat binding protein bound to DNA. SNAP output
4j1j viral protein-DNA X-ray (2.65 Å) Niu F, Shaw N, Wang YE, Jiao L, Ding W, Li X, Zhu P, Upur H, Ouyang S, Cheng G, Liu ZJ (2013) "Structure of the Leanyer orthobunyavirus nucleoprotein-RNA complex reveals unique architecture for RNA encapsidation." Proc.Natl.Acad.Sci.USA, 110, 9054-9059. doi: 10.1073/pnas.1300035110. Leanyer orthobunyavirus nucleoprotein-ssDNA complex. SNAP output
4j2a transferase-DNA X-ray (1.8 Å) Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH (2013) "Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics." Nucleic Acids Res., 41, 9077-9089. doi: 10.1093/nar/gkt674. Rb69 DNA polymerase l415a ternary complex. SNAP output
4j2b transferase-DNA X-ray (2.04 Å) Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH (2013) "Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics." Nucleic Acids Res., 41, 9077-9089. doi: 10.1093/nar/gkt674. Rb69 DNA polymerase l415g ternary complex. SNAP output
4j2d transferase-DNA X-ray (1.76 Å) Xia S, Wang J, Konigsberg WH "Role of L415 in the Replication of RB69 DNA Polymerase." Rb69 DNA polymerase l415k ternary complex. SNAP output
4j2e transferase-DNA X-ray (2.02 Å) Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg WH (2013) "Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics." Nucleic Acids Res., 41, 9077-9089. doi: 10.1093/nar/gkt674. Rb69 DNA polymerase l415m ternary complex. SNAP output
4j2x transcription-DNA binding protein-DNA X-ray (2.85 Å) Collins KJ, Yuan Z, Kovall RA (2014) "Structure and Function of the CSL-KyoT2 Corepressor Complex: A Negative Regulator of Notch Signaling." Structure, 22, 70-81. doi: 10.1016/j.str.2013.10.010. Csl (rbp-jk) with corepressor kyot2 bound to DNA. SNAP output
4j3n isomerase-DNA X-ray (2.3 Å) Wu CC, Li YC, Wang YR, Li TK, Chan NL (2013) "On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs." Nucleic Acids Res., 41, 10630-10640. doi: 10.1093/nar/gkt828. Human topoisomerase iibeta in complex with DNA. SNAP output
4j8u structural protein-DNA X-ray (2.38 Å) Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M, Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK, Hartinger CG (2013) "Novel metal(II) arene 2-pyridinecarbothioamides: a rationale to orally active organometallic anticancer agents." CHEM SCI, 4, 1837-1846. doi: 10.1039/C3SC22294B. X-ray structure of ncp145 with chlorido(eta-6-p-cymene)(n-phenyl-2-pyridinecarbothioamide)osmium(ii). SNAP output
4j8v structural protein-DNA X-ray (2.58 Å) Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M, Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK, Hartinger CG (2013) "Novel metal(II) arene 2-pyridinecarbothioamides: a rationale to orally active organometallic anticancer agents." CHEM SCI, 4, 1837-1846. doi: 10.1039/C3SC22294B. X-ray structure of ncp145 with bound chlorido(eta-6-p-cymene)(n-phenyl-2-pyridinecarbothioamide)ruthenium(ii). SNAP output
4j8w structural protein-DNA X-ray (2.41 Å) Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M, Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK, Hartinger CG (2013) "Novel metal(II) arene 2-pyridinecarbothioamides: a rationale to orally active organometallic anticancer agents." CHEM SCI, 4, 1837-1846. doi: 10.1039/C3SC22294B. X-ray structure of ncp145 with chlorido(eta-6-p-cymene)(n-fluorophenyl-2-pyridinecarbothioamide)osmium(ii). SNAP output
4j8x structural protein-DNA X-ray (2.87 Å) Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M, Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK, Hartinger CG (2013) "Novel metal(II) arene 2-pyridinecarbothioamides: a rationale to orally active organometallic anticancer agents." CHEM SCI, 4, 1837-1846. doi: 10.1039/C3SC22294B. X-ray structure of ncp145 with bound chlorido(eta-6-p-cymene)(n-fluorophenyl-2-pyridinecarbothioamide)ruthenium(ii). SNAP output
4j9k transferase-DNA X-ray (2.03 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA ternary complex: misincorporation g opposite t after a t at the primer 3' end (ta-g). SNAP output
4j9l transferase-DNA X-ray (1.85 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA ternary complex: misincorporation g opposite t after a c at the primer 3' end (ca-g). SNAP output
4j9m transferase-DNA X-ray (2.25 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA ternary complex: misincorporation g opposite t after an a at the primer 3' end (aa-g). SNAP output
4j9n transferase-DNA X-ray (1.956 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA ternary complex: misincorporation g opposite t after a g at the primer 3' end (ga-g). SNAP output
4j9o transferase-DNA X-ray (2.597 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA ternary complex: primer extension after a t:g mispair. SNAP output
4j9p transferase-DNA X-ray (2.3 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA postinsertion binary complex with ta base pair. SNAP output
4j9q transferase-DNA X-ray (1.96 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA postinsertion binary complex with tg mispair. SNAP output
4j9r transferase-DNA X-ray (2.35 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA translocated binary complex with tg mispair. SNAP output
4j9s transferase-DNA X-ray (1.95 Å) Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F, Yang W (2013) "Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta." Proc.Natl.Acad.Sci.USA, 110, 8146-8151. doi: 10.1073/pnas.1303126110. Human DNA polymerase eta-DNA translocated binary complex: with ta base pair. SNAP output
4jbk DNA binding protein-DNA X-ray (2.963 Å) Ru H, Ni X, Zhao L, Crowley C, Ding W, Hung L-W, Shaw N, Cheng G, Liu Z-J (2013) "Structural basis for termination of AIM2-mediated signaling by p202." Cell Res., 23, 855-858. doi: 10.1038/cr.2013.52. Molecular basis for abrogation of activation of pro-inflammatory cytokines. SNAP output
4jbm DNA binding protein-DNA X-ray (2.218 Å) Ru H, Ni X, Zhao L, Crowley C, Ding W, Hung L-W, Shaw N, Cheng G, Liu Z-J (2013) "Structural basis for termination of AIM2-mediated signaling by p202." Cell Res., 23, 855-858. doi: 10.1038/cr.2013.52. Structure of murine DNA binding protein bound with ds DNA. SNAP output
4jcx DNA binding protein-DNA X-ray (2.3 Å) Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A, McGeehan JE, Kneale GG (2015) "Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression." Acta Crystallogr.,Sect.D, 71, 398-407. doi: 10.1107/S139900471402690X. Crystal structure of the restriction-modification controller protein c.csp231i ol operator complex. SNAP output
4jcy DNA binding protein-DNA X-ray (1.8 Å) Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A, McGeehan JE, Kneale GG (2015) "Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression." Acta Crystallogr.,Sect.D, 71, 398-407. doi: 10.1107/S139900471402690X. Crystal structure of the restriction-modification controller protein c.csp231i or operator complex. SNAP output
4jgc hydrolase-DNA X-ray (2.582 Å) Hashimoto H, Zhang X, Cheng X (2013) "Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH." Dna Repair, 12, 535-540. doi: 10.1016/j.dnarep.2013.04.003. Human tdg n140a mutant in a complex with 5-carboxylcytosine (5cac). SNAP output
4jjn DNA binding protein-DNA X-ray (3.09 Å) Wang F, Li G, Altaf M, Lu C, Currie MA, Johnson A, Moazed D (2013) "Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA." Proc.Natl.Acad.Sci.USA, 110, 8495-8500. doi: 10.1073/pnas.1300126110. Crystal structure of heterochromatin protein sir3 in complex with a silenced yeast nucleosome. SNAP output
4jl3 transcription-DNA X-ray (2.5 Å) Yang S, Gao Z, Li T, Yang M, Zhang T, Dong Y, He ZG (2013) "Structural basis for interaction between Mycobacterium smegmatis Ms6564, a TetR family master regulator, and its target DNA." J.Biol.Chem., 288, 23687-23695. doi: 10.1074/jbc.M113.468694. Crystal structure of ms6564-DNA complex. SNAP output
4jqd transcription-DNA X-ray (2.75 Å) Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A, McGeehan JE, Kneale GG (2015) "Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression." Acta Crystallogr.,Sect.D, 71, 398-407. doi: 10.1107/S139900471402690X. Crystal structure of the restriction-modification controller protein c.csp231i ol operator complex. SNAP output
4jrp hydrolase-DNA X-ray (1.95 Å) Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE (2013) "Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion." Nucleic Acids Res., 41, 5887-5897. doi: 10.1093/nar/gkt278. Structure of e. coli exonuclease i in complex with a 5cy-dt13 oligonucleotide. SNAP output
4jrq hydrolase-DNA X-ray (3.0 Å) Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE (2013) "Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion." Nucleic Acids Res., 41, 5887-5897. doi: 10.1093/nar/gkt278. Crystal structure of e. coli exonuclease i in complex with a 5cy-da13 oligonucleotide. SNAP output
4js4 hydrolase-DNA X-ray (3.1 Å) Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE (2013) "Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion." Nucleic Acids Res., 41, 5887-5897. doi: 10.1093/nar/gkt278. Crystal structure of e. coli exonuclease i in complex with a da16 oligonucleotide. SNAP output
4js5 hydrolase-DNA X-ray (3.5 Å) Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA, Bell CE (2013) "Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion." Nucleic Acids Res., 41, 5887-5897. doi: 10.1093/nar/gkt278. Crystal structure of e. coli exonuclease i in complex with a dt13 oligonucleotide. SNAP output
4juo isomerase-DNA X-ray (6.53 Å) Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher LM, Sanderson MR (2013) "Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport." Nucleic Acids Res., 41, 9911-9923. doi: 10.1093/nar/gkt749. A low-resolution three-gate structure of topoisomerase iv from streptococcus pneumoniae in space group h32. SNAP output
4juz transferase-DNA X-ray (2.65 Å) Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP (2013) "Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4." Chem.Res.Toxicol., 26, 1348-1360. doi: 10.1021/tx400200b. Ternary complex of gamma-ohpdg adduct modified DNA (zero primer) with DNA polymerase iv and incoming dgtp. SNAP output
4jv0 transferase-DNA X-ray (2.95 Å) Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP (2013) "Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4." Chem.Res.Toxicol., 26, 1348-1360. doi: 10.1021/tx400200b. Ring-opening of the -oh-pdg adduct in ternary complexes with the sulfolobus solfataricus DNA polymerase dpo4. SNAP output
4jv1 transferase-DNA X-ray (2.3 Å) Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP (2013) "Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4." Chem.Res.Toxicol., 26, 1348-1360. doi: 10.1021/tx400200b. Ternary complex of gamma-ohpdg adduct modified DNA with DNA (-1 primer) polymerase iv and incoming dgtp. SNAP output
4jv2 transferase-DNA X-ray (2.74 Å) Shanmugam G, Minko IG, Banerjee S, Christov PP, Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP (2013) "Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4." Chem.Res.Toxicol., 26, 1348-1360. doi: 10.1021/tx400200b. Ternary complex of gamma-ohpdg adduct modified DNA with DNA (-1 primer) polymerase iv and incoming datp. SNAP output
4jwm transferase-DNA X-ray (2.0 Å) Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH (2013) "Amino Acid Substitution in the Active Site of DNA Polymerase beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction." J.Am.Chem.Soc., 135, 8078-8088. doi: 10.1021/ja403842j. Ternary complex of d256e mutant of DNA polymerase beta. SNAP output
4jwn transferase-DNA X-ray (2.39 Å) Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH (2013) "Amino Acid Substitution in the Active Site of DNA Polymerase beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction." J.Am.Chem.Soc., 135, 8078-8088. doi: 10.1021/ja403842j. Ternary complex of d256a mutant of DNA polymerase beta. SNAP output
4jzu hydrolase-RNA X-ray (1.7 Å) Piton J, Larue V, Thillier Y, Dorleans A, Pellegrini O, Li de la Sierra-Gallay I, Vasseur JJ, Debart F, Tisne C, Condon C (2013) "Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates." Proc.Natl.Acad.Sci.USA, 110, 8858-8863. doi: 10.1073/pnas.1221510110. Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pgpg) - first guanosine residue in guanosine binding pocket. SNAP output
4k1g hydrolase-DNA X-ray (1.9 Å) Mazouzi A, Vigouroux A, Aikeshev B, Brooks PJ, Saparbaev MK, Morera S, Ishchenko AA (2013) "Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases." Proc.Natl.Acad.Sci.USA, 110, E3071-E3080. doi: 10.1073/pnas.1305281110. Structure of e. coli nfo(endo iv)-h69a mutant bound to a cleaved DNA duplex containing a alphada:t basepair. SNAP output
4k4g transferase-DNA X-ray (2.15 Å) Vyas R, Zahurancik WJ, Suo Z (2014) "Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda." Proc.Natl.Acad.Sci.USA, 111, E3033-E3042. doi: 10.1073/pnas.1401286111. Ternary crystal structures of human DNA polymerase lambda in complex with DNA and l-dctp.. SNAP output
4k4h transferase-DNA X-ray (2.1 Å) Vyas R, Zahurancik WJ, Suo Z (2014) "Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda." Proc.Natl.Acad.Sci.USA, 111, E3033-E3042. doi: 10.1073/pnas.1401286111. Ternary crystal structures of a human DNA polymerase lambda in complex with DNA and (-)3tc-tp.. SNAP output
4k4i transferase-DNA X-ray (2.25 Å) Vyas R, Zahurancik WJ, Suo Z (2014) "Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda." Proc.Natl.Acad.Sci.USA, 111, E3033-E3042. doi: 10.1073/pnas.1401286111. Ternary crystal structures of a human DNA polymerase lambda in complex with DNA and (-)ftc-tp.. SNAP output
4k8x transferase-DNA X-ray (2.28 Å) Bergen K, Betz K, Welte W, Diederichs K, Marx A (2013) "Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex." Chembiochem, 14, 1058-1062. doi: 10.1002/cbic.201300175. Binary complex of 9n DNA polymerase in the replicative state. SNAP output
4k8z transferase-DNA X-ray (2.29 Å) Bergen K, Betz K, Welte W, Diederichs K, Marx A (2013) "Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex." Chembiochem, 14, 1058-1062. doi: 10.1002/cbic.201300175. Kod polymerase in binary complex with dsDNA. SNAP output
4k96 transferase-DNA X-ray (2.084 Å) Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL, Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G, Tuschl T, Patel DJ (2013) "Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase." Cell(Cambridge,Mass.), 153, 1094-1107. doi: 10.1016/j.cell.2013.04.046. Structure of binary complex of cgas with bound dsDNA. SNAP output
4k97 transferase-DNA X-ray (2.41 Å) Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL, Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G, Tuschl T, Patel DJ (2013) "Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase." Cell(Cambridge,Mass.), 153, 1094-1107. doi: 10.1016/j.cell.2013.04.046. Structure of ternary complex of cgas with dsDNA and bound atp. SNAP output
4k98 transferase-DNA X-ray (1.94 Å) Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL, Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G, Tuschl T, Patel DJ (2013) "Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase." Cell(Cambridge,Mass.), 153, 1094-1107. doi: 10.1016/j.cell.2013.04.046. Structure of ternary complex of cgas with dsDNA and bound 5 -pppg(2 ,5 )pg. SNAP output
4k99 transferase-DNA X-ray (1.95 Å) Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL, Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G, Tuschl T, Patel DJ (2013) "Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase." Cell(Cambridge,Mass.), 153, 1094-1107. doi: 10.1016/j.cell.2013.04.046. Structure of ternary complex of cgas with dsDNA and bound 5 -pppdg(2 ,5 )pdg. SNAP output
4k9a transferase-DNA X-ray (2.264 Å) Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL, Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G, Tuschl T, Patel DJ (2013) "Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase." Cell(Cambridge,Mass.), 153, 1094-1107. doi: 10.1016/j.cell.2013.04.046. Structure of ternary complex of cgas with dsDNA and bound 5 -pg(2 ,5 )pa. SNAP output
4k9b transferase-DNA X-ray (2.26 Å) Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL, Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G, Tuschl T, Patel DJ (2013) "Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase." Cell(Cambridge,Mass.), 153, 1094-1107. doi: 10.1016/j.cell.2013.04.046. Structure of ternary complex of cgas with dsDNA and bound c[g(2 ,5 )pa(3 ,5 )p]. SNAP output
4ka4 DNA binding protein-DNA X-ray (2.6 Å) Athanasiadis A, de Rosa M, De Sanctis D "Crystal structure of a proteolytically defined Zbeta domain of human DAI (ZBP1, DLM-1)." Crystal structure of a proteolytically defined zbeta domain of human dai (zbp1, dlm-1). SNAP output
4kaz hydrolase-DNA X-ray (1.9 Å) Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS (2014) "Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways." Plos Biol., 12, e1001803. doi: 10.1371/journal.pbio.1001803. Crystal structure of rnase t in complex with a y structured DNA. SNAP output
4kb0 hydrolase-DNA X-ray (2.004 Å) Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS (2014) "Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways." Plos Biol., 12, e1001803. doi: 10.1371/journal.pbio.1001803. Crystal structure of rnase t in complex with a bluge DNA (two nucleotide insertion cc ). SNAP output
4kb1 hydrolase-DNA X-ray (1.8 Å) Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS (2014) "Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways." Plos Biol., 12, e1001803. doi: 10.1371/journal.pbio.1001803. Crystal structure of rnase t in complex with a bluge DNA (two nucleotide insertion ct ). SNAP output
4kb6 transferase-DNA X-ray (3.08 Å) Civril F, Deimling T, de Oliveira Mann CC, Ablasser A, Moldt M, Witte G, Hornung V, Hopfner KP (2013) "Structural mechanism of cytosolic DNA sensing by cGAS." Nature, 498, 332-337. doi: 10.1038/nature12305. Structure of porcine cyclic gmp amp synthase (cgas) in complex with DNA, atp and gtp. SNAP output
4kdp transcription-DNA X-ray (3.6 Å) Chang YM, Ho CH, Chen CK, Maestre-Reyna M, Chang-Chien MW, Wang AH (2014) "TcaR-ssDNA complex crystal structure reveals new DNA binding mechanism of the MarR family proteins." Nucleic Acids Res., 42, 5314-5321. doi: 10.1093/nar/gku128. Tcar-ssDNA complex crystal structure reveals the novel ssDNA binding mechanism of the marr family proteins. SNAP output
4kfc transcription regulator-DNA X-ray (2.53 Å) Narayanan A, Kumar S, Evrard AN, Paul LN, Yernool DA (2014) "An asymmetric heterodomain interface stabilizes a response regulator-DNA complex." Nat Commun, 5, 3282. doi: 10.1038/ncomms4282. Crystal structure of a hyperactive mutant of response regulator kdpe complexed to its promoter DNA. SNAP output
4kgc structural protein-DNA X-ray (2.69 Å) Adhireksan Z, Davey GE, Campomanes P, Groessl M, Clavel CM, Yu H, Nazarov AA, Yeo CH, Ang WH, Droge P, Rothlisberger U, Dyson PJ, Davey CA (2014) "Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity." Nat Commun, 5, 3462. doi: 10.1038/ncomms4462. Nucleosome core particle containing (eta6-p-cymene)-(1, 2-ethylenediamine)-ruthenium. SNAP output
4khn hydrolase, transferase-DNA X-ray (2.55 Å) Jacewicz A, Trzemecka A, Guja KE, Plochocka D, Yakubovskaya E, Bebenek A, Garcia-Diaz M (2013) "A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site." Plos One, 8, e76700. doi: 10.1371/journal.pone.0076700. Crystal structure of the ternary complex of the d714a mutant of rb69 DNA polymerase. SNAP output
4khq transferase-DNA X-ray (2.186 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f wit dumpnpp. SNAP output
4khs transferase-DNA X-ray (2.12 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f with a ribonucleotide at 0 position. SNAP output
4khu transferase-DNA X-ray (2.05 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f with a ribonucleotide at -1 position. SNAP output
4khw transferase-DNA X-ray (2.371 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f with ribonucleotide at -2 position. SNAP output
4khy transferase-DNA X-ray (2.25 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f with ribonucleotide at -3 position. SNAP output
4ki2 transcription-DNA X-ray (3.3 Å) Feklistov A, Darst SA (2013) "Crystallographic analysis of an RNA polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes." Acta Crystallogr.,Sect.F, 69, 950-955. doi: 10.1107/S1744309113020368. Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA. SNAP output
4ki4 transferase-DNA X-ray (2.45 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f with ribonucleotides at 0 and -1 position. SNAP output
4ki6 transferase-DNA X-ray (2.55 Å) Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA (2013) "Structure-function analysis of ribonucleotide bypass by B family DNA replicases." Proc.Natl.Acad.Sci.USA, 110, 16802-16807. doi: 10.1073/pnas.1309119110. Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position. SNAP output
4kis recombination-DNA X-ray (3.2 Å) Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne GD (2013) "Attachment site recognition and regulation of directionality by the serine integrases." Nucleic Acids Res., 41, 8341-8356. doi: 10.1093/nar/gkt580. Crystal structure of a lsr-DNA complex. SNAP output
4kld transferase, lyase-DNA X-ray (1.916 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched substrate complex with ca2+, 0 s. SNAP output
4kle transferase, lyase-DNA X-ray (1.97 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched reactant complex with mg2+, 10 s. SNAP output
4klf transferase, lyase-DNA X-ray (1.85 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched reactant complex with mg2+, 20 s. SNAP output
4klg transferase, lyase-DNA X-ray (1.701 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched product complex with mg2+, 40 s. SNAP output
4klh transferase, lyase-DNA X-ray (1.876 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched product complex with mn2+, 40 s. SNAP output
4kli transferase, lyase-DNA X-ray (1.597 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched product complex with mg2+, 90 s. SNAP output
4klj transferase, lyase-DNA X-ray (1.799 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched product complex with mg2+, 5 min. SNAP output
4kll transferase, lyase-DNA X-ray (1.841 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched product complex with mg2+, 45 min. SNAP output
4klm transferase, lyase-DNA X-ray (1.747 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched product complex with mg2+, 11 h. SNAP output
4klo transferase, lyase-DNA X-ray (1.845 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta matched nick complex with mg2+ and ppi, 30 min. SNAP output
4klq transferase, lyase-DNA X-ray (1.999 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. Observing a DNA polymerase choose right from wrong.. SNAP output
4kls transferase, lyase-DNA X-ray (1.978 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta mismatched reactant complex with mn2+, 10 min. SNAP output
4klt transferase, lyase-DNA X-ray (1.979 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta mismatched product complex with mn2+, 30 min. SNAP output
4klu transferase, lyase-DNA X-ray (1.97 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta mismatched product complex with mn2+, 15 h. SNAP output
4kmf transferase-DNA X-ray (1.7 Å) Kim D, Hur J, Park K, Bae S, Shin D, Ha SC, Hwang HY, Hohng S, Lee JH, Lee S, Kim YG, Kim KK (2014) "Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)." Nucleic Acids Res., 42, 5937-5948. doi: 10.1093/nar/gku189. Crystal structure of zalpha domain from carassius auratus pkz in complex with z-DNA. SNAP output
4kny transcription regulator-DNA X-ray (2.945 Å) Narayanan A, Kumar S, Evrard AN, Paul LN, Yernool DA (2014) "An asymmetric heterodomain interface stabilizes a response regulator-DNA complex." Nat Commun, 5, 3282. doi: 10.1038/ncomms4282. Crystal structure of the response regulator kdpe complexed to DNA in an active-like conformation. SNAP output
4koe isomerase-DNA-inhibitor X-ray (3.02 Å) Laponogov I, Pan X-S, Veselkov DA, Fisher LM, Sanderson MR "Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions." Quinolone(trovafloxacin)-DNA cleavage complex of type iv topoisomerase from s. pneumoniae. SNAP output
4kpe isomerase-DNA-inhibitor X-ray (3.43 Å) Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR (2016) "Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones." Open Biol, 6. doi: 10.1098/rsob.160157. Novel fluoroquinolones in complex with topoisomerase iv from s. pneumoniae and e-site g-gate. SNAP output
4kpf isomerase-DNA-inhibitor X-ray (3.24 Å) Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR (2016) "Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones." Open Biol, 6. doi: 10.1098/rsob.160157. Novel fluoroquinolones in complex with topoisomerase iv from s. pneumoniae and e-site g-gate. SNAP output
4kpy DNA binding protein-DNA X-ray (2.406 Å) Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) "Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage." Proc.Natl.Acad.Sci.USA, 111, 652-657. doi: 10.1073/pnas.1321032111. DNA binding protein and DNA complex structure. SNAP output
4ktq transferase-DNA X-ray (2.5 Å) Li Y, Korolev S, Waksman G (1998) "Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation." EMBO J., 17, 7514-7525. doi: 10.1093/emboj/17.24.7514. Binary complex of the large fragment of DNA polymerase i from t. aquaticus bound to a primer-template DNA. SNAP output
4kud structural protein-transcription-DNA X-ray (3.203 Å) Yang D, Fang Q, Wang M, Ren R, Wang H, He M, Sun Y, Yang N, Xu RM (2013) "N alpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain." Nat.Struct.Mol.Biol., 20, 1116-1118. doi: 10.1038/nsmb.2637. Crystal structure of n-terminal acetylated sir3 bah domain d205n mutant in complex with yeast nucleosome core particle. SNAP output
4kxt hydrolase-RNA X-ray (2.294 Å) Nakanishi K, Ascano M, Gogakos T, Ishibe-Murakami S, Serganov AA, Briskin D, Morozov P, Tuschl T, Patel DJ (2013) "Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity." Cell Rep, 3, 1893-1900. doi: 10.1016/j.celrep.2013.06.010. Structure of human argonaute1 in complex with guide RNA. SNAP output
4kyw hydrolase-DNA X-ray (2.35 Å) Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M (2014) "Structural basis of the methylation specificity of R.DpnI." Nucleic Acids Res., 42, 8745-8754. doi: 10.1093/nar/gku546. Restriction endonuclease dpni in complex with two DNA molecules. SNAP output
4kzx ribosome X-ray (7.809 Å) Lomakin IB, Steitz TA (2013) "The initiation of mammalian protein synthesis and mRNA scanning mechanism." Nature, 500, 307-311. doi: 10.1038/nature12355. Rabbit 40s ribosomal subunit in complex with eif1.. SNAP output
4kzy ribosome X-ray (7.01 Å) Lomakin IB, Steitz TA (2013) "The initiation of mammalian protein synthesis and mRNA scanning mechanism." Nature, 500, 307-311. doi: 10.1038/nature12355. Rabbit 40s ribosomal subunit in complex with eif1 and eif1a.. SNAP output
4kzz ribosome X-ray (7.03 Å) Lomakin IB, Steitz TA (2013) "The initiation of mammalian protein synthesis and mRNA scanning mechanism." Nature, 500, 307-311. doi: 10.1038/nature12355. Rabbit 40s ribosomal subunit in complex with mrna, initiator trna and eif1a. SNAP output
4l0y transcription-DNA X-ray (2.5 Å) Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI, Rizzino A, Tahirov TH (2014) "Structural basis of Ets1 activation by Runx1." Leukemia, 28, 2040-2048. doi: 10.1038/leu.2014.111. Crystal structure of runx1 and ets1 bound to tcr alpha promoter (crystal form 1). SNAP output
4l0z transcription-DNA X-ray (2.7 Å) Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI, Rizzino A, Tahirov TH (2014) "Structural basis of Ets1 activation by Runx1." Leukemia, 28, 2040-2048. doi: 10.1038/leu.2014.111. Crystal structure of runx1 and ets1 bound to tcr alpha promoter (crystal form 2). SNAP output
4l18 transcription-DNA X-ray (2.3 Å) Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI, Rizzino A, Tahirov TH (2014) "Structural basis of Ets1 activation by Runx1." Leukemia, 28, 2040-2048. doi: 10.1038/leu.2014.111. Crystal structure of runx1 and ets1 bound to tcr alpha promoter (crystal form 3). SNAP output
4l5r DNA binding protein-DNA X-ray (1.873 Å) Yin Q, Sester DP, Tian Y, Hsiao YS, Lu A, Cridland JA, Sagulenko V, Thygesen SJ, Choubey D, Hornung V, Walz T, Stacey KJ, Wu H (2013) "Molecular Mechanism for p202-Mediated Specific Inhibition of AIM2 Inflammasome Activation." Cell Rep, 4, 327-339. doi: 10.1016/j.celrep.2013.06.024. Crystal structure of p202 hin1 in complex with 20-mer dsDNA. SNAP output
4l5s DNA binding protein-DNA X-ray (2.94 Å) Yin Q, Sester DP, Tian Y, Hsiao YS, Lu A, Cridland JA, Sagulenko V, Thygesen SJ, Choubey D, Hornung V, Walz T, Stacey KJ, Wu H (2013) "Molecular Mechanism for p202-Mediated Specific Inhibition of AIM2 Inflammasome Activation." Cell Rep, 4, 327-339. doi: 10.1016/j.celrep.2013.06.024. P202 hin1 in complex with 12-mer dsDNA. SNAP output
4l62 transcription-DNA X-ray (2.9 Å) Kim Y, Kang Y, Choe J (2013) "Crystal structure of Pseudomonas aeruginosa transcriptional regulator PA2196 bound to its operator DNA." Biochem.Biophys.Res.Commun., 440, 317-321. doi: 10.1016/j.bbrc.2013.09.074. Crystal structure of pseudomonas aeruginosa transcriptional regulator pa2196 bound to its operator DNA. SNAP output
4lb5 transferase-DNA X-ray (2.0 Å) de Rosa M, Zacarias S, Athanasiadis A (2013) "Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ." Nucleic Acids Res., 41, 9924-9933. doi: 10.1093/nar/gkt743. Crystal structure of pkz zalpha in complex with ds(cg)6 (hexagonal form). SNAP output
4lb6 transferase-DNA X-ray (1.8 Å) de Rosa M, Zacarias S, Athanasiadis A (2013) "Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ." Nucleic Acids Res., 41, 9924-9933. doi: 10.1093/nar/gkt743. Crystal structure of pkz zalpha in complex with ds(cg)6 (tetragonal form). SNAP output
4ld0 hydrolase-DNA X-ray (3.75 Å) Gorecka KM, Komorowska W, Nowotny M (2013) "Crystal structure of RuvC resolvase in complex with Holliday junction substrate." Nucleic Acids Res., 41, 9945-9955. doi: 10.1093/nar/gkt769. T. thermophilus ruvc in complex with holliday junction substrate. SNAP output
4ld9 nuclear protein-transcription-DNA X-ray (3.306 Å) Arnaudo N, Fernandez IS, McLaughlin SH, Peak-Chew SY, Rhodes D, Martino F (2013) "The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle." Nat.Struct.Mol.Biol., 20, 1119-1121. doi: 10.1038/nsmb.2641. Crystal structure of the n-terminally acetylated bah domain of sir3 bound to the nucleosome core particle. SNAP output
4ldx transcription-DNA X-ray (2.9 Å) Boer DR, Freire-Rios A, van den Berg WA, Saaki T, Manfield IW, Kepinski S, Lopez-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M (2014) "Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors." Cell(Cambridge,Mass.), 156, 577-589. doi: 10.1016/j.cell.2013.12.027. Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (arf1) in complex with protomor-like sequence er7. SNAP output
4ley transferase-DNA X-ray (2.5 Å) Li X, Shu C, Yi G, Chaton CT, Shelton CL, Diao J, Zuo X, Kao CC, Herr AB, Li P (2013) "Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization." Immunity, 39, 1019-1031. doi: 10.1016/j.immuni.2013.10.019. Structure of mouse cgas bound to 18 bp DNA. SNAP output
4lez transferase-DNA X-ray (2.36 Å) Li X, Shu C, Yi G, Chaton CT, Shelton CL, Diao J, Zuo X, Kao CC, Herr AB, Li P (2013) "Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization." Immunity, 39, 1019-1031. doi: 10.1016/j.immuni.2013.10.019. Structure of mouse cgas bound to an 18bp DNA and cgas product. SNAP output
4lg0 transcription-DNA X-ray (2.19 Å) Birrane G, Choy WC, Datta D, Geiger CA, Grant MA "Structure of a ternary FOXO1-ETS1 DNA complex." Structure of a ternary foxo1-ets1 DNA complex. SNAP output
4lg7 hydrolase-DNA X-ray (2.5 Å) Xu C, Tempel W, Wernimont AK, Bountra C, Arrowsmith CH, Edwards AM, Min J "Crystal structure MBD4 MBD domain in complex with methylated CpG DNA." Crystal structure mbd4 mbd domain in complex with methylated cpg DNA. SNAP output
4ljr DNA binding protein-DNA X-ray (1.8 Å) Wang W, Ding J, Zhang Y, Hu Y, Wang DC (2014) "Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA." Nucleic Acids Res., 42, 3478-3491. doi: 10.1093/nar/gkt1334. Structural insights into the unique single-stranded DNA binding mode of DNA processing protein a from helicobacter pylori. SNAP output
4lll transcription-DNA X-ray (3.036 Å) Birukou I, Seo SM, Schindler BD, Kaatz GW, Brennan RG (2014) "Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR." Nucleic Acids Res., 42, 2774-2788. doi: 10.1093/nar/gkt1215. Crystal structure of s. aureus mepr-DNA complex. SNAP output
4lln transcription-DNA X-ray (2.842 Å) Birukou I, Seo SM, Schindler BD, Kaatz GW, Brennan RG (2014) "Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR." Nucleic Acids Res., 42, 2774-2788. doi: 10.1093/nar/gkt1215. Crystal structure of s. aureus mepr-DNA complex. SNAP output
4lmg transcription activator-DNA X-ray (2.2 Å) Poor CB, Wegner SV, Li H, Dlouhy AC, Schuermann JP, Sanishvili R, Hinshaw JR, Riggs-Gelasco PJ, Outten CE, He C (2014) "Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2." Proc.Natl.Acad.Sci.USA, 111, 4043-4048. doi: 10.1073/pnas.1318869111. Crystal structure of aft2 in complex with DNA. SNAP output
4lnq DNA binding protein-DNA X-ray (2.0 Å) Li H, Wang J, Wang J, Cao LS, Wang ZX, Wu JW (2014) "Structural mechanism of DNA recognition by the p202 HINa domain: insights into the inhibition of Aim2-mediated inflammatory signalling." Acta Crystallogr F Struct Biol Commun, 70, 21-29. doi: 10.1107/S2053230X1303135X. Crystal structure of ifi202 hina domain in complex with 20bp dsDNA. SNAP output
4lox hydrolase-DNA X-ray (1.98 Å) Chik J, Shen B, Stoddard B "Crystal structure of a LAGLIDADG endonuclease from the Sordaria Macrospore." Crystal structure of the i-smami laglidadg homing endonuclease bound to cleaved DNA. SNAP output
4lq0 hydrolase-DNA X-ray (2.68 Å) Chik J, Shen B, Stoddard B "Structural Comparisons of LAGLIDADG Homing Endonucleases." Crystal structure of the i-ltrwi laglidadg homing endonuclease bound to target DNA.. SNAP output
4lt5 oxidoreductase-DNA X-ray (2.893 Å) Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Correa IR, Zheng Y, Cheng X (2014) "Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA." Nature, 506, 391-395. doi: 10.1038/nature12905. Structure of a naegleria tet-like dioxygenase in complex with 5-methylcytosine DNA. SNAP output
4lup transcription-DNA X-ray (1.2 Å) Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH (2014) "Structural basis for -10 promoter element melting by environmentally induced sigma factors." Nat.Struct.Mol.Biol., 21, 269-276. doi: 10.1038/nsmb.2777. Crystal structure of the complex formed by region of e. coli sigmae bound to its -10 element non template strand. SNAP output
4lvi DNA binding protein-DNA X-ray (1.9 Å) Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M (2017) "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance." Proc. Natl. Acad. Sci. U.S.A., 114, E6526-E6535. doi: 10.1073/pnas.1702971114. Mobm relaxase domain (mobv; mob_pre) bound to plasmid pmv158 orit DNA (22nt). mn-bound crystal structure at ph 4.6. SNAP output
4lvj DNA binding protein-DNA X-ray (2.17 Å) Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M (2017) "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance." Proc. Natl. Acad. Sci. U.S.A., 114, E6526-E6535. doi: 10.1073/pnas.1702971114. Mobm relaxase domain (mobv; mob_pre) bound to plasmid pmv158 orit DNA (22nt). mn-bound crystal structure at ph 5.5. SNAP output
4lvk DNA binding protein-DNA X-ray (2.37 Å) Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M (2017) "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance." Proc. Natl. Acad. Sci. U.S.A., 114, E6526-E6535. doi: 10.1073/pnas.1702971114. Mobm relaxase domain (mobv; mob_pre) bound to plasmid pmv158 orit DNA (22nt+3'phosphate). mn-bound crystal structure at ph 4.6. SNAP output
4lvl DNA binding protein-DNA X-ray (2.2 Å) Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M (2017) "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance." Proc. Natl. Acad. Sci. U.S.A., 114, E6526-E6535. doi: 10.1073/pnas.1702971114. Mobm relaxase domain (mobv; mob_pre) bound to plasmid pmv158 orit DNA (22nt+3'thiophosphate). mn-bound crystal structure at ph 6.8. SNAP output
4lvm DNA binding protein-DNA X-ray (3.1 Å) Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M (2017) "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance." Proc. Natl. Acad. Sci. U.S.A., 114, E6526-E6535. doi: 10.1073/pnas.1702971114. Mobm relaxase domain (mobv; mob_pre) bound to plasmid pmv158 orit DNA (23nt). mn-bound crystal structure at ph 6.5. SNAP output
4lvs transferase, lyase-DNA X-ray (2.002 Å) Freudenthal BD, Beard WA, Shock DD, Wilson SH (2013) "Observing a DNA polymerase choose right from wrong." Cell(Cambridge,Mass.), 154, 157-168. doi: 10.1016/j.cell.2013.05.048. DNA polymerase beta mismatched substrate complex with mn2+, 2.5 min. SNAP output
4lz1 hydrolase-hydrolase inhibitor-DNA X-ray (1.65 Å) Pica A, Russo Krauss I, Merlino A, Nagatoishi S, Sugimoto N, Sica F (2013) "Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer." Febs J., 280, 6581-6588. doi: 10.1111/febs.12561. X-ray structure of the complex between human thrombin and the tba deletion mutant lacking thymine 12 nucleobase. SNAP output
4lz4 hydrolase-hydrolase inhibitor-DNA X-ray (2.56 Å) Pica A, Russo Krauss I, Merlino A, Nagatoishi S, Sugimoto N, Sica F (2013) "Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer." Febs J., 280, 6581-6588. doi: 10.1111/febs.12561. X-ray structure of the complex between human thrombin and the tba deletion mutant lacking thymine 3 nucleobase. SNAP output
4lzg transferase-DNA X-ray (1.599 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2014) "Sustained active site rigidity during synthesis by human DNA polymerase mu." Nat.Struct.Mol.Biol., 21, 253-260. doi: 10.1038/nsmb.2766. Binary complex of human DNA polymerase mu with DNA. SNAP output
4m04 transferase-DNA X-ray (1.898 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2014) "Sustained active site rigidity during synthesis by human DNA polymerase mu." Nat.Struct.Mol.Biol., 21, 253-260. doi: 10.1038/nsmb.2766. Human DNA polymerase mu ternary complex. SNAP output
4m0a transferase-DNA X-ray (1.85 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2014) "Sustained active site rigidity during synthesis by human DNA polymerase mu." Nat.Struct.Mol.Biol., 21, 253-260. doi: 10.1038/nsmb.2766. Human DNA polymerase mu post-catalytic complex. SNAP output
4m2y transferase-DNA X-ray (2.27 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase beta complexed with 8-brg as the template base in a 1-nucleotide gapped DNA. SNAP output
4m3r hydrolase-DNA X-ray (2.07 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dt-dg at position n-1 of primer-template duplex. SNAP output
4m3t hydrolase-DNA X-ray (1.9 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dt-dg at position n-2 of primer-template duplex. SNAP output
4m3u hydrolase-DNA X-ray (2.07 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dt-dg at position n-3 of primer-template duplex. SNAP output
4m3w hydrolase-DNA X-ray (2.1 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dt-dg at position n-4 of primer-template duplex. SNAP output
4m3x hydrolase-DNA X-ray (2.2 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dt-dg at position n-5 of primer-template duplex. SNAP output
4m3y hydrolase-DNA X-ray (1.86 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dg-dt at position n-1 of primer-template duplex. SNAP output
4m3z hydrolase-DNA X-ray (1.84 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dg-dt at position n-2 of primer-template duplex. SNAP output
4m41 hydrolase-DNA X-ray (2.15 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dg-dt at position n-3 of primer-template duplex. SNAP output
4m42 hydrolase-DNA X-ray (2.04 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dg-dt at position n-4 of primer-template duplex. SNAP output
4m45 hydrolase-DNA X-ray (1.89 Å) Xia S, Konigsberg WH (2014) "Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant." Protein Sci., 23, 508-513. doi: 10.1002/pro.2434. Rb69 DNA polymerase ternary complex with dg-dt at position n-5 of primer-template duplex. SNAP output
4m47 transferase-DNA X-ray (2.37 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase complexed with 8-brg in the template base paired with incoming non-hydrolyzable gtp. SNAP output
4m6f hydrolase-DNA X-ray (4.99 Å) Ritacco CJ, Steitz TA, Wang J (2014) "Exploiting large non-isomorphous differences for phase determination of a G-segment invertase-DNA complex." Acta Crystallogr.,Sect.D, 70, 685-693. doi: 10.1107/S1399004713032392. Dimer of the g-segment invertase bound to a DNA substrate. SNAP output
4m8b transcription-DNA X-ray (2.61 Å) Lohse MB, Rosenberg OS, Cox JS, Stroud RM, Finer-Moore JS, Johnson AD (2014) "Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi." Proc.Natl.Acad.Sci.USA, 111, 10404-10410. doi: 10.1073/pnas.1410110111. Fungal protein. SNAP output
4m8o transferase-DNA X-ray (2.2 Å) Hogg M, Osterman P, Bylund GO, Ganai RA, Lundstrom EB, Sauer-Eriksson AE, Johansson E (2014) "Structural basis for processive DNA synthesis by yeast DNA polymerase epsilon." Nat.Struct.Mol.Biol., 21, 49-55. doi: 10.1038/nsmb.2712. Ternary complex of DNA polymerase epsilon with an incoming datp. SNAP output
4m94 transferase-DNA X-ray (2.14 Å) Singh I, Lian Y, Li L, Georgiadis MM (2014) "The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition." Acta Crystallogr.,Sect.D, 70, 752-759. doi: 10.1107/S1399004713032987. D(atccgttataacggat) complexed with moloney murine leukemia virus reverse transcriptase catalytic fragment. SNAP output
4m95 transferase-DNA X-ray (1.72 Å) Singh I, Lian Y, Li L, Georgiadis MM (2014) "The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition." Acta Crystallogr.,Sect.D, 70, 752-759. doi: 10.1107/S1399004713032987. D(atccgttataacggat)complexed with moloney murine leukemia virus reverse transcriptase catalytic fragment. SNAP output
4m9e transcription-DNA X-ray (1.851 Å) Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X (2014) "Structural basis for Klf4 recognition of methylated DNA." Nucleic Acids Res., 42, 4859-4867. doi: 10.1093/nar/gku134. Structure of klf4 zinc finger DNA binding domain in complex with methylated DNA. SNAP output
4m9g transferase-DNA X-ray (2.01 Å) Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S (2013) "The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection." J.Biol.Chem., 288, 34850-34860. doi: 10.1074/jbc.M113.510891. DNA polymerase beta e295k binary complex. SNAP output
4m9h transferase-DNA X-ray (2.394 Å) Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S (2013) "The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection." J.Biol.Chem., 288, 34850-34860. doi: 10.1074/jbc.M113.510891. DNA polymerase beta e295k soaked with dttp. SNAP output
4m9j transferase-DNA X-ray (2.038 Å) Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S (2013) "The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection." J.Biol.Chem., 288, 34850-34860. doi: 10.1074/jbc.M113.510891. DNA polymerase beta e295k soaked with dumpnpp. SNAP output
4m9l transferase-DNA X-ray (2.091 Å) Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S (2013) "The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection." J.Biol.Chem., 288, 34850-34860. doi: 10.1074/jbc.M113.510891. DNA polymerase beta e295k soaked with dctp. SNAP output
4m9n transferase-DNA X-ray (2.275 Å) Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S (2013) "The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection." J.Biol.Chem., 288, 34850-34860. doi: 10.1074/jbc.M113.510891. DNA polymerase beta e295k soaked with datp. SNAP output
4m9v transcription-DNA X-ray (0.969 Å) Liu Y, Olanrewaju YO, Zhang X, Cheng X (2013) "DNA recognition of 5-carboxylcytosine by a zfp57 mutant at an atomic resolution of 0.97 angstrom." Biochemistry, 52, 9310-9317. doi: 10.1021/bi401360n. Zfp57 mutant (e182q) in complex with 5-carboxylcytosine DNA. SNAP output
4mde transferase-DNA X-ray (1.8 Å) Das U, Wang LK, Smith P, Jacewicz A, Shuman S (2014) "Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition." Nucleic Acids Res., 42, 1152-1161. doi: 10.1093/nar/gkt936. Structure of bacterial polynucleotide kinase product complex bound to gdp and DNA. SNAP output
4mdf transferase-DNA X-ray (1.727 Å) Das U, Wang LK, Smith P, Jacewicz A, Shuman S (2014) "Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition." Nucleic Acids Res., 42, 1152-1161. doi: 10.1093/nar/gkt936. Structure of bacterial polynucleotide kinase michaelis complex bound to gtp and DNA. SNAP output
4mf2 transferase-DNA X-ray (2.4 Å) Koag MC, Lee S (2014) "Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta." J.Am.Chem.Soc., 136, 5709-5721. doi: 10.1021/ja500172d. Structure of human DNA polymerase beta complexed with o6mg as the template base in a 1-nucleotide gapped DNA. SNAP output
4mf8 transferase-DNA X-ray (2.32 Å) Koag MC, Min K, Monzingo AF, Lee S "Structures of human DNA polymerase beta inserting bases opposite templating O6MG." Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template o6mg and incoming ctp. SNAP output
4mfa transferase-DNA X-ray (2.27 Å) Koag MC, Min K, Monzingo AF, Lee S "Structures of human DNA polymerase beta inserting bases opposite templating O6MG." Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template o6mg and incoming ttp. SNAP output
4mfc transferase-DNA X-ray (2.13 Å) Koag MC, Lee S (2014) "Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta." J.Am.Chem.Soc., 136, 5709-5721. doi: 10.1021/ja500172d. Structure of human DNA polymerase beta complexed with o6mg in the template base paired with incoming non-hydrolyzable ctp. SNAP output
4mff transferase-DNA X-ray (2.55 Å) Koag MC, Lee S (2014) "Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta." J.Am.Chem.Soc., 136, 5709-5721. doi: 10.1021/ja500172d. Structure of human DNA polymerase beta complexed with o6mg in the template base paired with incoming non-hydrolyzable ttp. SNAP output
4mg2 oxidoreductase-DNA X-ray (2.3 Å) Chen B, Gan J, Yang CG (2014) "The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin." Sci China Chem, 57, 307-313. doi: 10.1007/s11426-013-5029-z. Alkbh2 f102a cross-linked to undamaged dsDNA. SNAP output
4mgt oxidoreductase-DNA X-ray (2.6 Å) Chen B, Gan J, Yang CG (2014) "The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin." Sci China Chem, 57, 307-313. doi: 10.1007/s11426-013-5029-z. Alkbh2 r110a cross-linked to undamaged dsDNA. SNAP output
4mgu virus-DNA X-ray (3.5 Å) Meng G, Zhang X, Plevka P, Yu Q, Tijssen P, Rossmann MG (2013) "The structure and host entry of an invertebrate parvovirus." J.Virol., 87, 12523-12530. doi: 10.1128/JVI.01822-13. Crystal structure of acheta domesticus densovirus. SNAP output
4mhg transcription-DNA X-ray (2.199 Å) De S, Chan AC, Coyne HJ, Bhachech N, Hermsdorf U, Okon M, Murphy ME, Graves BJ, McIntosh LP (2014) "Steric Mechanism of Auto-Inhibitory Regulation of Specific and Non-Specific DNA Binding by the ETS Transcriptional Repressor ETV6." J.Mol.Biol., 426, 1390-1406. doi: 10.1016/j.jmb.2013.11.031. Crystal structure of etv6 bound to a specific DNA sequence. SNAP output
4mht transferase-DNA X-ray (2.7 Å) O'Gara M, Klimasauskas S, Roberts RJ, Cheng X (1996) "Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes." J.Mol.Biol., 261, 634-645. doi: 10.1006/jmbi.1996.0489. Ternary structure of hhai methyltransferase with native DNA and adohcy. SNAP output
4mky transferase-DNA X-ray (2.4 Å) Brissett NC, Martin MJ, Bartlett EJ, Bianchi J, Blanco L, Doherty AJ (2013) "Molecular Basis for DNA Double-Strand Break Annealing and Primer Extension by an NHEJ DNA Polymerase." Cell Rep, 5, 1108-1120. doi: 10.1016/j.celrep.2013.10.016. Polymerase domain from mycobacterium tuberculosis ligase d in complex with an annealed double-strand DNA break.. SNAP output
4mtd DNA binding protein-DNA X-ray (2.5 Å) Gilston BA, Wang S, Marcus MD, Canalizo-Hernandez MA, Swindell EP, Xue Y, Mondragon A, O'Halloran TV (2014) "Structural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon." Plos Biol., 12, e1001987. doi: 10.1371/journal.pbio.1001987. Zinc uptake regulator complexed with zinc and DNA. SNAP output
4mte DNA binding protein-DNA X-ray (2.5 Å) Gilston BA, Wang S, Marcus MD, Canalizo-Hernandez MA, Swindell EP, Xue Y, Mondragon A, O'Halloran TV (2014) "Structural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon." Plos Biol., 12, e1001987. doi: 10.1371/journal.pbio.1001987. Zinc uptake regulator complexed with zinc and DNA. SNAP output
4mzr transcription-DNA X-ray (2.9 Å) Emamzadah S, Tropia L, Vincenti I, Falquet B, Halazonetis TD (2014) "Reversal of the DNA-Binding-Induced Loop L1 Conformational Switch in an Engineered Human p53 Protein." J.Mol.Biol., 426, 936-944. doi: 10.1016/j.jmb.2013.12.020. Crystal structure of a polypeptide p53 mutant bound to DNA. SNAP output
4n0o hydrolase-DNA X-ray (2.65 Å) Deng Z, Lehmann KC, Li X, Feng C, Wang G, Zhang Q, Qi X, Yu L, Zhang X, Feng W, Wu W, Gong P, Tao Y, Posthuma CC, Snijder EJ, Gorbalenya AE, Chen Z (2014) "Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase." Nucleic Acids Res., 42, 3464-3477. doi: 10.1093/nar/gkt1310. Complex structure of arterivirus nonstructural protein 10 (helicase) with DNA. SNAP output
4n41 nuclear protein-DNA X-ray (2.248 Å) Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) "Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage." Proc.Natl.Acad.Sci.USA, 111, 652-657. doi: 10.1073/pnas.1321032111. Structure of thermus thermophilus argonaute bound to guide DNA and 15-mer target DNA. SNAP output
4n47 nuclear protein-DNA X-ray (2.823 Å) Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) "Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage." Proc.Natl.Acad.Sci.USA, 111, 652-657. doi: 10.1073/pnas.1321032111. Structure of thermus thermophilus argonaute bound to guide DNA and 12-mer target DNA. SNAP output
4n56 transferase-DNA X-ray (2.2 Å) Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B, Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM, Kermekchiev MB (2015) "A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase." Biochemistry, 54, 881-889. doi: 10.1021/bi501198f. Binary complex structure of klenow fragment of taq DNA polymerase i707l mutant (cs3c klentaq) with DNA. SNAP output
4n5s transferase-DNA X-ray (1.67 Å) Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B, Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM, Kermekchiev MB (2015) "A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase." Biochemistry, 54, 881-889. doi: 10.1021/bi501198f. Ternary complex structure of klenow fragment of taq DNA polymerase i707l mutant (cs3c klentaq) with DNA and ddctp. SNAP output
4n76 nuclear protein-DNA X-ray (2.89 Å) Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) "Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage." Proc.Natl.Acad.Sci.USA, 111, 652-657. doi: 10.1073/pnas.1321032111. Structure of thermus thermophilus argonaute bound to guide DNA and cleaved target DNA with mn2+. SNAP output
4nca nuclear protein-DNA X-ray (2.489 Å) Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) "Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage." Proc.Natl.Acad.Sci.USA, 111, 652-657. doi: 10.1073/pnas.1321032111. Structure of thermus thermophilus argonaute bound to guide DNA 19-mer and target DNA in the presence of mg2+. SNAP output
4ncb nuclear protein-DNA X-ray (2.189 Å) Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) "Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage." Proc.Natl.Acad.Sci.USA, 111, 652-657. doi: 10.1073/pnas.1321032111. Structure of thermus thermophilus argonaute bound to guide DNA and 19-mer target DNA with mg2+. SNAP output
4ndf DNA binding protein-RNA-DNA X-ray (1.944 Å) Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS (2013) "Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity." Nature, 506, 111-115. doi: 10.1038/nature12824. Human aprataxin (aptx) bound to RNA-DNA, amp, and zn - product complex. SNAP output
4ndg DNA binding protein-RNA-DNA X-ray (2.541 Å) Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS (2013) "Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity." Nature, 506, 111-115. doi: 10.1038/nature12824. Human aprataxin (aptx) bound to RNA-DNA and zn - adenosine vanadate transition state mimic complex. SNAP output
4ndh DNA binding protein-DNA X-ray (1.848 Å) Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS (2013) "Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity." Nature, 506, 111-115. doi: 10.1038/nature12824. Human aprataxin (aptx) bound to DNA, amp, and zn - product complex. SNAP output
4ndi DNA binding protein-RNA-DNA X-ray (1.9 Å) Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS (2013) "Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity." Nature, 506, 111-115. doi: 10.1038/nature12824. Human aprataxin (aptx) aoa1 variant k197q bound to RNA-DNA, amp, and zn - product complex. SNAP output
4ndy DNA binding protein-DNA X-ray (6.999 Å) Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei AR, Sung P, Xiong Y (2014) "The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes." Nat Commun, 5, 2987. doi: 10.1038/ncomms3987. Human mhf1-mhf2 DNA complex. SNAP output
4ne1 DNA binding protein-DNA X-ray (6.499 Å) Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei AR, Sung P, Xiong Y (2014) "The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes." Nat Commun, 5, 2987. doi: 10.1038/ncomms3987. Human mhf1 mhf2 DNA complexes. SNAP output
4nhj transcription regulator-DNA X-ray (2.701 Å) Li YC, Chang CK, Chang CF, Cheng YH, Fang PJ, Yu T, Chen SC, Li YC, Hsiao CD, Huang TH (2014) "Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element." Nucleic Acids Res., 42, 8777-8788. doi: 10.1093/nar/gku572. Crystal structure of klebsiella pneumoniae rsta DNA-binding domain in complex with rsta box. SNAP output
4ni7 cytokine-DNA X-ray (2.4 Å) Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y, Jarvis TC, Janjic N (2014) "Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand." J.Biol.Chem., 289, 8720-8734. doi: 10.1074/jbc.M113.532697. Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (somamer sl1025). SNAP output
4ni9 cytokine-DNA X-ray (2.55 Å) Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y, Jarvis TC, Janjic N (2014) "Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand." J.Biol.Chem., 289, 8720-8734. doi: 10.1074/jbc.M113.532697. Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (somamer sl1025), form 2. SNAP output
4nia virus-RNA X-ray (1.82 Å) Larson SB, Day JS, McPherson A (2014) "Satellite tobacco mosaic virus refined to 1.4 angstrom resolution." Acta Crystallogr.,Sect.D, 70, 2316-2330. doi: 10.1107/S1399004714013789. Satellite tobacco mosaic virus refined at room temperature to 1.8 Å resolution using ncs restraints. SNAP output
4nid oxidoreductase-DNA X-ray (1.58 Å) Zhu C, Yi C (2014) "Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues." Angew.Chem.Int.Ed.Engl., 53, 3659-3662. doi: 10.1002/anie.201310050. Crystal structure of alkb protein with cofactors bound to dsDNA containing m6a. SNAP output
4nig oxidoreductase-DNA X-ray (1.52 Å) Zhu C, Yi C (2014) "Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues." Angew.Chem.Int.Ed.Engl., 53, 3659-3662. doi: 10.1002/anie.201310050. Crystal structure of alkb d135i-e136h mutant protein with cofactors bound to dsDNA containing m6a-a. SNAP output
4nih oxidoreductase-DNA X-ray (1.374 Å) Zhu C, Yi C (2014) "Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues." Angew.Chem.Int.Ed.Engl., 53, 3659-3662. doi: 10.1002/anie.201310050. Crystal structure of alkb e136l mutant protein with cofactors bound to dsDNA containing m6a-a. SNAP output
4nii oxidoreductase-DNA X-ray (1.622 Å) Zhu C, Yi C (2014) "Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues." Angew.Chem.Int.Ed.Engl., 53, 3659-3662. doi: 10.1002/anie.201310050. Crystal structure of alkb d135i mutant protein with cofactors bound to dsDNA containing m6a-a. SNAP output
4nlg transferase-DNA X-ray (2.4 Å) Mukherjee P, Wilson RC, Lahiri I, Pata JD (2014) "Three Residues of the Interdomain Linker Determine the Conformation and Single-base Deletion Fidelity of Y-family Translesion Polymerases." J.Biol.Chem., 289, 6323-6331. doi: 10.1074/jbc.M113.537860. Y-family DNA polymerase chimera dbh-dpo4(243-245)-dbh. SNAP output
4nlk transferase, lyase-DNA X-ray (2.494 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase beta complexed with 8brg in the template base-paired with incoming non-hydrolyzable ctp. SNAP output
4nln transferase, lyase-DNA X-ray (2.261 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8brg and incoming ctp. SNAP output
4nlz transferase, lyase-DNA X-ray (2.683 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template 8brg and incoming gtp. SNAP output
4nm1 transferase, lyase-DNA X-ray (2.415 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8brg-c at n-1 position and g-c at n position. SNAP output
4nm2 transferase, lyase-DNA X-ray (2.524 Å) Koag MC, Min K, Lee S (2014) "Structural basis for promutagenicity of 8-halogenated Guanine." J.Biol.Chem., 289, 6289-6298. doi: 10.1074/jbc.M113.537803. Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8brg-g at n-1 position and g-c at n position. SNAP output
4nm6 oxidoreductase-DNA X-ray (2.026 Å) Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y (2013) "Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation." Cell(Cambridge,Mass.), 155, 1545-1555. doi: 10.1016/j.cell.2013.11.020. Crystal structure of tet2-DNA complex. SNAP output
4nnu transcription-DNA X-ray (2.81 Å) Ngo HB, Lovely GA, Phillips R, Chan DC (2014) "Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation." Nat Commun, 5, 3077. doi: 10.1038/ncomms4077. Distinct structural features of tfam drive mitochondrial DNA packaging versus transcriptional activation. SNAP output
4nod transcription regulator-DNA X-ray (2.897 Å) Ngo HB, Lovely GA, Phillips R, Chan DC (2014) "Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation." Nat Commun, 5, 3077. doi: 10.1038/ncomms4077. Distinct structural features of tfam drive mitochondrial DNA packaging versus transcriptional activation. SNAP output
4noe DNA binding protein-DNA X-ray (2.2 Å) Sugiman-Marangos SN, Weiss YM, Junop MS (2016) "Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB." Proc.Natl.Acad.Sci.USA, 113, 4308-4313. doi: 10.1073/pnas.1520847113. Crystal structure of ddrb bound to 30b ssDNA. SNAP output
4nqa transcription regulator-DNA X-ray (3.102 Å) Lou X, Toresson G, Benod C, Suh JH, Philips KJ, Webb P, Gustafsson JA (2014) "Structure of the retinoid X receptor alpha-liver X receptor beta (RXR alpha-LXR beta ) heterodimer on DNA." Nat.Struct.Mol.Biol., 21, 277-281. doi: 10.1038/nsmb.2778. Crystal structure of liganded hrxr-alpha-hlxr-beta heterodimer on DNA. SNAP output
4nrw hydrolase, lyase-DNA X-ray (2.845 Å) Prakash A, Carroll BL, Sweasy JB, Wallace SS, Doublie S (2014) "Genome and cancer single nucleotide polymorphisms of the human NEIL1 DNA glycosylase: Activity, structure, and the effect of editing." Dna Repair, 14, 17-26. doi: 10.1016/j.dnarep.2013.12.003. Mvnei1-g86d. SNAP output
4nw3 DNA binding protein-DNA X-ray (2.82 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Crystal structure of mll cxxc domain in complex with a cpg DNA. SNAP output
4nxz transferase, lyase-DNA X-ray (2.557 Å) Koag MC, Lee S (2014) "Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta." J.Am.Chem.Soc., 136, 5709-5721. doi: 10.1021/ja500172d. DNA polymerase beta with o6mg in the template base opposite to incoming non-hydrolyzable ttp with manganese in the active site. SNAP output
4ny8 transferase, lyase-DNA X-ray (2.246 Å) Koag MC, Lee S (2014) "Metal-dependent conformational activation explains highly promutagenic replication across O6-methylguanine by human DNA polymerase beta." J.Am.Chem.Soc., 136, 5709-5721. doi: 10.1021/ja500172d. DNA polymerase beta with o6mg in the template base opposite to incoming non-hydrolyzable ctp with manganese in the active site. SNAP output
4o0i transferase-DNA X-ray (2.203 Å) Jiang S, Gan J, Sun H, Huang Z "Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA." Crystal structure of fragment DNA polymerase i from bacillus stearothermophilus with 2'-mese-arabino-guanosine derivatized DNA. SNAP output
4o3m hydrolase-DNA X-ray (2.3 Å) Swan MK, Legris V, Tanner A, Reaper PM, Vial S, Bordas R, Pollard JR, Charlton PA, Golec JM, Bertrand JA (2014) "Structure of human Bloom's syndrome helicase in complex with ADP and duplex DNA." Acta Crystallogr.,Sect.D, 70, 1465-1475. doi: 10.1107/S139900471400501X. Ternary complex of bloom's syndrome helicase. SNAP output
4o3n transferase-DNA X-ray (1.579 Å) Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M (2014) "Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta." J.Biol.Chem., 289, 16867-16882. doi: 10.1074/jbc.M114.551820. Crystal structure of human DNA polymerase eta in ternary complex with native DNA and incoming nucleotide (dcp). SNAP output
4o3o transferase-DNA X-ray (1.698 Å) Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M (2014) "Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta." J.Biol.Chem., 289, 16867-16882. doi: 10.1074/jbc.M114.551820. Crystal structure of human polymerase eta inserting datp opposite an 8-oxog containing DNA template. SNAP output
4o3p transferase-DNA X-ray (1.72 Å) Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M (2014) "Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta." J.Biol.Chem., 289, 16867-16882. doi: 10.1074/jbc.M114.551820. Crystal structure of human polymerase eta inserting dctp opposite an 8-oxog containing DNA template. SNAP output
4o3q transferase-DNA X-ray (1.72 Å) Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M (2014) "Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta." J.Biol.Chem., 289, 16867-16882. doi: 10.1074/jbc.M114.551820. Crystal structure of human polymerase eta inserting dgtp opposite an 8-oxog containing DNA template. SNAP output
4o3r transferase-DNA X-ray (1.62 Å) Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M (2014) "Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta." J.Biol.Chem., 289, 16867-16882. doi: 10.1074/jbc.M114.551820. Crystal structure of human polymerase eta extending an 8-oxog DNA lesion: post insertion of 8-oxog-da pair. SNAP output
4o3s transferase-DNA X-ray (1.717 Å) Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich FP, Egli M (2014) "Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta." J.Biol.Chem., 289, 16867-16882. doi: 10.1074/jbc.M114.551820. Crystal structure of human polymerase eta extending an 8-oxog DNA lesion: post insertion of 8-oxog-dc pair. SNAP output
4o5c transferase, lyase-DNA X-ray (2.363 Å) Koag MC, Kou Y, Ouzon-Shubeita H, Lee S (2014) "Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine." Nucleic Acids Res., 42, 8755-8766. doi: 10.1093/nar/gku554. Structure of human DNA polymerase complexed with n7-mg as the template base in a 1-nucleotide gapped DNA. SNAP output
4o5e transferase, lyase-DNA X-ray (2.532 Å) Koag MC, Kou Y, Ouzon-Shubeita H, Lee S (2014) "Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine." Nucleic Acids Res., 42, 8755-8766. doi: 10.1093/nar/gku554. Structure of human DNA polymerase complexed with n7mg in the template base paired with incoming non-hydrolyzable ttp. SNAP output
4o5k transferase, lyase-DNA X-ray (2.058 Å) Koag MC, Kou Y, Ouzon-Shubeita H, Lee S (2014) "Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine." Nucleic Acids Res., 42, 8755-8766. doi: 10.1093/nar/gku554. Structure of human DNA polymerase complexed with n7mg in the template base paired with incoming non-hydrolyzable ctp. SNAP output
4o6a transferase-DNA X-ray (1.859 Å) Zhang X, Wu J, Du F, Xu H, Sun L, Chen Z, Brautigam CA, Zhang X, Chen ZJ (2014) "The Cytosolic DNA Sensor cGAS Forms an Oligomeric Complex with DNA and Undergoes Switch-like Conformational Changes in the Activation Loop." Cell Rep, 6, 421-430. doi: 10.1016/j.celrep.2014.01.003. Mouse cyclic gmp-amp synthase (cgas) in complex with DNA. SNAP output
4o9m transferase-DNA X-ray (2.295 Å) Caglayan M, Batra VK, Sassa A, Prasad R, Wilson SH (2014) "Role of polymerase beta in complementing aprataxin deficiency during abasic-site base excision repair." Nat.Struct.Mol.Biol., 21, 497-499. doi: 10.1038/nsmb.2818. Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA. SNAP output
4ofa hydrolase-DNA X-ray (1.55 Å) Ouzon-Shubeita H, Lin Y-L, Lee S "Structure of MBD4 bound to G:T mispair DNA." Structural basis for thymine glycosylase activity on t:o6-methylg mismatch by methyl-cpg binding domain protein 4: implications for roles of arg468 in mismatch recognition and catalysis. SNAP output
4ofe hydrolase-DNA X-ray (2.15 Å) Ouzon-Shubeita H, Lin Y-L, Lee S "Structure of R468K/D560N MBD4 bound to G:T mispair DNA." Structural basis for thymine glycosylase activity on t:o6-methylg mismatch by methyl-cpg binding domain protein 4: implications for roles of arg468 in mismatch recognition and catalysis. SNAP output
4ofh hydrolase-DNA X-ray (2.22 Å) Ouzon-Shubeita H, Lin Y-L, Lee S "Structure of MBD4 bound to O6MeG:T mispair DNA." Structural basis for thymine glycosylase activity on t:o6-methylg mismatch by methyl-cpg binding domain protein 4: implications for roles of arg468 in mismatch recognition and catalysis. SNAP output
4oi7 transport protein,signaling protein-DNA X-ray (3.104 Å) Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L, Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS, Latz E (2013) "RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA." J.Exp.Med., 210, 2447-2463. doi: 10.1084/jem.20120201. Rage recognizes nucleic acids and promotes inflammatory responses to DNA. SNAP output
4oi8 transport protein,signaling protein-DNA X-ray (3.101 Å) Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L, Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS, Latz E (2013) "RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA." J.Exp.Med., 210, 2447-2463. doi: 10.1084/jem.20120201. Rage is a nucleic acid receptor that promotes inflammatory responses to DNA.. SNAP output
4oin transcription, transferase-antibiotic X-ray (2.8 Å) Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH (2014) "GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides." Elife, 3, e02450. Crystal structure of thermus thermophilus transcription initiation complex soaked with ge23077. SNAP output
4oio transcription, transferase X-ray (3.1 Å) Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH (2014) "GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides." Elife, 3, e02450. Crystal structure of thermus thermophilus pre-insertion substrate complex for de novo transcription initiation. SNAP output
4oip transcription, transferase-antibiotic X-ray (3.4 Å) Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH (2014) "GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides." Elife, 3, e02450. Crystal structure of thermus thermophilus transcription initiation complex soaked with ge23077, atp, and cmpcpp. SNAP output
4oiq transcription, transferase-antibiotic X-ray (3.624 Å) Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH (2014) "GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides." Elife, 3, e02450. Crystal structure of thermus thermophilus transcription initiation complex soaked with ge23077 and rifampicin. SNAP output
4oir transcription, transferase-antibiotic X-ray (3.105 Å) Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH (2014) "GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides." Elife, 3, e02450. Crystal structure of thermus thermophilus RNA polymerase transcription initiation complex soaked with ge23077 and rifamycin sv. SNAP output
4ol8 transferase, hydrolase-RNA-DNA X-ray (3.1 Å) Nowak E, Miller JT, Bona MK, Studnicka J, Szczepanowski RH, Jurkowski J, Le Grice SF, Nowotny M (2014) "Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry." Nat.Struct.Mol.Biol., 21, 389-396. doi: 10.1038/nsmb.2785. Ty3 reverse transcriptase bound to DNA-RNA. SNAP output
4oln transcription-DNA X-ray (1.7 Å) McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW (2014) "Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module." Cell(Cambridge,Mass.), 159, 58-68. doi: 10.1016/j.cell.2014.09.003. Ancestral steroid receptor 1 in complex with estrogen response element DNA. SNAP output
4omy transcription-DNA X-ray (3.062 Å) Lee SG, Krishnan HB, Jez JM (2014) "Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR." Proc.Natl.Acad.Sci.USA, 111, 6509-6514. doi: 10.1073/pnas.1402243111. Crystal structure of semet nolr from sinorhizobium fredii in complex with oligo at DNA. SNAP output
4on0 transcription-DNA X-ray (3.0 Å) Lee SG, Krishnan HB, Jez JM (2014) "Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR." Proc.Natl.Acad.Sci.USA, 111, 6509-6514. doi: 10.1073/pnas.1402243111. Crystal structure of nolr from sinorhizobium fredii in complex with oligo aa DNA. SNAP output
4ond transcription-DNA X-ray (2.253 Å) McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW (2014) "Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module." Cell(Cambridge,Mass.), 159, 58-68. doi: 10.1016/j.cell.2014.09.003. Ancestral steroid receptor 2 dbd helix mutant - ere DNA complex. SNAP output
4oo8 hydrolase-DNA-RNA X-ray (2.5 Å) Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O (2014) "Crystal structure of Cas9 in complex with guide RNA and target DNA." Cell(Cambridge,Mass.), 156, 935-949. doi: 10.1016/j.cell.2014.02.001. Crystal structure of streptococcus pyogenes cas9 in complex with guide RNA and target DNA. SNAP output
4oor transcription-DNA X-ray (2.701 Å) McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW (2014) "Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module." Cell(Cambridge,Mass.), 159, 58-68. doi: 10.1016/j.cell.2014.09.003. Ancestral steroid receptor 2 DNA binding domain in complex with a steroid response element. SNAP output
4opj hydrolase-DNA X-ray (1.541 Å) Egli M, Pallan PS "Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes." Methods Mol.Biol., 1320, 111-126. doi: 10.1007/978-1-4939-2763-0_8. Bh-rnaseh:tcda-DNA complex. SNAP output
4opk hydrolase-DNA X-ray (1.539 Å) Egli M, Pallan PS "Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes." Methods Mol.Biol., 1320, 111-126. doi: 10.1007/978-1-4939-2763-0_8. Bh-rnaseh:2'-sme-DNA complex. SNAP output
4opx transferase-DNA-transferase inhibitor X-ray (3.314 Å) Patel MR, Bhatt A, Steffen JD, Chergui A, Murai J, Pommier Y, Pascal JM, Trombetta LD, Fronczek FR, Talele TT (2014) "Discovery and Structure-Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-carboxamide and 2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide Derivatives as Poly(ADP-ribose)polymerase-1 Inhibitors." J.Med.Chem., 57, 5579-5601. doi: 10.1021/jm5002502. Structure of human parp-1 bound to a DNA double strand break in complex with (2r)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide. SNAP output
4oq9 virus-RNA X-ray (1.45 Å) Larson SB, Day JS, McPherson A (2014) "Satellite tobacco mosaic virus refined to 1.4 angstrom resolution." Acta Crystallogr.,Sect.D, 70, 2316-2330. doi: 10.1107/S1399004714013789. Satellite tobacco mosaic virus refined to 1.4 Å resolution using non-crystallographic symmetry restraints. SNAP output
4oqa transferase-DNA-transferase inhibitor X-ray (3.65 Å) Patel MR, Bhatt A, Steffen JD, Chergui A, Murai J, Pommier Y, Pascal JM, Trombetta LD, Fronczek FR, Talele TT (2014) "Discovery and Structure-Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-carboxamide and 2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide Derivatives as Poly(ADP-ribose)polymerase-1 Inhibitors." J.Med.Chem., 57, 5579-5601. doi: 10.1021/jm5002502. Structure of human parp-1 bound to a DNA double strand break in complex with (2z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide. SNAP output
4oqb transferase-DNA-transferase inhibitor X-ray (3.362 Å) Patel MR, Bhatt A, Steffen JD, Chergui A, Murai J, Pommier Y, Pascal JM, Trombetta LD, Fronczek FR, Talele TT (2014) "Discovery and Structure-Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-carboxamide and 2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide Derivatives as Poly(ADP-ribose)polymerase-1 Inhibitors." J.Med.Chem., 57, 5579-5601. doi: 10.1021/jm5002502. Structure of human parp-1 bound to a DNA double strand break in complex with (2z)-2-{4-[2-(morpholin-4-yl)ethoxy]benzylidene}-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide. SNAP output
4osh DNA binding protein-DNA X-ray (2.201 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the tal effector dhax3 with ni rvd at 2.2 angstrom resolution. SNAP output
4osi DNA binding protein-DNA X-ray (2.849 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the tal effector dhax3 with ni rvd at 2.8 angstrom resolution. SNAP output
4osj DNA binding protein-DNA X-ray (2.79 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of tal effector reveals the recognition between asparagine and adenine. SNAP output
4osk DNA binding protein-DNA X-ray (2.398 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of tal effector reveals the recognition between asparagine and guanine. SNAP output
4osl DNA binding protein-DNA X-ray (2.447 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of tal effector reveals the recognition between histidine and guanine. SNAP output
4osm DNA binding protein-DNA X-ray (2.454 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505h mutant of tal effector dhax3. SNAP output
4osq DNA binding protein-DNA X-ray (2.256 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505r mutant of tal effector dhax3. SNAP output
4osr DNA binding protein-DNA X-ray (1.944 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505k mutant of tal effector dhax3. SNAP output
4oss DNA binding protein-DNA X-ray (2.397 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505q mutant of tal effector dhax3. SNAP output
4ost DNA binding protein-DNA X-ray (1.996 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505c mutant of tal effector dhax3. SNAP output
4osv DNA binding protein-DNA X-ray (1.996 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505m mutant of tal effector dhax3. SNAP output
4osw DNA binding protein-DNA X-ray (2.302 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505e mutant of tal effector dhax3. SNAP output
4osz DNA binding protein-DNA X-ray (2.614 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505p mutant of tal effector dhax3. SNAP output
4ot0 DNA binding protein-DNA X-ray (2.491 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505t mutant of tal effector dhax3. SNAP output
4ot3 DNA binding protein-DNA X-ray (1.944 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505l mutant of tal effector dhax3. SNAP output
4oto DNA binding protein-DNA X-ray (2.588 Å) Deng D, Yan CY, Wu JP, Pan XJ, Yan N (2014) "Revisiting the TALE repeat." Protein Cell, 5, 297-306. doi: 10.1007/s13238-014-0035-2. Crystal structure of the s505w mutant of tal effector dhax3. SNAP output
4ou6 replication-DNA X-ray (1.96 Å) Liu Z, Chen P, Wang X, Cai G, Niu L, Teng M, Li X (2014) "Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode." Nucleic Acids Res., 42, 9470-9483. doi: 10.1093/nar/gku633. Crystal structure of dnat84-153-dt10 ssDNA complex form 1. SNAP output
4ou7 replication-DNA X-ray (2.83 Å) Liu Z, Chen P, Wang X, Cai G, Niu L, Teng M, Li X (2014) "Crystal structure of DnaT84-153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode." Nucleic Acids Res., 42, 9470-9483. doi: 10.1093/nar/gku633. Crystal structure of dnat84-153-dt10 ssDNA complex reveals a novel single-stranded DNA binding mode. SNAP output
4ov7 transcription-DNA X-ray (2.701 Å) McKeown AN, Bridgham JT, Anderson DW, Murphy MN, Ortlund EA, Thornton JW (2014) "Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module." Cell(Cambridge,Mass.), 159, 58-68. doi: 10.1016/j.cell.2014.09.003. Ancestral steroid receptor 2 dbd helix mutant - sre DNA complex. SNAP output
4oww DNA binding protein X-ray (2.3 Å) Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song H (2014) "Structural Basis of SOSS1 Complex Assembly and Recognition of ssDNA." Cell Rep, 6, 982-991. doi: 10.1016/j.celrep.2014.02.020. Structural basis of soss1 in complex with a 35nt ssDNA. SNAP output
4owx DNA binding protein-DNA X-ray (2.3 Å) Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song H (2014) "Structural Basis of SOSS1 Complex Assembly and Recognition of ssDNA." Cell Rep, 6, 982-991. doi: 10.1016/j.celrep.2014.02.020. Structural basis of soss1 in complex with a 12nt ssDNA. SNAP output
4p0p hydrolase-DNA X-ray (2.8 Å) Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y, Cho Y (2014) "Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates." Embo J., 33, 1061-1072. doi: 10.1002/embj.201487820. Crystal structure of human mus81-eme1 in complex with 5'-flap DNA, and mg2+. SNAP output
4p0q hydrolase-DNA X-ray (2.851 Å) Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y, Cho Y (2014) "Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates." Embo J., 33, 1061-1072. doi: 10.1002/embj.201487820. Crystal structure of human mus81-eme1 in complex with 5'-flap DNA. SNAP output
4p0r hydrolase-DNA X-ray (6.501 Å) Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y, Cho Y (2014) "Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates." Embo J., 33, 1061-1072. doi: 10.1002/embj.201487820. Human mus81-eme1-3'flap DNA complex. SNAP output
4p0s hydrolase-DNA X-ray (6.0 Å) Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y, Cho Y (2014) "Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates." Embo J., 33, 1061-1072. doi: 10.1002/embj.201487820. Human mus81-eme1-3'flap DNA complex. SNAP output
4p2h transferase-DNA X-ray (1.987 Å) Koag MC, Kou Y, Ouzon-Shubeita H, Lee S (2014) "Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine." Nucleic Acids Res., 42, 8755-8766. doi: 10.1093/nar/gku554. Structure of human DNA polymerase complexed with n7mg in the template opposite to incoming non-hydrolyzable ttp with manganese in the active site. SNAP output
4p4m transferase-DNA X-ray (1.92 Å) Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA, Bebenek K, Garcia-Diaz M (2014) "Structures of the Leishmania infantum polymerase beta." DNA Repair (Amst.), 18, 1-9. doi: 10.1016/j.dnarep.2014.03.001. Crystal structure of leishmania infantum polymerase beta: ternary p-t complex. SNAP output
4p4o transferase-DNA X-ray (2.3 Å) Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA, Bebenek K, Garcia-Diaz M (2014) "Structures of the Leishmania infantum polymerase beta." DNA Repair (Amst.), 18, 1-9. doi: 10.1016/j.dnarep.2014.03.001. Crystal structure of leishmania infantum polymerase beta: ternary gap complex. SNAP output
4p4p transferase-DNA X-ray (2.3 Å) Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA, Bebenek K, Garcia-Diaz M (2014) "Structures of the Leishmania infantum polymerase beta." DNA Repair (Amst.), 18, 1-9. doi: 10.1016/j.dnarep.2014.03.001. Crystal structure of leishmania infantum polymerase beta: nick complex. SNAP output
4p9u transcription regulator-DNA X-ray (3.208 Å) Shi W, Kovacikova G, Lin W, Taylor RK, Skorupski K, Kull FJ (2015) "The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand." Nat Commun, 6, 6032. doi: 10.1038/ncomms7032. Fadr, fatty acid responsive transcription factor from vibrio cholerae, in complex with DNA. SNAP output
4par DNA binding protein-DNA X-ray (2.89 Å) Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X (2014) "Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA." Nucleic Acids Res., 42, 7947-7959. doi: 10.1093/nar/gku497. The 5-hydroxymethylcytosine-specific restriction enzyme abasi in a complex with product-like DNA. SNAP output
4pba DNA binding protein-DNA X-ray (3.301 Å) Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X (2014) "Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA." Nucleic Acids Res., 42, 7947-7959. doi: 10.1093/nar/gku497. The 5-hydroxymethylcytosine-specific restriction enzyme abasi in a complex with substrate-like DNA. SNAP output
4pcb transferase-DNA X-ray (2.5 Å) Carballeira JD, Gonzalez-Perez B, Moncalian G, la Cruz Fd (2014) "A high security double lock and key mechanism in HUH relaxases controls oriT-processing for plasmid conjugation." Nucleic Acids Res., 42, 10632-10643. doi: 10.1093/nar/gku741. Conjugative relaxase trwc in complex with mutant orit DNA. SNAP output
4pcz hydrolase-DNA X-ray (1.7 Å) Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B (2014) "Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization." Nucleic Acids Res., 42, 10748-10761. doi: 10.1093/nar/gku613. Crystal structure of a complex between r247g llfpg mutant and a thf containing DNA. SNAP output
4pd2 hydrolase-DNA X-ray (1.65 Å) Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B (2014) "Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization." Nucleic Acids Res., 42, 10748-10761. doi: 10.1093/nar/gku613. Crystal structure of a complex between a c248gh llfpg mutant and a thf containing DNA. SNAP output
4pdg hydrolase-DNA X-ray (2.4 Å) Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B (2014) "Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization." Nucleic Acids Res., 42, 10748-10761. doi: 10.1093/nar/gku613. Crystal structure of a complex between an inhibited llfpg and a thf containing DNA. SNAP output
4pdi hydrolase-DNA X-ray (2.1 Å) Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B (2014) "Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization." Nucleic Acids Res., 42, 10748-10761. doi: 10.1093/nar/gku613. Crystal structure of a complex between an inhibited llfpg and a n7-benzyl-fapy-dg containing DNA. SNAP output
4pe8 hydrolase-DNA X-ray (2.894 Å) Chen YC, Li CL, Hsiao YY, Duh Y, Yuan HS (2014) "Structure and function of TatD exonuclease in DNA repair." Nucleic Acids Res., 42, 10776-10785. doi: 10.1093/nar/gku732. Crystal structure of tatd in complex with trinucleotide DNA. SNAP output
4peh hydrolase-RNA X-ray (2.1 Å) Montemayor EJ, Katolik A, Clark NE, Taylor AB, Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens SW, Damha MJ, Hart PJ (2014) "Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1." Nucleic Acids Res., 42, 10845-10855. doi: 10.1093/nar/gku725. Dbr1 in complex with synthetic linear RNA. SNAP output
4pei hydrolase-RNA X-ray (1.95 Å) Montemayor EJ, Katolik A, Clark NE, Taylor AB, Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens SW, Damha MJ, Hart PJ (2014) "Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1." Nucleic Acids Res., 42, 10845-10855. doi: 10.1093/nar/gku725. Dbr1 in complex with synthetic branched RNA analog. SNAP output
4pgq transferase,lyase-DNA X-ray (2.3 Å) Koag MC, Nam K, Lee S (2015) "The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta." Nucleic Acids Res., 42, 11233-11245. doi: 10.1093/nar/gku789. Structure of human DNA polymerase beta complexed with g in the template base paired with incoming non-hydrolyzable ttp. SNAP output
4pgx transferase,lyase-DNA X-ray (2.077 Å) Koag MC, Nam K, Lee S (2015) "The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta." Nucleic Acids Res., 42, 11233-11245. doi: 10.1093/nar/gku789. Structure of human DNA polymerase beta complexed with g in the template base paired with incoming non-hydrolyzable ttp and manganese. SNAP output
4pgy transferase,lyase-DNA X-ray (2.26 Å) Koag MC, Lee S "The spontaneous base substitution mechanisms of human DNA polymerase beta." Structure of human DNA polymerase beta complexed with a nicked DNA containing a gt at n-1 position and gc at n position. SNAP output
4ph5 transferase,lyase-DNA X-ray (2.55 Å) Koag MC, Lee S "The spontaneous base substitution mechanisms of human DNA polymerase beta." Structure of human DNA polymerase beta complexed with a nicked DNA containing a ac at n-1 position and gc at n position. SNAP output
4pha transferase,lyase-DNA X-ray (2.52 Å) Koag MC, Nam K, Lee S (2015) "The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta." Nucleic Acids Res., 42, 11233-11245. doi: 10.1093/nar/gku789. Structure of human DNA polymerase beta complexed with a in the template base paired with incoming non-hydrolyzable ctp. SNAP output
4phd transferase,lyase-DNA X-ray (2.21 Å) Koag MC, Nam K, Lee S (2015) "The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase beta." Nucleic Acids Res., 42, 11233-11245. doi: 10.1093/nar/gku789. Structure of human DNA polymerase beta complexed with a in the template base paired with incoming non-hydrolyzable ctp and manganese. SNAP output
4phe transferase,lyase-DNA X-ray (2.15 Å) Koag MC, Lee S "The spontaneous base substitution mechanisms of human DNA polymerase beta." Structure of human DNA polymerase beta complexed with t in the template base paired with incoming non-hydrolyzable gtp. SNAP output
4php transferase,lyase-DNA X-ray (2.6 Å) Koag MC, Lee S "The spontaneous base substitution mechanisms of human DNA polymerase beta." Structure of human DNA polymerase beta complexed with t in the template base paired with incoming non-hydrolyzable gtp and manganese. SNAP output
4plb isomerase-isomerase inhibitor-DNA X-ray (2.69 Å) Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen D, Lagrutta A, Bradley P, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Wei C, Fukuda H, Kishii R, Takei M, Fukuda Y (2014) "Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad spectrum antibacterial agents." Acs Med.Chem.Lett., 5, 609-614. doi: 10.1021/ml500069w. Crystal structure of s.a. gyrase-am8191 complex. SNAP output
4pog replication, DNA binding protein-DNA X-ray (3.203 Å) Froelich CA, Kang S, Epling LB, Bell SP, Enemark EJ (2014) "A conserved MCM single-stranded DNA binding element is essential for replication initiation." Elife, 3, e01993. doi: 10.7554/eLife.01993. Mcm-ssDNA co-crystal structure. SNAP output
4ppx transferase, lyase-DNA X-ray (2.08 Å) Eckenroth BE, Fleming AM, Sweasy JB, Burrows CJ, Doublie S (2014) "Crystal Structure of DNA Polymerase beta with DNA Containing the Base Lesion Spiroiminodihydantoin in a Templating Position." Biochemistry, 53, 2075-2077. doi: 10.1021/bi500270e. DNA polymerase beta e295k with spiroiminodihydantoin in templating position. SNAP output
4pqu transferase, hydrolase-DNA-RNA X-ray (2.508 Å) Das K, Martinez SE, Bandwar RP, Arnold E (2014) "Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage." Nucleic Acids Res., 42, 8125-8137. doi: 10.1093/nar/gku487. Crystal structure of hiv-1 reverse transcriptase in complex with RNA-DNA and datp. SNAP output
4pso DNA binding protein X-ray (2.9 Å) Ghalei H, Moeller Hv, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC (2014) "Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein." Nucleic Acids Res., 42, 6698-6708. doi: 10.1093/nar/gku259. Crystal structure of apethermo-dbp-rp2 bound to ssDNA dt10. SNAP output
4ptf transferase-DNA X-ray (2.809 Å) Jain R, Rajashankar KR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2014) "Crystal Structure of Yeast DNA Polymerase epsilon Catalytic Domain." Plos One, 9, e94835. doi: 10.1371/journal.pone.0094835. Ternary crystal structure of yeast DNA polymerase epsilon with template g. SNAP output
4pu3 toxin-antitoxin-DNA X-ray (3.39 Å) Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B, Devreese B, Savvides SN (2014) "The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence." Nucleic Acids Res., 42, 10134-10147. doi: 10.1093/nar/gku665. Shewanella oneidensis mr-1 toxin antitoxin system hipa, hipb and its operator DNA complex (space group p212121). SNAP output
4pu4 toxin-antitoxin-DNA X-ray (3.786 Å) Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B, Devreese B, Savvides SN (2014) "The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence." Nucleic Acids Res., 42, 10134-10147. doi: 10.1093/nar/gku665. Shewanella oneidensis mr-1 toxin antitoxin system hipa, hipb and its operator DNA complex (space group p21). SNAP output
4puo transferase, hydrolase-DNA-RNA-inhibitor X-ray (2.901 Å) Das K, Martinez SE, Bandwar RP, Arnold E (2014) "Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage." Nucleic Acids Res., 42, 8125-8137. doi: 10.1093/nar/gku487. Crystal structure of hiv-1 reverse transcriptase in complex with RNA-DNA and nevirapine. SNAP output
4puq hydrolase-DNA-RNA X-ray (1.6 Å) Gao R, Schellenberg MJ, Huang SY, Abdelmalak M, Marchand C, Nitiss KC, Nitiss JL, Williams RS, Pommier Y (2014) "Proteolytic Degradation of Topoisomerase II (Top2) Enables the Processing of Top2DNA and Top2RNA Covalent Complexes by Tyrosyl-DNA-Phosphodiesterase 2 (TDP2)." J.Biol.Chem., 289, 17960-17969. doi: 10.1074/jbc.M114.565374. Mus musculus tdp2 reaction product complex with 5'-phosphorylated RNA-DNA, glycerol, and mg2+. SNAP output
4pw5 ligase-DNA X-ray (2.204 Å) Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu RM (2014) "Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2." Mol.Cell, 54, 879-886. doi: 10.1016/j.molcel.2014.04.003. Structure of uhrf2-sra in complex with a 5hmc-containing DNA, complex i. SNAP output
4pw6 ligase-DNA X-ray (3.789 Å) Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu RM (2014) "Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2." Mol.Cell, 54, 879-886. doi: 10.1016/j.molcel.2014.04.003. Structure of uhrf2-sra in complex with a 5hmc-containing DNA, complex ii. SNAP output
4pw7 ligase-DNA X-ray (2.001 Å) Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu RM (2014) "Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2." Mol.Cell, 54, 879-886. doi: 10.1016/j.molcel.2014.04.003. Structure of uhrf2-sra in complex with a 5mc-containing DNA. SNAP output
4pwd transferase, hydrolase-DNA-RNA-inhibitor X-ray (3.0 Å) Das K, Martinez SE, Bandwar RP, Arnold E (2014) "Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage." Nucleic Acids Res., 42, 8125-8137. doi: 10.1093/nar/gku487. Crystal structure of hiv-1 reverse transcriptase in complex with bulge-RNA-DNA and nevirapine. SNAP output
4pxi transcription-DNA X-ray (3.2 Å) Bhukya H, Bhujbalrao R, Bitra A, Anand R (2014) "Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2)." Nucleic Acids Res., 42, 10122-10133. doi: 10.1093/nar/gku587. Elucidation of the structural and functional mechanism of action of the tetr family protein, cprb from s. coelicolor a3(2). SNAP output
4py5 hydrolase-DNA-RNA X-ray (2.1 Å) Figiel M, Nowotny M (2014) "Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition." Nucleic Acids Res., 42, 9285-9294. doi: 10.1093/nar/gku615. Thermovibrio ammonificans rnase h3 in complex with 19-mer RNA-DNA. SNAP output
4pzi transcription-DNA X-ray (2.15 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Zinc finger region of mll2 in complex with cpg DNA. SNAP output
4q0b transferase, hydrolase-RNA-DNA-inhibitor X-ray (3.3 Å) Das K, Martinez SE, Bandwar RP, Arnold E (2014) "Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage." Nucleic Acids Res., 42, 8125-8137. doi: 10.1093/nar/gku487. Crystal structure of hiv-1 reverse transcriptase in complex with gap-RNA-DNA and nevirapine. SNAP output
4q0r hydrolase-DNA X-ray (2.75 Å) Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M (2014) "Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding." Nucleic Acids Res., 42, 10762-10775. doi: 10.1093/nar/gku729. The catalytic core of rad2 (complex i). SNAP output
4q0w hydrolase-DNA X-ray (2.1 Å) Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M (2014) "Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding." Nucleic Acids Res., 42, 10762-10775. doi: 10.1093/nar/gku729. He catalytic core of rad2 in complex with DNA substrate (complex ii). SNAP output
4q0z hydrolase-DNA X-ray (2.398 Å) Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M (2014) "Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding." Nucleic Acids Res., 42, 10762-10775. doi: 10.1093/nar/gku729. The catalytic core of rad2 in complex with DNA substrate (complex iii). SNAP output
4q10 hydrolase-DNA X-ray (2.7 Å) Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M (2014) "Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding." Nucleic Acids Res., 42, 10762-10775. doi: 10.1093/nar/gku729. The catalytic core of rad2 in complex with DNA substrate (complex iv). SNAP output
4q43 transferase-DNA X-ray (2.45 Å) Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B, Pradeepkumar PI, Nair DT (2015) "Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic." Structure, 23, 56-67. doi: 10.1016/j.str.2014.10.019. Polymerase-damaged DNA complex. SNAP output
4q44 transferase-DNA X-ray (2.71 Å) Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B, Pradeepkumar PI, Nair DT (2015) "Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic." Structure, 23, 56-67. doi: 10.1016/j.str.2014.10.019. Polymerase-damaged DNA complex. SNAP output
4q45 transferase-DNA X-ray (2.176 Å) Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B, Pradeepkumar PI, Nair DT (2015) "Unique structural features in DNA polymerase IV enable efficient bypass of the N2 adduct induced by the nitrofurazone antibiotic." Structure, 23, 56-67. doi: 10.1016/j.str.2014.10.019. DNA polymerase- damaged DNA complex. SNAP output
4q4z transcription-DNA X-ray (2.9 Å) Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernandez-Tornero C, Kulbachinskiy A, Murakami KS (2014) "Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme." J.Biol.Chem., 289, 24549-24559. doi: 10.1074/jbc.M114.584037. Thermus thermophilus RNA polymerase de novo transcription initiation complex. SNAP output
4q5s transcription-DNA-RNA X-ray (3.0 Å) Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernandez-Tornero C, Kulbachinskiy A, Murakami KS (2014) "Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme." J.Biol.Chem., 289, 24549-24559. doi: 10.1074/jbc.M114.584037. Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA. SNAP output
4q5v transferase-DNA-RNA X-ray (2.52 Å) Baranovskiy AG, Babayeva ND, Suwa Y, Gu J, Pavlov YI, Tahirov TH (2014) "Structural basis for inhibition of DNA replication by aphidicolin." Nucleic Acids Res., 42, 14013-14021. doi: 10.1093/nar/gku1209. Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin. SNAP output
4q8e transferase-DNA X-ray (1.549 Å) Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W, Lippard SJ (2014) "Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage." Proc.Natl.Acad.Sci.USA, 111, 9133-9138. doi: 10.1073/pnas.1405739111. Human DNA polymerase eta inserting dcmpnpp opposite a phenanthriplatin adducted g. SNAP output
4q8f transferase-DNA X-ray (2.797 Å) Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W, Lippard SJ (2014) "Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage." Proc.Natl.Acad.Sci.USA, 111, 9133-9138. doi: 10.1073/pnas.1405739111. Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted g. SNAP output
4qcb hydrolase-DNA X-ray (2.89 Å) Schormann N, Banerjee S, Ricciardi R, Chattopadhyay D (2015) "Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase." BMC Struct. Biol., 15, 10. doi: 10.1186/s12900-015-0037-1. Protein-DNA complex of vaccinia virus d4 with double-stranded non-specific DNA. SNAP output
4qcl transferase-DNA-RNA X-ray (2.2 Å) Baranovskiy AG, Duong V, Babayeva ND, Zhang Y, Pavlov Y, Anderson K, Tahirov TH (2018) "Activity and fidelity of human DNA polymerase alpha depend on primer structure." J.Biol.Chem. Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dctp. SNAP output
4qen transcription-DNA X-ray (2.002 Å) Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504. doi: 10.1016/j.molcel.2014.06.009. Crystal structure of kryptonite in complex with mchh DNA and sah. SNAP output
4qeo transcription-DNA X-ray (2.0 Å) Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504. doi: 10.1016/j.molcel.2014.06.009. Crystal structure of kryptonite in complex with mchh DNA, h3(1-15) peptide and sah. SNAP output
4qep transcription-DNA X-ray (3.1 Å) Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504. doi: 10.1016/j.molcel.2014.06.009. Crystal structure of kryptonite in complex with mchg DNA and sah. SNAP output
4qgu transcription-DNA X-ray (2.545 Å) Ni X, Ru H, Ma F, Zhao L, Shaw N, Feng Y, Ding W, Gong W, Wang Q, Ouyang S, Cheng G, Liu ZJ (2016) "New insights into the structural basis of DNA recognition by HINa and HINb domains of IFI16." J Mol Cell Biol, 8, 51-61. doi: 10.1093/jmcb/mjv053. Protein domain complex with ssDNA. SNAP output
4qju DNA binding protein-DNA X-ray (2.16 Å) Kim D-H, Im H, Jee J-G, Jang S-B, Yoon H-J, Kwon A-R, Kang S-M, Lee B-J (2014) "beta-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism." Acta Crystallogr.,Sect.D, 70, 3273-3289. doi: 10.1107/S1399004714023931. Crystal structure of DNA-bound nucleoid associated protein, sav1473. SNAP output
4qlc chromatin binding protein-DNA X-ray (3.503 Å) Zhou BR, Jiang J, Feng H, Ghirlando R, Xiao TS, Bai Y (2015) "Structural Mechanisms of Nucleosome Recognition by Linker Histones." Mol.Cell, 33 Suppl 1, 2-3. doi: 10.1016/j.molcel.2015.06.025. Crystal structure of chromatosome at 3.5 angstrom resolution. SNAP output
4qm7 transferase-DNA X-ray (1.8 Å) Das U, Wang LK, Smith P, Munir A, Shuman S (2014) "Structures of bacterial polynucleotide kinase in a michaelis complex with nucleoside triphosphate (NTP)-Mg2+ and 5'-OH RNA and a mixed substrate-product complex with NTP-Mg2+ and a 5'-phosphorylated oligonucleotide." J.Bacteriol., 196, 4285-4292. doi: 10.1128/JB.02197-14. Structure of bacterial polynucleotide kinase bound to gtp and pDNA. SNAP output
4qpq transcription-DNA X-ray (3.106 Å) Peng Y, Lu J, Wong JJ, Edwards RA, Frost LS, Mark Glover JN (2014) "Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM." J.Mol.Biol., 426, 3783-3795. doi: 10.1016/j.jmb.2014.09.018. Mechanistic basis of plasmid-specific DNA binding of the f plasmid regulatory protein, tram. SNAP output
4qqw hydrolase-DNA X-ray (2.664 Å) Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A (2014) "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation." Nat.Struct.Mol.Biol., 21, 771-777. doi: 10.1038/nsmb.2875. Crystal structure of t. fusca cas3. SNAP output
4qqx hydrolase-DNA X-ray (3.34 Å) Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A (2014) "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation." Nat.Struct.Mol.Biol., 21, 771-777. doi: 10.1038/nsmb.2875. Crystal structure of t. fusca cas3-atp. SNAP output
4qqy hydrolase-DNA X-ray (3.12 Å) Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A (2014) "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation." Nat.Struct.Mol.Biol., 21, 771-777. doi: 10.1038/nsmb.2875. Crystal structure of t. fusca cas3-adp. SNAP output
4qqz hydrolase-DNA X-ray (2.93 Å) Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A (2014) "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation." Nat.Struct.Mol.Biol., 21, 771-777. doi: 10.1038/nsmb.2875. Crystal structure of t. fusca cas3-amppnp. SNAP output
4qr9 DNA binding protein X-ray (2.0 Å) Sanchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill ME, Campos JL (2015) "Two high-mobility group box domains act together to underwind and kink DNA." Acta Crystallogr.,Sect.D, 71, 1423-1432. doi: 10.1107/S1399004715007452. Crystal structure of two hmgb1 box a domains cooperating to underwind and kink a DNA. SNAP output
4qtj transcription-DNA X-ray (2.1 Å) Zhang S, Zhang T, Yan M, Ding J, Chen J (2014) "Crystal structure of the WOPR-DNA complex and implications for Wor1 function in white-opaque switching of Candida albicans." Cell Res., 24, 1108-1120. doi: 10.1038/cr.2014.102. Complex of wopr domain of wor1 in candida albicans with the 13bp dsDNA. SNAP output
4qtk transcription-DNA X-ray (2.99 Å) Zhang S, Zhang T, Yan M, Ding J, Chen J (2014) "Crystal structure of the WOPR-DNA complex and implications for Wor1 function in white-opaque switching of Candida albicans." Cell Res., 24, 1108-1120. doi: 10.1038/cr.2014.102. Complex of wopr domain of wor1 in candida albicans with the 17bp dsDNA. SNAP output
4qtr de novo design-DNA X-ray (3.2 Å) Mou Y, Yu JY, Wannier TM, Guo CL, Mayo SL (2015) "Computational design of co-assembling protein-DNA nanowires." Nature, 525, 230-233. doi: 10.1038/nature14874. Computational design of co-assembling protein-DNA nanowires. SNAP output
4qw8 transferase-DNA X-ray (2.29 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfolobus solfataricus in complex with DNA and d-dctp. SNAP output
4qw9 transferase-DNA X-ray (2.4 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfolobus solfataricus in complex with DNA and (-)ftc-ppnp. SNAP output
4qwa transferase-DNA X-ray (2.2 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfolobus solfataricus in complex with DNA and (-)3tc-dp. SNAP output
4qwb transferase-DNA X-ray (1.8 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Crystal structure of dpo4 linker region p236a mutant with an incoming d-dcdp. SNAP output
4qwc transferase-DNA X-ray (2.4 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfobus solfataricus in comples with DNA and l-dcdp. SNAP output
4qwd transferase-DNA X-ray (2.05 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfolobus solfataricus in complex with DNA and (-)3tc-ppnp. SNAP output
4qwe transferase-DNA X-ray (2.2 Å) Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z (2014) "Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase." Nucleic Acids Res., 42, 9984-9995. doi: 10.1093/nar/gku709. Ternary crystal structures of a y-family DNA polymerase dpo4 from sulfolobus solfataricus in complex with DNA and (-)ftc-dp. SNAP output
4qyz immune system-DNA-RNA X-ray (3.03 Å) Mulepati S, Heroux A, Bailey S (2014) "Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target." Science, 345, 1479-1484. doi: 10.1126/science.1256996. Crystal structure of a crispr RNA-guided surveillance complex, cascade, bound to a ssDNA target. SNAP output
4qz8 transferase-DNA X-ray (2.7 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt in complex with a dsb substrate, c-g base pair. SNAP output
4qz9 transferase-DNA X-ray (2.05 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt in complex with a dsb substrate, c-a base pair. SNAP output
4qza transferase-DNA X-ray (2.15 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt in complex with a dsb substrate, c-c base pair. SNAP output
4qzb transferase-DNA X-ray (2.15 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt in complex with a dsb substrate, c-t base pair. SNAP output
4qzc transferase-DNA X-ray (2.75 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f405a mutant, in complex with a dsb substrate, c-g base pair. SNAP output
4qzd transferase-DNA X-ray (2.7 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f405a mutant, in complex with a dsb substrate, c-c base pair. SNAP output
4qze transferase-DNA X-ray (2.25 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f401a mutant, in complex with a dsb substrate, c-g base pair. SNAP output
4qzf transferase-DNA X-ray (2.6 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f401a mutant, in complex with a dsb substrate, c-a base pair. SNAP output
4qzg transferase-DNA X-ray (2.75 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f401a mutant, in complex with a dsb substrate, c-c base pair. SNAP output
4qzh transferase-DNA X-ray (2.6 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f401a mutant, in complex with a dsb substrate, c-t base pair. SNAP output
4qzi transferase-DNA X-ray (2.65 Å) Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M (2015) "Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair." Embo J., 34, 1126-1142. doi: 10.15252/embj.201489643. Mouse tdt, f401a mutant, in complex with a dsb substrate and zn2+. SNAP output
4r22 transcription-DNA X-ray (2.6 Å) Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T (2015) "Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis." Genes Dev., 29, 451-464. doi: 10.1101/gad.254714.114. Tnra-DNA complex. SNAP output
4r24 transcrption-DNA X-ray (2.25 Å) Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T (2015) "Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis." Genes Dev., 29, 451-464. doi: 10.1101/gad.254714.114. Complete dissection of b. subtilis nitrogen homeostatic circuitry. SNAP output
4r28 hydrolase-DNA X-ray (3.055 Å) Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ, Zheng Y, Wilson GG, Cheng X (2014) "Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix." Nucleic Acids Res., 42, 12092-12101. doi: 10.1093/nar/gku871. Mspji restriction endonuclease in complex with 27-mer oligonucleotide. SNAP output
4r2a DNA binding protein-DNA X-ray (1.591 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Egr1-zif268 zinc fingers in complex with methylated DNA. SNAP output
4r2c DNA binding protein-DNA X-ray (1.89 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Egr1-zif268 zinc fingers in complex with hydroxymethylated DNA. SNAP output
4r2d DNA binding protein-DNA X-ray (2.088 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Egr1-zif268 zinc fingers in complex with formylated DNA. SNAP output
4r2e DNA binding protein-DNA X-ray (1.84 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) zinc fingers in complex with methylated DNA. SNAP output
4r2p DNA binding protein-DNA X-ray (1.788 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) zinc fingers in complex with hydroxymethylated DNA. SNAP output
4r2q DNA binding protein-DNA X-ray (1.54 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) zinc fingers in complex with formylated DNA. SNAP output
4r2r DNA binding protein-DNA X-ray (2.089 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) zinc fingers in complex with carboxylated DNA. SNAP output
4r2s DNA binding protein-DNA X-ray (2.489 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) q369p zinc fingers in complex with methylated DNA. SNAP output
4r4e transcription regulator-DNA X-ray (2.57 Å) Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK, Whitfill T (2015) "Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis." Genes Dev., 29, 451-464. doi: 10.1101/gad.254714.114. Structure of glnr-DNA complex. SNAP output
4r55 DNA binding protein-DNA X-ray (1.8 Å) Zhang ZF, Gong Y, Chen YY, Li HB, Huang L (2015) "Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4." Extremophiles, 19, 395-406. doi: 10.1007/s00792-014-0725-y. The crystal structure of a cren7 mutant protein gr and dsDNA complex. SNAP output
4r56 DNA binding protein-DNA X-ray (2.3 Å) Zhang ZF, Gong Y, Chen YY, Li HB, Huang L (2015) "Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4." Extremophiles, 19, 395-406. doi: 10.1007/s00792-014-0725-y. Crystal structure of sulfolobus cren7-dsDNA(gtgatcac) complex. SNAP output
4r5p transferase, hydrolase-DNA-inhibitor X-ray (2.894 Å) Balzarini J, Das K, Bernatchez JA, Martinez SE, Ngure M, Keane S, Ford A, Maguire N, Mullins N, John J, Kim Y, Dehaen W, Vande Voorde J, Liekens S, Naesens L, Gotte M, Maguire AR, Arnold E (2015) "Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics." Proc.Natl.Acad.Sci.USA, 112, 3475-3480. doi: 10.1073/pnas.1420233112. Crystal structure of hiv-1 reverse transcriptase (rt) with DNA and a nucleoside triphosphate mimic alpha-carboxy nucleoside phosphonate inhibitor. SNAP output
4r63 transferase-DNA X-ray (1.85 Å) Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH (2014) "Substrate-induced DNA Polymerase beta Activation." J.Biol.Chem., 289, 31411-31422. doi: 10.1074/jbc.M114.607432. Binary complex crystal structure of r258a mutant of DNA polymerase beta. SNAP output
4r64 transferase-DNA X-ray (2.2 Å) Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH (2014) "Substrate-induced DNA Polymerase beta Activation." J.Biol.Chem., 289, 31411-31422. doi: 10.1074/jbc.M114.607432. Binary complex crystal structure of e295k mutant of DNA polymerase beta. SNAP output
4r65 transferase-DNA X-ray (1.95 Å) Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH (2014) "Substrate-induced DNA Polymerase beta Activation." J.Biol.Chem., 289, 31411-31422. doi: 10.1074/jbc.M114.607432. Ternary complex crystal structure of r258a mutant of DNA polymerase beta. SNAP output
4r66 transferase-DNA X-ray (2.25 Å) Beard WA, Shock DD, Batra VK, Prasad R, Wilson SH (2014) "Substrate-induced DNA Polymerase beta Activation." J.Biol.Chem., 289, 31411-31422. doi: 10.1074/jbc.M114.607432. Ternary complex crystal structure of e295k mutant of DNA polymerase beta. SNAP output
4r79 recombination-DNA X-ray (3.1 Å) Trubitsyna M, Grey H, Houston DR, Finnegan DJ, Richardson JM (2015) "Structural Basis for the Inverted Repeat Preferences of mariner Transposases." J.Biol.Chem., 290, 13531-13540. doi: 10.1074/jbc.M115.636704. Mos1 transposase paired-end complex with left transposon end. SNAP output
4r89 hydrolase-DNA X-ray (4.002 Å) Gwon GH, Kim YR, Liu Y, Watson AT, Jo A, Etheridge TJ, Yuan F, Zhang Y, Kim YC, Carr AM, Cho Y (2014) "Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1." Genes Dev., 28, 2276-2290. doi: 10.1101/gad.248492.114. Crystal structure of pafan1 - 5' flap DNA complex with manganase. SNAP output
4r8a hydrolase-DNA X-ray (3.2 Å) Gwon GH, Kim YR, Liu Y, Watson AT, Jo A, Etheridge TJ, Yuan F, Zhang Y, Kim YC, Carr AM, Cho Y (2014) "Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1." Genes Dev., 28, 2276-2290. doi: 10.1101/gad.248492.114. Crystal structure of pafan1 - 5' flap DNA complex. SNAP output
4r8p structural protein-DNA X-ray (3.28 Å) McGinty RK, Henrici RC, Tan S (2014) "Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome." Nature, 514, 591-596. doi: 10.1038/nature13890. Crystal structure of the ring1b-bmi1-ubch5c prc1 ubiquitylation module bound to the nucleosome core particle. SNAP output
4r8u transferase-DNA X-ray (2.3 Å) Weinert T, Olieric V, Waltersperger S, Panepucci E, Chen L, Zhang H, Zhou D, Rose J, Ebihara A, Kuramitsu S, Li D, Howe N, Schnapp G, Pautsch A, Bargsten K, Prota AE, Surana P, Kottur J, Nair DT, Basilico F, Cecatiello V, Pasqualato S, Boland A, Weichenrieder O, Wang BC, Steinmetz MO, Caffrey M, Wang M (2015) "Fast native-SAD phasing for routine macromolecular structure determination." Nat.Methods, 12, 131-133. doi: 10.1038/nmeth.3211. S-sad structure of dinb-DNA complex. SNAP output
4rb1 metal binding protein-DNA X-ray (2.75 Å) Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP, Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi X, Li X, Wu W, Rohs R, Li Y, Chen Z "Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator." Nat Commun, 6, 7642. doi: 10.1038/ncomms8642. Crystal structure of magnetospirillum gryphiswaldense msr-1 fur-mn2+-e. coli fur box. SNAP output
4rb2 metal binding protein-DNA X-ray (2.82 Å) Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP, Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi X, Li X, Wu W, Rohs R, Li Y, Chen Z "Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator." Nat Commun, 6, 7642. doi: 10.1038/ncomms8642. Crystal structure of magnetospirillum gryphiswaldense msr-1 semet-fur-mn2+-feoab1 operator. SNAP output
4rb3 metal binding protein-DNA X-ray (2.6 Å) Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP, Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi X, Li X, Wu W, Rohs R, Li Y, Chen Z "Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator." Nat Commun, 6, 7642. doi: 10.1038/ncomms8642. Crystal structure of magnetospirillum gryphiswaldense msr-1 fur-mn2+-feoab1 operator. SNAP output
4rbo DNA binding protein, transcription-DNA X-ray (3.3 Å) Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ (2015) "Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells." Proc.Natl.Acad.Sci.USA, 112, 4666-4671. doi: 10.1073/pnas.1502855112. Crystal structure of a nanog homeobox (nanog) from homo sapiens at 3.30 Å resolution. SNAP output
4rd5 hydrolase-DNA X-ray (2.7 Å) Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V (2014) "Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII." Nucleic Acids Res., 42, 14022-14030. doi: 10.1093/nar/gku1237. Crystal structure of r.ngoavii restriction endonuclease b3 domain with cognate DNA. SNAP output
4rdm hydrolase-DNA X-ray (2.7 Å) Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V (2014) "Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII." Nucleic Acids Res., 42, 14022-14030. doi: 10.1093/nar/gku1237. Crystal structure of r.ngoavii restriction endonuclease b3 domain with cognate DNA. SNAP output
4rdu transcription-DNA X-ray (1.85 Å) Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL) "Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution." Crystal structure of a distal-less homeobox protein 5 (dlx5) from homo sapiens at 1.85 Å resolution. SNAP output
4rea hydrolase-DNA X-ray (3.81 Å) Zhao Q, Xue X, Longerich S, Sung P, Xiong Y (2014) "Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer." Nat Commun, 5, 5726. doi: 10.1038/ncomms6726. A nuclease DNA complex. SNAP output
4reb hydrolase-DNA X-ray (4.2 Å) Zhao Q, Xue X, Longerich S, Sung P, Xiong Y (2014) "Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer." Nat Commun, 5, 5726. doi: 10.1038/ncomms6726. Structural insights into 5' flap DNA unwinding and incision by the human fan1 dimer. SNAP output
4rec hydrolase-DNA X-ray (2.2 Å) Zhao Q, Xue X, Longerich S, Sung P, Xiong Y (2014) "Structural insights into 5' flap DNA unwinding and incision by the human FAN1 dimer." Nat Commun, 5, 5726. doi: 10.1038/ncomms6726. A nuclease-DNA complex form 3. SNAP output
4ri8 hydrolase-DNA X-ray (2.9 Å) Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska A, Elledge SJ, Pavletich NP (2014) "DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1." Science, 346, 1127-1130. doi: 10.1126/science.1258973. Fan1 nuclease bound to 5' phosphorylated p(dg)-3'(dt-dt-dt-dt) double flap DNA. SNAP output
4ri9 hydrolase-DNA X-ray (2.9 Å) Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska A, Elledge SJ, Pavletich NP (2014) "DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1." Science, 346, 1127-1130. doi: 10.1126/science.1258973. Fan1 nuclease bound to 5' phosphorylated p(dt)-3'(dt-dt-dt-dt-dt-dt-dt-dt) double flap DNA. SNAP output
4ria hydrolase-DNA X-ray (3.0 Å) Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska A, Elledge SJ, Pavletich NP (2014) "DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1." Science, 346, 1127-1130. doi: 10.1126/science.1258973. Fan1 nuclease bound to 5' phosphorylated nicked DNA. SNAP output
4rib hydrolase-DNA X-ray (3.25 Å) Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska A, Elledge SJ, Pavletich NP (2014) "DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1." Science, 346, 1127-1130. doi: 10.1126/science.1258973. Fan1 nuclease bound to 5' phosphorylated p(dt) single flap DNA. SNAP output
4ric hydrolase-DNA X-ray (2.8 Å) Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska A, Elledge SJ, Pavletich NP (2014) "DNA repair. Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1." Science, 346, 1127-1130. doi: 10.1126/science.1258973. Fan1 nuclease bound to 5' hydroxyl (dt-dt) single flap DNA. SNAP output
4rkg DNA binding protein-DNA X-ray (2.5 Å) Zheng S, Villa R, Wang J, Feng Y, Wang J, Becker PB, Ye K (2014) "Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation." Genes Dev., 28, 2652-2662. doi: 10.1101/gad.250936.114. Structure of the msl2 cxc domain bound with a non-specific (gc)6 DNA. SNAP output
4rkh DNA binding protein-DNA X-ray (2.0 Å) Zheng S, Villa R, Wang J, Feng Y, Wang J, Becker PB, Ye K (2014) "Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation." Genes Dev., 28, 2652-2662. doi: 10.1101/gad.250936.114. Structure of the msl2 cxc domain bound with a specific mre sequence. SNAP output
4rnm transferase-DNA X-ray (2.144 Å) Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich FP (2015) "Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase eta." J.Biol.Chem., 290, 8028-8038. doi: 10.1074/jbc.M115.637561. Crystal structure of human polymerase eta inserting dampnpp opposite DNA template containing an abasic site. SNAP output
4rnn transferase-DNA X-ray (1.808 Å) Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich FP (2015) "Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase eta." J.Biol.Chem., 290, 8028-8038. doi: 10.1074/jbc.M115.637561. Crystal structure of human polymerase eta inserting dgmpnpp opposite DNA template containing an abasic site. SNAP output
4rno transferase-DNA X-ray (2.82 Å) Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich FP (2015) "Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase eta." J.Biol.Chem., 290, 8028-8038. doi: 10.1074/jbc.M115.637561. Crystal structure of human polymerase eta extending an abasic site-da pair by inserting dctp opposite template g. SNAP output
4roc transcription X-ray (1.9 Å) Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ, Cousin P, Dergai O, Hernandez N, Vannini A (2015) "Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2." Cell(Cambridge,Mass.), 163, 1375-1387. doi: 10.1016/j.cell.2015.11.005. Human tfiib-related factor 2 (brf2) and tbp bound to u6#2 promoter. SNAP output
4rod transcription X-ray (2.7 Å) Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ, Cousin P, Dergai O, Hernandez N, Vannini A (2015) "Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2." Cell(Cambridge,Mass.), 163, 1375-1387. doi: 10.1016/j.cell.2015.11.005. Human tfiib-related factor 2 (brf2) and tbp bound to trnau1 promoter. SNAP output
4roe transcription X-ray (2.2 Å) Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ, Cousin P, Dergai O, Hernandez N, Vannini A (2015) "Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2." Cell(Cambridge,Mass.), 163, 1375-1387. doi: 10.1016/j.cell.2015.11.005. Human tfiib-related factor 2 (brf2) and tbp bound to rpph1 promoter. SNAP output
4rpx transferase-DNA X-ray (1.9 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Precatalytic ternary complex of human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog) and dctp in the presence of cacl2. SNAP output
4rpy transferase-DNA X-ray (1.9 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine(8-oxog) and dctp soaked with mgcl2 for 30 s. SNAP output
4rpz transferase-DNA X-ray (2.19 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog)and dctp soaked with mgcl2 for 60 s. SNAP output
4rq0 transferase-DNA X-ray (2.2 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog)and dctp soaked with mgcl2 for 80 s. SNAP output
4rq1 transferase-DNA X-ray (2.7 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine(8-oxog) and dctp soaked with mgcl2 for 1hr. SNAP output
4rq2 transferase-DNA X-ray (2.2 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog)and dctp soaked with mncl2 for 35 s. SNAP output
4rq3 transferase-DNA X-ray (2.0 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Precatalytic ternary complex of human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog) and datp in the presence of cacl2. SNAP output
4rq4 transferase-DNA X-ray (2.1 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine(8-oxog) and datp soaked with mgcl2 for 30 s. SNAP output
4rq5 transferase-DNA X-ray (2.32 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog)and datp soaked with mgcl2 for 60 s. SNAP output
4rq6 transferase-DNA X-ray (2.25 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine(8-oxog) and datp soaked with mgcl2 for 80 s. SNAP output
4rq7 transferase-DNA X-ray (2.0 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine (8-oxog)and datp soaked with mgcl2 for 1hr. SNAP output
4rq8 transferase-DNA X-ray (2.0 Å) Vyas R, Reed AJ, Tokarsky EJ, Suo Z (2015) "Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography." J.Am.Chem.Soc., 137, 5225-5230. doi: 10.1021/jacs.5b02109. Human DNA polymerase beta with gapped DNA containing an 8-oxo-7,8-dihydro-guanine(8-oxog) and datp soaked with mncl2 for 35 s. SNAP output
4rt2 transferase-DNA X-ray (1.92 Å) Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE (2015) "Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP." Org.Lett., 17, 2586-2589. doi: 10.1021/acs.orglett.5b00799. Ternary complex crystal structure of DNA polymerase beta with (alpha,beta)-ch2-(beta,gamma)-nh-dttp. SNAP output
4rt3 transferase-DNA X-ray (1.92 Å) Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE (2015) "Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP." Org.Lett., 17, 2586-2589. doi: 10.1021/acs.orglett.5b00799. Ternary complex crystal structure of DNA polymerase beta with (alpha, beta)-nh-(beta,gamma)-ch2-dttp. SNAP output
4rtj transferase-DNA X-ray (1.99 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. A non-cognate complex of escherichia coli DNA adenine methyltransferase (dam) with DNA and sinefungin. SNAP output
4rtk transferase-DNA X-ray (1.96 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with sah and with DNA containing distal pap regulon sequence. SNAP output
4rtl transferase-DNA X-ray (2.193 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with sinefungin and with DNA containing distal pap regulon sequence. SNAP output
4rtm transferase-DNA X-ray (2.5 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with adomet and with DNA containing distal pap regulon sequence. SNAP output
4rtn transferase-DNA X-ray (2.59 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with adohcy and with DNA containing proximal pap regulon sequence. SNAP output
4rto transferase-DNA X-ray (2.69 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with sinefungin and with DNA containing proximal pap regulon sequence. SNAP output
4rtp transferase-DNA X-ray (2.39 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with adomet and with DNA containing proximal pap regulon sequence. SNAP output
4rtq transferase-DNA X-ray (1.997 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with adohcy and a 5-bp non-canonical site (gttta ). SNAP output
4rtr transferase-DNA X-ray (2.393 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with adomet and a 5-bp non-canonical site (gttta ). SNAP output
4rts transferase-DNA X-ray (2.49 Å) Horton JR, Zhang X, Blumenthal RM, Cheng X (2015) "Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression." Nucleic Acids Res., 43, 4296-4308. doi: 10.1093/nar/gkv251. Complex of escherichia coli DNA adenine methyltransferase (dam) with adomet and a 5-bp non-canonical site (gtcta). SNAP output
4ru9 transferase-DNA X-ray (2.65 Å) Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M (2015) "Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV." J.Am.Chem.Soc., 137, 7011-7014. doi: 10.1021/jacs.5b02701. Crystal structure of human DNA polymerase eta inserting dcmpnpp opposite a mefapy-dg adducted DNA template. SNAP output
4rua transferase-DNA X-ray (3.07 Å) Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M (2015) "Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV." J.Am.Chem.Soc., 137, 7011-7014. doi: 10.1021/jacs.5b02701. Crystal structure of y-family DNA polymerase dpo4 bypassing a mefapy-dg adduct. SNAP output
4ruc transferase-DNA X-ray (2.9 Å) Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M (2015) "Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase eta and Sulfolobus solfataricus P2 Polymerase IV." J.Am.Chem.Soc., 137, 7011-7014. doi: 10.1021/jacs.5b02701. Crystal structure of y-family DNA polymerase dpo4 extending from a mefapy-dg:dc pair. SNAP output
4rul isomerase-DNA X-ray (2.9 Å) Tan K, Zhou Q, Cheng B, Zhang Z, Joachimiak A, Tse-Dinh YC (2015) "Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I." Nucleic Acids Res., 43, 11031-11046. doi: 10.1093/nar/gkv1073. Crystal structure of full-length e.coli topoisomerase i in complex with ssDNA. SNAP output
4rve hydrolase-DNA X-ray (3.0 Å) Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS (1993) "The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments." EMBO J., 12, 1781-1795. The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA segments. SNAP output
4rzr transferase-DNA X-ray (2.2 Å) Vyas R, Efthimiopoulos G, Tokarsky EJ, Malik CK, Basu AK, Suo Z (2015) "Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase." J.Am.Chem.Soc., 137, 12131-12142. doi: 10.1021/jacs.5b08027. Bypass of a bulky adduct dg1,8 by dpo4. SNAP output
4s04 transcription-DNA X-ray (3.2 Å) Lou YC, Weng TH, Li YC, Kao YF, Lin WF, Peng HL, Chou SH, Hsiao CD, Chen C (2015) "Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA." Nat Commun, 6, 8838. doi: 10.1038/ncomms9838. Crystal structure of klebsiella pneumoniae pmra in complex with pmra box DNA. SNAP output
4s05 transcription-DNA X-ray (3.8 Å) Lou YC, Weng TH, Li YC, Kao YF, Lin WF, Peng HL, Chou SH, Hsiao CD, Chen C (2015) "Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA." Nat Commun, 6, 8838. doi: 10.1038/ncomms9838. Crystal structure of klebsiella pneumoniae pmra in complex with pmra box DNA. SNAP output
4s0h transcription-DNA X-ray (2.817 Å) Pradhan L, Gopal S, Li S, Ashur S, Suryanarayanan S, Kasahara H, Nam HJ (2016) "Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5." Biochemistry, 55, 1702-1710. doi: 10.1021/acs.biochem.6b00171. Tbx5 db, nkx2.5 hd, anf DNA complex. SNAP output
4s0n DNA binding protein-DNA X-ray (1.501 Å) Kile AC, Chavez DA, Bacal J, Eldirany S, Korzhnev DM, Bezsonova I, Eichman BF, Cimprich KA (2015) "HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal." Mol.Cell, 58, 1090-1100. doi: 10.1016/j.molcel.2015.05.013. Crystal structure of hltf hiran domain bound to DNA. SNAP output
4s20 transferase-DNA-RNA X-ray (4.7 Å) Liu B, Zuo Y, Steitz TA (2015) "Structural basis for transcription reactivation by RapA." Proc.Natl.Acad.Sci.USA, 112, 2006-2010. doi: 10.1073/pnas.1417152112. Structural basis for transcription reactivation by rapa. SNAP output
4s2q DNA binding protein-DNA X-ray (2.7 Å) Vivekanandan S, Moovarkumudalvan B, Lescar J, Kolatkar PR "Crystal Structure of HMG domain of the chondrogenesis master regulator, Sox9 in complex with ChIP-Seq identified DNA element." Crystal structure of hmg domain of the chondrogenesis master regulator, sox9 in complex with chip-seq identified DNA element. SNAP output
4skn hydrolase-DNA X-ray (2.9 Å) Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA (1996) "A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA." Nature, 384, 87-92. doi: 10.1038/384087a0. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. SNAP output
4tmu hydrolase-DNA X-ray (2.4 Å) Manthei KA, Hill MC, Burke JE, Butcher SE, Keck JL (2015) "Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases." Proc.Natl.Acad.Sci.USA, 112, 4292-4297. doi: 10.1073/pnas.1416746112. Crystal structure of recq catalytic core from c. sakazakii bound to DNA. SNAP output
4tnt DNA binding protein-DNA X-ray (2.39 Å) Hudson WH, Youn C, Ortlund EA (2014) "Crystal structure of the mineralocorticoid receptor DNA binding domain in complex with DNA." Plos One, 9, e107000. doi: 10.1371/journal.pone.0107000. Structure of the human mineralocorticoid receptor in complex with DNA. SNAP output
4tqr transferase-DNA X-ray (1.58 Å) Xu W, Ouellette AM, Wawrzak Z, Shriver SJ, Anderson SM, Zhao L (2015) "Kinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA Replication Stalling." Biochemistry, 54, 639-651. doi: 10.1021/bi5014936. Ternary complex of y-family DNA polymerase dpo4 with (5's)-8,5'-cyclo-2'-deoxyguanosine and dttp. SNAP output
4tqs transferase-DNA X-ray (2.06 Å) Xu W, Ouellette AM, Wawrzak Z, Shriver SJ, Anderson SM, Zhao L (2015) "Kinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA Replication Stalling." Biochemistry, 54, 639-651. doi: 10.1021/bi5014936. Ternary complex of y-family DNA polymerase dpo4 with (5's)-8,5'-cyclo-2'-deoxyguanosine and dctp. SNAP output
4tu7 RNA binding protein-DNA X-ray (2.087 Å) Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf CL (2014) "Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA." Proc.Natl.Acad.Sci.USA, 111, 17420-17425. doi: 10.1073/pnas.1412743111. Structure of u2af65 d231v variant with bru5 DNA. SNAP output
4tu8 RNA binding protein-DNA X-ray (1.918 Å) Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf CL (2014) "Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA." Proc.Natl.Acad.Sci.USA, 111, 17420-17425. doi: 10.1073/pnas.1412743111. Structure of u2af65 variant with bru5a6 DNA. SNAP output
4tu9 RNA binding protein-DNA X-ray (1.992 Å) Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf CL (2014) "Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA." Proc.Natl.Acad.Sci.USA, 111, 17420-17425. doi: 10.1073/pnas.1412743111. Structure of u2af65 variant with bru5g6 DNA. SNAP output
4tug DNA binding protein-DNA X-ray (3.55 Å) Sung S, Li F, Park YB, Kim JS, Kim AK, Song OK, Kim J, Che J, Lee SE, Cho Y (2014) "DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA." Embo J., 33, 2422-2435. doi: 10.15252/embj.201488299. Crystal structure of mjmre11-dna2 complex. SNAP output
4tui DNA binding protein-DNA X-ray (3.59 Å) Sung S, Li F, Park YB, Kim JS, Kim AK, Song OK, Kim J, Che J, Lee SE, Cho Y (2014) "DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA." Embo J., 33, 2422-2435. doi: 10.15252/embj.201488299. Crystal structure of mjmre11-dna1 complex. SNAP output
4tup transferase,lyase-DNA X-ray (1.8 Å) Koag MC, Lai L, Lee S (2014) "Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta." J.Biol.Chem., 289, 31341-31348. doi: 10.1074/jbc.M114.605451. Structure of human DNA polymerase beta complexed with gg as the template (gg0b) in a 1-nucleotide gapped DNA. SNAP output
4tuq transferase,lyase-DNA X-ray (2.367 Å) Koag MC, Lai L, Lee S (2014) "Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta." J.Biol.Chem., 289, 31341-31348. doi: 10.1074/jbc.M114.605451. Human DNA polymerase beta inserting dcmpnpp opposite gg template (gg0b).. SNAP output
4tur transferase,lyase-DNA X-ray (2.169 Å) Koag MC, Lai L, Lee S (2014) "Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta." J.Biol.Chem., 289, 31341-31348. doi: 10.1074/jbc.M114.605451. Human DNA polymerase beta inserting dcmpnpp opposite the 5'g of cisplatin crosslinked gs (pt-gg2). SNAP output
4tus transferase,lyase-DNA X-ray (2.42 Å) Koag MC, Lai L, Lee S (2014) "Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta." J.Biol.Chem., 289, 31341-31348. doi: 10.1074/jbc.M114.605451. Human DNA polymerase beta inserting dcmpnpp opposite the 5'g of cisplatin crosslinked gs (pt-gg2) with manganese in the active site.. SNAP output
4tyn hydrolase-DNA X-ray (2.959 Å) Mallam AL, Sidote DJ, Lambowitz AM (2014) "Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase." Elife, 3, e04630. doi: 10.7554/eLife.04630. Dead-box helicase mss116 bound to ssDNA and adp-bef. SNAP output
4tzd carbohydrate binding protein-DNA X-ray (3.2 Å) Vieira DBHA, Delatorre P, Cavada BS, Nobrega RB, Teixeira CS, Silva-Filho JC, Lima EM, Rocha BAM "Crystal structure of Canavalia maritima lectin (ConM) complexed with interleukin 1 - beta primer." Crystal structure of canavalia maritima lectin (conm) complexed with interleukin - 1 beta primer. SNAP output
4u0y transcription X-ray (1.91 Å) Fillenberg SB, Grau FC, Seidel G, Muller YA (2015) "Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR." Nucleic Acids Res., 43, 1283-1296. doi: 10.1093/nar/gku1374. Crystal structure of the DNA-binding domains of yvoa in complex with palindromic operator DNA. SNAP output
4u6p transferase-DNA X-ray (2.593 Å) Jha V, Bian C, Xing G, Ling H (2016) "Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa." Nucleic Acids Res., 44, 4957-4967. doi: 10.1093/nar/gkw204. Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human polymerase kappa. SNAP output
4u7b hydrolase-DNA X-ray (3.09 Å) Dornan J, Grey H, Richardson JM (2015) "Structural role of the flanking DNA in mariner transposon excision." Nucleic Acids Res., 43, 2424-2432. doi: 10.1093/nar/gkv096. Crystal structure of a pre-cleavage mos1 transpososome. SNAP output
4u7c transferase-DNA X-ray (2.8 Å) Jha V, Bian C, Xing G, Ling H (2016) "Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa." Nucleic Acids Res., 44, 4957-4967. doi: 10.1093/nar/gkw204. Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA. SNAP output
4u7d hydrolase-DNA X-ray (3.4 Å) Pike AC, Gomathinayagam S, Swuec P, Berti M, Zhang Y, Schnecke C, Marino F, von Delft F, Renault L, Costa A, Gileadi O, Vindigni A (2015) "Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures." Proc.Natl.Acad.Sci.USA, 112, 4286-4291. doi: 10.1073/pnas.1417594112. Structure of human recq-like helicase in complex with an oligonucleotide. SNAP output
4uaw transferase, lyase-DNA X-ray (1.9 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta substrate complex with a templating adenine and incoming 8-oxodgtp, 0 s. SNAP output
4uay transferase, lyase-DNA X-ray (1.984 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta product complex with a templating adenine and inserted 8-oxodgmp, 40 s. SNAP output
4uaz transferase, lyase-DNA X-ray (1.88 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta reactant complex with a templating adenine and incoming 8-oxodgtp, 20 s. SNAP output
4ub1 transferase, lyase-DNA X-ray (2.341 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta product complex with a templating adenine and 8-oxodgmp, 90 s. SNAP output
4ub2 transferase, lyase-DNA X-ray (2.51 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta product complex with a templating cytosine and 8-oxodgmp, 120 s. SNAP output
4ub3 transferase, lyase-DNA X-ray (2.06 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta closed product complex with a templating cytosine and 8-oxodgmp, 60 s. SNAP output
4ub4 transferase, lyase-DNA X-ray (1.954 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta substrate complex with a templating cytosine and incoming dgtp, 0 s. SNAP output
4ub5 transferase, lyase-DNA X-ray (2.15 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta substrate complex with a templating cytosine, incoming 8-oxodgtp, and mn2+, 5 s. SNAP output
4ubb transferase, lyase-DNA X-ray (1.9 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta reactant complex with a templating cytosine and incoming 8-oxodgtp, 40 s. SNAP output
4ubc transferase, lyase-DNA X-ray (2.0 Å) Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T, Schlick T, Wilson SH (2015) "Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide." Nature, 517, 635-639. doi: 10.1038/nature13886. DNA polymerase beta substrate complex with a templating cytosine and incoming 8-oxodgtp, 0 s. SNAP output
4umk DNA binding protein-DNA X-ray (3.096 Å) Chen BW, Lin MH, Chu CH, Hsu CE, Sun YJ (2015) "Insights into ParB spreading from the complex structure of Spo0J and parS." Proc. Natl. Acad. Sci. U.S.A., 112, 6613-6618. doi: 10.1073/pnas.1421927112. The complex of spo0j and pars DNA in chromosomal partition system. SNAP output
4umm nuclear receptor cryo-EM (11.6 Å) Maletta M, Orlov I, Moras D, Billas IML, Klaholz BP (2014) "The Palindromic DNA-Bound Usp-Ecr Nuclear Receptor Adopts an Asymmetric Organization with Allosteric Domain Positioning." Nat.Commun., 5, 4139. doi: 10.1038/NCOMMS5139. The cryo-EM structure of the palindromic DNA-bound usp-ecr nuclear receptor reveals an asymmetric organization with allosteric domain positioning. SNAP output
4un3 hydrolase-DNA-RNA X-ray (2.593 Å) Anders C, Niewoehner O, Duerst A, Jinek M (2014) "Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease." Nature, 513, 569. doi: 10.1038/NATURE13579. Crystal structure of cas9 bound to pam-containing DNA target. SNAP output
4un4 hydrolase-DNA-RNA X-ray (2.371 Å) Anders C, Niewoehner O, Duerst A, Jinek M (2014) "Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease." Nature, 513, 569. doi: 10.1038/NATURE13579. Crystal structure of cas9 bound to pam-containing DNA target with mismatches at positions 1-2. SNAP output
4un5 hydrolase-DNA-RNA X-ray (2.4 Å) Anders C, Niewoehner O, Duerst A, Jinek M (2014) "Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease." Nature, 513, 569. doi: 10.1038/NATURE13579. Crystal structure of cas9 bound to pam-containing DNA target containing mismatches at positions 1-3. SNAP output
4un7 hydrolase-DNA X-ray (2.7 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA before incubation in 5mm mn (state 1). SNAP output
4un8 hydrolase-DNA X-ray (2.6 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 1h incubation in 5mm mn (state 2). SNAP output
4un9 hydrolase-DNA X-ray (2.734 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 8h incubation in 5mm mn (state 3). SNAP output
4una hydrolase-DNA X-ray (2.3 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 2 days incubation in 5mm mn (state 4). SNAP output
4unb hydrolase-DNA X-ray (2.55 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 6 days incubation in 5mm mn (state 5). SNAP output
4unc hydrolase-DNA X-ray (2.3 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 8 days incubation in 5mm mn (state 6). SNAP output
4uno DNA binding protein X-ray (1.95 Å) Cooper CDO, Newman JA, Aitkenhead H, Allerston CK, Gileadi O (2015) "Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation." J.Biol.Chem., 290, 13692. doi: 10.1074/JBC.M115.646737. Crystal structure of the ets domain of human etv5 in complex with DNA. SNAP output
4uqg transferase-DNA X-ray (2.0 Å) Tomas-Gamasa M, Serdjukow S, Su M, Muller M, Carell T (2015) ""Post-it" type connected DNA created with a reversible covalent cross-link." Angew. Chem. Int. Ed. Engl., 54, 796-800. doi: 10.1002/anie.201407854. A new bio-isosteric base pair based on reversible bonding. SNAP output
4uqm hydrolase-DNA X-ray (1.35 Å) Pedersen HL, Johnson KA, McVey CE, Leiros I, Moe E (2015) "Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA." Acta Crystallogr. D Biol. Crystallogr., 71, 2137-2149. doi: 10.1107/S1399004715014157. Crystal structure determination of uracil-DNA n-glycosylase (ung) from deinococcus radiodurans in complex with DNA - new insights into the role of the leucine-loop for damage recognition and repair. SNAP output
4usg transcription X-ray (1.973 Å) Huang J, Zhao Y, Liu H, Huang D, Cheng X, Zhao W, Taylor IA, Liu J, Peng YL (2015) "Substitution of Tryptophan 89 with Tyrosine Switches the DNA Binding Mode of Pc4." Sci.Rep., 5, 8789. doi: 10.1038/SREP08789. Crystal structure of pc4 w89y mutant complex with DNA. SNAP output
4ut0 hydrolase-DNA X-ray (2.4 Å) Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015) "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932. The crystal structure of i-dmoi in complex with its target DNA at 10 days incubation in 5mm mn (state 7). SNAP output
4uus transcription X-ray (2.55 Å) Foos N, Maurel-Zaffran C, Mate MJ, Vincentelli R, Hainaut M, Berenger H, Pradel J, Saurin AJ, Ortiz-Lombardia M, Graba Y (2015) "A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode." Structure, 23, 270. doi: 10.1016/J.STR.2014.12.011. Crystal structure of a ubx-exd-DNA complex including the ubda motif. SNAP output
4uuv transcription X-ray (2.8 Å) Cooper CDO, Newman JA, Aitkenhead H, Allerston CK, Gileadi O (2015) "Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation." J.Biol.Chem., 290, 13692. doi: 10.1074/JBC.M115.646737. Structure of the DNA binding ets domain of human etv4 in complex with DNA. SNAP output
4ux5 transcription X-ray (2.4 Å) Liu J, Huang J, Zhao Y, Liu H, Wang D, Yang J, Zhao W, Taylor IA, Peng Y (2015) "Structural Basis of DNA Recognition by Pcg2 Reveals a Novel DNA Binding Mode for Winged Helix-Turn-Helix Domains." Nucleic Acids Res., 43, 1231. doi: 10.1093/NAR/GKU1351. Structure of DNA complex of pcg2. SNAP output
4uzb viral protein-DNA X-ray (2.865 Å) Hellert J, Weidner-Glunde M, Krausze J, Lunsdorf H, Ritter C, Schulz TF, Luhrs T (2015) "The 3D Structure of Kaposi Sarcoma Herpesvirus Lana C-Terminal Domain Bound to DNA." Proc.Natl.Acad.Sci.USA, 112, 6694. doi: 10.1073/PNAS.1421804112. Kshv lana (orf73) c-terminal domain mutant bound to lbs1 DNA (r1039q, r1040q, k1055e, k1109a, d1110a, a1121e, k1138s, k1140d, k1141d). SNAP output
4v1m transcription cryo-EM (6.6 Å) Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P (2015) "Architecture of the RNA Polymerase II-Mediator Core Initiation Complex." Nature, 518, 376. doi: 10.1038/NATURE14229. Architecture of the RNA polymerase ii-mediator core transcription initiation complex. SNAP output
4v1n transcription cryo-EM (7.8 Å) Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P (2015) "Architecture of the RNA Polymerase II-Mediator Core Initiation Complex." Nature, 518, 376. doi: 10.1038/NATURE14229. Architecture of the RNA polymerase ii-mediator core transcription initiation complex. SNAP output
4v1o transcription cryo-EM (9.7 Å) Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P (2015) "Architecture of the RNA Polymerase II-Mediator Core Initiation Complex." Nature, 518, 376. doi: 10.1038/NATURE14229. Architecture of the RNA polymerase ii-mediator core transcription initiation complex. SNAP output
4w9m hydrolase X-ray (2.7 Å) Rojowska A, Lammens K, Seifert FU, Direnberger C, Feldmann H, Hopfner KP (2014) "Structure of the Rad50 DNA double-strand break repair protein in complex with DNA." Embo J., 33, 2847-2859. doi: 10.15252/embj.201488889. Amppnp bound rad50 in complex with dsDNA. SNAP output
4wal protein binding-RNA X-ray (2.2 Å) Jacewicz A, Chico L, Smith P, Schwer B, Shuman S (2015) "Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs." Rna, 21, 401-414. doi: 10.1261/rna.048942.114. Crystal structure of selenomethionine msl5 protein in complex with RNA at 2.2 a. SNAP output
4wan protein binding-RNA X-ray (1.8 Å) Jacewicz A, Chico L, Smith P, Schwer B, Shuman S (2015) "Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs." Rna, 21, 401-414. doi: 10.1261/rna.048942.114. Crystal structure of msl5 protein in complex with RNA at 1.8 a. SNAP output
4wb2 DNA-RNA hybrid X-ray (1.8 Å) Yatime L, Maasch C, Hoehlig K, Klussmann S, Andersen GR, Vater A (2015) "Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer." Nat Commun, 6, 6481. doi: 10.1038/ncomms7481. Crystal structure of the mirror-image l-RNA-l-DNA aptamer nox-d20 in complex with mouse c5a complement anaphylatoxin. SNAP output
4wb3 DNA-RNA hybrid X-ray (2.0 Å) Yatime L, Maasch C, Hoehlig K, Klussmann S, Andersen GR, Vater A (2015) "Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer." Nat Commun, 6, 6481. doi: 10.1038/ncomms7481. Crystal structure of the mirror-image l-RNA-l-DNA aptamer nox-d20 in complex with mouse c5a-desarg complement anaphylatoxin. SNAP output
4wcg DNA binding protein X-ray (1.5 Å) Kus K, Rakus K, Boutier M, Tsigkri T, Gabriel L, Vanderplasschen A, Athanasiadis A (2015) "The Structure of the Cyprinid herpesvirus 3 ORF112-Z alpha Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response." J.Biol.Chem., 290, 30713-30725. doi: 10.1074/jbc.M115.679407. The binding mode of cyprinid herpesvirus3 orf112-zalpha to z-DNA. SNAP output
4wk8 transcription-DNA X-ray (3.4 Å) Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen L (2015) "DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions." Nucleic Acids Res., 43, 1268-1282. doi: 10.1093/nar/gku1373. Foxp3 forms a domain-swapped dimer to bridge DNA. SNAP output
4wkr RNA binding protein X-ray (3.2 Å) Uchikawa E, Natchiar KS, Han X, Proux F, Roblin P, Zhang E, Durand A, Klaholz BP, Dock-Bregeon AC (2015) "Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7." Nucleic Acids Res., 43, 3373-3388. doi: 10.1093/nar/gkv173. Larp7 wrapping up the 3' hairpin of 7sk non-coding RNA (302-332). SNAP output
4wls transcription regulator-DNA X-ray (2.105 Å) Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz GC, Mondragon A, O'Halloran TV (2015) "Allosteric transcriptional regulation via changes in the overall topology of the core promoter." Science, 349, 877-881. doi: 10.1126/science.aaa9809. Crystal structure of the metal-free (repressor) form of e. coli cuer, a copper efflux regulator, bound to copa promoter DNA. SNAP output
4wlw transcription-DNA X-ray (2.8 Å) Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz GC, Mondragon A, O'Halloran TV (2015) "TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter." Science, 349, 877-881. doi: 10.1126/science.aaa9809. Crystal structure of the ag(i) (activator) form of e. coli cuer, a copper efflux regulator, bound to copa promoter DNA. SNAP output
4wqs transferase-DNA-RNA X-ray (4.306 Å) Sekine SI, Murayama Y, Svetlov V, Nudler E, Yokoyama S (2015) "The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions." Mol.Cell, 57, 408-421. doi: 10.1016/j.molcel.2014.12.014. Thermus thermophilus RNA polymerase backtracked complex. SNAP output
4wtg transferase-RNA X-ray (2.9 Å) Appleby TC, Perry JK, Murakami E, Barauskas O, Feng J, Cho A, Fox D, Wetmore DR, McGrath ME, Ray AS, Sofia MJ, Swaminathan S, Edwards TE (2015) "Structural basis for RNA replication by the hepatitis C virus polymerase." Science, 347, 771-775. doi: 10.1126/science.1259210. Crystal structure of hcv ns5b genotype 2a jfh-1 isolate with s15g e86q e87q c223h v321i mutations and delta8 beta hairpin loop deletion in complex with sofosbuvir diphosphate gs-607596, mn2+ and symmetrical primer template 5'-caaaauuu. SNAP output
4wu4 DNA binding protein-DNA X-ray (2.3 Å) Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR, Arias CA, Ladbury JE, Shamoo Y (2015) "A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin." Nucleic Acids Res., 43, 4758-4773. doi: 10.1093/nar/gkv321. Crystal structure of e. faecalis DNA binding domain liard191n complexed with 22bp DNA. SNAP output
4wu8 structural protein-DNA X-ray (2.45 Å) Chua EY, Davey GE, Chin CF, Droge P, Ang WH, Davey CA (2015) "Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents." Nucleic Acids Res., 43, 5284-5296. doi: 10.1093/nar/gkv356. Structure of trptnap-ncp145. SNAP output
4wu9 structural protein-DNA X-ray (2.6 Å) Chua EY, Davey GE, Chin CF, Droge P, Ang WH, Davey CA (2015) "Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents." Nucleic Acids Res., 43, 5284-5296. doi: 10.1093/nar/gkv356. Structure of cisptnap-ncp145. SNAP output
4wuh DNA binding protein-DNA X-ray (2.294 Å) Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR, Arias CA, Ladbury JE, Shamoo Y (2015) "A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin." Nucleic Acids Res., 43, 4758-4773. doi: 10.1093/nar/gkv321. Crystal structure of e. faecalis DNA binding domain liar wild type complexed with 22bp DNA. SNAP output
4wul DNA binding protein-DNA X-ray (2.4 Å) Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR, Arias CA, Ladbury JE, Shamoo Y (2015) "A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin." Nucleic Acids Res., 43, 4758-4773. doi: 10.1093/nar/gkv321. Crystal structure of e. faecalis DNA binding domain liard191n complexed with 26bp DNA. SNAP output
4wuz hydrolase-DNA X-ray (2.38 Å) Zhang J, Pan X, Bell CE (2014) "Crystal Structure of lambda Exonuclease in Complex with DNA and Ca(2+)." Biochemistry, 53, 7415-7425. doi: 10.1021/bi501155q. Crystal structure of lambda exonuclease in complex with DNA and ca2+. SNAP output
4wwc transcription X-ray (2.903 Å) Fillenberg SB, Grau FC, Seidel G, Muller YA (2015) "Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR." Nucleic Acids Res., 43, 1283-1296. doi: 10.1093/nar/gku1374. Crystal structure of full length yvoa in complex with palindromic operator DNA. SNAP output
4wx9 transferase X-ray (3.0 Å) Miggiano R, Perugino G, Ciaramella M, Serpe M, Rejman D, Pav O, Pohl R, Garavaglia S, Lahiri S, Rizzi M, Rossi F (2016) "Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA." Biochem.J., 473, 123-133. doi: 10.1042/BJ20150833. Crystal structure of mycobacterium tuberculosis ogt in complex with DNA. SNAP output
4wzs transcription X-ray (3.78 Å) Butryn A, Schuller JM, Stoehr G, Runge-Wollmann P, Forster F, Auble DT, Hopfner KP (2015) "Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1." Elife, 4. doi: 10.7554/eLife.07432. Crystal structure of the mot1 n-terminal domain in complex with tbp and nc2 bound to a promoter DNA fragment. SNAP output
4wzw DNA binding protein, RNA binding protein-DNA X-ray (2.95 Å) Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TM (2014) "A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization." Proc.Natl.Acad.Sci.USA, 111, 18554-18559. doi: 10.1073/pnas.1407634112. Crystal structure of human puf-a in complex with DNA. SNAP output
4x0g DNA binding protein-DNA X-ray (3.21 Å) Dai Q, Ren A, Westholm JO, Duan H, Patel DJ, Lai EC (2015) "Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family." Genes Dev., 29, 48-62. doi: 10.1101/gad.252122.114. Structure of bsg25a binding with DNA. SNAP output
4x0p transferase-DNA X-ray (3.911 Å) Zahn KE, Averill AM, Aller P, Wood RD, Doublie S (2015) "Human DNA polymerase theta grasps the primer terminus to mediate DNA repair." Nat.Struct.Mol.Biol., 22, 304-311. doi: 10.1038/nsmb.2993. Ternary complex of human DNA polymerase theta c-terminal domain binding ddatp opposite a tetrahydrofuran ap site analog. SNAP output
4x0q transferase-DNA X-ray (3.9 Å) Zahn KE, Averill AM, Aller P, Wood RD, Doublie S (2015) "Human DNA polymerase theta grasps the primer terminus to mediate DNA repair." Nat.Struct.Mol.Biol., 22, 304-311. doi: 10.1038/nsmb.2993. Ternary complex of human DNA polymerase theta c-terminal domain binding ddgtp opposite dcmp. SNAP output
4x23 structural protein-DNA X-ray (3.5 Å) Kato H, Jiang JS, Zhou BR, Rozendaal M, Feng H, Ghirlando R, Xiao TS, Straight AF, Bai Y (2013) "A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C." Science, 340, 1110-1113. doi: 10.1126/science.1235532. Crystal structure of cenp-c in complex with the nucleosome core particle. SNAP output
4x4b gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 2.1 mgy. SNAP output
4x4c gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 6.2 mgy. SNAP output
4x4d gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 10.3 mgy. SNAP output
4x4e gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 14.4 mgy. SNAP output
4x4f gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 20.6 mgy. SNAP output
4x4g gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 26.8 mgy. SNAP output
4x4h gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 35.7 mgy. SNAP output
4x4i gene regulation X-ray (2.8 Å) Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I, Kneale G, McGeehan JE (2015) "Radiation damage to nucleoprotein complexes in macromolecular crystallography." J.Synchrotron Radiat., 22, 213-224. doi: 10.1107/S1600577514026289. Radiation damage to the nucleoprotein complex c.esp1396i: dose (dwd) 44.6 mgy. SNAP output
4x5v transferase-DNA X-ray (2.15 Å) Burak MJ, Guja KE, Garcia-Diaz M (2015) "Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda." Nucleic Acids Res., 43, 8089-8099. doi: 10.1093/nar/gkv760. Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating a and incorporated 8-oxo-dgmp. SNAP output
4x67 transcription-DNA X-ray (4.1 Å) Walmacq C, Wang L, Chong J, Scibelli K, Lubkowska L, Gnatt A, Brooks PJ, Wang D, Kashlev M (2015) "Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions." Proc.Natl.Acad.Sci.USA, 112, E410-E419. doi: 10.1073/pnas.1415186112. Crystal structure of elongating yeast RNA polymerase ii stalled at oxidative cyclopurine DNA lesions.. SNAP output
4x6a transcription-DNA X-ray (3.96 Å) Walmacq C, Wang L, Chong J, Scibelli K, Lubkowska L, Gnatt A, Brooks PJ, Wang D, Kashlev M (2015) "Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions." Proc.Natl.Acad.Sci.USA, 112, E410-E419. doi: 10.1073/pnas.1415186112. Crystal structure of yeast RNA polymerase ii encountering oxidative cyclopurine DNA lesions. SNAP output
4x9e hydrolase-DNA X-ray (3.1 Å) Singh D, Gawel D, Itsko M, Hochkoeppler A, Krahn JM, London RE, Schaaper RM (2015) "Structure of Escherichia coli dGTP Triphosphohydrolase: A HEXAMERIC ENZYME WITH DNA EFFECTOR MOLECULES." J.Biol.Chem., 290, 10418-10429. doi: 10.1074/jbc.M115.636936. Deoxyguanosinetriphosphate triphosphohydrolase from escherichia coli with two DNA effector molecules. SNAP output
4x9j transcription regulator-DNA X-ray (1.412 Å) Zandarashvili L, White MA, Esadze A, Iwahara J (2015) "Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1." Febs Lett., 589, 1748-1753. doi: 10.1016/j.febslet.2015.05.022. Egr-1 with doubly methylated DNA. SNAP output
4xa5 transferase-DNA X-ray (1.9 Å) Burak MJ, Guja KE, Garcia-Diaz M (2015) "Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda." Nucleic Acids Res., 43, 8089-8099. doi: 10.1093/nar/gkv760. Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating a and an incoming 8-oxo-dgtp. SNAP output
4xeg hydrolase-DNA X-ray (1.72 Å) Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC (2015) "Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA." Nucleic Acids Res., 43, 9541-9552. doi: 10.1093/nar/gkv890. Structure of the enzyme-product complex resulting from tdg action on a g-hmu mismatch. SNAP output
4xic transcription regulator-DNA X-ray (2.69 Å) Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J (2015) "Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate." Biophys.J., 109, 1026-1037. doi: 10.1016/j.bpj.2015.07.032. Antphd with 15bp di-thioate modified DNA duplex. SNAP output
4xid transcription regulator-DNA X-ray (2.701 Å) Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J (2015) "Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate." Biophys.J., 109, 1026-1037. doi: 10.1016/j.bpj.2015.07.032. Antphd with 15bp DNA duplex. SNAP output
4xiu transferase-DNA X-ray (2.5 Å) Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B, Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM, Kermekchiev MB (2015) "A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase." Biochemistry, 54, 881-889. doi: 10.1021/bi501198f. Binary complex structure of klenow fragment of taq DNA polymerase i707l mutant with DNA containing ttt overhang. SNAP output
4xln transcription-DNA-RNA X-ray (4.0 Å) Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA (2015) "Structure of a bacterial RNA polymerase holoenzyme open promoter complex." Elife, 4. doi: 10.7554/eLife.08504. Crystal structure of t. aquaticus transcription initiation complex containing bubble promoter and RNA. SNAP output
4xlp transcription-DNA X-ray (4.0 Å) Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA (2015) "Structure of a bacterial RNA polymerase holoenzyme open promoter complex." Elife, 4. doi: 10.7554/eLife.08504. Crystal structure of t.aquaticus transcription initiation complex containing upstream fork promoter. SNAP output
4xlq transcription-DNA X-ray (4.6 Å) Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA (2015) "Structure of a bacterial RNA polymerase holoenzyme open promoter complex." Elife, 4. doi: 10.7554/eLife.08504. Crystal structure of t.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter. SNAP output
4xlr transcription-DNA X-ray (4.3 Å) Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA (2015) "CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex." Elife, 4. doi: 10.7554/eLife.08505. Crystal structure of t.aquaticus transcription initiation complex with card containing bubble promoter and RNA. SNAP output
4xls transcription X-ray (4.01 Å) Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA (2015) "CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex." Elife, 4. doi: 10.7554/eLife.08505. Crystal structure of t. aquaticus transcription initiation complex with card containing upstream fork promoter.. SNAP output
4xo0 transferase-DNA X-ray (1.7 Å) Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NG (2015) "Structural basis for a six nucleotide genetic alphabet." J. Am. Chem. Soc., 137, 6947-6955. doi: 10.1021/jacs.5b03482. Crystal structure of 5'-cttatpptazzataag in a host-guest complex. SNAP output
4xpc transferase-DNA X-ray (1.68 Å) Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NG (2015) "Structural basis for a six nucleotide genetic alphabet." J. Am. Chem. Soc., 137, 6947-6955. doi: 10.1021/jacs.5b03482. Crystal structure of 5'- cttataaatttataag in a host-guest complex. SNAP output
4xpe transferase-DNA X-ray (1.78 Å) Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NG (2015) "Structural basis for a six nucleotide genetic alphabet." J. Am. Chem. Soc., 137, 6947-6955. doi: 10.1021/jacs.5b03482. Crystal structure of 5'-cttatgggcccataag in a host-guest complex. SNAP output
4xq8 transferase-DNA X-ray (2.798 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda- mgdatp binary complex and complex with 6 paired DNA. SNAP output
4xqj DNA binding protein-DNA X-ray (1.9 Å) Rajasree K, Fasim A, Gopal B (2016) "Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression." Biochem Biophys Rep, 6, 124-134. doi: 10.1016/j.bbrep.2016.03.012. Crystal structure of agra lyttr domain in complex with promoters. SNAP output
4xqk hydrolase-DNA X-ray (2.7 Å) Chand MK, Nirwan N, Diffin FM, Aelst KV, Kulkarni M, Pernstich C, Szczelkun MD, Saikrishnan K (2015) "Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes." Nat.Chem.Biol., 11, 870-877. doi: 10.1038/nchembio.1926. Atp-dependent type isp restriction-modification enzyme llabiii bound to DNA. SNAP output
4xqn DNA-DNA binding protein X-ray (2.3 Å) Rajasree K, Fasim A, Gopal B (2016) "Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression." Biochem Biophys Rep, 6, 124-134. doi: 10.1016/j.bbrep.2016.03.012. Crystal structure of agra lyttr domain in complex with promoters. SNAP output
4xqq DNA binding protein-DNA X-ray (3.05 Å) Rajasree K, Fasim A, Gopal B (2016) "Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression." Biochem Biophys Rep, 6, 124-134. doi: 10.1016/j.bbrep.2016.03.012. Crystal structure of agra lyttr domain in complex with promoters. SNAP output
4xr0 replication-DNA X-ray (2.8 Å) Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM (2015) "Replisome speed determines the efficiency of the Tus-Ter replication termination barrier." Nature, 525, 394-398. doi: 10.1038/nature14866. Escherichia coli replication terminator protein (tus) complexed with DNA- g-t mismatch.. SNAP output
4xr1 replication-DNA X-ray (2.4 Å) Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM (2015) "Replisome speed determines the efficiency of the Tus-Ter replication termination barrier." Nature, 525, 394-398. doi: 10.1038/nature14866. Escherichia coli replication terminator protein (tus) complexed with DNA- ag-at mismatch.. SNAP output
4xr2 replication-DNA X-ray (2.35 Å) Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM (2015) "Replisome speed determines the efficiency of the Tus-Ter replication termination barrier." Nature, 525, 394-398. doi: 10.1038/nature14866. Escherichia coli replication terminator protein (tus) h114a mutant complexed with DNA- tera lock.. SNAP output
4xr3 replication-DNA X-ray (2.7 Å) Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M, Oakley AJ, Dixon NE, Hamdan SM (2015) "Replisome speed determines the efficiency of the Tus-Ter replication termination barrier." Nature, 525, 394-398. doi: 10.1038/nature14866. Escherichia coli replication terminator protein (tus) complexed with DNA- gc(6) swapped.. SNAP output
4xrh transferase-DNA X-ray (3.0 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda- mgdttp binary and complex with 6 paired DNA. SNAP output
4xrm transcription X-ray (1.6 Å) Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J (2015) "DNA-dependent formation of transcription factor pairs alters their binding specificity." Nature, 527, 384-388. doi: 10.1038/nature15518. Homodimer of tale type homeobox transcription factor meis1 complexes with specific DNA. SNAP output
4xrs transcription X-ray (3.5 Å) Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J (2015) "DNA-dependent formation of transcription factor pairs alters their binding specificity." Nature, 527, 384-388. doi: 10.1038/nature15518. Heterodimeric complex of transcription factors meis1 and dlx3 on specific DNA. SNAP output
4xuj DNA-binding protein-DNA X-ray (3.18 Å) Hanif M, Meier SM, Adhireksan Z, Henke H, Martic S, Labib M, Kandioller W, Jakupec MA, Kraatz HB, Davey CA, Keppler BK, Hartinger CG "Contrasting Cytotoxicity and Reactivity of RuII-Arene Complexes of Morpholine vs Thiomorpholine Substituted 3-Hydroxy-2-pyridone Ligands." Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)ru(3-hydroxy-2-pyridone)cl] compound. SNAP output
4xus transferase-DNA X-ray (2.4 Å) Burak MJ, Guja KE, Garcia-Diaz M (2015) "Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda." Nucleic Acids Res., 43, 8089-8099. doi: 10.1093/nar/gkv760. Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating a and an incoming dttp. SNAP output
4xvi transferase-DNA X-ray (3.1 Å) Lee YS, Gao Y, Yang W (2015) "How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis." Nat.Struct.Mol.Biol., 22, 298-303. doi: 10.1038/nsmb.2985. Binary complex of human polymerase nu and DNA with the finger domain ajar. SNAP output
4xvk transferase-DNA X-ray (2.95 Å) Lee YS, Gao Y, Yang W (2015) "How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis." Nat.Struct.Mol.Biol., 22, 298-303. doi: 10.1038/nsmb.2985. Binary complex of human polymerase nu and DNA with the finger domain closed. SNAP output
4xvl transferase-DNA X-ray (3.301 Å) Lee YS, Gao Y, Yang W (2015) "How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis." Nat.Struct.Mol.Biol., 22, 298-303. doi: 10.1038/nsmb.2985. Binary complex of human polymerase nu and DNA with the finger domain open. SNAP output
4xvm transferase-DNA X-ray (3.2 Å) Lee YS, Gao Y, Yang W (2015) "How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis." Nat.Struct.Mol.Biol., 22, 298-303. doi: 10.1038/nsmb.2985. Binary complex of human polymerase nu and DNA with the finger domain closed and thumb domain rotated out. SNAP output
4xxe transcription-DNA X-ray (3.2 Å) Rajasree K, Fasim A, Gopal B (2016) "Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression." Biochem Biophys Rep, 6, 124-134. doi: 10.1016/j.bbrep.2016.03.012. Structure of agra lyttr domain in complex with promoters. SNAP output
4xyq DNA-DNA binding protein X-ray (2.4 Å) Rajasree K, Fasim A, Gopal B (2016) "Conformational features of theStaphylococcus aureusAgrA-promoter interactions rationalize quorum-sensing triggered gene expression." Biochem Biophys Rep, 6, 124-134. doi: 10.1016/j.bbrep.2016.03.012. Structure of agra lyttr domain in complex with promoters. SNAP output
4xzf DNA binding protein-DNA X-ray (1.38 Å) Hishiki A, Hara K, Ikegaya Y, Yokoyama H, Shimizu T, Sato M, Hashimoto H (2015) "Structure of a Novel DNA-binding Domain of Helicase-like Transcription Factor (HLTF) and Its Functional Implication in DNA Damage Tolerance." J.Biol.Chem., 290, 13215-13223. doi: 10.1074/jbc.M115.643643. Crystal structure of hiran domain of human hltf in complex with DNA. SNAP output
4xzq structural protein-DNA X-ray (2.4 Å) Chatterjee N, North JA, Dechassa ML, Manohar M, Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew B (2015) "Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF." Mol.Cell.Biol., 35, 4083-4092. doi: 10.1128/MCB.00441-15. Nucleosome disassembly by rsc and swi-snf is enhanced by h3 acetylation near the nucleosome dyad axis. SNAP output
4y00 DNA binding protein-DNA X-ray (3.0 Å) Chiang CH, Grauffel C, Wu LS, Kuo PH, Doudeva LG, Lim C, Shen CK, Yuan HS (2016) "Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation." Sci Rep, 6, 21581. doi: 10.1038/srep21581. Crystal structure of human tdp-43 rrm1 domain with d169g mutation in complex with an unmodified single-stranded DNA. SNAP output
4y0f DNA binding protein-DNA X-ray (2.648 Å) Chiang CH, Grauffel C, Wu LS, Kuo PH, Doudeva LG, Lim C, Shen CK, Yuan HS (2016) "Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation." Sci Rep, 6, 21581. doi: 10.1038/srep21581. Crystal structure of human tdp-43 rrm1 domain in complex with an unmodified single-stranded DNA. SNAP output
4y52 transcription-DNA-RNA X-ray (3.5 Å) Wang L, Zhou Y, Xu L, Xiao R, Lu X, Chen L, Chong J, Li H, He C, Fu XD, Wang D (2015) "Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex." Nature, 523, 621-625. doi: 10.1038/nature14482. Crystal structure of 5-carboxycytosine recognition by RNA polymerase ii during transcription elongation.. SNAP output
4y5w transcription-DNA X-ray (3.104 Å) Li J, Rodriguez JP, Niu F, Pu M, Wang J, Hung LW, Shao Q, Zhu Y, Ding W, Liu Y, Da Y, Yao Z, Yang J, Zhao Y, Wei GH, Cheng G, Liu ZJ, Ouyang S (2016) "Structural basis for DNA recognition by STAT6." Proc.Natl.Acad.Sci.USA, 113, 13015-13020. doi: 10.1073/pnas.1611228113. Transcription factor-DNA complex. SNAP output
4y60 transcription-DNA X-ray (1.75 Å) Klaus M, Prokoph N, Girbig M, Wang X, Huang YH, Srivastava Y, Hou L, Narasimhan K, Kolatkar PR, Francois M, Jauch R (2016) "Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction." Nucleic Acids Res., 44, 3922-3935. doi: 10.1093/nar/gkw130. Structure of sox18-hmg-prox1-DNA. SNAP output
4y7n transcription-DNA-RNA X-ray (3.3 Å) Wang L, Zhou Y, Xu L, Xiao R, Lu X, Chen L, Chong J, Li H, He C, Fu XD, Wang D (2015) "Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex." Nature, 523, 621-625. doi: 10.1038/nature14482. The structure insight into 5-carboxycytosine recognition by RNA polymerase ii during transcription elongation.. SNAP output
4ycp oxidoreductase-RNA X-ray (2.55 Å) Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J, Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL, Antson AA (2015) "Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases." Proc.Natl.Acad.Sci.USA, 112, 6033-6037. doi: 10.1073/pnas.1500161112. E. coli dihydrouridine synthase c (dusc) in complex with trnatrp. SNAP output
4ycx transferase-DNA X-ray (2.1 Å) Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K (2015) "Creative template-dependent synthesis by human polymerase mu." Proc.Natl.Acad.Sci.USA, 112, E4530-E4536. doi: 10.1073/pnas.1505798112. Binary complex of human DNA polymerase mu with 2-nt gapped DNA substrate. SNAP output
4yd1 transferase-DNA X-ray (1.75 Å) Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K (2015) "Creative template-dependent synthesis by human polymerase mu." Proc.Natl.Acad.Sci.USA, 112, E4530-E4536. doi: 10.1073/pnas.1505798112. Ternary complex of human DNA polymerase mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dumpnpp. SNAP output
4yd2 transferase-DNA X-ray (2.471 Å) Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K (2015) "Creative template-dependent synthesis by human polymerase mu." Proc.Natl.Acad.Sci.USA, 112, E4530-E4536. doi: 10.1073/pnas.1505798112. Nicked complex of human DNA polymerase mu with 2-nt gapped DNA substrate. SNAP output
4yew DNA binding protein-DNA X-ray (2.683 Å) Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S (2016) "HU multimerization shift controls nucleoid compaction." Sci Adv, 2, e1600650. doi: 10.1126/sciadv.1600650. Huab-19bp. SNAP output
4yex DNA binding protein-DNA X-ray (3.2 Å) Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S (2016) "HU multimerization shift controls nucleoid compaction." Sci Adv, 2, e1600650. doi: 10.1126/sciadv.1600650. Huaa-19bp. SNAP output
4yey DNA binding protein-DNA X-ray (3.354 Å) Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S (2016) "HU multimerization shift controls nucleoid compaction." Sci Adv, 2, e1600650. doi: 10.1126/sciadv.1600650. Huaa-20bp. SNAP output
4yf0 DNA binding protein-DNA X-ray (2.79 Å) Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S (2016) "HU multimerization shift controls nucleoid compaction." Sci Adv, 2, e1600650. doi: 10.1126/sciadv.1600650. Hu38-19bp. SNAP output
4yfh DNA binding protein-DNA X-ray (3.49 Å) Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S (2016) "HU multimerization shift controls nucleoid compaction." Sci Adv, 2, e1600650. doi: 10.1126/sciadv.1600650. Hu38-20bp. SNAP output
4yft DNA binding protein-DNA X-ray (2.914 Å) Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HY, Larabell CA, Tainer JA, Adhya S (2016) "HU multimerization shift controls nucleoid compaction." Sci Adv, 2, e1600650. doi: 10.1126/sciadv.1600650. Huab-20bp. SNAP output
4yfu transferase-DNA X-ray (1.5 Å) Miller BR, Beese LS, Parish CA, Wu EY (2015) "The Closing Mechanism of DNA Polymerase I at Atomic Resolution." Structure, 23, 1609-1620. doi: 10.1016/j.str.2015.06.016. Crystal structure of open bacillus fragment DNA polymerase bound to DNA and dttp. SNAP output
4yg1 transcription-DNA X-ray (3.25 Å) Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulic M, Lewis K, Brennan RG (2015) "HipBA-promoter structures reveal the basis of heritable multidrug tolerance." Nature, 524, 59-64. doi: 10.1038/nature14662. Hipb-o1-o2 complex-p21212 crystal form. SNAP output
4yg4 transcription-DNA X-ray (3.5 Å) Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulic M, Lewis K, Brennan RG (2015) "HipBA-promoter structures reveal the basis of heritable multidrug tolerance." Nature, 524, 59-64. doi: 10.1038/nature14662. Hipb-o1-o1* complex. SNAP output
4yg7 transcription, transferase-DNA X-ray (3.77 Å) Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulic M, Lewis K, Brennan RG (2015) "HipBA-promoter structures reveal the basis of heritable multidrug tolerance." Nature, 524, 59-64. doi: 10.1038/nature14662. Structure of fl autorepression promoter complex. SNAP output
4ygi transferase-DNA X-ray (2.6 Å) Rajakumara E, Nakarakanti NK, Nivya MA, Satish M (2016) "Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain." Sci Rep, 6, 20161. doi: 10.1038/srep20161. Crystal structure of suvh5 sra bound to fully hydroxymethylated cg DNA. SNAP output
4yhx hydrolase-DNA X-ray (2.15 Å) Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure, 24, 862-873. doi: 10.1016/j.str.2016.03.024. Crystal structure of laglidadg meganuclease i-gpemi bound to uncleaved DNA. SNAP output
4yig hydrolase X-ray (2.7 Å) Burmeister WP, Tarbouriech N, Fender P, Contesto-Richefeu C, Peyrefitte CN, Iseni F (2015) "Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA." J.Biol.Chem., 290, 17923-17934. doi: 10.1074/jbc.M115.648352. Vaccinia virus d4-a20(1-50) in complex with dsDNA containing an abasic site and free uracyl. SNAP output
4yir DNA binding protein-DNA X-ray (3.05 Å) Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH (2015) "Kinetic gating mechanism of DNA damage recognition by Rad4/XPC." Nat Commun, 6, 5849. doi: 10.1038/ncomms6849. Crystal structure of rad4-rad23 crosslinked to an undamaged DNA. SNAP output
4yis hydrolase-DNA X-ray (2.89 Å) Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure, 24, 862-873. doi: 10.1016/j.str.2016.03.024. Crystal structure of laglidadg meganuclease i-cpami bound to uncleaved DNA. SNAP output
4yit hydrolase-DNA X-ray (3.24 Å) Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure, 24, 862-873. doi: 10.1016/j.str.2016.03.024. Crystal structure of laglidadg meganuclease i-aabmi bound to uncleaved DNA. SNAP output
4yj0 transcription X-ray (3.814 Å) Murphy MW, Lee JK, Rojo S, Gearhart MD, Kurahashi K, Banerjee S, Loeuille GA, Bashamboo A, McElreavey K, Zarkower D, Aihara H, Bardwell VJ (2015) "An ancient protein-DNA interaction underlying metazoan sex determination." Nat.Struct.Mol.Biol., 22, 442-451. doi: 10.1038/nsmb.3032. Crystal structure of the dm domain of human dmrt1 bound to 25mer target DNA. SNAP output
4ykl hydrolase-DNA X-ray (2.25 Å) Chauleau M, Jacewicz A, Shuman S (2015) "DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition." Nucleic Acids Res., 43, 6075-6083. doi: 10.1093/nar/gkv501. Hnt3 in complex with DNA and guanosine. SNAP output
4yln transcription-DNA-RNA X-ray (5.5 Å) Zuo Y, Steitz TA (2015) "Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble." Mol.Cell, 58, 534-540. doi: 10.1016/j.molcel.2015.03.010. E. coli transcription initiation complex - 17-bp spacer and 4-nt RNA. SNAP output
4ylo transcription-DNA-RNA X-ray (6.0 Å) Zuo Y, Steitz TA (2015) "Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble." Mol.Cell, 58, 534-540. doi: 10.1016/j.molcel.2015.03.010. E. coli transcription initiation complex - 16-bp spacer and 4-nt RNA. SNAP output
4ylp transcription-DNA-RNA X-ray (5.5 Å) Zuo Y, Steitz TA (2015) "Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble." Mol.Cell, 58, 534-540. doi: 10.1016/j.molcel.2015.03.010. E. coli transcription initiation complex - 16-bp spacer and 5-nt RNA. SNAP output
4ym5 structural protein-DNA X-ray (4.005 Å) Osakabe A, Tachiwana H, Kagawa W, Horikoshi N, Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J, Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka H (2015) "Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome." Sci Rep, 5, 16330. doi: 10.1038/srep16330. Crystal structure of the human nucleosome containing 6-4pp (inside). SNAP output
4ym6 structural protein-DNA X-ray (3.514 Å) Osakabe A, Tachiwana H, Kagawa W, Horikoshi N, Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J, Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka H (2015) "Structural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome." Sci Rep, 5, 16330. doi: 10.1038/srep16330. Crystal structure of the human nucleosome containing 6-4pp (outside). SNAP output
4ymm transferase-DNA X-ray (2.199 Å) Lee S, Koag M-C "Structure of human DNA polymerase beta complexed with 7BG as the template base in a 1-nucleotide gapped DNA." Structure of human DNA polymerase beta complexed with 7bg as the template base in a 1-nucleotide gapped DNA. SNAP output
4ymn transferase-DNA X-ray (2.591 Å) Kou Y, Koag MC, Lee S (2018) "Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication." Biochemistry. doi: 10.1021/acs.biochem.8b00331. Structure of human DNA polymerase beta complexed with n7bg in the template base paired with incoming non-hydrolyzable ctp. SNAP output
4ymo transferase-DNA X-ray (2.148 Å) Kou Y, Koag MC, Lee S (2018) "Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication." Biochemistry. doi: 10.1021/acs.biochem.8b00331. Structure of human DNA polymerase beta complexed with n7bg in the template opposite to incoming non-hydrolyzable ctp with manganese in the active site. SNAP output
4yn4 transferase-DNA X-ray (2.243 Å) Kou Y, Koag MC, Lee S (2018) "Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication." Biochemistry. doi: 10.1021/acs.biochem.8b00331. Structure of human DNA polymerase beta complexed with n7bg in the template opposite to incoming non-hydrolyzable dttp with manganese in the active site. SNAP output
4ynq hydrolase-DNA X-ray (2.8 Å) Grieves JL, Fye JM, Harvey S, Grayson JM, Hollis T, Perrino FW (2015) "Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease." Proc.Natl.Acad.Sci.USA, 112, 5117-5122. doi: 10.1073/pnas.1423804112. Trex1-dsDNA complex. SNAP output
4yo2 transcription X-ray (3.073 Å) Morgunova E, Yin Y, Jolma A, Dave K, Schmierer B, Popov A, Eremina N, Nilsson L, Taipale J (2015) "Structural insights into the DNA-binding specificity of E2F family transcription factors." Nat Commun, 6, 10050. doi: 10.1038/ncomms10050. Structure of e2f8, an atypical member of e2f family of transcription factors. SNAP output
4yoq hydrolase-DNA X-ray (2.21 Å) Wang L, Lee SJ, Verdine GL (2015) "Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase." J.Biol.Chem., 290, 17096-17105. doi: 10.1074/jbc.M115.657866. Crystal structure of muty bound to its anti-substrate. SNAP output
4yov hydrolase-DNA X-ray (2.05 Å) Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M (2015) "Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I." Nucleic Acids Res., 43, 7122-7136. doi: 10.1093/nar/gkv654. Crystal structure of a trimeric exonuclease phoexo i from pyrococcus horikoshii ot3 in complex with poly-da. SNAP output
4yow hydrolase-DNA X-ray (2.5 Å) Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M (2015) "Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I." Nucleic Acids Res., 43, 7122-7136. doi: 10.1093/nar/gkv654. Crystal structure of a trimeric exonuclease phoexo i from pyrococcus horikoshii ot3 in complex with poly-dc. SNAP output
4yox hydrolase-DNA X-ray (2.05 Å) Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M (2015) "Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I." Nucleic Acids Res., 43, 7122-7136. doi: 10.1093/nar/gkv654. Crystal structure of a trimeric exonuclease phoexo i from pyrococcus horikoshii ot3 in complex with poly-dt. SNAP output
4yoy hydrolase-DNA X-ray (1.95 Å) Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y, Tanokura M (2015) "Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I." Nucleic Acids Res., 43, 7122-7136. doi: 10.1093/nar/gkv654. Crystal structure of a trimeric exonuclease phoexo i from pyrococcus horikoshii ot3 in complex with poly-dt and mg2+ ion. SNAP output
4yp3 transferase-DNA X-ray (1.89 Å) Su Y, Patra A, Harp JM, Egli M, Guengerich FP (2015) "Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine." J.Biol.Chem., 290, 15921-15933. doi: 10.1074/jbc.M115.653691. Mutant human DNA polymerase eta q38a-r61a inserting dctp opposite an 8-oxoguanine lesion. SNAP output
4yph hydrolase-DNA X-ray (2.32 Å) Wang L, Lee SJ, Verdine GL (2015) "Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase." J.Biol.Chem., 290, 17096-17105. doi: 10.1074/jbc.M115.657866. Crystal structure of muty bound to its anti-substrate with the disulfide cross-linker reduced. SNAP output
4ypr hydrolase-DNA X-ray (2.59 Å) Wang L, Lee SJ, Verdine GL (2015) "Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase." J.Biol.Chem., 290, 17096-17105. doi: 10.1074/jbc.M115.657866. Crystal structure of d144n muty bound to its anti-substrate. SNAP output
4yqw transferase-DNA X-ray (2.064 Å) Su Y, Patra A, Harp JM, Egli M, Guengerich FP (2015) "Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine." J.Biol.Chem., 290, 15921-15933. doi: 10.1074/jbc.M115.653691. Mutant human DNA polymerase eta q38a-r61a inserting dctp opposite template g. SNAP output
4yr0 transferase-DNA X-ray (1.78 Å) Su Y, Patra A, Harp JM, Egli M, Guengerich FP (2015) "Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine." J.Biol.Chem., 290, 15921-15933. doi: 10.1074/jbc.M115.653691. Mutant human DNA polymerase eta r61m inserting dctp opposite an 8-oxoguanine lesion. SNAP output
4yr2 transferase-DNA X-ray (1.95 Å) Su Y, Patra A, Harp JM, Egli M, Guengerich FP (2015) "Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine." J.Biol.Chem., 290, 15921-15933. doi: 10.1074/jbc.M115.653691. Mutant human DNA polymerase eta r61m inserting datp opposite an 8-oxoguanine lesion. SNAP output
4yr3 transferase-DNA X-ray (2.0 Å) Su Y, Patra A, Harp JM, Egli M, Guengerich FP (2015) "Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine." J.Biol.Chem., 290, 15921-15933. doi: 10.1074/jbc.M115.653691. Mutant human DNA polymerase eta r61m inserting dctp opposite template g. SNAP output
4yrv transcription-DNA X-ray (2.8 Å) Hu HX, Jiang YL, Zhao MX, Cai K, Liu S, Wen B, Lv P, Zhang Y, Peng J, Zhong H, Yu HM, Ren YM, Zhang Z, Tian C, Wu Q, Oliveberg M, Zhang CC, Chen Y, Zhou CZ (2015) "Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation." Sci Rep, 5, 16470. doi: 10.1038/srep16470. Crystal structure of anabaena transcription factor hetr complexed with 21-bp DNA from hetp promoter. SNAP output
4ys3 structural protein-DNA X-ray (3.0 Å) Chatterjee N, North JA, Dechassa ML, Manohar M, Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew B (2015) "Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF." Mol.Cell.Biol., 35, 4083-4092. doi: 10.1128/MCB.00441-15. Nucleosome disassembly by rsc and swi-snf is enhanced by h3 acetylation near the nucleosome dyad axis. SNAP output
4z1x hydrolase-DNA X-ray (2.8 Å) Stoddard BL, Lambert AR, Kulshina N "Crystal structure of LAGLIDADG homing endonuclease I-GzeII in complex with DNA target." Crystal structure of laglidadg homing endonuclease i-gzeii in complex with DNA target. SNAP output
4z1z hydrolase-DNA X-ray (3.2 Å) Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure, 24, 862-873. doi: 10.1016/j.str.2016.03.024. Crystal structure of meganuclease i-smami bound to uncleaveable DNA with a ttct central four. SNAP output
4z20 hydrolase-DNA X-ray (3.2 Å) Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure, 24, 862-873. doi: 10.1016/j.str.2016.03.024. Crystal structure of meganuclease i-smami bound to uncleaveable DNA with a ttgt central four. SNAP output
4z2c isomerase X-ray (3.19 Å) Laponogov I, Veselkov DA, Pan X-S, Selvarajah J, Crevel IM-T, Fisher LM, Sanderson MR "Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae." Quinolone(moxifloxacin)-DNA cleavage complex of gyrase from s. pneumoniae. SNAP output
4z2d isomerase X-ray (3.38 Å) Laponogov I, Veselkov DA, Pan X-S, Selvarajah J, Crevel IM-T, Fisher LM, Sanderson MR "Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae." Quinolone(levofloxacin)-DNA cleavage complex of gyrase from s. pneumoniae. SNAP output
4z2e isomerase X-ray (3.46 Å) Laponogov I, Veselkov DA, Pan X-S, Selvarajah J, Crevel IM-T, Fisher LM, Sanderson MR "Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae." Quinolone(trovafloxacin)-DNA cleavage complex of gyrase from s. pneumoniae. SNAP output
4z3a hydrolase-DNA X-ray (1.72 Å) Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC (2015) "Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA." Nucleic Acids Res., 43, 9541-9552. doi: 10.1093/nar/gkv890. Acetate-free structure of the enzyme-product complex resulting from tdg action on a gu mismatch. SNAP output
4z3c DNA binding protein-DNA X-ray (1.57 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2017) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure. doi: 10.1016/j.str.2017.11.022. Zinc finger region of human tet3 in complex with cpg DNA. SNAP output
4z3o isomerase X-ray (3.44 Å) Laponogov I, Veselkov DA, Pan X-S, Selvarajah J, Crevel IM-T, Fisher LM, Sanderson MR "Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae." Quinolone(moxifloxacin)-DNA cleavage complex of topoisomerase iv from s. pneumoniae. SNAP output
4z47 DNA binding protein-DNA X-ray (1.45 Å) Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC (2015) "Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA." Nucleic Acids Res., 43, 9541-9552. doi: 10.1093/nar/gkv890. Structure of the enzyme-product complex resulting from tdg action on a gu mismatch in the presence of excess base. SNAP output
4z4q isomerase X-ray (3.04 Å) Laponogov I, Veselkov DA, Pan X-S, Selvarajah J, Crevel IM-T, Fisher LM, Sanderson MR "Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae." Quinazolinedione(pd 0305970)-DNA cleavage complex of topoisomerase iv from s. pneumoniae. SNAP output
4z53 isomerase X-ray (3.26 Å) Laponogov I, Veselkov DA, Pan X-S, Selvarajah J, Crevel IM-T, Fisher LM, Sanderson MR "Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae." Quinolone(trovafloxacin)-DNA cleavage complex of topoisomerase iv from s. pneumoniae. SNAP output
4z58 transcription-DNA X-ray (2.5 Å) Min J, Wang A, Brennan RG, Schumacher MA "Molecular mechanism on hipBA gene regulation." Hipb-o3 20mer complex. SNAP output
4z59 transcription-DNA X-ray (2.3 Å) Min J, Wang A, Brennan RG, Schumacher MA "Molecular mechanism on hipBA gene regulation." Hipb-o4 20mer complex. SNAP output
4z5c transcription-DNA X-ray (2.5 Å) Min J, Wang A, Brennan RG, Schumacher MA "Molecular mechanism on hipBA gene regulation." Hipb-o3 21mer complex. SNAP output
4z5d transcription-DNA X-ray (2.15 Å) Min J, Wang A, Brennan RG, Schumacher MA "Molecular mechanism on hipBA gene regulation." Hipb-o4 21mer complex. SNAP output
4z5h transcription-DNA X-ray (2.1 Å) Min J, Wang A, Brennan RG, Schumacher MA "Molecular mechanism on hipBA gene regulation." Hipb(s29a)-o2 20mer complex. SNAP output
4z5t structural protein-DNA X-ray (2.8 Å) Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H (2016) "Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis." Epigenetics Chromatin, 9, 2. doi: 10.1186/s13072-016-0051-y. The nucleosome containing human h3.5. SNAP output
4z66 structural protein-DNA X-ray (2.5 Å) Chatterjee N, North JA, Dechassa ML, Manohar M, Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew B (2015) "Histone Acetylation near the Nucleosome Dyad Axis Enhances Nucleosome Disassembly by RSC and SWI/SNF." Mol.Cell.Biol., 35, 4083-4092. doi: 10.1128/MCB.00441-15. Nucleosome disassembly by rsc and swi-snf is enhanced by h3 acetylation near the nucleosome dyad axis. SNAP output
4z6c transferase-DNA X-ray (2.677 Å) Koag MC, Lee S (2018) "Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta." Biochem. J., 475, 571-585. doi: 10.1042/BCJ20170787. Structure of human DNA polymerase beta 279na mutant complexed with g in the template base paired with incoming non-hydrolyzable ctp. SNAP output
4z6d transferase-DNA X-ray (2.51 Å) Koag MC, Lee S (2018) "Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta." Biochem. J., 475, 571-585. doi: 10.1042/BCJ20170787. Structure of human DNA polymerase beta 279na mutant complexed with g in the template base paired with incoming non-hydrolyzable ttp. SNAP output
4z6e transferase-DNA X-ray (2.752 Å) Koag MC, Lee S (2018) "Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta." Biochem. J., 475, 571-585. doi: 10.1042/BCJ20170787. Structure of human DNA polymerase beta 279na mutant complexed with g in the template base paired with incoming non-hydrolyzable ttp and manganese. SNAP output
4z6f transferase-DNA X-ray (2.444 Å) Koag MC, Lee S (2018) "Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta." Biochem. J., 475, 571-585. doi: 10.1042/BCJ20170787. Structure of human DNA polymerase beta 279na mutant complexed with g in the template base paired with incoming non-hydrolyzable ttp and manganese. SNAP output
4z7b hydrolase-DNA X-ray (2.02 Å) Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC (2015) "Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA." Nucleic Acids Res., 43, 9541-9552. doi: 10.1093/nar/gkv890. Structure of the enzyme-product complex resulting from tdg action on a gfc mismatch. SNAP output
4z7z hydrolase-DNA X-ray (1.83 Å) Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC (2015) "Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA." Nucleic Acids Res., 43, 9541-9552. doi: 10.1093/nar/gkv890. Structure of the enzyme-product complex resulting from tdg action on a gt mismatch in the presence of excess base. SNAP output
4z8f immune system-DNA X-ray (1.75 Å) Haji-Ghassemi O, Muller-Loennies S, Rodriguez T, Brade L, Kosma P, Brade H, Evans SV (2015) "Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA." J.Biol.Chem., 290, 19629-19640. doi: 10.1074/jbc.M115.657874. Fab structure of antibody s1-15 in complex with ssDNA DNA, 5'-p5(dt)p-3'. SNAP output
4zbn immune system-DNA X-ray (2.447 Å) Jarvis TC, Davies DR, Hisaminato A, Resnicow DI, Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H, Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y, Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider DJ, Janjic N (2015) "Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor." Structure, 23, 1293-1304. doi: 10.1016/j.str.2015.03.027. Non-helical DNA triplex forms a unique aptamer scaffold for high affinity recognition of nerve growth factor. SNAP output
4zcf hydrolase-DNA complex X-ray (2.6 Å) Gupta YK, Chan SH, Xu SY, Aggarwal AK (2015) "Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I." Nat Commun, 6, 7363. doi: 10.1038/ncomms8363. Structural basis of asymmetric DNA methylation and atp-triggered long-range diffusion by ecop15i. SNAP output
4zhn oxidoreductase-DNA X-ray (1.333 Å) Hall ML, Ergel B, Miller EB, Yu B, Rinaldo D, Hunt JF, Friesner R "DFT Studies of the Rate-Limiting Step in the Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related Experimental Studies." Crystal structure of alkb t208a mutant protein in complex with co(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
4zm0 transcription X-ray (3.17 Å) Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R (2016) "An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation." Nat.Chem.Biol., 12, 490-496. doi: 10.1038/nchembio.2078. Antitoxin phd from phage p1 in complex with its operator DNA inverted repeat. SNAP output
4zm2 transcription X-ray (3.88 Å) Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R (2016) "An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation." Nat.Chem.Biol., 12, 490-496. doi: 10.1038/nchembio.2078. Antitoxin phd from phage p1 in complex with its operator DNA inverted repeat in a monoclinic space group. SNAP output
4zpk protein transport-transcription-DNA X-ray (3.6 Å) Wu D, Potluri N, Lu J, Kim Y, Rastinejad F (2015) "Structural integration in hypoxia-inducible factors." Nature, 524, 303-308. doi: 10.1038/nature14883. Crystal structure of the heterodimeric hif-2a:arnt complex with hre DNA. SNAP output
4zpr protein transport-transcription-DNA X-ray (3.902 Å) Wu D, Potluri N, Lu J, Kim Y, Rastinejad F (2015) "Structural integration in hypoxia-inducible factors." Nature, 524, 303-308. doi: 10.1038/nature14883. Crystal structure of the heterodimeric hif-1a:arnt complex with hre DNA. SNAP output
4zq9 DNA binding protein-DNA X-ray (2.6 Å) Musayev FN, Zarate-Perez F, Bishop C, Burgner JW, Escalante CR (2015) "Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1." J.Biol.Chem., 290, 27487-27499. doi: 10.1074/jbc.M115.669960. X-ray structure of aav-2 obd bound to aavs1 site 3:1. SNAP output
4zsf protein-DNA X-ray (1.8 Å) Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V (2015) "Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI." Nucleic Acids Res., 43, 8100-8110. doi: 10.1093/nar/gkv768. Crystal structure of pre-specific restriction endonuclease bsawi-DNA complex. SNAP output
4ztf transferase-DNA-inhibitor X-ray (2.7 Å) Raheem IT, Walji AM, Klein D, Sanders JM, Powell DA, Abeywickrema P, Barbe G, Bennet A, Clas SD, Dubost D, Embrey M, Grobler J, Hafey MJ, Hartingh TJ, Hazuda DJ, Miller MD, Moore KP, Pajkovic N, Patel S, Rada V, Rearden P, Schreier JD, Sisko J, Steele TG, Truchon JF, Wai J, Xu M, Coleman PJ (2015) "Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors." J.Med.Chem., 58, 8154-8165. doi: 10.1021/acs.jmedchem.5b01037. Crystal structure of the prototype foamy virus intasome with a 2-pyridinone aminal inhibitor. SNAP output
4ztj transferase-DNA-inhibitor X-ray (2.67 Å) Raheem IT, Walji AM, Klein D, Sanders JM, Powell DA, Abeywickrema P, Barbe G, Bennet A, Clas SD, Dubost D, Embrey M, Grobler J, Hafey MJ, Hartingh TJ, Hazuda DJ, Miller MD, Moore KP, Pajkovic N, Patel S, Rada V, Rearden P, Schreier JD, Sisko J, Steele TG, Truchon JF, Wai J, Xu M, Coleman PJ (2015) "Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors." J.Med.Chem., 58, 8154-8165. doi: 10.1021/acs.jmedchem.5b01037. Crystal structure of the prototype foamy virus intasome with a 2-pyridinone aminal inhibitor. SNAP output
4ztu DNA binding protein-DNA X-ray (3.299 Å) Szymanski MR, Kuznestov VB, Shumate CK, Meng Q, Lee Y-S, Patel G, Patel SS, Yin YW (2015) "Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase." EMBO J., 34, 1959. doi: 10.15252/embj.201591520. Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase. SNAP output
4ztz DNA binding protein-DNA X-ray (3.442 Å) Szymanski MR, Kuznestov VB, Shumate CK, Meng Q, Lee Y-S, Patel G, Patel SS, Yin YW (2015) "Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase." EMBO J., 34, 1959. doi: 10.15252/embj.201591520. Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase. SNAP output
4zux hydrolase-DNA X-ray (3.82 Å) Morgan MT, Haj-Yahya M, Ringel AE, Bandi P, Brik A, Wolberger C (2016) "Structural basis for histone H2B deubiquitination by the SAGA DUB module." Science, 351, 725-728. doi: 10.1126/science.aac5681. Saga dub module ubp8-sgf11-sus1-sgf73 bound to ubiqitinated nucleosome. SNAP output
4zyd transferase X-ray (2.682 Å) Perugino G, Miggiano R, Serpe M, Vettone A, Valenti A, Lahiri S, Rossi F, Rossi M, Rizzi M, Ciaramella M (2015) "Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein." Nucleic Acids Res., 43, 8801-8816. doi: 10.1093/nar/gkv774. Crystal structure of sulfolobus solfataricus o6-methylguanine methyltransferase in complex with modified DNA. SNAP output
5a0m hydrolase-DNA X-ray (2.9 Å) Prieto J, Redondo P, Merino N, Villate M, Montoya G, Blanco FJ, Molina R (2016) "Structure of the I-Scei Nuclease Complexed with its DsDNA Target and Three Catalytic Metal Ions." Acta Crystallogr.,Sect.F, 72, 473. doi: 10.1107/S2053230X16007512. The crystal structure of i-scei in complex with its target DNA in the presence of mn. SNAP output
5a0v hydrolase-RNA X-ray (2.8 Å) Pei XY, Bralley P, Jones GH, Luisi BF (2015) "Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J." Nucleic Acids Res., 43, 8066. doi: 10.1093/NAR/GKV732. Catalysis and 5' end sensing by ribonuclease rnase j of the metallo- beta-lactamase family. SNAP output
5a0w hydrolase-DNA X-ray (2.2 Å) Molina R, Besker N, Prieto J, Montoya G, D'Abramo M "Structural and Dynamical Characterization of the I- Dmo Catalytic Activity." The crystal structure of i-dmoi e117a in complex with its target DNA and in the presence of 2mm mn. SNAP output
5a39 replication X-ray (2.8 Å) Koch SC, Kuper J, Gasteiger KL, Simon N, Strasser R, Eisen D, Geiger S, Schneider S, Kisker C, Carell T (2015) "Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion by Rad14 (Xpa)." Proc.Natl.Acad.Sci.USA, 112, 8272. doi: 10.1073/PNAS.1508509112. Structure of rad14 in complex with cisplatin containing DNA. SNAP output
5a3d DNA binding protein X-ray (1.8 Å) Koch SC, Kuper J, Gasteiger KL, Simon N, Strasser R, Eisen D, Geiger S, Schneider S, Kisker C, Carell T (2015) "Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion by Rad14 (Xpa)." Proc.Natl.Acad.Sci.USA, 112, 8272. doi: 10.1073/PNAS.1508509112. Structural insights into the recognition of cisplatin and aaf-dg lesions by rad14 (xpa). SNAP output
5a72 hydrolase-DNA X-ray (2.6 Å) Molina R, Redondo P, Lopez-Mendez B, Villate M, Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2015) "Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification." J.Biol.Chem., 290, 28727. doi: 10.1074/JBC.M115.678342. Crystal structure of the homing endonuclease i-cvui in complex with its target (sro1.3) in the presence of 2 mm ca. SNAP output
5a74 hydrolase-DNA X-ray (2.5 Å) Molina R, Redondo P, Lopez-Mendez B, Villate M, Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2015) "Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification." J.Biol.Chem., 290, 28727. doi: 10.1074/JBC.M115.678342. Crystal structure of the homing endonuclease i-cvui in complex with its target (sro1.3) in the presence of 2 mm mn. SNAP output
5a77 hydrolase-DNA X-ray (2.5 Å) Molina R, Redondo P, Lopez-Mendez B, Villate M, Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2015) "Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification." J.Biol.Chem., 290, 28727. doi: 10.1074/JBC.M115.678342. Crystal structure of the homing endonuclease i-cvui in complex with i- crei target (c1221) in the presence of 2 mm mg revealing DNA cleaved. SNAP output
5a78 hydrolase-DNA X-ray (2.5 Å) Molina R, Redondo P, Lopez-Mendez B, Villate M, Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P, Prieto J, Montoya G (2015) "Crystal Structure of the Homing Endonuclease I-Cvui Provides a New Template for Genome Modification." J.Biol.Chem., 290, 28727. doi: 10.1074/JBC.M115.678342. Crystal structure of the homing endonuclease i-cvui in complex with i- crei target (c1221) in the presence of 2 mm mg revealing DNA not cleaved. SNAP output
5ak9 hydrolase X-ray (2.601 Å) Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J (2015) "Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold." J.Biol.Chem., 290, 18534. doi: 10.1074/JBC.M115.658666. The crystal structure of i-dmoi q42ak120m in complex with its target DNA in the presence of 2mm mn. SNAP output
5akf hydrolase X-ray (2.45 Å) Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J (2015) "Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold." J.Biol.Chem., 290, 18534. doi: 10.1074/JBC.M115.658666. The crystal structure of i-dmoi q42ak120m in complex with its target DNA nicked in the coding strand a and in the presence of 2mm mn. SNAP output
5akm hydrolase X-ray (2.4 Å) Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J (2015) "Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold." J.Biol.Chem., 290, 18534. doi: 10.1074/JBC.M115.658666. The crystal structure of i-dmoi g20s in complex with its target DNA in the presence of 2mm mg. SNAP output
5akn hydrolase-DNA X-ray (2.75 Å) Molina R, Marcaida MJ, Redondo P, Marenchino M, Duchateau P, D'Abramo M, Montoya G, Prieto J (2015) "Engineering a Nickase on the Homing Endonuclease I-Dmoi Scaffold." J.Biol.Chem., 290, 18534. doi: 10.1074/JBC.M115.658666. The crystal structure of i-dmoi q42ak120m in complex with its target DNA nicked in the non-coding strand b and in the presence of 2mm mn. SNAP output
5aox translation X-ray (2.04 Å) Ahl V, Keller H, Schmidt S, Weichenrieder O (2015) "Retrotransposition and Crystal Structure of an Alu Rnp in the Ribosome-Stalling Conformation." Mol.Cell, 60, 715. doi: 10.1016/J.MOLCEL.2015.10.003. Human alu RNA retrotransposition complex in the ribosome-stalling conformation. SNAP output
5av5 DNA binding protein-DNA X-ray (2.4 Å) Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S (2015) "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation." Sci Rep, 5, 17204. doi: 10.1038/srep17204. Human nucleosome core particle. SNAP output
5av6 DNA binding protein-DNA X-ray (2.2 Å) Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S (2015) "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation." Sci Rep, 5, 17204. doi: 10.1038/srep17204. Human nucleosome core particle. SNAP output
5av8 DNA binding protein-DNA X-ray (2.2 Å) Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S (2015) "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation." Sci Rep, 5, 17204. doi: 10.1038/srep17204. Human nucleosome core particle. SNAP output
5av9 DNA binding protein-DNA X-ray (2.2 Å) Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S (2015) "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation." Sci Rep, 5, 17204. doi: 10.1038/srep17204. Human nucleosome core particle. SNAP output
5avb DNA binding protein-DNA X-ray (2.4 Å) Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S (2015) "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation." Sci Rep, 5, 17204. doi: 10.1038/srep17204. Human nucleosome core particle. SNAP output
5avc DNA binding protein-DNA X-ray (2.4 Å) Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S (2015) "Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation." Sci Rep, 5, 17204. doi: 10.1038/srep17204. Human nucleosome core particle. SNAP output
5awh RNA binding protein-DNA-RNA X-ray (2.0 Å) Miyoshi T, Ito K, Murakami R, Uchiumi T (2016) "Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute." Nat Commun, 7, 11846. doi: 10.1038/ncomms11846. Rhodobacter sphaeroides argonaute in complex with guide RNA-target DNA heteroduplex. SNAP output
5axw hydrolase-RNA-DNA X-ray (2.7 Å) Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O (2015) "Crystal Structure of Staphylococcus aureus Cas9." Cell, 162, 1113-1126. doi: 10.1016/j.cell.2015.08.007. Crystal structure of staphylococcus aureus cas9 in complex with sgrna and target DNA (ttgggt pam). SNAP output
5ay8 DNA binding protein-DNA X-ray (2.8 Å) Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H (2016) "Structure and function of human histone H3.Y nucleosome." Nucleic Acids Res., 44, 6127-6141. doi: 10.1093/nar/gkw202. Crystal structure of human nucleosome containing h3.y. SNAP output
5b0y DNA binding protein X-ray (2.557 Å) Suzuki Y, Horikoshi N, Kato D, Kurumizaka H (2016) "Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122." Biochem.Biophys.Res.Commun., 469, 483-489. doi: 10.1016/j.bbrc.2015.12.041. Crystal structure of the nucleosome containing histone h3 with the crotonylated lysine 122. SNAP output
5b0z DNA binding protein X-ray (1.987 Å) Suzuki Y, Horikoshi N, Kato D, Kurumizaka H (2016) "Crystal structure of the nucleosome containing histone H3 with crotonylated lysine 122." Biochem.Biophys.Res.Commun., 469, 483-489. doi: 10.1016/j.bbrc.2015.12.041. The crystal structure of the nucleosome containing h3.2, at 1.98 Å resolution. SNAP output
5b1l structural protein-DNA X-ray (2.35 Å) Ueda J, Harada A, Urahama T, Machida S, Maehara K, Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A, Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M, Iwamoto T, Isotani A, Ikawa M, Tachibana T, Okada Y, Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K (2017) "Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis." Cell Rep, 18, 593-600. doi: 10.1016/j.celrep.2016.12.065. The mouse nucleosome structure containing h3t. SNAP output
5b1m structural protein-DNA X-ray (2.34 Å) Ueda J, Harada A, Urahama T, Machida S, Maehara K, Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A, Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M, Iwamoto T, Isotani A, Ikawa M, Tachibana T, Okada Y, Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K (2017) "Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis." Cell Rep, 18, 593-600. doi: 10.1016/j.celrep.2016.12.065. The mouse nucleosome structure containing h3.1. SNAP output
5b24 structural protein-DNA X-ray (3.6 Å) Horikoshi N, Tachiwana H, Kagawa W, Osakabe A, Matsumoto S, Iwai S, Sugasawa K, Kurumizaka H (2016) "Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer." Biochem.Biophys.Res.Commun., 471, 117-122. doi: 10.1016/j.bbrc.2016.01.170. The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer. SNAP output
5b2i transcription-DNA X-ray (3.0 Å) Fujii Y, Wakamori M, Umehara T, Yokoyama S (2016) "Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation." Febs Open Bio, 6, 498-514. doi: 10.1002/2211-5463.12064. Human nucleosome containing cpg unmethylated DNA. SNAP output
5b2j transcription-DNA X-ray (2.6 Å) Fujii Y, Wakamori M, Umehara T, Yokoyama S (2016) "Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation." Febs Open Bio, 6, 498-514. doi: 10.1002/2211-5463.12064. Human nucleosome containing cpg methylated DNA. SNAP output
5b2o hydrolase-RNA-DNA X-ray (1.7 Å) Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O (2016) "Structure and Engineering of Francisella novicida Cas9." Cell, 164, 950-961. doi: 10.1016/j.cell.2016.01.039. Crystal structure of francisella novicida cas9 in complex with sgrna and target DNA (tgg pam). SNAP output
5b2p hydrolase-RNA-DNA X-ray (1.7 Å) Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O (2016) "Structure and Engineering of Francisella novicida Cas9." Cell, 164, 950-961. doi: 10.1016/j.cell.2016.01.039. Crystal structure of francisella novicida cas9 in complex with sgrna and target DNA (tga pam). SNAP output
5b2q hydrolase-RNA-DNA X-ray (1.7 Å) Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O (2016) "Structure and Engineering of Francisella novicida Cas9." Cell, 164, 950-961. doi: 10.1016/j.cell.2016.01.039. Crystal structure of francisella novicida cas9 rha in complex with sgrna and target DNA (tgg pam). SNAP output
5b2r hydrolase-RNA-DNA X-ray (2.0 Å) Hirano S, Nishimasu H, Ishitani R, Nureki O (2016) "Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9." Mol.Cell, 61, 886-894. doi: 10.1016/j.molcel.2016.02.018. Crystal structure of the streptococcus pyogenes cas9 vqr variant in complex with sgrna and target DNA (tga pam). SNAP output
5b2s hydrolase-RNA-DNA X-ray (2.2 Å) Hirano S, Nishimasu H, Ishitani R, Nureki O (2016) "Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9." Mol.Cell, 61, 886-894. doi: 10.1016/j.molcel.2016.02.018. Crystal structure of the streptococcus pyogenes cas9 eqr variant in complex with sgrna and target DNA (tgag pam). SNAP output
5b2t hydrolase-RNA-DNA X-ray (2.2 Å) Hirano S, Nishimasu H, Ishitani R, Nureki O (2016) "Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9." Mol.Cell, 61, 886-894. doi: 10.1016/j.molcel.2016.02.018. Crystal structure of the streptococcus pyogenes cas9 vrer variant in complex with sgrna and target DNA (tgcg pam). SNAP output
5b31 DNA binding protein X-ray (2.2 Å) Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H (2016) "Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A." Open Biology, 6. doi: 10.1098/rsob.160127. The crystal structure of the heterotypic h2az-h2a nucleosome with h3.1.. SNAP output
5b32 DNA binding protein X-ray (2.35 Å) Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H (2016) "Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A." Open Biology, 6. doi: 10.1098/rsob.160127. The crystal structure of the heterotypic h2az-h2a nucleosome with h3.3.. SNAP output
5b33 DNA binding protein X-ray (2.925 Å) Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H (2016) "Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A." Open Biology, 6. doi: 10.1098/rsob.160127. The crystal structure of the h2az nucleosome with h3.3.. SNAP output
5b40 structural protein-DNA X-ray (3.33 Å) Machida S, Sekine S, Nishiyama Y, Horikoshi N, Kurumizaka H "Monoubiquitination of histones H2B and H4 changes the nucleosome stability without affecting the nucleosome structure." The nucleosome structure containing h2b-k120 and h4-k31 monoubiquitinations. SNAP output
5b43 hydrolase-RNA-DNA X-ray (2.8 Å) Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O (2016) "Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA." Cell, 165, 949-962. doi: 10.1016/j.cell.2016.04.003. Crystal structure of acidaminococcus sp. cpf1 in complex with crrna and target DNA. SNAP output
5b7j DNA binding protein-DNA NMR Guan L, He P, Yang F, Zhang Y, Hu Y, Ding J, Hua Y, Zhang Y, Ye Q, Hu J, Wang T, Jin C, Kong D (2017) "Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe." J. Biol. Chem., 292, 6056-6075. doi: 10.1074/jbc.M116.767806. Structure model of sap1-DNA complex. SNAP output
5bk4 hydrolase-DNA cryo-EM (3.9 Å) Noguchi Y, Yuan Z, Bai L, Schneider S, Zhao G, Stillman B, Speck C, Li H (2017) "Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model." Proc. Natl. Acad. Sci. U.S.A., 114, E9529-E9538. doi: 10.1073/pnas.1712537114. cryo-EM structure of mcm2-7 double hexamer on dsDNA. SNAP output
5bmz transcription X-ray (3.001 Å) Kim Y, Joachimiak G, Biglow L, Cobb G, Joachimiak A "Crystal Structure of Putative MarR Family Transcriptional Regulator HcaR from Acinetobacter sp. ADP complexed with 24mer DNA." Crystal structure of putative marr family transcriptional regulator hcar from acinetobacter sp. adp complexed with 24mer DNA.. SNAP output
5bng protein-DNA X-ray (3.5 Å) Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J (2015) "DNA-dependent formation of transcription factor pairs alters their binding specificity." Nature, 527, 384-388. doi: 10.1038/nature15518. Monomer of tale type homeobox transcription factor meis1 complexes with specific DNA. SNAP output
5bnh DNA binding protein-DNA X-ray (1.7 Å) Neculai D, Walker JR, Weigelt J, Bountra C, Edwards AM, Arrowsmith CH, Dhe-Paganon S "Co-crystal structure of the HLTF HIRAN domain with a ssDNA fragment." Crystal structure of the hltf hiran domain with a ssDNA fragment. SNAP output
5bol transferase-DNA X-ray (1.981 Å) Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC, Li D, Delaney JC, Wilson SH, Essigmann JM (2015) "Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer." Proc.Natl.Acad.Sci.USA, 112, E4571-E4580. doi: 10.1073/pnas.1507709112. DNA polymerase beta ternary complex with a templating 5clc and incoming dgtp analog. SNAP output
5bom transferase, lyase-DNA X-ray (2.0 Å) Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC, Li D, Delaney JC, Wilson SH, Essigmann JM (2015) "Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer." Proc.Natl.Acad.Sci.USA, 112, E4571-E4580. doi: 10.1073/pnas.1507709112. DNA polymerase beta binary complex with a templating 5clc. SNAP output
5box DNA binding protein X-ray (2.5 Å) Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W (2015) "Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein." J.Mol.Biol., 427, 3216-3229. doi: 10.1016/j.jmb.2015.08.012. Structure of trmbl2, an archaeal chromatin protein, shows a novel mode of DNA binding.. SNAP output
5bpc transferase, ligase-DNA X-ray (2.0 Å) Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC, Li D, Delaney JC, Wilson SH, Essigmann JM (2015) "Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer." Proc.Natl.Acad.Sci.USA, 112, E4571-E4580. doi: 10.1073/pnas.1507709112. DNA polymerase beta ternary complex with a templating 5clc and incoming datp analog. SNAP output
5bpd DNA binding protein X-ray (2.4 Å) Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W (2015) "Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein." J.Mol.Biol., 427, 3216-3229. doi: 10.1016/j.jmb.2015.08.012. Structure of trmbl2, an archaeal chromatin protein, shows a novel mode of DNA binding.. SNAP output
5bpi DNA binding protein X-ray (3.198 Å) Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W (2015) "Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein." J.Mol.Biol., 427, 3216-3229. doi: 10.1016/j.jmb.2015.08.012. Structure of trmbl2, an archaeal chromatin protein, shows a novel mode of DNA binding.. SNAP output
5bs3 isomerase-DNA-RNA X-ray (2.65 Å) Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Black T, Nargund R, Meinke PT, Olsen DB, Lagrutta A, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Sherer E, Joyce LA, Wei C, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Takano H, Shibasaki M, Yajima M, Nishimura A, Shibata T, Fukuda Y (2015) "Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2)." Bioorg.Med.Chem.Lett., 25, 1831-1835. doi: 10.1016/j.bmcl.2015.03.044. Crystal structure of s.a. gyrase in complex with compound 7. SNAP output
5bs8 isomerase-DNA X-ray (2.399 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5bt2 DNA binding protein-DNA X-ray (2.2 Å) Chia JY, Tan WS, Ng CL, Hu NJ, Foo HL, Ho KL (2016) "A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence." Sci Rep, 6, 31210. doi: 10.1038/srep31210. Mecp2 mbd domain (a140v) in complex with methylated DNA. SNAP output
5bta isomerase-DNA X-ray (2.55 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5btc isomerase-DNA X-ray (2.55 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5btd isomerase-DNA X-ray (2.497 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5btf isomerase-DNA X-ray (2.61 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5btg isomerase-DNA X-ray (2.5 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5bti isomerase-DNA X-ray (2.501 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5btl isomerase-DNA X-ray (2.5 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5btn isomerase-DNA X-ray (2.5 Å) Blower TR, Williamson BH, Kerns RJ, Berger JM (2016) "Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis." Proc.Natl.Acad.Sci.USA, 113, 1706-1713. doi: 10.1073/pnas.1525047113. Crystal structure of a topoisomerase ii complex. SNAP output
5bua transcription X-ray (1.812 Å) Vainer R, Cohen S, Shahar A, Zarivach R, Arbely E (2016) "Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode." J.Mol.Biol., 428, 3013-3025. doi: 10.1016/j.jmb.2016.06.009. Lysine 120-acetylated p53 DNA binding domain in a complex with DNA.. SNAP output
5byg DNA binding protein-DNA X-ray (2.5 Å) Musayev FN, Zarate-Perez F, Bishop C, Burgner JW, Escalante CR (2015) "Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1." J.Biol.Chem., 290, 27487-27499. doi: 10.1074/jbc.M115.669960. X-ray structure of aav2 obd-aavs1 complex 2:1. SNAP output
5c0y hydrolase X-ray (2.1 Å) Makino DL, Schuch B, Stegmann E, Baumgartner M, Basquin C, Conti E (2015) "RNA degradation paths in a 12-subunit nuclear exosome complex." Nature, 524, 54-58. doi: 10.1038/nature14865. Crystal structure of the rrp6 catalytic domain bound to poly(u) RNA. SNAP output
5c3e transferase-DNA-RNA X-ray (3.7 Å) Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G (2015) "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble." Mol.Cell, 59, 258-269. doi: 10.1016/j.molcel.2015.06.034. Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble. SNAP output
5c44 transferase-DNA-RNA X-ray (3.95 Å) Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G (2015) "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble." Mol.Cell, 59, 258-269. doi: 10.1016/j.molcel.2015.06.034. Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble. SNAP output
5c4a transferase-RNA-DNA X-ray (4.2 Å) Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G (2015) "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble." Mol.Cell, 59, 258-269. doi: 10.1016/j.molcel.2015.06.034. Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble. SNAP output
5c4j transferase-DNA-RNA X-ray (4.0 Å) Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G (2015) "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble." Mol.Cell, 59, 258-269. doi: 10.1016/j.molcel.2015.06.034. Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble. SNAP output
5c4x transferase-RNA-DNA X-ray (4.0 Å) Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G (2015) "Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble." Mol.Cell, 59, 258-269. doi: 10.1016/j.molcel.2015.06.034. Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble. SNAP output
5c51 transferase-DNA X-ray (3.426 Å) Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW (2015) "Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma." Proc.Natl.Acad.Sci.USA, 112, 8596-8601. doi: 10.1073/pnas.1421733112. Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma. SNAP output
5c52 transferase-DNA X-ray (3.637 Å) Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW (2015) "Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma." Proc.Natl.Acad.Sci.USA, 112, 8596-8601. doi: 10.1073/pnas.1421733112. Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma. SNAP output
5c53 transferase-DNA X-ray (3.567 Å) Sohl CD, Szymanski MR, Mislak AC, Shumate CK, Amiralaei S, Schinazi RF, Anderson KS, Yin YW (2015) "Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma." Proc.Natl.Acad.Sci.USA, 112, 8596-8601. doi: 10.1073/pnas.1421733112. Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma. SNAP output
5c5j transferase-DNA X-ray (2.1 Å) Kottur J, Nair DT (2016) "Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics." Angew.Chem.Int.Ed.Engl., 55, 2397-2400. doi: 10.1002/anie.201509340. Poymerase nucleotide complex. SNAP output
5c8e transcription regulator-DNA X-ray (3.89 Å) Jost M, Fernandez-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PY, Kang G, Padmanabhan S, Elias-Arnanz M, Drennan CL (2015) "Structural basis for gene regulation by a B12-dependent photoreceptor." Nature, 526, 536-541. doi: 10.1038/nature14950. Crystal structure of thermus thermophilus carh bound to adenosylcobalamin and a 26-bp DNA segment. SNAP output
5ca7 transferase-DNA X-ray (2.522 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda- mgdgtp binary and complex with 6 paired DNA. SNAP output
5cbx DNA binding protein-DNA X-ray (2.0 Å) Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA (2016) "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space." Proc.Natl.Acad.Sci.USA, 113, 326-331. doi: 10.1073/pnas.1518960113. Ancgr DNA binding domain - (+)gre complex. SNAP output
5cby DNA binding protein-DNA X-ray (1.997 Å) Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA (2016) "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space." Proc.Natl.Acad.Sci.USA, 113, 326-331. doi: 10.1073/pnas.1518960113. Ancgr2 DNA binding domain - (+)gre complex. SNAP output
5cbz DNA binding protein-DNA X-ray (2.2 Å) Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA (2016) "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space." Proc.Natl.Acad.Sci.USA, 113, 326-331. doi: 10.1073/pnas.1518960113. Ancmr DNA binding domain - (+)gre complex. SNAP output
5cc0 DNA binding protein-DNA X-ray (2.405 Å) Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA (2016) "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space." Proc.Natl.Acad.Sci.USA, 113, 326-331. doi: 10.1073/pnas.1518960113. Ancsr2 - tslp ngre complex. SNAP output
5cc1 DNA binding protein-DNA X-ray (2.302 Å) Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund EA (2016) "Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space." Proc.Natl.Acad.Sci.USA, 113, 326-331. doi: 10.1073/pnas.1518960113. S425g glucocorticoid receptor DNA binding domain - (+)gre complex. SNAP output
5cdm isomerase X-ray (2.5 Å) Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN (2015) "Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin." Nat Commun, 6, 10048. doi: 10.1038/ncomms10048. 2.5a structure of qpt-1 with s.aureus DNA gyrase and DNA. SNAP output
5cdn isomerase X-ray (2.79 Å) Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN (2015) "Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin." Nat Commun, 6, 10048. doi: 10.1038/ncomms10048. 2.8a structure of etoposide with s.aureus DNA gyrase and DNA. SNAP output
5cdo isomerase X-ray (3.15 Å) Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN (2015) "Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin." Nat Commun, 6, 10048. doi: 10.1038/ncomms10048. 3.15a structure of qpt-1 with s.aureus DNA gyrase and DNA. SNAP output
5cdp isomerase X-ray (2.45 Å) Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN (2015) "Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin." Nat Commun, 6, 10048. doi: 10.1038/ncomms10048. 2.45a structure of etoposide with s.aureus DNA gyrase and DNA. SNAP output
5cdq hydrolase X-ray (2.95 Å) Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN (2015) "Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin." Nat Commun, 6, 10048. doi: 10.1038/ncomms10048. 2.95a structure of moxifloxacin with s.aureus DNA gyrase and DNA. SNAP output
5cdr isomerase X-ray (2.65 Å) Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R, Theobald AJ, Stavenger RA, Bax BD, Gwynn MN (2015) "Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin." Nat Commun, 6, 10048. doi: 10.1038/ncomms10048. 2.65 structure of s.aureus DNA gyrase and artificially nicked DNA. SNAP output
5cg8 oxidoreductase-DNA X-ray (2.702 Å) Hashimoto H, Pais JE, Dai N, Correa IR, Zhang X, Zheng Y, Cheng X (2015) "Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA." Nucleic Acids Res., 43, 10713-10721. doi: 10.1093/nar/gkv870. Ngtet1 in complex with 5hmc DNA. SNAP output
5cg9 oxidoreductase-DNA X-ray (2.693 Å) Hashimoto H, Pais JE, Dai N, Correa IR, Zhang X, Zheng Y, Cheng X (2015) "Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA." Nucleic Acids Res., 43, 10713-10721. doi: 10.1093/nar/gkv870. Ngtet1 in complex with 5mc DNA in space group p3221. SNAP output
5chg transferase-DNA X-ray (2.9 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda l431a mutant- mgdgtp binary and complex with 6 paired DNA. SNAP output
5chi hydrolase-DNA X-ray (2.472 Å) Kim JS, Sambalkhundev GD, Kim SH, Han A, Ko SM, Hwang KY, Lee WC "Structural basis of two-nucleotide removal of ssDNA by a cryptic RNase H fold 3'-5' exonuclease PF2046 from Pyrococcus furiosus." Crystal structure of pf2046 in complex with ssDNA. SNAP output
5chz hydrolase-DNA X-ray (1.83 Å) Ouzon-Shubeita H, Lin Y-L, Lee S "Structure of wild-type human MBD4 bound to a G:T mismatch." Structure of wild-type human mbd4 bound to a g:t mismatch. SNAP output
5ciy transferase-DNA X-ray (1.594 Å) Rondelet G, Dal Maso T, Willems L, Wouters J (2016) "Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B." J.Struct.Biol., 194, 357-367. doi: 10.1016/j.jsb.2016.03.013. Structural basis of the recognition of h3k36me3 by dnmt3b pwwp domain. SNAP output
5ciz gene regulation-DNA X-ray (5.01 Å) Lara-Gonzalez S, Machado ACD, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL (2020) "The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element." Biochemistry. doi: 10.1021/acs.biochem.0c00571. E. coli RNA polymerase alpha subunit ctd in complex with cap and DNA: a(5)-tract binding site for alpha ctd. SNAP output
5cj7 transferase-DNA X-ray (2.901 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda l431a mutant- mgdttp binary and complex with 6 paired DNA. SNAP output
5cky transcription-DNA X-ray (2.62 Å) Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C, Garcia-Diaz M (2016) "Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion." J.Mol.Biol., 428, 2542-2556. doi: 10.1016/j.jmb.2015.10.021. Crystal structure of the mterf1 r162a substitution bound to the termination sequence.. SNAP output
5cl3 hydrolase-DNA X-ray (1.971 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog (100% substrate at 4 hours). SNAP output
5cl4 hydrolase-DNA X-ray (1.866 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (71% substrate-29% product at 24 hours). SNAP output
5cl5 hydrolase-DNA X-ray (1.569 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (51% substrate-49% product at 48 hours). SNAP output
5cl6 hydrolase-DNA X-ray (1.541 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (33% substrate-67% product at 72 hours). SNAP output
5cl7 hydrolase-DNA X-ray (1.44 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (18% substrate-82% product at 96 hours). SNAP output
5cl8 hydrolase-DNA X-ray (1.38 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site and a free nucleobase (100% product at 144 hours). SNAP output
5cl9 hydrolase-DNA X-ray (1.538 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site and a free nucleobase (100% product at 240 hours). SNAP output
5cla hydrolase-DNA X-ray (1.541 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing an abasic site and a free nucleobase (100% product at 360 hours). SNAP output
5clb hydrolase-DNA X-ray (1.766 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog (9-mer a). SNAP output
5clc hydrolase-DNA X-ray (1.729 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing a 3-methyladenine analog (9-mer b). SNAP output
5cld hydrolase-DNA X-ray (1.541 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing an oxocarbenium-intermediate analog and a free 3-methyladenine nucleobase. SNAP output
5cle hydrolase-DNA X-ray (1.73 Å) Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF (2015) "The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions." Nature, 527, 254-258. doi: 10.1038/nature15728. Alkylpurine DNA glycosylase alkd bound to DNA containing an abasic-site analog and a free 3-methyladenine nucleobase. SNAP output
5clv transcription X-ray (2.5 Å) Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LE, Roessle M, Thomas CM, Hyde EI, White SA (2016) "Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator." Nucleic Acids Res., 44, 4947-4956. doi: 10.1093/nar/gkw191. Crystal structure of kora-operator DNA complex (kora-oa). SNAP output
5cm3 transcription X-ray (2.302 Å) Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LE, Roessle M, Thomas CM, Hyde EI, White SA (2016) "Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator." Nucleic Acids Res., 44, 4947-4956. doi: 10.1093/nar/gkw191. Crystal structure of kora, a plasmid-encoded, global transcription regulator. SNAP output
5cmx hydrolase X-ray (2.98 Å) Russo Krauss I, Spiridonova V, Pica A, Napolitano V, Sica F (2016) "Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding." Nucleic Acids Res., 44, 983-991. doi: 10.1093/nar/gkv1384. X-ray structure of the complex between human alpha thrombin and a duplex-quadruplex 31-mer DNA aptamer. SNAP output
5cnq replication X-ray (2.602 Å) Liu Y, Freeman AD, Declais AC, Wilson TJ, Gartner A, Lilley DM (2015) "Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA." Cell Rep, 13, 2565-2575. doi: 10.1016/j.celrep.2015.11.042. Crystal structure of the holliday junction-resolving enzyme gen1 (wt) in complex with product DNA, mg2+ and mn2+ ions. SNAP output
5co0 transcription-DNA X-ray (2.65 Å) Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C, Garcia-Diaz M (2016) "Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion." J.Mol.Biol., 428, 2542-2556. doi: 10.1016/j.jmb.2015.10.021. Crystal structure of the mterf1 y288a substitution bound to the termination sequence.. SNAP output
5co8 hydrolase X-ray (2.4 Å) Liu Y, Freeman AD, Declais AC, Wilson TJ, Gartner A, Lilley DM (2015) "Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA." Cell Rep, 13, 2565-2575. doi: 10.1016/j.celrep.2015.11.042. Crystal structure of the holliday junction-resolving enzyme gen1 (wt) in complex with product DNA and mg2+ ion. SNAP output
5cp2 transferase-DNA X-ray (2.36 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda l431a mutant- apoenzyme and complex with 6 paired DNA. SNAP output
5cp6 structural protein-DNA X-ray (2.6 Å) Ma Z, Palermo G, Adhireksan Z, Murray BS, von Erlach T, Dyson PJ, Rothlisberger U, Davey CA (2016) "An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode." Angew.Chem.Int.Ed.Engl., 55, 7441-7444. doi: 10.1002/anie.201602145. Nucleosome core particle with adducts from the anticancer compound, [(eta6-5,8,9,10-tetrahydroanthracene)ru(ethylenediamine)cl][pf6]. SNAP output
5cpi structural protein-DNA X-ray (2.902 Å) Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H (2015) "Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA." Open Biology, 5. doi: 10.1098/rsob.150128. Nucleosome containing unmethylated sat2r DNA. SNAP output
5cpj "structural protein-DNA X-ray (3.15 Å) Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H (2015) "Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA." Open Biology, 5. doi: 10.1098/rsob.150128. Nucleosome containing methylated sat2r DNA. SNAP output
5cpk structural protein-DNA X-ray (2.632 Å) Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H (2015) "Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA." Open Biology, 5. doi: 10.1098/rsob.150128. Nucleosome containing methylated sat2l DNA. SNAP output
5cqq transcription-DNA X-ray (3.1 Å) Gao GN, Wang M, Yang N, Huang Y, Xu RM (2015) "Structure of Zeste-DNA Complex Reveals a New Modality of DNA Recognition by Homeodomain-Like Proteins." J.Mol.Biol., 427, 3824-3833. doi: 10.1016/j.jmb.2015.10.008. Crystal structure of the drosophila zeste DNA binding domain in complex with DNA. SNAP output
5cr0 transferase-DNA X-ray (2.75 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda l431a mutant- mgdctp binary and complex with 6 paired DNA. SNAP output
5cr2 hydrolase X-ray (2.9 Å) Zorzini V, Mernik A, Lah J, Sterckx YG, De Jonge N, Garcia-Pino A, De Greve H, Versees W, Loris R (2016) "Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF." J.Biol.Chem., 291, 10950-10960. doi: 10.1074/jbc.M116.715912. E. coli mazf in complex with single strand DNA substrate analog. SNAP output
5crj transcription-DNA X-ray (2.59 Å) Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C, Garcia-Diaz M (2016) "Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion." J.Mol.Biol., 428, 2542-2556. doi: 10.1016/j.jmb.2015.10.021. Crystal structure of the mterf1 f322a substitution bound to the termination sequence.. SNAP output
5crk transcription-DNA X-ray (2.48 Å) Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C, Garcia-Diaz M (2016) "Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion." J.Mol.Biol., 428, 2542-2556. doi: 10.1016/j.jmb.2015.10.021. Crystal structure of the mterf1 f243a substitution bound to the termination sequence.. SNAP output
5crx protein-DNA X-ray (2.7 Å) Guo F, Gopaul DN, Van Duyne GD (1999) "Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse." Proc.Natl.Acad.Sci.USA, 96, 7143-7148. doi: 10.1073/pnas.96.13.7143. Asymmetric DNA-bending in the cre-loxp site-specific recombination synapse. SNAP output
5cwr transferase-DNA X-ray (2.5 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Crystal structure of human DNA polymerase lambda l431a mutant in complex with a one nucleotide DNA gap and dctp. SNAP output
5cy1 hydrolase, ligase-DNA X-ray (3.4 Å) Montano SP, Rice PA "Tn3 resolvase - accessory site complexes: DNA geometry dictates complex geometry." Tn3 resolvase - site iii complex crystal form i. SNAP output
5cy2 recombination-DNA X-ray (4.0 Å) Montano SP, Rice PA "Structures of resolvase - accessory site complexes." Tn3 resolvase - site iii complex crystal form ii. SNAP output
5cys hydrolase-DNA X-ray (2.45 Å) Malik SS, Varney KM, Pozharski E, Drohat AC (2015) "Characterizing the enzyme-product complexes of thymine DNA glycosylase using crystallography and NMR." Nucleic Acids Res. Structure of the enzyme-product complex resulting from tdg action on a gcac mismatch. SNAP output
5czz hydrolase-RNA-DNA X-ray (2.6 Å) Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O (2015) "Crystal Structure of Staphylococcus aureus Cas9." Cell, 162, 1113-1126. doi: 10.1016/j.cell.2015.08.007. Crystal structure of staphylococcus aureus cas9 in complex with sgrna and target DNA (ttgaat pam). SNAP output
5d23 transcription-DNA X-ray (1.95 Å) Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ (2016) "Structures of an all-alpha protein running along the DNA major groove." Nucleic Acids Res. doi: 10.1093/nar/gkw133. The crystal structure of stpr from bombyx mori in complex with 13-bp DNA derived from the +290 site of fibroin gene. SNAP output
5d2q transcription-DNA X-ray (2.4 Å) Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ (2016) "Structures of an all-alpha protein running along the DNA major groove." Nucleic Acids Res. doi: 10.1093/nar/gkw133. Crystal structure of stpr from bombyx mori in complex with 20-bp DNA derived from +290 site of the fibroin gene. SNAP output
5d2s transcription-DNA X-ray (2.2 Å) Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X, Wu Q, Chen Y, Zhou CZ (2016) "Structures of an all-alpha protein running along the DNA major groove." Nucleic Acids Res. doi: 10.1093/nar/gkw133. Crystal structure of stpr from bombyx mori in complex with 18-bp DNA containing four repetitive units of atac. SNAP output
5d39 transcription-DNA X-ray (3.2 Å) Li J, Rodriguez JP, Niu F, Pu M, Wang J, Hung LW, Shao Q, Zhu Y, Ding W, Liu Y, Da Y, Yao Z, Yang J, Zhao Y, Wei GH, Cheng G, Liu ZJ, Ouyang S (2016) "Structural basis for DNA recognition by STAT6." Proc.Natl.Acad.Sci.USA, 113, 13015-13020. doi: 10.1073/pnas.1611228113. Transcription factor-DNA complex. SNAP output
5d3g transferase X-ray (2.3 Å) Miller MT, Tuske S, Das K, DeStefano JJ, Arnold E (2016) "Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer." Protein Sci., 25, 46-55. doi: 10.1002/pro.2776. Structure of hiv-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer. SNAP output
5d46 transferase X-ray (2.8 Å) Loc'h J, Rosario S, Delarue M (2016) "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination." Structure, 24, 1452-1463. doi: 10.1016/j.str.2016.06.014. Structural basis for a new templated activity by terminal deoxynucleotidyl transferase: implications for v(d)j recombination. SNAP output
5d49 transferase X-ray (1.99 Å) Loc'h J, Rosario S, Delarue M (2016) "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination." Structure, 24, 1452-1463. doi: 10.1016/j.str.2016.06.014. Structural basis for a new templated activity by terminal deoxynucleotidyl transferase: implications for v(d)j recombination. SNAP output
5d4b transferase X-ray (2.66 Å) Loc'h J, Rosario S, Delarue M (2016) "Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination." Structure, 24, 1452-1463. doi: 10.1016/j.str.2016.06.014. Structural basis for a new templated activity by terminal deoxynucleotidyl transferase: implications for v(d)j recombination. SNAP output
5d4c transcription-DNA X-ray (3.28 Å) Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE (2016) "The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA." Nature, 535, 444-447. doi: 10.1038/nature18622. Crystal structure of thermus thermophilus product complex for transcription initiation with atp and ctp. SNAP output
5d4d transcription-DNA X-ray (3.0 Å) Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE (2016) "The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA." Nature, 535, 444-447. doi: 10.1038/nature18622. Crystal structure of thermus thermophilus product complex for transcription initiation with nad and ctp. SNAP output
5d4e transcription-DNA X-ray (3.08 Å) Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE (2016) "The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA." Nature, 535, 444-447. doi: 10.1038/nature18622. Crystal structure of thermus thermophilus product complex for transcription initiation with 3'-dephosphate-coa and ctp. SNAP output
5d4r transcription-DNA X-ray (2.07 Å) Jain D, Narayanan N, Nair DT (2016) "Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators." J.Biol.Chem., 291, 1235-1242. doi: 10.1074/jbc.M115.689695. Crystal structure of arar(dbd) in complex with operator ore1. SNAP output
5d4s transcription-DNA X-ray (1.972 Å) Jain D, Narayanan N, Nair DT (2016) "Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators." J.Biol.Chem., 291, 1235-1242. doi: 10.1074/jbc.M115.689695. Crystal structure of arar(dbd) in complex with operator orx1. SNAP output
5d5u transcription-DNA X-ray (2.91 Å) Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU, Bracher A (2016) "Structure of human heat-shock transcription factor 1 in complex with DNA." Nat.Struct.Mol.Biol., 23, 140-146. doi: 10.1038/nsmb.3149. Crystal structure of human hsf1 with hse DNA. SNAP output
5d5v transcription-DNA X-ray (2.55 Å) Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU, Bracher A (2016) "Structure of human heat-shock transcription factor 1 in complex with DNA." Nat.Struct.Mol.Biol., 23, 140-146. doi: 10.1038/nsmb.3149. Crystal structure of human hsf1 with satellite iii repeat DNA. SNAP output
5d5w transcription X-ray (2.35 Å) Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU, Bracher A (2016) "Structure of human heat-shock transcription factor 1 in complex with DNA." Nat.Struct.Mol.Biol., 23, 140-146. doi: 10.1038/nsmb.3149. Crystal structure of chaetomium thermophilum skn7 with hse DNA. SNAP output
5d5x transcription X-ray (2.4 Å) Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU, Bracher A (2016) "Structure of human heat-shock transcription factor 1 in complex with DNA." Nat.Struct.Mol.Biol., 23, 140-146. doi: 10.1038/nsmb.3149. Crystal structure of chaetomium thermophilum skn7 with ssre DNA. SNAP output
5d8c transcription-DNA X-ray (2.25 Å) Counago RM, Chen NH, Chang CW, Djoko KY, McEwan AG, Kobe B (2016) "Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region." Nucleic Acids Res., 44, 6981-6993. doi: 10.1093/nar/gkw543. Crystal structure of hinmlr, a merr family regulator lacking the sensor domain, bound to promoter DNA. SNAP output
5d8f DNA binding protein-DNA X-ray (2.35 Å) Li YH, Gao ZQ, Dong YH "crystal structure of SSB and ssDNA complex from homo sapiens." Crystal structure of ssb and ssDNA complex from homo sapiens. SNAP output
5d8k transcription-DNA X-ray (1.728 Å) Jaeger AM, Pemble CW, Sistonen L, Thiele DJ (2016) "Structures of HSF2 reveal mechanisms for differential regulation of human heat-shock factors." Nat.Struct.Mol.Biol., 23, 147-154. doi: 10.1038/nsmb.3150. Human hsf2 DNA-binding domain bound to 2-site hse DNA at 1.73 angstroms resolution. SNAP output
5d8l transcription-DNA X-ray (2.069 Å) Jaeger AM, Pemble CW, Sistonen L, Thiele DJ (2016) "Structures of HSF2 reveal mechanisms for differential regulation of human heat-shock factors." Nat.Struct.Mol.Biol., 23, 147-154. doi: 10.1038/nsmb.3150. Human hsf2 DNA binding domain in complex with 3-site hse DNA at 2.1 angstroms resolution. SNAP output
5d9i replication-DNA X-ray (1.7 Å) Meinke G, Phelan PJ, Fradet-Turcotte A, Bohm A, Archambault J, Bullock PA (2011) "Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA." J. Virol., 85, 818-827. doi: 10.1128/JVI.01738-10. Sv40 large t antigen origin binding domain bound to artificial DNA fork. SNAP output
5d9y oxidoreductase-DNA X-ray (1.971 Å) Hu L, Lu J, Cheng J, Rao Q, Li Z, Hou H, Lou Z, Zhang L, Li W, Gong W, Liu M, Sun C, Yin X, Li J, Tan X, Wang P, Wang Y, Fang D, Cui Q, Yang P, He C, Jiang H, Luo C, Xu Y (2015) "Structural insight into substrate preference for TET-mediated oxidation." Nature, 527, 118-122. doi: 10.1038/nature15713. Crystal structure of tet2-5fc complex. SNAP output
5dac hydrolase X-ray (2.503 Å) Seifert FU, Lammens K, Stoehr G, Kessler B, Hopfner KP (2016) "Structural mechanism of ATP-dependent DNA binding and DNA end bridging by eukaryotic Rad50." Embo J., 35, 759-772. doi: 10.15252/embj.201592934. Atp-gamma-s bound rad50 from chaetomium thermophilum in complex with DNA. SNAP output
5db6 transferase-DNA X-ray (2.83 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the n7mg base paired with a dc. SNAP output
5db7 transferase-DNA X-ray (2.209 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the n7mg base paired with a dt. SNAP output
5db8 transferase-DNA X-ray (2.547 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the n7mg base paired with a da. SNAP output
5db9 transferase-DNA X-ray (2.45 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the n7mg base paired with a dg. SNAP output
5dba transferase-DNA X-ray (1.965 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the dg base paired with a dt. SNAP output
5dbb transferase-DNA X-ray (2.25 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the dg base paired with a da. SNAP output
5dbc transferase-DNA X-ray (2.402 Å) Kou Y, Koag MC, Lee S (2015) "N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA." J.Am.Chem.Soc., 137, 14067-14070. doi: 10.1021/jacs.5b10172. Structure of human DNA polymerase beta host-guest complex with the dg base paired with a dg. SNAP output
5ddg transcription regulator-DNA X-ray (3.06 Å) Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A (2015) "A novel transcriptional regulator of L-arabinose utilization in human gut bacteria." Nucleic Acids Res., 43, 10546-10559. doi: 10.1093/nar/gkv1005. The structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with target double strand DNA. SNAP output
5ddm transferase-DNA X-ray (2.802 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Human DNA polymerase lambda- apoenzyme and complex with 6 paired DNA. SNAP output
5deu oxidoreductase-DNA X-ray (1.801 Å) Hu L, Lu J, Cheng J, Rao Q, Li Z, Hou H, Lou Z, Zhang L, Li W, Gong W, Liu M, Sun C, Yin X, Li J, Tan X, Wang P, Wang Y, Fang D, Cui Q, Yang P, He C, Jiang H, Luo C, Xu Y (2015) "Structural insight into substrate preference for TET-mediated oxidation." Nature, 527, 118-122. doi: 10.1038/nature15713. Crystal structure of tet2-5hmc complex. SNAP output
5dff lyase-DNA X-ray (1.57 Å) Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH (2015) "Capturing snapshots of APE1 processing DNA damage." Nat.Struct.Mol.Biol., 22, 924-931. doi: 10.1038/nsmb.3105. Human ape1 product complex. SNAP output
5dfh lyase-DNA X-ray (1.949 Å) Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH (2015) "Capturing snapshots of APE1 processing DNA damage." Nat.Struct.Mol.Biol., 22, 924-931. doi: 10.1038/nsmb.3105. Human ape1 mismatch product complex. SNAP output
5dfi lyase-DNA X-ray (1.63 Å) Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH (2015) "Capturing snapshots of APE1 processing DNA damage." Nat.Struct.Mol.Biol., 22, 924-931. doi: 10.1038/nsmb.3105. Human ape1 phosphorothioate substrate complex. SNAP output
5dfj lyase-DNA X-ray (1.85 Å) Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH (2015) "Capturing snapshots of APE1 processing DNA damage." Nat.Struct.Mol.Biol., 22, 924-931. doi: 10.1038/nsmb.3105. Human ape1 e96q-d210n mismatch substrate complex. SNAP output
5dg0 hydrolase,lyase-DNA X-ray (1.8 Å) Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS, Wilson SH (2015) "Capturing snapshots of APE1 processing DNA damage." Nat.Struct.Mol.Biol., 22, 924-931. doi: 10.1038/nsmb.3105. Human ape1 phosphorothioate substrate complex with mn2+. SNAP output
5dg7 transferase-DNA X-ray (2.26 Å) Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M (2016) "Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta." J.Biol.Chem., 291, 14134-14145. doi: 10.1074/jbc.M116.732487. Crystal structure of human DNA polymerase eta inserting dttp across a DNA template containing 1,n6-ethenodeoxyadenosine lesion. SNAP output
5dg8 transferase-DNA X-ray (2.12 Å) Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M (2016) "Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta." J.Biol.Chem., 291, 14134-14145. doi: 10.1074/jbc.M116.732487. Crystal structure of human DNA polymerase eta inserting dampnpp across a DNA template containing 1,n6-ethenodeoxyadenosine lesion. SNAP output
5dg9 transferase-DNA X-ray (2.15 Å) Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M (2016) "Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta." J.Biol.Chem., 291, 14134-14145. doi: 10.1074/jbc.M116.732487. Crystal structure of human DNA polymerase eta inserting dgmpnpp across a DNA template containing 1,n6-ethenodeoxyadenosine lesion. SNAP output
5dga transferase-DNA X-ray (2.3 Å) Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M (2016) "Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta." J.Biol.Chem., 291, 14134-14145. doi: 10.1074/jbc.M116.732487. Crystal structure of human DNA polymerase eta extending an 1,n6-ethenodeoxyadenosine : dt pair by inserting dtmpnpp opposite template da. SNAP output
5dgb transferase-DNA X-ray (1.79 Å) Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP, Egli M (2016) "Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta." J.Biol.Chem., 291, 14134-14145. doi: 10.1074/jbc.M116.732487. Crystal structure of human DNA polymerase eta extending an 1,n6-ethenodeoxyadenosine : da pair by inserting dtmpnpp opposite template da. SNAP output
5dkw transferase-DNA X-ray (2.689 Å) Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD (2016) "Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda." J.Am.Chem.Soc., 138, 2389-2398. doi: 10.1021/jacs.5b13368. Ternary crystal structure of polymerase lambda with a ga mispair at the primer terminus with ca2+ in the active. SNAP output
5dlf transferase-DNA X-ray (1.97 Å) O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ (2016) "Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta." Chem Sci, 7, 4896-4904. doi: 10.1039/C6SC00666C. Crystal structure of human DNA polymerase eta inserting datp opposite o4-methylhymidine. SNAP output
5dlg transferase-DNA X-ray (2.351 Å) O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ (2016) "Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta." Chem Sci, 7, 4896-4904. doi: 10.1039/C6SC00666C. Crystal structure of human DNA polymerase eta inserting dgmpnpp opposite o4-methylhymidine. SNAP output
5dlj hydrolase-DNA X-ray (2.6 Å) Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y (2015) "Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems." Cell, 163, 840-853. doi: 10.1016/j.cell.2015.10.008. Crystal structure of cas-DNA-n1 complex. SNAP output
5dlo hydrolase X-ray (1.401 Å) Zorzini V, Loris R "Substrate recognition, regulation mechanism and activity regulation of MazF mRNA interferase." S. aureus mazf in complex with substrate analogue. SNAP output
5dnm structural protein-DNA X-ray (2.81 Å) Adhireksan Z, Palermo G, Riedel T, Ma Z, Muhammad R, Rothlisberger U, Dyson PJ, Davey CA (2017) "Allosteric cross-talk in chromatin can mediate drug-drug synergy." Nat Commun, 8, 14860. doi: 10.1038/ncomms14860. Nucleosome core particle containing adducts of ruthenium(ii)-toluene pta complex. SNAP output
5dnn structural protein-DNA X-ray (2.8 Å) Adhireksan Z, Palermo G, Riedel T, Ma Z, Muhammad R, Rothlisberger U, Dyson PJ, Davey CA (2017) "Allosteric cross-talk in chromatin can mediate drug-drug synergy." Nat Commun, 8, 14860. doi: 10.1038/ncomms14860. Nucleosome core particle containing adducts of gold(i)-triethylphosphane and ruthenium(ii)-toluene pta complexes. SNAP output
5dny recombination-DNA X-ray (3.11 Å) Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim T, Song OK, Lee SE, Cho Y (2016) "ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex." Embo J., 35, 743-758. doi: 10.15252/embj.201592462. Structure of the atprs-mre11-rad50-DNA complex. SNAP output
5dqg transferase-DNA X-ray (2.29 Å) O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ (2016) "Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta." Chem Sci, 7, 4896-4904. doi: 10.1039/C6SC00666C. Crystal structure of human DNA polymerase eta inserting dampnpp opposite o4-ethylthymidine. SNAP output
5dqh transferase-DNA X-ray (1.99 Å) O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ (2016) "Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta." Chem Sci, 7, 4896-4904. doi: 10.1039/C6SC00666C. Crystal structure of human DNA polymerase eta inserting dgmpnpp opposite o4-ethylthymidine. SNAP output
5dqi transferase-DNA X-ray (2.3 Å) O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ (2016) "Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta." Chem Sci, 7, 4896-4904. doi: 10.1039/C6SC00666C. Crystal structure of human DNA polymerase eta extending an o4-ethylthymidine : da pair by inserting dctp opposite dg. SNAP output
5dqt hydrolase-DNA X-ray (3.1 Å) Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y (2015) "Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems." Cell, 163, 840-853. doi: 10.1016/j.cell.2015.10.008. Crystal structure of cas-DNA-22 complex. SNAP output
5dqu hydrolase-DNA X-ray (4.5 Å) Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y (2015) "Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems." Cell, 163, 840-853. doi: 10.1016/j.cell.2015.10.008. Crystal structure of cas-DNA-10 complex. SNAP output
5dqz hydrolase-DNA X-ray (2.7 Å) Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y (2015) "Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems." Cell, 163, 840-853. doi: 10.1016/j.cell.2015.10.008. Crystal structure of cas-DNA-pam complex. SNAP output
5ds4 hydrolase-DNA X-ray (3.2 Å) Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA (2015) "Foreign DNA capture during CRISPR-Cas adaptive immunity." Nature, 527, 535-538. doi: 10.1038/nature15760. Crystal structure the escherichia coli cas1-cas2 complex bound to protospacer DNA. SNAP output
5ds5 hydrolase-DNA X-ray (2.951 Å) Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA (2015) "Foreign DNA capture during CRISPR-Cas adaptive immunity." Nature, 527, 535-538. doi: 10.1038/nature15760. Crystal structure the escherichia coli cas1-cas2 complex bound to protospacer DNA and mg. SNAP output
5ds6 hydrolase-DNA X-ray (3.352 Å) Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA (2015) "Foreign DNA capture during CRISPR-Cas adaptive immunity." Nature, 527, 535-538. doi: 10.1038/nature15760. Crystal structure the escherichia coli cas1-cas2 complex bound to protospacer DNA with splayed ends. SNAP output
5ds9 DNA binding protein-DNA X-ray (2.561 Å) Hancock SP, Stella S, Cascio D, Johnson RC (2016) "DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis." Plos One, 11, e0150189. doi: 10.1371/journal.pone.0150189. Crystal structure of fis bound to 27bp DNA f1-8a (aaattagtttgaattttgagctaattt). SNAP output
5dtd DNA binding protein-DNA X-ray (2.642 Å) Hancock SP, Stella S, Cascio D, Johnson RC (2016) "DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis." Plos One, 11, e0150189. doi: 10.1371/journal.pone.0150189. Crystal structure of fis bound to 27bp DNA f1-8c (aaattcgtttgaattttgagcgaattt). SNAP output
5dui transcription-DNA X-ray (2.306 Å) Singh P, Han EH, Endrizzi JA, O'Brien RM, Chi YI (2017) "Crystal structures reveal a new and novel FoxO1 binding site within the human glucose-6-phosphatase catalytic subunit 1 gene promoter." J. Struct. Biol., 198, 54-64. doi: 10.1016/j.jsb.2017.02.006. Identification of a new foxo1 binding site that precludes creb binding at the glucose-6-phosphatase catalytic subunit gene promoter. SNAP output
5dwa hydrolase X-ray (1.5 Å) Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V (2017) "Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA." Nucleic Acids Res., 45, 3547-3558. doi: 10.1093/nar/gkw1310. Crystal structure of pre-specific restriction endonuclease agei-DNA complex. SNAP output
5dwb hydrolase X-ray (2.4 Å) Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V (2017) "Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA." Nucleic Acids Res., 45, 3547-3558. doi: 10.1093/nar/gkw1310. Crystal structure of specific restriction endonuclease agei-DNA complex. SNAP output
5dy0 DNA binding protein X-ray (3.0 Å) Palanca C, Rubio V (2016) "Structure of AmtR, the global nitrogen regulator of Corynebacterium glutamicum, in free and DNA-bound forms." Febs J., 283, 1039-1059. doi: 10.1111/febs.13643. Crystal of amtr from corynebacterium glutamicum in complex with DNA. SNAP output
5e01 transcription X-ray (2.3 Å) Counago RM, Chen NH, Chang CW, Djoko KY, McEwan AG, Kobe B (2016) "Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region." Nucleic Acids Res., 44, 6981-6993. doi: 10.1093/nar/gkw543. Crystal structure of hinmlr, a merr family regulator lacking the sensor domain, bound to palyndromic promoter DNA. SNAP output
5e17 transcription-DNA-RNA X-ray (3.2 Å) Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE (2016) "Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection." Science, 351, 1090-1093. doi: 10.1126/science.aad6881. T. thermophilus transcription initiation complex having a rrr discriminator sequence and a nontemplate-strand length corresponding to tss selection at position 7 (rpo-ggg-7). SNAP output
5e18 transcription-DNA-RNA X-ray (3.3 Å) Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE (2016) "Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection." Science, 351, 1090-1093. doi: 10.1126/science.aad6881. T. thermophilus transcription initiation complex having a yyy discriminator sequence and a nontemplate-strand length corresponding to tss selection at position 8 (rpo-ccc-8). SNAP output
5e24 transport-DNA binding-DNA X-ray (2.14 Å) Yuan Z, Praxenthaler H, Tabaja N, Torella R, Preiss A, Maier D, Kovall RA (2016) "Structure and Function of the Su(H)-Hairless Repressor Complex, the Major Antagonist of Notch Signaling in Drosophila melanogaster." Plos Biol., 14, e1002509. doi: 10.1371/journal.pbio.1002509. Structure of the su(h)-hairless-DNA repressor complex. SNAP output
5e3l DNA binding protein-DNA X-ray (2.66 Å) Hancock SP, Stella S, Cascio D, Johnson RC (2016) "DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis." Plos One, 11, e0150189. doi: 10.1371/journal.pone.0150189. Crystal structure of fis bound to 27bp DNA f1-8g (aaattggtttgaattttgagccaattt). SNAP output
5e3m DNA binding protein-DNA X-ray (2.886 Å) Hancock SP, Stella S, Cascio D, Johnson RC (2016) "DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis." Plos One, 11, e0150189. doi: 10.1371/journal.pone.0150189. Crystal structure of fis bound to 27bp DNA f35 (aaattagtttgaatctcgagctaattt). SNAP output
5e3n DNA binding protein-DNA X-ray (2.66 Å) Hancock SP, Stella S, Cascio D, Johnson RC (2016) "DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis." Plos One, 11, e0150189. doi: 10.1371/journal.pone.0150189. Crystal structure of fis bound to 27bp DNA f31 (aaatttgtaggaattttctgcaaattt). SNAP output
5e3o DNA binding protein-DNA X-ray (2.78 Å) Hancock SP, Stella S, Cascio D, Johnson RC (2016) "DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis." Plos One, 11, e0150189. doi: 10.1371/journal.pone.0150189. Crystal structure of fis bound to 27bp DNA f32 (aaatttggaggaattttctccaaattt). SNAP output
5e41 transferase X-ray (1.8 Å) Hottin A, Betz K, Diederichs K, Marx A (2017) "Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides." Chemistry, 23, 2109-2118. doi: 10.1002/chem.201604515. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with 5-(n-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate. SNAP output
5e5a protein binding-viral protein-DNA X-ray (2.809 Å) Fang Q, Chen P, Wang M, Fang J, Yang N, Li G, Xu RM (2016) "Human cytomegalovirus IE1 protein alters the higher-order chromatin structure by targeting the acidic patch of the nucleosome." Elife, 5. doi: 10.7554/eLife.11911. Crystal structure of the chromatin-tethering domain of human cytomegalovirus ie1 protein bound to the nucleosome core particle. SNAP output
5e5o hydrolase-DNA X-ray (2.36 Å) Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK (2016) "The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease." J.Mol.Biol., 428, 206-220. doi: 10.1016/j.jmb.2015.12.005. I-smami bound to uncleaved DNA target in the presence of calcium ions. SNAP output
5e5s hydrolase-DNA X-ray (2.29 Å) Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK (2016) "The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease." J.Mol.Biol., 428, 206-220. doi: 10.1016/j.jmb.2015.12.005. I-smami k103a mutant. SNAP output
5e63 hydrolase-DNA X-ray (2.6 Å) Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK (2016) "The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease." J.Mol.Biol., 428, 206-220. doi: 10.1016/j.jmb.2015.12.005. K262a mutant of i-smami. SNAP output
5e67 hydrolase-DNA X-ray (2.2 Å) Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK (2016) "The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease." J.Mol.Biol., 428, 206-220. doi: 10.1016/j.jmb.2015.12.005. K103a-k262a double mutant of i-smami. SNAP output
5e69 DNA binding protein-DNA X-ray (1.85 Å) Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA (2018) "Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements." Nat Commun, 9, 1337. doi: 10.1038/s41467-018-03780-1. Glucocorticoid receptor DNA binding domain - il8 nf-kb response element complex. SNAP output
5e6a DNA binding protein-DNA X-ray (2.197 Å) Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA (2018) "Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements." Nat Commun, 9, 1337. doi: 10.1038/s41467-018-03780-1. Glucocorticoid receptor DNA binding domain - plau nf-kb response element complex. SNAP output
5e6b DNA binding protein-DNA X-ray (2.25 Å) Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA (2018) "Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements." Nat Commun, 9, 1337. doi: 10.1038/s41467-018-03780-1. Glucocorticoid receptor DNA binding domain - relb nf-kb response element complex. SNAP output
5e6c DNA binding protein-DNA X-ray (2.2 Å) Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA (2018) "Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements." Nat Commun, 9, 1337. doi: 10.1038/s41467-018-03780-1. Glucocorticoid receptor DNA binding domain - ccl2 nf-kb response element complex. SNAP output
5e6d DNA binding protein-DNA X-ray (2.4 Å) Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA (2018) "Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements." Nat Commun, 9, 1337. doi: 10.1038/s41467-018-03780-1. Glucocorticoid receptor DNA binding domain - icam1 nf-kb response element complex. SNAP output
5e8i DNA binding protein-DNA X-ray (3.45 Å) Hou C, Tsodikov OV (2015) "Structural Basis for Dimerization and DNA Binding of Transcription Factor FLI1." Biochemistry, 54, 7365-7374. doi: 10.1021/acs.biochem.5b01121. Crystal structure of the DNA binding domain of human transcription factor fli1 in complex with a 10-mer DNA accggaagtg. SNAP output
5ean hydrolase-DNA X-ray (2.36 Å) Zhou C, Pourmal S, Pavletich NP (2015) "Dna2 nuclease-helicase structure, mechanism and regulation by Rpa." Elife, 4. doi: 10.7554/eLife.09832. Crystal structure of dna2 in complex with a 5' overhang DNA. SNAP output
5eax hydrolase-DNA X-ray (3.05 Å) Zhou C, Pourmal S, Pavletich NP (2015) "Dna2 nuclease-helicase structure, mechanism and regulation by Rpa." Elife, 4. doi: 10.7554/eLife.09832. Crystal structure of dna2 in complex with an ssDNA. SNAP output
5ed4 transcription-DNA X-ray (2.4 Å) He X, Wang L, Wang S (2016) "Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis." Sci Rep, 6, 24442. doi: 10.1038/srep24442. Structure of a phop-DNA complex. SNAP output
5edn transcription X-ray (3.2 Å) Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J (2018) "Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima." Elife, 7. doi: 10.7554/eLife.32963. Structure of hoxb13-DNA(tcg) complex. SNAP output
5edw transferase-DNA X-ray (2.62 Å) Koag M-C, Lee S "Structure of Dpo4 DNA polymerase replicating across the genotoxic N7-methylguanine lesion." Ternary structure of dpo4 bound to g in the template base paired with incoming dttp. SNAP output
5eea transcription X-ray (2.195 Å) Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J (2018) "Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima." Elife, 7. doi: 10.7554/eLife.32963. Structure of hoxb13-DNA(caa) complex. SNAP output
5ef6 transcription X-ray (3.0 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Structure of hoxb13 complex with methylated DNA. SNAP output
5eg0 transcription X-ray (3.101 Å) Morgunova E, Yin Y, Jolma A, Popov A, Taipale J "Molecular basis of recognition of two distinct DNA sequences by a single transcription factor." Hoxb13-meis1 heterodimer bound to DNA. SNAP output
5eg6 transcription-DNA binding protein-DNA X-ray (2.094 Å) Tabaja NH, Kovall RA "CSL-RITA complex bound to DNA." Csl-rita complex bound to DNA. SNAP output
5egb transcription-DNA X-ray (1.977 Å) Patel A, Horton JR, Wilson GG, Zhang X, Cheng X (2016) "Structural basis for human PRDM9 action at recombination hot spots." Genes Dev., 30, 257-265. doi: 10.1101/gad.274928.115. Human prdm9 allele-a znf domain with associated recombination hotspot DNA sequence ii. SNAP output
5ego transcription X-ray (2.54 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Hoxb13-meis1 heterodimer bound to methylated DNA. SNAP output
5eh2 transcription-DNA X-ray (2.05 Å) Patel A, Horton JR, Wilson GG, Zhang X, Cheng X (2016) "Structural basis for human PRDM9 action at recombination hot spots." Genes Dev., 30, 257-265. doi: 10.1101/gad.274928.115. Human prdm9 allele-a znf domain with associated recombination hotspot DNA sequence iii. SNAP output
5ei9 transcription-DNA X-ray (1.921 Å) Patel A, Horton JR, Wilson GG, Zhang X, Cheng X (2016) "Structural basis for human PRDM9 action at recombination hot spots." Genes Dev., 30, 257-265. doi: 10.1101/gad.274928.115. Human prdm9 allele-a znf domain with associated recombination hotspot DNA sequence i. SNAP output
5eix isomerase-DNA X-ray (3.35 Å) Veselkov DA, Laponogov I, Pan XS, Selvarajah J, Skamrova GB, Branstrom A, Narasimhan J, Prasad JV, Fisher LM, Sanderson MR (2016) "Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex." Acta Crystallogr D Struct Biol, 72, 488-496. doi: 10.1107/S2059798316001212. Quinolone-stabilized cleavage complex of topoisomerase iv from klebsiella pneumoniae. SNAP output
5ejk transferase-DNA X-ray (3.8 Å) Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H (2016) "Crystal structure of the Rous sarcoma virus intasome." Nature, 530, 362-366. doi: 10.1038/nature16950. Crystal structure of the rous sarcoma virus intasome. SNAP output
5elk RNA binding protein-RNA X-ray (2.3 Å) Murn J, Teplova M, Zarnack K, Shi Y, Patel DJ (2016) "Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt." Nat.Struct.Mol.Biol., 23, 16-23. doi: 10.1038/nsmb.3140. Crystal structure of mouse unkempt zinc fingers 4-6 (znf4-6), bound to RNA. SNAP output
5emc transcription-DNA X-ray (2.3 Å) Jin J, Lian T, SU XD "The effects of cytosine methylation on general transcription factors." Transcription factor grdbd and smgre complex. SNAP output
5emp transcription-DNA X-ray (2.3 Å) Lian T, Jin J, Su X "The effects of cytosine methylation on general transcription factors." Transcription factor grdbd and mmgre complex. SNAP output
5emq transcription-DNA X-ray (2.3 Å) Lian T, Jin J, Su X "The effects of cytosine methylation on general transcription factors." Transcription factor grdbd and gre complex. SNAP output
5eoz transferase-DNA X-ray (2.088 Å) Kou Y, Koag MC, Lee S (2018) "Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication." Biochemistry. doi: 10.1021/acs.biochem.8b00331. Mutagenicity of 7-benzyl guanine lesion and replication by human DNA polymerase beta. SNAP output
5esp hydrolase-DNA X-ray (2.995 Å) Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL (2016) "Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity." Structure, 24, 862-873. doi: 10.1016/j.str.2016.03.024. Crystal structure of laglidadg meganuclease i-panmi with coordinated calcium ions. SNAP output
5ev1 RNA binding protein-RNA X-ray (2.037 Å) Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL (2016) "An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal." Nat Commun, 7, 10950. doi: 10.1038/ncomms10950. Structure i of intact u2af65 recognizing a 3' splice site signal. SNAP output
5ev2 RNA binding protein-RNA X-ray (1.86 Å) Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL (2016) "An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal." Nat Commun, 7, 10950. doi: 10.1038/ncomms10950. Structure ii of intact u2af65 recognizing the 3' splice site signal. SNAP output
5ev3 RNA binding protein-RNA X-ray (1.5 Å) Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL (2016) "An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal." Nat Commun, 7, 10950. doi: 10.1038/ncomms10950. Structure iii of intact u2af65 recognizing the 3' splice site signal. SNAP output
5ev4 RNA binding protein-RNA X-ray (1.57 Å) Agrawal AA, Salsi E, Chatrikhi R, Henderson S, Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL (2016) "An extended U2AF(65)-RNA-binding domain recognizes the 3' splice site signal." Nat Commun, 7, 10950. doi: 10.1038/ncomms10950. Structure iv of intact u2af65 recognizing the 3' splice site signal. SNAP output
5ew1 protein-DNA X-ray (2.95 Å) Pica A, Russo Krauss I, Parente V, Tateishi-Karimata H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F (2017) "Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers." Nucleic Acids Res., 45, 461-469. doi: 10.1093/nar/gkw1113. Human thrombin sandwiched between two DNA aptamers: hd22 and hd1-deltat3. SNAP output
5ew2 protein-DNA X-ray (3.59 Å) Pica A, Russo Krauss I, Parente V, Tateishi-Karimata H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F (2017) "Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers." Nucleic Acids Res., 45, 461-469. doi: 10.1093/nar/gkw1113. Human thrombin sandwiched between two DNA aptamers: hd22 and hd1-deltat12. SNAP output
5ewe transferase-DNA X-ray (1.66 Å) Su Y, Egli M, Guengerich FP (2016) "Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta." J.Biol.Chem., 291, 3747-3756. doi: 10.1074/jbc.M115.706226. Ternary complex of human DNA polymerase eta inserting rctp opposite template g. SNAP output
5ewf transferase-DNA X-ray (1.782 Å) Su Y, Egli M, Guengerich FP (2016) "Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta." J.Biol.Chem., 291, 3747-3756. doi: 10.1074/jbc.M115.706226. Ternary complex of human DNA polymerase eta inserting rctp opposite an 8-oxodeoxyguanosine lesion. SNAP output
5ewg transferase-DNA X-ray (1.75 Å) Su Y, Egli M, Guengerich FP (2016) "Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta." J.Biol.Chem., 291, 3747-3756. doi: 10.1074/jbc.M115.706226. Ternary complex of human DNA polymerase eta inserting ratp opposite an 8-oxodeoxyguanosine lesion. SNAP output
5exh oxidoreductase-DNA X-ray (1.3 Å) Jin SG, Zhang ZM, Dunwell TL, Harter MR, Wu X, Johnson J, Li Z, Liu J, Szabo PE, Lu Q, Xu GL, Song J, Pfeifer GP (2016) "Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration." Cell Rep, 14, 493-505. doi: 10.1016/j.celrep.2015.12.044. Crystal structure of mtet3-cxxc domain in complex with 5-carboxylcytosine DNA at 1.3 angstroms resolution.. SNAP output
5eyb DNA binding protein-DNA X-ray (2.7 Å) Jaiswal R, Choudhury M, Zaman S, Singh S, Santosh V, Bastia D, Escalante CR (2016) "Functional architecture of the Reb1-Ter complex of Schizosaccharomyces pombe." Proc.Natl.Acad.Sci.USA, 113, E2267-E2276. doi: 10.1073/pnas.1525465113. X-ray structure of reb1-ter complex. SNAP output
5eyo transcription-DNA X-ray (2.39 Å) Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X (2017) "MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma." Nucleic Acids Res., 45, 2396-2407. doi: 10.1093/nar/gkw1184. The crystal structure of the max bhlh domain in complex with 5-carboxyl cytosine DNA. SNAP output
5f0q tranferase-DNA-RNA X-ray (2.21 Å) Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y, Pavlov YI, Tahirov TH (2016) "Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome." J.Biol.Chem., 291, 10006-10020. doi: 10.1074/jbc.M116.717405. Crystal structure of c-terminal domain of the human DNA primase large subunit with bound DNA template-RNA primer. SNAP output
5f0s replication-DNA-RNA X-ray (3.0 Å) Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y, Pavlov YI, Tahirov TH (2016) "Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome." J.Biol.Chem., 291, 10006-10020. doi: 10.1074/jbc.M116.717405. Crystal structure of c-terminal domain of the human DNA primase large subunit with bound DNA template-RNA primer and manganese ion. SNAP output
5f3w DNA binding protein-hydrolase-DNA X-ray (3.11 Å) Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim T, Song OK, Lee SE, Cho Y (2016) "ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex." Embo J., 35, 743-758. doi: 10.15252/embj.201592462. Structure of the atprs-mre11-rad50-DNA complex. SNAP output
5f55 DNA binding protein-DNA X-ray (2.6 Å) Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua Y (2016) "Structural basis for DNA 5 -end resection by RecJ." Elife, 5, e14294. doi: 10.7554/eLife.14294. Structure of recj complexed with DNA. SNAP output
5f56 DNA binding protein-DNA X-ray (2.3 Å) Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua Y (2016) "Structural basis for DNA 5 -end resection by RecJ." Elife, 5, e14294. doi: 10.7554/eLife.14294. Structure of recj complexed with DNA and ssb-ct. SNAP output
5f7q transcription-DNA X-ray (2.4 Å) Light SH, Cahoon LA, Halavaty AS, Freitag NE, Anderson WF (2016) "Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis." Nat Microbiol, 2, 16202. doi: 10.1038/nmicrobiol.2016.202. Rok repressor lmo0178 from listeria monocytogenes bound to operator. SNAP output
5f8a hydrolase-DNA X-ray (1.76 Å) Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L (2016) "Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex." Biochemistry, 55, 6115-6132. doi: 10.1021/acs.biochem.6b00919. Crystal structure of the ternary ecorv-DNA-lu complex with uncleaved DNA substrate. lanthanide binding to ecorv-DNA complex inhibits cleavage.. SNAP output
5f99 DNA binding protein X-ray (2.63 Å) Frouws TD, Duda SC, Richmond TJ (2016) "X-ray structure of the MMTV-A nucleosome core." Proc.Natl.Acad.Sci.USA, 113, 1214-1219. doi: 10.1073/pnas.1524607113. X-ray structure of the mmtv-a nucleosome core particle. SNAP output
5f9l transferase-DNA X-ray (2.592 Å) Patra A, Egli M "Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta." Crystal structure of human DNA polymerase eta inserting dampnpp across a DNA template containing 1,n2-ethenodeoxyguanosine lesion. SNAP output
5f9n transferase-DNA X-ray (2.23 Å) Patra A, Egli M "Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by Human DNA Polymerase Eta." Crystal structure of human DNA polymerase eta inserting dcmpnpp across a DNA template containing 1,n2-ethenodeoxyguanosine lesion. SNAP output
5f9r hydrolase-DNA-RNA X-ray (3.4 Å) Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA (2016) "Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage." Science, 351, 867-871. doi: 10.1126/science.aad8282. Crystal structure of catalytically-active streptococcus pyogenes crispr-cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage. SNAP output
5fb2 transcription-DNA X-ray (1.8 Å) Birukou I, Newman CE, Brennan RG "S. aureus MepR F27L Mutant bound to oligodeoxyribonucleotide." S. aureus mepr f27l mutant bound to oligodeoxyribonucleotide. SNAP output
5fd3 transcription-DNA X-ray (2.42 Å) Marceau AH, Felthousen JG, Goetsch PD, Iness AN, Lee HW, Tripathi SM, Strome S, Litovchick L, Rubin SM (2016) "Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters." Nat Commun, 7, 12301. doi: 10.1038/ncomms12301. Structure of lin54 tesmin domain bound to DNA. SNAP output
5fdk hydrolase X-ray (3.208 Å) Khavnekar S, Dantu SC, Sedelnikova S, Ayora S, Rafferty J, Kale A (2017) "Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state." Nucleic Acids Res., 45, 975-986. doi: 10.1093/nar/gkw1165. Crystal structure of recu(d88n) in complex with palindromic DNA duplex. SNAP output
5ff8 hydrolase-DNA X-ray (1.7 Å) Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC (2016) "Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues." Nucleic Acids Res., 44, 10248-10258. doi: 10.1093/nar/gkw768. Tdg enzyme-product complex. SNAP output
5ffj DNA binding protein-DNA X-ray (2.84 Å) Kulkarni M, Nirwan N, van Aelst K, Szczelkun MD, Saikrishnan K (2016) "Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes." Nucleic Acids Res., 44, 4396-4408. doi: 10.1093/nar/gkw154. Structure of a nuclease-deletion mutant of the type isp restriction-modification enzyme llagi in complex with a DNA substrate mimic. SNAP output
5fgp DNA binding protein X-ray (2.0 Å) Weber J, Bao H, Hartlmuller C, Wang Z, Windhager A, Janowski R, Madl T, Jin P, Niessing D (2016) "Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha." Elife, 5. doi: 10.7554/eLife.11297. Crystal structure of d. melanogaster pur-alpha repeat i-ii in complex with DNA.. SNAP output
5fhd hydrolase-DNA X-ray (2.0 Å) Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu Z, Li D, Song H (2016) "Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1." Cell Rep, 14, 2030-2039. doi: 10.1016/j.celrep.2016.02.008. Structure of bacteroides sp pif1 complexed with tailed dsDNA resulting in ssDNA bound complex. SNAP output
5fhe hydrolase-DNA X-ray (2.9 Å) Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu Z, Li D, Song H (2016) "Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1." Cell Rep, 14, 2030-2039. doi: 10.1016/j.celrep.2016.02.008. Crystal structure of bacteroides pif1 bound to ssDNA. SNAP output
5fj8 transcription cryo-EM (3.9 Å) Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJH, Sachse C, Muller CW (2015) "Molecular Structures of Unbound and Transcribing RNA Polymerase III." Nature, 528, 231. doi: 10.1038/NATURE16143. cryo-EM structure of yeast RNA polymerase iii elongation complex at 3. 9 a. SNAP output
5fkv transferase cryo-EM (8.04 Å) Fernandez-Leiro R, Conrad J, Scheres SH, Lamers MH (2015) "cryo-EM structures of theE. colireplicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease andtau." Elife, 4. doi: 10.7554/eLife.11134. cryo-EM structure of the e. coli replicative DNA polymerase complex bound to DNA (DNA polymerase iii alpha, beta, epsilon, tau complex). SNAP output
5fkw transferase cryo-EM (7.3 Å) Fernandez-Leiro R, Conrad J, Scheres SH, Lamers MH (2015) "cryo-EM structures of theE. colireplicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease andtau." Elife, 4. doi: 10.7554/eLife.11134. cryo-EM structure of the e. coli replicative DNA polymerase complex bound to DNA (DNA polymerase iii alpha, beta, epsilon). SNAP output
5flm transcription cryo-EM (3.4 Å) Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P (2016) "Structure of Transcribing Mammalian RNA Polymerase II." Nature, 529, 551. doi: 10.1038/NATURE16482. Structure of transcribing mammalian RNA polymerase ii. SNAP output
5flv transcription X-ray (3.005 Å) Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MAH, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Muller CW, Bruneau BG (2016) "Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis." Cell(Cambridge,Mass.), 164, 999. doi: 10.1016/J.CELL.2016.01.004. Crystal structure of nkx2-5 and tbx5 bound to the nppa promoter region. SNAP output
5fmf transcription cryo-EM (6.0 Å) Murakami K, Tsai K, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD (2015) "Structure of an RNA Polymerase II Pre-Initiation Complex." Proc.Natl.Acad.Sci.USA, 112, 13543. doi: 10.1073/PNAS.1518255112. The p-lobe of RNA polymerase ii pre-initiation complex. SNAP output
5fmp DNA binding protein X-ray (2.26 Å) Podust LM, Ouellet H "Kstr, Transcriptional Repressor of Cholesterol Degradation in Mycobacterium Tuberculosis." Kstr, transcriptional repressor of cholesterol degradation in mycobacterium tuberculosis, bound to the DNA operator. SNAP output
5fq5 hydrolase-DNA X-ray (2.136 Å) Olieric V, Weinert T, Finke AD, Anders C, Li D, Olieric N, Borca CN, Steinmetz MO, Caffrey M, Jinek M, Wang M (2016) "Data-Collection Strategy for Challenging Native Sad Phasing." Acta Crystallogr.,Sect.D, 72, 421. doi: 10.1107/S2059798315024110. Crystal structure of cas9-sgrna-DNA complex solved by native sad phasing. SNAP output
5frm recombination X-ray (2.58 Å) Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TRJ (2016) "HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases." Acs Chem.Biol., 11, 1074. doi: 10.1021/ACSCHEMBIO.5B00948. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz384 (compound 4a). SNAP output
5frn transferase X-ray (2.85 Å) Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TRJ (2016) "HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases." Acs Chem.Biol., 11, 1074. doi: 10.1021/ACSCHEMBIO.5B00948. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz419 (compound 4c). SNAP output
5fro transferase X-ray (2.67 Å) Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TRJ (2016) "HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases." Acs Chem.Biol., 11, 1074. doi: 10.1021/ACSCHEMBIO.5B00948. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz446 (compound 4f). SNAP output
5fte hydrolase X-ray (3.19 Å) Chen W-F, Dai Y-X, Duan X-L, Liu N-N, Shi W, Li N, Li M, Dou S-X, Dong Y-H, Rety S, Xi X-G (2016) "Crystal Structures of the Bspif1 Helicase Reveal that a Major Movement of the 2B SH3 Domain is Required for DNA Unwinding." Nucleic Acids Res., 44, 2949. doi: 10.1093/NAR/GKW033. Crystal structure of pif1 helicase from bacteroides in complex with adp-alf3 and ssDNA. SNAP output
5fur transcription cryo-EM (8.5 Å) Louder RK, He Y, Lopez-Blanco JR, Fang J, Chacon P, Nogales E (2016) "Structure of Promoter-Bound TFIID and Model of Human Pre-Initiation Complex Assembly." Nature, 531, 604. doi: 10.1038/NATURE17394. Structure of human tfiid-iia bound to core promoter DNA. SNAP output
5fw1 hydrolase-DNA X-ray (2.499 Å) Anders C, Bargsten K, Jinek M (2016) "Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9." Mol.Cell, 61, 895. doi: 10.1016/J.MOLCEL.2016.02.020. Crystal structure of spycas9 variant vqr bound to sgrna and tgag pam target DNA. SNAP output
5fw2 hydrolase-DNA-RNA X-ray (2.676 Å) Anders C, Bargsten K, Jinek M (2016) "Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9." Mol.Cell, 61, 895. doi: 10.1016/J.MOLCEL.2016.02.020. Crystal structure of spcas9 variant eqr bound to sgrna and tgag pam target DNA. SNAP output
5fw3 hydrolase-DNA-RNA X-ray (2.7 Å) Anders C, Bargsten K, Jinek M (2016) "Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9." Mol.Cell, 61, 895. doi: 10.1016/J.MOLCEL.2016.02.020. Crystal structure of spcas9 variant vrer bound to sgrna and tgcg pam target DNA. SNAP output
5fyw transcription cryo-EM (4.35 Å) Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P (2016) "Transcription Initiation Complex Structures Elucidate DNA Opening." Nature, 533, 353. doi: 10.1038/NATURE17990. Transcription initiation complex structures elucidate DNA opening (oc). SNAP output
5fz5 transcription cryo-EM (8.8 Å) Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P (2016) "Transcription Initiation Complex Structures Elucidate DNA Opening." Nature, 533, 353. doi: 10.1038/NATURE17990. Transcription initiation complex structures elucidate DNA opening (cc). SNAP output
5g32 cell cycle X-ray (2.2 Å) Schneider S, Simon N, Ebert C (2016) "Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14." Chemistry, 22, 10782. doi: 10.1002/CHEM.201602438. Structure of rad14 in complex with acetylaminophenyl-guanine containing DNA. SNAP output
5g33 cell cycle X-ray (2.4 Å) Schneider S, Simon N, Ebert C (2016) "Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14." Chemistry, 22, 10782. doi: 10.1002/CHEM.201602438. Structure of rad14 in complex with acetylnaphtyl-guanine containing DNA. SNAP output
5g34 cell cycle X-ray (1.9 Å) Schneider S, Simon N, Ebert C (2016) "Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14." Chemistry, 22, 10782. doi: 10.1002/CHEM.201602438. Structure of rad14 in complex with acetylaminoanthracene-c8-guanine containing DNA. SNAP output
5g35 cell cycle X-ray (2.0 Å) Schneider S, Simon N, Ebert C (2016) "Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14." Chemistry, 22, 10782. doi: 10.1002/CHEM.201602438. Structure of rad14 in complex with acetylaminopyren-c8-guanine containing DNA. SNAP output
5g5t hydrolase-DNA X-ray (2.85 Å) Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S (2017) "Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein." Nat Microbiol, 2, 17035. doi: 10.1038/nmicrobiol.2017.35. Structure of the argonaute protein from methanocaldcoccus janaschii in complex with guide DNA. SNAP output
5gat transcription-DNA NMR Starich MR, Wikstrom M, Arst Jr HN, Clore GM, Gronenborn AM (1998) "The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors." J.Mol.Biol., 277, 605-620. doi: 10.1006/jmbi.1998.1625. Solution NMR structure of the wild type DNA binding domain of area complexed to a 13bp DNA containing a cgata site, 35 structures. SNAP output
5gke hydrolase-DNA X-ray (2.4 Å) Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T (2016) "Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease." Structure, 24, 1960-1971. doi: 10.1016/j.str.2016.09.005. Structure of endoms-dsdna1 complex. SNAP output
5gkf hydrolase-DNA X-ray (2.8 Å) Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T (2016) "Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease." Structure, 24, 1960-1971. doi: 10.1016/j.str.2016.09.005. Structure of endoms-dsdna1' complex. SNAP output
5gkg hydrolase-DNA X-ray (2.6 Å) Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T (2016) "Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease." Structure, 24, 1960-1971. doi: 10.1016/j.str.2016.09.005. Structure of endoms-dsdna1'' complex. SNAP output
5gkh hydrolase-DNA X-ray (2.9 Å) Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T (2016) "Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease." Structure, 24, 1960-1971. doi: 10.1016/j.str.2016.09.005. Structure of endoms-dsdna2 complex. SNAP output
5gki hydrolase-DNA X-ray (2.9 Å) Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T (2016) "Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease." Structure, 24, 1960-1971. doi: 10.1016/j.str.2016.09.005. Structure of endoms-dsdna3 complex. SNAP output
5gkp hydrolase-DNA X-ray (2.3 Å) Lin JL, Wu CC, Yang WZ, Yuan HS (2016) "Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer." Nucleic Acids Res., 44, 10480-10490. doi: 10.1093/nar/gkw931. Crystal structure of the endog worm homologue cps-6 h148a-f122a in complex with DNA. SNAP output
5gkr immune system-DNA X-ray (2.1 Å) Sakakibara S, Arimori T, Yamashita K, Jinzai H, Motooka D, Nakamura S, Li S, Takeda K, Katayama J, El Hussien MA, Narazaki M, Tanaka T, Standley DM, Takagi J, Kikutani H (2017) "Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus." Sci Rep, 7, 16428. doi: 10.1038/s41598-017-16681-y. Crystal structure of sle patient-derived anti-DNA antibody in complex with oligonucleotide. SNAP output
5gnj DNA binding protein-DNA X-ray (2.7 Å) Lian TF, Xu YP, Li LF, Su XD (2017) "Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA." Cell Rep, 19, 1334-1342. doi: 10.1016/j.celrep.2017.04.057. Structure of a transcription factor and DNA complex. SNAP output
5gpc transcription, DNA binding protein-DNA X-ray (2.8 Å) Yeo HK, Park YW, Lee JY (2017) "Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR." Nucleic Acids Res., 45, 4244-4254. doi: 10.1093/nar/gkx009. Structural analysis of fatty acid degradation regulator fadr from bacillus halodurans. SNAP output
5gq9 DNA binding protein-DNA X-ray (2.7 Å) Zhao H, Sheng G, Wang Y "Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target." Crystal structure of thermus thermophilus argonaute in complex with g1c siDNA and DNA target. SNAP output
5gse structural protein-DNA X-ray (3.14 Å) Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H (2017) "Crystal structure of the overlapping dinucleosome composed of hexasome and octasome." Science, 356, 205-208. doi: 10.1126/science.aak9867. Crystal structure of unusual nucleosome. SNAP output
5gsu DNA binding protein-DNA X-ray (3.1 Å) Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2017) "Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b." Biophys. Chem., 221, 41-48. doi: 10.1016/j.bpc.2016.11.013. Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, th2a and th2b. SNAP output
5gt0 structural protein-DNA X-ray (2.82 Å) Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2017) "Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b." Biophys. Chem., 221, 41-48. doi: 10.1016/j.bpc.2016.11.013. Crystal structure of nucleosome complex with human testis-specific histone variants, th2a. SNAP output
5gt3 structural protein-DNA X-ray (2.91 Å) Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K, Kumasaka T, Ishii S, Kumarevel T (2017) "Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b." Biophys. Chem., 221, 41-48. doi: 10.1016/j.bpc.2016.11.013. Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hth2b. SNAP output
5gtc structural protein-DNA X-ray (2.7 Å) Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D, Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M (2017) "Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin." J. Am. Chem. Soc., 139, 7568-7576. doi: 10.1021/jacs.7b02138. Crystal structure of complex between dmap-sh conjugated with a kaposi's sarcoma herpesvirus lana peptide (5-15) and nucleosome core particle. SNAP output
5gwi isomerase-DNA-isomerase inhibitor X-ray (2.737 Å) Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT, Chen YS, Li TK, Chien TC, Chan NL (2017) "Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry." Nucleic Acids Res., 45, 10861-10871. doi: 10.1093/nar/gkx742. Structure of a human topoisomerase iibeta fragment in complex with DNA and e7873r. SNAP output
5gwj isomerase-DNA-isomerase inhibitor X-ray (2.566 Å) Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT, Chen YS, Li TK, Chien TC, Chan NL (2017) "Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry." Nucleic Acids Res., 45, 10861-10871. doi: 10.1093/nar/gkx742. Structure of a human topoisomerase iibeta fragment in complex with DNA and e7873s. SNAP output
5gwk isomerase-DNA-isomerase inhibitor X-ray (3.152 Å) Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT, Chen YS, Li TK, Chien TC, Chan NL (2017) "Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry." Nucleic Acids Res., 45, 10861-10871. doi: 10.1093/nar/gkx742. Human topoisomerase iialpha in complex with DNA and etoposide. SNAP output
5gxq structural protein-DNA X-ray (2.85 Å) Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H (2017) "Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8." Biochemistry, 56, 2184-2196. doi: 10.1021/acs.biochem.6b01098. The crystal structure of the nucleosome containing h3.6. SNAP output
5gzb transcription-DNA X-ray (2.704 Å) Shi ZB, He F, Chen M, Hua L, Wang W, Jiao S, Zhou ZC (2017) "DNA-binding mechanism of the Hippo pathway transcription factor TEAD4." Oncogene, 36, 4362-4369. doi: 10.1038/onc.2017.24. Crystal structure of transcription factor tead4 in complex with m-cat DNA. SNAP output
5h1b DNA binding protein-DNA cryo-EM (4.4 Å) Xu J, Zhao L, Xu Y, Zhao W, Sung P, Wang HW (2017) "Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange." Nat. Struct. Mol. Biol., 24, 40-46. doi: 10.1038/nsmb.3336. Human rad51 presynaptic complex. SNAP output
5h1c DNA binding protein-DNA cryo-EM (4.5 Å) Xu J, Zhao L, Xu Y, Zhao W, Sung P, Wang HW (2017) "Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange." Nat. Struct. Mol. Biol., 24, 40-46. doi: 10.1038/nsmb.3336. Human rad51 post-synaptic complexes. SNAP output
5h3r transcription-DNA X-ray (2.67 Å) Zhu R, Hao Z, Lou H, Song Y, Zhao J, Chen Y, Zhu J, Chen PR (2017) "Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator." J. Biol. Inorg. Chem., 22, 685-693. doi: 10.1007/s00775-017-1442-7. Crystal structure of mutant marr c80s from e.coli complexed with operator DNA. SNAP output
5h58 transcription-DNA X-ray (3.991 Å) Bhukya H, Jana AK, Sengupta N, Anand R (2017) "Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence." J. Struct. Biol., 198, 134-146. doi: 10.1016/j.jsb.2017.03.006. Structural and dynamics studies of the tetr family protein, cprb from streptomyces coelicolor in complex with its biological operator sequence. SNAP output
5h8w hydrolase X-ray (2.2 Å) Constantinescu-Aruxandei D, Petrovic-Stojanovska B, Penedo JC, White MF, Naismith JH (2016) "Mechanism of DNA loading by the DNA repair helicase XPD." Nucleic Acids Res., 44, 2806-2815. doi: 10.1093/nar/gkw102. Xpd mechanism. SNAP output
5h9e immune system-RNA X-ray (3.21 Å) Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, Wiedenheft B, Ke A (2016) "Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli." Nature, 530, 499-503. doi: 10.1038/nature16995. Crystal structure of e. coli cascade bound to a pam-containing dsDNA target (32-nt spacer) at 3.20 angstrom resolution.. SNAP output
5h9f immune system-RNA X-ray (2.45 Å) Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, Wiedenheft B, Ke A (2016) "Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli." Nature, 530, 499-503. doi: 10.1038/nature16995. Crystal structure of e. coli cascade bound to a pam-containing dsDNA target at 2.45 angstrom resolution.. SNAP output
5haw cell cycle-DNA X-ray (1.89 Å) Schumacher MA, Zeng W (2016) "Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ." Proc.Natl.Acad.Sci.USA, 113, 4988-4993. doi: 10.1073/pnas.1602327113. Structures of the no factor slma bound to DNA and the cytoskeletal cell division protein ftsz. SNAP output
5hbu cell cycle-DNA X-ray (2.6 Å) Schumacher MA, Zeng W (2016) "Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ." Proc.Natl.Acad.Sci.USA, 113, 4988-4993. doi: 10.1073/pnas.1602327113. Structure of the e. coli nucleoid occlusion protein slma bound to DNA and the c-terminal tail of the cytoskeletal cell division protein ftsz. SNAP output
5hch sugar binding protein X-ray (2.9 Å) Roethlisberger P, Istrate A, Marcaida Lopez MJ, Visini R, Stocker A, Reymond JL, Leumann CJ (2016) "X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair." Chem.Commun.(Camb.), 52, 4749-4752. doi: 10.1039/c6cc00374e. X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair. SNAP output
5hdn transcription X-ray (1.68 Å) Feng H, Liu W, Wang DC "HSF1-DBD crystal structure." Crystal structure of heat shock factor1-dbd complex with ds-DNA and ttt. SNAP output
5hf7 hydrolase-DNA X-ray (1.54 Å) Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC (2016) "Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues." Nucleic Acids Res., 44, 10248-10258. doi: 10.1093/nar/gkw768. Tdg enzyme-substrate complex. SNAP output
5hhh transferase, lyase-DNA X-ray (2.363 Å) Cheun Y, Koag MC, Naguib YW, Ouzon-Shubeita H, Cui Z, Pakotiprapha D, Lee S (2018) "Synthesis, structure, and biological evaluation of a platinum-carbazole conjugate." Chem Biol Drug Des, 91, 116-125. doi: 10.1111/cbdd.13062. Structure of human DNA polymerase beta host-guest complexed with the control g for n7-cbz-platination. SNAP output
5hhi transferase, lyase-DNA X-ray (2.517 Å) Cheun Y, Koag MC, Naguib YW, Ouzon-Shubeita H, Cui Z, Pakotiprapha D, Lee S (2018) "Synthesis, structure, and biological evaluation of a platinum-carbazole conjugate." Chem Biol Drug Des, 91, 116-125. doi: 10.1111/cbdd.13062. Structure of human DNA polymerase beta host-guest complexed with cbz-platinated n7-g. SNAP output
5hk0 hydrolase-RNA X-ray (2.25 Å) Yen TJ, Brennan RG "Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in complex with RNA." Crystal structure of m. tuberculosis mazf-mt3 (rv1991c) in complex with RNA. SNAP output
5hk3 hydrolase-DNA X-ray (1.56 Å) Yen TJ, Brennan RG "Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with DNA." Crystal structure of m. tuberculosis mazf-mt3 t52d-f62d mutant in complex with DNA. SNAP output
5hkc hydrolase-RNA X-ray (1.68 Å) Yen TJ, Brennan RG "Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with 8-mer RNA." Crystal structure of m. tuberculosis mazf-mt3 t52d-f62d mutant in complex with 8-mer RNA. SNAP output
5hlf transferase-inhibitor-DNA X-ray (2.95 Å) Mullins ND, Maguire NM, Ford A, Das K, Arnold E, Balzarini J, Maguire AR (2016) "Exploring the role of the alpha-carboxyphosphonate moiety in the HIV-RT activity of alpha-carboxy nucleoside phosphonates." Org.Biomol.Chem., 14, 2454-2465. doi: 10.1039/c5ob02507a. Structure of hiv-1 reverse transcriptase in complex with a 38-mer hairpin template-primer DNA aptamer and an alpha-carboxyphosphonate inhibitor. SNAP output
5hlg transcription regulator-DNA X-ray (3.0 Å) Liu G, Liu X, Xu H, Liu X, Zhou H, Huang Z, Gan J, Chen H, Lan L, Yang CG (2017) "Structural Insights into the Redox-Sensing Mechanism of MarR-Type Regulator AbfR." J. Am. Chem. Soc., 139, 1598-1608. doi: 10.1021/jacs.6b11438. Structure of reduced abfr bound to DNA. SNAP output
5hlh transcription regulator-DNA X-ray (3.0 Å) Liu G, Liu X, Xu H, Liu X, Zhou H, Huang Z, Gan J, Chen H, Lan L, Yang CG (2017) "Structural Insights into the Redox-Sensing Mechanism of MarR-Type Regulator AbfR." J. Am. Chem. Soc., 139, 1598-1608. doi: 10.1021/jacs.6b11438. Crystal structure of the overoxidized abfr bound to DNA. SNAP output
5hlk hydrolase-DNA X-ray (2.0 Å) Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson L (2016) "Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex." Biochemistry, 55, 6115-6132. doi: 10.1021/acs.biochem.6b00919. Crystal structure of the ternary ecorv-DNA-lu complex with cleaved DNA substrate.. SNAP output
5hlt hydrolase X-ray (2.672 Å) Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R (2016) "Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease." Nucleic Acids Res., 44, 7079-7089. doi: 10.1093/nar/gkw644. Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the bpuj1 endonuclease binding domain. SNAP output
5hnf hydrolase X-ray (1.546 Å) Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R (2016) "Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease." Nucleic Acids Res., 44, 7079-7089. doi: 10.1093/nar/gkw644. Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the bpuj1 endonuclease binding domain. SNAP output
5hnh hydrolase X-ray (1.876 Å) Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R (2016) "Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease." Nucleic Acids Res., 44, 7079-7089. doi: 10.1093/nar/gkw644. Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the bpuj1 endonuclease binding domain. SNAP output
5hnk hydrolase X-ray (2.22 Å) AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ (2016) "Direct observation of DNA threading in flap endonuclease complexes." Nat.Struct.Mol.Biol., 23, 640-646. doi: 10.1038/nsmb.3241. Crystal structure of t5fen in complex intact substrate and metal ions.. SNAP output
5hod transcription X-ray (2.682 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Structure of lhx4 transcription factor complexed with DNA. SNAP output
5hoo DNA X-ray (3.3 Å) Morris ER, Grey H, McKenzie G, Jones AC, Richardson JM (2016) "A bend, flip and trap mechanism for transposon integration." Elife, 5. doi: 10.7554/eLife.15537. Crystal structure of the mos1 strand transfer complex. SNAP output
5hp1 transferase-inhibitor-DNA X-ray (2.9 Å) Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E (2016) "Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet." Acs Chem.Biol., 11, 2158-2164. doi: 10.1021/acschembio.6b00187. Structure of hiv-1 reverse transcriptase in complex with a DNA aptamer and foscarnet, a pyrophosphate analog. SNAP output
5hp4 hydrolase X-ray (1.86 Å) AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ (2016) "Direct observation of DNA threading in flap endonuclease complexes." Nat.Struct.Mol.Biol., 23, 640-646. doi: 10.1038/nsmb.3241. Crystal structure bacteriohage t5 d15 flap endonuclease (d155k) pseudo-enzyme-product complex with DNA and metal ions. SNAP output
5hq2 transferase-DNA X-ray (4.5 Å) Girish TS, McGinty RK, Tan S (2016) "Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate." J.Mol.Biol., 428, 1531-1543. doi: 10.1016/j.jmb.2016.02.025. Structural model of set8 histone h4 lys20 methyltransferase bound to nucleosome core particle. SNAP output
5hr4 hydrolase-DNA X-ray (2.6 Å) Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts RJ, Morgan RD, Aggarwal AK (2016) "Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities." Plos Biol., 14, e1002442. doi: 10.1371/journal.pbio.1002442. Structure of type iil restriction-modification enzyme mmei in complex with DNA has implications for engineering of new specificities. SNAP output
5hr9 transferase-DNA X-ray (2.2 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of se-asfvpolx(l52-163m mutant) in complex with 1nt-gap dna1. SNAP output
5hrb transferase-DNA X-ray (1.7 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx:dna1 binary complex. SNAP output
5hrd transferase-DNA X-ray (1.8 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx:dna2 binary complex. SNAP output
5hre transferase-DNA X-ray (1.75 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx:dna3 binary complex. SNAP output
5hrf transferase-DNA X-ray (2.25 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx: dna5: dgtp ternary complex. SNAP output
5hrg transferase-DNA X-ray (2.0 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx(d51n mutant):dna4 binary complex. SNAP output
5hrh transferase-DNA X-ray (3.0 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx(h115f-r127a mutant): 1nt-gap(p) dna2:dgtp ternary complex. SNAP output
5hri transferase-DNA X-ray (2.2 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of AsfvPolX: 1nt-gap(P) DNA1: dGTP ternary complex." The crystal structure of asfvpolx:dna1 binary complex. SNAP output
5hrk transferase-DNA X-ray (2.9 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx(h115f mutant): 1nt-gap(p) dna2:dgtp ternary complex. SNAP output
5hrl transferase-DNA X-ray (2.4 Å) Chen YQ, Zhang J, Gan JH "The crystal structure of Se-AsfvPolX(L52/163M mutant) in complex with 1nt-gap DNA1." The crystal structure of asfvpolx: 1nt-gap(p) dna2: dgtp ternary complex.. SNAP output
5hro transferase-transferase inhibitor X-ray (2.75 Å) Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E (2016) "Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet." Acs Chem.Biol., 11, 2158-2164. doi: 10.1021/acschembio.6b00187. Structure of hiv-1 reverse transcriptase in complex with a DNA aptamer and an alpha-carboxy nucleoside phosphonate inhibitor (alpha-cnp). SNAP output
5hrt hydrolase X-ray (1.997 Å) Kato K, Ikeda H, Miyakawa S, Futakawa S, Nonaka Y, Fujiwara M, Okudaira S, Kano K, Aoki J, Morita J, Ishitani R, Nishimasu H, Nakamura Y, Nureki O (2016) "Structural basis for specific inhibition of Autotaxin by a DNA aptamer." Nat.Struct.Mol.Biol., 23, 395-401. doi: 10.1038/nsmb.3200. Crystal structure of mouse autotaxin in complex with a DNA aptamer. SNAP output
5hru oxidoreductase-DNA X-ray (1.71 Å) Choi SJ, Ban C (2016) "Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition." Sci Rep, 6, 34998. doi: 10.1038/srep34998. Crystal structure of plasmodium vivax ldh in complex with a DNA aptamer called pl1. SNAP output
5hso transcription X-ray (2.5 Å) Gao YR, Li DF, Fleming J, Zhou YF, Liu Y, Deng JY, Zhou L, Zhou J, Zhu GF, Zhang XE, Wang DC, Bi LJ (2017) "Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis." Sci Rep, 7, 6471. doi: 10.1038/s41598-017-01705-4. Crystal structure of mycobacterium tuberculosis marr family protein rv2887 complex with DNA. SNAP output
5ht2 hydrolase-DNA X-ray (1.43 Å) Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS (2016) "Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2." Nucleic Acids Res., 44, 3829-3844. doi: 10.1093/nar/gkw228. Mouse tdp2 reaction product (5'-phosphorylated DNA)-mg2+ complex with 1-n6-etheno-adenine. SNAP output
5hto oxidoreductase-DNA X-ray (1.9 Å) Choi SJ, Ban C (2016) "Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition." Sci Rep, 6, 34998. doi: 10.1038/srep34998. Crystal structure of plasmodium vivax ldh in complex with a DNA aptamer called pl1 (tetrameric ldh in an asymmetric unit). SNAP output
5i2d transcription-DNA-RNA X-ray (4.405 Å) Feng Y, Zhang Y, Ebright RH (2016) "Structural basis of transcription activation." Science, 352, 1330-1333. doi: 10.1126/science.aaf4417. Crystal structure of t. thermophilus tthb099 class ii transcription activation complex: tap-rpo. SNAP output
5i3u transferase-DNA X-ray (3.0 Å) Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E (2016) "Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet." Acs Chem.Biol., 11, 2158-2164. doi: 10.1021/acschembio.6b00187. Structure of hiv-1 reverse transcriptase n-site complex; catalytic incorporation of aztmp to a DNA aptamer in crystal. SNAP output
5i42 transferase-DNA X-ray (3.3 Å) Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ, Arnold E (2016) "Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet." Acs Chem.Biol., 11, 2158-2164. doi: 10.1021/acschembio.6b00187. Structure of hiv-1 reverse transcriptase in complex with a DNA aptamer, azttp, and ca(2+) ion. SNAP output
5i44 DNA binding protein-DNA X-ray (2.621 Å) Schumacher MA, Lee J, Zeng W (2016) "Molecular insights into DNA binding and anchoring by the Bacillus subtilis sporulation kinetochore-like RacA protein." Nucleic Acids Res., 44, 5438-5449. doi: 10.1093/nar/gkw248. Structure of raca-DNA complex; p21 form. SNAP output
5i4a RNA binding protein-RNA X-ray (1.949 Å) Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA (2016) "A bacterial Argonaute with noncanonical guide RNA specificity." Proc.Natl.Acad.Sci.USA, 113, 4057-4062. doi: 10.1073/pnas.1524385113. X-ray crystal structure of marinitoga piezophila argonaute in complex with 5' oh guide RNA. SNAP output
5i50 transcription X-ray (2.701 Å) Jung LA, Gebhardt A, Koelmel W, Ade CP, Walz S, Kuper J, von Eyss B, Letschert S, Redel C, d'Artista L, Biankin A, Zender L, Sauer M, Wolf E, Evan G, Kisker C, Eilers M (2017) "OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors." Oncogene, 36, 1911-1924. doi: 10.1038/onc.2016.354. Structure of omomyc bound to double-stranded DNA. SNAP output
5i9g RNA binding protein-RNA X-ray (2.288 Å) Shen C, Zhang D, Guan Z, Liu Y, Yang Z, Yang Y, Wang X, Wang Q, Zhang Q, Fan S, Zou T, Yin P (2016) "Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins." Nat Commun, 7, 11285. doi: 10.1038/ncomms11285. Crystal structure of designed pentatricopeptide repeat protein dppr-u8c2 in complex with its target RNA u8c2. SNAP output
5iff hydrolase-DNA X-ray (1.9 Å) Wang D, Miyazono KI, Tanokura M (2016) "Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA." Sci Rep, 6, 35197. doi: 10.1038/srep35197. Crystal structure of r.pabi-nonspecific DNA complex. SNAP output
5iii transferase-DNA X-ray (1.8 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dg and an incoming datp. SNAP output
5iij transferase-DNA X-ray (1.724 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dg and an incoming dctp. SNAP output
5iik transferase-DNA X-ray (1.982 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dg and incorporated dc. SNAP output
5iil transferase-DNA X-ray (1.96 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dg and incorporated da. SNAP output
5iim transferase-DNA X-ray (1.941 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dg:da base-pair. SNAP output
5iin transferase-DNA X-ray (2.15 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dg:dc base-pair. SNAP output
5iio transferase-DNA X-ray (2.08 Å) Burak MJ, Guja KE, Hambardjieva E, Derkunt B, Garcia-Diaz M (2016) "A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG." Embo J., 35, 2045-2059. doi: 10.15252/embj.201694332. Crystal structure of the DNA polymerase lambda binary complex. SNAP output
5ink hydrolase-DNA X-ray (2.15 Å) Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS (2016) "Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2." Nucleic Acids Res., 44, 3829-3844. doi: 10.1093/nar/gkw228. Mouse tdp2 reaction product (5'-phosphorylated DNA)-abasic-thf-mg2+ complex. SNAP output
5inl hydrolase-DNA X-ray (1.551 Å) Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS (2016) "Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2." Nucleic Acids Res., 44, 3829-3844. doi: 10.1093/nar/gkw228. Mouse tdp2 reaction product (5'-phosphorylated DNA)-mg2+ complex with deoxyadenosine. SNAP output
5ino hydrolase-DNA X-ray (3.205 Å) Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS (2016) "Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2." Nucleic Acids Res., 44, 3829-3844. doi: 10.1093/nar/gkw228. Human tdp2 reaction product (5'-phosphorylated DNA)-mg2+ complex. SNAP output
5inp hydrolase-DNA X-ray (1.947 Å) Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS (2016) "Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2." Nucleic Acids Res., 44, 3829-3844. doi: 10.1093/nar/gkw228. Mouse tdp2 reaction product (5'-phosphorylated DNA)-mn2+ complex. SNAP output
5inq hydrolase-DNA X-ray (1.848 Å) Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS (2016) "Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2." Nucleic Acids Res., 44, 3829-3844. doi: 10.1093/nar/gkw228. Mouse tdp2 reaction product (5'-phosphorylated DNA)-ca2+ complex. SNAP output
5ip3 viral protein-DNA X-ray (3.0 Å) Komoda K, Narita M, Yamashita K, Tanaka I, Yao M (2017) "Asymmetric Trimeric Ring Structure of the Nucleocapsid Protein of Tospovirus." J. Virol., 91. doi: 10.1128/JVI.01002-17. Tomato spotted wilt tospovirus nucleocapsid protein-ssDNA complex. SNAP output
5ipl transcription, transferase-DNA-RNA X-ray (3.6 Å) Liu B, Zuo Y, Steitz TA (2016) "Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism." Proc.Natl.Acad.Sci.USA, 113, 4051-4056. doi: 10.1073/pnas.1520555113. Sigmas-transcription initiation complex with 4-nt nascent RNA. SNAP output
5ipm transcription, transferase-DNA-RNA X-ray (4.2 Å) Liu B, Zuo Y, Steitz TA (2016) "Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism." Proc.Natl.Acad.Sci.USA, 113, 4051-4056. doi: 10.1073/pnas.1520555113. Sigmas-transcription initiation complex with 4-nt nascent RNA. SNAP output
5ipn transcription, transferase-DNA-RNA X-ray (4.61 Å) Liu B, Zuo Y, Steitz TA (2016) "Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism." Proc.Natl.Acad.Sci.USA, 113, 4051-4056. doi: 10.1073/pnas.1520555113. Sigmas-transcription initiation complex with 4-nt nascent RNA. SNAP output
5it9 ribosome cryo-EM (3.8 Å) Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS (2016) "Structural characterization of ribosome recruitment and translocation by type IV IRES." Elife, 5. doi: 10.7554/eLife.13567. Structure of the yeast kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus ires.. SNAP output
5ith RNA binding protein-DNA X-ray (2.31 Å) Waris S, Garcia-Maurino SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Diaz-Moreno I, Wilce MCJ, Wilce JA (2017) "TIA-1 RRM23 binding and recognition of target oligonucleotides." Nucleic Acids Res., 45, 4944-4957. doi: 10.1093/nar/gkx102. Tia-1 rrm2 recognition of target oligonucleotide. SNAP output
5itr DNA binding protein-DNA X-ray (2.46 Å) Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C (2016) "Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair." Proc.Natl.Acad.Sci.USA, 113, 7792-7797. doi: 10.1073/pnas.1604591113. Crystal structure of human neil1(p2g) bound to duplex DNA containing thf. SNAP output
5itt DNA binding protein-DNA X-ray (2.53 Å) Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C (2016) "Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair." Proc.Natl.Acad.Sci.USA, 113, 7792-7797. doi: 10.1073/pnas.1604591113. Crystal structure of human neil1 bound to duplex DNA containing thf. SNAP output
5itu DNA binding protein-DNA X-ray (2.41 Å) Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C (2016) "Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair." Proc.Natl.Acad.Sci.USA, 113, 7792-7797. doi: 10.1073/pnas.1604591113. Crystal structure of human neil1(242k) bound to duplex DNA containing thf. SNAP output
5itx DNA binding protein-DNA X-ray (2.65 Å) Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C (2016) "Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair." Proc.Natl.Acad.Sci.USA, 113, 7792-7797. doi: 10.1073/pnas.1604591113. Crystal structure of human neil1(p2g r242k) bound to duplex DNA containing thymine glycol. SNAP output
5ity DNA binding protein-DNA X-ray (2.48 Å) Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M, Stovicek O, Gao YQ, Yi C (2016) "Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair." Proc.Natl.Acad.Sci.USA, 113, 7792-7797. doi: 10.1073/pnas.1604591113. Crystal structure of human neil1(p2g) bound to duplex DNA containing thymine glycol. SNAP output
5iud transferase-DNA X-ray (3.3 Å) Coloma J, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2016) "Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer." Sci Rep, 6, 23784. doi: 10.1038/srep23784. Human DNA polymerase alpha in binary complex with a DNA:DNA template-primer. SNAP output
5ivw transcription-DNA cryo-EM (10.0 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human core tfiih bound to DNA within the pic. SNAP output
5iwi isomerase X-ray (1.98 Å) Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS, Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken JM, Giordano I, Hoover JL, Jones GE, Kusalakumari Sukmar SK, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN, Pearson ND (2016) "Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases." Bioorg.Med.Chem.Lett., 26, 2464-2469. doi: 10.1016/j.bmcl.2016.03.106. 1.98a structure of gsk945237 with s.aureus DNA gyrase and singly nicked DNA. SNAP output
5iwm isomerase X-ray (2.5 Å) Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS, Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken JM, Giordano I, Hoover JL, Jones GE, Kusalakumari Sukmar SK, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN, Pearson ND (2016) "Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases." Bioorg.Med.Chem.Lett., 26, 2464-2469. doi: 10.1016/j.bmcl.2016.03.106. 2.5a structure of gsk945237 with s.aureus DNA gyrase and DNA.. SNAP output
5iy6 transcription, transferase-DNA cryo-EM (7.2 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human holo-pic in the closed state. SNAP output
5iy7 transcription, transferase-DNA cryo-EM (8.6 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human holo-pic in the open state. SNAP output
5iy8 transcription, transferase-DNA cryo-EM (7.9 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human holo-pic in the initial transcribing state. SNAP output
5iy9 transcription, transferase-DNA-RNA cryo-EM (6.3 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human holo-pic in the initial transcribing state (no iis). SNAP output
5iya transcription, transferase-DNA cryo-EM (5.4 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human core-pic in the closed state. SNAP output
5iyb transcription, transferase-DNA cryo-EM (3.9 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human core-pic in the open state. SNAP output
5iyc transcription, transferase-DNA cryo-EM (3.9 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human core-pic in the initial transcribing state. SNAP output
5iyd transcription, transferase-DNA-RNA cryo-EM (3.9 Å) He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E (2016) "Near-atomic resolution visualization of human transcription promoter opening." Nature, 533, 359-365. doi: 10.1038/nature17970. Human core-pic in the initial transcribing state (no iis). SNAP output
5j0n transferase, hydrolase-DNA cryo-EM (11.0 Å) Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L, Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD (2016) "Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction." Elife, 5. doi: 10.7554/eLife.14313. Lambda excision hj intermediate. SNAP output
5j0o transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with a:a mismatch at the primer terminus. SNAP output
5j0p transferase-DNA X-ray (2.2 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with a:c mismatch at the primer terminus. SNAP output
5j0q transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with a:g mismatch at the primer terminus. SNAP output
5j0r transferase-DNA X-ray (2.001 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with c:a mismatch at the primer terminus. SNAP output
5j0s transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with c:t mismatch at the primer terminus. SNAP output
5j0t transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with g:a mismatch at the primer terminus. SNAP output
5j0u transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with g:g mismatch at the primer terminus. SNAP output
5j0w transferase-DNA X-ray (2.4 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with t:c mismatch at the primer terminus. SNAP output
5j0x transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with t:g mismatch at the primer terminus. SNAP output
5j0y transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with t:t mismatch at the primer terminus. SNAP output
5j29 transferase-DNA X-ray (2.2 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with a:a mismatch at the primer terminus. SNAP output
5j2a transferase-DNA X-ray (2.5 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with a:c mismatch at the primer terminus. SNAP output
5j2b transferase-DNA X-ray (2.5 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with a:c mismatch at the primer terminus. SNAP output
5j2c transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with c:a mismatch at the primer terminus. SNAP output
5j2d transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with c:c mismatch at the primer terminus. SNAP output
5j2e transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with c:t mismatch at the primer terminus. SNAP output
5j2f transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with g:a mismatch at the primer terminus. SNAP output
5j2g transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with g:g mismatch at the primer terminus. SNAP output
5j2h transferase-DNA X-ray (2.3 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with g:t mismatch at the primer terminus. SNAP output
5j2i transferase-DNA X-ray (2.4 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with t:c mismatch at the primer terminus. SNAP output
5j2j transferase-DNA X-ray (2.2 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with t:g mismatch at the primer terminus. SNAP output
5j2k transferase-DNA X-ray (2.1 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Ternary complex crystal structure of DNA polymerase beta with t:t mismatch at the primer terminus. SNAP output
5j2m transferase-DNA X-ray (2.432 Å) Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG (2016) "Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)." Proc.Natl.Acad.Sci.USA, 113, 9274-9279. doi: 10.1073/pnas.1605223113. Hiv-1 reverse transcriptase in complex with DNA and efda-triphosphate, a translocation-defective rt inhibitor. SNAP output
5j2n transferase-DNA X-ray (2.896 Å) Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG (2016) "Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)." Proc.Natl.Acad.Sci.USA, 113, 9274-9279. doi: 10.1073/pnas.1605223113. Hiv-1 reverse transcriptase in complex with DNA that has incorporated efda-mp at the p-(post-translocation) site and dtmp at the n-(pre-translocation) site. SNAP output
5j2p transferase-DNA X-ray (2.53 Å) Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG (2016) "Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)." Proc.Natl.Acad.Sci.USA, 113, 9274-9279. doi: 10.1073/pnas.1605223113. Hiv-1 reverse transcriptase in complex with DNA that has incorporated efda-mp at the p-(post-translocation) site and a second efda-mp at the n-(pre-translocation) site. SNAP output
5j2q transferase-DNA X-ray (2.789 Å) Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos SG (2016) "Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)." Proc.Natl.Acad.Sci.USA, 113, 9274-9279. doi: 10.1073/pnas.1605223113. Hiv-1 reverse transcriptase in complex with DNA that has incorporated a mismatched efda-mp at the n-(pre-translocation) site. SNAP output
5j2y gene regulation-DNA X-ray (2.4 Å) Kang H, Gan J, Zhao J, Kong W, Zhang J, Zhu M, Li F, Song Y, Qin J, Liang H (2017) "Crystal structure of Pseudomonas aeruginosa RsaL bound to promoter DNA reaffirms its role as a global regulator involved in quorum-sensing." Nucleic Acids Res., 45, 699-710. doi: 10.1093/nar/gkw954. Molecular insight into the regulatory mechanism of the quorum-sensing repressor rsal in pseudomonas aeruginosa. SNAP output
5j37 virus-DNA X-ray (2.3 Å) Sarker S, Terron MC, Khandokar Y, Aragao D, Hardy JM, Radjainia M, Jimenez-Zaragoza M, de Pablo PJ, Coulibaly F, Luque D, Raidal SR, Forwood JK (2016) "Structural insights into the assembly and regulation of distinct viral capsid complexes." Nat Commun, 7, 13014. doi: 10.1038/ncomms13014. Crystal structure of 60-mer bfdv capsid protein in complex with single stranded DNA. SNAP output
5j3e nuclear protein-DNA X-ray (2.6 Å) Halabelian L, Tempel W, Li Y, Bountra C, Edwards AM, Arrowsmith CH "Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA." Crystal structure of human thyn1 protein in complex with 5-methylcytosine containing DNA. SNAP output
5j5p isomerase-DNA X-ray (1.97 Å) Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR (2018) "Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase." Nat Commun, 9, 2579. doi: 10.1038/s41467-018-05005-x. Amp-pnp-stabilized atpase domain of topoisomerase iv from streptococcus pneumoniae, complex type i. SNAP output
5j5q isomerase-DNA X-ray (2.83 Å) Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR (2018) "Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase." Nat Commun, 9, 2579. doi: 10.1038/s41467-018-05005-x. Amp-pnp-stabilized atpase domain of topoisomerase iv from streptococcus pneumoniae, complex type ii. SNAP output
5j70 chromatin-binding protein-DNA X-ray (2.956 Å) Nodelman IM, Jenkins KR, Ren R, Horvath KC, Hauk G, Bowman GD "Chd1 domains communicate across the DNA gyres of the nucleosome." The chd1 DNA-binding domain in complex with 17mer DNA duplex. SNAP output
5jgh DNA binding protein X-ray (2.6 Å) Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Sola M (2017) "DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p." Nucleic Acids Res., 45, 951-967. doi: 10.1093/nar/gkw1147. Crystal structure of the mitochondrial DNA packaging protein abf2p in complex with DNA at 2.6 angstrom resolution. SNAP output
5jh0 DNA binding protein X-ray (2.18 Å) Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Sola M (2017) "DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p." Nucleic Acids Res., 45, 951-967. doi: 10.1093/nar/gkw1147. Crystal structure of the mitochondrial DNA packaging protein abf2p in complex with DNA at 2.18 angstrom resolution. SNAP output
5jjv recombination X-ray (2.4 Å) Bebel A, Karaca E, Kumar B, Stark WM, Barabas O (2016) "Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending." Elife, 5. doi: 10.7554/eLife.19706. Crystal structure of xerh site-specific recombinase bound to palindromic difh substrate: post-cleavage complex. SNAP output
5jk0 cell cycle X-ray (2.1 Å) Bebel A, Karaca E, Kumar B, Stark WM, Barabas O (2016) "Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending." Elife, 5. doi: 10.7554/eLife.19706. Crystal structure of xerh site-specific recombinase bound to difh substrate: pre-cleavage complex. SNAP output
5jlt viral protein-DNA X-ray (2.955 Å) Cuypers MG, Robertson RM, Knipling L, Waddell MB, Moon K, Hinton DM, White SW (2018) "The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA." Nucleic Acids Res., 46, 5308-5318. doi: 10.1093/nar/gky292. The crystal structure of the bacteriophage t4 mota c-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif. SNAP output
5jlw transcription regulator-DNA X-ray (2.088 Å) Nguyen D, Zandarashvili L, White MA, Iwahara J (2016) "Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity." Chembiochem, 17, 1636-1642. doi: 10.1002/cbic.201600265. Antphd with 15bp DNA duplex r-monothioated at cytidine-8. SNAP output
5jlx transcription regulator-DNA X-ray (2.748 Å) Nguyen D, Zandarashvili L, White MA, Iwahara J (2016) "Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity." Chembiochem, 17, 1636-1642. doi: 10.1002/cbic.201600265. Antphd with 15bp DNA duplex s-monothioated at cytidine-8. SNAP output
5jre DNA binding protein X-ray (2.1 Å) Zhang J, Liu H, Yao Q, Yu X, Chen Y, Cui R, Wu B, Zheng L, Zuo J, Huang Z, Ma J, Gan J (2016) "Structural basis for single-stranded RNA recognition and cleavage by C3PO." Nucleic Acids Res., 44, 9494-9504. doi: 10.1093/nar/gkw776. Crystal structure of nec3po in complex with ssDNA.. SNAP output
5jrg DNA binding protein-DNA X-ray (2.5 Å) Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H (2017) "Polymorphism of apyrimidinic DNA structures in the nucleosome." Sci Rep, 7, 41783. doi: 10.1038/srep41783. Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (thf). SNAP output
5jub transcription X-ray (2.57 Å) Talagas A, Fontaine L, Ledesma-Garca L, Mignolet J, Li de la Sierra-Gallay I, Lazar N, Aumont-Nicaise M, Federle MJ, Prehna G, Hols P, Nessler S (2016) "Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS." PLoS Pathog., 12, e1005980. doi: 10.1371/journal.ppat.1005980. Crystal structure of comr from s.thermophilus in complex with DNA and its signalling peptide coms.. SNAP output
5jum transferase-DNA X-ray (2.6 Å) Patra A, Politica DA, Chatterjee A, Tokarsky EJ, Suo Z, Basu AK, Stone MP, Egli M (2016) "Mechanism of Error-Free Bypass of the Environmental Carcinogen N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone Adduct by Human DNA Polymerase eta." Chembiochem, 17, 2033-2037. doi: 10.1002/cbic.201600420. Crystal structure of human DNA polymerase eta inserting dctp opposite n-(2'-deoxyguanosin-8- yl)-3-aminobenzanthrone (c8-dg-aba). SNAP output
5jvt transcription-DNA X-ray (3.1 Å) Hou C, Weidenbach S, Cano KE, Wang Z, Mitra P, Ivanov DN, Rohr J, Tsodikov OV (2016) "Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1." Nucleic Acids Res., 44, 8990-9004. doi: 10.1093/nar/gkw761. Crystal structure of the DNA binding domain of transcription factor fli1 in complex with an 11-mer DNA gaccggaagtg. SNAP output
5jxy hydrolase-DNA X-ray (1.71 Å) Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC (2016) "Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues." Nucleic Acids Res., 44, 10248-10258. doi: 10.1093/nar/gkw768. Enzyme-substrate complex of tdg catalytic domain bound to a g-u analog. SNAP output
5k07 DNA binding protein-DNA X-ray (2.0 Å) Tian L, Zhang ZF, Wang H, Zhao M, Dong Y, Gong Y (2016) "Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea." PLoS ONE, 11, e0163361. doi: 10.1371/journal.pone.0163361. Crystal structure of cren7-dsDNA (gtaattgc) complex. SNAP output
5k17 DNA binding protein-DNA X-ray (2.1 Å) Tian L, Zhang ZF, Wang H, Zhao M, Dong Y, Gong Y (2016) "Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea." PLoS ONE, 11, e0163361. doi: 10.1371/journal.pone.0163361. Crystal structure of cren7-dsDNA (gtgatcgc) complex. SNAP output
5k1y transcription-DNA X-ray (2.97 Å) Schumacher M "Detailed structural analysis of AspA-DNA contacts." P2(1) structure of pnob8 aspa-DNA complex. SNAP output
5k58 DNA binding protein-DNA X-ray (2.772 Å) Schumacher MA, Zeng W (2016) "Structures of the nucleoid occlusion protein SlmA bound to DNA and the C-terminal domain of the cytoskeletal protein FtsZ." Proc. Natl. Acad. Sci. U.S.A., 113, 4988-4993. doi: 10.1073/pnas.1602327113. Structure of the k. pneumonia slma-DNA complex bound to the c-terminal of the cell division protein ftsz. SNAP output
5k5h transcription-DNA X-ray (3.108 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Homo sapiens ccctc-binding factor (ctcf) znf4-7 and DNA complex structure. SNAP output
5k5i transcription-DNA X-ray (2.19 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Homo sapiens ccctc-binding factor (ctcf) znf5-8 and DNA complex structure in space group p65. SNAP output
5k5j transcription-DNA X-ray (2.287 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Homo sapiens ccctc-binding factor (ctcf) znf5-8 and DNA complex structure in space group p41212. SNAP output
5k5l transcription-DNA X-ray (3.125 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Homo sapiens ccctc-binding factor (ctcf) znf6-8 and h19 sequence DNA complex structure. SNAP output
5k5o transcription-DNA X-ray (3.2 Å) Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT, Shaw PL, Barilla D (2015) "Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages." Science, 349, 1120-1124. doi: 10.1126/science.aaa9046. Structure of aspa-26mer DNA complex. SNAP output
5k5q transcription-DNA X-ray (2.649 Å) Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT, Shaw PL, Barilla D (2015) "Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages." Science, 349, 1120-1124. doi: 10.1126/science.aaa9046. Structure of aspa-DNA complex: novel centromere bindng protein-centromere complex. SNAP output
5k5r transcription-DNA X-ray (3.09 Å) Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT, Shaw PL, Barilla D (2015) "Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages." Science, 349, 1120-1124. doi: 10.1126/science.aaa9046. Aspa-32mer DNA,crystal form 2. SNAP output
5k77 hydrolase-RNA X-ray (2.17 Å) Clark NE, Katolik A, Roberts KM, Taylor AB, Holloway SP, Schuermann JP, Montemayor EJ, Stevens SW, Fitzpatrick PF, Damha MJ, Hart PJ (2016) "Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1." Proc. Natl. Acad. Sci. U.S.A., 113, 14727-14732. doi: 10.1073/pnas.1612729114. Dbr1 in complex with 7-mer branched RNA. SNAP output
5k78 hydrolase-RNA X-ray (2.64 Å) Clark NE, Katolik A, Roberts K, Taylor AB, Holloway SP, Schuermann JP, Montemayor EJ, Stevens SW, Fitzpatrick PF, Damha MJ, Hart PJ (2016) "The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures." Proc.Natl.Acad.Sci.USA. doi: 10.1073/pnas.1612729114. Dbr1 in complex with 16-mer branched RNA. SNAP output
5k7z transcription X-ray (2.92 Å) Bock T, Volz C, Mueller R, Blankenfeldt W "Crystal structure of AibR in complex with isovaleryl coenzyme A and operator DNA." Crystal structure of aibr in complex with isovaleryl coenzyme a and operator DNA. SNAP output
5k83 hydrolase X-ray (2.39 Å) Xiao X, Li SX, Yang H, Chen XS (2016) "Crystal structures of APOBEC3G N-domain alone and its complex with DNA." Nat Commun, 7, 12193. doi: 10.1038/ncomms12193. Crystal structure of a primate apobec3g n-domain, in complex with ssDNA. SNAP output
5k97 hydrolase-DNA X-ray (2.102 Å) Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA (2017) "Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability." Nat Commun, 8, 15855. doi: 10.1038/ncomms15855. Flap endonuclease 1 (fen1) d233n with cleaved product fragment and sm3+. SNAP output
5k98 transcription-DNA X-ray (3.99 Å) Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulic M, Lewis K, Brennan RG (2015) "HipBA-promoter structures reveal the basis of heritable multidrug tolerance." Nature, 524, 59-64. doi: 10.1038/nature14662. Structure of hipa-hipb-o2-o3 complex. SNAP output
5kbd DNA binding protein-DNA X-ray (2.8 Å) Nguyen HT, Huang D "Structural Studies of Transcription Factor p73 DNA Binding Domain Bound to PA26 20-mer Response Element." Structural studies of transcription factor p73 DNA binding domain bound to pa26 20-mer response element. SNAP output
5kbj transcription-DNA X-ray (3.09 Å) Schumacher MA, Tonthat NK, Kwong SM, Chinnam NB, Liu MA, Skurray RA, Firth N (2014) "Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein." Proc. Natl. Acad. Sci. U.S.A., 111, 9121-9126. doi: 10.1073/pnas.1406065111. Structure of rep-DNA complex. SNAP output
5ke6 transcription-DNA X-ray (1.99 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 znf1-3 and tpg-cpa sequence DNA complex structure. SNAP output
5ke7 transcription-DNA X-ray (2.06 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 znf1-3 and tpg-mpa sequence DNA complex structure. SNAP output
5ke8 transcription-DNA X-ray (2.45 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 e446p znf1-3 and mpg-mpg sequence DNA complex structure. SNAP output
5ke9 transcription factor-DNA X-ray (2.336 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 e446p znf1-3 and tpg-cpa sequence DNA complex structure. SNAP output
5kea transcription factor-DNA X-ray (2.458 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 znf1-3 (e446d) and cpg-cpg sequence DNA complex structure: form i. SNAP output
5keb transcription factor-DNA X-ray (2.453 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 znf1-3 (e446d) and cpg-cpg sequence DNA complex structure: form ii. SNAP output
5keg hydrolase-DNA X-ray (2.2 Å) Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N, Matsuo H, Schiffer CA (2017) "Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity." Nat Commun, 8, 15024. doi: 10.1038/ncomms15024. Crystal structure of apobec3a in complex with a single-stranded DNA. SNAP output
5kfa replication, transferase-DNA X-ray (1.51 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: ground state at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
5kfb replication, transferase-DNA X-ray (1.55 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm mn2+ for 90s. SNAP output
5kfc replication, transferase-DNA X-ray (1.5 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm mn2+ for 180s. SNAP output
5kfd replication, transferase-DNA X-ray (1.65 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm mn2+ for 300s. SNAP output
5kfe replication, transferase-DNA X-ray (1.55 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm mn2+ for 600s. SNAP output
5kff replication, transferase-DNA X-ray (1.7 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm mn2+ for 1800s. SNAP output
5kfg replication, transferase-DNA X-ray (1.55 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 30s. SNAP output
5kfh replication, transferase-DNA X-ray (1.72 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 90s. SNAP output
5kfi replication, transferase-DNA X-ray (1.65 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 120s. SNAP output
5kfj replication, transferase-DNA X-ray (1.7 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 180s. SNAP output
5kfk replication, transferase-DNA X-ray (1.7 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 300s. SNAP output
5kfl replication, transferase-DNA X-ray (1.65 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 600s. SNAP output
5kfm replication, transferase-DNA X-ray (1.6 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-s: ground state at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
5kfn replication, transferase-DNA X-ray (1.45 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-s: reaction with 1 mm mg2+ for 1800s. SNAP output
5kfo replication, transferase-DNA X-ray (1.52 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-s: reaction with 1 mm mn2+ for 1800s. SNAP output
5kfp replication, transferase-DNA X-ray (1.7 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-s: reaction with 20 mm mg2+ for 600s. SNAP output
5kfq replication, transferase-DNA X-ray (1.55 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-s: reaction with 10 mm mn2+ for 600s. SNAP output
5kfr replication, transferase-DNA X-ray (1.75 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex with sp-datp-alpha-s: reaction with 20 mm mn2+ for 600s. SNAP output
5kfs replication, transferase-DNA X-ray (1.46 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta r61a-DNA ternary complex: ground state at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
5kft replication, transferase-DNA X-ray (1.52 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta r61a-DNA ternary complex: reaction with 1 mm mg2+ for 40s. SNAP output
5kfu replication, transferase-DNA X-ray (1.55 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta r61a-DNA ternary complex: reaction with 1 mm mg2+ for 80s. SNAP output
5kfv replication, transferase-DNA X-ray (1.6 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta r61a-DNA ternary complex: reaction with 1 mm mg2+ for 140s. SNAP output
5kfw replication, transferase-DNA X-ray (1.62 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta r61a-DNA ternary complex: reaction with 1 mm mg2+ for 200s. SNAP output
5kfx replication, transferase-DNA X-ray (1.52 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta r61a-DNA ternary complex: reaction with 1 mm mg2+ for 300s. SNAP output
5kfy replication, transferase-DNA X-ray (1.7 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for 60s at 4 degree. SNAP output
5kfz replication, transferase-DNA X-ray (1.44 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for 60s at 14 degree. SNAP output
5kg0 replication, transferase-DNA X-ray (1.6 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for 60s at 22 degree. SNAP output
5kg1 replication, transferase-DNA X-ray (1.62 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for 60s at 30 degree. SNAP output
5kg2 replication, transferase-DNA X-ray (1.6 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for 60s at 37 degree. SNAP output
5kg3 replication, transferase-DNA X-ray (1.7 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 10 mm mn2+ for 60s. SNAP output
5kg4 replication, transferase-DNA X-ray (1.6 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 10 mm mg2+ for 60s. SNAP output
5kg5 replication, transferase-DNA X-ray (1.6 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 10 mm cd2+ for 60s. SNAP output
5kg6 replication, transferase-DNA X-ray (1.55 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 10 mm ca2+ for 60s. SNAP output
5kg7 replication, transferase-DNA X-ray (1.75 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mm mn2+ for 1800s then with 10 mm zn2+ for 60s. SNAP output
5kgf structural protein-DNA cryo-EM (4.54 Å) Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A, Julien JP, McEwan A, Noordermeer SM, Sicheri F, Rubinstein JL, Durocher D (2016) "The structural basis of modified nucleosome recognition by 53BP1." Nature, 536, 100-103. doi: 10.1038/nature18951. Structural model of 53bp1 bound to a ubiquitylated and methylated nucleosome, at 4.5 Å resolution. SNAP output
5kk1 transcription-DNA X-ray (3.38 Å) Schumacher M "to be published." Structure of pnob8 aspa-DNA complex.. SNAP output
5kk5 hydrolase-DNA-RNA X-ray (3.289 Å) Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ (2016) "Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition." Cell Res., 26, 901-913. doi: 10.1038/cr.2016.88. Ascpf1(e993a)-crrna-DNA ternary complex. SNAP output
5kkq transcription-DNA X-ray (1.744 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Homo sapiens ccctc-binding factor (ctcf) znf3-7 and DNA complex structure. SNAP output
5kl2 transcription-DNA X-ray (1.692 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4 in complex with DNA. SNAP output
5kl3 transcription-DNA X-ray (1.449 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4 q369h in complex with DNA. SNAP output
5kl4 transcription-DNA X-ray (1.783 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4 q369h in complex with formylated DNA. SNAP output
5kl5 transcription-DNA X-ray (2.289 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4 q369h in complex with carboxylated DNA. SNAP output
5kl6 transcription-DNA X-ray (1.641 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) q369r znf2-4 in complex with DNA. SNAP output
5kl7 transcription-DNA X-ray (1.579 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4q369r in complex with carboxylated DNA. SNAP output
5kn8 hydrolase-DNA X-ray (1.81 Å) Wang L, Chakravarthy S, Verdine GL (2017) "Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase." J. Biol. Chem., 292, 5007-5017. doi: 10.1074/jbc.M116.757039. Muty n-terminal domain in complex with undamaged DNA. SNAP output
5kn9 hydrolase-DNA X-ray (1.93 Å) Wang L, Chakravarthy S, Verdine GL (2017) "Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase." J. Biol. Chem., 292, 5007-5017. doi: 10.1074/jbc.M116.757039. Muty n-terminal domain in complex with DNA containing an intrahelical oxog:a base-pair. SNAP output
5krb transcription-DNA X-ray (2.101 Å) Weikum ER, Tuntland ML, Murphy MN, Ortlund EA (2016) "A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1)." J. Mol. Biol., 428, 4981-4992. doi: 10.1016/j.jmb.2016.10.025. Gcnf DNA binding domain - oct4 dr0 complex. SNAP output
5kse hydrolase-DNA X-ray (2.105 Å) Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA (2017) "Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability." Nat Commun, 8, 15855. doi: 10.1038/ncomms15855. Flap endonuclease 1 (fen1) r100a with 5'-flap substrate DNA and sm3+. SNAP output
5kt2 transferase X-ray (2.488 Å) Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP (2016) "Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota." J.Biol.Chem., 291, 21063-21073. doi: 10.1074/jbc.M116.748285. Teranry complex of human DNA polymerase iota(26-445) inserting dcmpnpp opposite template g in the presence of mg2+. SNAP output
5kt3 transferase X-ray (2.64 Å) Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP (2016) "Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota." J.Biol.Chem., 291, 21063-21073. doi: 10.1074/jbc.M116.748285. Teranry complex of human DNA polymerase iota(26-445) inserting dcmpnpp opposite template g in the presence of mn2+. SNAP output
5kt4 transferase X-ray (2.78 Å) Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP (2016) "Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota." J.Biol.Chem., 291, 21063-21073. doi: 10.1074/jbc.M116.748285. Teranry complex of human DNA polymerase iota r96g inserting dcmpnpp opposite template g in the presence of mg2+. SNAP output
5kt5 transferase X-ray (2.798 Å) Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP (2016) "Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota." J.Biol.Chem., 291, 21063-21073. doi: 10.1074/jbc.M116.748285. Teranry complex of human DNA polymerase iota r96g inserting dcmpnpp opposite template g in the presence of mn2+. SNAP output
5kt6 transferase X-ray (3.54 Å) Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP (2016) "Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota." J.Biol.Chem., 291, 21063-21073. doi: 10.1074/jbc.M116.748285. Teranry complex of human DNA polymerase iota(1-445) inserting dcmpnpp opposite template g in the presence of mg2+. SNAP output
5kt7 transferase X-ray (3.151 Å) Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP (2016) "Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota." J.Biol.Chem., 291, 21063-21073. doi: 10.1074/jbc.M116.748285. Teranry complex of human DNA polymerase iota(1-445) inserting dcmpnpp opposite template g in the presence of mn2+. SNAP output
5kub hydrolase-DNA X-ray (1.73 Å) Parsons ZD, Bland JM, Mullins EA, Eichman BF (2016) "A Catalytic Role for C-H/ pi Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD." J.Am.Chem.Soc., 138, 11485-11488. doi: 10.1021/jacs.6b07399. Bacillus cereus DNA glycosylase alkd bound to 7-methylguanine nucleobase and DNA containing an oxocarbenium-intermediate analog. SNAP output
5kvy splicing-DNA X-ray (1.95 Å) Hsiao HT, Crichlow GV, Murphy JW, Folta-Stogniew EJ, Lolis EJ, Braddock DT (2020) "Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60." Plos One, 15, e0242725. doi: 10.1371/journal.pone.0242725. Crystal structure of the two tandem rrm domains of puf60 bound to a portion of an adml pre-mrna 3' splice site analog. SNAP output
5kw1 splicing-DNA X-ray (2.1 Å) Hsiao HT, Crichlow GV, Murphy JW, Folta-Stogniew EJ, Lolis EJ, Braddock DT (2020) "Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60." Plos One, 15, e0242725. doi: 10.1371/journal.pone.0242725. Crystal structure of the two tandem rrm domains of puf60 bound to a modified adml pre-mrna 3' splice site analogue. SNAP output
5kw6 splicing-DNA X-ray (1.91 Å) Hsiao HT, Crichlow GV, Murphy JW, Folta-Stogniew EJ, Lolis EJ, Braddock DT (2020) "Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60." Plos One, 15, e0242725. doi: 10.1371/journal.pone.0242725. Two tandem rrm domains of puf60 bound to an adml pre-mrna 3' splice site analogue with a modified binding-site nucleic acid base. SNAP output
5l0m transcription-DNA X-ray (2.197 Å) Weikum ER, Tuntland ML, Murphy MN, Ortlund EA (2016) "A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1)." J. Mol. Biol., 428, 4981-4992. doi: 10.1016/j.jmb.2016.10.025. Hlrh-1 DNA binding domain - 12bp oct4 promoter complex. SNAP output
5l1i transferase-DNA X-ray (2.78 Å) Patra A, Zhang Q, Guengerich FP, Egli M (2016) "Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta." J.Biol.Chem., 291, 24304-24313. doi: 10.1074/jbc.M116.755462. Crystal structure of human DNA polymerase eta inserting dctp opposite o6-methyl-2'-deoxyguanosine. SNAP output
5l1j transferase-DNA X-ray (1.94 Å) Patra A, Zhang Q, Guengerich FP, Egli M (2016) "Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta." J.Biol.Chem., 291, 24304-24313. doi: 10.1074/jbc.M116.755462. Crystal structure of human DNA polymerase eta inserting dtmpnpp opposite o6-methyl-2'-deoxyguanosine. SNAP output
5l1k transferase-DNA X-ray (1.82 Å) Patra A, Zhang Q, Guengerich FP, Egli M (2016) "Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta." J.Biol.Chem., 291, 24304-24313. doi: 10.1074/jbc.M116.755462. Postinsertion complex of human DNA polymerase eta bypassing an o6-methyl-2'-deoxyguanosine : dc site. SNAP output
5l1l transferase-DNA X-ray (1.62 Å) Patra A, Zhang Q, Guengerich FP, Egli M (2016) "Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta." J.Biol.Chem., 291, 24304-24313. doi: 10.1074/jbc.M116.755462. Postinsertion complex of human DNA polymerase eta bypassing an o6-methyl-2'-deoxyguanosine : dt site. SNAP output
5l2x transferase-DNA X-ray (2.2 Å) Rechkoblit O, Gupta YK, Malik R, Rajashankar KR, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2016) "Structure and mechanism of human PrimPol, a DNA polymerase with primase activity." Sci Adv, 2, e1601317. doi: 10.1126/sciadv.1601317. Crystal structure of human primpol ternary complex. SNAP output
5l6l hydrolase X-ray (2.7 Å) Bendtsen KL, Xu K, Luckmann M, Winther KS, Shah SA, Pedersen CNS, Brodersen DE (2017) "Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding." Nucleic Acids Res., 45, 2875-2886. doi: 10.1093/nar/gkw1266. Structure of caulobacter crescentus vapbc1 bound to operator DNA. SNAP output
5l9x transferase X-ray (1.9 Å) Gao Y, Yang W (2016) "Capture of a third Mg2+ is essential for catalyzing DNA synthesis." Science, 352, 1334-1337. doi: 10.1126/science.aad9633. Human DNA polymerase eta-DNA ternary complex: reaction with 10 mm mn2+ for 60s. SNAP output
5lcl DNA binding protein X-ray (2.2 Å) Ebert C, Simon N, Schneider S, Carell T (2017) "Structural Insights into the Recognition of N(2) -Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14." Chembiochem, 18, 1379-1382. doi: 10.1002/cbic.201700169. Structure of the rad14 DNA-binding domain in complex with c8-aminofluorene- guanine containing DNA. SNAP output
5lcm DNA binding protein X-ray (1.9 Å) Ebert C, Simon N, Schneider S, Carell T (2017) "Structural Insights into the Recognition of N(2) -Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14." Chembiochem, 18, 1379-1382. doi: 10.1002/cbic.201700169. Structure of the rad14 DNA-binding domain in complex with n2-acetylaminonaphtyl- guanine containing DNA. SNAP output
5ld2 hydrolase cryo-EM (3.83 Å) Wilkinson M, Chaban Y, Wigley DB (2016) "Mechanism for nuclease regulation in RecBCD." Elife, 5. doi: 10.7554/eLife.18227. cryo-EM structure of recbcd+DNA complex revealing activated nuclease domain. SNAP output
5lej transcription X-ray (2.7 Å) Hall M, Grundstrom C, Begum A, Lindberg MJ, Sauer UH, Almqvist F, Johansson J, Sauer-Eriksson AE (2016) "Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria." Proc. Natl. Acad. Sci. U.S.A., 113, 14733-14738. doi: 10.1073/pnas.1614028114. The transcriptional regulator prfa from listeria monocytogenes in complex with a 30-bp operator prfa-box motif. SNAP output
5lek transcription X-ray (2.8 Å) Hall M, Grundstrom C, Begum A, Lindberg MJ, Sauer UH, Almqvist F, Johansson J, Sauer-Eriksson AE (2016) "Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria." Proc. Natl. Acad. Sci. U.S.A., 113, 14733-14738. doi: 10.1073/pnas.1614028114. The transcriptional regulator prfa-g145s mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif. SNAP output
5lgy transcription X-ray (2.92 Å) Vainer R, Cohen S, Shahar A, Zarivach R, Arbely E (2016) "Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode." J.Mol.Biol., 428, 3013-3025. doi: 10.1016/j.jmb.2016.06.009. Lysine 120-acetylated p53 DNA binding domain in a complex with the bax response element.. SNAP output
5lrs transcription X-ray (2.9 Å) Hall M, Grundstrom C, Begum A, Lindberg MJ, Sauer UH, Almqvist F, Johansson J, Sauer-Eriksson AE (2016) "Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria." Proc. Natl. Acad. Sci. U.S.A., 113, 14733-14738. doi: 10.1073/pnas.1614028114. The transcriptional regulator prfa from listeria monocytogenes in complex with glutathione and a 30-bp operator prfa-box motif. SNAP output
5lty transcription X-ray (2.66 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Homeobox transcription factor cdx2 bound to methylated DNA. SNAP output
5lux transcription X-ray (3.23 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Homeobox transcription factor cdx1 bound to methylated DNA. SNAP output
5lxu DNA binding protein X-ray (2.14 Å) Zubieta C, Silva CS, Lai X, Wigge P, Nanao MH, Nayak A "Structure of the DNA-binding domain of LUX ARRHYTHMO." Structure of the DNA-binding domain of lux arrhythmo. SNAP output
5m0r hydrolase cryo-EM (8.2 Å) Ballandras-Colas A, Maskell DP, Serrao E, Locke J, Swuec P, Jonsson SR, Kotecha A, Cook NJ, Pye VE, Taylor IA, Andresdottir V, Engelman AN, Costa A, Cherepanov P (2017) "A supramolecular assembly mediates lentiviral DNA integration." Science, 355, 93-95. doi: 10.1126/science.aah7002. cryo-EM reconstruction of the maedi-visna virus (mvv) strand transfer complex. SNAP output
5m1s DNA binding protein cryo-EM (6.7 Å) Fernandez-Leiro R, Conrad J, Yang JC, Freund SM, Scheres SH, Lamers MH (2017) "Self-correcting mismatches during high-fidelity DNA replication." Nat. Struct. Mol. Biol., 24, 140-143. doi: 10.1038/nsmb.3348. cryo-EM structure of the e. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode. SNAP output
5m3f transcription cryo-EM (3.8 Å) Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau VV, Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis AS (2016) "Structure of RNA polymerase I transcribing ribosomal DNA genes." Nature, 540, 607-610. doi: 10.1038/nature20561. Yeast RNA polymerase i elongation complex at 3.8a. SNAP output
5m5w transcription cryo-EM (3.8 Å) Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW (2016) "Molecular Structures of Transcribing RNA Polymerase I." Mol. Cell, 64, 1135-1143. doi: 10.1016/j.molcel.2016.11.013. RNA polymerase i open complex. SNAP output
5m5x transcription cryo-EM (4.0 Å) Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW (2016) "Molecular Structures of Transcribing RNA Polymerase I." Mol. Cell, 64, 1135-1143. doi: 10.1016/j.molcel.2016.11.013. RNA polymerase i elongation complex 1. SNAP output
5m5y transcription cryo-EM (4.0 Å) Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW (2016) "Molecular Structures of Transcribing RNA Polymerase I." Mol. Cell, 64, 1135-1143. doi: 10.1016/j.molcel.2016.11.013. RNA polymerase i elongation complex 2. SNAP output
5m64 transcription cryo-EM (4.6 Å) Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R, Hagen WJ, Sachse C, Muller CW (2016) "Molecular Structures of Transcribing RNA Polymerase I." Mol. Cell, 64, 1135-1143. doi: 10.1016/j.molcel.2016.11.013. RNA polymerase i elongation complex with a49 tandem winged helix domain. SNAP output
5mct transcription X-ray (1.446 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-lhg1). SNAP output
5mcu transcription X-ray (1.7 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-lhg2). SNAP output
5mcv transcription X-ray (1.6 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-lwc1). SNAP output
5mcw transcription X-ray (1.897 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-lwc2). SNAP output
5mey transcription X-ray (2.05 Å) Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ (2017) "Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors." Nat Commun, 8, 2070. doi: 10.1038/s41467-017-02054-6. Crystal structure of smad4-mh1 bound to the ggcgc site.. SNAP output
5mez transcription X-ray (2.98 Å) Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ (2017) "Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors." Nat Commun, 8, 2070. doi: 10.1038/s41467-017-02054-6. Crystal structure of smad4-mh1 bound to the ggct site.. SNAP output
5mf0 transcription X-ray (3.03 Å) Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ (2017) "Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors." Nat Commun, 8, 2070. doi: 10.1038/s41467-017-02054-6. Crystal structure of smad4-mh1 bound to the ggccg site.. SNAP output
5mf7 transcription X-ray (1.59 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-gadd45). SNAP output
5mg7 transcription X-ray (1.45 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-p53r2). SNAP output
5mga hydrolase X-ray (3.0 Å) Stella S, Alcon P, Montoya G (2017) "Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage." Nature, 546, 559-563. doi: 10.1038/nature22398. Structure of the cpf1 endonuclease r-loop complex after DNA cleavage. SNAP output
5mhj transcription X-ray (2.117 Å) Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP (2017) "The herpes viral transcription factor ICP4 forms a novel DNA recognition complex." Nucleic Acids Res., 45, 8064-8078. doi: 10.1093/nar/gkx419. Icp4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter. SNAP output
5mhk transcription X-ray (2.28 Å) Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP, Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov AP (2017) "The herpes viral transcription factor ICP4 forms a novel DNA recognition complex." Nucleic Acids Res., 45, 8064-8078. doi: 10.1093/nar/gkx419. Icp4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter. SNAP output
5mht transferase-DNA X-ray (2.7 Å) O'Gara M, Roberts RJ, Cheng X (1996) "A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase." J.Mol.Biol., 263, 597-606. doi: 10.1006/jmbi.1996.0601. Ternary structure of hhai methyltransferase with hemimethylated DNA and adohcy. SNAP output
5mlu DNA binding protein X-ray (2.8 Å) Lesbats P, Serrao E, Maskell DP, Pye VE, O'Reilly N, Lindemann D, Engelman AN, Cherepanov P (2017) "Structural basis for spumavirus GAG tethering to chromatin." Proc. Natl. Acad. Sci. U.S.A., 114, 5509-5514. doi: 10.1073/pnas.1621159114. Crystal structure of the pfv gag cbs bound to a mononucleosome. SNAP output
5mma viral protein X-ray (2.55 Å) Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR (2017) "Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors." J. Med. Chem., 60, 7315-7332. doi: 10.1021/acs.jmedchem.7b00596. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz379 (compound 5'g). SNAP output
5mmb viral protein X-ray (2.77 Å) Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR (2017) "Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors." J. Med. Chem., 60, 7315-7332. doi: 10.1021/acs.jmedchem.7b00596. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz434 (compound 6p). SNAP output
5mpf transcription X-ray (2.918 Å) Ming Q, Roske Y, Schuetz A, Walentin K, Ibraimi I, Schmidt-Ott KM, Heinemann U (2018) "Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family." Nucleic Acids Res., 46, 2082-2095. doi: 10.1093/nar/gkx1299. Structural basis of gene regulation by the grainyhead transcription factor superfamily. SNAP output
5ms0 transcription-DNA-RNA cryo-EM (9.8 Å) Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O, Huang YH, Lee CT, Loll B, Behrmann E, Burger J, Mielke T, Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC (2017) "Structural basis for lambda N-dependent processive transcription antitermination." Nat Microbiol, 2, 17062. doi: 10.1038/nmicrobiol.2017.62. Pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM. SNAP output
5n2q DNA binding protein X-ray (2.0 Å) Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H, Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M, Coll M (2017) "Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance." Proc. Natl. Acad. Sci. U.S.A., 114, E6526-E6535. doi: 10.1073/pnas.1702971114. Mobm relaxase domain (mobv; mob_pre) bound to 26nt pmv158 orit DNA. SNAP output
5n61 transferase cryo-EM (3.4 Å) Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P (2017) "Structural Basis of RNA Polymerase I Transcription Initiation." Cell, 169, 120-131.e22. doi: 10.1016/j.cell.2017.03.003. RNA polymerase i initially transcribing complex. SNAP output
5n6i transferase X-ray (3.6 Å) Andreeva L, Hiller B, Kostrewa D, Lassig C, de Oliveira Mann CC, Jan Drexler D, Maiser A, Gaidt M, Leonhardt H, Hornung V, Hopfner KP (2017) "cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein-DNA ladders." Nature, 549, 394-398. doi: 10.1038/nature23890. Crystal structure of mouse cgas in complex with 39 bp DNA. SNAP output
5n8o transferase cryo-EM (3.9 Å) Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori E, Zechner EL, Zanetti G, Waksman G (2017) "Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation." Cell, 169, 708-721.e12. doi: 10.1016/j.cell.2017.04.010. Cryo em structure of the conjugative relaxase trai of the f-r1 plasmid system. SNAP output
5n8r hydrolase X-ray (2.2 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophilia dhx36 helicase in complex with gagcactgc. SNAP output
5n8s hydrolase X-ray (2.88 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophila dhx36 helicase in complex with polyt. SNAP output
5n8u hydrolase X-ray (2.62 Å) Chen W-F, Rety S, Guo H-L, Wu W-Q, Liu N-N, Liu Q-W, Dai Y-X, Xi X-G "Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding." Crystal structure of drosophila dhx36 helicase in complex with ctctcct. SNAP output
5n8z hydrolase X-ray (3.477 Å) Chen W-F, Rety S, Guo H-L, Wu W-Q, Liu N-N, Liu Q-W, Dai Y-X, Xi X-G "Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding." Crystal structure of drosophila dhx36 helicase in complex with ctctccctt. SNAP output
5n90 hydrolase X-ray (3.069 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophila dhx36 helicase in complex with ttgtggtgt. SNAP output
5n96 hydrolase X-ray (2.716 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophila dhx36 helicase in complex with agggtttttt. SNAP output
5n98 hydrolase X-ray (2.756 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophila dhx36 helicase in complex with tagggtttt. SNAP output
5n9a hydrolase X-ray (3.036 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophila dhx36 helicase in complex with gttagggtt. SNAP output
5n9d hydrolase X-ray (2.71 Å) Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG (2018) "Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model." Structure, 26, 403-415.e4. doi: 10.1016/j.str.2018.01.008. Crystal structure of drosophila dhx36 helicase in complex with gggttagggt. SNAP output
5n9e hydrolase X-ray (3.007 Å) Chen W-F, Rety S, Hai-Lei Guo H-L, Wu W-Q, Liu N-N, Liu Q-W, Dai Y-X, Xi X-G "Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding." Crystal structure of drosophila dhx36 helicase in complex with tggggattt. SNAP output
5n9f hydrolase X-ray (2.969 Å) Chen W-F, Rety S, Hai-Lei Guo H-L, Wu W-Q, Liu N-N, Liu Q-W, Dai Y-X, Xi X-G "Structural and mechanistic insights into DHX36-mediated innate immunity and G-quadruplex unfolding." Crystal structure of drosophila dhx36 helicase in complex with ssDNA cpg_a. SNAP output
5n9g transcription X-ray (2.7 Å) Gouge J, Guthertz N, Kramm K, Dergai O, Abascal-Palacios G, Satia K, Cousin P, Hernandez N, Grohmann D, Vannini A (2017) "Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation." Nat Commun, 8, 130. doi: 10.1038/s41467-017-00126-1. Tfiiib -tbp-brf2-DNA and sant domain of bdp1-. SNAP output
5nfv hydrolase X-ray (2.501 Å) Swarts DC, van der Oost J, Jinek M (2017) "Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a." Mol. Cell, 66, 221-233.e4. doi: 10.1016/j.molcel.2017.03.016. Crystal structure of catalytically inactive fncas12 mutant bound to an r-loop structure containing a pre-crrna mimic and full-length DNA target. SNAP output
5nj8 transcription X-ray (3.3 Å) Schulte KW, Green E, Wilz A, Platten M, Daumke O (2017) "Structural Basis for Aryl Hydrocarbon Receptor-Mediated Gene Activation." Structure, 25, 1025-1033.e3. doi: 10.1016/j.str.2017.05.008. Structural basis for aryl hydrocarbon receptor mediated gene activation. SNAP output
5nkl transferase X-ray (1.7 Å) Betz K, Kimoto M, Diederichs K, Hirao I, Marx A (2017) "Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair." Angew. Chem. Int. Ed. Engl., 56, 12000-12003. doi: 10.1002/anie.201704190. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with the artificial base pair dds-dpxtp. SNAP output
5nl0 chromatin binding protein - DNA X-ray (5.4 Å) Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai G, Reymer A, Syed SH, Lone IN, Tonchev O, Crucifix C, Menoni H, Papin C, Skoufias DA, Kurumizaka H, Lavery R, Hamiche A, Hayes JJ, Schultz P, Angelov D, Petosa C, Dimitrov S (2017) "Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1." Mol. Cell, 66, 384-397.e8. doi: 10.1016/j.molcel.2017.04.012. Crystal structure of a 197-bp palindromic 601l nucleosome in complex with linker histone h1. SNAP output
5nm9 transcription X-ray (2.43 Å) Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ (2017) "Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors." Nat Commun, 8, 2070. doi: 10.1038/s41467-017-02054-6. Crystal structure of the placozoa trichoplax adhaerens smad4-mh1 bound to the ggcgc site.. SNAP output
5nnu hydrolase X-ray (2.97 Å) Earl C, Bagneris C, Zeman K, Cole A, Barrett T, Savva R (2018) "A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping." Nucleic Acids Res., 46, 4286-4300. doi: 10.1093/nar/gky217. Kshv uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping. SNAP output
5nnx transcription X-ray (3.29 Å) Morgunova E, Jolma A, Yin Y, Popov A, Taipale J "TEAD1 bound to DNA." Tead1 bound to DNA. SNAP output
5no1 viral protein X-ray (2.6 Å) Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR (2017) "Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors." J. Med. Chem., 60, 7315-7332. doi: 10.1021/acs.jmedchem.7b00596. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz407 (compound 5g). SNAP output
5no6 transcription X-ray (2.88 Å) Morgunova E, Jolma A, Yin Y, Popov A, Taipale J "TEAD4-HOXB13 complex bound to DNA." Tead4-hoxb13 complex bound to DNA. SNAP output
5npk isomerase X-ray (1.98 Å) Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacque E, Checchia A, Chen D, Cui H, Ding X, Ingraham K, McCloskey L, Raha K, Srikannathasan V, Maxwell A, Stavenger RA (2017) "Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase." Proc. Natl. Acad. Sci. U.S.A., 114, E4492-E4500. doi: 10.1073/pnas.1700721114. 1.98a structure of thiophene1 with s.aureus DNA gyrase and DNA. SNAP output
5npp isomerase X-ray (2.22 Å) Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacque E, Checchia A, Chen D, Cui H, Ding X, Ingraham K, McCloskey L, Raha K, Srikannathasan V, Maxwell A, Stavenger RA (2017) "Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase." Proc. Natl. Acad. Sci. U.S.A., 114, E4492-E4500. doi: 10.1073/pnas.1700721114. 2.22a structure of thiophene2 and gsk945237 with s.aureus DNA gyrase and DNA. SNAP output
5nsr transcription cryo-EM (3.8 Å) Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X (2017) "Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation." Mol. Cell, 67, 106-116.e4. doi: 10.1016/j.molcel.2017.05.010. cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex. SNAP output
5nss transcription cryo-EM (5.8 Å) Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X (2017) "Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation." Mol. Cell, 67, 106-116.e4. doi: 10.1016/j.molcel.2017.05.010. cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator pspf intermedate complex. SNAP output
5nw5 DNA binding protein X-ray (6.502 Å) Mattarocci S, Reinert JK, Bunker RD, Fontana GA, Shi T, Klein D, Cavadini S, Faty M, Shyian M, Hafner L, Shore D, Thoma NH, Rass U (2017) "Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends." Nat. Struct. Mol. Biol., 24, 588-595. doi: 10.1038/nsmb.3420. Crystal structure of the rif1 n-terminal domain (rif1-ntd) from saccharomyces cerevisiae in complex with DNA. SNAP output
5nw9 hydrolase X-ray (2.04 Å) Flett FJ, Ruksenaite E, Armstrong LA, Bharati S, Carloni R, Morris ER, Mackay CL, Interthal H, Richardson JM (2018) "Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1." Nat Commun, 9, 24. doi: 10.1038/s41467-017-02530-z. Crystal structure of the complex of tdp1 with duplex DNA. SNAP output
5nwa hydrolase X-ray (3.2 Å) Flett FJ, Ruksenaite E, Armstrong LA, Bharati S, Carloni R, Morris ER, Mackay CL, Interthal H, Richardson JM (2018) "Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1." Nat Commun, 9, 24. doi: 10.1038/s41467-017-02530-z. Crystal structure of the complex of tdp1 with duplex DNA. SNAP output
5o20 transcription X-ray (3.53 Å) Franco-Echevarria E, Gonzalez-Polo N, Zorrilla S, Martinez-Lumbreras S, Santiveri CM, Campos-Olivas R, Sanchez M, Calvo O, Gonzalez B, Perez-Canadillas JM (2017) "The structure of transcription termination factor Nrd1 reveals an original mode for GUAA recognition." Nucleic Acids Res., 45, 10293-10305. doi: 10.1093/nar/gkx685. Structure of nrd1 RNA binding domain in complex with RNA (uuaguaaucc). SNAP output
5o63 hydrolase X-ray (1.6 Å) Sasnauskas G, Tamulaitiene G, Tamulaitis G, Calyseva J, Laime M, Rimseliene R, Lubys A, Siksnys V (2017) "UbaLAI is a monomeric Type IIE restriction enzyme." Nucleic Acids Res., 45, 9583-9594. doi: 10.1093/nar/gkx634. Crystal structure of ubalai restriction endonuclease b3 domain domain (mutant l24m l53m l95m) with cognate DNA. SNAP output
5o6b hydrolase X-ray (2.029 Å) Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG (2018) "Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase." Nucleic Acids Res., 46, 1486-1500. doi: 10.1093/nar/gkx1217. Structure of scpif1 in complex with gggtttt and adp-alf4. SNAP output
5o6d hydrolase X-ray (3.283 Å) Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG (2018) "Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase." Nucleic Acids Res., 46, 1486-1500. doi: 10.1093/nar/gkx1217. Structure of scpif1 in complex with polydt and atpgs. SNAP output
5o6e hydrolase X-ray (3.345 Å) Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG (2018) "Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase." Nucleic Acids Res., 46, 1486-1500. doi: 10.1093/nar/gkx1217. Structure of scpif1 in complex with tttgggtt and adp-alf4. SNAP output
5o6g DNA binding protein X-ray (2.75 Å) Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R, D'Abramo M (2017) "Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI." J. Comput. Aided Mol. Des., 31, 1063-1072. doi: 10.1007/s10822-017-0087-5. Structures and dynamics of mesophilic variants from the homing endonuclease i-dmoi. SNAP output
5o6i DNA binding protein X-ray (2.25 Å) Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R, D'Abramo M (2017) "Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI." J. Comput. Aided Mol. Des., 31, 1063-1072. doi: 10.1007/s10822-017-0087-5. Structures and dynamics of mesophilic variants from the homing endonuclease i-dmoi. SNAP output
5o6u antiviral protein X-ray (3.25 Å) Pausch P, Muller-Esparza H, Gleditzsch D, Altegoer F, Randau L, Bange G (2017) "Structural Variation of Type I-F CRISPR RNA Guided DNA Surveillance." Mol. Cell, 67, 622-632.e4. doi: 10.1016/j.molcel.2017.06.036. Structure of the cascade-i-fv r-loop complex from shewanella putrefaciens. SNAP output
5o7t transferase X-ray (1.8 Å) Betz K, Nilforoushan A, Wyss LA, Diederichs K, Sturla SJ, Marx A (2017) "Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase." Chem. Commun. (Camb.), 53, 12704-12707. doi: 10.1039/c7cc07173f. Crystal structure of klentaq mutant m747k in a closed ternary complex with a dg:dctp base pair. SNAP output
5o9g DNA binding protein cryo-EM (4.8 Å) Farnung L, Vos SM, Wigge C, Cramer P (2017) "Nucleosome-Chd1 structure and implications for chromatin remodelling." Nature, 550, 539-542. doi: 10.1038/nature24046. Structure of nucleosome-chd1 complex. SNAP output
5oa1 transcription cryo-EM (4.4 Å) Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJ, Beck M, Sachse C, Muller CW (2017) "Structural insights into transcription initiation by yeast RNA polymerase I." EMBO J., 36, 2698-2709. doi: 10.15252/embj.201796958. RNA polymerase i pre-initiation complex. SNAP output
5od6 transcription X-ray (2.0 Å) Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ (2017) "Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors." Nat Commun, 8, 2070. doi: 10.1038/s41467-017-02054-6. Crystal structure of smad3-mh1 bound to the ggcgc site.. SNAP output
5odg transcription X-ray (2.12 Å) Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ (2017) "Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors." Nat Commun, 8, 2070. doi: 10.1038/s41467-017-02054-6. Crystal structure of smad3-mh1 bound to the ggct site.. SNAP output
5odl DNA binding protein X-ray (1.56 Å) Cernooka E, Rumnieks J, Tars K, Kazaks A (2017) "Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34." Sci Rep, 7, 15529. doi: 10.1038/s41598-017-15774-y. Single-stranded DNA-binding protein from bacteriophage enc34 in complex with ssDNA. SNAP output
5odn DNA binding protein X-ray (2.598 Å) Pierechod M, Rothweiler U "Salinibacter ruber Single-Strand Binding protein." Salinibacter ruber single-strand binding protein. SNAP output
5odp DNA binding protein X-ray (2.535 Å) Pierechod M, Rothweiler U "Salinibacter ruber Single-Strand Binding protein D17K D71K mutant." Salinibacter ruber single-strand binding protein d17k d71k mutant. SNAP output
5oik transcription cryo-EM (3.7 Å) Bernecky C, Plitzko JM, Cramer P (2017) "Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp." Nat. Struct. Mol. Biol., 24, 809-815. doi: 10.1038/nsmb.3465. Structure of an RNA polymerase ii-dsif transcription elongation complex. SNAP output
5ola transcription X-ray (3.904 Å) Hillen HS, Parshin AV, Agaronyan K, Morozov YI, Graber JJ, Chernev A, Schwinghammer K, Urlaub H, Anikin M, Cramer P, Temiakov D (2017) "Mechanism of Transcription Anti-termination in Human Mitochondria." Cell, 171, 1082-1093.e13. doi: 10.1016/j.cell.2017.09.035. Structure of mitochondrial transcription elongation complex in complex with elongation factor tefm. SNAP output
5omf DNA binding protein X-ray (2.092 Å) Kropp HM, Betz K, Wirth J, Diederichs K, Marx A (2017) "Crystal structures of ternary complexes of archaeal B-family DNA polymerases." PLoS ONE, 12, e0188005. doi: 10.1371/journal.pone.0188005. Closed, ternary structure of kod DNA polymerase. SNAP output
5omq transferase X-ray (2.199 Å) Kropp HM, Betz K, Wirth J, Diederichs K, Marx A (2017) "Crystal structures of ternary complexes of archaeal B-family DNA polymerases." PLoS ONE, 12, e0188005. doi: 10.1371/journal.pone.0188005. Ternary complex of 9n DNA polymerase in the replicative state with three metal ions in the active site. SNAP output
5omv transferase X-ray (2.003 Å) Kropp HM, Betz K, Wirth J, Diederichs K, Marx A (2017) "Crystal structures of ternary complexes of archaeal B-family DNA polymerases." PLoS ONE, 12, e0188005. doi: 10.1371/journal.pone.0188005. Ternary complex of 9n DNA polymerase in the replicative state with two metal ions in the active site. SNAP output
5omx DNA binding protein X-ray (2.32 Å) Frouws TD, Barth PD, Richmond TJ (2018) "Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability." J. Mol. Biol., 430, 45-57. doi: 10.1016/j.jmb.2017.10.029. X-ray structure of the h2a-n38c nucleosome core particle. SNAP output
5ond transcription X-ray (2.1 Å) Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rosch P, Knauer SH (2018) "The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand." Elife, 7. doi: 10.7554/eLife.36349. Rfah from escherichia coli in complex with ops DNA. SNAP output
5ong DNA binding protein X-ray (2.797 Å) Frouws TD, Barth PD, Richmond TJ (2018) "Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability." J. Mol. Biol., 430, 45-57. doi: 10.1016/j.jmb.2017.10.029. X-ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer. SNAP output
5onw DNA binding protein X-ray (2.8 Å) Frouws TD, Barth PD, Richmond TJ (2018) "Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability." J. Mol. Biol., 430, 45-57. doi: 10.1016/j.jmb.2017.10.029. X-ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two h2a-h2b dimers crosslinked via h2a n38c. SNAP output
5oqj transcription cryo-EM (4.7 Å) Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P (2017) "Structures of transcription pre-initiation complex with TFIIH and Mediator." Nature, 551, 204-209. doi: 10.1038/nature24282. Structure of yeast transcription pre-initiation complex with tfiih. SNAP output
5oqm transcription cryo-EM (5.8 Å) Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P (2017) "Structures of transcription pre-initiation complex with TFIIH and Mediator." Nature, 551, 204-209. doi: 10.1038/nature24282. Structure of yeast transcription pre-initiation complex with tfiih and core mediator. SNAP output
5oqn cell cycle X-ray (3.15 Å) Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V, Hassler M, Haering CH (2017) "Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes." Cell, 171, 588-600.e24. doi: 10.1016/j.cell.2017.09.008. Crystal structure of the s. cerevisiae condensin ycg1-brn1 subcomplex bound to DNA (short kleisin loop). SNAP output
5oqo cell cycle X-ray (3.25 Å) Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V, Hassler M, Haering CH (2017) "Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes." Cell, 171, 588-600.e24. doi: 10.1016/j.cell.2017.09.008. Crystal structure of the s. cerevisiae condensin ycg1-brn1 subcomplex bound to DNA (crystal form ii). SNAP output
5oqp cell cycle X-ray (2.98 Å) Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V, Hassler M, Haering CH (2017) "Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes." Cell, 171, 588-600.e24. doi: 10.1016/j.cell.2017.09.008. Crystal structure of the s. cerevisiae condensin ycg1-brn1 subcomplex bound to DNA (crystal form i). SNAP output
5or5 transcription NMR Campagne S, Vorholt JA, Allain FH "Engineered promoter selectivity of an ECF sigma factor." Not published. NMR structure of the complex formed by an engineered region 2 of sigmae in complex with gtaaaa. SNAP output
5orq de novo protein X-ray (1.95 Å) Spahr H, Chia T, Lingford JP, Siira SJ, Cohen SB, Filipovska A, Rackham O (2018) "Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins." Nat Commun, 9, 2212. doi: 10.1038/s41467-018-04388-1. Crystal structure of designed cppr-telo1 in complex with ssDNA. SNAP output
5ot2 transcription X-ray (3.2 Å) Malvezzi S, Farnung L, Aloisi CMN, Angelov T, Cramer P, Sturla SJ (2017) "Mechanism of RNA polymerase II stalling by DNA alkylation." Proc. Natl. Acad. Sci. U.S.A., 114, 12172-12177. doi: 10.1073/pnas.1706592114. RNA polymerase ii elongation complex in the presence of 3d-napht-a. SNAP output
5oxj transferase X-ray (2.0 Å) Betz K, Nilforoushan A, Wyss LA, Diederichs K, Sturla SJ, Marx A (2017) "Structural basis for the selective incorporation of an artificial nucleotide opposite a DNA adduct by a DNA polymerase." Chem. Commun. (Camb.), 53, 12704-12707. doi: 10.1039/c7cc07173f. Crystal structure of klentaq mutant m747k in a closed ternary complex with a o6-meg:benzitp base pair. SNAP output
5oxv gene regulation X-ray (6.721 Å) Ekundayo B, Richmond TJ, Schalch T (2017) "Capturing Structural Heterogeneity in Chromatin Fibers." J. Mol. Biol., 429, 3031-3042. doi: 10.1016/j.jmb.2017.09.002. Structure of the 4_601_157 tetranucleosome (c2 form). SNAP output
5oy7 gene regulation X-ray (5.774 Å) Ekundayo B, Richmond TJ, Schalch T (2017) "Capturing Structural Heterogeneity in Chromatin Fibers." J. Mol. Biol., 429, 3031-3042. doi: 10.1016/j.jmb.2017.09.002. Structure of the 4_601_157 tetranucleosome (p1 form). SNAP output
5sva transcription, transferase-DNA cryo-EM (15.3 Å) Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei PJ, Burlingame AL, Kornberg RD (2016) "Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex." Cell, 166, 1411-1422.e16. doi: 10.1016/j.cell.2016.08.050. Mediator-RNA polymerase ii pre-initiation complex. SNAP output
5swm hydrolase-RNA-DNA X-ray (1.5 Å) Pallan PS, Prakash TP, de Leon AR, Egli M (2016) "Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid." Biochemistry, 55, 5321-5325. doi: 10.1021/acs.biochem.6b00849. Bacillus halodurans rnase h mutant d132n in complex with 12-mer frna-DNA hybrid. SNAP output
5sww hydrolase-DNA X-ray (3.151 Å) Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir O, Amaro RE, Harki DA, Harris RS, Aihara H (2017) "Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B." Nat. Struct. Mol. Biol., 24, 131-139. doi: 10.1038/nsmb.3344. Crystal structure of human apobec3a complexed with ssDNA. SNAP output
5sy7 transcription-DNA X-ray (4.2 Å) Wu D, Su X, Potluri N, Kim Y, Rastinejad F (2016) "NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors." Elife, 5. doi: 10.7554/eLife.18790. Crystal structure of the heterodimeric npas3-arnt complex with hre DNA. SNAP output
5szt transferase X-ray (1.8 Å) Hottin A, Betz K, Diederichs K, Marx A (2017) "Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides." Chemistry, 23, 2109-2118. doi: 10.1002/chem.201604515. Crystal structure of the large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with 7-(n-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-datp. SNAP output
5szx transcription regulator-DNA X-ray (2.251 Å) Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X (2017) "Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta." Nucleic Acids Res., 45, 2503-2515. doi: 10.1093/nar/gkx057. Epstein-barr virus zta DNA binding domain homodimer in complex with methylated DNA. SNAP output
5t00 transcription regulator-DNA X-ray (2.19 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Human ctcf znf3-7 and methylated DNA complex. SNAP output
5t01 transcription regulator-DNA X-ray (1.89 Å) Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X (2017) "Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta." Nucleic Acids Res., 45, 2503-2515. doi: 10.1093/nar/gkx057. Human c-jun DNA binding domain homodimer in complex with methylated DNA. SNAP output
5t0u transcription regulator-DNA X-ray (3.199 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Ctcf znf2-7 and DNA complex structure. SNAP output
5t14 transferase-DNA X-ray (3.0 Å) Jha V, Ling H (2017) "Structural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa." DNA Repair (Amst.), 49, 43-50. doi: 10.1016/j.dnarep.2016.11.001. DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct. SNAP output
5t1j transcription-DNA X-ray (2.947 Å) Liu CF, Brandt GS, Hoang QQ, Naumova N, Lazarevic V, Hwang ES, Dekker J, Glimcher LH, Ringe D, Petsko GA (2016) "Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites." Proc.Natl.Acad.Sci.USA, 113, E6572-E6581. doi: 10.1073/pnas.1613914113. Crystal structure of the tbox DNA binding domain of the transcription factor t-bet. SNAP output
5t2h hydrolase-DNA X-ray (2.517 Å) Werther R, Hallinan JP, Lambert AR, Havens K, Pogson M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan T, Stoddard BL (2017) "Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity." Nucleic Acids Res., 45, 8621-8634. doi: 10.1093/nar/gkx544. Engineered variant of i-onui meganuclease targeting the human tcra gene; harbors 43 point mutations relative to wild-type i-onui. SNAP output
5t2n hydrolase-DNA X-ray (2.079 Å) Werther R, Hallinan JP, Lambert AR, Havens K, Pogson M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan T, Stoddard BL (2017) "Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity." Nucleic Acids Res., 45, 8621-8634. doi: 10.1093/nar/gkx544. Engineered variant of i-onui meganuclease targeting the anopheles agap007280 gene; harbors 38 point mutations relative to wild-type i-onui. SNAP output
5t2o hydrolase-DNA X-ray (2.801 Å) Werther R, Hallinan JP, Lambert AR, Havens K, Pogson M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan T, Stoddard BL (2017) "Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity." Nucleic Acids Res., 45, 8621-8634. doi: 10.1093/nar/gkx544. Engineered variant of i-onui meganuclease targeting the anopheles agap011377 gene; harbors 53 point mutations relative to wild-type i-onui. SNAP output
5t2w hydrolase-DNA X-ray (2.2 Å) Pidugu LS, Flowers JW, Coey CT, Pozharski E, Greenberg MM, Drohat AC (2016) "Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase." Biochemistry, 55, 6205-6208. doi: 10.1021/acs.biochem.6b00982. Structure of thymine DNA glycosylase bound to substrate analog 2'-f-5-formyl-dc. SNAP output
5t4i hydrolase-DNA X-ray (2.389 Å) Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW (2017) "A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease." Nat Commun, 8, 14959. doi: 10.1038/ncomms14959. A novel domain in human exog converts apoptotic endonuclease to DNA-repair enzyme. SNAP output
5t5c hydrolase-DNA X-ray (1.851 Å) Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW (2017) "A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease." Nat Commun, 8, 14959. doi: 10.1038/ncomms14959. A novel domain in human exog converts apoptotic endonuclease to DNA-repair enzyme. SNAP output
5t5k DNA binding protein-DNA X-ray (4.0 Å) Mattiroli F, Bhattacharyya S, Dyer PN, White AE, Sandman K, Burkhart BW, Byrne KR, Lee T, Ahn NG, Santangelo TJ, Reeve JN, Luger K (2017) "Structure of histone-based chromatin in Archaea." Science, 357, 609-612. doi: 10.1126/science.aaj1849. Structure of histone-based chromatin in archaea. SNAP output
5t7x DNA binding protein-DNA X-ray (2.35 Å) Dheekollu J, Malecka K, Wiedmer A, Delecluse HJ, Chiang AK, Altieri DC, Messick TE, Lieberman PM (2017) "Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency." Oncotarget, 8, 7248-7264. doi: 10.18632/oncotarget.14540. Crystal structure of hhv-4 ebna1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA. SNAP output
5t8d hydrolase-DNA X-ray (2.15 Å) Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR (2017) "Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses." Protein Eng.Des.Sel., 30, 503-522. doi: 10.1093/protein/gzx037. Engineered variant of i-onui meganuclease targeting the hiv integrase gene; harbors 47 point mutations relative to wild-type i-onui. SNAP output
5t9j hydrolase X-ray (3.0 Å) Lee SH, Princz LN, Klugel MF, Habermann B, Pfander B, Biertumpfel C (2015) "Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage." Elife, 4. doi: 10.7554/eLife.12256. Crystal structure of human gen1 in complex with holliday junction DNA in the upper interface. SNAP output
5tb8 transferase-DNA X-ray (2.0 Å) Reed AJ, Vyas R, Raper AT, Suo Z (2017) "Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase." J. Am. Chem. Soc., 139, 465-471. doi: 10.1021/jacs.6b11258. Precatalytic ternary complex of human DNA polymerase beta in closed conformation with gapped DNA substrate incoming (-)3tc-tp and mn2+.. SNAP output
5tb9 transferase-DNA X-ray (2.49 Å) Reed AJ, Vyas R, Raper AT, Suo Z (2017) "Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase." J. Am. Chem. Soc., 139, 465-471. doi: 10.1021/jacs.6b11258. Precatalytic ternary complex of human DNA polymerase beta in closed conformation with gapped DNA substrate incoming (-)ftc-tp and mn2+.. SNAP output
5tba transferase-DNA X-ray (2.49 Å) Reed AJ, Vyas R, Raper AT, Suo Z (2017) "Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase." J. Am. Chem. Soc., 139, 465-471. doi: 10.1021/jacs.6b11258. Postcatalytic ternary complex of human DNA polymerase beta with gapped DNA substrate, incorporated (-)3tc and ppi.. SNAP output
5tbb transferase-DNA X-ray (2.39 Å) Reed AJ, Vyas R, Raper AT, Suo Z (2017) "Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase." J. Am. Chem. Soc., 139, 465-471. doi: 10.1021/jacs.6b11258. Postcatalytic ternary complex of human DNA polymerase beta with gapped DNA substrate, incorporated (-)ftc and ppi.. SNAP output
5tbc transferase-DNA X-ray (1.85 Å) Reed AJ, Vyas R, Raper AT, Suo Z (2017) "Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase." J. Am. Chem. Soc., 139, 465-471. doi: 10.1021/jacs.6b11258. Precatalytic ternary complex of human DNA polymerase beta with gapped DNA substrate, incorporated (-)3tc-mp and an another incoming (-)3tc-tp nucleotide.. SNAP output
5td5 hydrolase-DNA X-ray (1.718 Å) Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir O, Amaro RE, Harki DA, Harris RS, Aihara H (2017) "Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B." Nat. Struct. Mol. Biol., 24, 131-139. doi: 10.1038/nsmb.3344. Crystal structure of human apobec3b variant complexed with ssDNA. SNAP output
5tgx DNA binding protein X-ray (2.3 Å) Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL (2017) "DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target." Nucleic Acids Res., 45, 1516-1528. doi: 10.1093/nar/gkw1200. Restriction-modification system-type ii r-swai complexed with partially cleaved DNA. SNAP output
5th3 DNA binding protein X-ray (2.33 Å) Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL (2017) "DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target." Nucleic Acids Res., 45, 1516-1528. doi: 10.1093/nar/gkw1200. Restriction-modification system-type ii r.swai cleaved DNA complex. SNAP output
5thg hydrolase-DNA X-ray (3.106 Å) Werther R, Hallinan JP, Lambert A, Haven K, Jarjor J, Stoddard BL "The structural basis of altered gene specificity resulting from meganuclease and MegaTAL engineering." Engineered variant of i-onui meganuclease targeting the hiv ccr5 gene; harbors 43 point mutations relative to wild-type i-onui. SNAP output
5tjg transferase-DNA X-ray (2.6 Å) Feklistov A, Bae B, Hauver J, Lass-Napiorkowska A, Kalesse M, Glaus F, Altmann KH, Heyduk T, Landick R, Darst SA (2017) "RNA polymerase motions during promoter melting." Science, 356, 863-866. doi: 10.1126/science.aam7858. Thermus aquaticus delta1.1-sigmaa holoenzyme-downstream-fork promoter complex with an open clamp. SNAP output
5tkz splicing X-ray (1.529 Å) Soufari H, Mackereth CD (2017) "Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family." RNA, 23, 308-316. doi: 10.1261/rna.059733.116. Mec-8 n-terminal rrm bound to tandem gcac ligand. SNAP output
5trd transferase-DNA X-ray (1.85 Å) Vetting MW, Rodionova IA, Li X, Osterman AL, Rodionov DA, Almo SC "Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator." Structure of rbkr (riboflavin kinase) from thermoplasma acidophilum determined in complex with ctp and its cognate DNA operator. SNAP output
5tvp hydrolase-DNA X-ray (2.399 Å) Schellenberg MJ, Lieberman JA, Herrero-Ruiz A, Butler LR, Williams JG, Munoz-Cabello AM, Mueller GA, London RE, Cortes-Ledesma F, Williams RS (2017) "ZATT (ZNF451)-mediated resolution of topoisomerase 2 DNA-protein cross-links." Science, 357, 1412-1416. doi: 10.1126/science.aam6468. Sumo2 bound to mouse tdp2 catalytic domain with a 5'-phosphorylated DNA ternary complex. SNAP output
5tw1 transcription activator-transferase-DNA X-ray (2.76 Å) Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA (2017) "Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA." Elife, 6. doi: 10.7554/eLife.22520. Crystal structure of a mycobacterium smegmatis transcription initiation complex with rbpa. SNAP output
5twp transferase-DNA X-ray (2.001 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Pre-catalytic ternary complex of human polymerase mu with incoming nonhydrolyzable umpnpp. SNAP output
5twq transferase-DNA X-ray (1.8 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic nicked complex of human polymerase mu with newly incorporated utp. SNAP output
5twr transferase-DNA X-ray (1.9 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Pre-catalytic ternary complex of human polymerase mu (h329a) mutant with incoming nonhydrolyzable umpnpp. SNAP output
5tws transferase-DNA X-ray (1.85 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (h329a) with newly incorporated utp. SNAP output
5txl transferase-DNA X-ray (2.501 Å) Das K, Martinez SE, Arnold E (2017) "Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance." Antimicrob. Agents Chemother., 61. doi: 10.1128/AAC.00224-17. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming datp. SNAP output
5txm transferase-DNA X-ray (2.7 Å) Das K, Martinez SE, Arnold E (2017) "Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance." Antimicrob. Agents Chemother., 61. doi: 10.1128/AAC.00224-17. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming ddatp. SNAP output
5txn transferase-DNA X-ray (2.55 Å) Das K, Martinez SE, Arnold E (2017) "Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance." Antimicrob. Agents Chemother., 61. doi: 10.1128/AAC.00224-17. Structure of q151m mutant hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming datp. SNAP output
5txo transferase-DNA X-ray (2.546 Å) Das K, Martinez SE, Arnold E (2017) "Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance." Antimicrob. Agents Chemother., 61. doi: 10.1128/AAC.00224-17. Structure of q151m complex (a62v, v75i, f77l, f116y, q151m) mutant hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming datp. SNAP output
5txp transferase-DNA X-ray (2.7 Å) Das K, Martinez SE, Arnold E (2017) "Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance." Antimicrob. Agents Chemother., 61. doi: 10.1128/AAC.00224-17. Structure of q151m complex (a62v, v75i, f77l, f116y, q151m) mutant hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming ddatp. SNAP output
5txx transferase-DNA X-ray (1.948 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu pre-catalytic ground state ternary complex, ca2+. SNAP output
5txz transferase-DNA X-ray (1.651 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, 100mm mg2+ (15 min). SNAP output
5tyb transferase-DNA X-ray (1.848 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, 10mm mg2+ (7.5 min). SNAP output
5tyc transferase-DNA X-ray (2.101 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, 10mm mg2+ (15 min). SNAP output
5tyd transferase-DNA X-ray (1.899 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, 10 mm mg2+ (45 min). SNAP output
5tye transferase-DNA X-ray (2.047 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu product complex, 10 mm mg2+ (60 min). SNAP output
5tyf transferase-DNA X-ray (1.971 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu product complex, 10 mm mg2+ (270 min). SNAP output
5tyg transferase-DNA X-ray (1.726 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu product complex, 10 mm mg2+ (960 min). SNAP output
5tyu transferase-DNA X-ray (2.048 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, mn2+ (4 min). SNAP output
5tyv transferase-DNA X-ray (1.93 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, mn2+ (7.5 min). SNAP output
5tyw transferase-DNA X-ray (1.88 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu reactant complex, mn2+ (10 min). SNAP output
5tyx transferase-DNA X-ray (1.948 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu product complex, mn2+ (15 min). SNAP output
5tyy transferase-DNA X-ray (1.931 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu product complex, mn2+ (60 min). SNAP output
5tyz transferase-DNA X-ray (1.977 Å) Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH (2017) "Time-lapse crystallography snapshots of a double-strand break repair polymerase in action." Nat Commun, 8, 253. doi: 10.1038/s41467-017-00271-7. DNA polymerase mu product complex, mn2+ (960 min). SNAP output
5tzv transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Pedersen LC, Wilson SH (2016) "Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism." Structure, 24, 1863-1875. doi: 10.1016/j.str.2016.08.006. Binary complex crystal structure of DNA polymerase beta with g:t mismatch at the primer terminus. SNAP output
5u01 transcription-DNA X-ray (2.5 Å) Mulero MC, Huang DB, Nguyen HT, Wang VY, Li Y, Biswas T, Ghosh G (2017) "DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor kappa B are not correlated." J. Biol. Chem., 292, 18821-18830. doi: 10.1074/jbc.M117.813980. Cooperative DNA binding by two rela dimers. SNAP output
5u07 immune system cryo-EM (3.8 Å) Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A (2017) "Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System." Cell, 170, 48-60.e11. doi: 10.1016/j.cell.2017.06.012. Crispr RNA-guided surveillance complex. SNAP output
5u0a immune system cryo-EM (3.3 Å) Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A (2017) "Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System." Cell, 170, 48-60.e11. doi: 10.1016/j.cell.2017.06.012. Crispr RNA-guided surveillance complex. SNAP output
5u1c viral protein cryo-EM (3.9 Å) Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D (2017) "Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome." Science, 355, 89-92. doi: 10.1126/science.aah5163. Structure of tetrameric hiv-1 strand transfer complex intasome. SNAP output
5u1j DNA binding protein-DNA X-ray (2.95 Å) Zhang H, Schumacher MA (2017) "Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation." Genes Dev., 31, 481-492. doi: 10.1101/gad.296319.117. Structure of pnob8 para bound to nonspecific DNA. SNAP output
5u2r transferase-DNA X-ray (1.8 Å) Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer PC, Suo Z (2017) "Structural basis for the D-stereoselectivity of human DNA polymerase beta." Nucleic Acids Res., 45, 6228-6237. doi: 10.1093/nar/gkx252. Precatalytic ternary complex of human DNA polymerase beta with gapped DNA substarte, incoming l-dctp and ca2+. SNAP output
5u2s transferase-DNA X-ray (2.3 Å) Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer PC, Suo Z (2017) "Structural basis for the D-stereoselectivity of human DNA polymerase beta." Nucleic Acids Res., 45, 6228-6237. doi: 10.1093/nar/gkx252. Pre-catalytic ternary complex of human DNA polymerase beta with gapped DNA substrate incoming (-)3tc-tp and ca2+.. SNAP output
5u2t transferase-DNA X-ray (1.79 Å) Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer PC, Suo Z (2017) "Structural basis for the D-stereoselectivity of human DNA polymerase beta." Nucleic Acids Res., 45, 6228-6237. doi: 10.1093/nar/gkx252. Pre-catalytic ternary complex of human DNA polymerase beta with gapped DNA substrate incoming (-)ftc-tp and ca2+.. SNAP output
5u30 hydrolase-DNA X-ray (2.92 Å) Yang H, Gao P, Rajashankar KR, Patel DJ (2016) "PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease." Cell, 167, 1814-1828.e12. doi: 10.1016/j.cell.2016.11.053. Crystal structure of aacc2c1-sgrna-extended target DNA ternary complex. SNAP output
5u31 hydrolase-DNA X-ray (2.89 Å) Yang H, Gao P, Rajashankar KR, Patel DJ (2016) "PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease." Cell, 167, 1814-1828.e12. doi: 10.1016/j.cell.2016.11.053. Crystal structure of aacc2c1-sgrna-8mer substrate DNA ternary complex. SNAP output
5u33 hydrolase-DNA X-ray (3.75 Å) Yang H, Gao P, Rajashankar KR, Patel DJ (2016) "PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease." Cell, 167, 1814-1828.e12. doi: 10.1016/j.cell.2016.11.053. Crystal structure of aacc2c1-sgrna-extended non-target DNA ternary complex. SNAP output
5u8g transferase,lyase-DNA X-ray (2.166 Å) Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL, Sweasy JB, Doublie S (2017) "Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta." Biochemistry, 56, 2363-2371. doi: 10.1021/acs.biochem.6b01287. DNA polymerase beta crystallized in peg 400. SNAP output
5u8h transferase,lyase-DNA X-ray (2.155 Å) Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL, Sweasy JB, Doublie S (2017) "Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta." Biochemistry, 56, 2363-2371. doi: 10.1021/acs.biochem.6b01287. DNA polymerase beta g231d crystallized in peg 400. SNAP output
5u8i transferase,lyase-DNA X-ray (2.45 Å) Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL, Sweasy JB, Doublie S (2017) "Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta." Biochemistry, 56, 2363-2371. doi: 10.1021/acs.biochem.6b01287. DNA polymerase beta s229l crystallized in peg 400. SNAP output
5u8s replication cryo-EM (6.1 Å) Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R, Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME (2017) "Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation." Proc. Natl. Acad. Sci. U.S.A., 114, E697-E706. doi: 10.1073/pnas.1620500114. Structure of eukaryotic cmg helicase at a replication fork. SNAP output
5u8t replication cryo-EM (4.9 Å) Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R, Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME (2017) "Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation." Proc. Natl. Acad. Sci. U.S.A., 114, E697-E706. doi: 10.1073/pnas.1620500114. Structure of eukaryotic cmg helicase at a replication fork and implications. SNAP output
5u91 isomerase-DNA X-ray (3.104 Å) Meinke G, Karpinski J, Buchholz F, Bohm A (2017) "Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA." Nucleic Acids Res., 45, 9726-9740. doi: 10.1093/nar/gkx603. Crystal structure of tre-loxltr complex. SNAP output
5u9h transferase-DNA X-ray (1.85 Å) Perera L, Freudenthal BD, Beard WA, Pedersen LG, Wilson SH (2017) "Revealing the role of the product metal in DNA polymerase beta catalysis." Nucleic Acids Res., 45, 2736-2745. doi: 10.1093/nar/gkw1363. DNA polymerase beta product complex with inserted sp-isomer of dctp-alpha-s. SNAP output
5ua1 transcription-DNA X-ray (2.9 Å) Ho NAT, Dawes SS, Baker EN, Lott JS "Crystal structure of KstR in complex with cognate DNA operator." Mycobacterium tuberculosis kstr in complex with a 18-bp DNA operator. SNAP output
5ua2 transcription-DNA X-ray (2.9 Å) Ho NAT, Dawes SS, Baker EN, Lott JS "Crystal structure of KstR in complex with cognate DNA operator." Mycobacterium tuberculosis kstr in complex with a 26-bp DNA operator. SNAP output
5uan transcription-DNA X-ray (3.508 Å) Chandra V, Wu D, Li S, Potluri N, Kim Y, Rastinejad F (2017) "The quaternary architecture of RAR beta-RXR alpha heterodimer facilitates domain-domain signal transmission." Nat Commun, 8, 868. doi: 10.1038/s41467-017-00981-y. Crystal structure of multi-domain rar-beta-rxr-alpha heterodimer on DNA. SNAP output
5uc6 immune system-DNA X-ray (2.1 Å) Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM (2017) "Structural basis for IL-1 alpha recognition by a modified DNA aptamer that specifically inhibits IL-1 alpha signaling." Nat Commun, 8, 810. doi: 10.1038/s41467-017-00864-2. Structural insights into il-1 alpha recognition by a naphthyl-modified aptamer that mimics il-1ri domain iii. SNAP output
5ugn transferase-DNA X-ray (1.997 Å) Shock DD, Freudenthal BD, Beard WA, Wilson SH (2017) "Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction." Nat. Chem. Biol., 13, 1074-1080. doi: 10.1038/nchembio.2450. DNA polymerase beta imidodiphosphate reactant complex. SNAP output
5ugo transferase-DNA X-ray (1.897 Å) Shock DD, Freudenthal BD, Beard WA, Wilson SH (2017) "Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction." Nat. Chem. Biol., 13, 1074-1080. doi: 10.1038/nchembio.2450. DNA polymerase beta nick complex with imidodiphosphate. SNAP output
5ugp transferase-DNA X-ray (1.955 Å) Shock DD, Freudenthal BD, Beard WA, Wilson SH (2017) "Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction." Nat. Chem. Biol., 13, 1074-1080. doi: 10.1038/nchembio.2450. DNA polymerase beta complex with a 1nt gap and dcmppnp. SNAP output
5uh5 transcription-DNA-RNA X-ray (3.746 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 3 nt of RNA. SNAP output
5uh6 transcription-DNA-RNA-antibiotic X-ray (3.837 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 2ntrna in complex with rifampin. SNAP output
5uh8 transcription-DNA-RNA X-ray (4.176 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 4nt RNA. SNAP output
5uh9 transcription-DNA-RNA X-ray (4.402 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 2nt RNA. SNAP output
5uha transcription-DNA X-ray (3.906 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex. SNAP output
5uhb transcription-DNA-RNA X-ray (4.29 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex in complex with rifampin. SNAP output
5uhc transcription-DNA-RNA X-ray (3.796 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 3nt RNA in complex with rifampin. SNAP output
5uhd transcription-DNA-RNA X-ray (4.01 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex containing 4nt RNA in complex with rifampin. SNAP output
5uhe transcription-DNA-RNA X-ray (4.039 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex in complex with d-aap1. SNAP output
5uhf transcription-DNA-RNA X-ray (4.345 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex in complex with d-ix336. SNAP output
5uhg transcription-DNA-RNA X-ray (3.971 Å) Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH (2017) "Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition." Mol. Cell, 66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Crystal structure of mycobacterium tuberculosis transcription initiation complex in complex with d-aap1 and rifampin. SNAP output
5ui5 transcription-DNA X-ray (3.4 Å) Campbell EA, Kamath S, Rajashankar KR, Wu M, Darst SA (2017) "Crystal structure of Aquifex aeolicus sigma (N) bound to promoter DNA and the structure of sigma (N)-holoenzyme." Proc. Natl. Acad. Sci. U.S.A., 114, E1805-E1814. doi: 10.1073/pnas.1619464114. Crystal structure of aquifex aeolicus sigman bound to promoter DNA. SNAP output
5uj2 immune system-RNA X-ray (2.9 Å) Kirschberg TA, Metobo S, Clarke MO, Aktoudianakis V, Babusis D, Barauskas O, Birkus G, Butler T, Byun D, Chin G, Doerffler E, Edwards TE, Fenaux M, Lee R, Lew W, Mish MR, Murakami E, Park Y, Squires NH, Tirunagari N, Wang T, Whitcomb M, Xu J, Yang H, Ye H, Zhang L, Appleby TC, Feng JY, Ray AS, Cho A, Kim CU (2017) "Discovery of a 2'-fluoro-2'-C-methyl C-nucleotide HCV polymerase inhibitor and a phosphoramidate prodrug with favorable properties." Bioorg. Med. Chem. Lett., 27, 1840-1847. doi: 10.1016/j.bmcl.2017.02.037. Crystal structure of hcv ns5b genotype 2a jfh-1 isolate with s15g e86q e87q c223h v321i mutations and delta8 neta hairpoin loop deletion in complex with gs-639476 (diphsohate version of gs-9813), mn2+ and symmetrical primer template 5'-auaaauuu. SNAP output
5uk7 DNA binding protein-DNA X-ray (3.0 Å) Orans J, Kovach AR, Hoff KE, Brennan RG "Crystal structure of Escherichia coli Hfq DNA complex reveals multifunctional nucleic acid binding site." Escherichia coli hfq bound to dsDNA. SNAP output
5ulw thansferase-DNA X-ray (2.617 Å) Jain R, Choudhury JR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2017) "Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-iota." Sci Rep, 7, 43904. doi: 10.1038/srep43904. Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine. SNAP output
5ulx thansferase-DNA X-ray (1.96 Å) Jain R, Choudhury JR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2017) "Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-iota." Sci Rep, 7, 43904. doi: 10.1038/srep43904. Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine crystallized in the presence of dctp. SNAP output
5um9 hydrolase-DNA X-ray (2.805 Å) Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA (2017) "Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability." Nat Commun, 8, 15855. doi: 10.1038/ncomms15855. Flap endonuclease 1 (fen1) d86n with 5'-flap substrate DNA and sm3+. SNAP output
5und transcription-DNA X-ray (2.549 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Crystal structure of ctcf(znf 4-10) with 28-mer DNA. SNAP output
5uop transferase-DNA-inhibitor X-ray (2.85 Å) Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ, Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N, Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J, Steele TG, Wai J, Walji A, Xu M, Coleman PJ (2017) "Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV." Bioorg. Med. Chem. Lett., 27, 2038-2046. doi: 10.1016/j.bmcl.2017.02.039. Crystal structure of the prototype foamy virus intasome with a 2- pyridinone aminal inhibitor (compound 18). SNAP output
5uoq transferase-DNA-inhibitor X-ray (2.61 Å) Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ, Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N, Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J, Steele TG, Wai J, Walji A, Xu M, Coleman PJ (2017) "Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV." Bioorg. Med. Chem. Lett., 27, 2038-2046. doi: 10.1016/j.bmcl.2017.02.039. Crystal structure of the prototype foamy virus intasome with a 2- pyridinone aminal inhibitor (compound 31). SNAP output
5us2 hydrolase - RNA - DNA X-ray (1.9 Å) Fang Z, Yang F, Huang Z "2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant." 2-se-t2-DNA and native RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5usa hydrolase - RNA - DNA X-ray (1.8 Å) Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z (2023) "Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate." Chemistryselect, 8. doi: 10.1002/slct.202302253. 5-se-t2-DNA and native RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5usb DNA binding protein-DNA-RNA X-ray (1.615 Å) Lloyd NR, Wuttke DS (2018) "Discrimination against RNA Backbones by a ssDNA Binding Protein." Structure, 26, 722-733.e2. doi: 10.1016/j.str.2018.03.016. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssrna-ssDNA chimera (rggttacggt). SNAP output
5use hydrolase - RNA - DNA X-ray (1.73 Å) Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z (2023) "Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate." Chemistryselect, 8. doi: 10.1002/slct.202302253. 5-se-t4-DNA and native RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5usg hydrolase - RNA - DNA X-ray (1.7 Å) Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z (2023) "Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate." Chemistryselect, 8. doi: 10.1002/slct.202302253. 5-se-t2-4-DNA and native RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5usn DNA binding protein-DNA-RNA X-ray (1.9 Å) Lloyd NR, Wuttke DS (2018) "Discrimination against RNA Backbones by a ssDNA Binding Protein." Structure, 26, 722-733.e2. doi: 10.1016/j.str.2018.03.016. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssrna-ssDNA chimera (rgrgrutacggt). SNAP output
5uso DNA binding protein-DNA-RNA X-ray (2.0 Å) Lloyd NR, Wuttke DS (2018) "Discrimination against RNA Backbones by a ssDNA Binding Protein." Structure, 26, 722-733.e2. doi: 10.1016/j.str.2018.03.016. Crystal structure of schizosaccharomyces pombe pot1pc bound to ssrna-ssDNA chimera (ggttacrgrgru). SNAP output
5uuf hydrolase-DNA-antibiotic X-ray (1.612 Å) Mullins EA, Shi R, Eichman BF (2017) "Toxicity and repair of DNA adducts produced by the natural product yatakemycin." Nat. Chem. Biol., 13, 1002-1008. doi: 10.1038/nchembio.2439. Bacillus cereus DNA glycosylase alkd bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (12-mer product complex). SNAP output
5uug hydrolase-DNA-antibiotic X-ray (1.712 Å) Mullins EA, Shi R, Eichman BF (2017) "Toxicity and repair of DNA adducts produced by the natural product yatakemycin." Nat. Chem. Biol., 13, 1002-1008. doi: 10.1038/nchembio.2439. Bacillus cereus DNA glycosylase alkd bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex). SNAP output
5uuh hydrolase-DNA-antibiotic X-ray (1.569 Å) Mullins EA, Shi R, Eichman BF (2017) "Toxicity and repair of DNA adducts produced by the natural product yatakemycin." Nat. Chem. Biol., 13, 1002-1008. doi: 10.1038/nchembio.2439. Bacillus cereus DNA glycosylase alkd bound to a yatakemycin-adenine nucleobase adduct and DNA containing a fluorinated abasic site (9-mer product complex). SNAP output
5ux0 hydrolase-RNA-DNA X-ray (3.197 Å) Doxzen KW, Doudna JA (2017) "DNA recognition by an RNA-guided bacterial Argonaute." PLoS ONE, 12, e0177097. doi: 10.1371/journal.pone.0177097. X-ray crystal structure of marinitoga piezophila argonaute in complex with 5' oh guide RNA and target DNA. SNAP output
5uzv hydrolase-DNA X-ray (2.45 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (ri). SNAP output
5v04 hydrolase-DNA X-ray (2.65 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (rii). SNAP output
5v05 hydrolase-DNA X-ray (2.902 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (riii). SNAP output
5v06 hydrolase-DNA X-ray (2.75 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (riv). SNAP output
5v07 hydrolase-DNA X-ray (2.15 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (d173a) in complex with 5' recessed-end DNA (rv). SNAP output
5v08 hydrolase-DNA X-ray (2.812 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (d173a) in complex with 5' recessed-end DNA (rvi). SNAP output
5v09 hydrolase-DNA X-ray (2.75 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (d225a) in complex with 5' recessed-end DNA (rvii). SNAP output
5v0a hydrolase-DNA X-ray (2.38 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (d225a) in complex with 5' recessed-end DNA (rviii). SNAP output
5v0b hydrolase-DNA X-ray (2.63 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (rix). SNAP output
5v0c hydrolase-DNA X-ray (2.58 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' flap DNA (f2i). SNAP output
5v0d hydrolase-DNA X-ray (2.63 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' flap DNA (f2ii). SNAP output
5v0e hydrolase-DNA X-ray (2.744 Å) Shi Y, Hellinga HW, Beese LS (2017) "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proc. Natl. Acad. Sci. U.S.A., 114, 6010-6015. doi: 10.1073/pnas.1704845114. Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' flap DNA (f5i). SNAP output
5v0l transcription-DNA X-ray (4.0 Å) Seok SH, Lee W, Jiang L, Molugu K, Zheng A, Li Y, Park S, Bradfield CA, Xing Y (2017) "Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex." Proc. Natl. Acad. Sci. U.S.A., 114, 5431-5436. doi: 10.1073/pnas.1617035114. Crystal structure of the ahr-arnt heterodimer in complex with the dre. SNAP output
5v0q hydrolase-DNA X-ray (2.4 Å) Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR (2017) "Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses." Protein Eng. Des. Sel., 30, 503-522. doi: 10.1093/protein/gzx037. Original engineered variant of i-onui meganuclease targeting the hiv integrase gene; harbors 49 point mutations relative to wild-type i-onui. SNAP output
5v1f transferase-DNA, ligase-DNA X-ray (2.181 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta substrate complex with 8-oxog at the primer terminus and incoming dctp. SNAP output
5v1g transferase-DNA, ligase-DNA X-ray (1.798 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta binary complex with 8-oxog at the primer terminus. SNAP output
5v1h transferase-DNA, ligase-DNA X-ray (1.946 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta binary complex with 8-oxog:a at the primer terminus. SNAP output
5v1i transferase-DNA, ligase-DNA X-ray (2.035 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta ternary product complex with 8-oxog:c and inserted dctp. SNAP output
5v1j transferase-DNA, ligase-DNA X-ray (2.616 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta open product complex with 8-oxog:c and inserted dctp. SNAP output
5v1n transferase-DNA, ligase-DNA X-ray (2.005 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta substrate complex with 8-oxog:a at the primer terminus and incoming dctp. SNAP output
5v1o transferase-DNA, ligase-DNA X-ray (1.801 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta product complex with 8-oxog:a and inserted dctp. SNAP output
5v1p transferase-DNA, ligase-DNA X-ray (1.991 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta substrate complex with 8-oxog:c at the primer terminus and incoming dctp analog. SNAP output
5v1r transferase-DNA, ligase-DNA X-ray (2.077 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta reactant complex with 8-oxog:c at the primer terminus and incoming dctp. SNAP output
5v3g transferase-DNA X-ray (2.416 Å) Patel A, Zhang X, Blumenthal RM, Cheng X (2017) "Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence." J. Biol. Chem., 292, 15994-16002. doi: 10.1074/jbc.M117.805754. Prdm9-allele-c znf8-13. SNAP output
5v3j transferase-DNA X-ray (2.064 Å) Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X (2018) "DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins." Cell, 173, 221-233.e12. doi: 10.1016/j.cell.2018.02.058. Mousezfp568-znf1-10 in complex with DNA. SNAP output
5v3m DNA binding protein-DNA X-ray (2.091 Å) Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X (2018) "DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins." Cell, 173, 221-233.e12. doi: 10.1016/j.cell.2018.02.058. Mousezfp568-znf1-11 in complex with DNA. SNAP output
5v8f replication cryo-EM (3.9 Å) Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H (2017) "Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1." Nat. Struct. Mol. Biol., 24, 316-324. doi: 10.1038/nsmb.3372. Structural basis of mcm2-7 replicative helicase loading by orc-cdc6 and cdt1. SNAP output
5v9x hydrolase-DNA X-ray (2.797 Å) Ejaz A, Ordonez H, Jacewicz A, Ferrao R, Shuman S (2018) "Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases." Nucleic Acids Res., 46, 442-455. doi: 10.1093/nar/gkx1163. Structure of mycobacterium smegmatis helicase lhr bound to ssDNA and amp-pnp. SNAP output
5va0 transcription-DNA X-ray (2.295 Å) Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH, Nettles KW, Kojetin DJ, Ortlund EA (2017) "Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes." Nucleic Acids Res., 45, 8596-8608. doi: 10.1093/nar/gkx509. Glucocorticoid receptor DNA binding domain in complex with ap-1 response element from vcam-1 promoter. SNAP output
5va7 transcription-DNA X-ray (2.153 Å) Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH, Nettles KW, Kojetin DJ, Ortlund EA (2017) "Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes." Nucleic Acids Res., 45, 8596-8608. doi: 10.1093/nar/gkx509. Glucocorticoid receptor DNA binding domain - il11 ap-1 recognition element complex. SNAP output
5vaj hydrolase-RNA-DNA X-ray (1.95 Å) Mutisya D, Hardcastle T, Cheruiyot SK, Pallan PS, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E (2017) "Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs." Nucleic Acids Res., 45, 8142-8155. doi: 10.1093/nar/gkx558. Bhrnase h - amide-RNA-DNA complex. SNAP output
5vbs transferase-DNA X-ray (1.749 Å) Singh I, Kim MJ, Molt RW, Hoshika S, Benner SA, Georgiadis MM (2017) "Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K)." ACS Synth Biol, 6, 2118-2129. doi: 10.1021/acssynbio.7b00150. Structural basis for a six letter alphabet including gatckx. SNAP output
5vc8 DNA binding protein X-ray (1.8 Å) Zhang M, Yang Y, Zhou M, Dong A, Yan X, Loppnau P, Min J, Liu Y (2021) "Histone and DNA binding ability studies of the NSD subfamily of PWWP domains." Biochem.Biophys.Res.Commun., 569, 199-206. doi: 10.1016/j.bbrc.2021.07.017. Crystal structure of the whsc1 pwwp1 domain. SNAP output
5vc9 DNA binding protein X-ray (2.1 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Zinc finger of human cxxc4 in complex with cpg DNA. SNAP output
5vez transferase-DNA, ligase-DNA X-ray (2.039 Å) Whitaker AM, Smith MR, Schaich MA, Freudenthal BD (2017) "Capturing a mammalian DNA polymerase extending from an oxidized nucleotide." Nucleic Acids Res., 45, 6934-6944. doi: 10.1093/nar/gkx293. DNA polymerase beta substrate complex with 8-oxog:a at the primer terminus and incoming dctp analog. SNAP output
5vfx DNA binding protein-DNA X-ray (2.81 Å) Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ, Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI, Whisstock JC (2018) "Crystal structure of TcpK in complex with oriT DNA of the antibiotic resistance plasmid pCW3." Nat Commun, 9, 3732. doi: 10.1038/s41467-018-06096-2. Structure of an accessory protein of the pcw3 relaxosome in complex with the origin of transfer (orit) DNA. SNAP output
5vhe hydrolase X-ray (3.793 Å) Chen MC, Tippana R, Demeshkina NA, Murat P, Balasubramanian S, Myong S, Ferre-D'Amare AR (2018) "Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36." Nature, 558, 465-469. doi: 10.1038/s41586-018-0209-9. Dhx36 in complex with the c-myc g-quadruplex. SNAP output
5vhv hydrolase-DNA X-ray (1.799 Å) Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF (2018) "Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC." EMBO J., 37, 63-74. doi: 10.15252/embj.201797833. Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an oxocarbenium-intermediate analog. SNAP output
5vi0 hydrolase-DNA X-ray (2.396 Å) Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF (2018) "Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC." EMBO J., 37, 63-74. doi: 10.15252/embj.201797833. Pseudomonas fluorescens alkylpurine DNA glycosylase alkc bound to DNA containing an abasic site analog. SNAP output
5vi5 transcription X-ray (3.196 Å) Hubin EA, Lilic M, Darst SA, Campbell EA (2017) "Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures." Nat Commun, 8, 16072. doi: 10.1038/ncomms16072. Structure of mycobacterium smegmatis transcription initiation complex with a full transcription bubble. SNAP output
5vi8 transcription X-ray (2.76 Å) Hubin EA, Lilic M, Darst SA, Campbell EA (2017) "Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures." Nat Commun, 8, 16072. doi: 10.1038/ncomms16072. Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter fragment. SNAP output
5vl9 transcription-DNA X-ray (2.16 Å) Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP (2018) "Jungle Express is a versatile repressor system for tight transcriptional control." Nat Commun, 9, 3617. doi: 10.1038/s41467-018-05857-3. Crystal structure of eilr in complex with eilo DNA element. SNAP output
5vmu transcription-DNA X-ray (2.346 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs). SNAP output
5vmv transcription-DNA X-ray (2.313 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with its double cpg-methylated DNA consensus binding site. SNAP output
5vmw transcription-DNA X-ray (2.397 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs). SNAP output
5vmx transcription-DNA X-ray (2.05 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a hemi cpg-methylated DNA resembling the specific kaiso binding sequence (kbs). SNAP output
5vmy transcription-DNA X-ray (2.002 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a hemi cpg-methylated DNA resembling the specific kaiso binding sequence (kbs). SNAP output
5vmz transcription-DNA X-ray (2.319 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) e535q mutant zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs). SNAP output
5vo8 transcription-DNA-RNA X-ray (3.3 Å) Murakami KS, Shin Y, Turnbough CL, Molodtsov V (2017) "X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway." Proc. Natl. Acad. Sci. U.S.A., 114, 8211-8216. doi: 10.1073/pnas.1702741114. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter. SNAP output
5voi transcription-DNA-RNA X-ray (2.8 Å) Murakami KS, Shin Y, Turnbough CL, Molodtsov V (2017) "X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway." Proc. Natl. Acad. Sci. U.S.A., 114, 8211-8216. doi: 10.1073/pnas.1702741114. X-ray crystal structure of bacterial RNA polymerase and pyrg promoter complex. SNAP output
5vpe transcription-DNA X-ray (2.053 Å) Yin Z, Machius M, Nestler EJ, Rudenko G (2017) "Activator Protein-1: redox switch controlling structure and DNA-binding." Nucleic Acids Res., 45, 11425-11436. doi: 10.1093/nar/gkx795. Transcription factor fosb-jund bzip domain in complex with cognate DNA, type-i crystal. SNAP output
5vpf transcription-DNA X-ray (2.694 Å) Yin Z, Machius M, Nestler EJ, Rudenko G (2017) "Activator Protein-1: redox switch controlling structure and DNA-binding." Nucleic Acids Res., 45, 11425-11436. doi: 10.1093/nar/gkx795. Transcription factor fosb-jund bzip domain in complex with cognate DNA, type-ii crystal. SNAP output
5vrw transferase, lyase-DNA X-ray (2.58 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta pre-catalytic 8-oxog:dc extension complex with dttp bound in non-planar conformation. SNAP output
5vrx transferase, lyase-DNA X-ray (2.2 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta pre-catalytic 8-oxog:dc extension complex with dttp bound in watson-crick conformation. SNAP output
5vry transferase, lyase-DNA X-ray (1.9 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta 8-oxog:dc extension with dttp after 20 s. SNAP output
5vrz transferase, lyase-DNA X-ray (2.05 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta 8-oxog:dc extension with dttp after 60 s. SNAP output
5vs0 transferase, lyase-DNA X-ray (2.1 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta 8-oxog:dc extension with dttp after 80 s. SNAP output
5vs1 transferase, lyase-DNA X-ray (2.5 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta pre-catalytic 8-oxog:da extension complex with dttp bound in non-planar conformation. SNAP output
5vs2 transferase, lyase-DNA X-ray (2.33 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta pre-catalytic 8-oxog:da extension complex with dttp bound in watson-crick conformation. SNAP output
5vs3 transferase, lyase-DNA X-ray (1.7 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta 8-oxog:da extension with dttp after 90 s. SNAP output
5vs4 transferase, lyase-DNA X-ray (1.87 Å) Reed AJ, Suo Z (2017) "Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta." J. Am. Chem. Soc., 139, 9684-9690. doi: 10.1021/jacs.7b05048. Human DNA polymerase beta 8-oxog:da extension with dttp after 120 s. SNAP output
5vu6 transferase-DNA X-ray (3.0 Å) Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC (2017) "Structural basis for TNA synthesis by an engineered TNA polymerase." Nat Commun, 8, 1810. doi: 10.1038/s41467-017-02014-0. Tna polymerase binary complex with primer-template duplex. SNAP output
5vu7 transferase-DNA X-ray (2.72 Å) Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC (2017) "Structural basis for TNA synthesis by an engineered TNA polymerase." Nat Commun, 8, 1810. doi: 10.1038/s41467-017-02014-0. Tna polymerase, open ternary complex. SNAP output
5vu8 transferase-DNA X-ray (3.2 Å) Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC (2017) "Structural basis for TNA synthesis by an engineered TNA polymerase." Nat Commun, 8, 1810. doi: 10.1038/s41467-017-02014-0. Tna polymerase, closed ternary complex. SNAP output
5vu9 transferase-DNA X-ray (2.05 Å) Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC (2017) "Structural basis for TNA synthesis by an engineered TNA polymerase." Nat Commun, 8, 1810. doi: 10.1038/s41467-017-02014-0. Tna polymerase, translocated product. SNAP output
5vvj hydrolase-DNA X-ray (3.89 Å) Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA (2017) "Structures of the CRISPR genome integration complex." Science, 357, 1113-1118. doi: 10.1126/science.aao0679. Cas1-cas2 bound to half-site intermediate. SNAP output
5vvk hydrolase-DNA X-ray (2.9 Å) Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA (2017) "Structures of the CRISPR genome integration complex." Science, 357, 1113-1118. doi: 10.1126/science.aao0679. Cas1-cas2 bound to full-site mimic. SNAP output
5vvl hydrolase-DNA X-ray (3.31 Å) Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA (2017) "Structures of the CRISPR genome integration complex." Science, 357, 1113-1118. doi: 10.1126/science.aao0679. Cas1-cas2 bound to full-site mimic with ni. SNAP output
5vvr transcription-RNA-DNA cryo-EM (5.8 Å) Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D (2017) "Structural basis for the initiation of eukaryotic transcription-coupled DNA repair." Nature, 551, 653-657. doi: 10.1038/nature24658. Ternary complex of RNA pol ii, transcription scaffold and rad26. SNAP output
5vvs transcription-RNA-DNA cryo-EM (6.4 Å) Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D (2017) "Structural basis for the initiation of eukaryotic transcription-coupled DNA repair." Nature, 551, 653-657. doi: 10.1038/nature24658. RNA pol ii elongation complex. SNAP output
5vxn DNA binding protein-DNA X-ray (3.375 Å) Filippova EV, Zemaitaitis B, Aung T, Wolfe AJ, Anderson WF (2018) "Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB." MBio, 9. doi: 10.1128/mBio.01993-17. Structure of two rcsb dimers bound to two parallel dnas.. SNAP output
5vz7 transferase-DNA X-ray (1.551 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Pre-catalytic ternary complex of human polymerase mu (g433a) mutant with incoming nonhydrolyzable umpnpp. SNAP output
5vz8 transferase-DNA X-ray (1.601 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (g433a) mutant with incoming utp. SNAP output
5vz9 transferase-DNA X-ray (1.65 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (g433a) mutant with incoming dttp. SNAP output
5vza transferase-DNA X-ray (1.501 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Pre-catalytic ternary complex of human polymerase mu (g433s) mutant with incoming nonhydrolyzable umpnpp. SNAP output
5vzb transferase-DNA X-ray (1.5 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (g433s) mutant with incoming utp. SNAP output
5vzc transferase-DNA X-ray (1.552 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (g433s) mutant with incoming dttp. SNAP output
5vzd transferase-DNA X-ray (1.602 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Pre-catalytic ternary complex of human polymerase mu (w434a) mutant with incoming nonhydrolyzable umpnpp. SNAP output
5vze transferase-DNA X-ray (1.506 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (w434a) mutant with incoming utp. SNAP output
5vzf transferase-DNA X-ray (1.65 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (w434a) mutant with incoming dttp. SNAP output
5vzg transferase-DNA X-ray (1.85 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Pre-catalytic ternary complex of human polymerase mu (w434h) mutant with incoming nonhydrolyzable umpnpp. SNAP output
5vzh transferase-DNA X-ray (1.95 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (w434h) mutant with incoming utp. SNAP output
5vzi transferase-DNA X-ray (1.5 Å) Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2017) "Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu." Nucleic Acids Res., 45, 9138-9148. doi: 10.1093/nar/gkx527. Post-catalytic complex of human polymerase mu (w434h) mutant with incoming dttp. SNAP output
5w0u hydrolase-DNA X-ray (2.9 Å) Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H (2017) "AID Recognizes Structured DNA for Class Switch Recombination." Mol. Cell, 67, 361-373.e4. doi: 10.1016/j.molcel.2017.06.034. Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with dcmp. SNAP output
5w1c DNA binding protein-DNA X-ray (3.18 Å) Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H (2017) "AID Recognizes Structured DNA for Class Switch Recombination." Mol. Cell, 67, 361-373.e4. doi: 10.1016/j.molcel.2017.06.034. Crystal structure of mbp fused activation-induced cytidine deaminase (aid) in complex with cytidine. SNAP output
5w1i RNA binding protein-RNA X-ray (2.2 Å) Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA (2017) "Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme." Nat. Struct. Mol. Biol., 24, 825-833. doi: 10.1038/nsmb.3466. Crystal structure of lbacas13a (c2c2) bound to mature crrna (20-nt spacer). SNAP output
5w2a replication X-ray (2.9 Å) Yockey OP, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L (2017) "Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa." Chem. Res. Toxicol., 30, 2023-2032. doi: 10.1021/acs.chemrestox.7b00227. Structure of human DNA polymerase kappa in complex with lucidin-derived DNA adduct and incoming dcmpnpp. SNAP output
5w2c replication X-ray (2.5 Å) Yockey OP, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L (2017) "Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa." Chem. Res. Toxicol., 30, 2023-2032. doi: 10.1021/acs.chemrestox.7b00227. Structure of human DNA polymerase kappa in complex with lucidin-derived DNA adduct and incoming dampnpp. SNAP output
5w2m DNA binding protein X-ray (3.7 Å) Fang Y, Xiao X, Li SX, Wolfe A, Chen XS (2018) "Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA." J. Mol. Biol., 430, 87-101. doi: 10.1016/j.jmb.2017.11.007. Apobec3f catalytic domain complex with a single-stranded DNA. SNAP output
5w34 transferase X-ray (2.95 Å) Hou C, Biswas T, Tsodikov OV (2018) "Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events." Biochemistry, 57, 2084-2093. doi: 10.1021/acs.biochem.8b00036. Crystal structure of the RNA polymerase domain (rpd) of mycobacterium tuberculosis primase dnag in complex with double-stranded DNA gaccggaagtgg. SNAP output
5w35 transferase-DNA X-ray (3.31 Å) Hou C, Biswas T, Tsodikov OV (2018) "Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events." Biochemistry, 57, 2084-2093. doi: 10.1021/acs.biochem.8b00036. Crystal structure of the RNA polymerase domain (rpd) of mycobacterium tuberculosis primase dnag in complex with a double-stranded DNA oligomer with a 1-nucleotide overhang. SNAP output
5w36 transferase X-ray (2.46 Å) Hou C, Biswas T, Tsodikov OV (2018) "Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events." Biochemistry, 57, 2084-2093. doi: 10.1021/acs.biochem.8b00036. Crystal structure of the RNA polymerase domain (rpd) of mycobacterium tuberculosis primase dnag in complex with a double-stranded DNA oligomer with a 6-nucleotide overhang. SNAP output
5w43 DNA binding protein X-ray (3.15 Å) Filippova EV, Zemaitaitis B, Aung T, Wolfe AJ, Anderson WF (2018) "Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB." MBio, 9. doi: 10.1128/mBio.01993-17. Structure of the two-component response regulator rcsb-DNA complex. SNAP output
5w4u DNA binding protein-RNA-DNA X-ray (3.6 Å) Wang W, Xu L, Hu L, Chong J, He C, Wang D (2017) "Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing." J.Am.Chem.Soc., 139, 14436-14442. doi: 10.1021/jacs.7b06381. Pol ii elongation complex with an n6-methyladenine-containing template. SNAP output
5w51 DNA binding protein-RNA-DNA X-ray (3.404 Å) Wang W, Xu L, Hu L, Chong J, He C, Wang D (2017) "Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing." J.Am.Chem.Soc., 139, 14436-14442. doi: 10.1021/jacs.7b06381. Pol ii elongation complex with an n6-methyladenine-containing template and a matched umpnpp. SNAP output
5w5y transcription cryo-EM (3.8 Å) Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y (2017) "Structural mechanism of ATP-independent transcription initiation by RNA polymerase I." Elife, 6. doi: 10.7554/eLife.27414. RNA polymerase i initial transcribing complex. SNAP output
5w64 transcription cryo-EM (4.2 Å) Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y (2017) "Structural mechanism of ATP-independent transcription initiation by RNA polymerase I." Elife, 6. doi: 10.7554/eLife.27414. RNA polymerase i initial transcribing complex state 1. SNAP output
5w65 transcription cryo-EM (4.3 Å) Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y (2017) "Structural mechanism of ATP-independent transcription initiation by RNA polymerase I." Elife, 6. doi: 10.7554/eLife.27414. RNA polymerase i initial transcribing complex state 2. SNAP output
5w66 transcription cryo-EM (3.9 Å) Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y (2017) "Structural mechanism of ATP-independent transcription initiation by RNA polymerase I." Elife, 6. doi: 10.7554/eLife.27414. RNA polymerase i initial transcribing complex state 3. SNAP output
5w6k DNA binding protein-DNA X-ray (2.339 Å) Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM (2018) "Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide." Nucleic Acids Res., 46, 7977-7988. doi: 10.1093/nar/gky552. Structure of mutant taq polymerase incorporating unnatural base pairs z:p. SNAP output
5w6q DNA binding protein-DNA X-ray (2.66 Å) Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM (2018) "Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide." Nucleic Acids Res., 46, 7977-7988. doi: 10.1093/nar/gky552. Structural basis for recognition of artificial DNA by an evolved klentaq variant. SNAP output
5w7g virus cryo-EM (4.5 Å) Egelman EH, Kasson PM, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D (2017) "Model for a novel membrane envelope in a filamentous hyperthermophilic virus." Elife, 6. doi: 10.7554/eLife.26268. An envelope of a filamentous hyperthermophilic virus carries lipids in a horseshoe conformation. SNAP output
5w7n hydrolase-DNA-RNA X-ray (1.8 Å) Fang Z, Yang F, Huang Z "2-Se-T2/4-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant." 2-se-t2-4-DNA and native RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5w7o hydrolase-DNA-RNA X-ray (1.75 Å) Fang Z, Yang F, Huang Z "2-Se-T-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant." 2-se-t4-DNA and native RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5w9q DNA binding protein-DNA X-ray (1.8 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Zinc finger region of mbd1 in complex with cpg DNA. SNAP output
5w9s DNA binding protein-DNA X-ray (2.1 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Zinc finger of human cxxc5 in complex with cpg DNA. SNAP output
5wc9 DNA binding protein X-ray (3.15 Å) Agarwal S, Cho TY (2018) "Biochemical and structural characterization of a novel cooperative binding mode by Pit-1 with CATT repeats in the macrophage migration inhibitory factor promoter." Nucleic Acids Res., 46, 929-941. doi: 10.1093/nar/gkx1183. Human pit-1 and 4xcatt DNA complex. SNAP output
5wcu chromatin binding protein-DNA X-ray (5.53 Å) Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y (2018) "Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures." J. Mol. Biol., 430, 3093-3110. doi: 10.1016/j.jmb.2018.06.020. Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone h5. SNAP output
5wfe DNA binding protein-DNA cryo-EM (3.64 Å) Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA (2017) "Structures of the CRISPR genome integration complex." Science, 357, 1113-1118. doi: 10.1126/science.aao0679. Cas1-cas2-ihf-DNA holo-complex. SNAP output
5wjq gene regulation-DNA X-ray (2.794 Å) Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X (2018) "DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins." Cell, 173, 221-233.e12. doi: 10.1016/j.cell.2018.02.058. Mousezfp568-znf2-11 in complex with DNA. SNAP output
5wjr hydrolase X-ray (1.7 Å) Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z (2023) "Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate." Chemistryselect, 8. doi: 10.1002/slct.202302253. High resolution native hexamer DNA and RNA hybrid in complex with rnase h catalytic domain d132n mutant. SNAP output
5wm1 transferase-DNA X-ray (1.85 Å) Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK (2017) "Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase." Nat Commun, 8, 965. doi: 10.1038/s41467-017-01013-5. Structure of the 10s (+)-trans-bp-dg modified rev1 ternary complex. SNAP output
5wm8 transferase-DNA X-ray (1.92 Å) Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK (2017) "Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase." Nat Commun, 8, 965. doi: 10.1038/s41467-017-01013-5. Structure of the 10r (+)-cis-bp-dg modified rev1 ternary complex. SNAP output
5wmb transferase-DNA X-ray (2.25 Å) Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK (2017) "Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase." Nat Commun, 8, 965. doi: 10.1038/s41467-017-01013-5. Structure of the 10s (-)-cis-bp-dg modified rev1 ternary complex (the bp residue is disordered). SNAP output
5wn0 hydrolase, lyase-DNA X-ray (2.6 Å) Whitaker AM, Flynn TS, Freudenthal BD (2018) "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage." Nat Commun, 9, 399. doi: 10.1038/s41467-017-02175-y. Ape1 exonuclease substrate complex with a c-g match. SNAP output
5wn1 hydrolase, lyase-DNA X-ray (2.3 Å) Whitaker AM, Flynn TS, Freudenthal BD (2018) "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage." Nat Commun, 9, 399. doi: 10.1038/s41467-017-02175-y. Ape1 exonuclease product complex. SNAP output
5wn2 hydrolase, lyase-DNA X-ray (2.288 Å) Whitaker AM, Flynn TS, Freudenthal BD (2018) "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage." Nat Commun, 9, 399. doi: 10.1038/s41467-017-02175-y. Ape1 exonuclease substrate complex with phosphoglycolate. SNAP output
5wn3 hydrolase, lyase-DNA X-ray (2.0 Å) Whitaker AM, Flynn TS, Freudenthal BD (2018) "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage." Nat Commun, 9, 399. doi: 10.1038/s41467-017-02175-y. Ape1 f266a exonuclease substrate complex with a c-t mismatch. SNAP output
5wn4 hydrolase, lyase-DNA X-ray (2.1 Å) Whitaker AM, Flynn TS, Freudenthal BD (2018) "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage." Nat Commun, 9, 399. doi: 10.1038/s41467-017-02175-y. Ape1 exonuclease substrate complex with a c-t mismatch. SNAP output
5wn5 hydrolase, lyase-DNA X-ray (2.2 Å) Whitaker AM, Flynn TS, Freudenthal BD (2018) "Molecular snapshots of APE1 proofreading mismatches and removing DNA damage." Nat Commun, 9, 399. doi: 10.1038/s41467-017-02175-y. Ape1 exonuclease substrate complex with a c-t mismatch and mn2+. SNAP output
5wnx DNA ligase-DNA, transferase X-ray (2.55 Å) Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD (2017) "Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues." Chem. Res. Toxicol., 30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173. DNA polymerase beta substrate complex with incoming 6-tdgtp. SNAP output
5wny DNA ligase-DNA, transferase X-ray (2.1 Å) Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD (2017) "Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues." Chem. Res. Toxicol., 30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173. DNA polymerase beta substrate complex with incoming 5-fdutp. SNAP output
5wnz DNA ligase-DNA, transferase X-ray (2.2 Å) Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD (2017) "Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues." Chem. Res. Toxicol., 30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173. DNA polymerase beta substrate complex with incoming 5-fodctp. SNAP output
5wo0 DNA ligase-DNA, transferase X-ray (1.6 Å) Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD (2017) "Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues." Chem. Res. Toxicol., 30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173. DNA polymerase beta substrate complex with incoming 5-fodutp. SNAP output
5wti hydrolase-DNA-RNA X-ray (2.682 Å) Wu D, Guan X, Zhu Y, Ren K, Huang Z (2017) "Structural basis of stringent PAM recognition by CRISPR-C2c1 in complex with sgRNA." Cell Res., 27, 705-708. doi: 10.1038/cr.2017.46. Crystal structure of the crispr-associated protein in complex with crrna and DNA. SNAP output
5wvw DNA binding protein-DNA X-ray (1.8 Å) Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y, Huang L (2017) "Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA." Biochem. J., 474, 1727-1739. doi: 10.1042/BCJ20170036. The crystal structure of cren7 mutant l28a in complex with dsDNA. SNAP output
5wvy DNA binding protein-DNA X-ray (2.0 Å) Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y, Huang L (2017) "Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA." Biochem. J., 474, 1727-1739. doi: 10.1042/BCJ20170036. The crystal structure of cren7 mutant l28v in complex with dsDNA. SNAP output
5wvz DNA binding protein-DNA X-ray (2.3 Å) Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y, Huang L (2017) "Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA." Biochem. J., 474, 1727-1739. doi: 10.1042/BCJ20170036. The crystal structure of cren7 mutant l28f in complex with dsDNA. SNAP output
5wwc DNA binding protein-DNA X-ray (1.9 Å) Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y, Huang L (2017) "Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA." Biochem. J., 474, 1727-1739. doi: 10.1042/BCJ20170036. The crystal structure of cren7 mutant l28m in complex with dsDNA. SNAP output
5wx9 DNA binding protein-DNA X-ray (1.76 Å) Chen CY, Lin PH, Chen KH, Cheng YS (2020) "Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box." Plant Mol.Biol., 104, 483-498. doi: 10.1007/s11103-020-01052-5. Crystal structure of aterf96 with gcc-box. SNAP output
5x07 DNA binding protein-DNA X-ray (2.796 Å) Li J, Machado ACD, Guo M, Sagendorf JM, Zhou Z, Jiang L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen Y (2017) "Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site." Biochemistry, 56, 3745-3753. doi: 10.1021/acs.biochem.7b00211. Crystal structure of foxa2 DNA binding domain bound to a full consensus DNA site. SNAP output
5x0x structural protein-hydrolase-DNA cryo-EM (3.97 Å) Liu X, Li M, Xia X, Li X, Chen Z (2017) "Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure." Nature, 544, 440-445. doi: 10.1038/nature22036. Complex of snf2-nucleosome complex with snf2 bound to position +6 of the nucleosome. SNAP output
5x0y structural protein-hydrolase-DNA cryo-EM (4.69 Å) Liu X, Li M, Xia X, Li X, Chen Z (2017) "Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure." Nature, 544, 440-445. doi: 10.1038/nature22036. Complex of snf2-nucleosome complex with snf2 bound to shl2 of the nucleosome. SNAP output
5x11 transcription-DNA X-ray (2.65 Å) Park SC, Kwak YM, Song WS, Hong M, Yoon SI (2017) "Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR." Nucleic Acids Res., 45, 13080-13093. doi: 10.1093/nar/gkx1055. Crystal structure of bacillus subtilis padr in complex with operator DNA. SNAP output
5x21 transferase-DNA X-ray (3.323 Å) Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Deho G, Donadio S, Ebright RH (2017) "Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase." Cell, 169, 1240-1248.e23. doi: 10.1016/j.cell.2017.05.042. Crystal structure of thermus thermophilus transcription initiation complex with gpa and pseudouridimycin (pum). SNAP output
5x22 transferase-DNA X-ray (3.35 Å) Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Deho G, Donadio S, Ebright RH (2017) "Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase." Cell, 169, 1240-1248.e23. doi: 10.1016/j.cell.2017.05.042. Crystal structure of thermus thermophilus transcription initiation complex with gpa and cmpcpp. SNAP output
5x2g hydrolase-RNA-DNA X-ray (2.4 Å) Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran FA, Nakane T, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) "Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems." Mol. Cell, 65, 1109-1121.e3. doi: 10.1016/j.molcel.2017.02.007. Crystal structure of campylobacter jejuni cas9 in complex with sgrna and target DNA (agaaacc pam). SNAP output
5x2h hydrolase-RNA-DNA X-ray (2.3 Å) Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran FA, Nakane T, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) "Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems." Mol. Cell, 65, 1109-1121.e3. doi: 10.1016/j.molcel.2017.02.007. Crystal structure of campylobacter jejuni cas9 in complex with sgrna and target DNA (agaaaca pam). SNAP output
5x5l DNA binding protein-DNA X-ray (2.75 Å) Wen Y, Ouyang Z, Yu Y, Zhou X, Pei Y, Devreese B, Higgins PG, Zheng F (2017) "Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region." Nucleic Acids Res., 45, 9773-9787. doi: 10.1093/nar/gkx624. Crystal structure of response regulator ader DNA binding domain in complex with an intercistronic region. SNAP output
5x6d DNA binding proten-DNA X-ray (2.94 Å) Wang Y, Feng H, Zhu Y, Gao P (2017) "Structural insights into glutathione-mediated activation of the master regulator PrfA in Listeria monocytogenes." Protein Cell, 8, 308-312. doi: 10.1007/s13238-017-0390-x. Crystal structure of prfa-DNA binary complex. SNAP output
5x6e DNA binding protein-DNA X-ray (2.99 Å) Wang Y, Feng H, Zhu Y, Gao P (2017) "Structural insights into glutathione-mediated activation of the master regulator PrfA in Listeria monocytogenes." Protein Cell, 8, 308-312. doi: 10.1007/s13238-017-0390-x. Crystal structure of prfa-DNA binary complex. SNAP output
5x6g metal binding protein-DNA X-ray (3.05 Å) Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW (2015) "Structural basis for the Smad5 MH1 domain to recognize different DNA sequences." Nucleic Acids Res., 43, 9051-9064. doi: 10.1093/nar/gkv848. Crystal structure of smad5-mh1-palindromic sbe DNA complex. SNAP output
5x6h metal binding protein-DNA X-ray (3.1 Å) Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW (2015) "Structural basis for the Smad5 MH1 domain to recognize different DNA sequences." Nucleic Acids Res., 43, 9051-9064. doi: 10.1093/nar/gkv848. Crystal structure of smad5-mh1-gc-bre DNA complex. SNAP output
5x6m metal binding protein-DNA X-ray (3.2 Å) Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW (2015) "Structural basis for the Smad5 MH1 domain to recognize different DNA sequences." Nucleic Acids Res., 43, 9051-9064. doi: 10.1093/nar/gkv848. Crystal structure of smad5-mh1 in complex with a composite DNA sequence. SNAP output
5x7x structural protein-DNA X-ray (2.184 Å) Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H (2017) "Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8." Biochemistry, 56, 2184-2196. doi: 10.1021/acs.biochem.6b01098. The crystal structure of the nucleosome containing h3.3 at 2.18 angstrom resolution. SNAP output
5xf3 structural protein-DNA X-ray (2.6 Å) Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA (2017) "Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation." Nat Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4. Nucleosome core particle with an adduct of a binuclear rapta (ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (r,r-configuration). SNAP output
5xf4 structural protein-DNA X-ray (2.87 Å) Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA (2017) "Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation." Nat Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4. Nucleosome core particle with an adduct of a binuclear rapta (ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (s,s-configuration). SNAP output
5xf5 structural protein-DNA X-ray (2.82 Å) Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA (2017) "Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation." Nat Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4. Nucleosome core particle with an adduct of a binuclear rapta (ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (r,s-configuration). SNAP output
5xf6 structural protein-DNA X-ray (2.63 Å) Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA (2017) "Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation." Nat Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4. Nucleosome core particle with an adduct of a binuclear rapta (ru-arene-phosphaadamantane) compound having an ethylenediamine linker. SNAP output
5xfp transcription-DNA X-ray (2.3 Å) Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z (2017) "Polycomb-like proteins link the PRC2 complex to CpG islands." Nature, 549, 287-291. doi: 10.1038/nature23881. Binary complex of phf1 and a double stranded DNA. SNAP output
5xfq transcription-DNA X-ray (2.4 Å) Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z (2017) "Polycomb-like proteins link the PRC2 complex to CpG islands." Nature, 549, 287-291. doi: 10.1038/nature23881. Ternary complex of phf1, a DNA duplex and a histone peptide. SNAP output
5xfr transcription-DNA X-ray (2.25 Å) Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z (2017) "Polycomb-like proteins link the PRC2 complex to CpG islands." Nature, 549, 287-291. doi: 10.1038/nature23881. Ternary complex of mtf2, DNA and histone. SNAP output
5xh6 hydrolase-RNA-DNA X-ray (2.0 Å) Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O (2017) "Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1." Mol. Cell, 67, 139-147.e2. doi: 10.1016/j.molcel.2017.04.019. Crystal structure of the acidaminococcus sp. bv3l6 cpf1 rvr variant in complex with crrna and target DNA (tata pam). SNAP output
5xh7 hydrolase-RNA-DNA X-ray (2.0 Å) Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O (2017) "Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1." Mol. Cell, 67, 139-147.e2. doi: 10.1016/j.molcel.2017.04.019. Crystal structure of the acidaminococcus sp. bv3l6 cpf1 rr variant in complex with crrna and target DNA (tcca pam). SNAP output
5xm0 structural protein-DNA X-ray (2.874 Å) Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K, Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S, Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H, Ohkawa Y (2018) "Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration." Nat Commun, 9, 1400. doi: 10.1038/s41467-018-03845-1. The mouse nucleosome structure containing h2a, h2b type3-a, h3.3, and h4. SNAP output
5xm1 structural protein-DNA X-ray (3.45 Å) Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K, Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S, Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H, Ohkawa Y (2018) "Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration." Nat Commun, 9, 1400. doi: 10.1038/s41467-018-03845-1. The mouse nucleosome structure containing h2a, h2b type3-a, h3mm7, and h4. SNAP output
5xm8 transferase-DNA X-ray (2.55 Å) Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J (2017) "Crystal structure of an RNA-cleaving DNAzyme." Nat Commun, 8, 2006. doi: 10.1038/s41467-017-02203-x. Crystal structure of asfvpolx in complex with DNA enzyme and pb.. SNAP output
5xm9 transferase-DNA X-ray (3.053 Å) Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J (2017) "Crystal structure of an RNA-cleaving DNAzyme." Nat Commun, 8, 2006. doi: 10.1038/s41467-017-02203-x. Crystal structure of asfvpolx in complex with DNA enzyme.. SNAP output
5xma transferase-DNA X-ray (3.8 Å) Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J (2017) "Crystal structure of an RNA-cleaving DNAzyme." Nat Commun, 8, 2006. doi: 10.1038/s41467-017-02203-x. Crystal structure of asfvpolx in complex with DNA enzyme at p43212 space group. SNAP output
5xn0 transferase-DNA X-ray (2.596 Å) Yasutake Y, Hattori SI, Hayashi H, Matsuda K, Tamura N, Kohgo S, Maeda K, Mitsuya H (2018) "HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir." Sci Rep, 8, 1624. doi: 10.1038/s41598-018-19602-9. Hiv-1 reverse transcriptase q151m:DNA binary complex. SNAP output
5xn1 transferase-DNA X-ray (2.446 Å) Yasutake Y, Hattori SI, Hayashi H, Matsuda K, Tamura N, Kohgo S, Maeda K, Mitsuya H (2018) "HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir." Sci Rep, 8, 1624. doi: 10.1038/s41598-018-19602-9. Hiv-1 reverse transcriptase q151m:DNA:entecavir-triphosphate ternary complex. SNAP output
5xn2 transferase-DNA X-ray (2.381 Å) Yasutake Y, Hattori SI, Hayashi H, Matsuda K, Tamura N, Kohgo S, Maeda K, Mitsuya H (2018) "HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir." Sci Rep, 8, 1624. doi: 10.1038/s41598-018-19602-9. Hiv-1 reverse transcriptase q151m:DNA:dgtp ternary complex. SNAP output
5xog transcription X-ray (3.0 Å) Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI (2017) "Structure of the complete elongation complex of RNA polymerase II with basal factors." Science, 357, 921-924. doi: 10.1126/science.aan8552. RNA polymerase ii elongation complex bound with spt5 kow5 and elf1. SNAP output
5xon transcription-RNA cryo-EM (3.83 Å) Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI (2017) "Structure of the complete elongation complex of RNA polymerase II with basal factors." Science, 357, 921-924. doi: 10.1126/science.aan8552. RNA polymerase ii elongation complex bound with spt4-5 and tfiis. SNAP output
5xou DNA binding protein X-ray (2.63 Å) Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y (2017) "Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes." Nucleic Acids Res., 45, 9149-9163. doi: 10.1093/nar/gkx547. Crystal structure of t. thermophilus argonaute protein complexed with a bulge 7t8 on the guide strand. SNAP output
5xow DNA binding protein X-ray (2.902 Å) Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y (2017) "Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes." Nucleic Acids Res., 45, 9149-9163. doi: 10.1093/nar/gkx547. Crystal structure of t. thermophilus argonaute protein complexed with a bulge 6'a7' on the target strand. SNAP output
5xp8 DNA binding protein X-ray (3.1 Å) Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y (2017) "Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes." Nucleic Acids Res., 45, 9149-9163. doi: 10.1093/nar/gkx547. Crystal structure of t. thermophilus argonaute protein complexed with a bulge 4a5 on the guide strand. SNAP output
5xpa DNA binding protein X-ray (2.9 Å) Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y (2017) "Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes." Nucleic Acids Res., 45, 9149-9163. doi: 10.1093/nar/gkx547. Crystal structure of t. thermophilus argonaute protein complexed with a bulge 9'u10' on the target strand. SNAP output
5xpg DNA binding protein X-ray (2.8 Å) Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y (2017) "Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes." Nucleic Acids Res., 45, 9149-9163. doi: 10.1093/nar/gkx547. Crystal structure of t. thermophilus argonaute protein complexed with a bulge 6'u7' on the target strand. SNAP output
5xq2 DNA binding protein X-ray (3.33 Å) Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y (2017) "Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes." Nucleic Acids Res., 45, 9149-9163. doi: 10.1093/nar/gkx547. Crystal structure of t. thermophilus argonaute protein complexed with a bulge 5a6 on the guide strand. SNAP output
5xrz recombination X-ray (3.6 Å) Saotome M, Saito K, Yasuda T, Ohtomo H, Sugiyama S, Nishimura Y, Kurumizaka H, Kagawa W (2018) "Structural Basis of Homology-Directed DNA Repair Mediated by RAD52." iScience, 3, 50-62. doi: 10.1016/j.isci.2018.04.005. Structure of a ssDNA bound to the inner DNA binding site of rad52. SNAP output
5xs0 recombination X-ray (3.0 Å) Saotome M, Saito K, Yasuda T, Ohtomo H, Sugiyama S, Nishimura Y, Kurumizaka H, Kagawa W (2018) "Structural Basis of Homology-Directed DNA Repair Mediated by RAD52." iScience, 3, 50-62. doi: 10.1016/j.isci.2018.04.005. Structure of a ssDNA bound to the outer DNA binding site of rad52. SNAP output
5xsk hormone X-ray (2.84 Å) Chen LY, Huang YC, Hsieh YC, Lin PJ "Structure of PWWP-DNA complex at 2.84 Angstroms resolution." Crystal structure of pwwp-DNA complex for human hepatoma-derived growth factor. SNAP output
5xus hydrolase-RNA-DNA X-ray (2.5 Å) Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) "Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1." Mol. Cell, 67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035. Crystal structure of lachnospiraceae bacterium nd2006 cpf1 in complex with crrna and target DNA (ttta pam). SNAP output
5xut hydrolase-RNA-DNA X-ray (2.4 Å) Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) "Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1." Mol. Cell, 67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035. Crystal structure of lachnospiraceae bacterium nd2006 cpf1 in complex with crrna and target DNA (tcta pam). SNAP output
5xuu hydrolase-RNA-DNA X-ray (2.5 Å) Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) "Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1." Mol. Cell, 67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035. Crystal structure of lachnospiraceae bacterium nd2006 cpf1 in complex with crrna and target DNA (tcca pam). SNAP output
5xuz hydrolase-RNA-DNA X-ray (2.4 Å) Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O (2017) "Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1." Mol. Cell, 67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035. Crystal structure of lachnospiraceae bacterium nd2006 cpf1 in complex with crrna and target DNA (ccca pam). SNAP output
5xvn immune system X-ray (3.25 Å) Xiao Y, Ng S, Hyun Nam K, Ke A (2017) "How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration." Nature, 550, 137-141. doi: 10.1038/nature24020. E. far cas1-cas2-prespacer binary complex. SNAP output
5xvo immune system X-ray (3.1 Å) Xiao Y, Ng S, Hyun Nam K, Ke A (2017) "How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration." Nature, 550, 137-141. doi: 10.1038/nature24020. E. fae cas1-cas2-prespacer-target ternary complex revealing DNA sampling and half-integration states. SNAP output
5xvp immune system X-ray (3.0 Å) Xiao Y, Ng S, Hyun Nam K, Ke A (2017) "How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration." Nature, 550, 137-141. doi: 10.1038/nature24020. E. fae cas1-cas2-prespacer-target ternary complex revealing the fully integrated states. SNAP output
5xxp DNA binding protein X-ray (2.55 Å) Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda T (2018) "Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region." FEBS J., 285, 977-989. doi: 10.1111/febs.14380. Crystal structure of cbnr_dbd-DNA complex. SNAP output
5xzb immune system-inhibitor X-ray (2.13 Å) Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M (2017) "Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice." Nat Commun, 8, 750. doi: 10.1038/s41467-017-00833-9. Mouse cgas bound to the inhibitor ru365. SNAP output
5xze immune system-inhibitor X-ray (2.177 Å) Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M (2017) "Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice." Nat Commun, 8, 750. doi: 10.1038/s41467-017-00833-9. Mouse cgas bound to the inhibitor ru332. SNAP output
5xzg immune system-inhibitor X-ray (1.828 Å) Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M (2017) "Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice." Nat Commun, 8, 750. doi: 10.1038/s41467-017-00833-9. Mouse cgas bound to the inhibitor ru521. SNAP output
5y0c DNA binding protein-DNA X-ray (2.087 Å) Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H (2018) "Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome." Nucleic Acids Res., 46, 10007-10018. doi: 10.1093/nar/gky661. Crystal structure of the human nucleosome at 2.09 angstrom resolution. SNAP output
5y0d DNA binding protein-DNA X-ray (1.99 Å) Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H (2018) "Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome." Nucleic Acids Res., 46, 10007-10018. doi: 10.1093/nar/gky661. Crystal structure of the human nucleosome containing the h2b e76k mutant. SNAP output
5y36 hydrolase-RNA-DNA cryo-EM (5.2 Å) Huai C, Li G, Yao R, Zhang Y, Cao M, Kong L, Jia C, Yuan H, Chen H, Lu D, Huang Q (2017) "Structural insights into DNA cleavage activation of CRISPR-Cas9 system." Nat Commun, 8, 1375. doi: 10.1038/s41467-017-01496-2. cryo-EM structure of spcas9-sgrna-DNA ternary complex. SNAP output
5y3j immune system X-ray (1.81 Å) Ohto U, Ishida H, Shibata T, Sato R, Miyake K, Shimizu T (2018) "Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation." Immunity, 48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013. Crystal structure of horse tlr9 in complex with two dnas (cpg DNA and tcgcac DNA). SNAP output
5y3k immune system X-ray (2.7 Å) Ohto U, Ishida H, Shibata T, Sato R, Miyake K, Shimizu T (2018) "Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation." Immunity, 48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013. Crystal structure of horse tlr9 in complex with two dnas (cpg DNA and gcgcac DNA). SNAP output
5y3l immune system X-ray (2.6 Å) Ohto U, Ishida H, Shibata T, Sato R, Miyake K, Shimizu T (2018) "Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation." Immunity, 48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013. Crystal structure of horse tlr9 in complex with two dnas (cpg DNA and ccgcac DNA). SNAP output
5y3m immune system X-ray (2.5 Å) Ohto U, Ishida H, Shibata T, Sato R, Miyake K, Shimizu T (2018) "Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation." Immunity, 48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013. Crystal structure of bovine tlr9 in complex with two dnas (cpg DNA and tcgttt DNA). SNAP output
5y3r DNA binding protein cryo-EM (6.6 Å) Yin X, Liu M, Tian Y, Wang J, Xu Y (2017) "Cryo-EM structure of human DNA-PK holoenzyme." Cell Res., 27, 1341-1350. doi: 10.1038/cr.2017.110. cryo-EM structure of human DNA-pk holoenzyme. SNAP output
5y7g hydrolase-DNA X-ray (3.4 Å) Jin H, Roy U, Lee G, Scharer OD, Cho Y (2018) "Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease." J. Biol. Chem., 293, 6482-6496. doi: 10.1074/jbc.RA118.002171. Crystal structure of pafan1 bound to 1nt 5'flap DNA with gap. SNAP output
5y7q hydrolase-DNA X-ray (2.7 Å) Jin H, Roy U, Lee G, Scharer OD, Cho Y (2018) "Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease." J. Biol. Chem., 293, 6482-6496. doi: 10.1074/jbc.RA118.002171. Crystal structure of pafan1 bound to 2nt 5'flap DNA with gap. SNAP output
5ybb DNA binding protein-DNA X-ray (3.2 Å) Liu YP, Tang Q, Zhang JZ, Tian LF, Gao P, Yan XX (2017) "Structural basis underlying complex assembly and conformational transition of the type I R-M system." Proc. Natl. Acad. Sci. U.S.A., 114, 11151-11156. doi: 10.1073/pnas.1711754114. Structural basis underlying complex assembly andconformational transition of the type i r-m system. SNAP output
5ybd DNA binding protein X-ray (2.769 Å) Sharma R, Gangwar SP, Saxena AK (2018) "Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence." Acta Crystallogr F Struct Biol Commun, 74, 656-663. doi: 10.1107/S2053230X1801110X. X-ray structure of ets domain of ergp55 in complex with e74DNA. SNAP output
5yef DNA binding protein-DNA X-ray (2.807 Å) Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y (2017) "Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites." Cell Res., 27, 1365-1377. doi: 10.1038/cr.2017.131. Crystal structure of ctcf zfs2-8-hs5-1ae. SNAP output
5yeg DNA binding protein X-ray (2.0 Å) Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y (2017) "Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites." Cell Res., 27, 1365-1377. doi: 10.1038/cr.2017.131. Crystal structure of ctcf zfs4-8-hs5-1a complex. SNAP output
5yeh DNA binding protein-DNA X-ray (2.328 Å) Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y (2017) "Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites." Cell Res., 27, 1365-1377. doi: 10.1038/cr.2017.131. Crystal structure of ctcf zfs4-8-ecbs. SNAP output
5yej DNA binding protein-DNA X-ray (2.698 Å) Yan L, Tang Q, Guan Z, Pei K, Zou T, He J (2018) "Structural insights into operator recognition by BioQ in the Mycobacterium smegmatis biotin synthesis pathway." Biochim Biophys Acta Gen Subj, 1862, 1843-1851. doi: 10.1016/j.bbagen.2018.05.015. Crystal structure of bioq with its naturel double-stranded DNA operator. SNAP output
5yel DNA binding protein-DNA X-ray (2.96 Å) Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang Y (2017) "Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites." Cell Res., 27, 1365-1377. doi: 10.1038/cr.2017.131. Crystal structure of ctcf zfs6-11-gb7cse. SNAP output
5yi2 metal binding protein X-ray (2.6 Å) Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen PR (2017) "Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation." Proc.Natl.Acad.Sci.USA, 114, 13661-13666. doi: 10.1073/pnas.1708563115. Structure of lactococcus lactis zitr, wild type in complex with DNA. SNAP output
5yi3 metal binding protein-DNA X-ray (2.9 Å) Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen PR (2017) "Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation." Proc.Natl.Acad.Sci.USA, 114, 13661-13666. doi: 10.1073/pnas.1708563115. Structure of lactococcus lactis zitr, c30s mutant in complex with DNA. SNAP output
5yiv DNA binding protein-DNA X-ray (2.914 Å) Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L, Zhuang N, Laub MT, Zhang Y (2018) "Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA." Nucleic Acids Res., 46, 3245-3256. doi: 10.1093/nar/gky161. Caulobacter crescentus gcra DNA-binding domain(dbd) in complex with methylated dsDNA(crystal form 1). SNAP output
5yiw DNA binding protein-DNA X-ray (1.551 Å) Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L, Zhuang N, Laub MT, Zhang Y (2018) "Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA." Nucleic Acids Res., 46, 3245-3256. doi: 10.1093/nar/gky161. Caulobacter crescentus gcra DNA-binding domain (dbd) in complex with methylated dsDNA (crystal form 2). SNAP output
5yj3 DNA binding protein-DNA X-ray (2.845 Å) Zhao Y, Zhang G, He C, Mei Y, Shi Y, Li F (2018) "The 11th C2H2 zinc finger and an adjacent C-terminal arm are responsible for TZAP recognition of telomeric DNA." Cell Res., 28, 130-134. doi: 10.1038/cr.2017.141. Crystal structure of tzap and telomeric DNA complex. SNAP output
5ytc transferase-DNA X-ray (2.28 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with the unnatural base m-fc pair with datp in the active site. SNAP output
5ytd replication-DNA X-ray (2.0 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with the natural base pair 5fc:dgtp. SNAP output
5yte replication-DNA X-ray (2.21 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Large fragment of DNA polymerase i from thermus aquaticus in a closed ternary complex with with natural dt:datp base pair. SNAP output
5ytf transferase-DNA X-ray (1.98 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Structure of large fragment of DNA polymerase i from thermus aquaticus host-guest complex with the unnatural base m-fc pair with da. SNAP output
5ytg transferase-DNA X-ray (2.07 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Structure of large fragment of DNA polymerase i from thermus aquaticus host-guest complex with the unnatural base i-fc pair with da. SNAP output
5yth transferase-DNA X-ray (2.53 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Structure of large fragment of DNA polymerase i from thermus aquaticus host-guest complex with the unnatural base m-fc pair with dg. SNAP output
5yty antibiotic-DNA X-ray (1.58 Å) Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH (2018) "Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex." Nucleic Acids Res., 46, 7396-7404. doi: 10.1093/nar/gky345. Crystal structure of echinomycin-d(acgacgt-acgtcgt) complex. SNAP output
5ytz antibiotic-DNA X-ray (1.55 Å) Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH (2018) "Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex." Nucleic Acids Res., 46, 7396-7404. doi: 10.1093/nar/gky345. Crystal structure of echinomycin-d(acgtcgt)2 complex. SNAP output
5yur DNA binding protein-DNA X-ray (2.035 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 1. SNAP output
5yus DNA binding protein-DNA X-ray (1.94 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 2. SNAP output
5yut DNA binding protein-DNA X-ray (2.15 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 3. SNAP output
5yuu DNA binding protein-DNA X-ray (1.892 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 4. SNAP output
5yuv DNA binding protein-DNA X-ray (2.06 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 5. SNAP output
5yuw DNA binding protein-dan X-ray (2.124 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 6. SNAP output
5yux DNA binding protein-DNA X-ray (2.04 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 8. SNAP output
5yuy DNA binding protein-DNA X-ray (1.74 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 9. SNAP output
5yuz DNA binding protein-DNA X-ray (1.83 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 11. SNAP output
5yv0 DNA binding protein-DNA X-ray (2.09 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 12. SNAP output
5yv1 DNA binding protein-DNA X-ray (2.09 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 13. SNAP output
5yv2 DNA binding protein X-ray (1.9 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 14. SNAP output
5yv3 DNA binding protein-DNA X-ray (2.03 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 7. SNAP output
5yws DNA binding protein-DNA X-ray (2.0 Å) Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW, Hsiao YY (2018) "Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1." PLoS Biol., 16, e2005653. doi: 10.1371/journal.pbio.2005653. Crystal structure of trex1 in complex with a y structured DNA. SNAP output
5ywt DNA binding protein X-ray (1.7 Å) Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW, Hsiao YY (2018) "Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1." PLoS Biol., 16, e2005653. doi: 10.1371/journal.pbio.2005653. Crystal structure of trex1 in complex with a duplex DNA with 3' overhang. SNAP output
5ywu DNA binding protein-DNA X-ray (3.4 Å) Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW, Hsiao YY (2018) "Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1." PLoS Biol., 16, e2005653. doi: 10.1371/journal.pbio.2005653. Crystal structure of trex1 in complex with a inosine contained dsDNA. SNAP output
5ywv DNA binding protein-DNA X-ray (2.3 Å) Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW, Hsiao YY (2018) "Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1." PLoS Biol., 16, e2005653. doi: 10.1371/journal.pbio.2005653. Crystal structure of trex1 in complex with a inosine contained ssDNA. SNAP output
5yx2 transferase-transferase regulator-DNA X-ray (2.653 Å) Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J (2018) "Structural basis for DNMT3A-mediated de novo DNA methylation." Nature, 554, 387-391. doi: 10.1038/nature25477. Crystal structure of dnmt3a-dnmt3l in complex with DNA containing two cpg sites. SNAP output
5yyd DNA binding protein-DNA X-ray (2.05 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - ternary complex 15. SNAP output
5yye DNA binding protein-DNA X-ray (2.325 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - ternary complex 16. SNAP output
5yzy transcription-DNA X-ray (2.61 Å) Wu BX, Zhang MM, Su SC, Liu HH, Gan JH, Ma JB (2018) "Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana." Biochem. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2018.05.002. Atval1 b3 domain in complex with 13bp-DNA. SNAP output
5yzz transcription-DNA X-ray (2.58 Å) Wu BX, Zhang MM, Su SC, Liu HH, Gan JH, Ma JB (2018) "Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana." Biochem. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2018.05.002. Atval1 b3 domain in complex with 13bp-DNA. SNAP output
5z00 transcription-DNA X-ray (2.587 Å) Wu BX, Zhang MM, Su SC, Liu HH, Gan JH, Ma JB (2018) "Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana." Biochem. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2018.05.002. Atval1 b3 domain in complex with 15bp-DNA. SNAP output
5z23 DNA binding protein-DNA X-ray (2.73 Å) Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H (2019) "The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism." Nat Commun, 10, 576. doi: 10.1038/s41467-019-08314-x. Crystal structure of the nucleosome containing a chimeric histone h3-cenp-a catd. SNAP output
5z2t DNA binding protein-DNA X-ray (2.623 Å) Dong X, Zhang W, Wu H, Huang J, Zhang M, Wang P, Zhang H, Chen Z, Chen SJ, Meng G (2018) "Structural basis of DUX4/IGH-driven transactivation." Leukemia, 32, 1466-1476. doi: 10.1038/s41375-018-0093-1. Crystal structure of DNA-bound dux4-hd2. SNAP output
5z30 DNA binding protein-DNA X-ray (2.45 Å) Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H (2018) "Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome." Nucleic Acids Res., 46, 10007-10018. doi: 10.1093/nar/gky661. The crystal structure of the nucleosome containing a cancer-associated histone h2a.z r80c mutant. SNAP output
5z3l structural protein-hydrolase-DNA cryo-EM (4.31 Å) Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z (2019) "Mechanism of DNA translocation underlying chromatin remodelling by Snf2." Nature, 567, 409-413. doi: 10.1038/s41586-019-1029-2. Structure of snf2-nucleosome complex in apo state. SNAP output
5z3n replication-DNA X-ray (1.91 Å) Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C (2019) "Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry." Angew. Chem. Int. Ed. Engl., 58, 130-133. doi: 10.1002/anie.201807845. Structure of large fragment of DNA polymerase i from thermus aquaticus host-guest complex with the unnatural base 5fc pair with da. SNAP output
5z3o structural protein-hydrolase-DNA cryo-EM (3.62 Å) Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z (2019) "Mechanism of DNA translocation underlying chromatin remodelling by Snf2." Nature, 567, 409-413. doi: 10.1038/s41586-019-1029-2. Structure of snf2-nucleosome complex in adp state. SNAP output
5z3u structural protein-hydrolase-DNA cryo-EM (4.31 Å) Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z (2019) "Mechanism of DNA translocation underlying chromatin remodelling by Snf2." Nature, 567, 409-413. doi: 10.1038/s41586-019-1029-2. Structure of snf2-nucleosome complex at shl2 in adp befx state. SNAP output
5z3v structural protein-hydrolase-DNA cryo-EM (4.22 Å) Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z (2019) "Mechanism of DNA translocation underlying chromatin remodelling by Snf2." Nature, 567, 409-413. doi: 10.1038/s41586-019-1029-2. Structure of snf2-nucleosome complex at shl-2 in adp befx state. SNAP output
5z6w hydrolase-DNA X-ray (3.2 Å) Jin H, Roy U, Lee G, Scharer OD, Cho Y (2018) "Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease." J. Biol. Chem., 293, 6482-6496. doi: 10.1074/jbc.RA118.002171. Crystal structure of pafan1 bound to 2nt 5'flap DNA with gap with manganese. SNAP output
5z6z transcription-DNA X-ray (2.301 Å) Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J, Chen Y, Gu Y, Li J, Ma J, Gan J (2018) "Structural basis for multiple gene regulation by human DUX4." Biochem. Biophys. Res. Commun., 505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056. Crystal structure of human dux4 homeodomains bound to DNA. SNAP output
5z7d immune system X-ray (4.5 Å) Fan X, Jiang J, Zhao D, Chen F, Ma H, Smith P, Unterholzner L, Xiao TS, Jin T (2021) "Structural mechanism of DNA recognition by the p204 HIN domain." Nucleic Acids Res. doi: 10.1093/nar/gkab076. P204hinab-dsDNA complex structure. SNAP output
5z7i DNA binding protein-DNA X-ray (1.601 Å) Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L, Zhuang N, Laub MT, Zhang Y (2018) "Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA." Nucleic Acids Res., 46, 3245-3256. doi: 10.1093/nar/gky161. Caulobacter crescentus gcra DNA-binding domain(dbd)in complex with unmethylated dsDNA. SNAP output
5z98 antiviral protein-RNA X-ray (2.2 Å) Matsuoka T, Nagae T, Ode H, Awazu H, Kurosawa T, Hamano A, Matsuoka K, Hachiya A, Imahashi M, Yokomaku Y, Watanabe N, Iwatani Y (2018) "Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA." Nucleic Acids Res., 46, 10368-10379. doi: 10.1093/nar/gky676. Crystal structure of the primate apobec3h dimer mediated by RNA duplex. SNAP output
5zad DNA binding protein-DNA X-ray (2.54 Å) Sun LY, Zhu LW, Tang YJ (2018) "Increasing the distance between two monomers of topoisomerase II beta under the action of antitumor agent 4 beta-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin." Sci Rep, 8, 14949. doi: 10.1038/s41598-018-33366-2. Human topoisomerase ii beta in complex with DNA. SNAP output
5zbx DNA binding protein-DNA X-ray (2.58 Å) Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H, Fukagawa T, Kurumizaka H (2019) "The CENP-A centromere targeting domain facilitates H4K20 monomethylation in the nucleosome by structural polymorphism." Nat Commun, 10, 576. doi: 10.1038/s41467-019-08314-x. The crystal structure of the nucleosome containing histone h3.1 catd(v76q, k77d). SNAP output
5zcw DNA binding protein-DNA X-ray (2.7 Å) Maestre-Reyna M, Yamamoto J, Huang WC, Tsai MD, Essen LO, Bessho Y (2018) "Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA." IUCrJ, 5, 608-618. doi: 10.1107/S205225251800996X. Structure of the methanosarcina mazei class ii cpd-photolyase in complex with intact, phosphodiester linked, cpd-lesion. SNAP output
5zd4 transcription X-ray (2.17 Å) Nosaki S, Miyakawa T, Xu Y, Nakamura A, Hirabayashi K, Asami T, Nakano T, Tanokura M (2018) "Structural basis for brassinosteroid response by BIL1/BZR1." Nat Plants, 4, 771-776. doi: 10.1038/s41477-018-0255-1. Crystal structure of mbp-fused bil1-bzr1 in complex with double-stranded DNA. SNAP output
5zdz DNA binding protein X-ray (2.8 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Hairpin forming complex, rag1-2-nicked 12rss-23rss complex in ca2+. SNAP output
5ze0 DNA binding protein X-ray (2.75 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Hairpin forming complex, rag1-2-nicked(with dideoxy) 12rss-23rss complex in mg2+. SNAP output
5ze1 DNA binding protein X-ray (3.0 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Hairpin forming complex, rag1-2-nicked 12rss-23rss complex in 2mm mn2+ for 10 min at 4'c. SNAP output
5ze2 DNA binding protein X-ray (3.3 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Hairpin complex, rag1-2-hairpin 12rss-23rss complex in 5mm mn2+ for 2 min at 4'c. SNAP output
5zen isomerase-DNA X-ray (2.75 Å) Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL (2018) "Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate." Nat Commun, 9, 3085. doi: 10.1038/s41467-018-05406-y. Crystal structure of human topoisomerase ii beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate. SNAP output
5zfw transcription-DNA X-ray (2.103 Å) Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J, Chen Y, Gu Y, Li J, Ma J, Gan J (2018) "Structural basis for multiple gene regulation by human DUX4." Biochem. Biophys. Res. Commun., 505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056. Crystal structure of human dux4 homeodomains bound to a11g DNA mutant. SNAP output
5zfy transcription-DNA X-ray (2.3 Å) Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J, Chen Y, Gu Y, Li J, Ma J, Gan J (2018) "Structural basis for multiple gene regulation by human DUX4." Biochem. Biophys. Res. Commun., 505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056. Crystal structure of human dux4 homeodomains bound to a12c DNA mutant. SNAP output
5zfz transcription-DNA X-ray (1.9 Å) Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J, Chen Y, Gu Y, Li J, Ma J, Gan J (2018) "Structural basis for multiple gene regulation by human DUX4." Biochem. Biophys. Res. Commun., 505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056. Crystal structure of human dux4 homeodomains bound to a12t DNA mutant. SNAP output
5zg9 DNA binding protein-DNA X-ray (2.04 Å) Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu M, Fang X, Liu J (2019) "The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus." Proteins, 87, 257-264. doi: 10.1002/prot.25647. Crystal structure of mosub1-ssDNA complex in phosphate buffer. SNAP output
5zgn toxin X-ray (2.24 Å) Qian HL, Yao QQ, Gan JH, Ou HY "The crystal structure of KacTA-DNA complex." The crystal structure of kacta-DNA complex. SNAP output
5zjq transcription-DNA X-ray (2.443 Å) Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS (2018) "Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites." Cell Rep, 24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100. Structure of abdb-exd complex bound to a 'red14' DNA sequence. SNAP output
5zjr transcription-DNA X-ray (3.03 Å) Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS (2018) "Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites." Cell Rep, 24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100. Structure of abdb-exd complex bound to a 'magenta14' DNA sequence. SNAP output
5zjs transcription-DNA X-ray (2.896 Å) Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS (2018) "Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites." Cell Rep, 24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100. Structure of abdb-exd complex bound to a 'blue14' DNA sequence. SNAP output
5zjt transcription-DNA X-ray (2.4 Å) Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS (2018) "Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites." Cell Rep, 24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100. Structure of abdb-exd complex bound to a 'black14' DNA sequence. SNAP output
5zk1 transcription-DNA X-ray (3.05 Å) Song Y, Zhai L, Valencia Swain J, Chen Y, Wang P, Chen L, Liu Y, Xiang S (2018) "Structural Insights into the CRTC2-CREB Complex Assembly on CRE." J. Mol. Biol., 430, 1926-1939. doi: 10.1016/j.jmb.2018.04.038. Crystal structure of the crtc2(semet)-creb-cre complex. SNAP output
5zki hydrolase-DNA X-ray (2.321 Å) Wu CC, Lin JLJ, Yang-Yen HF, Yuan HS (2019) "A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication." Nucleic Acids Res., 47, 5405-5419. doi: 10.1093/nar/gkz241. Human exog-h140a in complex with duplex DNA. SNAP output
5zkj hydrolase-RNA-DNA X-ray (2.798 Å) Wu CC, Lin JLJ, Yang-Yen HF, Yuan HS (2019) "A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication." Nucleic Acids Res., 47, 5405-5419. doi: 10.1093/nar/gkz241. Human exog-h140a in complex with RNA-DNA hybrid duplex. SNAP output
5zkl unknown function-DNA X-ray (1.951 Å) Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y (2020) "Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins." Nucleic Acids Res., 48, 432-444. doi: 10.1093/nar/gkz1045. Crystal structure of streptococcus pneumoniae sp_0782 (residues 7-79) in complex with single-stranded DNA dt12. SNAP output
5zkm unknown function-DNA X-ray (1.65 Å) Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y (2020) "Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins." Nucleic Acids Res., 48, 432-444. doi: 10.1093/nar/gkz1045. Crystal structure of streptococcus pneumoniae sp_0782 (residues 7-79) in complex with single-stranded DNA tcttcc. SNAP output
5zko transcription-DNA X-ray (3.05 Å) Song Y, Zhai L, Valencia Swain J, Chen Y, Wang P, Chen L, Liu Y, Xiang S (2018) "Structural Insights into the CRTC2-CREB Complex Assembly on CRE." J. Mol. Biol., 430, 1926-1939. doi: 10.1016/j.jmb.2018.04.038. Crystal structure of the crtc2-creb-cre complex. SNAP output
5zln immune system X-ray (2.3 Å) Ishida H, Ohto U, Shibata T, Miyake K, Shimizu T (2018) "Structural basis for species-specific activation of mouse Toll-like receptor 9." FEBS Lett., 592, 2636-2646. doi: 10.1002/1873-3468.13176. Crystal structure of mouse tlr9 in complex with two dnas (cpg DNA and tcgcca DNA). SNAP output
5zlv DNA binding protein-DNA X-ray (2.35 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex with 50mm mgcl2. SNAP output
5zmc transcription-DNA X-ray (2.99 Å) Xu X, Li Y, Bharath SR, Ozturk MB, Bowler MW, Loo BZL, Tergaonkar V, Song H (2018) "Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1." Nat Commun, 9, 3183. doi: 10.1038/s41467-018-05644-0. Structural basis for reactivation of -146c>t mutant tert promoter by cooperative binding of p52 and ets1-2. SNAP output
5zmd oxidoreductase-DNA X-ray (3.3 Å) Zhang X, Wei LH, Wang Y, Xiao Y, Liu J, Zhang W, Yan N, Amu G, Tang X, Zhang L, Jia G (2019) "Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates." Proc. Natl. Acad. Sci. U.S.A., 116, 2919-2924. doi: 10.1073/pnas.1820574116. Crystal structure of fto in complex with m6da modified ssDNA. SNAP output
5zmn DNA binding protein-DNA X-ray (3.29 Å) Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X, Zhao Y, Deng Z, Wu G, He X (2018) "Structural basis for the recognition of sulfur in phosphorothioated DNA." Nat Commun, 9, 4689. doi: 10.1038/s41467-018-07093-1. Sulfur binding domain and sra domain of scomcra complexed with phosphorothioated DNA. SNAP output
5zmo DNA binding protein-DNA X-ray (1.69 Å) Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X, Zhao Y, Deng Z, Wu G, He X (2018) "Structural basis for the recognition of sulfur in phosphorothioated DNA." Nat Commun, 9, 4689. doi: 10.1038/s41467-018-07093-1. Sulfur binding domain of scomcra complexed with phosphorothioated DNA. SNAP output
5zoe hydrolase-DNA X-ray (1.95 Å) Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L, Tian B, Zheng L, Shen B, Hua Y, Zhao Y (2018) "Structural basis of 5' flap recognition and protein-protein interactions of human flap endonuclease 1." Nucleic Acids Res., 46, 11315-11325. doi: 10.1093/nar/gky911. Crystal structure of d181a hfen1 in complex with DNA. SNAP output
5zof hydrolase-DNA X-ray (2.249 Å) Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L, Tian B, Zheng L, Shen B, Hua Y, Zhao Y (2018) "Structural basis of 5' flap recognition and protein-protein interactions of human flap endonuclease 1." Nucleic Acids Res., 46, 11315-11325. doi: 10.1093/nar/gky911. Crystal structure of d181a-r192f hfen1 in complex with DNA. SNAP output
5zog hydrolase-DNA X-ray (2.299 Å) Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L, Tian B, Zheng L, Shen B, Hua Y, Zhao Y (2018) "Structural basis of 5' flap recognition and protein-protein interactions of human flap endonuclease 1." Nucleic Acids Res., 46, 11315-11325. doi: 10.1093/nar/gky911. Crystal structure of r192f hfen1 in complex with DNA. SNAP output
5zqf isomerase-DNA X-ray (3.873 Å) Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL (2018) "Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate." Nat Commun, 9, 3085. doi: 10.1038/s41467-018-05406-y. Crystal structure of human topoisomerase ii beta in complex with 5-iodouridine-containing-DNA in space group p3221. SNAP output
5zr1 DNA binding protein-DNA cryo-EM (3.0 Å) Li N, Lam WH, Zhai Y, Cheng J, Cheng E, Zhao Y, Gao N, Tye BK (2018) "Structure of the origin recognition complex bound to DNA replication origin." Nature, 559, 217-222. doi: 10.1038/s41586-018-0293-x. Saccharomyces cerevisiae origin recognition complex bound to a 72-bp origin DNA containing acs and b1 element. SNAP output
5zrf isomerase-DNA X-ray (2.3 Å) Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL (2018) "Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate." Nat Commun, 9, 3085. doi: 10.1038/s41467-018-05406-y. Crystal structure of human topoisomerase ii beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21. SNAP output
5zu1 hydrolase-DNA X-ray (3.009 Å) Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S, Sugiyama H, Kim KK (2018) "Sequence preference and structural heterogeneity of BZ junctions." Nucleic Acids Res., 46, 10504-10513. doi: 10.1093/nar/gky784. Crystal structure of bz junction in diverse sequence. SNAP output
5zuo hydrolase-DNA X-ray (2.902 Å) Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S, Sugiyama H, Kim KK (2018) "Sequence preference and structural heterogeneity of BZ junctions." Nucleic Acids Res., 46, 10504-10513. doi: 10.1093/nar/gky784. Crystal structure of bz junction in diverse sequence. SNAP output
5zup hydrolase-DNA X-ray (2.9 Å) Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S, Sugiyama H, Kim KK (2018) "Sequence preference and structural heterogeneity of BZ junctions." Nucleic Acids Res., 46, 10504-10513. doi: 10.1093/nar/gky784. Crystal structure of bz junction in diverse sequence. SNAP output
5zux DNA binding protein-DNA NMR Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B (2018) "How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome." Nucleic Acids Res., 46, 10514-10529. doi: 10.1093/nar/gky836. Solution structure of the DNA complex of the c-terminal domain of rok. SNAP output
5zva structural protein-DNA X-ray (2.3 Å) Cheng C, Zhang T, Wang C, Lan W, Ding J, Cao C (2018) "Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA." Chin.J.Chem., 36, 1241-1248. doi: 10.1002/cjoc.201800508. Apobec3f chimeric catalytic domain in complex with DNA(dc9). SNAP output
5zvb structural protein-DNA X-ray (2.0 Å) Cheng C, Zhang T, Wang C, Lan W, Ding J, Cao C (2018) "Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA." Chin.J.Chem., 36, 1241-1248. doi: 10.1002/cjoc.201800508. Apobec3f chimeric catalytic domain in complex with DNA(dt9). SNAP output
5zx2 transcription-DNA-RNA X-ray (2.8 Å) Li L, Fang C, Zhuang N, Wang T, Zhang Y (2019) "Structural basis for transcription initiation by bacterial ECF sigma factors." Nat Commun, 10, 1153. doi: 10.1038/s41467-019-09096-y. Mycobacterium tuberculosis RNA polymerase transcription initiation complex with ecf sigma factor sigma h and 7nt RNA. SNAP output
5zyt DNA binding protein X-ray (2.702 Å) Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma J, Li J, Gan J (2018) "Structural insights into DNA degradation by human mitochondrial nuclease MGME1." Nucleic Acids Res., 46, 11075-11088. doi: 10.1093/nar/gky855. Crystal structure of human mgme1 with 3' overhang double strand dna3. SNAP output
5zyu DNA binding protein-DNA X-ray (1.752 Å) Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma J, Li J, Gan J (2018) "Structural insights into DNA degradation by human mitochondrial nuclease MGME1." Nucleic Acids Res., 46, 11075-11088. doi: 10.1093/nar/gky855. The crystal structure of humanmgme1 with single strand dna2. SNAP output
5zyv DNA binding protein-DNA X-ray (2.72 Å) Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma J, Li J, Gan J (2018) "Structural insights into DNA degradation by human mitochondrial nuclease MGME1." Nucleic Acids Res., 46, 11075-11088. doi: 10.1093/nar/gky855. Crystal structure of human mgme1 with single strand dna2 and ca2+. SNAP output
6a2h DNA binding protein-DNA X-ray (2.3 Å) Zhang Z, Zhao M, Chen Y, Wang L, Liu Q, Dong Y, Gong Y, Huang L (2019) "Architectural roles of Cren7 in folding crenarchaeal chromatin filament." Mol. Microbiol., 111, 556-569. doi: 10.1111/mmi.14173. Architectural roles of cren7 in folding crenarchaeal chromatin filament. SNAP output
6a2i DNA binding protein-DNA X-ray (2.4 Å) Zhang Z, Zhao M, Chen Y, Wang L, Liu Q, Dong Y, Gong Y, Huang L (2019) "Architectural roles of Cren7 in folding crenarchaeal chromatin filament." Mol. Microbiol., 111, 556-569. doi: 10.1111/mmi.14173. Architectural roles of cren7 in folding crenarchaeal chromatin filament. SNAP output
6a47 DNA binding protein X-ray (1.9 Å) Cheng HL, Lin CT, Huang KW, Wang S, Lin YT, Toh SI, Hsiao YY (2018) "Structural insights into the duplex DNA processing of TREX2." Nucleic Acids Res., 46, 12166-12176. doi: 10.1093/nar/gky970. Structure of trex2 in complex with a y structured dsDNA. SNAP output
6a4b DNA binding protein X-ray (2.7 Å) Cheng HL, Lin CT, Huang KW, Wang S, Lin YT, Toh SI, Hsiao YY (2018) "Structural insights into the duplex DNA processing of TREX2." Nucleic Acids Res., 46, 12166-12176. doi: 10.1093/nar/gky970. Structure of trex2 in complex with a duplex DNA with 2 nucleotide 3'-overhang. SNAP output
6a57 DNA binding protein-DNA X-ray (2.7 Å) Tian Z, Li X, Li M, Wu W, Zhang M, Tang C, Li Z, Liu Y, Chen Z, Yang M, Ma L, Caba C, Tong Y, Lam HM, Dai S, Chen Z (2020) "Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms." Cell Discov, 6, 17. doi: 10.1038/s41421-020-0150-6. Structure of histone demethylase ref6 complexed with DNA. SNAP output
6a5l transcription-RNA-DNA cryo-EM (5.6 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign DNA. SNAP output
6a5n gene regulation-DNA X-ray (2.4 Å) Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J (2018) "Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation." Proc. Natl. Acad. Sci. U.S.A., 115, E8793-E8802. doi: 10.1073/pnas.1809841115. Crystal structure of arabidopsis thaliana suvh6 in complex with methylated DNA. SNAP output
6a5o transcription-RNA-DNA cryo-EM (9.9 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-6) of the nucleosome. SNAP output
6a5p transcription-RNA-DNA cryo-EM (7.0 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-5) of the nucleosome. SNAP output
6a5r transcription-RNA-DNA cryo-EM (8.7 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-2) of the nucleosome. SNAP output
6a5t transcription-RNA-DNA cryo-EM (6.7 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-1) of the nucleosome. SNAP output
6a5u transcription-RNA-DNA cryo-EM (7.6 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign DNA, tilt conformation. SNAP output
6a8r DNA binding protein-DNA X-ray (1.6 Å) Dong X, Zhang H, Cheng N, Li K, Meng G (2019) "DUX4HD2-DNAERGstructure reveals new insight into DUX4-Responsive-Element." Leukemia, 33, 550-553. doi: 10.1038/s41375-018-0273-z. Crystal structure of dux4 hd2 domain associated with erg DNA binding site. SNAP output
6aeb DNA binding protein-RNA X-ray (3.004 Å) Guo M, Ren K, Zhu Y, Tang Z, Wang Y, Zhang B, Huang Z (2019) "Structural insights into a high fidelity variant of SpCas9." Cell Res., 29, 183-192. doi: 10.1038/s41422-018-0131-6. Crystal structure of xcas9 in complex with sgrna and target DNA (aag pam). SNAP output
6aeg DNA binding protein-DNA-RNA X-ray (2.701 Å) Guo M, Ren K, Zhu Y, Tang Z, Wang Y, Zhang B, Huang Z (2019) "Structural insights into a high fidelity variant of SpCas9." Cell Res., 29, 183-192. doi: 10.1038/s41422-018-0131-6. Crystal structure of xcas9 in complex with sgrna and target DNA (gat pam). SNAP output
6ai6 hydrolase-RNA-DNA X-ray (2.7 Å) Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O (2018) "Engineered CRISPR-Cas9 nuclease with expanded targeting space." Science, 361, 1259-1262. doi: 10.1126/science.aas9129. Crystal structure of spcas9-ng. SNAP output
6ajo DNA binding protein X-ray (2.269 Å) Ahn WC, Aroli S, Kim JH, Moon JH, Lee GS, Lee MH, Sang PB, Oh BH, Varshney U, Woo EJ (2019) "Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision." Nat.Chem.Biol., 15, 607-614. doi: 10.1038/s41589-019-0289-3. Complex form of uracil DNA glycosylase x and uracil-DNA.. SNAP output
6ak8 transferase-DNA X-ray (1.74 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Pre-catalytic ternary complex of human DNA polymerase mu with templating adenine and incoming ca-8oxodgtp. SNAP output
6ak9 transferase-DNA X-ray (1.91 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Pre-catalytic ternary complex of human DNA polymerase mu with templating cytosine and incoming ca-8oxodgtp. SNAP output
6akh transferase-DNA X-ray (1.75 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Pre-catalytic ternary complex of human DNA polymerase mu with templating adenine and incoming mn-dumpnpp. SNAP output
6ako DNA binding protein-DNA X-ray (2.396 Å) Chen X, Wei H, Li J, Liang X, Dai S, Jiang L, Guo M, Qu L, Chen Z, Chen L, Chen Y (2019) "Structural basis for DNA recognition by FOXC2." Nucleic Acids Res., 47, 3752-3764. doi: 10.1093/nar/gkz077. Crystal structure of foxc2 dbd bound to dbe2 DNA. SNAP output
6akp DNA binding protein-DNA X-ray (2.323 Å) Chen X, Wei H, Li J, Liang X, Dai S, Jiang L, Guo M, Qu L, Chen Z, Chen L, Chen Y (2019) "Structural basis for DNA recognition by FOXC2." Nucleic Acids Res., 47, 3752-3764. doi: 10.1093/nar/gkz077. Crystal structural of foxc2 DNA binding domain bound to pc promoter. SNAP output
6alf transcription-DNA-RNA cryo-EM (4.1 Å) Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA (2017) "Structural basis of transcription arrest by coliphage HK022 Nun in anEscherichia coliRNA polymerase elongation complex." Elife, 6. doi: 10.7554/eLife.25478. Cryoem structure of crosslinked e.coli RNA polymerase elongation complex. SNAP output
6alg transcription-DNA-RNA cryo-EM (3.7 Å) Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA (2017) "Structural basis of transcription arrest by coliphage HK022 Nun in anEscherichia coliRNA polymerase elongation complex." Elife, 6. doi: 10.7554/eLife.25478. Cryoem structure of hk022 nun - e.coli RNA polymerase elongation complex. SNAP output
6alh transcription-DNA-RNA cryo-EM (4.4 Å) Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA (2017) "Structural basis of transcription arrest by coliphage HK022 Nun in anEscherichia coliRNA polymerase elongation complex." Elife, 6. doi: 10.7554/eLife.25478. Cryoem structure of e.coli RNA polymerase elongation complex. SNAP output
6ama DNA binding protein-DNA X-ray (3.09 Å) Schumacher MA, den Hengst CD, Bush MJ, Le TBK, Tran NT, Chandra G, Zeng W, Travis B, Brennan RG, Buttner MJ (2018) "The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development." Nat Commun, 9, 1139. doi: 10.1038/s41467-018-03576-3. Structure of s. coelicolor-s. venezuelae bldc-smea-ssfa complex to 3.09 angstrom. SNAP output
6amk DNA binding protein-DNA X-ray (3.288 Å) Schumacher MA, den Hengst CD, Bush MJ, Le TBK, Tran NT, Chandra G, Zeng W, Travis B, Brennan RG, Buttner MJ (2018) "The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development." Nat Commun, 9, 1139. doi: 10.1038/s41467-018-03576-3. Structure of streptomyces venezuelae bldc-whii opt complex. SNAP output
6amo transferase-DNA X-ray (2.497 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 7.0. SNAP output
6an2 transferase-DNA X-ray (2.7 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 7.5. SNAP output
6an8 transferase-DNA X-ray (2.596 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 8.0. SNAP output
6anq transferase-DNA X-ray (2.586 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 8.5. SNAP output
6ar1 RNA binding protein-RNA-DNA X-ray (3.01 Å) Stamos JL, Lentzsch AM, Lambowitz AM (2017) "Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications." Mol. Cell, 68, 926-939.e4. doi: 10.1016/j.molcel.2017.10.024. Structure of a thermostable group ii intron reverse transcriptase with template-primer and its functional and evolutionary implications (rt-duplex (nat)). SNAP output
6ar3 RNA binding protein-RNA-DNA X-ray (3.41 Å) Stamos JL, Lentzsch AM, Lambowitz AM (2017) "Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications." Mol. Cell, 68, 926-939.e4. doi: 10.1016/j.molcel.2017.10.024. Structure of a thermostable group ii intron reverse transcriptase with template-primer and its functional and evolutionary implications (rt-duplex (se-met)). SNAP output
6as7 replication-DNA X-ray (2.95 Å) Baranovskiy AG, Duong VN, Babayeva ND, Zhang Y, Pavlov YI, Anderson KS, Tahirov TH (2018) "Activity and fidelity of human DNA polymerase alpha depend on primer structure." J. Biol. Chem., 293, 6824-6843. doi: 10.1074/jbc.RA117.001074. Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an DNA-primed DNA template and dctp. SNAP output
6asb DNA binding protein-DNA X-ray (2.85 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Cxxc and phd-type zinc finger regions of fbxl19 in complex with DNA. SNAP output
6asd DNA binding protein-DNA X-ray (1.85 Å) Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J (2018) "DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants." Structure, 26, 85-95.e3. doi: 10.1016/j.str.2017.11.022. Zinc finger region of human tet1 in complex with cpg DNA. SNAP output
6asw transferase-DNA X-ray (2.605 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 9.0. SNAP output
6asx transcription-DNA-RNA cryo-EM (3.8 Å) Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R (2018) "RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing." Mol. Cell, 69, 802-815.e1. doi: 10.1016/j.molcel.2018.01.018. Cryoem structure of e.coli his pause elongation complex. SNAP output
6avm transferase-DNA X-ray (2.502 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 9.5 with cross-linking to second base template overhang. SNAP output
6avt transferase-DNA X-ray (2.603 Å) Martinez SE, Bauman JD, Das K, Arnold E (2019) "Structure of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA cross-linking site and pH-dependent conformational changes." Protein Sci., 28, 587-597. doi: 10.1002/pro.3559. Structure of hiv-1 reverse transcriptase (rt) ternary complex with a double stranded DNA and an incoming d4ttp at ph 9.5 with cross-linking to first base template overhang. SNAP output
6b0o transcription-DNA X-ray (1.552 Å) Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) "Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites." Nucleic Acids Res., 46, 3864-3877. doi: 10.1093/nar/gkx1274. Zinc finger domain of wt1(-kts form) with 12+1mer oligonucleotide with 3' triplet tgt. SNAP output
6b0p transcription-DNA X-ray (2.077 Å) Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) "Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites." Nucleic Acids Res., 46, 3864-3877. doi: 10.1093/nar/gkx1274. Zinc finger domain of wt1(-kts form) with 12+1mer oligonucleotide with 3' triplet ggt. SNAP output
6b0q transcription-DNA X-ray (2.794 Å) Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) "Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites." Nucleic Acids Res., 46, 3864-3877. doi: 10.1093/nar/gkx1274. Zinc finger domain of wt1(-kts form) with 13+1mer oligonucleotide with 3' triplet tgt. SNAP output
6b0r transcription-DNA X-ray (1.818 Å) Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) "Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites." Nucleic Acids Res., 46, 3864-3877. doi: 10.1093/nar/gkx1274. Zinc finger domain of wt1(-kts form) with m342r mutation and 14+1mer oligonucleotide with 3' triplet tgg. SNAP output
6b19 viral protein-RNA cryo-EM (4.5 Å) Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV (2018) "Architecture of an HIV-1 reverse transcriptase initiation complex." Nature, 557, 118-122. doi: 10.1038/s41586-018-0055-9. Architecture of hiv-1 reverse transcriptase initiation complex core. SNAP output
6b1q DNA binding protein-DNA X-ray (1.9 Å) Hoshika S, Singh I, Switzer C, Molt Jr RW, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA (2018) ""Skinny" and "Fat" DNA: Two New Double Helices." J. Am. Chem. Soc., 140, 11655-11660. doi: 10.1021/jacs.8b05042. Hydrogen bonding complementary, not size complementarity is key in the formation of the double helix. SNAP output
6b1r DNA binding protein-DNA X-ray (1.69 Å) Hoshika S, Singh I, Switzer C, Molt Jr RW, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA (2018) ""Skinny" and "Fat" DNA: Two New Double Helices." J. Am. Chem. Soc., 140, 11655-11660. doi: 10.1021/jacs.8b05042. Hydrogen bonding complementary, not size complementarity is key in the formation of the double helix. SNAP output
6b1s DNA binding protein-DNA X-ray (2.0 Å) Hoshika S, Singh I, Switzer C, Molt Jr RW, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA (2018) ""Skinny" and "Fat" DNA: Two New Double Helices." J. Am. Chem. Soc., 140, 11655-11660. doi: 10.1021/jacs.8b05042. Hydrogen bonding complementary, not size complementarity is key in the formation of the double helix. SNAP output
6b40 recombination cryo-EM (4.3 Å) Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz DG (2019) "Transposon molecular domestication and the evolution of the RAG recombinase." Nature, 569, 79-84. doi: 10.1038/s41586-019-1093-7. Bbragl-3'tir synaptic complex with nicked DNA refined with c2 symmetry. SNAP output
6b44 immune system-RNA-DNA cryo-EM (2.9 Å) Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S (2017) "Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex." Cell, 171, 414-426.e12. doi: 10.1016/j.cell.2017.09.006. cryo-EM structure of type i-f crispr crrna-guided csy surveillance complex with bound target dsDNA. SNAP output
6b6h transcription-transferase-DNA-RNA cryo-EM (3.9 Å) Liu B, Hong C, Huang RK, Yu Z, Steitz TA (2017) "Structural basis of bacterial transcription activation." Science, 358, 947-951. doi: 10.1126/science.aao1923. The cryo-EM structure of a bacterial class i transcription activation complex. SNAP output
6bce hydrolase-DNA X-ray (1.75 Å) McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR (2018) "Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases." Nucleic Acids Res., 46, 11990-12007. doi: 10.1093/nar/gky976. Wild-type i-ltri bound to cognate substrate (pre-cleavage complex). SNAP output
6bcf hydrolase-DNA X-ray (2.92 Å) McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR (2018) "Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases." Nucleic Acids Res., 46, 11990-12007. doi: 10.1093/nar/gky976. I-ltri g183a bound to cognate substrate (pre-cleavage complex). SNAP output
6bcg hydrolase-DNA X-ray (2.9 Å) McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR (2018) "Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases." Nucleic Acids Res., 46, 11990-12007. doi: 10.1093/nar/gky976. I-ltri a28g bound to cognate substrate (pre-cleavage complex). SNAP output
6bch hydrolase-DNA X-ray (3.0 Å) McMurrough TA, Brown C, Zhang K, Junop M, Gloor GB, Edgell DR "I-LtrI E29D bound to cognate substrate (nicked complex)." I-ltri e29d bound to cognate substrate (nicked complex). SNAP output
6bci hydrolase-DNA X-ray (2.28 Å) McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR (2018) "Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases." Nucleic Acids Res., 46, 11990-12007. doi: 10.1093/nar/gky976. Wild-type i-ltri bound to non-cognate c4 substrate (pre-cleavage complex). SNAP output
6bcn hydrolase-DNA X-ray (2.5 Å) McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR (2018) "Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases." Nucleic Acids Res., 46, 11990-12007. doi: 10.1093/nar/gky976. I-ltri e184d bound to cognate substrate (pre-cleavage complex). SNAP output
6bct hydrolase-DNA X-ray (2.73 Å) McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR (2018) "Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases." Nucleic Acids Res., 46, 11990-12007. doi: 10.1093/nar/gky976. I-ltri e184d bound to non-cognate c4 substrate (pre-cleavage complex). SNAP output
6bd0 hydrolase-DNA X-ray (1.45 Å) Laforet M, McMurrough TA, Brown C, Zhang K, Junop M, Gloor GB, Edgell DR "I-OnuI K227Y, D236A bound to cognate substrate (pre-cleavage complex)." I-onui k227y, d236a bound to cognate substrate (pre-cleavage complex). SNAP output
6bda hydrolase-DNA X-ray (1.88 Å) Laforet M, McMurrough T, Brown C, Zhang K, Junop M, Gloor GB, Edgell DR "Wild-type I-OnuI bound to A3G substrate (post-cleavage complex)." Wild-type i-onui bound to a3g substrate (post-cleavage complex). SNAP output
6bdb hydrolase X-ray (1.5 Å) Laforet M, McMurrough TA, Brown C, Junop M, Zhang K, Gloor GB "I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex)." I-onui k227y, d236a bound to a3g substrate (pre-cleavage complex). SNAP output
6bek DNA binding protein-DNA X-ray (1.7 Å) Nanji T, Gehrke EJ, Shen Y, Gloyd M, Zhang X, Firby CD, Huynh A, Razi A, Ortega J, Elliot MA, Guarne A (2019) "Streptomyces IHF uses multiple interfaces to bind DNA." Biochim Biophys Acta Gen Subj, 1863, 129405. doi: 10.1016/j.bbagen.2019.07.014. Structure of sihf bound to an 8bp palindromic DNA. SNAP output
6bel transferase-DNA X-ray (1.898 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with r-isomer of beta-gamma-chf-dctp. SNAP output
6bem transferase-DNA X-ray (1.88 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with s-isomer of beta-gamma-chcl-dctp. SNAP output
6bhj transferase-DNA X-ray (2.81 Å) Tuske S, Zheng J, Olson ED, Ruiz FX, Pascal BD, Bauman JD, Das K, DeStefano JJ, Musier-Forsyth K, Griffin PR, Arnold E (2020) "Integrative Structural Biology Studies of HIV-1 Reverse Transcriptase Binding to a High-Affinity DNA Aptamer." Curr Res Struct Biol. doi: 10.1016/j.crstbi.2020.06.002. Structure of hiv-1 reverse transcriptase bound to a 38-mer hairpin template-primer RNA-DNA aptamer. SNAP output
6bhx DNA binding protein-DNA X-ray (2.936 Å) Dubiel K, Myers AR, Kozlov AG, Yang O, Zhang J, Ha T, Lohman TM, Keck JL (2019) "Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins." J. Mol. Biol., 431, 178-195. doi: 10.1016/j.jmb.2018.11.019. B. subtilis ssba with DNA. SNAP output
6bjs transcription-DNA-RNA cryo-EM (5.5 Å) Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R (2018) "RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing." Mol. Cell, 69, 802-815.e1. doi: 10.1016/j.molcel.2018.01.018. Cryoem structure of e.coli his pause elongation complex without pause hairpin. SNAP output
6bkf ligase-DNA X-ray (3.25 Å) Kaminski AM, Tumbale PP, Schellenberg MJ, Williams RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K (2018) "Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis." Nat Commun, 9, 2642. doi: 10.1038/s41467-018-05024-8. Lysyl-adenylate form of human ligiv catalytic domain with bound DNA substrate in open conformation. SNAP output
6bkg ligase-DNA X-ray (2.402 Å) Kaminski AM, Tumbale PP, Schellenberg MJ, Williams RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K (2018) "Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis." Nat Commun, 9, 2642. doi: 10.1038/s41467-018-05024-8. Human ligiv catalytic domain with bound DNA-adenylate intermediate in closed conformation. SNAP output
6blo transcription X-ray (3.401 Å) Wang W, Walmacq C, Chong J, Kashlev M, Wang D (2018) "Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II." Proc. Natl. Acad. Sci. U.S.A., 115, E2538-E2545. doi: 10.1073/pnas.1722050115. Pol ii elongation complex with an abasic lesion at i+1 position. SNAP output
6blp transcription X-ray (3.203 Å) Wang W, Walmacq C, Chong J, Kashlev M, Wang D (2018) "Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II." Proc. Natl. Acad. Sci. U.S.A., 115, E2538-E2545. doi: 10.1073/pnas.1722050115. Pol ii elongation complex with an abasic lesion at i+1 position, soaking ampcpp. SNAP output
6blw DNA binding protein-DNA X-ray (1.835 Å) Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X, Cheng X (2018) "Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites." Nucleic Acids Res., 46, 3864-3877. doi: 10.1093/nar/gkx1274. Zinc finger domain of wt1(+kts form) with m342r mutation and 17+1mer oligonucleotide with triplet ggt. SNAP output
6bm2 transcription X-ray (3.403 Å) Wang W, Walmacq C, Chong J, Kashlev M, Wang D (2018) "Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II." Proc. Natl. Acad. Sci. U.S.A., 115, E2538-E2545. doi: 10.1073/pnas.1722050115. Pol ii elongation complex with an abasic lesion at i-1 position. SNAP output
6bm4 transcription X-ray (2.951 Å) Wang W, Walmacq C, Chong J, Kashlev M, Wang D (2018) "Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II." Proc. Natl. Acad. Sci. U.S.A., 115, E2538-E2545. doi: 10.1073/pnas.1722050115. Pol ii elongation complex with an abasic lesion at i-1 position,soaking umpnpp. SNAP output
6boq DNA binding protein-DNA X-ray (1.96 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an a-a mismatch adjacent the thf. SNAP output
6bor DNA binding protein-DNA X-ray (1.84 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an g-g mismatch adjacent the thf. SNAP output
6bos DNA binding protein-DNA X-ray (2.304 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an a-c mismatch adjacent the thf. SNAP output
6bot DNA binding protein-DNA X-ray (2.3 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an c-c mismatch adjacent the thf. SNAP output
6bou DNA binding protein-DNA X-ray (2.538 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an t-c mismatch adjacent the thf. SNAP output
6bov DNA binding protein-DNA X-ray (1.975 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an a-g mismatch adjacent the thf. SNAP output
6bow DNA binding protein-DNA X-ray (1.59 Å) Fairlamb MS, Whitaker AM, Freudenthal BD (2018) "Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches." Acta Crystallogr D Struct Biol, 74, 760-768. doi: 10.1107/S2059798318003340. Human ape1 substrate complex with an t-t mismatch adjacent the thf. SNAP output
6bqf transferase-transcription X-ray (3.35 Å) Wang W, Walmacq C, Chong J, Kashlev M, Wang D (2018) "Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II." Proc. Natl. Acad. Sci. U.S.A., 115, E2538-E2545. doi: 10.1073/pnas.1722050115. Pol ii elongation complex with 'dt-ap' at i+1, i-1 position. SNAP output
6bqu DNA binding protein-DNA X-ray (2.5 Å) Pufall MA "General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry." Human gr (418-507) in complex with monomeric DNA binding site. SNAP output
6brr transferase-DNA X-ray (2.97 Å) Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J (2018) "Structural basis for DNMT3A-mediated de novo DNA methylation." Nature, 554, 387-391. doi: 10.1038/nature25477. Crystal structure of dnmt3a (r836a)-dnmt3l in complex with DNA containing two cpg sites. SNAP output
6brx replication X-ray (2.8 Å) Jha V, Ling H (2018) "Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender." J. Mol. Biol., 430, 1577-1589. doi: 10.1016/j.jmb.2018.04.023. Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion. SNAP output
6bs1 replication X-ray (3.15 Å) Jha V, Ling H (2018) "Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender." J. Mol. Biol., 430, 1577-1589. doi: 10.1016/j.jmb.2018.04.023. Crystal structure of human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion. SNAP output
6bse gene regulation X-ray (2.35 Å) Pufall MA, Zhang L "General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry." Glucocorticoid receptor bound to high cooperativity monomer sequence. SNAP output
6bsf DNA binding protein-DNA X-ray (2.4 Å) Pufall MA "General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry." Human gr (418-507) in complex with monomeric DNA binding site. SNAP output
6bsg viral protein-DNA-RNA-inhibitor X-ray (2.44 Å) Tian L, Kim MS, Li H, Wang J, Yang W (2018) "Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid." Proc. Natl. Acad. Sci. U.S.A., 115, 507-512. doi: 10.1073/pnas.1719746115. Structure of hiv-1 rt complexed with RNA-DNA hybrid in an RNA hydrolysis-off mode. SNAP output
6bsh viral protein-DNA-RNA-inhibitor X-ray (2.649 Å) Tian L, Kim MS, Li H, Wang J, Yang W (2018) "Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid." Proc. Natl. Acad. Sci. U.S.A., 115, 507-512. doi: 10.1073/pnas.1719746115. Structure of hiv-1 rt complexed with RNA-DNA hybrid in the RNA hydrolysis mode. SNAP output
6bsi viral protein-DNA-RNA-inhibitor X-ray (3.25 Å) Tian L, Kim MS, Li H, Wang J, Yang W (2018) "Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid." Proc. Natl. Acad. Sci. U.S.A., 115, 507-512. doi: 10.1073/pnas.1719746115. Structure of hiv-1 rt complexed with an RNA-DNA hybrid containing the polypurine-tract sequence. SNAP output
6bsj viral protein-DNA-RNA-inhibitor X-ray (2.89 Å) Tian L, Kim MS, Li H, Wang J, Yang W (2018) "Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid." Proc. Natl. Acad. Sci. U.S.A., 115, 507-512. doi: 10.1073/pnas.1719746115. Structure of hiv-1 rt complexed with an RNA-DNA hybrid sequence non-preferred for RNA hydrolysis. SNAP output
6bte transferase,lyase-DNA X-ray (2.2 Å) Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S, Loria JP, Sweasy JB (2018) "I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity." Nucleic Acids Res., 46, 10740-10756. doi: 10.1093/nar/gky825. DNA polymerase beta i260q binary complex. SNAP output
6btf transferase,lyase-DNA X-ray (1.75 Å) Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S, Loria JP, Sweasy JB (2018) "I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity." Nucleic Acids Res., 46, 10740-10756. doi: 10.1093/nar/gky825. DNA polymerase beta i260q ternary complex. SNAP output
6bux hydrolase-DNA X-ray (1.856 Å) Maiti A, Myint W, Kanai T, Delviks-Frankenberry K, Sierra Rodriguez C, Pathak VK, Schiffer CA, Matsuo H (2018) "Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA." Nat Commun, 9, 2460. doi: 10.1038/s41467-018-04872-8. Crystal structure of apobec3g catalytic domain complex with substrate ssDNA. SNAP output
6buz structural protein-DNA cryo-EM (3.92 Å) Chittori S, Hong J, Saunders H, Feng H, Ghirlando R, Kelly AE, Bai Y, Subramaniam S (2018) "Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N." Science, 359, 339-343. doi: 10.1126/science.aar2781. cryo-EM structure of cenp-a nucleosome in complex with kinetochore protein cenp-n. SNAP output
6bwy hydrolase X-ray (2.9 Å) Ziegler SJ, Liu C, Landau M, Buzovetsky O, Desimmie BA, Zhao Q, Sasaki T, Burdick RC, Pathak VK, Anderson KS, Xiong Y (2018) "Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies." PLoS ONE, 13, e0195048. doi: 10.1371/journal.pone.0195048. DNA substrate selection by apobec3g. SNAP output
6byy transcription-DNA X-ray (2.3 Å) Lei X, Kou Y, Fu Y, Rajashekar N, Shi H, Wu F, Xu J, Luo Y, Chen L (2018) "The Cancer Mutation D83V Induces an alpha-Helix to beta-Strand Conformation Switch in MEF2B." J. Mol. Biol., 430, 1157-1172. doi: 10.1016/j.jmb.2018.02.012. Mef2 chimera-DNA complex. SNAP output
6bz1 transcription-DNA X-ray (2.97 Å) Lei X, Kou Y, Fu Y, Rajashekar N, Shi H, Wu F, Xu J, Luo Y, Chen L (2018) "The Cancer Mutation D83V Induces an alpha-Helix to beta-Strand Conformation Switch in MEF2B." J. Mol. Biol., 430, 1157-1172. doi: 10.1016/j.jmb.2018.02.012. Mef2 chimera d83v mutant-DNA complex. SNAP output
6bzo transcription-DNA-antibiotic cryo-EM (3.38 Å) Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA (2018) "Fidaxomicin jamsMycobacterium tuberculosisRNA polymerase motions needed for initiation via RbpA contacts." Elife, 7. doi: 10.7554/eLife.34823. Mtb rnap holo-rbpa-fidaxomicin-upstream fork DNA. SNAP output
6c04 transcription-DNA cryo-EM (3.27 Å) Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA (2018) "Fidaxomicin jamsMycobacterium tuberculosisRNA polymerase motions needed for initiation via RbpA contacts." Elife, 7. doi: 10.7554/eLife.34823. Mtb rnap holo-rbpa-double fork DNA -closed clamp. SNAP output
6c0w structural protein-DNA cryo-EM (4.0 Å) Pentakota S, Zhou K, Smith C, Maffini S, Petrovic A, Morgan GP, Weir JR, Vetter IR, Musacchio A, Luger K (2017) "Decoding the centromeric nucleosome through CENP-N." Elife, 6. doi: 10.7554/eLife.33442. cryo-EM structure of human kinetochore protein cenp-n with the centromeric nucleosome containing cenp-a. SNAP output
6c1a DNA binding protein-DNA X-ray (2.05 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with methylated DNA. SNAP output
6c1t DNA binding protein-DNA X-ray (1.84 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with a partially methylated DNA. SNAP output
6c1u DNA binding protein-DNA X-ray (2.3 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with a deoxy-oligonucleotide. SNAP output
6c1v DNA binding protein-DNA X-ray (2.3 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with double-stranded DNA. SNAP output
6c1y DNA binding protein-DNA X-ray (2.3 Å) Lei M, Tempel W, Chen S, Liu K, Min J (2019) "Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain." Biochim Biophys Acta Gene Regul Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409. Mbd of human mecp2 in complex with methylated DNA. SNAP output
6c2f DNA binding protein-DNA X-ray (2.65 Å) Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C, Edwards AM, Min J, Structural Genomics Consortium "MBD2 in complex with methylated DNA." Mbd2 in complex with methylated DNA. SNAP output
6c2s DNA binding protein-DNA X-ray (2.85 Å) Cogan DP, Baraquet C, Harwood CS, Nair SK (2018) "Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism, inRhodopseudomonas palustris." J. Biol. Chem., 293, 11727-11735. doi: 10.1074/jbc.RA118.003561. Transcriptional repressor, cour, bound to a 23-mer DNA duplex. SNAP output
6c31 DNA binding protein-DNA X-ray (3.0 Å) Samanovic MI, Hsu HC, Jones MB, Jones V, McNeil MR, Becker SH, Jordan AT, Strnad M, Xu C, Jackson M, Li H, Darwin KH (2018) "Cytokinin Signaling in Mycobacterium tuberculosis." MBio, 9. doi: 10.1128/mBio.00989-18. Crystal structure of tetr family protein rv0078 in complex with DNA. SNAP output
6c66 DNA binding protein-DNA-RNA cryo-EM (3.66 Å) Xiao Y, Luo M, Dolan AE, Liao M, Ke A (2018) "Structure basis for RNA-guided DNA degradation by Cascade and Cas3." Science, 361. doi: 10.1126/science.aat0839. Crispr RNA-guided surveillance complex, pre-nicking. SNAP output
6c6s transcription-DNA-RNA cryo-EM (3.7 Å) Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA (2018) "Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators." Cell, 173, 1650-1662.e14. doi: 10.1016/j.cell.2018.05.017. Cryoem structure of e.coli RNA polymerase elongation complex bound with rfah. SNAP output
6c6t transcription-DNA-RNA cryo-EM (3.5 Å) Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA (2018) "Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators." Cell, 173, 1650-1662.e14. doi: 10.1016/j.cell.2018.05.017. Cryoem structure of e.coli RNA polymerase elongation complex bound with rfah. SNAP output
6c6u transcription-DNA-RNA cryo-EM (3.7 Å) Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA (2018) "Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators." Cell, 173, 1650-1662.e14. doi: 10.1016/j.cell.2018.05.017. Cryoem structure of e.coli RNA polymerase elongation complex bound with nusg. SNAP output
6ca0 transcription-DNA cryo-EM (5.75 Å) Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS (2018) "Cryo-EM structure ofEscherichia colisigma70RNA polymerase and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation." J. Biol. Chem., 293, 7367-7375. doi: 10.1074/jbc.RA118.002161. cryo-EM structure of e. coli rnap sigma70 open complex. SNAP output
6cc8 DNA binding protein-DNA X-ray (1.95 Å) Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J (2019) "Structural analyses reveal that MBD3 is a methylated CG binder." Febs J., 286, 3240-3254. doi: 10.1111/febs.14850. Crystal structure mbd3 mbd domain in complex with methylated cpg DNA. SNAP output
6cce transcription-DNA-antibiotic X-ray (3.05 Å) Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF (2018) "Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism." Nat Commun, 9, 4147. doi: 10.1038/s41467-018-06587-2. Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor kanglemycin a. SNAP output
6ccg transcription X-ray (1.9 Å) Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J (2019) "Structural analyses reveal that MBD3 is a methylated CG binder." Febs J., 286, 3240-3254. doi: 10.1111/febs.14850. Crystal structure mbd3 mbd domain in complex with methylated cpg DNA. SNAP output
6ccv transcription X-ray (3.05 Å) Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF (2018) "Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism." Nat Commun, 9, 4147. doi: 10.1038/s41467-018-06587-2. Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor rifampicin. SNAP output
6ceu transcription-DNA X-ray (2.005 Å) Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J (2019) "Structural analyses reveal that MBD3 is a methylated CG binder." Febs J., 286, 3240-3254. doi: 10.1111/febs.14850. Mbd3 mbd in complex with methylated, non-palindromic cpg DNA: alternative interpretation of crystallographic data. SNAP output
6cfi DNA binding protein-DNA X-ray (3.36 Å) Paul D, Mu H, Zhao H, Ouerfelli O, Jeffrey PD, Broyde S, Min JH (2019) "Structure and mechanism of pyrimidine-pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex." Nucleic Acids Res., 47, 6015-6028. doi: 10.1093/nar/gkz359. Crystal structure of rad4-rad23 bound to a 6-4 photoproduct uv lesion. SNAP output
6cg0 recombination cryo-EM (3.17 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. cryo-EM structure of mouse rag1-2 hfc complex (3.17 a). SNAP output
6cg8 DNA binding protein-DNA X-ray (2.299 Å) Guo MS, Haakonsen DL, Zeng W, Schumacher MA, Laub MT (2018) "A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication." Cell, 175, 583. doi: 10.1016/j.cell.2018.08.029. Structure of c. crescentus gapr-DNA. SNAP output
6chv antitoxin-DNA X-ray (2.9 Å) Schureck MA, Meisner J, Hoffer ED, Wang D, Onuoha N, Ei Cho S, Lollar 3rd P, Dunham CM (2019) "Structural basis of transcriptional regulation by the HigA antitoxin." Mol.Microbiol., 111, 1449-1462. doi: 10.1111/mmi.14229. Proteus vulgaris higa antitoxin bound to DNA. SNAP output
6cij recombination-DNA cryo-EM (3.9 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. cryo-EM structure of mouse rag1-2 hfc complex containing partial hmgb1 linker(3.9 a). SNAP output
6cik recombination-DNA X-ray (3.15 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Pre-reaction complex, rag1(e962q)-2-intact-nicked 12-23rss complex in mn2+. SNAP output
6cil recombination-DNA X-ray (4.15 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Pre-reaction complex, rag1(e962q)-2-intact-intact 12-23rss complex in mn2+. SNAP output
6cim recombination-DNA X-ray (3.6 Å) Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018) "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008. Pre-reaction complex, rag1(e962q)-2-nicked-intact 12-23rss complex in mn2+. SNAP output
6cly transferase, lyase-DNA X-ray (2.186 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8-ClG as the template base in a 1-nucleotide gapped DNA." Structure of human DNA polymerase beta complexed with 8-clg as the template base in a 1-nucleotide gapped DNA. SNAP output
6cnb transcription-DNA cryo-EM (4.1 Å) Han Y, Yan C, Fishbain S, Ivanov I, He Y (2018) "Structural visualization of RNA polymerase III transcription machineries." Cell Discov, 4, 40. doi: 10.1038/s41421-018-0044-z. Yeast RNA polymerase iii initial transcribing complex. SNAP output
6cnc transcription-DNA cryo-EM (4.1 Å) Han Y, Yan C, Fishbain S, Ivanov I, He Y (2018) "Structural visualization of RNA polymerase III transcription machineries." Cell Discov, 4, 40. doi: 10.1038/s41421-018-0044-z. Yeast RNA polymerase iii open complex. SNAP output
6cnd transcription-DNA cryo-EM (4.8 Å) Han Y, Yan C, Fishbain S, Ivanov I, He Y (2018) "Structural visualization of RNA polymerase III transcription machineries." Cell Discov, 4, 40. doi: 10.1038/s41421-018-0044-z. Yeast RNA polymerase iii natural open complex (noc). SNAP output
6cnf transcription-DNA cryo-EM (4.5 Å) Han Y, Yan C, Fishbain S, Ivanov I, He Y (2018) "Structural visualization of RNA polymerase III transcription machineries." Cell Discov, 4, 40. doi: 10.1038/s41421-018-0044-z. Yeast RNA polymerase iii elongation complex. SNAP output
6cnp transcription-DNA X-ray (2.1 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Crystal structure of mbd2 complex with methylated cpg island. SNAP output
6cnq transcription-DNA X-ray (2.151 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with methylated DNA. SNAP output
6cpq transferase-DNA X-ray (1.93 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP." Structure of human DNA polymerase beta complexed with 8-clg in the template base paired with incoming non-hydrolyzable ctp. SNAP output
6cq2 isomerase-DNA X-ray (3.004 Å) Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC (2018) "Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site." Nucleic Acids Res., 46, 7296-7308. doi: 10.1093/nar/gky492. Crystal structure of mycobacterium tuberculosis topoisomerase i in complex with oligonucleotide mts2-12 and magnesium. SNAP output
6cqi isomerase-DNA X-ray (2.42 Å) Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC (2018) "Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site." Nucleic Acids Res., 46, 7296-7308. doi: 10.1093/nar/gky492. 2.42a crystal structure of mycobacterium tuberculosis topoisomerase i in complex with an oligonucleotide mts2-11. SNAP output
6cr3 transcription-DNA X-ray (1.95 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cbr2, beta, gamma datp analogue. SNAP output
6cr4 transferase-DNA X-ray (1.8 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with datp. SNAP output
6cr5 transferase-DNA X-ray (1.982 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ch2-beta, gamma datp analogue. SNAP output
6cr6 transferase-DNA X-ray (2.097 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ch-ch3, beta, gamma datp analogue. SNAP output
6cr7 transferase-DNA X-ray (2.29 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chf, beta, gamma datp analogue. SNAP output
6cr8 transferase-DNA X-ray (2.05 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chcl (r & s isomers), beta, gamma datp analogue. SNAP output
6cr9 transferase-DNA X-ray (1.96 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cfcl, beta, gamma datp analogue. SNAP output
6crb transferase-DNA X-ray (2.151 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cf2, beta, gamma datp analogue. SNAP output
6crc transferase-DNA X-ray (2.3 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ccl2, beta, gamma datp analogue. SNAP output
6crh transferase, lyase-DNA X-ray (2.327 Å) Kou Y, Koag MC, Lee S (2019) "Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion." Molecules, 24. doi: 10.3390/molecules24193507. Structure of human DNA polymerase beta complexed with 8-clg in the template base paired with incoming non-hydrolyzable gtp. SNAP output
6crm hydrolase-DNA X-ray (2.19 Å) Voter AF, Qiu Y, Tippana R, Myong S, Keck JL (2018) "A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases." Nat Commun, 9, 4201. doi: 10.1038/s41467-018-06751-8. Crystal structure of recq catalytic core from c. sakazakii bound to an unfolded g-quadruplex. SNAP output
6cro gene regulation-DNA X-ray (3.0 Å) Albright RA, Matthews BW (1998) "Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution." J.Mol.Biol., 280, 137-151. doi: 10.1006/jmbi.1998.1848. Crystal structure of lambda-cro bound to a consensus operator at 3.0 angstrom resolution. SNAP output
6cst replication, transferase-DNA X-ray (2.0 Å) Jha V, Ling H (2018) "2.0 angstrom resolution crystal structure of human pol kappa reveals a new catalytic function of N-clasp in DNA replication." Sci Rep, 8, 15125. doi: 10.1038/s41598-018-33371-5. Structure of human DNA polymerase kappa with DNA. SNAP output
6ct9 transferase-DNA X-ray (2.26 Å) Zhou W, Whiteley AT, de Oliveira Mann CC, Morehouse BR, Nowak RP, Fischer ES, Gray NS, Mekalanos JJ, Kranzusch PJ (2018) "Structure of the Human cGAS-DNA Complex Reveals Enhanced Control of Immune Surveillance." Cell, 174, 300-311.e11. doi: 10.1016/j.cell.2018.06.026. Structure of the human cgas-DNA complex. SNAP output
6cta transferase-DNA X-ray (2.779 Å) Zhou W, Whiteley AT, de Oliveira Mann CC, Morehouse BR, Nowak RP, Fischer ES, Gray NS, Mekalanos JJ, Kranzusch PJ (2018) "Structure of the Human cGAS-DNA Complex Reveals Enhanced Control of Immune Surveillance." Cell, 174, 300-311.e11. doi: 10.1016/j.cell.2018.06.026. Structure of the human cgas-DNA complex with atp. SNAP output
6cti transcription-DNA X-ray (2.001 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ccl2, beta, gamma dttp analogue. SNAP output
6ctj transcription-DNA X-ray (2.1 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chch3, beta, gamma dttp analogue. SNAP output
6ctk transcription-DNA X-ray (2.153 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chf-r-s isomers, beta, gamma dttp analogue. SNAP output
6ctl transcription-DNA X-ray (2.0 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chcl-r-s isomers, beta, gamma dttp analogue. SNAP output
6ctm transcription-DNA X-ray (2.101 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chcl(r-isomer), beta, gamma dttp analogue. SNAP output
6ctn transcription-DNA X-ray (1.92 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cfcl,beta-gamma dttp analogue. SNAP output
6cto transcription-DNA X-ray (2.04 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cf2, beta, gamma dttp analogue. SNAP output
6ctp transcription-DNA X-ray (2.2 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ch2, beta, gamma dttp analogue. SNAP output
6ctq transcription-DNA X-ray (1.87 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with dctp. SNAP output
6ctr transcription-DNA X-ray (1.85 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chf (r & s isomers), beta, gamma dctp analogue. SNAP output
6ctt transcription-DNA X-ray (2.0 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chcl (r & s isomers, beta, gamma dctp analogue. SNAP output
6ctu transcription-DNA X-ray (1.9 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cfcl, beta, gamma dctp analogue. SNAP output
6ctv transcription-DNA X-ray (2.02 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cf2, beta, gamma dctp analogue. SNAP output
6ctw transcription-DNA X-ray (1.981 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with ccl2, beta, gamma dctp analogue. SNAP output
6ctx transcription-DNA X-ray (2.02 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with cbr2, beta, gamma dctp analogue. SNAP output
6cu9 transferase, lyase-DNA X-ray (2.04 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP and MANGANESE." Structure of human DNA polymerase beta complexed with 8-clg in the template base paired with incoming non-hydrolyzable ctp and manganese. SNAP output
6cua transferase, lyase-DNA X-ray (2.17 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP and MANGANESE." Structure of human DNA polymerase beta complexed with 8-clg in the template base paired with incoming non-hydrolyzable gtp and manganese. SNAP output
6cub transferase, lyase-DNA X-ray (2.05 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable ATP and MANGANESE." Structure of human DNA polymerase beta complexed with 8-clg in the template base paired with incoming non-hydrolyzable atp and manganese. SNAP output
6cuu transcription-DNA-antibiotic X-ray (2.994 Å) Mosaei H, Molodtsov V, Kepplinger B, Harbottle J, Moon CW, Jeeves RE, Ceccaroni L, Shin Y, Morton-Laing S, Marrs ECL, Wills C, Clegg W, Yuzenkova Y, Perry JD, Bacon J, Errington J, Allenby NEE, Hall MJ, Murakami KS, Zenkin N (2018) "Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis." Mol. Cell, 72, 263-274.e5. doi: 10.1016/j.molcel.2018.08.028. Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic kanglemycin a. SNAP output
6cvo hydrolase-DNA-RNA X-ray (2.4 Å) Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS (2018) "Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease." EMBO J., 37. doi: 10.15252/embj.201798875. Human aprataxin (aptx) bound to nicked RNA-DNA, amp and zn product complex. SNAP output
6cvp hydrolase-DNA-RNA X-ray (1.999 Å) Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS (2018) "Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease." EMBO J., 37. doi: 10.15252/embj.201798875. Human aprataxin (aptx) r199h bound to RNA-DNA, amp and zn product complex. SNAP output
6cvq hydrolase-DNA-RNA X-ray (1.65 Å) Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS (2018) "Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease." EMBO J., 37. doi: 10.15252/embj.201798875. Human aprataxin (aptx) h201q bound to RNA-DNA, amp and zn product complex. SNAP output
6cvr hydrolase-DNA-RNA X-ray (1.88 Å) Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS (2018) "Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease." EMBO J., 37. doi: 10.15252/embj.201798875. Human aprataxin (aptx) s242n bound to RNA-DNA, amp and zn product complex. SNAP output
6cvs hydrolase-DNA X-ray (2.11 Å) Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS (2018) "Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease." EMBO J., 37. doi: 10.15252/embj.201798875. Human aprataxin (aptx) l248m bound to DNA, amp and zn product. SNAP output
6cvt hydrolase-DNA-RNA X-ray (2.941 Å) Tumbale P, Schellenberg MJ, Mueller GA, Fairweather E, Watson M, Little JN, Krahn J, Waddell I, London RE, Williams RS (2018) "Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease." EMBO J., 37. doi: 10.15252/embj.201798875. Human aprataxin (aptx) v263g bound to RNA-DNA, amp and zn product complex. SNAP output
6d0m transferase-DNA X-ray (1.832 Å) Rechkoblit O, Choudhury JR, Buku A, Prakash L, Prakash S, Aggarwal AK (2018) "Structural basis for polymerase eta-promoted resistance to the anticancer nucleoside analog cytarabine." Sci Rep, 8, 12702. doi: 10.1038/s41598-018-30796-w. Polymerase eta post-insertion binary complex with cytarabine (arac). SNAP output
6d0z transferase X-ray (1.75 Å) Rechkoblit O, Choudhury JR, Buku A, Prakash L, Prakash S, Aggarwal AK (2018) "Structural basis for polymerase eta-promoted resistance to the anticancer nucleoside analog cytarabine." Sci Rep, 8, 12702. doi: 10.1038/s41598-018-30796-w. Polymerase eta cytarabine (arac) extension ternary complex. SNAP output
6d1t DNA binding protein-DNA X-ray (2.25 Å) Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C, Edwards AM, Min J, Structural Genomics Consortium "Complex of MBD1-MBD and methylated DNA." Complex of mbd1-mbd and methylated DNA. SNAP output
6d5f virus cryo-EM (3.7 Å) Liu Y, Osinski T, Wang F, Krupovic M, Schouten S, Kasson P, Prangishvili D, Egelman EH (2018) "Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile." Nat Commun, 9, 3360. doi: 10.1038/s41467-018-05684-6. cryo-EM reconstruction of membrane-enveloped filamentous virus sfv1 (sulfolobus filamentous virus 1). SNAP output
6d6q hydrolase cryo-EM (3.45 Å) Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia MA, Lima CD (2018) "Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex." Cell, 173, 1663. doi: 10.1016/j.cell.2018.05.041. Human nuclear exosome-mtr4 RNA complex - overall reconstruction. SNAP output
6d6r hydrolase cryo-EM (3.45 Å) Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia MA, Lima CD (2018) "Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex." Cell, 173, 1663. doi: 10.1016/j.cell.2018.05.041. Human nuclear exosome-mtr4 RNA complex - composite map after focused reconstruction. SNAP output
6d6v replication cryo-EM (4.8 Å) Jiang J, Wang Y, Susac L, Chan H, Basu R, Zhou ZH, Feigon J (2018) "Structure of Telomerase with Telomeric DNA." Cell, 173, 1179-1190.e13. doi: 10.1016/j.cell.2018.04.038. Cryoem structure of tetrahymena telomerase with telomeric DNA at 4.8 angstrom resolution. SNAP output
6d8a RNA binding protein X-ray (2.251 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Rsago ternary complex with guide RNA and target DNA containing a-a bulge within the seed segment of the target strand. SNAP output
6d8f RNA binding protein X-ray (2.15 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Rsago ternary complex with guide RNA and target DNA containing t-t bulge within the seed segment. SNAP output
6d8p RNA binding protein X-ray (2.1 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Ternary rsago complex containing guide RNA paired with target DNA. SNAP output
6d92 RNA binding protein X-ray (1.81 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Ternary rsago complex with guide RNA and target DNA containing a-a non-canonical pair at position 3. SNAP output
6d95 RNA binding protein X-ray (1.85 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Ternary rsago complex with guide RNA paired and target DNA containing a8-a8' non-canonical pair. SNAP output
6d9k RNA binding protein-RNA-DNA X-ray (2.0 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Ternary rsago complex with guide RNA and target DNA containing a-g non-canonical pair. SNAP output
6d9l RNA binding protein-RNA-DNA X-ray (2.6 Å) Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ (2018) "Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA." Cell Rep, 24, 453-462. doi: 10.1016/j.celrep.2018.06.021. Ternary rsago complex with guide RNA and target DNA containing g-a non-canonical pair. SNAP output
6dbi recombination-DNA cryo-EM (3.4 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss nicked DNA intermediates. SNAP output
6dbj recombination-DNA cryo-EM (3.0 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss nicked DNA intermediates. SNAP output
6dbl recombination-DNA cryo-EM (5.001 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas. SNAP output
6dbo recombination-DNA cryo-EM (4.4 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas. SNAP output
6dbq recombination-DNA cryo-EM (4.22 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas. SNAP output
6dbr recombination-DNA cryo-EM (4.0 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with one melted rss and one unmelted rss. SNAP output
6dbt recombination-DNA cryo-EM (4.3 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas. SNAP output
6dbu recombination-DNA cryo-EM (3.9 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas. SNAP output
6dbv recombination-DNA cryo-EM (4.291 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas. SNAP output
6dbw recombination-DNA cryo-EM (4.7 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss substrate DNA. SNAP output
6dbx recombination-DNA cryo-EM (4.2 Å) Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H (2018) "DNA melting initiates the RAG catalytic pathway." Nat. Struct. Mol. Biol., 25, 732-742. doi: 10.1038/s41594-018-0098-5. cryo-EM structure of rag in complex with 12-rss substrate DNA. SNAP output
6dcf transcription-DNA-antibiotic X-ray (3.45 Å) Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF (2018) "Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism." Nat Commun, 9, 4147. doi: 10.1038/s41467-018-06587-2. Crystal structure of a mycobacterium smegmatis transcription initiation complex with rifampicin-resistant RNA polymerase and bound to kanglemycin a. SNAP output
6df5 DNA binding protein-DNA X-ray (1.819 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences." Biochemistry. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs). SNAP output
6df8 DNA binding protein-DNA X-ray (2.536 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences." Biochemistry. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs), ph 6.5. SNAP output
6df9 DNA binding protein-DNA X-ray (2.319 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences." Biochemistry. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) e535q zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs). SNAP output
6dfa DNA binding protein-DNA X-ray (1.908 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences." Biochemistry. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) e535a zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs). SNAP output
6dfb DNA binding protein-DNA X-ray (1.66 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences." Biochemistry. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) k539a zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs). SNAP output
6dfc DNA binding protein-DNA X-ray (1.85 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences." Biochemistry. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) zinc finger DNA binding domain in complex with the specific kaiso binding sequence (kbs) with a t-to-u substitution. SNAP output
6dfy DNA binding protein-DNA X-ray (2.623 Å) Aihara H, Shi K, Lee JK, Bosnakovski D, Kyba M (2018) "Comment on structural basis of DUX4/IGH-driven transactivation." Leukemia, 32, 2090-2092. doi: 10.1038/s41375-018-0217-7. Remodeled crystal structure of DNA-bound dux4-hd2. SNAP output
6dg0 RNA binding protein-DNA X-ray (2.457 Å) Soufari H, Mackereth CD "Structure of MEC-8 RRM2 in complex with AGCACA." Mec-8 c-terminal rrm domain bound to agcaca. SNAP output
6dgd DNA binding protein-DNA X-ray (2.823 Å) Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL (2018) "Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase." Proc. Natl. Acad. Sci. U.S.A., 115, E9075-E9084. doi: 10.1073/pnas.1809842115. Pria helicase bound to dsDNA of a DNA replication fork. SNAP output
6dia DNA binding protein-DNA X-ray (1.969 Å) Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH (2019) "A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition." Nucleic Acids Res., 47, 3197-3207. doi: 10.1093/nar/gkz002. DNA polymerase beta substrate complex with templating cytosine and incoming fapy-dgtp analog. SNAP output
6dic DNA binding protein-DNA X-ray (1.992 Å) Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH (2019) "A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition." Nucleic Acids Res., 47, 3197-3207. doi: 10.1093/nar/gkz002. D276g DNA polymerase beta substrate complex with templating cytosine and incoming fapy-dgtp analog. SNAP output
6dks transcription-DNA X-ray (2.78 Å) Yuan Z, VanderWielen BD, Giaimo BD, Pan L, Collins CE, Turkiewicz A, Hein K, Oswald F, Borggrefe T, Kovall RA (2019) "Structural and Functional Studies of the RBPJ-SHARP Complex Reveal a Conserved Corepressor Binding Site." Cell Rep, 26, 845-854.e6. doi: 10.1016/j.celrep.2018.12.097. Structure of the rbpj-sharp-DNA repressor complex. SNAP output
6dmn hydrolase-DNA-RNA X-ray (1.27 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: soaked in 2 mm ca2+ and 200 mm k+ at 21 c. SNAP output
6dmv hydrolase-DNA-RNA X-ray (1.52 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: soaked for 40 s in 2 mm mg2+ and 200 mm k+ at 21 c. SNAP output
6dnw DNA binding protein X-ray (2.849 Å) Li H, Sharp R, Rutherford K, Gupta K, Van Duyne GD (2018) "Serine Integrase attP Binding and Specificity." J. Mol. Biol., 430, 4401-4418. doi: 10.1016/j.jmb.2018.09.007. Sequence requirements of the listeria innocua prophage attp site. SNAP output
6do8 hydrolase-DNA-RNA X-ray (1.414 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 80 s at 21 c. SNAP output
6do9 hydrolase-DNA-RNA X-ray (1.36 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 120 s at 21 c. SNAP output
6doa hydrolase-DNA-RNA X-ray (1.474 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 480 s at 21 c. SNAP output
6dob hydrolase-DNA-RNA X-ray (1.343 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 200 s at 21 c. SNAP output
6doc hydrolase-DNA-RNA X-ray (1.496 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 240 s at 21 c. SNAP output
6dod hydrolase-DNA-RNA X-ray (1.535 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 360 s at 21 c. SNAP output
6doe hydrolase-DNA-RNA X-ray (1.451 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 420 s at 21 c. SNAP output
6dof hydrolase-DNA-RNA X-ray (1.433 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 540 s at 21 c. SNAP output
6dog hydrolase-RNA-DNA X-ray (1.285 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 600 s at 21 c. SNAP output
6doh hydrolase-RNA-DNA X-ray (1.363 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: soak in 0.5 mm egta and 200 mm k+ at 21 c. SNAP output
6doi hydrolase-RNA-DNA X-ray (1.948 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid (1.54 angstrom wavelength): soak in 0.5 mm egta and 200 mm k+ at 21 c. SNAP output
6doj hydrolase-DNA-RNA X-ray (1.403 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 5 mm k+ for 120 s at 21 c. SNAP output
6dok hydrolase-DNA-RNA X-ray (1.38 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 25 mm k+ for 120 s at 21 c (dataset 1). SNAP output
6dol hydrolase-DNA-RNA X-ray (1.433 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 25 mm k+ for 120 s at 21 c (dataset 2). SNAP output
6dom hydrolase-DNA-RNA X-ray (1.425 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 50 mm k+ for 120 s at 21 c. SNAP output
6don hydrolase-DNA-RNA X-ray (1.422 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 100 mm k+ for 120 s at 21 c (dataset 1). SNAP output
6doo hydrolase-DNA-RNA X-ray (1.44 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 100 mm k+ for 120 s at 21 c (dataset 2). SNAP output
6dop hydrolase-DNA-RNA X-ray (1.25 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 120 s at 21 c (dataset 1). SNAP output
6doq hydrolase-DNA-RNA X-ray (1.422 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 120 s at 21 c (dataset 2). SNAP output
6dor hydrolase-DNA-RNA X-ray (1.5 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 300 mm k+ for 120 s at 21 c (dataset 1). SNAP output
6dos hydrolase-DNA-RNA X-ray (1.318 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 300 mm k+ for 120 s at 21 c (dataset 2). SNAP output
6dot hydrolase-RNA-DNA X-ray (1.423 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm rb+ for 40 s at 21 c. SNAP output
6dou hydrolase-RNA-DNA X-ray (1.487 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm rb+ for 120 s at 21 c. SNAP output
6dov hydrolase-RNA-DNA X-ray (1.521 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm rb+ for 80 s at 21 c. SNAP output
6dow hydrolase-RNA-DNA X-ray (1.495 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm rb+ for 160 s at 21 c. SNAP output
6dox hydrolase-RNA-DNA X-ray (1.45 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm rb+ for 360 s at 21 c. SNAP output
6doy hydrolase-DNA-RNA X-ray (1.45 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm li+ for 120 s at 21 c. SNAP output
6doz hydrolase-DNA-RNA X-ray (1.573 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 1 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp0 hydrolase-DNA-RNA X-ray (1.451 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2.5 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp1 hydrolase-DNA-RNA X-ray (1.42 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp2 hydrolase-DNA-RNA X-ray (1.662 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 7.5 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp3 hydrolase-DNA-RNA X-ray (1.461 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 10 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp4 hydrolase-DNA-RNA X-ray (1.374 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 20 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp5 hydrolase-DNA-RNA X-ray (1.432 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 40 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp6 hydrolase-DNA-RNA X-ray (1.403 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 80 mm mg2+ and 75 mm k+ for 40 s at 21 c. SNAP output
6dp7 hydrolase-DNA-RNA X-ray (1.381 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 500 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dp8 hydrolase-DNA-RNA X-ray (1.323 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm li+ for 240 s at 21 c. SNAP output
6dp9 hydrolase-DNA-RNA X-ray (1.4 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 2 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpa hydrolase-DNA-RNA X-ray (1.489 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 4 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpb hydrolase-DNA-RNA X-ray (1.324 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 8 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpc hydrolase-DNA-RNA X-ray (1.34 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 12 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpd hydrolase-DNA-RNA X-ray (1.46 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 16 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpe hydrolase-DNA-RNA X-ray (1.56 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 20 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpf hydrolase-DNA-RNA X-ray (1.56 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 40 mm mn2+ and 200 mm k+ for 40 s at 21 c. SNAP output
6dpg hydrolase-RNA-DNA X-ray (1.38 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 e188a in complex with an RNA-DNA hybrid: reaction in 4 mm mn2+ and 200 mm k+ for 240 s at 21 c. SNAP output
6dph hydrolase-RNA-DNA X-ray (1.339 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 e188a in complex with an RNA-DNA hybrid: reaction in 2 mm mn2+ and 200 mm k+ for 120 s at 21 c. SNAP output
6dpi hydrolase-RNA-DNA X-ray (1.347 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 k196a in complex with an RNA-DNA hybrid: reaction in 10 mm mg2+ and 200 mm rb+ for 40 s at 21 c. SNAP output
6dpj hydrolase-RNA-DNA X-ray (1.55 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 k196a in complex with an RNA-DNA hybrid: reaction in 4 mm mn2+ and 200 mm k+ for 80 s at 21 c. SNAP output
6dpk hydrolase-RNA-DNA X-ray (1.391 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 k196a in complex with an RNA-DNA hybrid: reaction in 4 mm mn2+ and 200 mm k+ for 240 s at 21 c. SNAP output
6dpl hydrolase-RNA-DNA X-ray (1.45 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 k196a in complex with an RNA-DNA hybrid: reaction in 10 mm mg2+ and 200 mm rb+ for 720 s at 21 c. SNAP output
6dpm hydrolase-RNA-DNA X-ray (1.677 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 k196a in complex with an RNA-DNA hybrid: reaction in 10 mm mg2+ and 200 mm rb+ for 1800 s at 21 c. SNAP output
6dpn hydrolase-RNA-DNA X-ray (1.493 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 e188a in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 200 s at 21 c. SNAP output
6dpo hydrolase-RNA-DNA X-ray (1.45 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 e188a in complex with an RNA-DNA hybrid: reaction in 2 mm mg2+ and 200 mm k+ for 360 s at 21 c. SNAP output
6dpp hydrolase-RNA-DNA X-ray (1.45 Å) Samara NL, Yang W (2018) "Cation trafficking propels RNA hydrolysis." Nat. Struct. Mol. Biol., 25, 715-721. doi: 10.1038/s41594-018-0099-4. Crystal structure of bacillus halodurans ribonuclease h1 in complex with an RNA-DNA hybrid: reaction in 5 mm mg2+ and 200 mm rb+ for 240 s at 21 c. SNAP output
6dsu transferase-DNA X-ray (1.98 Å) Chim N, Jackson LN, Trinh AM, Chaput JC (2018) "Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway." Elife, 7. doi: 10.7554/eLife.40444. Bst DNA polymerase i pre-insertion complex structure. SNAP output
6dsv transferase-DNA X-ray (1.99 Å) Chim N, Jackson LN, Trinh AM, Chaput JC (2018) "Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway." Elife, 7. doi: 10.7554/eLife.40444. Bst DNA polymerase i post-chemistry (n+2) structure. SNAP output
6dsw transferase-DNA X-ray (1.589 Å) Chim N, Jackson LN, Trinh AM, Chaput JC (2018) "Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway." Elife, 7. doi: 10.7554/eLife.40444. Bst DNA polymerase i pre-chemistry (n) structure. SNAP output
6dsx transferase-DNA X-ray (1.99 Å) Chim N, Jackson LN, Trinh AM, Chaput JC (2018) "Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway." Elife, 7. doi: 10.7554/eLife.40444. Bst DNA polymerase i post-chemistry (n+1 with datp soak) structure. SNAP output
6dsy transferase-DNA X-ray (1.98 Å) Chim N, Jackson LN, Trinh AM, Chaput JC (2018) "Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway." Elife, 7. doi: 10.7554/eLife.40444. Bst DNA polymerase i post-chemistry (n+1) structure. SNAP output
6dt1 ligase-DNA X-ray (2.75 Å) Shi K, Bohl TE, Park J, Zasada A, Malik S, Banerjee S, Tran V, Li N, Yin Z, Kurniawan F, Orellana K, Aihara H (2018) "T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction." Nucleic Acids Res., 46, 10474-10488. doi: 10.1093/nar/gky776. Crystal structure of the ligase from bacteriophage t4 complexed with DNA intermediate. SNAP output
6dt7 transcription-DNA X-ray (2.5 Å) Molodtsov V, Murakami KS (2018) "Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II." J. Biol. Chem., 293, 13616-13625. doi: 10.1074/jbc.RA118.003447. Bacteriophage n4 RNA polymerase ii and DNA complex. SNAP output
6dt8 transcription-DNA-RNA X-ray (3.2 Å) Molodtsov V, Murakami KS (2018) "Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II." J. Biol. Chem., 293, 13616-13625. doi: 10.1074/jbc.RA118.003447. Bacteriophage n4 RNA polymerase ii elongation complex 1. SNAP output
6dta transcription-DNA-RNA X-ray (2.694 Å) Molodtsov V, Murakami KS (2018) "Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II." J. Biol. Chem., 293, 13616-13625. doi: 10.1074/jbc.RA118.003447. Bacteriophage n4 RNA polymerase ii elongation complex 2. SNAP output
6dv9 transferase-DNA-RNA X-ray (3.8 Å) Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH (2019) "Structural basis of ECF-sigma-factor-dependent transcription initiation." Nat Commun, 10, 710. doi: 10.1038/s41467-019-08443-3. Crystal structure of mycobacterium tuberculosis transcription initiation complex(ecf sigma factor l) containing 5nt RNA with 4nt spacer. SNAP output
6dvb transferase-DNA-RNA X-ray (3.8 Å) Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH (2019) "Structural basis of ECF-sigma-factor-dependent transcription initiation." Nat Commun, 10, 710. doi: 10.1038/s41467-019-08443-3. Crystal structure of mycobacterium tuberculosis transcription initiation complex(ecf sigma factor l) containing 5nt RNA with 5nt spacer. SNAP output
6dvc transferase-DNA-RNA X-ray (3.3 Å) Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH (2019) "Structural basis of ECF-sigma-factor-dependent transcription initiation." Nat Commun, 10, 710. doi: 10.1038/s41467-019-08443-3. Crystal structure of mycobacterium tuberculosis transcription initiation complex(ecf sigma factor l) containing 5nt RNA with 6nt spacer. SNAP output
6dvd transferase-DNA X-ray (3.899 Å) Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH (2019) "Structural basis of ECF-sigma-factor-dependent transcription initiation." Nat Commun, 10, 710. doi: 10.1038/s41467-019-08443-3. Crystal structure of mycobacterium tuberculosis transcription initiation complex(ecf sigma factor l) with 6 nt spacer and bromine labelled in position "-11. SNAP output
6dve transferase-DNA X-ray (3.812 Å) Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH (2019) "Structural basis of ECF-sigma-factor-dependent transcription initiation." Nat Commun, 10, 710. doi: 10.1038/s41467-019-08443-3. Crystal structure of mycobacterium tuberculosis transcription initiation complex(ecf selenomethionine-labelled sigma factor l) with 6 nt spacer. SNAP output
6dww DNA binding protein-DNA X-ray (2.851 Å) Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F (2018) "Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase." Nucleic Acids Res., 46, 10286-10301. doi: 10.1093/nar/gky838. Hermes transposase deletion dimer complex with (a-t) DNA and mn2+. SNAP output
6dwy DNA binding protein-DNA X-ray (3.2 Å) Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F (2018) "Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase." Nucleic Acids Res., 46, 10286-10301. doi: 10.1093/nar/gky838. Hermes transposase deletion dimer complex with (c-g) DNA and ca2+. SNAP output
6dwz DNA binding protein-DNA X-ray (3.2 Å) Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F (2018) "Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase." Nucleic Acids Res., 46, 10286-10301. doi: 10.1093/nar/gky838. Hermes transposase deletion dimer complex with (c-g) DNA. SNAP output
6dx0 DNA binding protein-DNA X-ray (2.9 Å) Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F (2018) "Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase." Nucleic Acids Res., 46, 10286-10301. doi: 10.1093/nar/gky838. Hermes transposase deletion dimer complex with (a-t) DNA. SNAP output
6dzt nuclear protein cryo-EM (2.99 Å) Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P (2019) "Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment." Nat Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4. cryo-EM structure of nucleosome in complex with a single chain antibody fragment. SNAP output
6e0c nuclear protein cryo-EM (2.63 Å) Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P (2019) "Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment." Nat Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4. cryo-EM structure of the cenp-a nucleosome (w601) in complex with a single chain antibody fragment. SNAP output
6e0p nuclear protein cryo-EM (2.6 Å) Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P (2019) "Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment." Nat Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4. cryo-EM structure of the centromeric nucleosome (native alpha satellite DNA) in complex with a single chain antibody fragment. SNAP output
6e33 transcription X-ray (1.705 Å) Garg A, Goldgur Y, Schwer B, Shuman S (2018) "Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis." Nucleic Acids Res., 46, 11262-11273. doi: 10.1093/nar/gky827. Crystal structure of pho7-DNA complex. SNAP output
6e3r DNA binding protein-DNA X-ray (2.26 Å) Koag MC, Jung H, Lee S (2019) "Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases." J. Am. Chem. Soc., 141, 4584-4596. doi: 10.1021/jacs.8b08551. Structure of human DNA polymerase beta complexed with 8oa as the template base in a 1-nucleotide gapped DNA. SNAP output
6e3v DNA binding protein-DNA X-ray (1.96 Å) Koag MC, Jung H, Lee S (2019) "Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases." J. Am. Chem. Soc., 141, 4584-4596. doi: 10.1021/jacs.8b08551. Structure of human DNA polymerase beta complexed with 8oa in the template base paired with incoming non-hydrolyzable ttp. SNAP output
6e3w DNA binding protein-DNA X-ray (2.02 Å) Koag MC, Jung H, Lee S (2019) "Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases." J. Am. Chem. Soc., 141, 4584-4596. doi: 10.1021/jacs.8b08551. Structure of human DNA polymerase beta complexed with 8oa in the template base paired with incoming non-hydrolyzable gtp. SNAP output
6e3x DNA binding protein-DNA X-ray (2.65 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP." Structure of human DNA polymerase beta complexed with 8oa in the template base paired with incoming non-hydrolyzable atp. SNAP output
6e53 transferase-transferase inhibitor X-ray (2.8 Å) Hernandez-Sanchez W, Huang W, Plucinsky B, Garcia-Vazquez N, Robinson NJ, Schiemann WP, Berdis AJ, Skordalakes E, Taylor DJ (2019) "A non-natural nucleotide uses a specific pocket to selectively inhibit telomerase activity." Plos Biol., 17, e3000204. doi: 10.1371/journal.pbio.3000204. Structure of tert in complex with a novel telomerase inhibitor. SNAP output
6e8c DNA binding protein-DNA X-ray (2.12 Å) Lee JK, Bosnakovski D, Toso EA, Dinh T, Banerjee S, Bohl TE, Shi K, Orellana K, Kyba M, Aihara H (2018) "Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA." Cell Rep, 25, 2955-2962.e3. doi: 10.1016/j.celrep.2018.11.060. Crystal structure of the double homeodomain of dux4 in complex with DNA. SNAP output
6e93 DNA binding protein-DNA X-ray (1.747 Å) Hudson NO, Whitby FG, Buck-Koehntop BA (2018) "Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38." J. Biol. Chem., 293, 19835-19843. doi: 10.1074/jbc.RA118.005147. Crystal structure of zbtb38 c-terminal zinc fingers 6-9 in complex with methylated DNA. SNAP output
6e94 DNA binding protein-DNA X-ray (1.594 Å) Hudson NO, Whitby FG, Buck-Koehntop BA (2018) "Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38." J. Biol. Chem., 293, 19835-19843. doi: 10.1074/jbc.RA118.005147. Crystal structure of zbtb38 c-terminal zinc fingers 6-9 k1055r in complex with methylated DNA. SNAP output
6edb transferase-DNA X-ray (3.209 Å) Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl T, Patel DJ (2019) "Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation." Proc.Natl.Acad.Sci.USA, 116, 11946-11955. doi: 10.1073/pnas.1905013116. Crystal structure of sry.hcgas-21bp dsDNA complex. SNAP output
6edc transferase-DNA X-ray (2.712 Å) Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl T, Patel DJ (2019) "Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation." Proc.Natl.Acad.Sci.USA, 116, 11946-11955. doi: 10.1073/pnas.1905013116. Hcgas-16bp dsDNA complex. SNAP output
6edt transcription-DNA cryo-EM Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA (2019) "Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding." Nature, 565, 382-385. doi: 10.1038/s41586-018-0840-5. Mycobacterium tuberculosis rnap open promoter complex with rbpa-card and ap3 promoter. SNAP output
6ee8 transcription-DNA cryo-EM (3.92 Å) Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA (2019) "Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding." Nature, 565, 382-385. doi: 10.1038/s41586-018-0840-5. Mycobacterium tuberculosis rnap promoter unwinding intermediate complex with rbpa-card and ap3 promoter. SNAP output
6eec transcription-DNA cryo-EM (3.55 Å) Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA (2019) "Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding." Nature, 565, 382-385. doi: 10.1038/s41586-018-0840-5. Mycobacterium tuberculosis rnap promoter unwinding intermediate complex with rbpa-card and ap3 promoter captured by corallopyronin. SNAP output
6eht DNA binding protein X-ray (3.2 Å) De March M, Barrera-Vilarmau S, Crespan E, Mentegari E, Merino N, Gonzalez-Magana A, Romano-Moreno M, Maga G, Crehuet R, Onesti S, Blanco FJ, De Biasio A (2018) "p15PAF binding to PCNA modulates the DNA sliding surface." Nucleic Acids Res., 46, 9816-9828. doi: 10.1093/nar/gky723. Modulation of pcna sliding surface by p15paf suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme. SNAP output
6eko hydrolase X-ray (2.284 Å) Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V (2019) "Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family." Nucleic Acids Res., 47, 997-1010. doi: 10.1093/nar/gky1137. Crystal structure of type iip restriction endonuclease pfoi with cognate DNA. SNAP output
6el8 DNA binding protein X-ray (1.61 Å) Newman JA, Aitkenhead HA, Pinkas DM, von Delft F, Arrowsmith CH, Edwards A, Bountra C, Gileadi O "Crystal structure of the Forkhead domain of human FOXN1 in complex with DNA." Crystal structure of the forkhead domain of human foxn1 in complex with DNA. SNAP output
6emy recombination X-ray (2.5 Å) Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O (2018) "Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance." Cell, 173, 208-220.e20. doi: 10.1016/j.cell.2018.02.032. Structure of the tn1549 transposon integrase (aa 82-397, y379f) in complex with transposon right end DNA. SNAP output
6emz recombination X-ray (2.79 Å) Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O (2018) "Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance." Cell, 173, 208-220.e20. doi: 10.1016/j.cell.2018.02.032. Structure of the tn1549 transposon integrase (aa 82-397, r225k) in complex with circular intermediate DNA (ci5-DNA). SNAP output
6en0 recombination X-ray (2.8 Å) Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O (2018) "Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance." Cell, 173, 208-220.e20. doi: 10.1016/j.cell.2018.02.032. Structure of the tn1549 transposon integrase (aa 82-397) in complex with circular intermediate DNA (ci5-DNA). SNAP output
6en1 recombination X-ray (2.67 Å) Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O (2018) "Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance." Cell, 173, 208-220.e20. doi: 10.1016/j.cell.2018.02.032. Structure of the tn1549 transposon integrase (aa 82-397, r225k) in complex with a circular intermediate DNA (ci6a-DNA). SNAP output
6en2 recombination X-ray (2.67 Å) Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O (2018) "Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance." Cell, 173, 208-220.e20. doi: 10.1016/j.cell.2018.02.032. Structure of the tn1549 transposon integrase (aa 82-397, r225k) in complex with a circular intermediate DNA (ci6b-DNA). SNAP output
6en8 transcription X-ray (3.29 Å) Wang K, Sybers D, Maklad HR, Lemmens L, Lewyllie C, Zhou X, Schult F, Brasen C, Siebers B, Valegard K, Lindas AC, Peeters E (2019) "A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius." Nat Commun, 10, 1542. doi: 10.1038/s41467-019-09479-1. Safadr in complex with dsDNA. SNAP output
6eo6 hydrolase-DNA X-ray (1.69 Å) Dolot R, Lam CH, Sierant M, Zhao Q, Liu FW, Nawrot B, Egli M, Yang X (2018) "Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity." Nucleic Acids Res., 46, 4819-4830. doi: 10.1093/nar/gky268. X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(2-(1h-indol-3-yl)acetamide-n-yl)-1-propen-1-yl)-2'-deoxyuridine residue. SNAP output
6eo7 hydrolase-DNA X-ray (2.24 Å) Dolot R, Lam CH, Sierant M, Zhao Q, Liu FW, Nawrot B, Egli M, Yang X (2018) "Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity." Nucleic Acids Res., 46, 4819-4830. doi: 10.1093/nar/gky268. X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(acetamide-n-yl)-1-propen-1-yl)-2'-deoxyuridine residue. SNAP output
6erf DNA binding protein X-ray (3.01 Å) Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB (2018) "XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining." Nat.Struct.Mol.Biol., 25, 971-980. doi: 10.1038/s41594-018-0133-6. Complex of aplf factor and ku heterodimer bound to DNA. SNAP output
6erg DNA binding protein X-ray (2.9 Å) Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB (2018) "XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining." Nat. Struct. Mol. Biol., 25, 971-980. doi: 10.1038/s41594-018-0133-6. Complex of xlf and heterodimer ku bound to DNA. SNAP output
6erh DNA binding protein X-ray (2.8 Å) Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB (2018) "XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining." Nat. Struct. Mol. Biol., 25, 971-980. doi: 10.1038/s41594-018-0133-6. Complex of xlf and heterodimer ku bound to DNA. SNAP output
6erp transcription X-ray (4.502 Å) Hillen HS, Morozov YI, Sarfallah A, Temiakov D, Cramer P (2017) "Structural Basis of Mitochondrial Transcription Initiation." Cell, 171, 1072-1081.e10. doi: 10.1016/j.cell.2017.10.036. Structure of the human mitochondrial transcription initiation complex at the lsp promoter. SNAP output
6erq transcription X-ray (4.5 Å) Hillen HS, Morozov YI, Sarfallah A, Temiakov D, Cramer P (2017) "Structural Basis of Mitochondrial Transcription Initiation." Cell, 171, 1072-1081.e10. doi: 10.1016/j.cell.2017.10.036. Structure of the human mitochondrial transcription initiation complex at the hsp promoter. SNAP output
6es2 transcription X-ray (2.95 Å) Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J (2018) "Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima." Elife, 7. doi: 10.7554/eLife.32963. Structure of cdx2-DNA(caa). SNAP output
6es3 transcription X-ray (2.57 Å) Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J (2018) "Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima." Elife, 7. doi: 10.7554/eLife.32963. Structure of cdx2-DNA(tcg). SNAP output
6esf gene regulation cryo-EM (3.7 Å) Bilokapic S, Strauss M, Halic M (2018) "Histone octamer rearranges to adapt to DNA unwrapping." Nat. Struct. Mol. Biol., 25, 101-108. doi: 10.1038/s41594-017-0005-5. Nucleosome : class 1. SNAP output
6esg gene regulation cryo-EM (5.4 Å) Bilokapic S, Strauss M, Halic M (2018) "Histone octamer rearranges to adapt to DNA unwrapping." Nat. Struct. Mol. Biol., 25, 101-108. doi: 10.1038/s41594-017-0005-5. Nucleosome breathing : class 2. SNAP output
6esh gene regulation cryo-EM (5.1 Å) Bilokapic S, Strauss M, Halic M (2018) "Histone octamer rearranges to adapt to DNA unwrapping." Nat. Struct. Mol. Biol., 25, 101-108. doi: 10.1038/s41594-017-0005-5. Nucleosome breathing : class 3. SNAP output
6esi gene regulation cryo-EM (6.3 Å) Bilokapic S, Strauss M, Halic M (2018) "Histone octamer rearranges to adapt to DNA unwrapping." Nat. Struct. Mol. Biol., 25, 101-108. doi: 10.1038/s41594-017-0005-5. Nucleosome breathing : class 4. SNAP output
6eu0 transcription cryo-EM (4.0 Å) Abascal-Palacios G, Ramsay EP, Beuron F, Morris E, Vannini A (2018) "Structural basis of RNA polymerase III transcription initiation." Nature, 553, 301-306. doi: 10.1038/nature25441. RNA polymerase iii open pre-initiation complex (oc-pic). SNAP output
6eu1 transcription cryo-EM (3.4 Å) Abascal-Palacios G, Ramsay EP, Beuron F, Morris E, Vannini A (2018) "Structural basis of RNA polymerase III transcription initiation." Nature, 553, 301-306. doi: 10.1038/nature25441. RNA polymerase iii - open DNA complex (oc-pol3).. SNAP output
6evv hydrolase X-ray (2.5 Å) Troisi R, Napolitano V, Spiridonova V, Russo Krauss I, Sica F (2018) "Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer." Nucleic Acids Res., 46, 12177-12185. doi: 10.1093/nar/gky990. X-ray structure of the complex between human alpha thrombin and nu172, a duplex-quadruplex 26-mer DNA aptamer, in the presence of potassium ions.. SNAP output
6exv transcription cryo-EM (3.6 Å) Liu X, Farnung L, Wigge C, Cramer P (2018) "Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by alpha-amanitin." J. Biol. Chem., 293, 7189-7194. doi: 10.1074/jbc.RA118.002545. Structure of mammalian RNA polymerase ii elongation complex inhibited by alpha-amanitin. SNAP output
6f0l hydrolase cryo-EM (4.77 Å) Abid Ali F, Douglas ME, Locke J, Pye VE, Nans A, Diffley JFX, Costa A (2017) "Cryo-EM structure of a licensed DNA replication origin." Nat Commun, 8, 2241. doi: 10.1038/s41467-017-02389-0. S. cerevisiae mcm double hexamer bound to duplex DNA. SNAP output
6f1k DNA binding protein X-ray (2.2 Å) Obaji E, Haikarainen T, Lehtio L (2018) "Structural basis for DNA break recognition by ARTD2/PARP2." Nucleic Acids Res., 46, 12154-12165. doi: 10.1093/nar/gky927. Structure of artd2-parp2 wgr domain bound to double strand DNA without 5'phosphate. SNAP output
6f2s virus cryo-EM (3.3 Å) Hesketh EL, Saunders K, Fisher C, Potze J, Stanley J, Lomonossoff GP, Ranson NA (2018) "The 3.3 angstrom structure of a plant geminivirus using cryo-EM." Nat Commun, 9, 2369. doi: 10.1038/s41467-018-04793-6. Cryoem structure of ageratum yellow vein virus (ayvv). SNAP output
6f40 transcription cryo-EM (3.7 Å) Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller CW (2018) "Molecular mechanism of promoter opening by RNA polymerase III." Nature, 553, 295-300. doi: 10.1038/nature25440. RNA polymerase iii open complex. SNAP output
6f41 transcription cryo-EM (4.3 Å) Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller CW (2018) "Molecular mechanism of promoter opening by RNA polymerase III." Nature, 553, 295-300. doi: 10.1038/nature25440. RNA polymerase iii initially transcribing complex. SNAP output
6f42 transcription cryo-EM (5.5 Å) Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller CW (2018) "Molecular mechanism of promoter opening by RNA polymerase III." Nature, 553, 295-300. doi: 10.1038/nature25440. RNA polymerase iii closed complex cc1.. SNAP output
6f44 transcription cryo-EM (4.2 Å) Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller CW (2018) "Molecular mechanism of promoter opening by RNA polymerase III." Nature, 553, 295-300. doi: 10.1038/nature25440. RNA polymerase iii closed complex cc2.. SNAP output
6f57 transferase-DNA X-ray (3.098 Å) Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J (2018) "Structural basis for DNMT3A-mediated de novo DNA methylation." Nature, 554, 387-391. doi: 10.1038/nature25477. Crystal structure of dnmt3a-dnmt3l in complex with single cpg-containing DNA. SNAP output
6f58 transcription X-ray (2.253 Å) Newman JA, Gavard AE, Krojer T, Shrestha L, Burgess-Brown NA, von Delft F, Arrowsmith CH, Edwards A, Bountra C, Gileadi O "Crystal structure of human Brachyury (T) in complex with DNA." Crystal structure of human brachyury (t) in complex with DNA. SNAP output
6f59 transcription X-ray (2.151 Å) Newman JA, Gavard AE, Krojer T, Shrestha L, Burgess-Brown NA, von Delft F, Arrowsmith CH, Edwards A, Bountra C, Gileadi O "Crystal structure of human Brachyury (T) G177D variant in complex with DNA." Crystal structure of human brachyury (t) g177d variant in complex with DNA. SNAP output
6f5b DNA binding protein X-ray (2.8 Å) Obaji E, Haikarainen T, Lehtio L (2018) "Structural basis for DNA break recognition by ARTD2/PARP2." Nucleic Acids Res., 46, 12154-12165. doi: 10.1093/nar/gky927. Structure of artd2-parp2 wgr domain bound to double stranded DNA with 5'phosphate. SNAP output
6f5f DNA binding protein X-ray (2.98 Å) Obaji E, Haikarainen T, Lehtio L (2018) "Structural basis for DNA break recognition by ARTD2/PARP2." Nucleic Acids Res., 46, 12154-12165. doi: 10.1093/nar/gky927. Structure of artd2-parp2 wgr domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate. SNAP output
6fas DNA binding protein X-ray (1.9 Å) Sasnauskas G, Kauneckaite K, Siksnys V (2018) "Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1." Nucleic Acids Res., 46, 4316-4324. doi: 10.1093/nar/gky256. Crystal structure of val1 b3 domain in complex with cognate DNA. SNAP output
6fb0 DNA binding protein X-ray (2.15 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of a tailored i-crei homing endonuclease protein (3115 variant) in complex with its target DNA (haemoglobin beta subunit gene) in the presence of calcium. SNAP output
6fb1 DNA binding protein X-ray (3.024 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of a tailored i-crei homing endonuclease protein (3115 variant) in complex with its target DNA (haemoglobin beta subunit gene) in the presence of magnesium. SNAP output
6fb2 DNA binding protein X-ray (2.95 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of a tailored i-crei homing endonuclease protein (3115 variant) in complex with its target DNA (haemoglobin beta subunit gene) in the presence of manganese. SNAP output
6fb5 DNA binding protein X-ray (2.2 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of a tailored i-crei homing endonuclease protein (3115 variant) in complex with an altered version of its target DNA (haemoglobin beta subunit gene) at 5nnn region in the presence of magnesium. SNAP output
6fb6 DNA binding protein X-ray (2.6 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of a tailored i-crei homing endonuclease protein (3115 variant) in complex with an altered version of its target DNA (haemoglobin beta subunit gene) at 5nnn region in the presence of manganese. SNAP output
6fb7 DNA binding protein X-ray (2.689 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of the i-crei homing endonuclease d75n variant in complex with its target DNA in the presence of manganese. SNAP output
6fb8 DNA binding protein X-ray (2.45 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of the i-crei homing endonuclease d75n variant in complex with an altered version of its target DNA at 5nnn region in the presence of magnesium. SNAP output
6fb9 DNA binding protein X-ray (2.95 Å) Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R (2018) "Understanding the indirect DNA read-out specificity of I-CreI Meganuclease." Sci Rep, 8, 10286. doi: 10.1038/s41598-018-28599-0. Crystal structure of the i-crei homing endonuclease d75n variant in complex with an altered version of its target DNA at 5nnn region in the presence of manganese. SNAP output
6fbc DNA binding protein X-ray (1.54 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.. SNAP output
6fbd DNA binding protein X-ray (2.099 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide.. SNAP output
6fbe DNA binding protein X-ray (1.589 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the third primer nucleotide.. SNAP output
6fbf DNA binding protein X-ray (2.001 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the fourth primer nucleotide.. SNAP output
6fbg DNA binding protein X-ray (1.702 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer nucleotide.. SNAP output
6fbh DNA binding protein X-ray (1.8 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the sixth primer nucleotide.. SNAP output
6fbi DNA binding protein X-ray (1.9 Å) Kropp HM, Durr SL, Peter C, Diederichs K, Marx A (2018) "Snapshots of a modified nucleotide moving through the confines of a DNA polymerase." Proc. Natl. Acad. Sci. U.S.A., 115, 9992-9997. doi: 10.1073/pnas.1811518115. Klentaq DNA polymerase in a closed, ternary complex with dgpnhpp bound in the active site. SNAP output
6fbq transcription X-ray (1.6 Å) Osz J, McEwen AG, Wolf J, Poussin-Courmontagne P, Peluso-Iltis C, Chebaro Y, Kieffer B, Rochel N (2019) "Modulation of RXR-DNA complex assembly by DNA context." Mol. Cell. Endocrinol., 481, 44-52. doi: 10.1016/j.mce.2018.11.008. Crystal structure of the human retinoid x receptor DNA-binding domain bound to the human mep dr1 response element, ph 7.0. SNAP output
6fbr transcription X-ray (2.1 Å) Osz J, McEwen AG, Wolf J, Poussin-Courmontagne P, Peluso-Iltis C, Chebaro Y, Kieffer B, Rochel N (2019) "Modulation of RXR-DNA complex assembly by DNA context." Mol. Cell. Endocrinol., 481, 44-52. doi: 10.1016/j.mce.2018.11.008. Crystal structure of the human retinoid x receptor DNA-binding domain bound to the human mep dr1 response element, ph 4.2. SNAP output
6fbu hydrolase X-ray (2.0 Å) Pomyalov S, Lansky S, Golan G, Zharkov DO, Grollman AP, Shoham G "Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli (e2q) in complex with ap-site containing DNA substrate. SNAP output
6fi8 DNA binding protein X-ray (2.598 Å) Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S, Guynet C, Hickman AB, Chandler M, Dyda F, Barabas O (2018) "Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering." Nucleic Acids Res., 46, 4152-4163. doi: 10.1093/nar/gky235. Crystal structure of the is608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complex. SNAP output
6fix antitoxin X-ray (3.8 Å) Talavera A, Tamman H, Ainelo A, Konijnenberg A, Hadzi S, Sobott F, Garcia-Pino A, Horak R, Loris R (2019) "A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT." Nat Commun, 10, 972. doi: 10.1038/s41467-019-08865-z. Antitoxin graa in complex with its operator. SNAP output
6fj5 transcription X-ray (2.051 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-agg-hg). SNAP output
6fk4 DNA binding protein X-ray (2.297 Å) Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang CM, Freemont PS, Baldwin GS (2018) "Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis." Nucleic Acids Res., 46, 11980-11989. doi: 10.1093/nar/gky934. Structure of 3' phosphatase nexo (wt) from neisseria bound to DNA substrate. SNAP output
6fk5 DNA binding protein X-ray (2.02 Å) Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang CM, Freemont PS, Baldwin GS (2018) "Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis." Nucleic Acids Res., 46, 11980-11989. doi: 10.1093/nar/gky934. Structure of 3' phosphatase nexo (d146n) from neisseria bound to DNA substrate in presence of magnesium ion. SNAP output
6fke DNA binding protein X-ray (2.151 Å) Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang CM, Freemont PS, Baldwin GS (2018) "Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis." Nucleic Acids Res., 46, 11980-11989. doi: 10.1093/nar/gky934. Structure of 3' phosphatase nexo (d146n) from neisseria bound to product DNA hairpin. SNAP output
6fl1 hydrolase X-ray (1.6 Å) Coste F, Castaing B, Ober M, Carell T "Crystal structure of the complex between the Lactococcus lactis FPG mutant T221P and a Fapy-dG containing DNA." Crystal structure of the complex between the lactococcus lactis fpg mutant t221p and a fapy-dg containing DNA. SNAP output
6flp transcription cryo-EM (4.1 Å) Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A (2018) "Structural Basis for NusA Stabilized Transcriptional Pausing." Mol. Cell, 69, 816-827.e4. doi: 10.1016/j.molcel.2018.02.008. Cryoem structure of e.coli RNA polymerase paused elongation complex without RNA hairpin bound to nusa. SNAP output
6flq transcription cryo-EM (3.6 Å) Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A (2018) "Structural Basis for NusA Stabilized Transcriptional Pausing." Mol. Cell, 69, 816-827.e4. doi: 10.1016/j.molcel.2018.02.008. Cryoem structure of e.coli RNA polymerase paused elongation complex bound to nusa. SNAP output
6fm4 isomerase X-ray (2.7 Å) Magaro G, Prati F, Garofalo B, Corso G, Furlotti G, Apicella C, Mangano G, D'Atanasio N, Robinson D, Di Giorgio FP, Ombrato R (2019) "Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens." J.Med.Chem., 62, 7445-7472. doi: 10.1021/acs.jmedchem.9b00394. The crystal structure of s. aureus gyrase complex with id-130 and DNA. SNAP output
6fml DNA binding protein cryo-EM (4.34 Å) Eustermann S, Schall K, Kostrewa D, Lakomek K, Strauss M, Moldt M, Hopfner KP (2018) "Structural basis for ATP-dependent chromatin remodelling by the INO80 complex." Nature, 556, 386-390. doi: 10.1038/s41586-018-0029-y. Cryoem structure ino80core nucleosome complex. SNAP output
6fn0 flavoprotein X-ray (2.9 Å) Franz S, Ignatz E, Wenzel S, Zielosko H, Putu EPGN, Maestre-Reyna M, Tsai MD, Yamamoto J, Mittag M, Essen LO (2018) "Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii." Nucleic Acids Res., 46, 8010-8022. doi: 10.1093/nar/gky621. The animal-like cryptochrome from chlamydomonas reinhardtii in complex with 6-4 DNA. SNAP output
6fq5 gene regulation cryo-EM (3.8 Å) Bilokapic S, Strauss M, Halic M (2018) "Structural rearrangements of the histone octamer translocate DNA." Nat Commun, 9, 1330. doi: 10.1038/s41467-018-03677-z. Class 1 : canonical nucleosome. SNAP output
6fq6 gene regulation cryo-EM (4.0 Å) Bilokapic S, Strauss M, Halic M (2018) "Structural rearrangements of the histone octamer translocate DNA." Nat Commun, 9, 1330. doi: 10.1038/s41467-018-03677-z. Class 2 : distorted nucleosome. SNAP output
6fq8 gene regulation cryo-EM (4.8 Å) Bilokapic S, Strauss M, Halic M (2018) "Structural rearrangements of the histone octamer translocate DNA." Nat Commun, 9, 1330. doi: 10.1038/s41467-018-03677-z. Class 3 : translocated nucleosome. SNAP output
6fqm isomerase X-ray (3.06 Å) Germe T, Voros J, Jeannot F, Taillier T, Stavenger RA, Bacque E, Maxwell A, Bax BD (2018) "A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance." Nucleic Acids Res., 46, 4114-4128. doi: 10.1093/nar/gky181. 3.06a complex of s.aureus gyrase with imidazopyrazinone t1 and DNA. SNAP output
6fqp transcription X-ray (2.42 Å) Guca E, Sunol D, Ruiz L, Konkol A, Cordero J, Torner C, Aragon E, Martin-Malpartida P, Riera A, Macias MJ (2018) "TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-beta signaling." Nucleic Acids Res., 46, 9220-9235. doi: 10.1093/nar/gky680. Crystal structure of tale homeobox domain transcription factor tgif1 with its consensus DNA. SNAP output
6fqq transcription X-ray (3.25 Å) Guca E, Sunol D, Ruiz L, Konkol A, Cordero J, Torner C, Aragon E, Martin-Malpartida P, Riera A, Macias MJ (2018) "TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-beta signaling." Nucleic Acids Res., 46, 9220-9235. doi: 10.1093/nar/gky680. Crystal structure of tale homeobox domain transcription factor tgif1 double alanine mutant bound to its consensus DNA. SNAP output
6fqs isomerase X-ray (3.11 Å) Germe T, Voros J, Jeannot F, Taillier T, Stavenger RA, Bacque E, Maxwell A, Bax BD (2018) "A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance." Nucleic Acids Res., 46, 4114-4128. doi: 10.1093/nar/gky181. 3.11a complex of s.aureus gyrase with imidazopyrazinone t3 and DNA. SNAP output
6fqv isomerase X-ray (2.6 Å) Germe T, Voros J, Jeannot F, Taillier T, Stavenger RA, Bacque E, Maxwell A, Bax BD (2018) "A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance." Nucleic Acids Res., 46, 4114-4128. doi: 10.1093/nar/gky181. 2.60a binary complex of s.aureus gyrase with uncleaved DNA. SNAP output
6ftx motor protein cryo-EM (4.5 Å) Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T (2018) "Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome." Elife, 7. doi: 10.7554/eLife.35720. Structure of the chromatin remodelling enzyme chd1 bound to a ubiquitinylated nucleosome. SNAP output
6fwk DNA binding protein X-ray (2.503 Å) Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV, Kamerlin SCL, Johansson E (2019) "Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon." Nat Commun, 10, 373. doi: 10.1038/s41467-018-08114-9. The crystal structure of pol2core-m644g in complex with DNA and an incoming nucleotide. SNAP output
6fwr DNA binding protein X-ray (2.5 Å) Cheng K, Wigley DB (2018) "DNA translocation mechanism of an XPD family helicase." Elife, 7. doi: 10.7554/eLife.42400. Structure of ding in complex with ssDNA. SNAP output
6fws DNA binding protein X-ray (2.5 Å) Cheng K, Wigley DB (2018) "DNA translocation mechanism of an XPD family helicase." Elife, 7. doi: 10.7554/eLife.42400. Structure of ding in complex with ssDNA and adpbef. SNAP output
6fzs transcription X-ray (2.31 Å) Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, Marquez JA, Cordeiro TN, Pluta R, Macias MJ (2021) "Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes." Computational and Structural Biotechnology Journal, 19. doi: 10.1016/j.csbj.2020.12.044. Crystal structure of smad5-mh1 bound to the ggcgc site.. SNAP output
6fzt transcription X-ray (2.46 Å) Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, Marquez JA, Cordeiro TN, Pluta R, Macias MJ (2021) "Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes." Computational and Structural Biotechnology Journal, 19. doi: 10.1016/j.csbj.2020.12.044. Crystal structure of smad8_9-mh1 bound to the ggcgc site.. SNAP output
6g0a DNA binding protein X-ray (2.62 Å) Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV, Kamerlin SCL, Johansson E (2019) "Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon." Nat Commun, 10, 373. doi: 10.1038/s41467-018-08114-9. The crystal structure of the pol2 catalytic domain of DNA polymerase epsilon carrying a p301r substitution.. SNAP output
6g0l motor protein cryo-EM (10.0 Å) Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T (2018) "Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome." Elife, 7. doi: 10.7554/eLife.35720. Structure of two molecules of the chromatin remodelling enzyme chd1 bound to a nucleosome. SNAP output
6g1l transcription X-ray (2.4 Å) Moller K, Sigurbjornsdottir S, Arnthorsson AO, Pogenberg V, Dilshat R, Fock V, Brynjolfsdottir SH, Bindesboll C, Bessadottir M, Ogmundsdottir HM, Simonsen A, Larue L, Wilmanns M, Thorsson V, Steingrimsson E, Ogmundsdottir MH (2019) "MITF has a central role in regulating starvation-induced autophagy in melanoma." Sci Rep, 9, 1055. doi: 10.1038/s41598-018-37522-6. Mitf-clearbox structure. SNAP output
6g1t DNA binding protein X-ray (1.93 Å) Kohler V, Goessweiner-Mohr N, Aufschnaiter A, Fercher C, Probst I, Pavkov-Keller T, Hunger K, Wolinski H, Buttner S, Grohmann E, Keller W (2018) "TraN: A novel repressor of an Enterococcus conjugative type IV secretion system." Nucleic Acids Res., 46, 9201-9219. doi: 10.1093/nar/gky671. Tran, a repressor of an enterococcus conjugative type iv secretion system. SNAP output
6g2q replication X-ray (2.148 Å) Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH (2018) "Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs." Biochemistry, 57, 3934-3944. doi: 10.1021/acs.biochem.8b00418. Ternary complex crystal structure of DNA polymerase beta with a dideoxy terminated primer with chcl (s-isomer), beta, gamma dttp analogue. SNAP output
6g3b hydrolase X-ray (1.8 Å) Kisiala M, Kowalska M, Pastor M, Korza H, Czapinska H, Bochtler M (2020) "Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation." Nucleic Acids Res. Avaii restriction endonuclease in complex with an RNA-DNA hybrid. SNAP output
6gat transcription-DNA NMR Starich MR, Wikstrom M, Schumacher S, Arst Jr HN, Gronenborn AM, Clore GM (1998) "The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity." J.Mol.Biol., 277, 621-634. doi: 10.1006/jmbi.1997.1626. Solution NMR structure of the l22v mutant DNA binding domain of area complexed to a 13 bp DNA containing a tgata site, regularized mean structure. SNAP output
6gcd DNA binding protein X-ray (1.8 Å) Zagorskaite E, Manakova E, Sasnauskas G (2018) "Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC." FEBS Lett., 592, 3335-3345. doi: 10.1002/1873-3468.13244. DNA binding domain of restriction endonuclease mcrbc in complex with 5-hydroxymethylcytosine DNA. SNAP output
6gce DNA binding protein X-ray (1.6 Å) Zagorskaite E, Manakova E, Sasnauskas G (2018) "Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC." FEBS Lett., 592, 3335-3345. doi: 10.1002/1873-3468.13244. DNA binding domain of restriction endonuclease mcrbc in complex with 5-formylcytosine DNA. SNAP output
6gcf DNA binding protein X-ray (1.55 Å) Zagorskaite E, Manakova E, Sasnauskas G (2018) "Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC." FEBS Lett., 592, 3335-3345. doi: 10.1002/1873-3468.13244. DNA binding domain of restriction endonuclease mcrbc in complex with n4-methylcytosine DNA. SNAP output
6gdr ligase X-ray (2.33 Å) Williamson A, Grgic M, Leiros HS (2018) "DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases." Nucleic Acids Res., 46, 8616-8629. doi: 10.1093/nar/gky622. DNA binding with a minimal scaffold: structure-function analysis of lig e DNA ligases. SNAP output
6ged cell adhesion X-ray (1.794 Å) Schmitt A, Jiang K, Camacho MI, Jonna VR, Hofer A, Westerlund F, Christie PJ, Berntsson RP (2018) "PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction." Mol. Microbiol., 109, 291-305. doi: 10.1111/mmi.13980. Adhesin domain of prgb from enterococcus faecalis bound to DNA. SNAP output
6gej nuclear protein cryo-EM (3.6 Å) Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M, Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS, Wigley DB (2018) "Structure and dynamics of the yeast SWR1-nucleosome complex." Science, 362. doi: 10.1126/science.aat7716. Chromatin remodeller-nucleosome complex at 3.6 Å resolution.. SNAP output
6gen nuclear protein cryo-EM (3.6 Å) Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M, Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS, Wigley DB (2018) "Structure and dynamics of the yeast SWR1-nucleosome complex." Science, 362. doi: 10.1126/science.aat7716. Chromatin remodeller-nucleosome complex at 4.5 Å resolution.. SNAP output
6gfw transcription cryo-EM (3.7 Å) Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X (2018) "Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation." Mol. Cell, 70, 1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021. cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing complex. SNAP output
6gh5 transcription cryo-EM (3.4 Å) Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X (2018) "Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation." Mol. Cell, 70, 1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021. cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open complex. SNAP output
6gh6 transcription cryo-EM (4.1 Å) Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X (2018) "Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation." Mol. Cell, 70, 1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021. cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex. SNAP output
6gis DNA binding protein X-ray (2.82 Å) De March M, Merino N, Barrera-Vilarmau S, Crehuet R, Onesti S, Blanco FJ, De Biasio A (2017) "Structural basis of human PCNA sliding on DNA." Nat Commun, 8, 13935. doi: 10.1038/ncomms13935. Structural basis of human clamp sliding on DNA. SNAP output
6gmh transcription cryo-EM (3.1 Å) Vos SM, Farnung L, Boehning M, Wigge C, Linden A, Urlaub H, Cramer P (2018) "Structure of activated transcription complex Pol II-DSIF-PAF-SPT6." Nature, 560, 607-612. doi: 10.1038/s41586-018-0440-4. Structure of activated transcription complex pol ii-dsif-paf-spt6. SNAP output
6gml transcription cryo-EM (3.2 Å) Vos SM, Farnung L, Urlaub H, Cramer P (2018) "Structure of paused transcription complex Pol II-DSIF-NELF." Nature, 560, 601-606. doi: 10.1038/s41586-018-0442-2. Structure of paused transcription complex pol ii-dsif-nelf. SNAP output
6gn7 hydrolase X-ray (2.8 Å) Troisi R, Napolitano V, Spiridonova V, Russo Krauss I, Sica F (2018) "Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer." Nucleic Acids Res., 46, 12177-12185. doi: 10.1093/nar/gky990. X-ray structure of the complex between human alpha thrombin and nu172, a duplex-quadruplex 26-mer DNA aptamer, in the presence of sodium ions.. SNAP output
6go5 DNA binding protein X-ray (2.35 Å) Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M (2019) "Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction." J.Biol.Chem., 294, 10579-10595. doi: 10.1074/jbc.RA119.008739. Tdt chimera (loop1 of pol mu) - ternary complex with 1-nt gapped DNA substrate. SNAP output
6go6 DNA binding protein X-ray (2.09 Å) Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M (2019) "Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction." J.Biol.Chem., 294, 10579-10595. doi: 10.1074/jbc.RA119.008739. Tdt chimera (loop1 of pol mu) - ternary complex with downstream dsDNA. SNAP output
6go7 DNA binding protein X-ray (2.55 Å) Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M (2019) "Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction." J.Biol.Chem., 294, 10579-10595. doi: 10.1074/jbc.RA119.008739. Tdt chimera (loop1 of pol mu) - full DNA synapsis complex. SNAP output
6gov transcription cryo-EM (3.7 Å) Krupp F, Said N, Huang YH, Loll B, Burger J, Mielke T, Spahn CMT, Wahl MC (2019) "Structural Basis for the Action of an All-Purpose Transcription Anti-termination Factor." Mol.Cell, 74, 143-157.e5. doi: 10.1016/j.molcel.2019.01.016. Structure of the RNA polymerase lambda-based antitermination complex. SNAP output
6grb DNA X-ray (2.4 Å) Liu Y, Freeman AD, Declais AC, Lilley DMJ (2018) "A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1." Nucleic Acids Res., 46, 11089-11098. doi: 10.1093/nar/gky863. Eukaryotic junction-resolving enzyme gen-1 binding with potassium. SNAP output
6grc DNA X-ray (2.452 Å) Liu Y, Freeman AD, Declais AC, Lilley DMJ (2018) "A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1." Nucleic Acids Res., 46, 11089-11098. doi: 10.1093/nar/gky863. Eukaryotic junction-resolving enzyme gen-1 binding with sodium. SNAP output
6grd DNA X-ray (2.66 Å) Liu Y, Freeman AD, Declais AC, Lilley DMJ (2018) "A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1." Nucleic Acids Res., 46, 11089-11098. doi: 10.1093/nar/gky863. Eukaryotic junction-resolving enzyme gen-1 binding with cesium. SNAP output
6gtc hydrolase cryo-EM (3.91 Å) Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G (2018) "Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity." Cell, 175, 1856-1871.e21. doi: 10.1016/j.cell.2018.10.045. Transition state structure of cpf1(cas12a) i1 conformation. SNAP output
6gtd hydrolase cryo-EM (4.24 Å) Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G (2018) "Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity." Cell, 175, 1856-1871.e21. doi: 10.1016/j.cell.2018.10.045. Transient state structure of crispr-cpf1 (cas12a) i2 conformation. SNAP output
6gte hydrolase cryo-EM (4.07 Å) Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G (2018) "Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity." Cell, 175, 1856-1871.e21. doi: 10.1016/j.cell.2018.10.045. Transient state structure of crispr-cpf1 (cas12a) i3 conformation. SNAP output
6gtf hydrolase cryo-EM (3.63 Å) Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G (2018) "Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity." Cell, 175, 1856-1871.e21. doi: 10.1016/j.cell.2018.10.045. Transient state structure of crispr-cpf1 (cas12a) i5 conformation. SNAP output
6gtg hydrolase cryo-EM (3.27 Å) Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G (2018) "Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity." Cell, 175, 1856-1871.e21. doi: 10.1016/j.cell.2018.10.045. Transition state structure of cpf1(cas12a) i4 conformation. SNAP output
6gts transcription X-ray (3.357 Å) Jurenas D, Van Melderen L, Garcia-Pino A (2019) "Mechanism of regulation and neutralization of the AtaR-AtaT toxin-antitoxin system." Nat. Chem. Biol., 15, 285-294. doi: 10.1038/s41589-018-0216-z. Structure of the atat-atar complex bound DNA. SNAP output
6gvq DNA binding protein NMR Boudet J, Devillier JC, Wiegand T, Salmon L, Meier BH, Lipps G, Allain FH (2019) "A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template." Cell, 176, 154-166.e13. doi: 10.1016/j.cell.2018.11.031. DNA-bound prn1 helix bundle domain with atp and magnesium in the interaction buffer. SNAP output
6gvt DNA binding protein multiple methods: solution nmr, solid-state nmr Boudet J, Devillier JC, Wiegand T, Salmon L, Meier BH, Lipps G, Allain FH (2019) "A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template." Cell, 176, 154-166.e13. doi: 10.1016/j.cell.2018.11.031. Hybrid structure of the prn1 helix bundle domain in complex with DNA and 2 atp molecules. SNAP output
6gvu DNA binding protein NMR Boudet J, Devillier JC, Wiegand T, Salmon L, Meier BH, Lipps G, Allain FH (2019) "A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template." Cell, 176, 154-166.e13. doi: 10.1016/j.cell.2018.11.031. NMR structure of the DNA-bound helix bundle domain from the functional prn1 primase. SNAP output
6gy3 transcription X-ray (2.68 Å) Schwab C, Sevvana M, Seidel G, Sandmann A, Grau FC, Muller YA "The role of DNA flexibility in transcription regulator AmtR-DNA interaction." Crystal structure of c. glutamicum amtr bound to glna operator DNA. SNAP output
6gyk transcription cryo-EM (5.1 Å) Dienemann C, Schwalb B, Schilbach S, Cramer P (2019) "Promoter Distortion and Opening in the RNA Polymerase II Cleft." Mol. Cell, 73, 97-106.e4. doi: 10.1016/j.molcel.2018.10.014. Structure of a yeast closed complex (core cc1). SNAP output
6gyl transcription cryo-EM (4.8 Å) Dienemann C, Schwalb B, Schilbach S, Cramer P (2019) "Promoter Distortion and Opening in the RNA Polymerase II Cleft." Mol. Cell, 73, 97-106.e4. doi: 10.1016/j.molcel.2018.10.014. Structure of a yeast closed complex with distorted DNA (core ccdist). SNAP output
6gym transcription cryo-EM (6.7 Å) Dienemann C, Schwalb B, Schilbach S, Cramer P (2019) "Promoter Distortion and Opening in the RNA Polymerase II Cleft." Mol. Cell, 73, 97-106.e4. doi: 10.1016/j.molcel.2018.10.014. Structure of a yeast closed complex with distorted DNA (ccdist). SNAP output
6gys DNA binding protein cryo-EM (4.4 Å) Yan K, Zhang Z, Yang J, McLaughlin SH, Barford D (2018) "Architecture of the CBF3-centromere complex of the budding yeast kinetochore." Nat. Struct. Mol. Biol., 25, 1103-1110. doi: 10.1038/s41594-018-0154-1. cryo-EM structure of the cbf3-cen3 complex of the budding yeast kinetochore. SNAP output
6h0s hydrolase X-ray (1.75 Å) Coste F, Castaing B, Carell T "Crystal structure of the complex between the Lactococcus lactis FPG mutant G226P and a Fapy-dG containing DNA." Crystal structure of the complex between the lactococcus lactis fpg mutant g226p and a fapy-dg containing DNA. SNAP output
6h1v DNA binding protein X-ray (2.7 Å) Ter Beek J, Parkash V, Bylund GO, Osterman P, Sauer-Eriksson AE, Johansson E (2019) "Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ε." Nucleic Acids Res., 47, 5712-5722. doi: 10.1093/nar/gkz248. The crystal structure of pol2core in complex with DNA and an incoming nucleotide, carrying an fe-s cluster. SNAP output
6h3r transcription X-ray (2.75 Å) Aragon E, Wang Q, Zou Y, Morgani SM, Ruiz L, Kaczmarska Z, Su J, Torner C, Tian L, Hu J, Shu W, Agrawal S, Gomes T, Marquez JA, Hadjantonakis A-K, Macias MJ, Massague J (2020) "Structural basis for distinct roles of SMAD2 and SMAD3 in FOXH1 pioneer-directed TGF-beta signaling." Genes Dev. doi: 10.1101/gad.330837.119. Crystal structure of smad2 without exon -mh1 bound to the cagac site.. SNAP output
6h67 transcription cryo-EM (3.6 Å) Sanz-Murillo M, Xu J, Belogurov GA, Calvo O, Gil-Carton D, Moreno-Morcillo M, Wang D, Fernandez-Tornero C (2018) "Structural basis of RNA polymerase I stalling at UV light-induced DNA damage." Proc. Natl. Acad. Sci. U.S.A., 115, 8972-8977. doi: 10.1073/pnas.1802626115. Yeast RNA polymerase i elongation complex stalled by cyclobutane pyrimidine dimer (cpd). SNAP output
6h68 transcription cryo-EM (4.6 Å) Sanz-Murillo M, Xu J, Belogurov GA, Calvo O, Gil-Carton D, Moreno-Morcillo M, Wang D, Fernandez-Tornero C (2018) "Structural basis of RNA polymerase I stalling at UV light-induced DNA damage." Proc. Natl. Acad. Sci. U.S.A., 115, 8972-8977. doi: 10.1073/pnas.1802626115. Yeast RNA polymerase i elongation complex stalled by cyclobutane pyrimidine dimer (cpd) with fully-ordered a49. SNAP output
6h8q cell cycle X-ray (3.631 Å) Li Y, Muir K, Bowler MW, Metz J, Haering CH, Panne D (2018) "Structural basis for Scc3-dependent cohesin recruitment to chromatin." Elife, 7. doi: 10.7554/eLife.38356. Structural basis for scc3-dependent cohesin recruitment to chromatin. SNAP output
6hb4 DNA binding protein X-ray (3.05 Å) Cuppari A, Fernandez-Millan P, Battistini F, Tarres-Sole A, Lyonnais S, Iruela G, Ruiz-Lopez E, Enciso Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Toth K, Rivas G, Orozco M, Sola M (2019) "DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region." Nucleic Acids Res., 47, 6519-6537. doi: 10.1093/nar/gkz406. Tfam in complex with site-y. SNAP output
6hc3 DNA binding protein X-ray (3.1 Å) Cuppari A, Fernandez-Millan P, Battistini F, Tarres-Sole A, Lyonnais S, Iruela G, Ruiz-Lopez E, Enciso Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Toth K, Rivas G, Orozco M, Sola M (2019) "DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region." Nucleic Acids Res., 47, 6519-6537. doi: 10.1093/nar/gkz406. Tfam bound to site-x. SNAP output
6hko transcription cryo-EM (3.42 Å) Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Muller CW (2019) "The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2." Elife, 8. doi: 10.7554/eLife.43204. Yeast RNA polymerase i elongation complex bound to nucleotide analog gmpcpp. SNAP output
6hkt DNA binding protein X-ray (9.7 Å) Garcia-Saez I, Menoni H, Boopathi R, Shukla MS, Soueidan L, Noirclerc-Savoye M, Le Roy A, Skoufias DA, Bednar J, Hamiche A, Angelov D, Petosa C, Dimitrov S (2018) "Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation." Mol. Cell, 72, 902-915.e7. doi: 10.1016/j.molcel.2018.09.027. Structure of an h1-bound 6-nucleosome array. SNAP output
6hlq transcription cryo-EM (3.18 Å) Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Muller CW (2019) "The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2." Elife, 8. doi: 10.7554/eLife.43204. Yeast RNA polymerase i* elongation complex bound to nucleotide analog gmpcpp. SNAP output
6hlr transcription cryo-EM (3.18 Å) Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Muller CW (2019) "The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2." Elife, 8. doi: 10.7554/eLife.43204. Yeast RNA polymerase i elongation complex bound to nucleotide analog gmpcpp (core focused). SNAP output
6hp7 DNA binding protein X-ray (2.2 Å) Gallego Del Sol F, Penades JR, Marina A (2019) "Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems." Mol.Cell, 74, 59-72.e3. doi: 10.1016/j.molcel.2019.01.025. Arbitrium peptide receptor from spbeta phage in complex with 43 mer DNA. SNAP output
6ht5 transcription X-ray (3.451 Å) Vahokoski J, Pogenberg V, Wilmanns M "Oct4/Sox2:UTF1 structure." Oct4-sox2:utf1 structure. SNAP output
6hts DNA binding protein cryo-EM (4.8 Å) Ayala R, Willhoft O, Aramayo RJ, Wilkinson M, McCormack EA, Ocloo L, Wigley DB, Zhang X (2018) "Structure and regulation of the human INO80-nucleosome complex." Nature, 556, 391-395. doi: 10.1038/s41586-018-0021-6. cryo-EM structure of the human ino80 complex bound to nucleosome. SNAP output
6hv9 DNA binding protein cryo-EM (4.98 Å) Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC, Diffley JFX, Costa A (2018) "Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome." Nat Commun, 9, 5061. doi: 10.1038/s41467-018-07417-1. S. cerevisiae cmg-pol epsilon-DNA. SNAP output
6hyu RNA binding protein X-ray (3.22 Å) Felisberto-Rodrigues C, Thomas JC, McAndrew C, Le Bihan YV, Burke R, Workman P, van Montfort RLM (2019) "Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release." Biochem.J., 476, 2521-2543. doi: 10.1042/BCJ20190383. Crystal structure of dhx8 helicase bound to single stranded poly-adenine RNA. SNAP output
6i1k hydrolase X-ray (2.65 Å) Swarts DC, Jinek M (2019) "Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a." Mol. Cell, 73, 589-600.e4. doi: 10.1016/j.molcel.2018.11.021. Crystal structure of catalytically inactive fncas12a in complex with a crrna guide and a dsDNA target. SNAP output
6i1l hydrolase X-ray (2.98 Å) Swarts DC, Jinek M (2019) "Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a." Mol. Cell, 73, 589-600.e4. doi: 10.1016/j.molcel.2018.11.021. Crystal structure of fncas12a in complex with a crrna guide and ssDNA target. SNAP output
6i52 DNA binding protein cryo-EM (4.7 Å) Yates LA, Aramayo RJ, Pokhrel N, Caldwell CC, Kaplan JA, Perera RL, Spies M, Antony E, Zhang X (2018) "A structural and dynamic model for the assembly of Replication Protein A on single-stranded DNA." Nat Commun, 9, 5447. doi: 10.1038/s41467-018-07883-7. Yeast rpa bound to ssDNA. SNAP output
6i84 transcription cryo-EM (4.4 Å) Farnung L, Vos SM, Cramer P (2018) "Structure of transcribing RNA polymerase II-nucleosome complex." Nat Commun, 9, 5432. doi: 10.1038/s41467-018-07870-y. Structure of transcribing RNA polymerase ii-nucleosome complex. SNAP output
6i8a DNA binding protein X-ray (2.652 Å) Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV, Kamerlin SCL, Johansson E (2019) "Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon." Nat Commun, 10, 373. doi: 10.1038/s41467-018-08114-9. The crystal structure of the pol2 catalytic domain of DNA polymerase epsilon carrying a p301r substitution.. SNAP output
6ide transcription-DNA X-ray (2.51 Å) Wu H, Li M, Guo H, Zhou H, Li B, Xu Q, Xu C, Yu F, He J (2019) "Crystal structure of theVibrio choleraeVqmA-ligand-DNA complex provides insight into ligand-binding mechanisms relevant for drug design." J. Biol. Chem., 294, 2580-2592. doi: 10.1074/jbc.RA118.006082. Crystal structure of the vibrio cholera vqma-ligand-DNA complex provides molecular mechanisms for drug design. SNAP output
6idg immune system X-ray (2.0 Å) Yokoyama H, Mizutani R, Noguchi S, Hayashida N (2019) "Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms." Acta Crystallogr.,Sect.F, 75, 80-88. doi: 10.1107/S2053230X18017661. Antibody 64m-5 fab in complex with dt(6-4)t. SNAP output
6ido transcription X-ray (3.748 Å) Lou YC, Chou CC, Yeh HH, Chien CY, Sadotra S, Hsu CH, Chen C (2020) "Structural basis for -35 element recognition by sigma4chimera proteins and their interactions with PmrA response regulator." Proteins, 88, 69-81. doi: 10.1002/prot.25768. Crystal structure of klebsiella pneumoniae sigma4 of sigmas fusing with the RNA polymerase beta-flap-tip-helix in complex with -35 element DNA. SNAP output
6ifm toxin-antitoxin-DNA X-ray (2.804 Å) Park D, Yoon HJ, Lee KY, Park SJ, Cheon SH, Lee HH, Lee SJ, Lee BJ (2020) "Crystal structure of proteolyzed VapBC and DNA-bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca2+-dependent ribonuclease." Faseb J., 34, 3051-3068. doi: 10.1096/fj.201901989R. Crystal structure of DNA bound vapbc from salmonella typhimurium. SNAP output
6ig1 DNA binding protein X-ray (1.97 Å) Kottur J, Nair DT (2018) "Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction." Nucleic Acids Res., 46, 5875-5885. doi: 10.1093/nar/gky402. DNA polymerase iv - DNA ternary complex 10. SNAP output
6iid hydrolase-DNA X-ray (2.986 Å) Wu CC, Lin JLJ, Yang-Yen HF, Yuan HS (2019) "A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication." Nucleic Acids Res., 47, 5405-5419. doi: 10.1093/nar/gkz241. Human exog-h140a in complex with RNA-DNA chimeric duplex. SNAP output
6iiq DNA binding protein-DNA X-ray (1.85 Å) Wang Z, Tian W (2019) "Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA." Nucleic Acids Res. Complex structure of the hrp3 pwwp domain with a 16-bp ta-rich DNA. SNAP output
6iir DNA binding protein-DNA X-ray (2.2 Å) Wang Z, Tian W (2019) "Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA." Nucleic Acids Res. Complex structure of the hrp3 pwwp domain with a 10-bp gc-rich DNA. SNAP output
6iis DNA binding protein-DNA X-ray (2.358 Å) Wang Z, Tian W (2019) "Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide." Nucleic Acids Res. Complex structure of the hrp3 pwwp domain with both a 16-bp ta-rich DNA and an h3k36me3-containing histone peptide. SNAP output
6iit DNA binding protein-DNA X-ray (2.1 Å) Wang Z, Tian W (2019) "Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and a H3K36me2-containing histone peptide." Nucleic Acids Res. Complex structure of the hrp3 pwwp domain with both a 16-bp ta-rich DNA and an h3k36me2-containing histone peptide. SNAP output
6ik9 transferase-DNA X-ray (2.435 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2019) "Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors." Biochem. Biophys. Res. Commun., 509, 943-948. doi: 10.1016/j.bbrc.2019.01.026. Hiv-1 reverse transcriptase with q151m-g112s-d113a-y115f-f116y-f160l-i159l:DNA:dgtp ternary complex. SNAP output
6ika transferase-DNA X-ray (2.598 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2019) "Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors." Biochem. Biophys. Res. Commun., 509, 943-948. doi: 10.1016/j.bbrc.2019.01.026. Hiv-1 reverse transcriptase with q151m-g112s-d113a-y115f-f116y-f160l-i159l:DNA:entecavir-triphosphate ternary complex. SNAP output
6imj ligase-DNA X-ray (2.554 Å) Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R, Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J (2019) "Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues." Nat Commun, 10, 387. doi: 10.1038/s41467-019-08296-w. The crystal structure of se-asfvlig:DNA complex. SNAP output
6imk ligase-DNA X-ray (2.502 Å) Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R, Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J (2019) "Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues." Nat Commun, 10, 387. doi: 10.1038/s41467-019-08296-w. The crystal structure of asfvlig:cg complex. SNAP output
6iml ligase-DNA X-ray (2.35 Å) Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R, Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J (2019) "Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues." Nat Commun, 10, 387. doi: 10.1038/s41467-019-08296-w. The crystal structure of asfvlig:ct1 complex. SNAP output
6imn ligase-DNA X-ray (2.7 Å) Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R, Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J (2019) "Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues." Nat Commun, 10, 387. doi: 10.1038/s41467-019-08296-w. The crystal structure of asfvlig:ct2 complex. SNAP output
6inq transcription-RNA-DNA cryo-EM (6.9 Å) Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine S, Kurumizaka H (2018) "Structural basis of the nucleosome transition during RNA polymerase II passage." Science, 362, 595-598. doi: 10.1126/science.aau9904. RNA polymerase ii elongation complex stalled at shl(-1) of the nucleosome, with foreign DNA (+1 position). SNAP output
6iod DNA binding protein-DNA X-ray (1.66 Å) Tu J, Chen R, Yang Y, Cao W, Xie W (2019) "Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation." Nat.Chem.Biol., 15, 615-622. doi: 10.1038/s41589-019-0290-x. The structure of udgx in complex with single-stranded DNA. SNAP output
6ipd transferase-DNA X-ray (1.7 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Post-catalytic complex of human DNA polymerase mu with templating adenine and mn-8oxodgmp. SNAP output
6ipe transferase-DNA X-ray (1.7 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Post-catalytic complex of human DNA polymerase mu with templating adenine and mg-8oxodgmp. SNAP output
6ipf transferase-DNA X-ray (1.77 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Post-catalytic complex of human DNA polymerase mu with templating cytosine and mn-8oxodgmp. SNAP output
6ipg transferase-DNA X-ray (1.62 Å) Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano Y, Maestre-Reyna M, Wu WJ, Tsai MD (2019) "Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." J.Am.Chem.Soc., 141, 8489-8502. doi: 10.1021/jacs.9b01741. Post-catalytic complex of human DNA polymerase mu with templating cytosine and mg-8oxodgmp. SNAP output
6ipu DNA binding protein-DNA X-ray (1.99 Å) Sharma D, De Falco L, Padavattan S, Rao C, Geifman-Shochat S, Liu CF, Davey CA (2019) "PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome." Nat Commun, 10, 5751. doi: 10.1038/s41467-019-13641-0. Human nucleosome core particle containing 145 bp of DNA. SNAP output
6iq4 DNA binding protein-DNA X-ray (2.25 Å) Batchelor LK, De Falco L, von Erlach T, Sharma D, Adhireksan Z, Roethlisberger U, Davey CA, Dyson PJ (2019) "Crosslinking Allosteric Sites on the Nucleosome." Angew.Chem.Int.Ed.Engl., 58, 15660-15664. doi: 10.1002/anie.201906423. Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing rapta and gold(i) 4-(diphenylphosphino)benzoic acid groups.. SNAP output
6ir8 transcription-DNA X-ray (2.3 Å) Cheng X, Zhao Y, Jiang Q, Yang J, Zhao W, Taylor IA, Peng YL, Wang D, Liu J (2019) "Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain." Nucleic Acids Res., 47, 4308-4318. doi: 10.1093/nar/gkz113. Rice wrky-DNA complex. SNAP output
6ir9 transcription-RNA-DNA cryo-EM (3.8 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-1) of the nucleosome. SNAP output
6iro DNA binding protein-DNA cryo-EM (3.4 Å) Yan L, Wu H, Li X, Gao N, Chen Z (2019) "Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling." Nat. Struct. Mol. Biol., 26, 258-266. doi: 10.1038/s41594-019-0199-9. The crosslinked complex of iswi-nucleosome in the adp-bound state. SNAP output
6irq DNA binding protein-DNA X-ray (1.91 Å) Huang YH, Chen IC, Huang CY (2019) "Characterization of an SSB-dT25 complex: structural insights into the S-shaped ssDNA binding conformation." Rsc Adv, 9, 40388-40396. doi: 10.1039/C9RA09406G. Complexed crystal structure of passb with ssDNA dt25 at 1.91 angstrom resolution. SNAP output
6is7 transferase-DNA X-ray (2.8 Å) LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD (2019) "Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing." Commun Biol, 2, 224. doi: 10.1038/s42003-019-0458-7. Structure of 9n-i DNA polymerase incorporation with da in the active site. SNAP output
6is8 DNA binding protein-DNA X-ray (1.68 Å) Lin H, Zhang D, Zuo K, Yuan C, Li J, Huang M, Lin Z (2019) "Structural basis of sequence-specific Holliday junction cleavage by MOC1." Nat.Chem.Biol., 15, 1241-1248. doi: 10.1038/s41589-019-0377-4. Crystal structure of zmmoc1 d115n mutant in complex with holliday junction. SNAP output
6isf transferase-DNA X-ray (2.8 Å) LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD (2019) "Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing." Commun Biol, 2, 224. doi: 10.1038/s42003-019-0458-7. Structure of 9n-i DNA polymerase incorporation with dt in the active site. SNAP output
6isg transferase-DNA X-ray (3.401 Å) LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD (2019) "Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing." Commun Biol, 2, 224. doi: 10.1038/s42003-019-0458-7. Structure of 9n-i DNA polymerase incorporation with dg in the active site. SNAP output
6ish transferase-DNA X-ray (3.3 Å) LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD (2019) "Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing." Commun Biol, 2, 224. doi: 10.1038/s42003-019-0458-7. Structure of 9n-i DNA polymerase incorporation with 3'-al in the active site. SNAP output
6isi transferase-DNA X-ray (3.2 Å) LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J, Tsai MD (2019) "Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing." Commun Biol, 2, 224. doi: 10.1038/s42003-019-0458-7. Structure of 9n-i DNA polymerase incorporation with 3'-cl in the active site. SNAP output
6iuc DNA binding protein-DNA X-ray (3.4 Å) Chu CH, Yen CY, Chen BW, Lin MG, Wang LH, Tang KZ, Hsiao CD, Sun YJ (2019) "Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation." Nucleic Acids Res., 47, 2113-2129. doi: 10.1093/nar/gky1251. Structure of helicobacter pylori soj-atp complex bound to DNA. SNAP output
6iud DNA binding protein-DNA X-ray (2.506 Å) Chu CH, Yen CY, Chen BW, Lin MG, Wang LH, Tang KZ, Hsiao CD, Sun YJ (2019) "Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation." Nucleic Acids Res., 47, 2113-2129. doi: 10.1093/nar/gky1251. Structure of helicobacter pylori soj-adp complex bound to DNA. SNAP output
6iy2 structural protein-hydrolase-DNA cryo-EM (3.47 Å) Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z (2019) "Mechanism of DNA translocation underlying chromatin remodelling by Snf2." Nature, 567, 409-413. doi: 10.1038/s41586-019-1029-2. Structure of snf2-mmtv-a nucleosome complex at shl2 in adp state. SNAP output
6iy3 structural protein-hydrolase-DNA cryo-EM (3.67 Å) Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z (2019) "Mechanism of DNA translocation underlying chromatin remodelling by Snf2." Nature, 567, 409-413. doi: 10.1038/s41586-019-1029-2. Structure of snf2-mmtv-a nucleosome complex at shl-2 in adp state. SNAP output
6j0h DNA-antibiotic X-ray (1.52 Å) Satange R, Chuang CY, Neidle S, Hou MH (2019) "Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation." Nucleic Acids Res., 47, 8899-8912. doi: 10.1093/nar/gkz653. Crystal structure of actinomycin d- d(ttggcgaa) complex. SNAP output
6j4e DNA binding protein-DNA X-ray (3.126 Å) Xu YP, Xu H, Wang B, Su XD "Crystal structure of the AtWRKY1 domain." Crystal structure of the atwrky1 domain. SNAP output
6j4f DNA binding protein-DNA X-ray (2.4 Å) Xu YP, Xu H, Wang B, Su XD "Crystal structure of the AtWRKY2 domain." Crystal structure of the atwrky2 domain. SNAP output
6j4g DNA binding protein X-ray (3.0 Å) Xu YP, Xu H, Wang B, Su XD "Crystal structure of the N-terminal DNA binding domain of AtWRKY33." Crystal structure of the atwrky33 domain. SNAP output
6j4r transcription-DNA X-ray (2.8 Å) Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang Q, Wang Q, Yang W, Wu Y (2019) "Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1." Febs J., 286, 2809-2821. doi: 10.1111/febs.14846. Structural basis for the target DNA recognition and binding by the myb domain of phosphate starvation response regulator 1. SNAP output
6j4w transcription-RNA-DNA cryo-EM (7.9 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-5) of the nucleosome. SNAP output
6j4x transcription-RNA-DNA cryo-EM (4.3 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-1) of the nucleosome (+1a). SNAP output
6j4y transcription-RNA-DNA cryo-EM (4.3 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-1) of the nucleosome (+1b). SNAP output
6j4z transcription-RNA-DNA cryo-EM (4.1 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with spt4-5 and foreign DNA, stalled at shl(-1) of the nucleosome. SNAP output
6j50 transcription-RNA-DNA cryo-EM (4.7 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with spt4-5 and foreign DNA, stalled at shl(-1) of the nucleosome (tilted conformation). SNAP output
6j51 transcription-RNA-DNA cryo-EM (4.2 Å) Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI (2019) "Structural insight into nucleosome transcription by RNA polymerase II with elongation factors." Science, 363, 744-747. doi: 10.1126/science.aav8912. RNA polymerase ii elongation complex bound with spt4-5 and foreign DNA, stalled at shl(-1) of the nucleosome, weak elf1 (+1 position). SNAP output
6j5b transcription-DNA X-ray (2.7 Å) Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang Q, Wang Q, Yang W, Wu Y (2019) "Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1." Febs J., 286, 2809-2821. doi: 10.1111/febs.14846. Structural basis for the target DNA recognition and binding by the myb domain of phosphate starvation response regulator 1. SNAP output
6j7y hydrolase X-ray (2.203 Å) Chu LY, Agrawal S, Chen YP, Yang WZ, Yuan HS (2019) "Structural insights into nanoRNA degradation by human Rexo2." Rna, 25, 737-746. doi: 10.1261/rna.070557.119. Human mitochondrial oligoribonuclease in complex with DNA. SNAP output
6j80 hydrolase-DNA X-ray (1.812 Å) Chu LY, Agrawal S, Chen YP, Yang WZ, Yuan HS (2019) "Structural insights into nanoRNA degradation by human Rexo2." Rna, 25, 737-746. doi: 10.1261/rna.070557.119. Human mitochondrial oligoribonuclease in complex with poly-dt DNA. SNAP output
6j99 transcription cryo-EM (4.1 Å) Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan G, Lei M, Huang J (2019) "Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome." Cell Res., 29, 330-333. doi: 10.1038/s41422-019-0146-7. cryo-EM structure of human dot1l in complex with an h2b-monoubiquitinated nucleosome. SNAP output
6j9a transcription-DNA X-ray (2.915 Å) Tao Z, Hu H, Luo X, Jia B, Du J, He Y (2019) "Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis." Nat.Plants, 5, 424-435. doi: 10.1038/s41477-019-0402-3. Crystal structure of arabidopsis thaliana val1 in complex with flc DNA fragment. SNAP output
6j9b transcription-DNA X-ray (1.9 Å) Tao Z, Hu H, Luo X, Jia B, Du J, He Y (2019) "Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis." Nat.Plants, 5, 424-435. doi: 10.1038/s41477-019-0402-3. Arabidopsis fus3-DNA complex. SNAP output
6j9c transcription-DNA X-ray (3.102 Å) Tao Z, Hu H, Luo X, Jia B, Du J, He Y (2019) "Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis." Nat.Plants, 5, 424-435. doi: 10.1038/s41477-019-0402-3. Crystal structure of arabidopsis thaliana transcription factor lec2-DNA complex. SNAP output
6j9e transcription cryo-EM (3.41 Å) You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W, Feng Y, Zhang Y (2019) "Structural basis for transcription antitermination at bacterial intrinsic terminator." Nat Commun, 10, 3048. doi: 10.1038/s41467-019-10955-x. cryo-EM structure of xanthomonos oryzae transcription elongation complex with nusa and the bacteriophage protein p7. SNAP output
6j9f transcription cryo-EM (3.95 Å) You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W, Feng Y, Zhang Y (2019) "Structural basis for transcription antitermination at bacterial intrinsic terminator." Nat Commun, 10, 3048. doi: 10.1038/s41467-019-10955-x. cryo-EM structure of xanthomonos oryzae transcription elongation complex with the bacteriophage protein p7. SNAP output
6jbq transcription-DNA-RNA cryo-EM (4.02 Å) Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y (2019) "Structures and mechanism of transcription initiation by bacterial ECF factors." Nucleic Acids Res., 47, 7094-7104. doi: 10.1093/nar/gkz470. Cryoem structure of escherichia coli sigmae transcription initiation complex containing 5nt of RNA. SNAP output
6jbx transcription-DNA X-ray (2.2 Å) Zuo G, Chen ZP, Jiang YL, Zhu Z, Ding C, Zhang Z, Chen Y, Zhou CZ, Li Q (2019) "Structural insights into repression of the Pneumococcal fatty acid synthesis pathway by repressor FabT and co-repressor acyl-ACP." Febs Lett., 593, 2730-2741. doi: 10.1002/1873-3468.13534. Crystal structure of streptococcus pneumoniae fabt in complex with DNA. SNAP output
6jcx transcription X-ray (2.903 Å) Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y (2019) "Structures and mechanism of transcription initiation by bacterial ECF factors." Nucleic Acids Res., 47, 7094-7104. doi: 10.1093/nar/gkz470. Mycobacterium tuberculosis transcription initiation complex with ecf sigma factor sigma h and 6nt RNA. SNAP output
6jcy transcription X-ray (3.106 Å) Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y (2019) "Structures and mechanism of transcription initiation by bacterial ECF factors." Nucleic Acids Res., 47, 7094-7104. doi: 10.1093/nar/gkz470. Mycobacterium tuberculosis RNA polymerase transcription initiation open complex with a chimeric ecf sigma factor sigh-e. SNAP output
6jdg DNA binding protein-DNA X-ray (2.388 Å) Huang YH, Lin ES, Huang CY (2019) "Complexed crystal structure of SSB reveals a novel single-stranded DNA binding mode (SSB)3:1: Phe60 is not crucial for defining binding paths." Biochem.Biophys.Res.Commun., 520, 353-358. doi: 10.1016/j.bbrc.2019.10.036. Complexed crystal structure of passb with ssDNA dt20 at 2.39 angstrom resolution. SNAP output
6jdv hydrolase-RNA-DNA X-ray (3.1 Å) Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y (2019) "Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States." Mol.Cell, 76, 938. doi: 10.1016/j.molcel.2019.09.025. Crystal structure of nme1cas9 in complex with sgrna and target DNA (atatgatt pam) in catalytic state. SNAP output
6je3 hydrolase-RNA-DNA X-ray (2.931 Å) Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y (2019) "Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States." Mol.Cell, 76, 938. doi: 10.1016/j.molcel.2019.09.025. Crystal structure of nme2cas9 in complex with sgrna and target DNA (aggccc pam) with 5 nt overhang. SNAP output
6je4 hydrolase-hydrolase inhibitor-DNA-RNA X-ray (3.069 Å) Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y (2019) "Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States." Mol.Cell, 76, 938. doi: 10.1016/j.molcel.2019.09.025. Crystal structure of nme1cas9-sgrna-dsDNA dimer mediated by double protein inhibitor acriic3 monomers. SNAP output
6jfu hydrolase-RNA-DNA X-ray (3.2 Å) Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y (2019) "Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States." Mol.Cell, 76, 938. doi: 10.1016/j.molcel.2019.09.025. Crystal structure of nme2cas9 in complex with sgrna and target DNA (aggccc pam). SNAP output
6jg8 peptide binding protein-DNA X-ray (2.097 Å) Guan ZY, Pei K, Wang J, Cui YQ, Zhu X, Su X, Zhou YB, Zhang DL, Tang C, Yin P, Liu Z, Zou TT (2019) "Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage." Cell Discov, 5, 29. doi: 10.1038/s41421-019-0101-2. Crystal structure of aimr in complex with DNA. SNAP output
6jgw transcription-DNA X-ray (2.8 Å) Liu X, Hu Q, Yang J, Huang S, Wei T, Chen W, He Y, Wang D, Liu Z, Wang K, Gan J, Chen H (2019) "Selective cadmium regulation mediated by a cooperative binding mechanism in CadR." Proc.Natl.Acad.Sci.USA, 116, 20398-20403. doi: 10.1073/pnas.1908610116. Crystal structure of the transcriptional regulator cadr from p. putida in complex with DNA. SNAP output
6jgx transcription-DNA X-ray (2.71 Å) Liu X, Hu Q, Yang J, Huang S, Wei T, Chen W, He Y, Wang D, Liu Z, Wang K, Gan J, Chen H (2019) "Selective cadmium regulation mediated by a cooperative binding mechanism in CadR." Proc.Natl.Acad.Sci.USA, 116, 20398-20403. doi: 10.1073/pnas.1908610116. Crystal structure of the transcriptional regulator cadr from p. putida in complex with cadmium(ii) and DNA. SNAP output
6jhe transcription-DNA X-ray (3.101 Å) Kwon E, Devkota SR, Pathak D, Dahal P, Kim DY (2019) "Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis." Plos One, 14, e0221666. doi: 10.1371/journal.pone.0221666. Crystal structure of bacillus subtilis sigw domain 4 in complexed with -35 element DNA. SNAP output
6jip DNA binding protein-DNA X-ray (1.659 Å) Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y (2020) "Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins." Nucleic Acids Res., 48, 432-444. doi: 10.1093/nar/gkz1045. Crystal structure of streptococcus pneumoniae sp_0782 (residues 7-79) in complex with single-stranded DNA dt6. SNAP output
6jiq DNA binding protein-DNA X-ray (1.67 Å) Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y (2020) "Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins." Nucleic Acids Res., 48, 432-444. doi: 10.1093/nar/gkz1045. Crystal structure of streptococcus pneumoniae sp_0782 (residues 7-79) in complex with single-stranded DNA dt6. SNAP output
6jm9 gene regulation cryo-EM (7.3 Å) Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY, Kim SJ, Hohng S, Song JJ (2019) "Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase." Genes Dev., 33, 620-625. doi: 10.1101/gad.323790.118. cryo-EM structure of dot1l bound to unmodified nucleosome. SNAP output
6jma gene regulation cryo-EM (6.8 Å) Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY, Kim SJ, Hohng S, Song JJ (2019) "Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase." Genes Dev., 33, 620-625. doi: 10.1101/gad.323790.118. cryo-EM structure of dot1l bound to h2b ubiquitinated nucleosome. SNAP output
6jni transcription-DNA X-ray (2.9 Å) Liu X, Hu Q, Yang J, Huang S, Wei T, Chen W, He Y, Wang D, Liu Z, Wang K, Gan J, Chen H (2019) "Selective cadmium regulation mediated by a cooperative binding mechanism in CadR." Proc.Natl.Acad.Sci.USA, 116, 20398-20403. doi: 10.1073/pnas.1908610116. Crystal structure of the transcriptional regulator cadr from p. putida in complex with zinc(ii) and DNA. SNAP output
6jnl DNA binding protein-DNA X-ray (2.15 Å) Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X (2019) "DNA methylation repels targeting of Arabidopsis REF6." Nat Commun, 10, 2063. doi: 10.1038/s41467-019-10026-1. Ref6 znf2-4-nac004 complex. SNAP output
6jnm DNA binding protein-DNA X-ray (2.05 Å) Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X (2019) "DNA methylation repels targeting of Arabidopsis REF6." Nat Commun, 10, 2063. doi: 10.1038/s41467-019-10026-1. Ref6 znf2-4-nac004-mc3 complex. SNAP output
6jnn DNA binding protein-DNA X-ray (2.6 Å) Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X (2019) "DNA methylation repels targeting of Arabidopsis REF6." Nat Commun, 10, 2063. doi: 10.1038/s41467-019-10026-1. Ref6 znf2-4-nac004-mc1 complex. SNAP output
6jnx transcription,DNA,RNA cryo-EM (4.08 Å) Shi J, Gao X, Tian T, Yu Z, Gao B, Wen A, You L, Chang S, Zhang X, Zhang Y, Feng Y (2019) "Structural basis of Q-dependent transcription antitermination." Nat Commun, 10, 2925. doi: 10.1038/s41467-019-10958-8. cryo-EM structure of a q-engaged arrested complex. SNAP output
6joo hydrolase-DNA-RNA X-ray (2.9 Å) Hirano S, Abudayyeh OO, Gootenberg JS, Horii T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O (2019) "Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9." Nat Commun, 10, 1968. doi: 10.1038/s41467-019-09741-6. Crystal structure of corynebacterium diphtheriae cas9 in complex with sgrna and target DNA. SNAP output
6jou DNA binding protein-DNA X-ray (2.17 Å) Horikoshi N, Kujirai T, Sato K, Kimura H, Kurumizaka H (2019) "Structure-based design of an H2A.Z.1 mutant stabilizing a nucleosome in vitro and in vivo." Biochem.Biophys.Res.Commun., 515, 719-724. doi: 10.1016/j.bbrc.2019.06.012. Crystal structure of the human nucleosome containing h2a.z.1 s42r. SNAP output
6jpi antitoxin-DNA X-ray (3.143 Å) Liu Y, Gao Z, Zhang H, Dong Y "Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa." Crystal structure of pa4674 in complex with its operator DNA (28bp) from pseudomonas aeruginosa. SNAP output
6jr0 gene regulation-DNA X-ray (2.5 Å) Saotome M, Horikoshi N, Urano K, Kujirai T, Yuzurihara H, Kurumizaka H, Kagawa W (2019) "Structure determination of the nucleosome core particle by selenium SAD phasing." Acta Crystallogr D Struct Biol, 75, 930-936. doi: 10.1107/S2059798319012713. Crystal structure of the human nucleosome phased with 12 selenium atoms. SNAP output
6jr1 gene regulation-DNA X-ray (2.4 Å) Saotome M, Horikoshi N, Urano K, Kujirai T, Yuzurihara H, Kurumizaka H, Kagawa W (2019) "Structure determination of the nucleosome core particle by selenium SAD phasing." Acta Crystallogr D Struct Biol, 75, 930-936. doi: 10.1107/S2059798319012713. Crystal structure of the human nucleosome phased with 16 selenium atoms. SNAP output
6jrf DNA binding protein-DNA X-ray (2.047 Å) Lin H, Zhang D, Zuo K, Yuan C, Li J, Huang M, Lin Z (2019) "Structural basis of sequence-specific Holliday junction cleavage by MOC1." Nat.Chem.Biol., 15, 1241-1248. doi: 10.1038/s41589-019-0377-4. Crystal structure of zmmoc1-holliday junction complex in the presence of calcium. SNAP output
6jrg DNA binding protein-DNA X-ray (2.005 Å) Lin H, Zhang D, Zuo K, Yuan C, Li J, Huang M, Lin Z (2019) "Structural basis of sequence-specific Holliday junction cleavage by MOC1." Nat.Chem.Biol., 15, 1241-1248. doi: 10.1038/s41589-019-0377-4. Crystal structure of zmmoc1 h253a mutant in complex with holliday junction. SNAP output
6jrp transcription X-ray (3.0 Å) Lee H, Song JJ (2019) "The crystal structure of Capicua HMG-box domain complexed with the ETV5-DNA and its implications for Capicua-mediated cancers." Febs J., 286, 4951-4963. doi: 10.1111/febs.15008. Crystal structure of cic-hmg-etv5-DNA complex. SNAP output
6jtq DNA binding protein-DNA X-ray (2.48 Å) Liu L, Yi C "RVD HA specifically contacts 5mC through van der Waals interactions." Rvd ha specifically contacts 5mc through van der waals interactions. SNAP output
6jul replication-DNA X-ray (2.3 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Msdpo4-DNA complex 1. SNAP output
6jum replication-DNA X-ray (1.78 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Msdpo4-DNA complex 2. SNAP output
6jun replication-DNA X-ray (2.51 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Msdpo4-DNA complex 3. SNAP output
6juo replication-DNA X-ray (2.16 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Msdpo4-DNA complex 4. SNAP output
6jup replication-DNA X-ray (2.44 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Mutant poliv-DNA incoming nucleotide complex. SNAP output
6juq replication-DNA X-ray (2.74 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Mutant poliv-DNA incoming nucleotide complex 2. SNAP output
6jur replication-DNA X-ray (2.06 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Msdpo4-DNA complex 5. SNAP output
6jus replication-DNA X-ray (2.5 Å) Johnson MK, Kottur J, Nair DT (2019) "A polar filter in DNA polymerases prevents ribonucleotide incorporation." Nucleic Acids Res., 47, 10693-10705. doi: 10.1093/nar/gkz792. Msdpo4-DNA complex 6. SNAP output
6jvy RNA binding protein-DNA X-ray (2.003 Å) Qian K, Li M, Wang J, Zhang M, Wang M (2020) "Structural basis for mRNA recognition by human RBM38." Biochem.J., 477, 161-172. doi: 10.1042/BCJ20190652. Crystal structure of rbm38 in complex with single-stranded DNA. SNAP output
6jvz DNA binding protein-DNA X-ray (2.48 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Rvd ha specifically contacts 5mc through van der waals interactions. SNAP output
6jw0 DNA binding protein-DNA X-ray (2.2 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Universal rvd r* accommodates cytosine via water-mediated interactions. SNAP output
6jw1 DNA binding protein-DNA X-ray (2.49 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Universal rvd r* accommodates 5mc via water-mediated interactions. SNAP output
6jw2 DNA binding protein-DNA X-ray (3.03 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Universal rvd r* accommodates 5hmc via water-mediated interactions. SNAP output
6jw3 DNA binding protein-DNA X-ray (3.1 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Degenerate rvd rg forms a distinct loop conformation. SNAP output
6jw4 DNA binding protein-DNA X-ray (3.09 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Degenerate rvd rg forms a distinct loop conformation. SNAP output
6jw5 DNA binding protein-DNA X-ray (2.99 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Rvd q* recognizes 5hmc through water-mediated h bonds. SNAP output
6jxd DNA binding protein-DNA X-ray (2.25 Å) Sharma D, De Falco L, Padavattan S, Rao C, Geifman-Shochat S, Liu CF, Davey CA (2019) "PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome." Nat Commun, 10, 5751. doi: 10.1038/s41467-019-13641-0. Human nucleosome core particle with cohesive end DNA termini. SNAP output
6jyl DNA binding protein-DNA cryo-EM (3.37 Å) Yan L, Wu H, Li X, Gao N, Chen Z (2019) "Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling." Nat.Struct.Mol.Biol., 26, 258-266. doi: 10.1038/s41594-019-0199-9. The crosslinked complex of iswi-nucleosome in the adp.bef-bound state. SNAP output
6jyw transcription-DNA X-ray (2.95 Å) Liu XC, Chen H "Crystal structure of the transcription regulator CadR N81M mutant from P. putida in complex with Cadmium(II) and DNA." Crystal structure of the transcription regulator cadr n81m mutant from p. putida in complex with cadmium(ii) and DNA. SNAP output
6k1i DNA binding protein-DNA X-ray (2.75 Å) Sharma D, De Falco L, Padavattan S, Rao C, Geifman-Shochat S, Liu CF, Davey CA (2019) "PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome." Nat Commun, 10, 5751. doi: 10.1038/s41467-019-13641-0. Human nucleosome core particle with gammah2a.x variant. SNAP output
6k1j DNA binding protein-DNA X-ray (2.85 Å) Sharma D, De Falco L, Padavattan S, Rao C, Geifman-Shochat S, Liu CF, Davey CA (2019) "PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome." Nat Commun, 10, 5751. doi: 10.1038/s41467-019-13641-0. Human nucleosome core particle with h2a.x variant. SNAP output
6k1k DNA binding protein-DNA X-ray (2.2 Å) Sharma D, De Falco L, Padavattan S, Rao C, Geifman-Shochat S, Liu CF, Davey CA (2019) "PARP1 exhibits enhanced association and catalytic efficiency with gamma H2A.X-nucleosome." Nat Commun, 10, 5751. doi: 10.1038/s41467-019-13641-0. Human nucleosome core particle with h2a.x s139e variant. SNAP output
6k1p DNA binding protein-DNA cryo-EM (3.87 Å) Yan L, Wu H, Li X, Gao N, Chen Z (2019) "Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling." Nat.Struct.Mol.Biol., 26, 258-266. doi: 10.1038/s41594-019-0199-9. The complex of iswi-nucleosome in the adp.bef-bound state. SNAP output
6k2j DNA binding protein-DNA X-ray (2.4 Å) Huang Q, Duan B, Dong X, Fan S, Xia B (2020) "GapR binds DNA through dynamic opening of its tetrameric interface." Nucleic Acids Res., 48, 9372-9386. doi: 10.1093/nar/gkaa644. Crystal structure of the DNA complex of c. crescentus gapr. SNAP output
6k3j hydrolase-DNA NMR Yan X, Lan W, Wang C, Cao C (2019) "Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA." Chem Asian J, 14, 2235-2241. doi: 10.1002/asia.201900480. Solution structure of apobec3g-cd2 with ssDNA, product a. SNAP output
6k3k hydrolase-DNA NMR Yan X, Lan W, Wang C, Cao C (2019) "Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA." Chem Asian J, 14, 2235-2241. doi: 10.1002/asia.201900480. Solution structure of apobec3g-cd2 with ssDNA, product b. SNAP output
6k3z hydrolase-DNA-RNA X-ray (3.2 Å) Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q (2019) "Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease." Plos Biol., 17, e3000496. doi: 10.1371/journal.pbio.3000496. Crystal structure of dcas9 in complex with sgrna and DNA (tga pam). SNAP output
6k4p hydrolase-DNA-RNA X-ray (2.9 Å) Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q (2019) "Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease." Plos Biol., 17, e3000496. doi: 10.1371/journal.pbio.3000496. Crystal structure of xcas9 in complex with sgrna and DNA (tgg pam). SNAP output
6k4q hydrolase-DNA-RNA X-ray (2.7 Å) Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q (2019) "Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease." Plos Biol., 17, e3000496. doi: 10.1371/journal.pbio.3000496. Crystal structure of xcas9 in complex with sgrna and DNA (cgg pam). SNAP output
6k4s hydrolase-DNA-RNA X-ray (3.01 Å) Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q (2019) "Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease." Plos Biol., 17, e3000496. doi: 10.1371/journal.pbio.3000496. Crystal structure of xcas9 in complex with sgrna and DNA (tgc pam). SNAP output
6k4u hydrolase-DNA X-ray (3.2 Å) Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q (2019) "Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease." Plos Biol., 17, e3000496. doi: 10.1371/journal.pbio.3000496. Crystal structure of xcas9 in complex with sgrna and DNA (tga pam). SNAP output
6k4y transcription cryo-EM (3.79 Å) Shi J, Wen A, Zhao M, You L, Zhang Y, Feng Y (2019) "Structural basis of sigma appropriation." Nucleic Acids Res., 47, 9423-9432. doi: 10.1093/nar/gkz682. Cryoem structure of sigma appropriation complex. SNAP output
6k57 hydrolase-RNA-DNA X-ray (2.98 Å) Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q (2019) "Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease." Plos Biol., 17, e3000496. doi: 10.1371/journal.pbio.3000496. Crystal structure of dcas9 in complex with sgrna and DNA (cga pam). SNAP output
6k8o isomerase, DNA binding protein-DNA X-ray (2.5 Å) Wang HQ, Zhang JH, Zheng X, Zheng ZF, Dong YH, Huang L, Gong Y "Crystal structures of the Sulfolobus solfataricus topoisomerase III reveal that its C-terminal novel zinc finger part is a unique decatenation domain." Crystal structure of the sulfolobus solfataricus topoisomerase iii in complex with DNA. SNAP output
6kbs DNA binding protein X-ray (1.601 Å) Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H (2019) "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK." Nucleic Acids Res., 47, 10388-10399. doi: 10.1093/nar/gkz744. Crystal structure of yedk in complex with ssDNA. SNAP output
6kbx DNA binding protein X-ray (1.221 Å) Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H (2019) "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK." Nucleic Acids Res., 47, 10388-10399. doi: 10.1093/nar/gkz744. Crystal structure of yedk in complex with ssDNA containing abasic site. SNAP output
6kbz DNA binding protein X-ray (1.653 Å) Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H (2019) "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK." Nucleic Acids Res., 47, 10388-10399. doi: 10.1093/nar/gkz744. Crystal structure of yedk with ssDNA containing a tetrahydrofuran abasic site. SNAP output
6kc7 hydrolase-RNA-DNA X-ray (3.3 Å) Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y (2019) "Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States." Mol.Cell, 76, 938. doi: 10.1016/j.molcel.2019.09.025. Crystal structure of nme1cas9 in complex with sgrna and target DNA (atatgatt pam) in seed-base paring state. SNAP output
6kc8 hydrolase-RNA-DNA X-ray (2.9 Å) Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y (2019) "Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States." Mol.Cell, 76, 938. doi: 10.1016/j.molcel.2019.09.025. Crystal structure of wt nme1cas9 in complex with sgrna and target DNA (atatgatt pam) in post-cleavage state. SNAP output
6kcp DNA binding protein-DNA X-ray (1.8 Å) Liu YC, Huang Y "Shuguo PWWP in complex with ssDNA." Shuguo pwwp in complex with ssDNA. SNAP output
6kcq DNA binding protein X-ray (1.701 Å) Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H (2019) "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK." Nucleic Acids Res., 47, 10388-10399. doi: 10.1093/nar/gkz744. Crystal structure of yedk with ssDNA containing an abasic site. SNAP output
6kcs DNA binding protein-DNA X-ray (2.1 Å) Hishiki A, Sato M, Hashimoto H (2020) "Structure of HIRAN domain of human HLTF bound to duplex DNA provides structural basis for DNA unwinding to initiate replication fork regression." J.Biochem., 167, 597-602. doi: 10.1093/jb/mvaa008. Crystal structure of hiran domain of hltf in complex with duplex DNA. SNAP output
6kda transferase-DNA X-ray (2.909 Å) Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS (2020) "Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B." Nucleic Acids Res., 48, 3949-3961. doi: 10.1093/nar/gkaa111. Crystal structure of human dnmt3b-dnmt3l in complex with DNA containing cpgpg site. SNAP output
6kdb transferase-DNA X-ray (2.862 Å) Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS (2020) "Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B." Nucleic Acids Res., 48, 3949-3961. doi: 10.1093/nar/gkaa111. Crystal structure of human dnmt3b-dnmt3l in complex with DNA containing cpgpt site. SNAP output
6kdi immune system X-ray (2.7 Å) Yokoyama H, Mizutani R, Noguchi S, Hayashida N (2019) "Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab." Sci Rep, 9, 18494. doi: 10.1038/s41598-019-54918-0. Antibody 64m-5 fab including isoasp in complex with dt(6-4)t. SNAP output
6kdj transferase-DNA X-ray (2.51 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2020) "Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine." Sci Rep, 10, 3021. doi: 10.1038/s41598-020-59775-w. Hiv-1 reverse transcriptase with q151m-y115f-f116y:DNA:lamivudine 5'-triphosphate ternary complex. SNAP output
6kdk transferase-DNA X-ray (2.56 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2020) "Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine." Sci Rep, 10, 3021. doi: 10.1038/s41598-020-59775-w. Hiv-1 reverse transcriptase with q151m-y115f-f116y:DNA:dctp ternary complex. SNAP output
6kdm transferase-DNA X-ray (2.32 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2020) "Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine." Sci Rep, 10, 3021. doi: 10.1038/s41598-020-59775-w. Hiv-1 reverse transcriptase with q151m-y115f-f116y:DNA:entecavir 5'-triphosphate ternary complex. SNAP output
6kdn transferase-DNA X-ray (2.303 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2020) "Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine." Sci Rep, 10, 3021. doi: 10.1038/s41598-020-59775-w. Hiv-1 reverse transcriptase with q151m-y115f-f116y:DNA:dgtp ternary complex. SNAP output
6kdo transferase-DNA X-ray (2.573 Å) Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H (2020) "Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine." Sci Rep, 10, 3021. doi: 10.1038/s41598-020-59775-w. Hiv-1 reverse transcriptase with q151m-y115f-f116y-m184v-f160m:DNA:lamivudine 5'-triphosphate ternary complex. SNAP output
6kdv DNA binding protein-DNA X-ray (3.11 Å) Yang J, Li J, Wang J, Sheng G, Wang M, Zhao H, Yang Y, Wang Y (2020) "Crystal structure of Cas1 in complex with branched DNA." Sci China Life Sci, 63, 516-528. doi: 10.1007/s11427-019-9827-x. Crystal structure of ttcas1-DNA complex. SNAP output
6ke9 DNA binding protein-DNA X-ray (2.22 Å) Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V, Korolev N, Rhodes D, Nordenskiold L (2020) "The human telomeric nucleosome displays distinct structural and dynamic properties." Nucleic Acids Res., 48, 5383-5396. doi: 10.1093/nar/gkaa289. The human telomeric nucleosome displays distinct structural and dynamic properties. SNAP output
6kf9 transcription cryo-EM (3.79 Å) Jun SH, Hyun J, Cha JS, Kim H, Bartlett MS, Cho HS, Murakami KS (2020) "Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase." Nat Commun, 11, 6123. doi: 10.1038/s41467-020-19998-x. cryo-EM structure of thermococcus kodakarensis RNA polymerase. SNAP output
6khy DNA binding protein X-ray (3.008 Å) Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C, Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J (2020) "A unique DNA-binding mode of African swine fever virus AP endonuclease." Cell Discov, 6, 13. doi: 10.1038/s41421-020-0146-2. The crystal structure of asfvap:ag. SNAP output
6ki3 DNA binding protein-DNA X-ray (2.354 Å) Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C, Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J (2020) "A unique DNA-binding mode of African swine fever virus AP endonuclease." Cell Discov, 6, 13. doi: 10.1038/s41421-020-0146-2. The crystal structure of asfvap:df commplex. SNAP output
6ki6 transcription-DNA X-ray (2.5 Å) Yang Y, Xu Z, He C, Zhang B, Shi Y, Li F (2019) "Structural insights into the recognition of gamma-globin gene promoter by BCL11A." Cell Res., 29, 960-963. doi: 10.1038/s41422-019-0221-0. Crystal structure of bcl11a in complex with gamma-globin -115 hpfh region. SNAP output
6kij DNA binding protein X-ray (1.58 Å) Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H (2019) "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK." Nucleic Acids Res., 47, 10388-10399. doi: 10.1093/nar/gkz744. Crystal structure of yedk with ssDNA containing an abasic site. SNAP output
6kiu transcription-DNA cryo-EM (3.2 Å) Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J (2019) "Structural basis of nucleosome recognition and modification by MLL methyltransferases." Nature, 573, 445-449. doi: 10.1038/s41586-019-1528-1. cryo-EM structure of human mll1-ubncp complex (3.2 angstrom). SNAP output
6kiv transcription-DNA cryo-EM (4.0 Å) Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J (2019) "Structural basis of nucleosome recognition and modification by MLL methyltransferases." Nature, 573, 445-449. doi: 10.1038/s41586-019-1528-1. cryo-EM structure of human mll1-ubncp complex (4.0 angstrom). SNAP output
6kiw transcription-DNA cryo-EM (4.0 Å) Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J (2019) "Structural basis of nucleosome recognition and modification by MLL methyltransferases." Nature, 573, 445-449. doi: 10.1038/s41586-019-1528-1. cryo-EM structure of human mll3-ubncp complex (4.0 angstrom). SNAP output
6kix transcription-DNA cryo-EM (4.1 Å) Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J (2019) "Structural basis of nucleosome recognition and modification by MLL methyltransferases." Nature, 573, 445-449. doi: 10.1038/s41586-019-1528-1. cryo-EM structure of human mll1-ncp complex, binding mode1. SNAP output
6kiz transcription-DNA cryo-EM (4.5 Å) Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J (2019) "Structural basis of nucleosome recognition and modification by MLL methyltransferases." Nature, 573, 445-449. doi: 10.1038/s41586-019-1528-1. cryo-EM structure of human mll1-ncp complex, binding mode2. SNAP output
6kj6 transcription cryo-EM (3.8 Å) Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y (2019) "Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor." Elife, 8. doi: 10.7554/eLife.50928. cryo-EM structure of escherichia coli crl transcription activation complex. SNAP output
6kks DNA binding protein-DNA X-ray (2.15 Å) Wang B, Luo Q, Li Y, Yin L, Zhou N, Li X, Gan J, Dong A (2020) "Structural insights into target DNA recognition by R2R3-MYB transcription factors." Nucleic Acids Res., 48, 460-471. doi: 10.1093/nar/gkz1081. Structural insights into target DNA recognition by r2r3-type myb transcription factor. SNAP output
6knb replication-DNA cryo-EM (6.9 Å) Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T, Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y (2020) "Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy." Bmc Biol., 18, 152. doi: 10.1186/s12915-020-00889-y. Pold-pcna-DNA (form a). SNAP output
6knc replication-DNA cryo-EM (9.3 Å) Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T, Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y (2020) "Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy." Bmc Biol., 18, 152. doi: 10.1186/s12915-020-00889-y. Pold-pcna-DNA (form b). SNAP output
6kon transcription X-ray (3.0 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Mycobacterium tuberculosis initial transcription complex comprising sigma h and 5'-oh RNA of 5 nt. SNAP output
6koo transcription X-ray (2.8 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Mycobacterium tuberculosis initial transcription complex comprising sigma h and 5'-oh RNA of 7 nt. SNAP output
6kop transcription X-ray (3.303 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Mycobacterium tuberculosis initial transcription complex comprising sigma h and 5'-oh RNA of 9 nt. SNAP output
6koq transcription X-ray (3.353 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Mycobacterium tuberculosis initial transcription complex comprising sigma h and 5'-oh RNA of 10 nt. SNAP output
6kqd transcription X-ray (3.3 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-oh RNA of 3 nt. SNAP output
6kqe translation X-ray (3.3 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-oh RNA of 4 nt. SNAP output
6kqf transcription X-ray (2.45 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-oh RNA of 5 nt. SNAP output
6kqg transcription X-ray (2.783 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-oh RNA of 6 nt. SNAP output
6kqh transcription X-ray (3.18 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-oh RNA of 7 nt. SNAP output
6kql transcription X-ray (2.89 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 4 nt. SNAP output
6kqm transcription X-ray (3.197 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 5 nt. SNAP output
6kqn transcription X-ray (3.489 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 6 nt. SNAP output
6ksf gene regulation X-ray (2.4 Å) Zhang M, Yang S, Nelakanti R, Zhao W, Liu G, Li Z, Liu X, Wu T, Xiao A, Li H (2020) "Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA." Cell Res., 30, 197-210. doi: 10.1038/s41422-019-0237-5. Crystal structure of alkbh1 bound to 21-mer DNA bulge. SNAP output
6kvd DNA binding protein-DNA X-ray (2.21 Å) Tanaka H, Sato S, Koyama M, Kujirai T, Kurumizaka H (2020) "Biochemical and structural analyses of the nucleosome containing human histone H2A.J." J.Biochem., 167, 419-427. doi: 10.1093/jb/mvz109. Crystal structure of human nucleosome containing h2a.j. SNAP output
6kvo plant protein-DNA X-ray (2.5 Å) Yan J, Hong S, Guan Z, He W, Zhang D, Yin P (2020) "Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1." Nat Commun, 11, 1417. doi: 10.1038/s41467-020-15242-8. Crystal structure of chloroplast resolvase in complex with holliday junction. SNAP output
6kw3 DNA binding protein-DNA cryo-EM (7.13 Å) Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z (2019) "Structure of the RSC complex bound to the nucleosome." Science, 366, 838-843. doi: 10.1126/science.aay0033. The classa rsc-nucleosome complex. SNAP output
6kw4 DNA binding protein-DNA cryo-EM (7.55 Å) Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z (2019) "Structure of the RSC complex bound to the nucleosome." Science, 366, 838-843. doi: 10.1126/science.aay0033. The classb rsc-nucleosome complex. SNAP output
6kw5 DNA binding protein-DNA cryo-EM (10.13 Å) Ye YP, Wu H, Chen KJ, Verma N, Cairns B, Gao N, Chen ZC "Structure of the RSC complex bound to the nucleosome." The classc rsc-nucleosome complex. SNAP output
6kxv DNA binding protein-DNA X-ray (3.63 Å) Dacher M, Tachiwana H, Horikoshi N, Kujirai T, Taguchi H, Kimura H, Kurumizaka H (2019) "Incorporation and influence of Leishmania histone H3 in chromatin." Nucleic Acids Res., 47, 11637-11648. doi: 10.1093/nar/gkz1040. Crystal structure of a nucleosome containing leishmania histone h3. SNAP output
6l2n hydrolase-DNA X-ray (2.45 Å) Miyazono KI, Wang D, Ito T, Tanokura M (2020) "Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI." Nucleic Acids Res., 48, 5106-5118. doi: 10.1093/nar/gkaa184. Crystal structure of the r.pabi(y68f-k154a)-dsDNA(gtac-3bp-gtac) complex. SNAP output
6l2o hydrolase-DNA X-ray (2.2 Å) Miyazono KI, Wang D, Ito T, Tanokura M (2020) "Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI." Nucleic Acids Res., 48, 5106-5118. doi: 10.1093/nar/gkaa184. Crystal structure of the r.pabi(y68f-k154a)-dsDNA(gtac-5bp-gtac) complex. SNAP output
6l3g hydrolase-DNA X-ray (3.3 Å) Su N, Byrd AK, Bharath SR, Yang O, Jia Y, Tang X, Ha T, Raney KD, Song H (2019) "Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases." Nat Commun, 10, 5375. doi: 10.1038/s41467-019-13414-9. Structural basis for DNA unwinding at forked dsDNA by two coordinating pif1 helicases. SNAP output
6l49 nuclear protein cryo-EM (18.9 Å) Takizawa Y, Ho CH, Tachiwana H, Matsunami H, Kobayashi W, Suzuki M, Arimura Y, Hori T, Fukagawa T, Ohi MD, Wolf M, Kurumizaka H (2020) "Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome." Structure, 28, 44. doi: 10.1016/j.str.2019.10.016. H3-ca-h3 tri-nucleosome with the 22 base-pair linker DNA. SNAP output
6l4a nuclear protein cryo-EM (12.3 Å) Takizawa Y, Ho CH, Tachiwana H, Matsunami H, Kobayashi W, Suzuki M, Arimura Y, Hori T, Fukagawa T, Ohi MD, Wolf M, Kurumizaka H (2020) "Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome." Structure, 28, 44. doi: 10.1016/j.str.2019.10.016. H3-h3-h3 tri-nucleosome with the 22 base-pair linker DNA. SNAP output
6l6l DNA binding protein X-ray (2.781 Å) Jiang L, Dai S, Li J, Liang X, Qu L, Chen X, Guo M, Chen Z, Chen L, Wei H, Chen Y (2019) "Structural basis of binding of homodimers of the nuclear receptor NR4A2 to selective Nur-responsive DNA elements." J.Biol.Chem., 294, 19795-19803. doi: 10.1074/jbc.RA119.010730. Structural basis of nr4a2 homodimers binding to selective nur-responsive elements. SNAP output
6l6q DNA binding protein X-ray (2.601 Å) Jiang L, Dai S, Li J, Liang X, Qu L, Chen X, Guo M, Chen Z, Chen L, Wei H, Chen Y (2019) "Structural basis of binding of homodimers of the nuclear receptor NR4A2 to selective Nur-responsive DNA elements." J.Biol.Chem., 294, 19795-19803. doi: 10.1074/jbc.RA119.010730. Structural basis of nr4a2 homodimers binding to selective nur-responsive elements. SNAP output
6l6s DNA binding protein X-ray (2.06 Å) Jia Q, Zeng H, Tu J, Sun L, Cao W, Xie W (2021) "Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability." DNA Repair (Amst), 97, 103008. doi: 10.1016/j.dnarep.2020.103008. The structure of the udgx mutant h109e crosslinked to single-stranded DNA. SNAP output
6l6y DNA binding protein-DNA,transcription X-ray (3.0 Å) Balasubramanian M, Kolatkar PR "Crystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain bound to DNA." Crystal structure of pluripotency reprogramming factor sox17 mutant (sox17ek) hmg domain bound to DNA. SNAP output
6l74 transcription X-ray (3.12 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 2 nt. SNAP output
6l84 DNA binding protein-DNA X-ray (2.602 Å) An J, Choi J, Hwang D, Park J, Pemble 4th CW, Duong THM, Kim KR, Ahn H, Chung HS, Ahn DR (2020) "The crystal structure of a natural DNA polymerase complexed with mirror DNA." Chem.Commun.(Camb.), 56, 2186-2189. doi: 10.1039/c9cc09351f. Complex of DNA polymerase iv and d-DNA duplex. SNAP output
6l8e antitoxin-toxin-DNA X-ray (2.35 Å) Xue L, Yue J, Ke J, Khan MH, Wen W, Sun B, Zhu Z, Niu L (2020) "Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system." Nucleic Acids Res., 48, 10527-10541. doi: 10.1093/nar/gkaa706. Crystal structure of heterohexameric yoeb-yefm complex bound to 26bp-DNA. SNAP output
6l97 DNA binding protein-DNA X-ray (2.362 Å) An J, Choi J, Hwang D, Park J, Pemble 4th CW, Duong THM, Kim KR, Ahn H, Chung HS, Ahn DR (2020) "The crystal structure of a natural DNA polymerase complexed with mirror DNA." Chem.Commun.(Camb.), 56, 2186-2189. doi: 10.1039/c9cc09351f. Complex of DNA polymerase iv and l-DNA duplex. SNAP output
6l9h DNA binding protein-DNA X-ray (2.6 Å) Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V, Korolev N, Rhodes D, Nordenskiold L (2020) "The human telomeric nucleosome displays distinct structural and dynamic properties." Nucleic Acids Res., 48, 5383-5396. doi: 10.1093/nar/gkaa289. The human telomeric nucleosome displays distinct structural and dynamic properties. SNAP output
6l9z DNA binding protein X-ray (2.5 Å) Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA (2021) "Engineering nucleosomes for generating diverse chromatin assemblies." Nucleic Acids Res., 49, e52. doi: 10.1093/nar/gkab070. 338 bp di-nucleosome assembled with linker histone h1.x. SNAP output
6la2 DNA binding protein X-ray (3.89 Å) Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA (2021) "Engineering nucleosomes for generating diverse chromatin assemblies." Nucleic Acids Res., 49, e52. doi: 10.1093/nar/gkab070. 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone h1.0. SNAP output
6la8 DNA binding protein X-ray (3.4 Å) Adhireksan Z, Sharma D, Lee PL, Davey CA (2020) "Near-atomic resolution structures of interdigitated nucleosome fibres." Nat Commun, 11, 4747. doi: 10.1038/s41467-020-18533-2. 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone h1.0. SNAP output
6la9 DNA binding protein X-ray (3.7 Å) Adhireksan Z, Sharma D, Lee PL, Davey CA (2020) "Near-atomic resolution structures of interdigitated nucleosome fibres." Nat Commun, 11, 4747. doi: 10.1038/s41467-020-18533-2. 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone h1.0 (high cryoprotectant). SNAP output
6lab DNA binding protein X-ray (3.2 Å) Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA (2021) "Engineering nucleosomes for generating diverse chromatin assemblies." Nucleic Acids Res., 49, e52. doi: 10.1093/nar/gkab070. 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone h1.0. SNAP output
6lae DNA binding protein-DNA X-ray (2.81 Å) Lian FM, Yang X, Jiang YL, Yang F, Li C, Yang W, Qian C (2020) "New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA." Int.J.Biol.Macromol., 148, 466-474. doi: 10.1016/j.ijbiomac.2020.01.169. Crystal structure of the DNA-binding domain of human xpa in complex with DNA. SNAP output
6lb3 antitoxin-DNA X-ray (2.497 Å) Liu Y, Zhang H, Gao Z, Dong Y "Crystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas aeruginosa." Crystal structure of pa4674 in complex with its operator DNA (18bp) from pseudomonas aeruginosa. SNAP output
6lbi DNA binding protein X-ray (3.067 Å) Li J, Dai S, Chen X, Liang X, Qu L, Jiang L, Guo M, Zhou Z, Wei H, Zhang H, Chen Z, Chen L, Chen Y (2021) "Mechanism of forkhead transcription factors binding to a novel palindromic DNA site." Nucleic Acids Res., 49, 3573-3583. doi: 10.1093/nar/gkab086. Crystal structure of foxo1-dbd homodimer bound to a palindromic DNA sequence. SNAP output
6lbm transcription X-ray (2.841 Å) Li J, Dai S, Chen X, Liang X, Qu L, Jiang L, Guo M, Zhou Z, Wei H, Zhang H, Chen Z, Chen L, Chen Y (2021) "Mechanism of forkhead transcription factors binding to a novel palindromic DNA site." Nucleic Acids Res., 49, 3573-3583. doi: 10.1093/nar/gkab086. Crystal structure of foxc2-dbd bound to a palindromic DNA sequence. SNAP output
6lbr DNA binding protein-DNA X-ray (2.5 Å) Ge Y, Wu Z, Chen H, Zhong Q, Shi S, Li G, Wu J, Lei M (2020) "Structural insights into telomere protection and homeostasis regulation by yeast CST complex." Nat.Struct.Mol.Biol., 27, 752-762. doi: 10.1038/s41594-020-0459-8. Crystal structure of yeast cdc13 and ssDNA. SNAP output
6lc1 DNA binding protein-DNA X-ray (3.12 Å) Jiang L, Wei H, Yan N, Dai S, Li J, Qu L, Chen X, Guo M, Chen Z, Chen Y (2020) "Structural basis of NR4A1 bound to the human pituitary proopiomelanocortin gene promoter." Biochem.Biophys.Res.Commun., 523, 1-5. doi: 10.1016/j.bbrc.2019.11.192. Structural basis of nr4a1 bound to the human pituitary proopiomelanocortin gene promoter. SNAP output
6lct hydrolase-DNA X-ray (2.55 Å) Yan J, Hong S, Guan Z, He W, Zhang D, Yin P (2020) "Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1." Nat Commun, 11, 1417. doi: 10.1038/s41467-020-15242-8. Crystal structure of catalytic inactive chloroplast resolvase ntmoc1 in complex with holliday junction. SNAP output
6ldi transcription (DNA to RNA) cryo-EM (3.69 Å) Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O'Halloran TV, Zhang Y (2021) "CueR activates transcription through a DNA distortion mechanism." Nat.Chem.Biol., 17, 57-64. doi: 10.1038/s41589-020-00653-x. The cryo-EM structure of e. coli cuer transcription activation complex. SNAP output
6ldm DNA binding protein-DNA X-ray (2.4 Å) Traczyk A, Liew CW, Gill DJ, Rhodes D (2020) "Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1." Nucleic Acids Res., 48, 4562-4571. doi: 10.1093/nar/gkaa171. Structural basis of g-quadruplex DNA recognition by the yeast telomeric protein rap1. SNAP output
6le9 DNA binding protein-DNA X-ray (2.6 Å) Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V, Korolev N, Rhodes D, Nordenskiold L (2020) "The human telomeric nucleosome displays distinct structural and dynamic properties." Nucleic Acids Res., 48, 5383-5396. doi: 10.1093/nar/gkaa289. The human telomeric nucleosome displays distinct structural and dynamic properties. SNAP output
6ler DNA binding protein X-ray (3.0 Å) Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA (2021) "Engineering nucleosomes for generating diverse chromatin assemblies." Nucleic Acids Res., 49, e52. doi: 10.1093/nar/gkab070. 169 bp nucleosome harboring non-identical cohesive DNA termini.. SNAP output
6lew DNA binding protein-DNA X-ray (2.48 Å) Liu L, Yi C "RVD HA specifically contacts 5mC through van der Waals interactions." Rvd ha specifically contacts 5mc through van der waals interactions. SNAP output
6lff transcription-DNA X-ray (1.79 Å) Yamasaki K, Akutsu Y, Yamasaki T, Miyagishi M, Kubota T (2020) "Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts." Nucleic Acids Res., 48, 4551-4561. doi: 10.1093/nar/gkaa170. Transcription factor satb1 cutr1 domain in complex with a phosphorothioate DNA. SNAP output
6lmj DNA binding protein-DNA X-ray (2.8 Å) Liu R, Sun Y, Chai Y, Li S, Li S, Wang L, Su J, Yu S, Yan J, Gao F, Zhang G, Qiu HJ, Gao GF, Qi J, Wang H (2020) "The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives." Proc.Natl.Acad.Sci.USA, 117, 11000-11009. doi: 10.1073/pnas.1922523117. Asfv pa104r in complex with double-strand DNA. SNAP output
6lmr DNA binding protein NMR Zhang J, Fan JS, Li S, Yang Y, Sun P, Zhu Q, Wang J, Jiang B, Yang D, Liu M (2020) "Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation." Nucleic Acids Res., 48, 9361-9371. doi: 10.1093/nar/gkaa619. Solution structure of cold shock domain and ssDNA complex. SNAP output
6lnb immune system cryo-EM (3.18 Å) Wang B, Xu W, Yang H (2020) "Structural basis of a Tn7-like transposase recruitment and DNA loading to CRISPR-Cas surveillance complex." Cell Res., 30, 185-187. doi: 10.1038/s41422-020-0274-0. Cryoem structure of cascade-tniq-dsDNA complex. SNAP output
6lqf gene regulation X-ray (1.5 Å) Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y, Chen L, Du X, Li S, Shao CR, Su YN, Cai XW, Lin RN, Li L, Chen S, Du J, He XJ (2020) "Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis." Plant Cell, 32, 2178-2195. doi: 10.1105/tpc.19.00944. Crystal structure of arabidopsis arid5 arid-phd cassette in complex with h3k4me3 peptide and DNA. SNAP output
6lrd DNA binding protein-DNA X-ray (1.9 Å) Cheng K, Xu Y, Chen X, Lu H, He Y, Wang L, Hua Y (2020) "Participation of RecJ in the base excision repair pathway of Deinococcus radiodurans." Nucleic Acids Res., 48, 9859-9871. doi: 10.1093/nar/gkaa714. Structure of recj complexed with a 5'-p-dspacer-modified ssDNA. SNAP output
6ltj gene regulation cryo-EM (3.7 Å) He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, Li J, Liu B, Xu Y (2020) "Structure of nucleosome-bound human BAF complex." Science, 367, 875-881. doi: 10.1126/science.aaz9761. Structure of nucleosome-bound human baf complex. SNAP output
6ltr hydrolase-RNA-DNA X-ray (2.51 Å) Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng G, Gong W, Wang Y (2020) "Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2." Nat Commun, 11, 5241. doi: 10.1038/s41467-020-19072-6. Crystal structure of cas12i2 ternary complex with single mg2+ bound in catalytic pocket. SNAP output
6lts transcription X-ray (3.45 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Crystal structure of thermus thermophilus transcription initiation complex comprising a truncated sigma finger. SNAP output
6ltu hydrolase-RNA-DNA X-ray (2.57 Å) Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng G, Gong W, Wang Y (2020) "Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2." Nat Commun, 11, 5241. doi: 10.1038/s41467-020-19072-6. Crystal structure of cas12i2 ternary complex with double mg2+ bound in catalytic pocket. SNAP output
6lty antitoxin, DNA binding protein-DNA X-ray (3.28 Å) Park JY, Kim HJ, Pathak C, Yoon HJ, Kim DH, Park SJ, Lee BJ (2020) "Induced DNA bending by unique dimerization of HigA antitoxin." Iucrj, 7, 748-760. doi: 10.1107/S2052252520006466. DNA bound antitoxin higa3. SNAP output
6lu0 hydrolase-RNA-DNA X-ray (3.22 Å) Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng G, Gong W, Wang Y (2020) "Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2." Nat Commun, 11, 5241. doi: 10.1038/s41467-020-19072-6. Crystal structure of cas12i2 ternary complex with 12 nt spacer. SNAP output
6lui DNA binding protein X-ray (1.781 Å) Stielow B, Zhou Y, Cao Y, Simon C, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R (2021) "The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands." Sci Adv, 7. doi: 10.1126/sciadv.abf2229. Crystal structure of the samd1 wh domain and DNA complex. SNAP output
6lwa DNA binding protein-DNA X-ray (2.76 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, k242) bound to duplex DNA containing 5-hydroxyuracil (5-ohu). SNAP output
6lwb DNA binding protein-DNA X-ray (2.55 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, r242) bound to duplex DNA containing 5-hydroxyuracil (5-ohu). SNAP output
6lwc DNA binding protein-DNA X-ray (2.91 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, k242) bound to duplex DNA containing spiroiminodihydantoin (sp). SNAP output
6lwd DNA binding protein-DNA X-ray (2.41 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, r242) bound to duplex DNA containing spiroiminodihydantoin (sp). SNAP output
6lwf DNA binding protein-DNA X-ray (2.79 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, k242) bound to duplex DNA containing guanidinohydantoin (gh). SNAP output
6lwg DNA binding protein-DNA X-ray (2.53 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, r242) bound to duplex DNA containing guanidinohydantoin (gh). SNAP output
6lwh DNA binding protein-DNA X-ray (2.78 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, k242) bound to duplex DNA containing dihydrothymine (dht). SNAP output
6lwi DNA binding protein-DNA X-ray (2.72 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, r242) bound to duplex DNA containing dihydrothymine (dht). SNAP output
6lwj DNA binding protein-DNA X-ray (2.83 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, k242) bound to duplex DNA containing dihydrouracil (dhu). SNAP output
6lwk DNA binding protein-DNA X-ray (2.88 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(p2g, e3q, r242) bound to duplex DNA containing dihydrouracil (dhu). SNAP output
6lwl DNA binding protein-DNA X-ray (2.55 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(r242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine. SNAP output
6lwm DNA binding protein-DNA X-ray (2.67 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(k242) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine. SNAP output
6lwn DNA binding protein-DNA X-ray (2.74 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(r242, g249p) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine. SNAP output
6lwo DNA binding protein-DNA X-ray (2.51 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(r242, y244h) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine. SNAP output
6lwp DNA binding protein-DNA X-ray (2.64 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(r242, y244r) bound to duplex DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine. SNAP output
6lwq DNA binding protein X-ray (2.89 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(r242) bound to duplex DNA containing a c:t mismatch. SNAP output
6lwr DNA binding protein-DNA X-ray (2.9 Å) Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C (2021) "DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes." Nat Commun, 12, 4108. doi: 10.1038/s41467-021-24431-y. Crystal structure of human neil1(k242) bound to duplex DNA containing a cleaved c:t mismatch. SNAP output
6lxn DNA binding protein X-ray (2.93 Å) Sadotra S, Lou YC, Tang HC, Chiu YC, Hsu CH, Chen C (2020) "Structural basis for promoter DNA recognition by the response regulator OmpR." J.Struct.Biol., 213, 107638. doi: 10.1016/j.jsb.2020.107638. Crystal structure of c-terminal DNA-binding domain of escherichia coli ompr in complex with f1-DNA. SNAP output
6m0v hydrolase-DNA-RNA X-ray (3.0 Å) Zhang Y, Zhang H, Xu X, Wang Y, Chen W, Wang Y, Wu Z, Tang N, Wang Y, Zhao S, Gan J, Ji Q (2020) "Catalytic-state structure and engineering of Streptococcus thermophilus Cas9." Nat Catal. doi: 10.1038/s41929-020-00506-9. Crsytal structure of streptococcus thermophilus cas9 in complex with the ggaa pam. SNAP output
6m0w hydrolase-DNA-RNA X-ray (2.76 Å) Zhang Y, Zhang H, Xu X, Wang Y, Chen W, Wang Y, Wu Z, Tang N, Wang Y, Zhao S, Gan J, Ji Q (2020) "Catalytic-state structure and engineering of Streptococcus thermophilus Cas9." Nat Catal. doi: 10.1038/s41929-020-00506-9. Crystal structure of streptococcus thermophilus cas9 in complex with the agaa pam. SNAP output
6m0x DNA binding protein X-ray (2.561 Å) Zhang Y, Zhang H, Xu X, Wang Y, Chen W, Wang Y, Wu Z, Tang N, Wang Y, Zhao S, Gan J, Ji Q (2020) "Catalytic-state structure and engineering of Streptococcus thermophilus Cas9." Nat Catal. doi: 10.1038/s41929-020-00506-9. Crystal structure of streptococcus thermophilus cas9 in complex with agga pam. SNAP output
6m2v DNA binding protein-DNA X-ray (3.0 Å) Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara E (2021) "Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA." Int.J.Biol.Macromol., 170, 514-522. doi: 10.1016/j.ijbiomac.2020.12.149. Crystal structure of uhrf1 sra complexed with fully-mchg DNA.. SNAP output
6m3d DNA binding protein-DNA X-ray (1.6 Å) Sunami T, Hirano Y, Tamada T, Kono H (2020) "Structural basis for designing an array of engrailed homeodomains." Acta Crystallogr D Struct Biol, 76, 824-833. doi: 10.1107/S2059798320009237. X-ray crystal structure of tandemly connected engrailed homeodomains (ehd) with r53a mutations and DNA complex. SNAP output
6m3l hydrolase-DNA X-ray (2.75 Å) Miyazono KI, Wang D, Ito T, Tanokura M (2020) "Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI." Nucleic Acids Res., 48, 5106-5118. doi: 10.1093/nar/gkaa184. Crystal structure of the r.pabi(y68f-k154a)-dsDNA(nonspecific) complex. SNAP output
6m3v DNA binding protein X-ray (4.6 Å) Adhireksan Z, Sharma D, Lee PL, Davey CA (2020) "Near-atomic resolution structures of interdigitated nucleosome fibres." Nat Commun, 11, 4747. doi: 10.1038/s41467-020-18533-2. 355 bp di-nucleosome harboring cohesive DNA termini. SNAP output
6m44 DNA binding protein X-ray (3.81 Å) Adhireksan Z, Sharma D, Lee PL, Davey CA (2020) "Near-atomic resolution structures of interdigitated nucleosome fibres." Nat Commun, 11, 4747. doi: 10.1038/s41467-020-18533-2. 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant). SNAP output
6m4d nuclear protein cryo-EM (4.4 Å) Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P, Zhou Z (2021) "Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2." Embo J., 40, e105907. doi: 10.15252/embj.2020105907. Structural mechanism of nucleosome dynamics governed by human histone variants h2a.b and h2a.z.2.2. SNAP output
6m4g nuclear protein cryo-EM (2.8 Å) Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P, Zhou Z (2021) "Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2." Embo J., 40, e105907. doi: 10.15252/embj.2020105907. Structural mechanism of nucleosome dynamics governed by human histone variants h2a.b and h2a.z.2.2. SNAP output
6m4h nuclear protein cryo-EM (3.9 Å) Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P, Zhou Z (2021) "Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2." Embo J., 40, e105907. doi: 10.15252/embj.2020105907. Structural mechanism of nucleosome dynamics governed by human histone variants h2a.b and h2a.z.2.2. SNAP output
6m6a transcription cryo-EM (5.0 Å) Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y (2020) "Structural basis of Mfd-dependent transcription termination." Nucleic Acids Res., 48, 11762-11772. doi: 10.1093/nar/gkaa904. cryo-EM structure of thermus thermophilus mfd in complex with RNA polymerase. SNAP output
6m6b transcription cryo-EM (4.1 Å) Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y (2020) "Structural basis of Mfd-dependent transcription termination." Nucleic Acids Res., 48, 11762-11772. doi: 10.1093/nar/gkaa904. cryo-EM structure of thermus thermophilus mfd in complex with RNA polymerase and atp-gamma-s. SNAP output
6m6c transcription cryo-EM (3.1 Å) Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S, Hua X, Zhang Y, Feng Y (2020) "Structural basis of Mfd-dependent transcription termination." Nucleic Acids Res., 48, 11762-11772. doi: 10.1093/nar/gkaa904. Cryoem structure of thermus thermophilus RNA polymerase elongation complex. SNAP output
6m75 DNA binding protein-DNA X-ray (2.57 Å) Aggarwal P, Bhavesh NS (2021) "Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter." Nucleic Acids Res., 49, 5943-5955. doi: 10.1093/nar/gkab363. C-myc DNA binding protein complex. SNAP output
6m7j transcription cryo-EM (4.4 Å) Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA (2019) "Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding." Nature, 565, 382-385. doi: 10.1038/s41586-018-0840-5. Mycobacterium tuberculosis rnap with rbpa-us fork and corallopyronin. SNAP output
6m7o transferase-DNA X-ray (3.0 Å) Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W (2018) "Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution." Proc. Natl. Acad. Sci. U.S.A., 115, 10660-10665. doi: 10.1073/pnas.1812856115. Human DNA polymerase eta ternary complex with mn2+ and dtmpnpp oppositing cda. SNAP output
6m7p transferase-DNA X-ray (1.75 Å) Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W (2018) "Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution." Proc. Natl. Acad. Sci. U.S.A., 115, 10660-10665. doi: 10.1073/pnas.1812856115. Human DNA polymerase eta extension complex with cda at the -2 position. SNAP output
6m7t transferase-DNA X-ray (2.8 Å) Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W (2018) "Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution." Proc. Natl. Acad. Sci. U.S.A., 115, 10660-10665. doi: 10.1073/pnas.1812856115. Human DNA polymerase eta in a non-productive ternary complex with ca2+ and dttp oppositing cda. SNAP output
6m7u transferase-DNA X-ray (3.4 Å) Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W (2018) "Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution." Proc. Natl. Acad. Sci. U.S.A., 115, 10660-10665. doi: 10.1073/pnas.1812856115. Human DNA polymerase eta in a non-productive ternary complex with mg2+ and dtmpnpp oppositing cda. SNAP output
6m7v transferase-DNA X-ray (3.062 Å) Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang W (2018) "Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution." Proc. Natl. Acad. Sci. U.S.A., 115, 10660-10665. doi: 10.1073/pnas.1812856115. Human DNA polymerase eta extension complex with cda at the -1 position. SNAP output
6mdz hydrolase-RNA X-ray (3.4 Å) Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ (2019) "Structural Basis for Target-Directed MicroRNA Degradation." Mol.Cell, 75, 1243-1255.e7. doi: 10.1016/j.molcel.2019.06.019. Human argonaute2-mir-122 bound to a target RNA with two central mismatches (bu2). SNAP output
6me0 RNA-DNA-nucleic acid binding protein cryo-EM (3.6 Å) Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N (2019) "Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA." Cell, 178, 612-623.e12. doi: 10.1016/j.cell.2019.06.035. Structure of a group ii intron retroelement prior to DNA integration. SNAP output
6mec RNA-DNA-RNA binding protein cryo-EM (3.6 Å) Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N (2019) "Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA." Cell, 178, 612-623.e12. doi: 10.1016/j.cell.2019.06.035. Structure of a group ii intron retroelement after DNA integration. SNAP output
6mfr hydrolase-RNA X-ray (3.6 Å) Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ (2019) "Structural Basis for Target-Directed MicroRNA Degradation." Mol.Cell, 75, 1243-1255.e7. doi: 10.1016/j.molcel.2019.06.019. Human argonaute2-mir-122 bound to a target RNA with three central mismatches (bu3). SNAP output
6mg1 transcription-DNA X-ray (1.75 Å) Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for effects of CpA modifications on C/EBP beta binding of DNA." Nucleic Acids Res., 47, 1774-1785. doi: 10.1093/nar/gky1264. C-terminal bzip domain of human c-ebpbeta with 16bp methylated oligonucleotide containing consensus recognition sequence-c2 crystal form. SNAP output
6mg2 transcription-DNA X-ray (1.928 Å) Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for effects of CpA modifications on C/EBP beta binding of DNA." Nucleic Acids Res., 47, 1774-1785. doi: 10.1093/nar/gky1264. C-terminal bzip domain of human c-ebpbeta with 16bp methylated oligonucleotide containing consensus recognition sequence-c2221 crystal form. SNAP output
6mg3 transcription-DNA X-ray (2.05 Å) Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for effects of CpA modifications on C/EBP beta binding of DNA." Nucleic Acids Res., 47, 1774-1785. doi: 10.1093/nar/gky1264. V285a mutant of the c-terminal bzip domain of human c-ebpbeta with 16bp methylated oligonucleotide containing consensus recognition sequence. SNAP output
6mht transferase-DNA X-ray (2.05 Å) Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ, Cheng X (1997) "DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase." Nucleic Acids Res., 25, 2773-2783. doi: 10.1093/nar/25.14.2773. Ternary structure of hhai methyltransferase with adohcy and DNA containing 4'-thio-2'deoxycytidine at the target. SNAP output
6mig hydrolase-DNA X-ray (1.7 Å) Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins Jr NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr J, Georgiadis MM, Benner SA (2019) "Hachimoji DNA and RNA: A genetic system with eight building blocks." Science, 363, 884-887. doi: 10.1126/science.aat0971. Crystal structure of host-guest complex with pb hachimoji DNA. SNAP output
6mih hydrolase-DNA X-ray (1.6 Å) Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins Jr NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr J, Georgiadis MM, Benner SA (2019) "Hachimoji DNA and RNA: A genetic system with eight building blocks." Science, 363, 884-887. doi: 10.1126/science.aat0971. Crystal structure of host-guest complex with pc hachimoji DNA. SNAP output
6mii hydrolase-DNA X-ray (3.15 Å) Meagher M, Epling LB, Enemark EJ (2019) "DNA translocation mechanism of the MCM complex and implications for replication initiation." Nat Commun, 10, 3117. doi: 10.1038/s41467-019-11074-3. Crystal structure of minichromosome maintenance protein mcm-DNA complex. SNAP output
6mik hydrolase-DNA X-ray (1.7 Å) Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins Jr NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr J, Georgiadis MM, Benner SA (2019) "Hachimoji DNA and RNA: A genetic system with eight building blocks." Science, 363, 884-887. doi: 10.1126/science.aat0971. Crystal structure of host-guest complex with pp hachimoji DNA. SNAP output
6ml2 transcription-DNA X-ray (1.874 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 1). SNAP output
6ml3 transcription-DNA X-ray (1.683 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 2). SNAP output
6ml4 transcription-DNA X-ray (1.482 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Btb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 3). SNAP output
6ml5 transcription-DNA X-ray (1.65 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 4). SNAP output
6ml6 transcription-DNA X-ray (1.54 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 4 with a cpa 5mc modification). SNAP output
6ml7 transcription-DNA X-ray (1.75 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 4 with a cpg 5mc modification). SNAP output
6mp3 transferase-DNA X-ray (1.907 Å) Hawkins MA, Hunmin J, Lee S "Structural Analysis of Translesion Synthesis Across Hypoxanthine Lesion Using Human DNA Polymerase Eta." Binary structure of DNA polymerase eta in complex with templating hypoxanthine. SNAP output
6mq8 transferase-DNA X-ray (1.969 Å) Jung H, Hawkins M, Lee S (2020) "Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase." Biochem.J. doi: 10.1042/BCJ20200800. Binary structure of DNA polymerase eta in complex with templating hypoxanthine. SNAP output
6mr7 DNA binding protein-DNA X-ray (2.144 Å) Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH (2019) "A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition." Nucleic Acids Res., 47, 3197-3207. doi: 10.1093/nar/gkz002. DNA polymerase beta substrate complex with templating adenine and incoming fapy-dgtp analog. SNAP output
6mr8 DNA binding protein-DNA X-ray (1.897 Å) Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH (2019) "A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition." Nucleic Acids Res., 47, 3197-3207. doi: 10.1093/nar/gkz002. D276g DNA polymerase beta substrate complex with templating adenine and incoming fapy-dgtp analog. SNAP output
6mrj DNA binding protein-DNA X-ray (2.8 Å) Pozharski E, de Serrano V "Crystal structure of H.pylori NikR in complex with DNA." Crystal structure of h.pylori nikr in complex with DNA. SNAP output
6mu4 transferase-DNA X-ray (1.62 Å) Jackson LN, Chim N, Shi C, Chaput JC (2019) "Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase." Nucleic Acids Res., 47, 6973-6983. doi: 10.1093/nar/gkz513. Bst DNA polymerase i fana-DNA binary complex. SNAP output
6mu5 transferase-DNA X-ray (1.912 Å) Jackson LN, Chim N, Shi C, Chaput JC (2019) "Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase." Nucleic Acids Res., 47, 6973-6983. doi: 10.1093/nar/gkz513. Bst DNA polymerase i tna-DNA binary complex. SNAP output
6muo nuclear protein cryo-EM (3.6 Å) Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE (2019) "Structure of the Human Core Centromeric Nucleosome Complex." Curr.Biol., 29, 2625-2639.e5. doi: 10.1016/j.cub.2019.06.062. Cenp-a nucleosome bound by two copies of cenp-c(cd) and one copy cenp-n(nt). SNAP output
6mup nuclear protein cryo-EM (3.5 Å) Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE (2019) "Structure of the Human Core Centromeric Nucleosome Complex." Curr.Biol., 29, 2625-2639.e5. doi: 10.1016/j.cub.2019.06.062. Cenp-a nucleosome bound by two copies of cenp-c(cd) and two copies cenp-n(nt). SNAP output
6mxo nuclear protein-DNA X-ray (2.04 Å) Ouzon-Shubeita H, Baker M, Koag MC, Lee S (2019) "Structural basis for the bypass of the major oxaliplatin-DNA adducts by human DNA polymerase eta." Biochem. J., 476, 747-758. doi: 10.1042/BCJ20180848. Structure of hpoleta incorporating dctp opposite the 3-prime pt(dach)-gg. SNAP output
6mzm transcription-DNA cryo-EM (7.5 Å) Patel AB, Louder RK, Greber BJ, Grunberg S, Luo J, Fang J, Liu Y, Ranish J, Hahn S, Nogales E (2018) "Structure of human TFIID and mechanism of TBP loading onto promoter DNA." Science, 362. doi: 10.1126/science.aau8872. Human tfiid bound to promoter DNA and tfiia. SNAP output
6n1p isomerase-DNA cryo-EM (6.35 Å) Soczek KM, Grant T, Rosenthal PB, Mondragon A (2018) "CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage." Elife, 7. doi: 10.7554/eLife.41215. Dihedral oligomeric complex of gyra n-terminal fragment with DNA, solved by cryoem in c2 symmetry. SNAP output
6n2r gene regulation-DNA X-ray (2.1 Å) Howard MJ, Foley KG, Shock DD, Batra VK, Wilson SH (2019) "Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta." J.Biol.Chem., 294, 7194-7201. doi: 10.1074/jbc.RA118.006809. Binary complex crystal structure of DNA polymerase beta with 5-carboxy-dc (5-cac) at the templating position. SNAP output
6n2s gene regulation-DNA X-ray (2.457 Å) Howard MJ, Foley KG, Shock DD, Batra VK, Wilson SH (2019) "Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta." J.Biol.Chem., 294, 7194-7201. doi: 10.1074/jbc.RA118.006809. Ternary complex crystal structure of DNA polymerase beta with 5-carboxy-dc (5-cac) at the templating position. SNAP output
6n2t gene regulation-DNA X-ray (2.6 Å) Howard MJ, Foley KG, Shock DD, Batra VK, Wilson SH (2019) "Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta." J.Biol.Chem., 294, 7194-7201. doi: 10.1074/jbc.RA118.006809. Ternary complex crystal structure of DNA polymerase beta with 5-hydroxymethyl-dc (5-hmc) at the templating position. SNAP output
6n4c transcription-DNA cryo-EM (17.0 Å) Sosa R, Florez-Ariza A, Diaz-Celis C, Onoa B, Cassago A, de Oliveira PSL, Portugal RV, Guerra DG, Bustamante C (2020) "Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation." Biorxiv. doi: 10.1101/2020.05.13.070375. Em structure of the DNA wrapping in bacterial open transcription initiation complex. SNAP output
6n60 transferase-DNA X-ray (3.68 Å) Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link AJ, Darst SA (2019) "Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin." Proc. Natl. Acad. Sci. U.S.A., 116, 1273-1278. doi: 10.1073/pnas.1817352116. Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and microcin j25 (mccj25). SNAP output
6n61 transferase-DNA X-ray (3.253 Å) Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link AJ, Darst SA (2019) "Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin." Proc. Natl. Acad. Sci. U.S.A., 116, 1273-1278. doi: 10.1073/pnas.1817352116. Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and capistruin. SNAP output
6n62 transferase-DNA X-ray (3.803 Å) Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link AJ, Darst SA (2019) "Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin." Proc. Natl. Acad. Sci. U.S.A., 116, 1273-1278. doi: 10.1073/pnas.1817352116. Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA. SNAP output
6n7i hydrolase,transferase-DNA cryo-EM (3.2 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 e343q mutant gp4 helicase-primase in complex with ssDNA, dttp, ac dinucleotide and ctp (gp4(5)-DNA). SNAP output
6n7n hydrolase,transferase-DNA cryo-EM (3.5 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 e343q mutant gp4 helicase-primase in complex with ssDNA, dttp, ac dinucleotide and ctp (form i). SNAP output
6n7s hydrolase,transferase-DNA cryo-EM (4.6 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 e343q mutant gp4 helicase-primase in complex with ssDNA, dttp, ac dinucleotide and ctp (form ii). SNAP output
6n7t hydrolase,transferase-DNA cryo-EM (3.9 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 e343q mutant gp4 helicase-primase in complex with ssDNA, dttp, ac dinucleotide and ctp (form iii). SNAP output
6n7v hydrolase,transferase-DNA cryo-EM (3.8 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 gp4 (helicase-primase, e343q mutant) in complex with ssDNA, dttp, ac dinucleotide, and ctp (from multiple lead complexes). SNAP output
6n7w transferase-DNA cryo-EM (4.5 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 leading-strand DNA polymerase (d5a-e7a)-trx in complex with a DNA fork and incoming dttp (from multiple lead complexes). SNAP output
6n9u hydrolase,transferase-DNA cryo-EM (3.7 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 lagging-strand DNA polymerase (d5a-e7a) interacting with primase domains of two gp4 subunits bound to an RNA-DNA hybrid and dttp (from lags1). SNAP output
6n9v hydrolase,transferase-DNA cryo-EM (4.0 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 lagging-strand DNA polymerase (d5a-e7a) and gp4 (helicase-primase) bound to DNA including RNA-DNA hybrid, and an incoming dttp (lags1). SNAP output
6n9w hydrolase,transferase-DNA cryo-EM (4.0 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 lagging-strand DNA polymerase (d5a-e7a) and gp4 (helicase-primase) bound to DNA including RNA-DNA hybrid, and an incoming dttp (lags2). SNAP output
6n9x hydrolase,transferase-DNA cryo-EM (4.1 Å) Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W (2019) "Structures and operating principles of the replisome." Science, 363. doi: 10.1126/science.aav7003. Structure of bacteriophage t7 lagging-strand DNA polymerase (d5a-e7a) and gp4 (helicase-primase) bound to DNA including RNA-DNA hybrid, and an incoming dttp (lags3). SNAP output
6nce DNA binding protein-DNA X-ray (2.598 Å) Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML (2019) "Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes." Mol. Cell, 74, 245. doi: 10.1016/j.molcel.2019.01.019. Crystal structure of the human foxn3 DNA binding domain in complex with a forkhead DNA sequence. SNAP output
6ncm DNA binding protein-DNA X-ray (2.704 Å) Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML (2019) "Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes." Mol. Cell, 74, 245. doi: 10.1016/j.molcel.2019.01.019. Crystal structure of the human foxn3 DNA binding domain in complex with a forkhead-like (fhl) DNA sequence. SNAP output
6ne0 immune system-RNA cryo-EM (3.4 Å) Rollins MF, Chowdhury S, Carter J, Golden SM, Miettinen HM, Santiago-Frangos A, Faith D, Lawrence CM, Lander GC, Wiedenheft B (2019) "Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry." Mol. Cell, 74, 132-142.e5. doi: 10.1016/j.molcel.2019.02.001. Structure of double-stranded target DNA engaged csy complex from pseudomonas aeruginosa (pa-14). SNAP output
6ne3 DNA binding protein-DNA cryo-EM (3.9 Å) Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y (2019) "Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome." Elife, 8. doi: 10.7554/eLife.46057. cryo-EM structure of singly-bound snf2h-nucleosome complex with snf2h bound at shl-2. SNAP output
6nit RNA binding protein-RNA X-ray (3.8 Å) Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ (2019) "Structural Basis for Target-Directed MicroRNA Degradation." Mol.Cell, 75, 1243-1255.e7. doi: 10.1016/j.molcel.2019.06.019. Human argonaute2-mir-122 bound to a target RNA with four central mismatches (bu4). SNAP output
6nj9 structural protein-transferase-DNA cryo-EM (2.96 Å) Worden EJ, Hoffmann NA, Hicks CW, Wolberger C (2019) "Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L." Cell, 176, 1490-1501.e12. doi: 10.1016/j.cell.2019.02.002. Active state dot1l bound to the h2b-ubiquitinated nucleosome, 2-to-1 complex. SNAP output
6njq DNA binding protein-DNA X-ray (2.75 Å) Stelling AL, Liu AY, Zeng W, Salinas R, Schumacher MA, Al-Hashimi HM (2019) "Infrared Spectroscopic Observation of a G-C+Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions." Angew.Chem.Int.Ed.Engl., 58, 12010-12013. doi: 10.1002/anie.201902693. Structure of tbp-hoogsteen containing DNA complex. SNAP output
6nju recombination X-ray (2.35 Å) Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho PS (2020) "Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function." Nucleic Acids Res., 48, 3962-3974. doi: 10.1093/nar/gkaa117. Mouse endonuclease g mutant h97a bound to a-DNA. SNAP output
6nkr transcription-DNA X-ray (2.45 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with dgtp. SNAP output
6nks transcription-DNA X-ray (2.349 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with beta-gamma chf analog of dgtp. SNAP output
6nkt transcription-DNA X-ray (2.6 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with beta-gamma difluoro analogue of dgtp. SNAP output
6nku transcription-DNA X-ray (1.9 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of DNA polymerase beta with "hot-spot sequence" with dgtp. SNAP output
6nkv transcription-DNA X-ray (1.85 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of DNA polymerase beta with "hot-spot sequence" with beta-gamma chf analogue of dgtp. SNAP output
6nkw transcription-DNA X-ray (1.98 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of DNA polymerase beta with "hot-spot sequence" with beta-gamma-methylene dgtp. SNAP output
6nkx transcription-DNA X-ray (1.98 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with "hot-spot sequence" with dgtp. SNAP output
6nky transcription-DNA X-ray (2.094 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with "hot-spot sequence" with beta-gamma chf analogue of dgtp. SNAP output
6nkz transcription-DNA X-ray (2.01 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with "hot-spot sequence" with beta-gamma methylene dgtp. SNAP output
6nl0 transcription-DNA X-ray (1.97 Å) Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH (2020) "Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography." Biochemistry, 59, 955-963. doi: 10.1021/acs.biochem.9b01072. Ternary complex crystal structure of k289m variant of DNA polymerase beta with "hot-spot sequence" with beta-gamma cf2 analogue of dgtp. SNAP output
6nn6 gene regulation cryo-EM (3.9 Å) Anderson CJ, Baird MR, Hsu A, Barbour EH, Koyama Y, Borgnia MJ, McGinty RK (2019) "Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase." Cell Rep, 26, 1681-1690.e5. doi: 10.1016/j.celrep.2019.01.058. Structure of dot1l-h2bk120ub nucleosome complex. SNAP output
6nog structural protein-transferase-DNA cryo-EM (3.9 Å) Worden EJ, Hoffmann NA, Hicks CW, Wolberger C (2019) "Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L." Cell, 176, 1490-1501.e12. doi: 10.1016/j.cell.2019.02.002. Poised-state dot1l bound to the h2b-ubiquitinated nucleosome. SNAP output
6nqa structural protein-transferase-DNA cryo-EM (3.54 Å) Worden EJ, Hoffmann NA, Hicks CW, Wolberger C (2019) "Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L." Cell, 176, 1490-1501.e12. doi: 10.1016/j.cell.2019.02.002. Active state dot1l bound to the h2b-ubiquitinated nucleosome, 1-to-1 complex. SNAP output
6nsm transcription-DNA X-ray (2.8 Å) He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F, Madden DR (2024) "Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa." Nucleic Acids Res. doi: 10.1093/nar/gkae889. Tetr family transcriptional regulator cifr c99t-c107s-c181r cysteines mutant complexed with 26bp double-strand operator DNA. SNAP output
6nsn transcription-DNA X-ray (2.6 Å) He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F, Madden DR (2024) "Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa." Nucleic Acids Res. doi: 10.1093/nar/gkae889. Tetr family transcriptional regulator cifr c99t-c181r cysteines mutant complexed with 26bp double-strand operator DNA. SNAP output
6nsr transcription-DNA X-ray (3.0 Å) He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ, Bahl CD, Hickman AB, Dyda F, Madden DR (2024) "Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa." Nucleic Acids Res. doi: 10.1093/nar/gkae889. Tetr family transcriptional regulator cifr c99t-c181r cysteine mutant complexed with 26bp double-strand operator DNA and apo-cifr c99t-c181r. SNAP output
6nua DNA binding protein-DNA X-ray (1.64 Å) Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman BF (2019) "Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link." Nat.Struct.Mol.Biol., 26, 613-618. doi: 10.1038/s41594-019-0255-5. DNA-protein crosslink between e. coli yedk and ssDNA containing an abasic site. SNAP output
6nuh DNA binding protein-DNA X-ray (1.594 Å) Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman BF (2019) "Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link." Nat.Struct.Mol.Biol., 26, 613-618. doi: 10.1038/s41594-019-0255-5. Non-covalent DNA-protein complex between e. coli yedk and ssDNA containing an abasic site analog. SNAP output
6ny1 RNA binding protein-RNA-DNA cryo-EM (4.2 Å) Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA (2019) "CasX enzymes comprise a distinct family of RNA-guided genome editors." Nature, 566, 218-223. doi: 10.1038/s41586-019-0908-x. Casx-grna-DNA(30bp) state ii. SNAP output
6ny2 RNA binding protein-RNA-DNA cryo-EM (3.2 Å) Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA (2019) "CasX enzymes comprise a distinct family of RNA-guided genome editors." Nature, 566, 218-223. doi: 10.1038/s41586-019-0908-x. Casx-grna-DNA(45bp) state i. SNAP output
6ny3 RNA binding protein-RNA-DNA cryo-EM (3.7 Å) Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA (2019) "CasX enzymes comprise a distinct family of RNA-guided genome editors." Nature, 566, 218-223. doi: 10.1038/s41586-019-0908-x. Casx ternary complex with 30bp target DNA. SNAP output
6nzo gene regulation cryo-EM (3.8 Å) Bilokapic S, Halic M (2019) "Nucleosome and ubiquitin position Set2 to methylate H3K36." Nat Commun, 10, 3795. doi: 10.1038/s41467-019-11726-4. Set2 bound to nucleosome. SNAP output
6o0x hydrolase-RNA-DNA cryo-EM (3.28 Å) Zhu X, Clarke R, Puppala AK, Chittori S, Merk A, Merrill BJ, Simonovic M, Subramaniam S (2019) "Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9." Nat.Struct.Mol.Biol., 26, 679-685. doi: 10.1038/s41594-019-0258-2. Conformational states of cas9-sgrna-DNA ternary complex in the presence of magnesium. SNAP output
6o0y hydrolase-RNA-DNA cryo-EM (3.37 Å) Zhu X, Clarke R, Puppala AK, Chittori S, Merk A, Merrill BJ, Simonovic M, Subramaniam S (2019) "Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9." Nat.Struct.Mol.Biol., 26, 679-685. doi: 10.1038/s41594-019-0258-2. Conformational states of cas9-sgrna-DNA ternary complex in the presence of magnesium. SNAP output
6o0z hydrolase-RNA-DNA cryo-EM (3.3 Å) Zhu X, Clarke R, Puppala AK, Chittori S, Merk A, Merrill BJ, Simonovic M, Subramaniam S (2019) "Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9." Nat.Struct.Mol.Biol., 26, 679-685. doi: 10.1038/s41594-019-0258-2. Conformational states of cas9-sgrna-DNA ternary complex in the presence of magnesium. SNAP output
6o19 transcription-DNA X-ray (1.596 Å) Garg A, Goldgur Y, Sanchez AM, Schwer B, Shuman S (2019) "Structure of Fission Yeast Transcription Factor Pho7 Bound topho1Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis." Mol.Cell.Biol., 39. doi: 10.1128/MCB.00132-19. Crystal structure of pho7 complex with pho1 promoter site 2. SNAP output
6o1d nuclear protein cryo-EM (3.395 Å) Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P (2019) "Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment." Nat Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4. cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA. SNAP output
6o3t gene regulation-DNA X-ray (3.06 Å) Li S, Pradhan L, Ashur S, Joshi A, Nam HJ (2019) "Crystal Structure of FOXC2 in Complex with DNA Target." Acs Omega, 4, 10906-10914. doi: 10.1021/acsomega.9b00756. Structural basis of foxc2 and DNA interactions. SNAP output
6o6c transferase-DNA-RNA cryo-EM (3.1 Å) Lahiri I, Xu J, Han BG, Oh J, Wang D, DiMaio F, Leschziner AE (2019) "3.1 angstrom structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids." J.Struct.Biol., 207, 270-278. doi: 10.1016/j.jsb.2019.06.004. RNA polymerase ii elongation complex arrested at a cpd lesion. SNAP output
6o6k DNA binding protein-DNA X-ray (3.601 Å) Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M (2020) "Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling." Nat Commun, 11, 2905. doi: 10.1038/s41467-020-16724-5. Huaa 19bp sym DNA ph 5.5. SNAP output
6o6p transcription-DNA X-ray (3.851 Å) Lara J, Diacovich L, Trajtenberg F, Larrieux N, Malchiodi EL, Fernandez MM, Gago G, Gramajo H, Buschiazzo A (2020) "Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine." Nat Commun, 11, 3703. doi: 10.1038/s41467-020-17504-x. Structure of the regulator fasr from mycobacterium tuberculosis in complex with DNA. SNAP output
6o71 immune system-DNA X-ray (2.55 Å) Jia N, Jones R, Yang G, Ouerfelli O, Patel DJ (2019) "CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity." Mol.Cell, 75, 944-956.e6. doi: 10.1016/j.molcel.2019.06.014. Crystal structure of csm6 in complex with cda4 by soaking cda4 into csm6. SNAP output
6o8e DNA binding protein-DNA X-ray (2.61 Å) Lee SJ, Sung RJ, Verdine GL (2019) "Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System." Res, 2019, 5641746. doi: 10.34133/2019/5641746. Crystal structure of uvrb bound to duplex DNA with adp. SNAP output
6o8f DNA binding protein-DNA X-ray (2.81 Å) Lee SJ, Sung RJ, Verdine GL (2019) "Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System." Res, 2019, 5641746. doi: 10.34133/2019/5641746. Crystal structure of uvrb bound to duplex DNA. SNAP output
6o8g DNA binding protein-DNA X-ray (2.64 Å) Lee SJ, Sung RJ, Verdine GL (2019) "Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System." Res, 2019, 5641746. doi: 10.34133/2019/5641746. Crystal structure of uvrb bound to fully duplex DNA. SNAP output
6o8h DNA binding protein-DNA X-ray (2.39 Å) Lee SJ, Sung RJ, Verdine GL (2019) "Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System." Res, 2019, 5641746. doi: 10.34133/2019/5641746. Crystal structure of uvrb mutant bound to duplex DNA. SNAP output
6o8q DNA binding protein-DNA X-ray (3.216 Å) Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M (2020) "Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling." Nat Commun, 11, 2905. doi: 10.1038/s41467-020-16724-5. Huaa 19bp sym DNA ph 4.5. SNAP output
6o96 structural protein-DNA-transferase cryo-EM (3.5 Å) Valencia-Sanchez MI, De Ioannes P, Wang M, Vasilyev N, Chen R, Nudler E, Armache J-P, Armache KJ (2019) "Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination." Mol.Cell, 74, 1010. doi: 10.1016/j.molcel.2019.03.029. Dot1l bound to the h2bk120 ubiquitinated nucleosome. SNAP output
6o9e transferase-DNA X-ray (2.4 Å) Ruiz FX, Hoang A, Das K, Arnold E (2019) "Structural Basis of HIV-1 Inhibition by Nucleotide-Competing Reverse Transcriptase Inhibitor INDOPY-1." J.Med.Chem., 62, 9996-10002. doi: 10.1021/acs.jmedchem.9b01289. Structure of hiv-1 reverse transcriptase in complex with DNA and indopy-1. SNAP output
6o9l transcription-DNA cryo-EM (7.2 Å) Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I (2019) "Transcription preinitiation complex structure and dynamics provide insight into genetic diseases." Nat.Struct.Mol.Biol., 26, 397-406. doi: 10.1038/s41594-019-0220-3. Human holo-pic in the closed state. SNAP output
6oaj DNA binding protein-DNA X-ray (4.092 Å) Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M (2020) "Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling." Nat Commun, 11, 2905. doi: 10.1038/s41467-020-16724-5. Huae34k 19bp sym DNA. SNAP output
6obj hydrolase-DNA cryo-EM (3.5 Å) Polley S, Lyumkis D, Horton NC (2019) "Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease." Structure, 27, 1497-1507.e3. doi: 10.1016/j.str.2019.08.001. Structure of a DNA-bound dimer extracted from filamentous sgrai endonuclease in its activated form. SNAP output
6od3 transcription-DNA X-ray (1.494 Å) Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine." Nucleic Acids Res., 47, 8375-8387. doi: 10.1093/nar/gkz381. Human tcf4 c-terminal bhlh domain in complex with 13-bp oligonucleotide containing e-box sequence. SNAP output
6od4 transcription-DNA X-ray (1.699 Å) Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine." Nucleic Acids Res., 47, 8375-8387. doi: 10.1093/nar/gkz381. Human tcf4 c-terminal bhlh domain in complex with 11-bp oligonucleotide containing e-box sequence. SNAP output
6od5 transcription-DNA X-ray (2.05 Å) Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine." Nucleic Acids Res., 47, 8375-8387. doi: 10.1093/nar/gkz381. Human tcf4 c-terminal bhlh domain in complex with 12-bp oligonucleotide containing e-box sequence with 5-carboxylcytosines. SNAP output
6oe7 DNA binding protein-DNA X-ray (2.2 Å) Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH (2019) "Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition." Nat.Struct.Mol.Biol., 26, 607-612. doi: 10.1038/s41594-019-0246-6. Crystal structure of hmces cross-linked to DNA abasic site. SNAP output
6oea DNA binding protein-DNA X-ray (2.1 Å) Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH (2019) "Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition." Nat.Struct.Mol.Biol., 26, 607-612. doi: 10.1038/s41594-019-0246-6. Crystal structure of hmces srap domain in complex with longer 3' overhang DNA. SNAP output
6oeb DNA binding protein-DNA X-ray (2.1 Å) Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH (2019) "Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition." Nat.Struct.Mol.Biol., 26, 607-612. doi: 10.1038/s41594-019-0246-6. Crystal structure of hmces srap domain in complex with 3' overhang DNA. SNAP output
6oem recombination-DNA cryo-EM (3.6 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse rag1-2 prc complex (dna0). SNAP output
6oen recombination-DNA cryo-EM (4.3 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse rag1-2 prc complex (dna1). SNAP output
6oeo recombination-DNA cryo-EM (3.69 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse rag1-2 nfc complex (dna1). SNAP output
6oep recombination-DNA cryo-EM (3.7 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse rag1-2 12rss-nfc-23rss-prc complex (dna1). SNAP output
6oeq recombination-DNA cryo-EM (4.3 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse rag1-2 12rss-prc-23rss-nfc complex (dna1). SNAP output
6oer recombination-DNA cryo-EM (3.29 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse rag1-2 nfc complex (dna2). SNAP output
6oes recombination-DNA cryo-EM (3.06 Å) Chen X, Cui Y, Wang H, Zhou ZH, Gellert M, Yang W (2020) "How mouse RAG recombinase avoids DNA transposition." Nat.Struct.Mol.Biol., 27, 127-133. doi: 10.1038/s41594-019-0366-z. cryo-EM structure of mouse rag1-2 stc complex (without nbd domain). SNAP output
6oet recombination-DNA cryo-EM (3.4 Å) Chen X, Cui Y, Wang H, Zhou ZH, Gellert M, Yang W (2020) "How mouse RAG recombinase avoids DNA transposition." Nat.Struct.Mol.Biol., 27, 127-133. doi: 10.1038/s41594-019-0366-z. cryo-EM structure of mouse rag1-2 stc complex. SNAP output
6ogj DNA binding protein-DNA X-ray (1.8 Å) Lei M, Tempel W, Chen S, Liu K, Min J (2019) "Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain." Biochim Biophys Acta Gene Regul Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409. Mecp2 mbd in complex with DNA. SNAP output
6ogk DNA binding protein-DNA X-ray (1.65 Å) Lei M, Tempel W, Chen S, Liu K, Min J (2019) "Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain." Biochim Biophys Acta Gene Regul Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409. Mecp2 mbd in complex with DNA. SNAP output
6om3 structural protein-DNA X-ray (3.3 Å) De Ioannes P, Leon VA, Kuang Z, Wang M, Boeke JD, Hochwagen A, Armache KJ (2019) "Structure and function of the Orc1 BAH-nucleosome complex." Nat Commun, 10, 2894. doi: 10.1038/s41467-019-10609-y. Crystal structure of the orc1 bah domain in complex with a nucleosome core particle. SNAP output
6omf transcription, transferase-DNA cryo-EM (3.26 Å) Cartagena AJ, Banta AB, Sathyan N, Ross W, Gourse RL, Campbell EA, Darst SA (2019) "Structural basis for transcription activation by Crl through tethering of sigmaSand RNA polymerase." Proc.Natl.Acad.Sci.USA, 116, 18923-18927. doi: 10.1073/pnas.1910827116. Cryoem structure of sigmas-transcription initiation complex with activator crl. SNAP output
6omv unknown function-DNA-RNA cryo-EM (3.9 Å) Zhang H, Li Z, Daczkowski CM, Gabel C, Mesecar AD, Chang L (2019) "Structural Basis for the Inhibition of CRISPR-Cas12a by Anti-CRISPR Proteins." Cell Host Microbe, 25, 815. doi: 10.1016/j.chom.2019.05.004. Cryoem structure of the lbcas12a-crrna-acrva4-DNA complex. SNAP output
6on0 transcription-DNA X-ray (1.6 Å) Hall BM, Roberts SA, Cordes MHJ (2019) "Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the lambda Cro complex." Nucleic Acids Res., 47, 7118-7129. doi: 10.1093/nar/gkz507. Structure of n15 cro complexed with consensus operator DNA. SNAP output
6oov DNA binding protein-DNA X-ray (2.2 Å) Halabelian L, Zeng H, Li Y, Bountra C, Edwards AM, Arrowsmith CH, Structural Genomics Consortium (SGC) "Crystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA." Crystal structure of hmces srap domain in complex with palindromic 3' overhang DNA. SNAP output
6opm hydrolase-DNA X-ray (3.1 Å) Hickman AB, Kailasan S, Genzor P, Haase AD, Dyda F (2020) "Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas." Elife, 9. doi: 10.7554/eLife.50004. Casposase bound to integration product. SNAP output
6or7 transferase-DNA X-ray (2.53 Å) Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS (2019) "Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine." Protein Sci., 28, 1664-1675. doi: 10.1002/pro.3681. Structure of hiv-1 reverse transcriptase (rt) in complex with DNA and (-)ftc-tp. SNAP output
6otz transferase-DNA X-ray (2.857 Å) Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS (2019) "Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine." Protein Sci., 28, 1664-1675. doi: 10.1002/pro.3681. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and (+)ftc-tp. SNAP output
6oul transcription cryo-EM (3.4 Å) Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA (2019) "E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation." Elife, 8. doi: 10.7554/eLife.49375. cryo-EM structure of escherichia coli rnap polymerase bound to rpstp2 promoter DNA. SNAP output
6oun transferase-DNA X-ray (2.656 Å) Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS (2019) "Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine." Protein Sci., 28, 1664-1675. doi: 10.1002/pro.3681. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and (-)3tc-tp. SNAP output
6ovr transcription-DNA-RNA X-ray (2.843 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter variant -1g. SNAP output
6ovy transcription-DNA-RNA X-ray (2.999 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter variant -1c. SNAP output
6ow3 transcription-DNA-RNA X-ray (2.766 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter variant -1t. SNAP output
6oy5 transcription-DNA-RNA X-ray (3.1 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter at 3 min. SNAP output
6oy6 transcription-DNA-RNA X-ray (3.096 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter at 5 min. SNAP output
6oy7 transcription-DNA-RNA X-ray (3.04 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter at 7 min. SNAP output
6ozf hydrolase X-ray (1.8 Å) Wu J, Samara NL, Kuraoka I, Yang W (2019) "Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase." Mol.Cell, 76, 44. doi: 10.1016/j.molcel.2019.06.046. Crystal structure of thermotoga maritima (tm) endonuclease v (d110n) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine. SNAP output
6ozg hydrolase X-ray (1.93 Å) Wu J, Samara NL, Kuraoka I, Yang W (2019) "Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase." Mol.Cell, 76, 44. doi: 10.1016/j.molcel.2019.06.046. Crystal structure of thermotoga maritima (tm) endonuclease v (e89q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine. SNAP output
6ozh hydrolase X-ray (3.026 Å) Wu J, Samara NL, Kuraoka I, Yang W (2019) "Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase." Mol.Cell, 76, 44. doi: 10.1016/j.molcel.2019.06.046. Crystal structure of ciona intestinalis (ci) endonuclease v in complex with a 24mer DNA containing an inosine followed by a ribo-adenosine. SNAP output
6ozi hydrolase X-ray (2.302 Å) Wu J, Samara NL, Kuraoka I, Yang W (2019) "Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase." Mol.Cell, 76, 44. doi: 10.1016/j.molcel.2019.06.046. Crystal structure of ciona intestinalis (ci) endonuclease v (d234n) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine. SNAP output
6p09 ligase-DNA X-ray (2.052 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 bound to an adenylated, dideoxy terminated DNA nick with 200 mm mg2+. SNAP output
6p0a ligase X-ray (2.05 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 bound to an adenylated, dideoxy terminated DNA nick with 2 mm mg2+. SNAP output
6p0b ligase X-ray (2.203 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 (e346a-e592a) bound to an adenylated, dideoxy terminated DNA nick with 200 mm mg2+. SNAP output
6p0c ligase-DNA X-ray (1.55 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 bound to an adenylated, hydroxyl terminated DNA nick in edta. SNAP output
6p0d ligase X-ray (1.75 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 (e346a-e592a) bound to an adenylated, hydroxyl terminated DNA nick. SNAP output
6p0e ligase X-ray (1.85 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 (e346a,e592a) bound to adenylated DNA containing an 8-oxo guanine:adenine base-pair. SNAP output
6p0g DNA binding protein-DNA X-ray (2.27 Å) Hosford CJ, Bui AQ, Chappie JS (2020) "The structure of theThermococcus gammatoleransMcrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs." J.Biol.Chem., 295, 743-756. doi: 10.1074/jbc.RA119.010188. N-terminal domain of thermococcus gammatolerans mcrb bound to m5c DNA. SNAP output
6p0s DNA binding protein-DNA X-ray (2.7 Å) Hancock SP, Cascio D, Johnson RC (2019) "Cooperative DNA binding by proteins through DNA shape complementarity." Nucleic Acids Res., 47, 8874-8887. doi: 10.1093/nar/gkz642. Crystal structure of ternary DNA complex "fx2" containing e. coli fis and phage lambda xis. SNAP output
6p0t DNA binding protein-DNA X-ray (3.603 Å) Hancock SP, Cascio D, Johnson RC (2019) "Cooperative DNA binding by proteins through DNA shape complementarity." Nucleic Acids Res., 47, 8874-8887. doi: 10.1093/nar/gkz642. Crystal structure of ternary DNA complex "fx(1-2)-1xis" containing e. coli fis and phage lambda xis. SNAP output
6p0u DNA binding protein-DNA X-ray (3.3 Å) Hancock SP, Cascio D, Johnson RC (2019) "Cooperative DNA binding by proteins through DNA shape complementarity." Nucleic Acids Res., 47, 8874-8887. doi: 10.1093/nar/gkz642. Crystal structure of ternary DNA complex " fx(1-2)-2xis" containing e. coli fis and phage lambda xis. SNAP output
6p18 gene regulation cryo-EM (3.5 Å) Yin Z, Kaelber JT, Ebright RH (2019) "Structural basis of Q-dependent antitermination." Proc.Natl.Acad.Sci.USA, 116, 18384-18390. doi: 10.1073/pnas.1909801116. Q21 transcription antitermination complex: loading complex. SNAP output
6p19 gene regulation cryo-EM (3.8 Å) Yin Z, Kaelber JT, Ebright RH (2019) "Structural basis of Q-dependent antitermination." Proc.Natl.Acad.Sci.USA, 116, 18384-18390. doi: 10.1073/pnas.1909801116. Q21 transcription antitermination complex: loaded complex. SNAP output
6p1a gene regulation X-ray (2.837 Å) Yin Z, Kaelber JT, Ebright RH (2019) "Structural basis of Q-dependent antitermination." Proc.Natl.Acad.Sci.USA, 116, 18384-18390. doi: 10.1073/pnas.1909801116. Transcription antitermination factor q21 in complex with q21-binding-element DNA. SNAP output
6p1h DNA binding protein-DNA cryo-EM (3.2 Å) Jain R, Rice WJ, Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK (2019) "Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme." Nat.Struct.Mol.Biol., 26, 955-962. doi: 10.1038/s41594-019-0305-z. cryo-EM structure of DNA polymerase delta holoenzyme. SNAP output
6p1i transferase-DNA X-ray (2.74 Å) Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS (2019) "Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine." Protein Sci., 28, 1664-1675. doi: 10.1002/pro.3681. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and dctp. SNAP output
6p1m transferase X-ray (1.65 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Binary complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og. SNAP output
6p1n transferase X-ray (1.6 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Pre-catalytic ternary complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and bound incoming dampnpp. SNAP output
6p1o transferase X-ray (1.65 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Post-catalytic nicked complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and newly incorporated damp. SNAP output
6p1p transferase X-ray (1.75 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Pre-catalytic ternary complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and bound incoming dcmpnpp. SNAP output
6p1q transferase X-ray (1.9 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Post-catalytic nicked complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and newly incorporated dcmp. SNAP output
6p1r transferase X-ray (1.701 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Pre-catalytic ternary complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and bound incoming ampnpp. SNAP output
6p1s transferase-DNA X-ray (1.75 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Post-catalytic nicked complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and newly incorporated amp. SNAP output
6p1t transferase X-ray (1.7 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Pre-catalytic ternary complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and bound cmpcpp. SNAP output
6p1u transferase X-ray (1.75 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Post-catalytic nicked complex of human DNA polymerase mu with 1-nt gapped substrate containing template 8og and newly incorporated cmp. SNAP output
6p1v transferase X-ray (1.95 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Pre-catalytic ternary complex of human DNA polymerase mu with 1-nt gapped substrate containing undamaged template dg and bound incoming dcmpnpp. SNAP output
6p1w transferase X-ray (1.751 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA, Bebenek K, Pedersen LC (2019) "Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids Res., 47, 9410-9422. doi: 10.1093/nar/gkz680. Pre-catalytic ternary complex of human DNA polymerase mu with 1-nt gapped substrate containing undamaged template dg and bound incoming cmpcpp. SNAP output
6p1x transferase-DNA X-ray (2.553 Å) Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS (2019) "Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine." Protein Sci., 28, 1664-1675. doi: 10.1002/pro.3681. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and l-ddctp. SNAP output
6p2g transferase-DNA X-ray (2.99 Å) Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson KS (2019) "Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine." Protein Sci., 28, 1664-1675. doi: 10.1002/pro.3681. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and d-ddctp. SNAP output
6p4f hydrolase-DNA X-ray (3.55 Å) He F, DuPrez K, Hilario E, Chen Z, Fan L (2020) "Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA." Nucleic Acids Res., 48, 11695-11705. doi: 10.1093/nar/gkaa801. Crystal structure of the xpb-bax1-forked DNA ternary complex. SNAP output
6p5a transferase-DNA cryo-EM (3.6 Å) Ghanim GE, Kellogg EH, Nogales E, Rio DC (2019) "Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts." Nat.Struct.Mol.Biol., 26, 1013-1022. doi: 10.1038/s41594-019-0319-6. Drosophila p element transposase strand transfer complex. SNAP output
6p5c replication-DNA X-ray (2.2 Å) Hamm ML, Garcia AA, Gilbert R, Johri M, Ricart M, Sholes SL, Murray-Nerger LA, Wu EY (2020) "The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase." DNA Repair (Amst.), 89, 102826. doi: 10.1016/j.dnarep.2020.102826. Bacillus fragment DNA polymerase mutant i716m. SNAP output
6p70 transcription-DNA X-ray (3.052 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of bacterial RNA polymerase and pyrbi promoter complex. SNAP output
6p71 transcription-DNA-RNA X-ray (2.92 Å) Shin Y, Hedglin M, Murakami KS (2020) "Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase." Nucleic Acids Res., 48, 2144-2155. doi: 10.1093/nar/gkz1221. X-ray crystal structure of a bacterial reiterative transcription complex of pyrbi promoter. SNAP output
6p7b hydrolase-DNA X-ray (3.317 Å) Li N, Shi K, Rao T, Banerjee S, Aihara H (2020) "Structural insights into the promiscuous DNA binding and broad substrate selectivity of fowlpox virus resolvase." Sci Rep, 10, 393. doi: 10.1038/s41598-019-56825-w. Crystal structure of fowlpox virus resolvase and substrate holliday junction DNA complex. SNAP output
6p7e transferase-DNA binding protein-DNA X-ray (3.001 Å) Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR (2019) "Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome." Biochemistry, 58, 4466-4479. doi: 10.1021/acs.biochem.9b00525. Structure of t7 DNA polymerase bound to a primer-template DNA and a peptide that mimics the c-terminal tail of the primase-helicase. SNAP output
6p93 lyase-DNA X-ray (2.1 Å) McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM (2020) "Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance." Mutagenesis, 35, 27-38. doi: 10.1093/mutage/gez046. Human ape1 k98a ap-endonuclease product complex. SNAP output
6p94 lyase-DNA X-ray (2.09 Å) McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM (2020) "Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance." Mutagenesis, 35, 27-38. doi: 10.1093/mutage/gez046. Human ape1 c65a ap-endonuclease product complex. SNAP output
6pa7 transferase-DNA cryo-EM (2.94 Å) Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE, Melcher K, Jones PA (2020) "Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B." Nature, 586, 151-155. doi: 10.1038/s41586-020-2747-1. The cryo-EM structure of the human dnmt3a2-dnmt3b3 complex bound to nucleosome.. SNAP output
6pax gene regulation-DNA X-ray (2.5 Å) Xu HE, Rould MA, Xu W, Epstein JA, Maas RL, Pabo CO (1999) "Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding." Genes Dev., 13, 1263-1275. Crystal structure of the human pax-6 paired domain-DNA complex reveals a general model for pax protein-DNA interactions. SNAP output
6pb4 transcription-DNA-RNA cryo-EM (4.35 Å) Shi W, Jiang Y, Deng Y, Dong Z, Liu B (2020) "Visualization of two architectures in class-II CAP-dependent transcription activation." Plos Biol., 18, e3000706. doi: 10.1371/journal.pbio.3000706. The e. coli class-ii cap-dependent transcription activation complex with de novo RNA transcript at the state 2. SNAP output
6pb5 transcription-DNA cryo-EM (4.52 Å) Shi W, Jiang Y, Deng Y, Dong Z, Liu B (2020) "Visualization of two architectures in class-II CAP-dependent transcription activation." Plos Biol., 18, e3000706. doi: 10.1371/journal.pbio.3000706. The e. coli class-ii cap-dependent transcription activation complex at the state 1 architecture. SNAP output
6pb6 transcription-DNA cryo-EM (4.29 Å) Shi W, Jiang Y, Deng Y, Dong Z, Liu B (2020) "Visualization of two architectures in class-II CAP-dependent transcription activation." Plos Biol., 18, e3000706. doi: 10.1371/journal.pbio.3000706. The e. coli class-ii cap-dependent transcription activation complex at the state 2. SNAP output
6pbd transferase-DNA X-ray (2.343 Å) Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X, Cheng X (2019) "The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site." Nat Commun, 10, 4600. doi: 10.1038/s41467-019-12498-7. DNA n6-adenine methyltransferase ccrm in complex with double-stranded DNA oligonucleotide containing its recognition sequence gaatc. SNAP output
6pcm isomerase-DNA X-ray (3.107 Å) Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC (2020) "Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains." Nucleic Acids Res., 48, 4448-4462. doi: 10.1093/nar/gkaa201. Crystal structure of mycobacterium smegmatis topoisomerase i with ssDNA bound to both n- and c-terminal domains. SNAP output
6pe2 transferase-DNA cryo-EM (4.0 Å) Ghanim GE, Kellogg EH, Nogales E, Rio DC (2019) "Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts." Nat.Struct.Mol.Biol., 26, 1013-1022. doi: 10.1038/s41594-019-0319-6. Drosophila p element transposase strand transfer complex. SNAP output
6ph5 transcription-DNA X-ray (2.602 Å) Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard WA, Wilson SH (2020) "DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context." J.Biol.Chem., 295, 529-538. doi: 10.1074/jbc.RA119.010594. Binary product complex crystal structure of DNA polymerase beta with an extra-helical template base. SNAP output
6ph6 transcription-DNA X-ray (2.6 Å) Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard WA, Wilson SH (2020) "DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context." J.Biol.Chem., 295, 529-538. doi: 10.1074/jbc.RA119.010594. Ternary complex crystal structure of DNA polymerase beta with 2nt-gap with dctp bound downstream. SNAP output
6pij RNA binding protein-RNA-DNA cryo-EM (2.9 Å) Halpin-Healy TS, Klompe SE, Sternberg SH, Fernandez IS (2020) "Structural basis of DNA targeting by a transposon-encoded CRISPR-Cas system." Nature, 577, 271-274. doi: 10.1038/s41586-019-1849-0. Target DNA-bound v. cholerae tniq-cascade complex, closed conformation. SNAP output
6pkz DNA binding protein-DNA X-ray (2.74 Å) Koag MC, Lee S "Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP." Structure of human DNA polymerase beta n279a complexed with 8oa in the template base paired with incoming non-hydrolyzable gtp. SNAP output
6pl7 DNA binding protein-DNA X-ray (2.5 Å) Koag MC, Lee S "Structure of human DNA polymerase eta complexed with A in the template base paired with incoming non-hydrolyzable TTP." Structure of human DNA polymerase eta complexed with a in the template base paired with incoming non-hydrolyzable ttp. SNAP output
6pl8 DNA binding protein-DNA X-ray (2.17 Å) Koag MC, Lee S "Structure of human DNA polymerase eta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP." Structure of human DNA polymerase eta complexed with 8oa in the template base paired with incoming non-hydrolyzable ttp. SNAP output
6plc DNA binding protein-DNA X-ray (2.5 Å) Koag MC, Jung H, Lee S (2020) "Mutagenesis mechanism of the major oxidative adenine lesion 7,8-dihydro-8-oxoadenine." Nucleic Acids Res., 48, 5119-5134. doi: 10.1093/nar/gkaa193. Structure of human DNA polymerase eta complexed with 8oa in the template base paired with incoming non-hydrolyzable gtp. SNAP output
6pmi transcription cryo-EM (3.86 Å) Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B (2020) "Structural basis of bacterial sigma28-mediated transcription reveals roles of the RNA polymerase zinc-binding domain." Embo J., 39, e104389. doi: 10.15252/embj.2020104389. Sigm28-transcription initiation complex with specific promoter at the state 1. SNAP output
6pmj transcription cryo-EM (3.91 Å) Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B (2020) "Structural basis of bacterial sigma28-mediated transcription reveals roles of the RNA polymerase zinc-binding domain." Embo J., 39, e104389. doi: 10.15252/embj.2020104389. Sigm28-transcription initiation complex with specific promoter at the state 2. SNAP output
6ppr DNA binding protein-DNA cryo-EM (3.5 Å) Jia N, Unciuleac MC, Xue C, Greene EC, Patel DJ, Shuman S (2019) "Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection." Proc.Natl.Acad.Sci.USA, 116, 24507-24516. doi: 10.1073/pnas.1913546116. cryo-EM structure of aDNA(d934a)-adnb(d1014a) in complex with amppnp and DNA. SNAP output
6ppu DNA binding protein-DNA cryo-EM (3.5 Å) Jia N, Unciuleac MC, Xue C, Greene EC, Patel DJ, Shuman S (2019) "Structures and single-molecule analysis of bacterial motor nuclease AdnAB illuminate the mechanism of DNA double-strand break resection." Proc.Natl.Acad.Sci.USA, 116, 24507-24516. doi: 10.1073/pnas.1913546116. cryo-EM structure of adnab-amppnp-DNA complex. SNAP output
6pqr recombination-DNA cryo-EM (3.4 Å) Liu C, Yang Y, Schatz DG (2019) "Structures of a RAG-like transposase during cut-and-paste transposition." Nature, 575, 540-544. doi: 10.1038/s41586-019-1753-7. cryo-EM structure of hztransib-intact tir substrate DNA pre-reaction complex (prc). SNAP output
6pqu recombination-DNA cryo-EM (3.3 Å) Liu C, Yang Y, Schatz DG (2019) "Structures of a RAG-like transposase during cut-and-paste transposition." Nature, 575, 540-544. doi: 10.1038/s41586-019-1753-7. cryo-EM structure of hztransib-nicked tir substrate DNA pre-reaction complex (prc). SNAP output
6pqx recombination-DNA cryo-EM (4.6 Å) Liu C, Yang Y, Schatz DG (2019) "Structures of a RAG-like transposase during cut-and-paste transposition." Nature, 575, 540-544. doi: 10.1038/s41586-019-1753-7. cryo-EM structure of hztransib-nicked tir substrate DNA hairpin forming complex (hfc). SNAP output
6pqy recombination cryo-EM (4.2 Å) Liu C, Yang Y, Schatz DG (2019) "Structures of a RAG-like transposase during cut-and-paste transposition." Nature, 575, 540-544. doi: 10.1038/s41586-019-1753-7. cryo-EM structure of hztransib-tir DNA transposon end complex (tec). SNAP output
6pr5 recombination-DNA cryo-EM (3.3 Å) Liu C, Yang Y, Schatz DG (2019) "Structures of a RAG-like transposase during cut-and-paste transposition." Nature, 575, 540-544. doi: 10.1038/s41586-019-1753-7. cryo-EM structure of hztransib strand transfer complex (stc). SNAP output
6psq transcription-DNA cryo-EM (3.4 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase closed complex (trpc) with trar and rpst p2 promoter. SNAP output
6psr transcription-DNA cryo-EM (3.4 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase promoter unwinding intermediate (trpi1) with trar and rpst p2 promoter. SNAP output
6pss transcription-DNA cryo-EM (3.5 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase promoter unwinding intermediate (trpi1.5a) with trar and mutant rpst p2 promoter. SNAP output
6pst transcription-DNA cryo-EM (3.0 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase promoter unwinding intermediate (trpi1.5b) with trar and mutant rpst p2 promoter. SNAP output
6psu transcription-DNA cryo-EM (3.9 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase promoter unwinding intermediate (trpi2) with trar and rpst p2 promoter. SNAP output
6psv transcription-DNA cryo-EM (3.5 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase promoter unwinding intermediate (tprerpo) with trar and rpst p2 promoter. SNAP output
6psw transcription-DNA cryo-EM (3.7 Å) Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA (2020) "Stepwise Promoter Melting by Bacterial RNA Polymerase." Mol.Cell, 78, 275. doi: 10.1016/j.molcel.2020.02.017. Escherichia coli RNA polymerase promoter unwinding intermediate (trpo) with trar and rpst p2 promoter. SNAP output
6put viral protein-DNA cryo-EM (2.9 Å) Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr TR, Craigie R, Lyumkis D (2020) "Structural basis for strand-transfer inhibitor binding to HIV intasomes." Science, 367, 810-814. doi: 10.1126/science.aay8015. Structure of hiv cleaved synaptic complex (csc) intasome bound with calcium. SNAP output
6puw viral protein-DNA cryo-EM (2.9 Å) Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr TR, Craigie R, Lyumkis D (2020) "Structural basis for strand-transfer inhibitor binding to HIV intasomes." Science, 367, 810-814. doi: 10.1126/science.aay8015. Structure of hiv cleaved synaptic complex (csc) intasome bound with magnesium and bictegravir (bic). SNAP output
6puy viral protein-DNA cryo-EM (2.8 Å) Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr TR, Craigie R, Lyumkis D (2020) "Structural basis for strand-transfer inhibitor binding to HIV intasomes." Science, 367, 810-814. doi: 10.1126/science.aay8015. Structure of hiv cleaved synaptic complex (csc) intasome bound with magnesium and insti xz426 (compound 4d). SNAP output
6puz viral protein-DNA cryo-EM (2.8 Å) Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr TR, Craigie R, Lyumkis D (2020) "Structural basis for strand-transfer inhibitor binding to HIV intasomes." Science, 367, 810-814. doi: 10.1126/science.aay8015. Structure of hiv cleaved synaptic complex (csc) intasome bound with magnesium and insti xz446 (compound 4f). SNAP output
6pw2 viral protein-DNA X-ray (3.01 Å) Malecka KA, Dheekollu J, Deakyne JS, Wiedmer A, Ramirez UD, Lieberman PM, Messick TE (2019) "Structural Basis for Cooperative Binding of EBNA1 to the Epstein-Barr Virus Dyad Symmetry Minimal Origin of Replication." J.Virol., 93. doi: 10.1128/JVI.00487-19. Structural basis for cooperative binding of ebna1 to the epstein-barr virus dyad symmetry minimal origin of replication. SNAP output
6pwe structural protein-DNA cryo-EM (3.95 Å) Chittori S, Hong J, Bai Y, Subramaniam S (2019) "Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome." Nucleic Acids Res., 47, 9400-9409. doi: 10.1093/nar/gkz670. cryo-EM structure of nucleosome core particle. SNAP output
6pwf structural protein-DNA cryo-EM (4.07 Å) Chittori S, Hong J, Bai Y, Subramaniam S (2019) "Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome." Nucleic Acids Res., 47, 9400-9409. doi: 10.1093/nar/gkz670. cryo-EM structure of the atpase domain of chromatin remodeling factor iswi bound to the nucleosome. SNAP output
6pwv histone binding-DNA binding-DNA cryo-EM (6.2 Å) Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US (2019) "Cryo-EM structure of the human MLL1 core complex bound to the nucleosome." Nat Commun, 10, 5540. doi: 10.1038/s41467-019-13550-2. cryo-EM structure of mll1 core complex bound to the nucleosome. SNAP output
6pww histone binding-DNA binding-DNA cryo-EM (4.4 Å) Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US (2019) "Cryo-EM structure of the human MLL1 core complex bound to the nucleosome." Nat Commun, 10, 5540. doi: 10.1038/s41467-019-13550-2. cryo-EM structure of mll1 in complex with rbbp5 and wdr5 bound to the nucleosome. SNAP output
6pwx histone binding-DNA binding-DNA cryo-EM (4.2 Å) Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US (2019) "Cryo-EM structure of the human MLL1 core complex bound to the nucleosome." Nat Commun, 10, 5540. doi: 10.1038/s41467-019-13550-2. cryo-EM structure of rbbp5 bound to the nucleosome. SNAP output
6px1 gene regulation cryo-EM (3.3 Å) Bilokapic S, Halic M (2019) "Nucleosome and ubiquitin position Set2 to methylate H3K36." Nat Commun, 10, 3795. doi: 10.1038/s41467-019-11726-4. Set2 bound to nucleosome. SNAP output
6px3 gene regulation cryo-EM (4.1 Å) Bilokapic S, Halic M (2019) "Nucleosome and ubiquitin position Set2 to methylate H3K36." Nat Commun, 10, 3795. doi: 10.1038/s41467-019-11726-4. Set2 bound to nucleosome. SNAP output
6py8 DNA binding protein-DNA X-ray (3.75 Å) Jarrett SM, Seegar TCM, Andrews M, Adelmant G, Marto JA, Aster JC, Blacklow SC (2019) "Extension of the Notch intracellular domain ankyrin repeat stack by NRARP promotes feedback inhibition of Notch signaling." Sci.Signal., 12. doi: 10.1126/scisignal.aay2369. Crystal structure of the rbpj-notch1-nrarp ternary complex bound to DNA. SNAP output
6pz3 transferase X-ray (2.395 Å) Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash S, Aggarwal AK (2019) "Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase eta." Sci Rep, 9, 16400. doi: 10.1038/s41598-019-52703-7. Polymerase eta-catalyzed insertion of correct g opposite template cytarabine (arac) residue. SNAP output
6q02 transferase-DNA X-ray (2.09 Å) Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash S, Aggarwal AK (2019) "Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase eta." Sci Rep, 9, 16400. doi: 10.1038/s41598-019-52703-7. Polymerase eta-catalyzed insertion of the mismatched a opposite template cytarabine (arac) residue. SNAP output
6q0c hydrolase-DNA X-ray (2.0 Å) Russelburg LP, O'Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP (2020) "Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY." Acs Chem.Biol., 15, 93-102. doi: 10.1021/acschembio.9b00639. Muty adenine glycosylase bound to DNA containing a transition state analog (1n) paired with undamaged dg. SNAP output
6q1v ligase-DNA X-ray (1.85 Å) Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS (2019) "Two-tiered enforcement of high-fidelity DNA ligation." Nat Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7. Human DNA ligase 1 (e592r) bound to an adenylated, hydroxyl terminated DNA nick. SNAP output
6q2b transcription X-ray (2.72 Å) Kim Y, Tesar C, Clancy S, Joachimiak A, Midwest Center for Structural Genomics (MCSG) "Crystal Structure of Putative MarR Family Transcriptional Regulator from Listeria monocytogenes complexed with 26mer DNA." Crystal structure of putative marr family transcriptional regulator from listeria monocytogenes complexed with 26mer DNA. SNAP output
6q4t DNA binding protein X-ray (1.997 Å) Kropp HM, Diederichs K, Marx A (2019) "The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide." Angew.Chem.Int.Ed.Engl., 58, 5457-5461. doi: 10.1002/anie.201900315. Kod DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-n-(prop-2-yn-1-yl)acetamide)-2-datp. SNAP output
6q4u DNA binding protein X-ray (2.005 Å) Kropp HM, Diederichs K, Marx A (2019) "The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide." Angew.Chem.Int.Ed.Engl., 58, 5457-5461. doi: 10.1002/anie.201900315. Klentaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-n-(prop-2-yn-1-yl)acetamide)-2-datp. SNAP output
6q4v DNA binding protein X-ray (2.006 Å) Kropp HM, Diederichs K, Marx A (2019) "The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide." Angew.Chem.Int.Ed.Engl., 58, 5457-5461. doi: 10.1002/anie.201900315. Klentaq DNA polymerase in complex with datp. SNAP output
6q6r DNA binding protein X-ray (1.5 Å) Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan AT (2020) "Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex." J.Struct.Biol., 209, 107399. doi: 10.1016/j.jsb.2019.10.001. Recognition of different base tetrads by rhau: x-ray crystal structure of g4 recognition motif bound to the 3-end tetrad of a DNA g-quadruplex. SNAP output
6qec circadian clock protein X-ray (1.9 Å) Silva CS, Nayak A, Lai X, Hutin S, Hugouvieux V, Jung JH, Lopez-Vidriero I, Franco-Zorrilla JM, Panigrahi KCS, Nanao MH, Wigge PA, Zubieta C (2020) "Molecular mechanisms of Evening Complex activity inArabidopsis." Proc.Natl.Acad.Sci.USA, 117, 6901-6909. doi: 10.1073/pnas.1920972117. DNA binding domain of lux arrythmo in complex with DNA. SNAP output
6qem replication cryo-EM (3.4 Å) Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q, Berger JM (2019) "Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA." Mol.Cell, 74, 173-184.e4. doi: 10.1016/j.molcel.2019.01.023. E. coli dnabc complex bound to ssDNA. SNAP output
6qfd DNA binding protein X-ray (2.133 Å) Kutnowski N, Shmulevich F, Davidov G, Shahar A, Bar-Zvi D, Eichler J, Zarivach R, Shaanan B (2019) "Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR." Nucleic Acids Res., 47, 8860-8873. doi: 10.1093/nar/gkz604. The complex structure of hsrosr-s4 (vng0258-rosr-s4). SNAP output
6qh0 DNA binding protein X-ray (2.436 Å) Kutnowski N, Shmulevich F, Davidov G, Shahar A, Bar-Zvi D, Eichler J, Zarivach R, Shaanan B (2019) "Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR." Nucleic Acids Res., 47, 8860-8873. doi: 10.1093/nar/gkz604. The complex structure of hsrosr-s5 (vng0258h-rosr-s5). SNAP output
6qhd transcription X-ray (2.85 Å) Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O, Shahar A, Zarivach R, Gordan R, Arbely E (2019) "Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine." Biochim Biophys Acta Gen Subj, 1863, 1343-1350. doi: 10.1016/j.bbagen.2019.05.019. Lysine acetylated and tyrosine phosphorylated stat3 in a complex with DNA. SNAP output
6qib DNA binding protein X-ray (2.8 Å) Ter Beek J, Parkash V, Bylund GO, Osterman P, Sauer-Eriksson AE, Johansson E (2019) "Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ε." Nucleic Acids Res., 47, 5712-5722. doi: 10.1093/nar/gkz248. The crystal structure of pol2core in complex with DNA and an incoming nucleotide, carrying an fe-s cluster. SNAP output
6qil DNA binding protein X-ray (2.0 Å) Kutnowski N, Shmulevich F, Davidov G, Shahar A, Bar-Zvi D, Eichler J, Zarivach R, Shaanan B (2019) "Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR." Nucleic Acids Res., 47, 8860-8873. doi: 10.1093/nar/gkz604. The complex structure of hsrosr-s1 (vng0258h-rosr-s1). SNAP output
6qld DNA binding protein cryo-EM (4.15 Å) Yan K, Yang J, Zhang Z, McLaughlin SH, Chang L, Fasci D, Ehrenhofer-Murray AE, Heck AJR, Barford D (2019) "Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome." Nature, 574, 278-282. doi: 10.1038/s41586-019-1609-1. Structure of inner kinetochore ccan-cenp-a complex. SNAP output
6qtk isomerase X-ray (2.31 Å) Gibson EG, Bax B, Chan PF, Osheroff N (2019) "Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase." Acs Infect Dis., 5, 570-581. doi: 10.1021/acsinfecdis.8b00315. 2.31a structure of gepotidacin with s.aureus DNA gyrase and doubly nicked DNA. SNAP output
6qtp isomerase X-ray (2.37 Å) Gibson EG, Bax B, Chan PF, Osheroff N (2019) "Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase." Acs Infect Dis., 5, 570-581. doi: 10.1021/acsinfecdis.8b00315. 2.37a structure of gepotidacin with s.aureus DNA gyrase and uncleaved DNA. SNAP output
6qua DNA binding protein X-ray (2.681 Å) Kutnowski N, Shmulevich F, Davidov G, Shahar A, Bar-Zvi D, Eichler J, Zarivach R, Shaanan B (2019) "Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR." Nucleic Acids Res., 47, 8860-8873. doi: 10.1093/nar/gkz604. The complex structure of hsrosr-sg (vng0258-rosr-sg). SNAP output
6qwf DNA binding protein X-ray (2.7 Å) Hansen S, Hall M, Grundstrom C, Brannstrom K, Sauer-Eriksson AE, Johansson J (2020) "A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes." J.Bacteriol., 202. doi: 10.1128/JB.00115-20. The transcriptional regulator prfa-a94v mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif. SNAP output
6qwh DNA binding protein X-ray (2.9 Å) Hansen S, Hall M, Grundstrom C, Brannstrom K, Sauer-Eriksson AE, Johansson J (2020) "A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes." J.Bacteriol., 202. doi: 10.1128/JB.00115-20. The transcriptional regulator prfa-l140h mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif. SNAP output
6qwk DNA binding protein X-ray (2.9 Å) Hansen S, Hall M, Grundstrom C, Brannstrom K, Sauer-Eriksson AE, Johansson J (2020) "A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes." J.Bacteriol., 202. doi: 10.1128/JB.00115-20. The transcriptional regulator prfa-l140f mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif. SNAP output
6qwm DNA binding protein X-ray (2.9 Å) Hansen S, Hall M, Grundstrom C, Brannstrom K, Sauer-Eriksson AE, Johansson J (2020) "A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes." J.Bacteriol., 202. doi: 10.1128/JB.00115-20. The transcriptional regulator prfa-a218g mutant from listeria monocytogenes in complex with a 30-bp operator prfa-box motif. SNAP output
6qx1 isomerase X-ray (2.65 Å) Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA (2019) "Structure-guided design of antibacterials that allosterically inhibit DNA gyrase." Bioorg.Med.Chem.Lett., 29, 1407-1412. doi: 10.1016/j.bmcl.2019.03.029. 2.7a structure of benzoisoxazole 3 with s.aureus DNA gyrase and DNA.. SNAP output
6qx2 isomerase X-ray (3.4 Å) Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA (2019) "Structure-guided design of antibacterials that allosterically inhibit DNA gyrase." Bioorg.Med.Chem.Lett., 29, 1407-1412. doi: 10.1016/j.bmcl.2019.03.029. 3.4a structure of benzoisoxazole 3 with s.aureus DNA gyrase and DNA. SNAP output
6qxf DNA binding protein cryo-EM (3.6 Å) Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB (2019) "Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System." Mol.Cell, 75, 90-101.e5. doi: 10.1016/j.molcel.2019.04.020. Cas1-cas2-csn2-DNA complex from the type ii-a crispr-cas system. SNAP output
6qxt DNA binding protein cryo-EM (8.9 Å) Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB (2019) "Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System." Mol.Cell, 75, 90-101.e5. doi: 10.1016/j.molcel.2019.04.020. Cas1-cas2-csn2-DNA dimer complex from the type ii-a crispr-cas system. SNAP output
6qy3 DNA binding protein cryo-EM (9.1 Å) Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB (2019) "Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System." Mol.Cell, 75, 90-101.e5. doi: 10.1016/j.molcel.2019.04.020. Segment of the cas1-cas2-csn2-DNA filament complex from the type ii-a crispr-cas system. SNAP output
6qzk hydrolase X-ray (3.548 Å) Hegge JW, Swarts DC, Chandradoss SD, Cui TJ, Kneppers J, Jinek M, Joo C, van der Oost J (2019) "DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute." Nucleic Acids Res., 47, 5809-5821. doi: 10.1093/nar/gkz306. Structure of clostridium butyricum argonaute bound to a guide DNA (5' deoxycytidine) and a 19-mer target DNA. SNAP output
6r0c DNA binding protein cryo-EM (4.2 Å) Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE, Nans A, Rueda DS, Cherepanov P, Costa A (2019) "Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer." Nat Commun, 10, 4189. doi: 10.1038/s41467-019-12007-w. Human-d02 nucleosome core particle with biotin-streptavidin label. SNAP output
6r1t gene regulation cryo-EM (4.02 Å) Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A (2019) "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex." Cell Rep, 27, 387-399.e7. doi: 10.1016/j.celrep.2019.03.061. Structure of lsd2-npac-linker-nucleosome core particle complex: class 1, free nuclesome. SNAP output
6r1u gene regulation cryo-EM (4.36 Å) Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A (2019) "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex." Cell Rep, 27, 387-399.e7. doi: 10.1016/j.celrep.2019.03.061. Structure of lsd2-npac-linker-nucleosome core particle complex: class 2. SNAP output
6r25 gene regulation cryo-EM (4.61 Å) Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A (2019) "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex." Cell Rep, 27, 387-399.e7. doi: 10.1016/j.celrep.2019.03.061. Structure of lsd2-npac-linker-nucleosome core particle complex: class 3. SNAP output
6r2v transcription X-ray (2.503 Å) Chaves-Sanjuan A, Gnesutta N, Gobbini A, Martignago D, Bernardini A, Fornara F, Mantovani R, Nardini M (2021) "Structural determinants for NF-Y subunit organization and NF-Y/DNA association in plants." Plant J., 105, 49-61. doi: 10.1111/tpj.15038. Arabidopsis nf-y-ccaat-box complex. SNAP output
6r64 hydrolase X-ray (2.64 Å) Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M (2019) "Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping." Nucleic Acids Res., 47, 11943-11955. doi: 10.1093/nar/gkz1017. N-terminal domain of modification dependent ecokmcra restriction endonuclease (neco) in complex with c5mcgg target sequence. SNAP output
6r8y DNA binding protein cryo-EM (4.3 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp-6-4pp(-1)-uv-ddb. SNAP output
6r8z DNA binding protein cryo-EM (3.9 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp_thf2(-1)-uv-ddb. SNAP output
6r90 DNA binding protein cryo-EM (4.5 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp-thf2(+1)-uv-ddb class a. SNAP output
6r91 DNA binding protein cryo-EM (4.1 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp_thf2(-3)-uv-ddb. SNAP output
6r92 DNA binding protein cryo-EM (4.8 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp-thf2(+1)-uv-ddb class b. SNAP output
6r93 DNA cryo-EM (4.0 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp-6-4pp. SNAP output
6r94 DNA binding protein cryo-EM (3.5 Å) Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH (2019) "DNA damage detection in nucleosomes involves DNA register shifting." Nature, 571, 79-84. doi: 10.1038/s41586-019-1259-3. cryo-EM structure of ncp_thf2(-3). SNAP output
6rar DNA binding protein X-ray (1.785 Å) Williamson A, Leiros HS (2019) "Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation." Nucleic Acids Res., 47, 7147-7162. doi: 10.1093/nar/gkz596. Pmar-lig_pres3-mn. SNAP output
6ras DNA binding protein X-ray (2.75 Å) Williamson A, Leiros HS (2019) "Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation." Nucleic Acids Res., 47, 7147-7162. doi: 10.1093/nar/gkz596. Pmar-lig_pre.. SNAP output
6rau DNA binding protein X-ray (1.99 Å) Williamson A, Leiros HS (2019) "Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation." Nucleic Acids Res., 47, 7147-7162. doi: 10.1093/nar/gkz596. Posts3_pmar_lig4_wt. SNAP output
6raw replication cryo-EM (3.7 Å) Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A (2019) "Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome." Cell Rep, 28, 2673-2688.e8. doi: 10.1016/j.celrep.2019.07.104. D. melanogaster cmg-DNA, state 1a. SNAP output
6rax hydolase cryo-EM (3.99 Å) Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A (2019) "Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome." Cell Rep, 28, 2673-2688.e8. doi: 10.1016/j.celrep.2019.07.104. D. melanogaster cmg-DNA, state 1b. SNAP output
6ray replication cryo-EM (4.28 Å) Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A (2019) "Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome." Cell Rep, 28, 2673-2688.e8. doi: 10.1016/j.celrep.2019.07.104. D. melanogaster cmg-DNA, state 2a. SNAP output
6raz hydrolase cryo-EM (4.46 Å) Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR, Yardimci H, Costa A (2019) "Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome." Cell Rep, 28, 2673-2688.e8. doi: 10.1016/j.celrep.2019.07.104. D. melanogaster cmg-DNA, state 2b. SNAP output
6rce DNA binding protein X-ray (1.946 Å) Williamson A, Leiros HS (2019) "Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation." Nucleic Acids Res., 47, 7147-7162. doi: 10.1093/nar/gkz596. Pmar-lig_pres3. SNAP output
6rcn hydrolase X-ray (2.25 Å) Nicholls TJ, Spahr H, Jiang S, Siira SJ, Koolmeister C, Sharma S, Kauppila JHK, Jiang M, Kaever V, Rackham O, Chabes A, Falkenberg M, Filipovska A, Larsson NG, Gustafsson CM (2019) "Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria." Mol.Cell, 76, 784-796.e6. doi: 10.1016/j.molcel.2019.09.010. Crystal structure of rexo2-d199a-dada. SNAP output
6rh3 transcription cryo-EM (3.6 Å) Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A (2019) "Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation." Mol.Cell, 75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029. cryo-EM structure of e. coli RNA polymerase elongation complex bound to ctp substrate. SNAP output
6ri7 transcription cryo-EM (3.9 Å) Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A (2019) "Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation." Mol.Cell, 75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029. cryo-EM structure of e. coli RNA polymerase elongation complex bound to greb transcription factor. SNAP output
6ri9 transcription cryo-EM (3.7 Å) Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A (2019) "Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation." Mol.Cell, 75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029. cryo-EM structure of e. coli RNA polymerase backtracked elongation complex in non-swiveled state. SNAP output
6rid viral protein cryo-EM (2.9 Å) Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K, Szalay AA, Fischer U, Cramer P (2019) "Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes." Cell, 179, 1525. doi: 10.1016/j.cell.2019.11.023. Structure of vaccinia virus DNA-dependent RNA polymerase elongation complex. SNAP output
6rie viral protein cryo-EM (3.1 Å) Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K, Szalay AA, Fischer U, Cramer P (2019) "Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes." Cell, 179, 1525. doi: 10.1016/j.cell.2019.11.023. Structure of vaccinia virus DNA-dependent RNA polymerase co-transcriptional capping complex. SNAP output
6rin transcription cryo-EM (3.7 Å) Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A (2019) "Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation." Mol.Cell, 75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029. cryo-EM structure of e. coli RNA polymerase backtracked elongation complex bound to greb transcription factor. SNAP output
6rip transcription cryo-EM (3.4 Å) Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A (2019) "Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation." Mol.Cell, 75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029. cryo-EM structure of e. coli RNA polymerase backtracked elongation complex in swiveled state. SNAP output
6rj9 hydrolase cryo-EM (3.2 Å) Fuchsbauer O, Swuec P, Zimberger C, Amigues B, Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A, Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M, Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A (2019) "Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6." Mol.Cell, 76, 922. doi: 10.1016/j.molcel.2019.09.012. cryo-EM structure of st1cas9-sgrna-tdna20-acriia6 monomeric assembly.. SNAP output
6rja hydrolase cryo-EM (3.0 Å) Fuchsbauer O, Swuec P, Zimberger C, Amigues B, Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A, Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M, Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A (2019) "Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6." Mol.Cell, 76, 922. doi: 10.1016/j.molcel.2019.09.012. cryo-EM structure of st1cas9-sgrna-tdna20-acriia6 dimeric assembly.. SNAP output
6rjd hydrolase cryo-EM (3.3 Å) Fuchsbauer O, Swuec P, Zimberger C, Amigues B, Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A, Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M, Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A (2019) "Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6." Mol.Cell, 76, 922. doi: 10.1016/j.molcel.2019.09.012. cryo-EM structure of st1cas9-sgrna-tdna59-ntpam complex.. SNAP output
6rjg hydrolase cryo-EM (3.2 Å) Fuchsbauer O, Swuec P, Zimberger C, Amigues B, Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A, Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M, Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A (2019) "Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6." Mol.Cell, 76, 922. doi: 10.1016/j.molcel.2019.09.012. cryo-EM structure of st1cas9-sgrna-acriia6-tdna59-ntpam complex.. SNAP output
6rks isomerase cryo-EM (4.0 Å) Vanden Broeck A, Lotz C, Ortiz J, Lamour V (2019) "Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex." Nat Commun, 10, 4935. doi: 10.1038/s41467-019-12914-y. E. coli DNA gyrase - DNA binding and cleavage domain in state 1 without toprim insertion. SNAP output
6rku isomerase cryo-EM (4.0 Å) Vanden Broeck A, Lotz C, Ortiz J, Lamour V (2019) "Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex." Nat Commun, 10, 4935. doi: 10.1038/s41467-019-12914-y. E. coli DNA gyrase - DNA binding and cleavage domain in state 1. SNAP output
6rkv isomerase cryo-EM (4.6 Å) Vanden Broeck A, Lotz C, Ortiz J, Lamour V (2019) "Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex." Nat Commun, 10, 4935. doi: 10.1038/s41467-019-12914-y. E. coli DNA gyrase - DNA binding and cleavage domain in state 2. SNAP output
6rkw isomerase cryo-EM (6.6 Å) Vanden Broeck A, Lotz C, Ortiz J, Lamour V (2019) "Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex." Nat Commun, 10, 4935. doi: 10.1038/s41467-019-12914-y. Cryoem structure of the complete e. coli DNA gyrase complex bound to a 130 bp DNA duplex. SNAP output
6rnm hydrolase X-ray (1.76 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. Crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6rno hydrolase X-ray (2.25 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. Crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6rnr hydrolase X-ray (2.003 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. The crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6rny DNA binding protein cryo-EM (3.9 Å) Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE, Nans A, Rueda DS, Cherepanov P, Costa A (2019) "Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer." Nat Commun, 10, 4189. doi: 10.1038/s41467-019-12007-w. Pfv intasome - nucleosome strand transfer complex. SNAP output
6ro2 hydrolase X-ray (1.821 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. The crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6ro4 translocase cryo-EM (3.5 Å) Kokic G, Chernev A, Tegunov D, Dienemann C, Urlaub H, Cramer P (2019) "Structural basis of TFIIH activation for nucleotide excision repair." Nat Commun, 10, 2885. doi: 10.1038/s41467-019-10745-5. Structure of the core tfiih-xpa-DNA complex. SNAP output
6rok hydrolase X-ray (1.95 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. The crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6rp0 hydrolase X-ray (2.25 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. The crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6rp7 hydrolase X-ray (2.0 Å) Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V, Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V, Agrofoglio L, Garnier N, Castaing B (2020) "Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights." Int J Mol Sci, 21. doi: 10.3390/ijms21062058. The crystal structure of a complex between the llfpg protein, a thf-DNA and an inhibitor. SNAP output
6rqh transcription cryo-EM (3.7 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i closed conformation 1 (cc1). SNAP output
6rql transcription cryo-EM (2.9 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i closed conformation 2 (cc2). SNAP output
6rqt transcription cryo-EM (4.0 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i-twh-rrn3-DNA. SNAP output
6rrd transcription cryo-EM (3.1 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i pre-initiation complex DNA opening intermediate 1. SNAP output
6rt4 RNA binding protein X-ray (1.49 Å) Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A (2019) "Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif." J Chem Theory Comput, 15, 7004-7014. doi: 10.1021/acs.jctc.9b00987. The yth domain of ythdc1 protein in complex with m6acu oligonucleotide. SNAP output
6rt5 RNA binding protein X-ray (2.303 Å) Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A (2019) "Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif." J Chem Theory Comput, 15, 7004-7014. doi: 10.1021/acs.jctc.9b00987. The yth domain of ythdc1 protein in complex with gm6ac oligonucleotide. SNAP output
6rt6 RNA binding protein X-ray (1.461 Å) Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A (2019) "Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif." J Chem Theory Comput, 15, 7004-7014. doi: 10.1021/acs.jctc.9b00987. The yth domain of ythdc1 protein in complex with ggm6ac oligonucleotide. SNAP output
6rt7 RNA binding protein X-ray (1.73 Å) Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A (2019) "Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif." J Chem Theory Comput, 15, 7004-7014. doi: 10.1021/acs.jctc.9b00987. The yth domain of ythdc1 protein in complex with gm6acu oligonucleotide. SNAP output
6rui transcription cryo-EM (2.7 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i pre-initiation complex DNA opening intermediate 2. SNAP output
6ruo transcription cryo-EM (3.5 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i open complex conformation 1. SNAP output
6rwe transcription cryo-EM (3.0 Å) Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW (2019) "Molecular insight into RNA polymerase I promoter recognition and promoter melting." Nat Commun, 10, 5543. doi: 10.1038/s41467-019-13510-w. RNA polymerase i open complex conformation 2. SNAP output
6rwl recombination cryo-EM (3.36 Å) Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P (2020) "Structural basis of second-generation HIV integrase inhibitor action and viral resistance." Science, 367, 806-810. doi: 10.1126/science.aay4919. Sivrcm intasome. SNAP output
6rwm recombination cryo-EM (2.81 Å) Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P (2020) "Structural basis of second-generation HIV integrase inhibitor action and viral resistance." Science, 367, 806-810. doi: 10.1126/science.aay4919. Sivrcm intasome in complex with bictegravir. SNAP output
6rwn recombination cryo-EM (3.1 Å) Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P (2020) "Structural basis of second-generation HIV integrase inhibitor action and viral resistance." Science, 367, 806-810. doi: 10.1126/science.aay4919. Sivrcm intasome in complex with dolutegravir. SNAP output
6rwo recombination cryo-EM (3.05 Å) Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P (2020) "Structural basis of second-generation HIV integrase inhibitor action and viral resistance." Science, 367, 806-810. doi: 10.1126/science.aay4919. Sivrcm intasome (q148h-g140s) in complex with bictegravir. SNAP output
6ryd DNA binding protein X-ray (1.575 Å) Sloan J, Hakenjos JP, Gebert M, Ermakova O, Gumiero A, Stier G, Wild K, Sinning I, Lohmann JU (2020) "Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL." Nat Commun, 11, 2223. doi: 10.1038/s41467-020-16024-y. Wus-hd bound to tgaa DNA. SNAP output
6ryi DNA binding protein X-ray (2.691 Å) Sloan J, Hakenjos JP, Gebert M, Ermakova O, Gumiero A, Stier G, Wild K, Sinning I, Lohmann JU (2020) "Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL." Nat Commun, 11, 2223. doi: 10.1038/s41467-020-16024-y. Wus-hd bound to g-box DNA. SNAP output
6ryl DNA binding protein X-ray (2.63 Å) Sloan J, Hakenjos JP, Gebert M, Ermakova O, Gumiero A, Stier G, Wild K, Sinning I, Lohmann JU (2020) "Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL." Nat Commun, 11, 2223. doi: 10.1038/s41467-020-16024-y. Wus-hd bound to taat DNA. SNAP output
6ryr transcription cryo-EM (3.1 Å) Farnung L, Ochmann M, Cramer P (2020) "Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations." Elife, 9. doi: 10.7554/eLife.56178. Nucleosome-chd4 complex structure (single chd4 copy). SNAP output
6ryu transcription cryo-EM (4.0 Å) Farnung L, Ochmann M, Cramer P (2020) "Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations." Elife, 9. doi: 10.7554/eLife.56178. Nucleosome-chd4 complex structure (two chd4 copies). SNAP output
6s01 transcription cryo-EM (3.2 Å) Wang H, Farnung L, Dienemann C, Cramer P (2020) "Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding." Nat.Struct.Mol.Biol., 27, 8-13. doi: 10.1038/s41594-019-0345-4. Structure of ledgf pwwp domain bound h3k36 methylated nucleosome. SNAP output
6s16 hydrolase X-ray (3.409 Å) Gorecka KM, Krepl M, Szlachcic A, Poznanski J, Sponer J, Nowotny M (2019) "RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution." Nat Commun, 10, 4102. doi: 10.1038/s41467-019-11900-8. T. thermophilus ruvc in complex with holliday junction substrate. SNAP output
6s1m replication cryo-EM (4.27 Å) Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A (2020) "Structure of the processive human Pol delta holoenzyme." Nat Commun, 11, 1109. doi: 10.1038/s41467-020-14898-6. Human polymerase delta holoenzyme conformer 1. SNAP output
6s1n replication cryo-EM (4.86 Å) Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A (2020) "Structure of the processive human Pol delta holoenzyme." Nat Commun, 11, 1109. doi: 10.1038/s41467-020-14898-6. Human polymerase delta holoenzyme conformer 2. SNAP output
6s1o replication cryo-EM (8.1 Å) Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A (2020) "Structure of the processive human Pol delta holoenzyme." Nat Commun, 11, 1109. doi: 10.1038/s41467-020-14898-6. Human polymerase delta holoenzyme conformer 3. SNAP output
6s3h hydrolase X-ray (2.06 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with adp-alf4 and (dt)7ds11bp. SNAP output
6s3i hydrolase X-ray (2.455 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with ssDNA (dt)18 and adp-mgf4. SNAP output
6s3m hydrolase X-ray (2.113 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with ssDNA (dt)18 and adp-alf4. SNAP output
6s3n hydrolase X-ray (2.533 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with ssDNA (dt)18 and adp-vo4. SNAP output
6s3o hydrolase X-ray (1.974 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with ssDNA (dt)18 and adp. SNAP output
6s3p hydrolase X-ray (1.926 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with (dt)18. SNAP output
6s48 hydrolase X-ray (1.9 Å) Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M (2020) "Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation." Nucleic Acids Res., 48, 6954-6969. doi: 10.1093/nar/gkaa403. Avaii restriction endonuclease in complex with partially cleaved dsDNA. SNAP output
6s6h DNA binding protein X-ray (2.4 Å) Jalal ASB, Tran NT, Stevenson CE, Chan EW, Lo R, Tan X, Noy A, Lawson DM, Le TBK (2020) "Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family." Cell Rep, 32, 107928. doi: 10.1016/j.celrep.2020.107928. Crystal structure of the DNA binding domain of the chromosome-partitioning protein parb complexed to the centromeric pars site. SNAP output
6s85 DNA binding protein cryo-EM (4.2 Å) Kashammer L, Saathoff JH, Lammens K, Gut F, Bartho J, Alt A, Kessler B, Hopfner KP (2019) "Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex." Mol.Cell, 76, 382. doi: 10.1016/j.molcel.2019.07.035. Cutting state of the e. coli mre11-rad50 (sbccd) head complex bound to adp and dsDNA.. SNAP output
6sa0 transferase X-ray (2.209 Å) Brissett NC, Zabrady K, Plocinski P, Bianchi J, Korycka-Machala M, Brzostek A, Dziadek J, Doherty AJ (2020) "Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C." Nat Commun, 11, 4196. doi: 10.1038/s41467-020-18012-8. Ternary complex of prim-polc from mycobacterium smegmatis with 2nt gapped DNA and upnhpp. SNAP output
6sa1 transferase X-ray (2.01 Å) Brissett NC, Zabrady K, Plocinski P, Bianchi J, Korycka-Machala M, Brzostek A, Dziadek J, Doherty AJ (2020) "Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C." Nat Commun, 11, 4196. doi: 10.1038/s41467-020-18012-8. Post catalytic complex of prim-polc from mycobacterium smegmatis with gapped DNA and 3'-dutp. SNAP output
6sdg transcription X-ray (2.96 Å) Kato H, Mutte SK, Suzuki H, Crespo I, Das S, Radoeva T, Fontana M, Yoshitake Y, Hainiwa E, van den Berg W, Lindhoud S, Ishizaki K, Hohlbein J, Borst JW, Boer DR, Nishihama R, Kohchi T, Weijers D (2020) "Design principles of a minimal auxin response system." Nat.Plants, 6, 473-482. doi: 10.1038/s41477-020-0662-y. Crystal structure of the DNA binding domain of m. polymorpha auxin response factor 2 (mparf2) in complex with high affinity DNA. SNAP output
6se0 nuclear protein cryo-EM (3.8 Å) Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M, Sekulic N (2019) "CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail." Embo Rep., 20, e48913. doi: 10.15252/embr.201948913. Class 1 : cenp-a nucleosome. SNAP output
6se6 nuclear protein cryo-EM (3.5 Å) Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M, Sekulic N (2019) "CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail." Embo Rep., 20, e48913. doi: 10.15252/embr.201948913. Class2 : cenp-a nucleosome in complex with cenp-c central region. SNAP output
6see nuclear protein cryo-EM (4.2 Å) Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M, Sekulic N (2019) "CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail." Embo Rep., 20, e48913. doi: 10.15252/embr.201948913. Class2a : cenp-a nucleosome in complex with cenp-c central region. SNAP output
6sef nuclear protein cryo-EM (3.7 Å) Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M, Sekulic N (2019) "CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail." Embo Rep., 20, e48913. doi: 10.15252/embr.201948913. Class2c : cenp-a nucleosome in complex with cenp-c central region. SNAP output
6seg nuclear protein cryo-EM (3.1 Å) Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M, Sekulic N (2019) "CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail." Embo Rep., 20, e48913. doi: 10.15252/embr.201948913. Class1: cenp-a nucleosome in complex with cenp-c central region. SNAP output
6sei DNA binding protein X-ray (2.69 Å) Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapinska M, Nowotny M (2019) "Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease." Nucleic Acids Res., 47, 11681-11690. doi: 10.1093/nar/gkz842. Recognition and processing of branched DNA substrates by slx1-slx4 nuclease. SNAP output
6sjb hydrolase cryo-EM (3.7 Å) Cheng K, Wilkinson M, Chaban Y, Wigley DB (2020) "A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair." Nat.Struct.Mol.Biol., 27, 71-77. doi: 10.1038/s41594-019-0355-2. cryo-EM structure of the recbcd chi recognised complex. SNAP output
6sje hydrolase cryo-EM (4.1 Å) Cheng K, Wilkinson M, Chaban Y, Wigley DB (2020) "A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair." Nat.Struct.Mol.Biol., 27, 71-77. doi: 10.1038/s41594-019-0355-2. cryo-EM structure of the recbcd chi partially-recognised complex. SNAP output
6sjf hydrolase cryo-EM (3.9 Å) Cheng K, Wilkinson M, Chaban Y, Wigley DB (2020) "A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair." Nat.Struct.Mol.Biol., 27, 71-77. doi: 10.1038/s41594-019-0355-2. cryo-EM structure of the recbcd chi unrecognised complex. SNAP output
6sjg hydrolase cryo-EM (3.8 Å) Cheng K, Wilkinson M, Chaban Y, Wigley DB (2020) "A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair." Nat.Struct.Mol.Biol., 27, 71-77. doi: 10.1038/s41594-019-0355-2. cryo-EM structure of the recbcd no chi negative control complex. SNAP output
6sko replication cryo-EM (3.4 Å) Baretic D, Jenkyn-Bedford M, Aria V, Cannone G, Skehel M, Yeeles JTP (2020) "Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork." Mol.Cell, 78, 926-940.e13. doi: 10.1016/j.molcel.2020.04.012. cryo-EM structure of the fork protection complex bound to cmg at a replication fork - conformation 2 mcm ctd:ssDNA. SNAP output
6sxb DNA binding protein cryo-EM (7.9 Å) Jones M, Beuron F, Borg A, Nans A, Earl CP, Briggs DC, Snijders AP, Bowles M, Morris EP, Linch M, McDonald NQ (2020) "Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation." Nat Commun, 11, 1120. doi: 10.1038/s41467-020-14856-2. Xpf-ercc1 cryo-EM structure, DNA-bound form. SNAP output
6sy0 DNA binding protein X-ray (3.102 Å) Niederwieser I, Reiter D, Kantsadi A, Voss T, Vakonakis I "Structural and functional analysis of the Plasmodium falciparum SIP2 DNA binding domain." Structure of the plasmodium falciparum sip2 DNA-binding ap2 tandem repeat in complex with two spe2 half-sites. SNAP output
6t1f DNA binding protein X-ray (2.9 Å) Jalal AS, Tran NT, Stevenson CE, Chimthanawala A, Badrinarayanan A, Lawson DM, Le TB (2021) "A CTP-dependent gating mechanism enables ParB spreading on DNA." Elife, 10. doi: 10.7554/eLife.69676. Crystal structure of the c-terminally truncated chromosome-partitioning protein parb from caulobacter crescentus complexed to the centromeric pars site. SNAP output
6t21 hydrolase X-ray (2.07 Å) Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M (2019) "Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping." Nucleic Acids Res., 47, 11943-11955. doi: 10.1093/nar/gkz1017. N-terminal domain of ecokmcra restriction endonuclease (neco) in complex with t5mcga target sequence. SNAP output
6t22 hydrolase X-ray (2.21 Å) Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M (2019) "Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping." Nucleic Acids Res., 47, 11943-11955. doi: 10.1093/nar/gkz1017. N-terminal domain of ecokmcra restriction endonuclease (neco) in complex with t5hmcga target sequence. SNAP output
6t2u hydrolase cryo-EM (3.6 Å) Cheng K, Wilkinson M, Chaban Y, Wigley DB (2020) "A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair." Nat.Struct.Mol.Biol., 27, 71-77. doi: 10.1038/s41594-019-0355-2. cryo-EM structure of the recbcd in complex with chi-minus2 substrate. SNAP output
6t2v hydrolase cryo-EM (3.8 Å) Cheng K, Wilkinson M, Chaban Y, Wigley DB (2020) "A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair." Nat.Struct.Mol.Biol., 27, 71-77. doi: 10.1038/s41594-019-0355-2. cryo-EM structure of the recbcd in complex with chi-plus2 substrate. SNAP output
6t5t DNA binding protein X-ray (1.7 Å) Golovinas E, Manakova E, Sasnauskas G, Zaremba M "Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTGGCCACAAT." Crystal structure of archaeoglobus fulgidus argonaute protein with cognate DNA oligoduplex 5'-pattgtggccacaat. SNAP output
6t78 nuclear protein X-ray (2.504 Å) Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P (2020) "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function." Nature, 580, 669-672. doi: 10.1038/s41586-020-2195-y. Structure of human sox11 transcription factor in complex with a short DNA fragment. SNAP output
6t79 nuclear protein cryo-EM (3.2 Å) Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P (2020) "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function." Nature, 580, 669-672. doi: 10.1038/s41586-020-2195-y. Structure of a human nucleosome at 3.2 Å resolution. SNAP output
6t7a nuclear protein cryo-EM (3.7 Å) Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P (2020) "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function." Nature, 580, 669-672. doi: 10.1038/s41586-020-2195-y. Structure of human sox11 transcription factor in complex with a nucleosome. SNAP output
6t7b nuclear protein cryo-EM (5.1 Å) Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P (2020) "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function." Nature, 580, 669-672. doi: 10.1038/s41586-020-2195-y. Structure of human sox2 transcription factor in complex with a nucleosome. SNAP output
6t7c nuclear protein cryo-EM (4.0 Å) Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P (2020) "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function." Nature, 580, 669-672. doi: 10.1038/s41586-020-2195-y. Structure of two copies of human sox11 transcription factor in complex with a nucleosome. SNAP output
6t7d nuclear protein cryo-EM (4.4 Å) Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P (2020) "Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function." Nature, 580, 669-672. doi: 10.1038/s41586-020-2195-y. Structure of human sox11 transcription factor in complex with a nucleosome. SNAP output
6t8b DNA binding protein cryo-EM (3.65 Å) Jean NL, Rutherford TJ, Lowe J (2020) "FtsK in motion reveals its mechanism for double-stranded DNA translocation." Proc.Natl.Acad.Sci.USA, 117, 14202-14208. doi: 10.1073/pnas.2001324117. Ftsk motor domain with dsDNA, translocating state. SNAP output
6t8g DNA binding protein cryo-EM (4.34 Å) Jean NL, Rutherford TJ, Lowe J (2020) "FtsK in motion reveals its mechanism for double-stranded DNA translocation." Proc.Natl.Acad.Sci.USA, 117, 14202-14208. doi: 10.1073/pnas.2001324117. Stalled ftsk motor domain bound to dsDNA. SNAP output
6t8h replication cryo-EM (3.77 Å) Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L (2020) "Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA." Nat Commun, 11, 1591. doi: 10.1038/s41467-020-15392-9. cryo-EM structure of the DNA-bound pold-pcna processive complex from p. abyssi. SNAP output
6t8o DNA binding protein cryo-EM (3.99 Å) Jean NL, Rutherford TJ, Lowe J (2020) "FtsK in motion reveals its mechanism for double-stranded DNA translocation." Proc.Natl.Acad.Sci.USA, 117, 14202-14208. doi: 10.1073/pnas.2001324117. Stalled ftsk motor domain bound to dsDNA end. SNAP output
6t90 transcription cryo-EM (3.05 Å) Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH (2020) "Mechanisms of OCT4-SOX2 motif readout on nucleosomes." Science, 368, 1460-1465. doi: 10.1126/science.abb0074. Oct4-sox2-bound nucleosome - shl-6. SNAP output
6t93 transcription cryo-EM (3.49 Å) Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH (2020) "Mechanisms of OCT4-SOX2 motif readout on nucleosomes." Science, 368, 1460-1465. doi: 10.1126/science.abb0074. Nucleosome with oct4-sox2 motif at shl-6. SNAP output
6t9l gene regulation cryo-EM (3.6 Å) Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM, Cramer P (2020) "Structure of the transcription coactivator SAGA." Nature, 577, 717-720. doi: 10.1038/s41586-020-1933-5. Saga dub module bound to a ubiqitinated nucleosome. SNAP output
6tbz transcription X-ray (1.782 Å) Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, de Martin Garrido N, Marquez JA, Cordeiro TN, Pluta R, Macias MJ (2021) "Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes." Comput Struct Biotechnol J, 19, 632-646. doi: 10.1016/j.csbj.2020.12.044. Crystal structure of the mh1 domain of smad5-smad3 chimera construct bound to the ggcgc site. SNAP output
6tc9 DNA binding protein X-ray (2.175 Å) Landova B, Silhan J (2020) "Conformational changes of DNA repair glycosylase MutM triggered by DNA binding." Febs Lett., 594, 3032-3044. doi: 10.1002/1873-3468.13876. Crystal structure of mutm from neisseria meningitidis. SNAP output
6tce transcription X-ray (2.92 Å) Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, de Martin Garrido N, Marquez JA, Cordeiro TN, Pluta R, Macias MJ (2021) "Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes." Comput Struct Biotechnol J, 19, 632-646. doi: 10.1016/j.csbj.2020.12.044. Crystal structure of the ggct site-bound mh1 domain of smad5 containing a gggs insertion in the loop1. SNAP output
6tda DNA binding protein cryo-EM (15.0 Å) Wagner FR, Dienemann C, Wang H, Stutzer A, Tegunov D, Urlaub H, Cramer P (2020) "Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome." Nature, 579, 448-451. doi: 10.1038/s41586-020-2088-0. Structure of swi-snf chromatin remodeler rsc bound to a nucleosome. SNAP output
6ted transcription cryo-EM (3.1 Å) Vos SM, Farnung L, Linden A, Urlaub H, Cramer P (2020) "Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation." Nat.Struct.Mol.Biol., 27, 668-677. doi: 10.1038/s41594-020-0437-1. Structure of complete, activated transcription complex pol ii-dsif-paf-spt6 uncovers allosteric elongation activation by rtf1. SNAP output
6tem DNA binding protein cryo-EM (3.9 Å) Boopathi R, Danev R, Khoshouei M, Kale S, Nahata S, Ramos L, Angelov D, Dimitrov S, Hamiche A, Petosa C, Bednar J (2020) "Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends." Nucleic Acids Res., 48, 5735-5748. doi: 10.1093/nar/gkaa246. Cenp-a nucleosome core particle with 145 base pairs of the widom 601 sequence by cryo-EM. SNAP output
6tny replication cryo-EM (3.08 Å) Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A (2020) "Structure of the processive human Pol delta holoenzyme." Nat Commun, 11, 1109. doi: 10.1038/s41467-020-14898-6. Processive human polymerase delta holoenzyme. SNAP output
6tnz replication cryo-EM (4.05 Å) Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N, Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ, Hamdan SM, De Biasio A (2020) "Structure of the processive human Pol delta holoenzyme." Nat Commun, 11, 1109. doi: 10.1038/s41467-020-14898-6. Human polymerase delta-fen1-pcna toolbelt. SNAP output
6tps transcription cryo-EM (3.54 Å) Pilsl M, Engel C (2020) "Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting." Nat Commun, 11, 1206. doi: 10.1038/s41467-020-15052-y. Early intermediate RNA polymerase i pre-initiation complex - eipic. SNAP output
6tqn transcription cryo-EM (3.8 Å) Huang YH, Hilal T, Loll B, Burger J, Mielke T, Bottcher C, Said N, Wahl MC (2020) "Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis." Mol.Cell, 79, 1024-1036.e5. doi: 10.1016/j.molcel.2020.08.010. Rrn anti-termination complex without s4. SNAP output
6tqo transcription cryo-EM (3.8 Å) Huang YH, Hilal T, Loll B, Burger J, Mielke T, Bottcher C, Said N, Wahl MC (2020) "Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis." Mol.Cell, 79, 1024-1036.e5. doi: 10.1016/j.molcel.2020.08.010. Rrn anti-termination complex. SNAP output
6tuo DNA binding protein X-ray (1.8 Å) Golovinas E, Manakova E, Sasnauskas G, Zaremba M "Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA oligoduplex 5'-pATTGTACGTACAAT." Crystal structure of archaeoglobus fulgidus argonaute protein with cognate DNA oligoduplex 5'-pattgtacgtacaat. SNAP output
6tup virus cryo-EM (3.2 Å) Tarafder AK, von Kugelgen A, Mellul AJ, Schulze U, Aarts DGAL, Bharat TAM (2020) "Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria." Proc.Natl.Acad.Sci.USA, 117, 4724-4731. doi: 10.1073/pnas.1917726117. cryo-EM structure of pf4 bacteriophage coat protein with single-stranded DNA. SNAP output
6tuw DNA binding protein X-ray (3.5 Å) Gonzalez-Corrochano R, Ruiz FM, Taylor NMI, Huecas S, Drakulic S, Spinola-Amilibia M, Fernandez-Tornero C (2020) "The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair." Nucleic Acids Res., 48, 9943-9958. doi: 10.1093/nar/gkaa688. Human xpg-DNA, complex 1. SNAP output
6tux DNA binding protein X-ray (3.1 Å) Gonzalez-Corrochano R, Ruiz FM, Taylor NMI, Huecas S, Drakulic S, Spinola-Amilibia M, Fernandez-Tornero C (2020) "The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair." Nucleic Acids Res., 48, 9943-9958. doi: 10.1093/nar/gkaa688. Human xpg-DNA, complex 2. SNAP output
6tye transcription X-ray (3.79 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Crystal structure of mtb sigma l transcription initiation complex with 5 nt long RNA primer. SNAP output
6tyf transcription X-ray (3.8 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Crystal structure of mtb sigma l transcription initiation complex with 6 nt long RNA primer. SNAP output
6tyg transcription X-ray (3.5 Å) Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y (2020) "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription." Proc.Natl.Acad.Sci.USA, 117, 5801-5809. doi: 10.1073/pnas.1920747117. Crystal structure of mtb sigma l transcription initiation complex with 9 nt long RNA primer. SNAP output
6u0m replication-DNA cryo-EM (3.9 Å) Yuan Z, Georgescu R, Bai L, Zhang D, Li H, O'Donnell ME (2020) "DNA unwinding mechanism of a eukaryotic replicative CMG helicase." Nat Commun, 11, 688. doi: 10.1038/s41467-020-14577-6. Structure of the s. cerevisiae replicative helicase cmg in complex with a forked DNA. SNAP output
6u15 hydrolase X-ray (2.4 Å) Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat AC (2019) "Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase." J.Am.Chem.Soc., 141, 18851-18861. doi: 10.1021/jacs.9b10376. Human thymine DNA glycosylase n140a mutant bound to DNA with 2'-f-5-carboxyl-dc substrate analog. SNAP output
6u16 hydrolase X-ray (1.6 Å) Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat AC (2019) "Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase." J.Am.Chem.Soc., 141, 18851-18861. doi: 10.1021/jacs.9b10376. Human thymine DNA glycosylase n140a mutant bound to DNA with 5-carboxyl-dc substrate. SNAP output
6u17 hydrolase X-ray (1.55 Å) Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat AC (2019) "Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase." J.Am.Chem.Soc., 141, 18851-18861. doi: 10.1021/jacs.9b10376. Human thymine DNA glycosylase bound to DNA with 2'-f-5-carboxyl-dc substrate analog. SNAP output
6u2o transferase-DNA X-ray (2.3 Å) Ouzon-Shubeita H, Vilas CK, Lee S "Structures of the Mutagenic Bypass of the Major Cisplatin-DNA Lesion by Human DNA Polymerase Beta Reveal Insights into Cisplatin-Induced Mutagenesis." Structure of human DNA polymerase beta misinserting dampnpp opposite the 5'g of the cisplatin pt-gg intrastrand crosslink. SNAP output
6u6b transferase-DNA X-ray (3.108 Å) Ouzon-Shubeita H, Vilas CK, Lee S (2020) "Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion." Biochem.J., 477, 937-951. doi: 10.1042/BCJ20190906. Structure of human DNA polymerase beta misinserting dampnpp opposite the 5'g of the cisplatin pt-gg intrastrand crosslink with manganese in the active site. SNAP output
6u6x hydrolase X-ray (2.58 Å) Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z, Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov DN (2021) "Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification." Nat Commun, 12, 731. doi: 10.1038/s41467-021-21023-8. Human samhd1 bound to deoxyribo(c*g*c*c*t)-oligonucleotide. SNAP output
6u6z hydrolase X-ray (2.1 Å) Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z, Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov DN (2021) "Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification." Nat Commun, 12, 731. doi: 10.1038/s41467-021-21023-8. Human samhd1 bound to deoxyribo(tg*ttca)-oligonucleotide. SNAP output
6u7t hydrolase-DNA X-ray (2.0 Å) Russelburg LP, O'Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP (2020) "Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY." Acs Chem.Biol., 15, 93-102. doi: 10.1021/acschembio.9b00639. Muty adenine glycosylase bound to DNA containing a transition state analog (1n) paired with d(8-oxo-g). SNAP output
6u81 DNA binding protein-DNA X-ray (2.34 Å) Klingler C, Ashley J, Shi K, Stiefvater A, Kyba M, Sinnreich M, Aihara H, Kinter J (2020) "DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD." Faseb J., 34, 4573-4590. doi: 10.1096/fj.201902696. Crystal structure of the double homeodomain of dux4 in complex with a DNA aptamer. SNAP output
6u82 DNA binding protein-DNA X-ray (3.21 Å) Klingler C, Ashley J, Shi K, Stiefvater A, Kyba M, Sinnreich M, Aihara H, Kinter J (2020) "DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD." Faseb J., 34, 4573-4590. doi: 10.1096/fj.201902696. Crystal structure of the double homeodomain of dux4 in complex with a DNA aptamer containing bulge and loop. SNAP output
6u8p transferase-DNA X-ray (3.05 Å) Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J (2020) "Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms." Nat Commun, 11, 3355. doi: 10.1038/s41467-020-17109-4. Crystal structure of dnmt3b-dnmt3l in complex with cpgpa DNA. SNAP output
6u8q transferase-transferase inhibitor-DNA cryo-EM (4.67 Å) Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie R (2020) "A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies." J.Mol.Biol., 432, 2055-2066. doi: 10.1016/j.jmb.2020.01.040. Cryoem structure of hiv-1 cleaved synaptic complex (csc) intasome. SNAP output
6u8v transferase-DNA X-ray (3.0 Å) Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J (2020) "Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms." Nat Commun, 11, 3355. doi: 10.1038/s41467-020-17109-4. Crystal structure of dnmt3b-dnmt3l in complex with cpgpt DNA. SNAP output
6u8w transferase-DNA X-ray (2.95 Å) Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J (2020) "Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms." Nat Commun, 11, 3355. doi: 10.1038/s41467-020-17109-4. Crystal structure of dnmt3b(k777a)-dnmt3l in complex with cpgpt DNA. SNAP output
6u8x transferase-DNA X-ray (2.95 Å) Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S, Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H, Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang GG, Jeltsch A, Song J (2020) "Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms." Nat Commun, 11, 3355. doi: 10.1038/s41467-020-17109-4. Crystal structure of dnmt3b-dnmt3l in complex with cpapg DNA. SNAP output
6u90 transferase-DNA X-ray (3.0 Å) Gao L "Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms." Crystal structure of dnmt3b(n779a)-dnmt3l in complex with cpgpt DNA. SNAP output
6u91 transferase-DNA X-ray (3.0 Å) Gao L "Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms." Crystal structure of dnmt3b(q772r)-dnmt3l in complex with cpgpt DNA. SNAP output
6u9q transcription-DNA X-ray (1.83 Å) Viennet T, Yin M, Jayaraj A, Kim W, Sun ZYJ, Fujiwara Y, Zhang K, Seruggia D, Seo HS, Dhe-Paganon S, Orkin SH, Arthanari H (2024) "Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6." Structure. doi: 10.1016/j.str.2024.09.022. Crystal structure analysis of DNA-bcl11a znf domain complex. SNAP output
6ubf DNA binding protein-DNA X-ray (4.597 Å) Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH (2015) "Kinetic gating mechanism of DNA damage recognition by Rad4/XPC." Nat Commun, 6, 5849. doi: 10.1038/ncomms6849. Role of beta-hairpin motifs in the DNA duplex opening by the rad4-xpc nucleotide excision repair complex. SNAP output
6ueo DNA binding protein-DNA X-ray (2.0 Å) Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan R (2020) "DNA mismatches reveal conformational penalties in protein-DNA recognition." Nature, 587, 291-296. doi: 10.1038/s41586-020-2843-2. Structure of a. thaliana tbp-ac mismatch DNA site. SNAP output
6uep DNA binding protein-DNA X-ray (2.05 Å) Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan R (2020) "DNA mismatches reveal conformational penalties in protein-DNA recognition." Nature, 587, 291-296. doi: 10.1038/s41586-020-2843-2. Structure of a. thaliana tbp bound to a DNA site with a c-c mismatch. SNAP output
6ueq DNA binding protein-DNA X-ray (2.4 Å) Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan R (2020) "DNA mismatches reveal conformational penalties in protein-DNA recognition." Nature, 587, 291-296. doi: 10.1038/s41586-020-2843-2. Structure of tbp bound to c-c mismatch containing tata site. SNAP output
6uer DNA binding protein-DNA X-ray (2.5 Å) Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan R (2020) "DNA mismatches reveal conformational penalties in protein-DNA recognition." Nature, 587, 291-296. doi: 10.1038/s41586-020-2843-2. Crystal form 2: structure of tbp bound to c-c mismatch at ph 7. SNAP output
6ueu replication X-ray (1.8 Å) Walsh AR, Beese LS, Wu EY "Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase." Crystal structure of bf DNA polymerase f710y mutant bound to tetrahydrofuran and datp. SNAP output
6ug1 DNA binding protein-DNA X-ray (2.833 Å) Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C, Ansari A, Broyde S, Min JH (2021) "Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex." DNA Repair (Amst), 107, 103194. doi: 10.1016/j.dnarep.2021.103194. Sequence impact in DNA duplex opening by the rad4-xpc nucleotide excision repair complex. SNAP output
6ugm transferase-structural protein-DNA cryo-EM (3.7 Å) Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng N (2019) "Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS." Mol.Cell, 76, 712. doi: 10.1016/j.molcel.2019.10.013. Structural basis of compass ecm recognition of an unmodified nucleosome. SNAP output
6uh5 transferase-structural protein-DNA cryo-EM (3.5 Å) Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng N (2019) "Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS." Mol.Cell, 76, 712. doi: 10.1016/j.molcel.2019.10.013. Structural basis of compass ecm recognition of the h2bub nucleosome. SNAP output
6ui2 DNA binding protein-DNA X-ray (2.35 Å) Koag MC, Jung H, Kou Y, Lee S (2019) "Bypass of the Major Alkylative DNA Lesion by Human DNA Polymerase eta." Molecules, 24. doi: 10.3390/molecules24213928. Structure of human DNA polymerase eta complexed with n7mg in the template base paired with incoming non-hydrolyzable ctp. SNAP output
6uin DNA binding protein-DNA X-ray (3.348 Å) Paul D, Mu H, Tavakoli A, Dai Q, Chen X, Chakraborty S, He C, Ansari A, Broyde S, Min JH (2021) "Tethering-facilitated DNA 'opening' and complementary roles of beta-hairpin motifs in the Rad4/XPC DNA damage sensor protein." Nucleic Acids Res., 48, 12348-12364. doi: 10.1093/nar/gkaa909. Role of beta-hairpin motifs in the DNA duplex opening by the rad4-xpc nucleotide excision repair complex. SNAP output
6uir viral protein X-ray (2.64 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 m184v reverse transcriptase-DNA complex with (-)-ftc-tp. SNAP output
6uis viral protein X-ray (2.75 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 m184v reverse transcriptase-DNA complex with dctp. SNAP output
6uit viral protein X-ray (2.81 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 wild-type reverse transcriptase-DNA complex with dctp. SNAP output
6ujx viral protein X-ray (2.7 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 wild-type reverse transcriptase-DNA complex with (-)-ftc-tp. SNAP output
6ujy viral protein X-ray (2.59 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 wild-type reverse transcriptase-DNA complex with (-)-3tc-tp. SNAP output
6ujz viral protein-DNA X-ray (2.56 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 wild-type reverse transcriptase-DNA complex with (+)-ftc-tp. SNAP output
6uk0 viral protein X-ray (2.76 Å) Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z, Lansdon EB (2019) "Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance." Commun Biol, 2, 469. doi: 10.1038/s42003-019-0706-x. Hiv-1 m184v reverse transcriptase-DNA complex. SNAP output
6uke hydrolase-DNA X-ray (1.62 Å) Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X (2020) "Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom." Nucleic Acids Res., 48, 1466-1478. doi: 10.1093/nar/gkz1195. Hhai endonuclease in complex with iodine-labelled DNA. SNAP output
6ukf hydrolase-DNA X-ray (1.0 Å) Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X (2020) "Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom." Nucleic Acids Res., 48, 1466-1478. doi: 10.1093/nar/gkz1195. Hhai endonuclease in complex with DNA at 1 angstrom resolution. SNAP output
6ukg hydrolase-DNA X-ray (1.16 Å) Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X (2020) "Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom." Nucleic Acids Res., 48, 1466-1478. doi: 10.1093/nar/gkz1195. Hhai endonuclease in complex with DNA in space group p21 (ph 4.2). SNAP output
6ukh hydrolase-DNA X-ray (2.82 Å) Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X (2020) "Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom." Nucleic Acids Res., 48, 1466-1478. doi: 10.1093/nar/gkz1195. Hhai endonuclease in complex with DNA in space group p41212 (ph 6.0). SNAP output
6uki hydrolase-DNA X-ray (2.7 Å) Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X (2020) "Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom." Nucleic Acids Res., 48, 1466-1478. doi: 10.1093/nar/gkz1195. Hhai endonuclease in complex with DNA in space group p212121 (ph 6.0). SNAP output
6uok transferase-DNA X-ray (2.55 Å) Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB, Freudenthal BD (2020) "Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta." J.Biol.Chem., 295, 1613-1622. doi: 10.1074/jbc.RA119.011569. Y271g DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-gtp. SNAP output
6uol transferase-DNA X-ray (1.936 Å) Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB, Freudenthal BD (2020) "Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta." J.Biol.Chem., 295, 1613-1622. doi: 10.1074/jbc.RA119.011569. Y271g DNA polymerase beta substrate complex with a templating cytosine and incoming rgtp. SNAP output
6uom transferase-DNA X-ray (2.05 Å) Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB, Freudenthal BD (2020) "Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta." J.Biol.Chem., 295, 1613-1622. doi: 10.1074/jbc.RA119.011569. Y271g DNA polymerase beta ternary complex with templating adenine and incoming r8-oxo-gtp. SNAP output
6uph cell cycle cryo-EM (2.7 Å) Migl D, Kschonsak M, Arthur CP, Khin Y, Harrison SC, Ciferri C, Dimitrova YN (2020) "Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 angstrom Resolution." Structure, 28, 363-370.e3. doi: 10.1016/j.str.2019.12.002. Structure of a yeast centromeric nucleosome at 2.7 angstrom resolution. SNAP output
6upk transcription-DNA cryo-EM (4.9 Å) Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D'Arcy S, Luger K (2020) "FACT caught in the act of manipulating the nucleosome." Nature, 577, 426-431. doi: 10.1038/s41586-019-1820-0. Structure of fact_subnucleosome complex 1. SNAP output
6upl transcription-DNA cryo-EM (7.4 Å) Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D'Arcy S, Luger K (2020) "FACT caught in the act of manipulating the nucleosome." Nature, 577, 426-431. doi: 10.1038/s41586-019-1820-0. Structure of fact_subnucleosome complex 2. SNAP output
6upx transcription-RNA-DNA X-ray (3.4 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with 5-guanidinohydantoin lesion in state 1. SNAP output
6upy transcription-RNA-DNA X-ray (3.4 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with 5-guanidinohydantoin lesion in state 2e. SNAP output
6upz transcription-RNA-DNA X-ray (3.1 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with 5-guanidinohydantoin lesion in state 3. SNAP output
6uq0 transcription-RNA-DNA X-ray (3.56 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with 5-guanidinohydantoin lesion in state 4. SNAP output
6uq1 transcription-DNA-RNA X-ray (3.6 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with 5-guanidinohydantoin lesion in state 6. SNAP output
6uq2 transcription-RNA-DNA X-ray (3.2 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with dg in state 1. SNAP output
6uq3 transcription-RNA-DNA X-ray (3.47 Å) Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D (2020) "RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions." Proc.Natl.Acad.Sci.USA, 117, 9338-9348. doi: 10.1073/pnas.1919904117. RNA polymerase ii elongation complex with 5-guanidinohydantoin lesion in state 5. SNAP output
6uqi transferase-DNA X-ray (2.5 Å) Jung H, Lee S "Crystal structure of Q38A human DNA polymerase eta bound with 8-oxoadenine (oxoA) and non-hydrolyzable dGTP analog (dGTP*)." Crystal structure of q38a human DNA polymerase eta bound with 8-oxoadenine (oxoa) and non-hydrolyzable dgtp analog (dgtp*). SNAP output
6ur2 replication-DNA X-ray (2.27 Å) Lelyveld VS, Zhang W, Szostak JW (2020) "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 7276-7283. doi: 10.1073/pnas.1922400117. DNA polymerase i large fragment from bacillus stearothermophilus with DNA template and primer containing an n3'-> p5' linkage. SNAP output
6ur4 replication-DNA X-ray (2.25 Å) Lelyveld VS, Zhang W, Szostak JW (2020) "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 7276-7283. doi: 10.1073/pnas.1922400117. DNA polymerase i large fragment from bacillus stearothermophilus with DNA template and 3'-amino primer. SNAP output
6ur9 replication-DNA X-ray (2.1 Å) Lelyveld VS, Zhang W, Szostak JW (2020) "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 7276-7283. doi: 10.1073/pnas.1922400117. DNA polymerase i large fragment from bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddgtp (ngtp), and ca2+. SNAP output
6us5 replication-DNA X-ray (2.25 Å) Lelyveld VS, Zhang W, Szostak JW (2020) "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 7276-7283. doi: 10.1073/pnas.1922400117. DNA polymerase i large fragment from bacillus stearothermophilus with DNA template, 3'-amino primer, dgpnhpp analog, and mn2+. SNAP output
6usj DNA binding protein-DNA cryo-EM (10.5 Å) Gaullier G, Roberts G, Muthurajan UM, Bowerman S, Rudolph J, Mahadevan J, Jha A, Rae PS, Luger K (2020) "Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1." Plos One, 15, e0240932. doi: 10.1371/journal.pone.0240932. Structure of two nucleosomes bridged by human parp2. SNAP output
6uso nuclear protein, transferase-RNA-DNA X-ray (2.54 Å) Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD (2020) "Mechanisms of nucleotide selection by telomerase." Elife, 9. doi: 10.7554/eLife.55438. Telomerase reverse transcriptase prenucleotide binary complex, tert:DNA. SNAP output
6usp nuclear protein, transferase-RNA-DNA X-ray (3.56 Å) Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD (2020) "Mechanisms of nucleotide selection by telomerase." Elife, 9. doi: 10.7554/eLife.55438. Telomerase reverse transcriptase product complex, tert:DNA. SNAP output
6usq nuclear protein, transferase-RNA-DNA X-ray (3.62 Å) Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD (2020) "Mechanisms of nucleotide selection by telomerase." Elife, 9. doi: 10.7554/eLife.55438. Telomerase reverse transcriptase binary complex with y256a mutation, tert:DNA. SNAP output
6usr nuclear protein, transferase-RNA-DNA X-ray (2.93 Å) Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang TH, Opresko PL, Freudenthal BD (2020) "Mechanisms of nucleotide selection by telomerase." Elife, 9. doi: 10.7554/eLife.55438. Telomerase reverse transcriptase ternary complex, tert:DNA:dgpcpp. SNAP output
6uvn hydrolase-RNA cryo-EM (3.1 Å) Li Z, Zhang H, Xiao R, Chang L (2020) "Cryo-EM structure of a type I-F CRISPR RNA guided surveillance complex bound to transposition protein TniQ." Cell Res., 30, 179-181. doi: 10.1038/s41422-019-0268-y. Cryoem structure of vccascasde-tniq complex. SNAP output
6uvw DNA binding protein-DNA X-ray (2.551 Å) Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard BL (2020) "Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition." Structure, 28, 760-775.e8. doi: 10.1016/j.str.2020.04.009. Engineered variant of i-onui meganuclease with improved thermostability. SNAP output
6uw0 DNA binding protein-DNA X-ray (2.72 Å) Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard BL (2020) "Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition." Structure, 28, 760-775.e8. doi: 10.1016/j.str.2020.04.009. Engineered variant of i-onui meganuclease with improved thermostability and fully altered specificity targeting cholera toxin a subunit. SNAP output
6uwg DNA binding protein-DNA X-ray (2.22 Å) Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard BL (2020) "Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition." Structure, 28, 760-775.e8. doi: 10.1016/j.str.2020.04.009. Engineered variant of i-onui meganuclease with improved thermostability and e178d mutation at catalytic site. SNAP output
6uwh DNA binding protein-DNA X-ray (2.299 Å) Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard BL (2020) "Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition." Structure, 28, 760-775.e8. doi: 10.1016/j.str.2020.04.009. Intermediate engineered variant of i-onui meganuclease with improved thermostability and partially altered specificity. SNAP output
6uwj DNA binding protein-DNA X-ray (1.852 Å) Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard BL (2020) "Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition." Structure, 28, 760-775.e8. doi: 10.1016/j.str.2020.04.009. Intermediate engineered variant of i-onui meganuclease with improved thermostability and partially altered specificity. SNAP output
6uwk DNA binding protein-DNA X-ray (2.533 Å) Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard BL (2020) "Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition." Structure, 28, 760-775.e8. doi: 10.1016/j.str.2020.04.009. Engineered variant of i-onui meganuclease with improved stability and fully altered specificity targeting human chromosome 11 trans integration site. SNAP output
6uxw transcription-DNA cryo-EM (8.96 Å) Han Y, Reyes AA, Malik S, He Y (2020) "Cryo-EM structure of SWI/SNF complex bound to a nucleosome." Nature, 579, 452-455. doi: 10.1038/s41586-020-2087-1. Swi-snf nucleosome complex with adp-befx. SNAP output
6v0v recombination-DNA cryo-EM (3.61 Å) Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, Gellert M (2020) "Cutting antiparallel DNA strands in a single active site." Nat.Struct.Mol.Biol., 27, 119-126. doi: 10.1038/s41594-019-0363-2. cryo-EM structure of mouse wt rag1-2 nfc complex (dna0). SNAP output
6v2k nuclear protein-DNA X-ray (2.6 Å) Hirano R, Arimura Y, Kujirai T, Shibata M, Okuda A, Morishima K, Inoue R, Sugiyama M, Kurumizaka H (2021) "Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome." Commun Biol, 4, 191. doi: 10.1038/s42003-021-01707-z. The nucleosome structure after h2a-h2b exchange. SNAP output
6v3k viral protein-DNA cryo-EM (3.4 Å) Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr TR, Craigie R, Lyumkis D (2020) "Structural basis for strand-transfer inhibitor binding to HIV intasomes." Science, 367, 810-814. doi: 10.1126/science.aay8015. Structure of hiv cleaved synaptic complex (csc) intasome bound with magnesium and insti xz419 (compound 4c). SNAP output
6v5k transferase X-ray (2.69 Å) Jung H, Lee S "Crystal structure of human DNA polymerase eta complexed with N7-nitrogen half-mustard guanine (NHMG) and dCTP*." Crystal structure of human DNA polymerase eta complexed with n7-nitrogen half-mustard guanine (nhmg) and dctp*. SNAP output
6v7b virus cryo-EM (3.4 Å) Wang F, Baquero DP, Su Z, Osinski T, Prangishvili D, Egelman EH, Krupovic M (2020) "Structure of a filamentous virus uncovers familial ties within the archaeal virosphere." Virus Evol, 6, veaa023. doi: 10.1093/ve/veaa023. cryo-EM reconstruction of pyrobaculum filamentous virus 2 (pfv2). SNAP output
6v8u DNA binding protein X-ray (2.103 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2020) "A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences." Biochemistry, 59, 1909-1926. doi: 10.1021/acs.biochem.0c00253. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a modified kaiso binding sequence (kbs). SNAP output
6v92 gene regulation-DNA cryo-EM (20.0 Å) Patel AB, Moore CM, Greber BJ, Luo J, Zukin SA, Ranish J, Nogales E (2019) "Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement." Elife, 8. doi: 10.7554/eLife.54449. Rsc-ncp. SNAP output
6v93 DNA binding protein cryo-EM (3.1 Å) Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK (2020) "Structure and mechanism of B-family DNA polymerase zeta specialized for translesion DNA synthesis." Nat.Struct.Mol.Biol., 27, 913-924. doi: 10.1038/s41594-020-0476-7. Structure of DNA polymerase zeta-DNA-dntp ternary complex. SNAP output
6vaa DNA binding protein-DNA cryo-EM (3.4 Å) Wang R, Wang S, Dhar A, Peralta C, Pavletich NP (2020) "DNA clamp function of the monoubiquitinated Fanconi anaemia ID complex." Nature, 580, 278-282. doi: 10.1038/s41586-020-2110-6. Structure of the fanconi anemia id complex bound to icl DNA. SNAP output
6vae DNA binding protein-DNA cryo-EM (3.6 Å) Wang R, Wang S, Dhar A, Peralta C, Pavletich NP (2020) "DNA clamp function of the monoubiquitinated Fanconi anaemia ID complex." Nature, 580, 278-282. doi: 10.1038/s41586-020-2110-6. Mono-ubiquitinated fanconi anemia id complex bound to icl DNA. SNAP output
6vaf DNA binding protein-DNA cryo-EM (3.9 Å) Wang R, Wang S, Dhar A, Peralta C, Pavletich NP (2020) "DNA clamp function of the monoubiquitinated Fanconi anaemia ID complex." Nature, 580, 278-282. doi: 10.1038/s41586-020-2110-6. Structure of mono-ubiquitinated fancd2 bound to non-ubiquitinated fanci and to DNA. SNAP output
6vbw immune system cryo-EM (3.2 Å) Jia N, Xie W, de la Cruz MJ, Eng ET, Patel DJ (2020) "Structure-function insights into the initial step of DNA integration by a CRISPR-Cas-Transposon complex." Cell Res., 30, 182-184. doi: 10.1038/s41422-019-0272-2. cryo-EM structure of cascade-tniq-dsDNA ternary complex. SNAP output
6vcs DNA binding protein-DNA X-ray (1.7 Å) Dong C, Tempel W, Bountra C, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "SRA domain of UHRF1 in complex with DNA." Sra domain of uhrf1 in complex with DNA. SNAP output
6vdd transferase-DNA X-ray (1.9 Å) Ghosh S, Goldgur Y, Shuman S (2020) "Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme." Nucleic Acids Res., 48, 3165-3180. doi: 10.1093/nar/gkaa075. Pol domain of pol1 from m. smegmatis complex with DNA primer-template and dntp. SNAP output
6vdk transferase-DNA cryo-EM (4.5 Å) Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie R (2020) "A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies." J.Mol.Biol., 432, 2055-2066. doi: 10.1016/j.jmb.2020.01.040. Cryoem structure of hiv-1 conserved intasome core. SNAP output
6ven transferase-structural protein-DNA cryo-EM (3.37 Å) Worden EJ, Zhang X, Wolberger C (2020) "Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome." Elife, 9. doi: 10.7554/eLife.53199. Yeast compass in complex with a ubiquitinated nucleosome. SNAP output
6vez replication X-ray (1.875 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Pre-Catalytic Ternary Complex, 20 mM Ca2+ (60 min)." DNA polymerase mu, 8-oxorgtp:at pre-catalytic ternary complex, 20 mm ca2+ (60 min). SNAP output
6vf0 replication X-ray (1.58 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Reaction State Ternary Complex, 50 mM Mg2+ (30 min)." DNA polymerase mu, 8-oxorgtp:at reaction state ternary complex, 50 mm mg2+ (30 min). SNAP output
6vf1 replication X-ray (1.68 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mg2+ (120 min)." DNA polymerase mu, 8-oxorgtp:at product state ternary complex, 50 mm mg2+ (120 min). SNAP output
6vf2 replication X-ray (1.6 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mg2+ (960 min)." DNA polymerase mu, 8-oxorgtp:at product state ternary complex, 50 mm mg2+ (960 min). SNAP output
6vf3 replication X-ray (1.521 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)." DNA polymerase mu, 8-oxorgtp:at ground state ternary complex, 50 mm mn2+ (15 min). SNAP output
6vf4 replication X-ray (1.75 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Reaction State Ternary Complex, 50 mM Mn2+ (30 min)." DNA polymerase mu, 8-oxorgtp:at reaction state ternary complex, 50 mm mn2+ (30 min). SNAP output
6vf5 replication X-ray (1.6 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mn2+ (120 min)." DNA polymerase mu, 8-oxorgtp:at product state ternary complex, 50 mm mn2+ (120 min). SNAP output
6vf6 replication X-ray (1.69 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:At Product State Ternary Complex, 50 mM Mn2+ (960 min)." DNA polymerase mu, 8-oxorgtp:at product state ternary complex, 50 mm mn2+ (960 min). SNAP output
6vf7 replication X-ray (1.871 Å) Jamsen JA, Sassa A, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxodGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)." DNA polymerase mu, 8-oxodgtp:at ground state ternary complex, 50 mm mn2+ (15 min). SNAP output
6vf8 replication X-ray (1.7 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:Ct Pre-Catalytic Ternary Complex, 20 mM Ca2+ (120 min)." DNA polymerase mu, 8-oxorgtp:ct pre-catalytic ternary complex, 20 mm ca2+ (120 min). SNAP output
6vf9 replication X-ray (1.56 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:Ct Ternary Complex, 50 mM Mg2+ (2160 min)." DNA polymerase mu, 8-oxorgtp:ct ternary complex, 50 mm mg2+ (2160 min). SNAP output
6vfa replication X-ray (1.76 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:Ct Ground State Ternary Complex, 50 mM Mn2+ (15 min)." DNA polymerase mu, 8-oxorgtp:ct ground state ternary complex, 50 mm mn2+ (15 min). SNAP output
6vfb replication X-ray (1.55 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (960 min)." DNA polymerase mu, 8-oxorgtp:ct reaction state ternary complex, 50 mm mn2+ (960 min). SNAP output
6vfc replication X-ray (1.59 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH "DNA Polymerase Mu, 8-oxorGTP:Ct Product State Ternary Complex, 50 mM Mn2+ (2160 min)." DNA polymerase mu, 8-oxorgtp:ct product state ternary complex, 50 mm mn2+ (2160 min). SNAP output
6vg2 transcription X-ray (3.9 Å) Hou C, Mandal A, Rohr J, Tsodikov OV (2021) "Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins." Structure, 29, 404-412.e4. doi: 10.1016/j.str.2020.11.012. Crystal structure of the DNA binding domain of human transcription factor fli1 in complex with 16-mer DNA cagaggatgtggcttc. SNAP output
6vg6 transferase-DNA X-ray (3.08 Å) Jung H, Lee S (2020) "Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4." Biochem.J., 477, 2859-2871. doi: 10.1042/BCJ20200449. Crystal structure of dpo4 with 8-oxoadenine (oxoa) and dgtp*. SNAP output
6vg8 transcription X-ray (4.31 Å) Hou C, Mandal A, Rohr J, Tsodikov OV (2021) "Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins." Structure, 29, 404-412.e4. doi: 10.1016/j.str.2020.11.012. Crystal structure of the DNA binding domains of human fli1 and runx2 in complex with 16-mer DNA cagaggatgtggcttc. SNAP output
6vgd transcription X-ray (4.2 Å) Hou C, Mandal A, Rohr J, Tsodikov OV (2021) "Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins." Structure, 29, 404-412.e4. doi: 10.1016/j.str.2020.11.012. Crystal structure of the DNA binding domain (dbd) of human fli1 and the complex of the dbd of human runx2 with core binding factor beta (cbfb), in complex with 16mer DNA cagaggatgtggcttc. SNAP output
6vge transcription X-ray (4.25 Å) Hou C, Mandal A, Rohr J, Tsodikov OV (2021) "Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins." Structure, 29, 404-412.e4. doi: 10.1016/j.str.2020.11.012. Crystal structure of the DNA binding domains of human transcription factor erg, human runx2 bound to core binding factor beta (cbfb), in complex with 16mer DNA cagaggatgtggcttc. SNAP output
6vgg transcription X-ray (4.31 Å) Hou C, Mandal A, Rohr J, Tsodikov OV (2021) "Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins." Structure, 29, 404-412.e4. doi: 10.1016/j.str.2020.11.012. Crystal structure of the DNA binding domains of human transcription factor erg, human runx2 bound to core binding factor beta (cbfb), and mithramycin, in complex with 16mer DNA cagaggatgtggcttc. SNAP output
6vgm transferase X-ray (2.84 Å) Jung H, Lee S (2020) "Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4." Biochem.J., 477, 2859-2871. doi: 10.1042/BCJ20200449. Crystal structure of dpo4 with 8-oxoadenine (oxoa) and dttp*. SNAP output
6vjw transferase X-ray (2.02 Å) Ouzon-Shubeita H, Jung H, Lee MH, Koag MC, Lee S (2020) "Catalytic mechanism of the mismatch-specific DNA glycosylase methyl-CpG-binding domain 4." Biochem.J., 477, 1601-1612. doi: 10.1042/BCJ20200125. Crystal structure of wt hmbd4 complexed with t:g mismatch DNA. SNAP output
6vkp transferase-DNA X-ray (2.54 Å) Jung H, Lee S (2021) "Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4." Biochem.J., 478, 1769-1781. doi: 10.1042/BCJ20210162. Crystal structure of dpo4 extension past 8-oxoadenine (oxoa) and dg. SNAP output
6vnp transferase-DNA X-ray (2.42 Å) Jung H, Lee S "Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT." Crystal structure of dpo4 extension past 8-oxoadenine (oxoa) and dt. SNAP output
6voy DNA binding protein-DNA cryo-EM (3.7 Å) Bhatt V, Shi K, Salamango DJ, Moeller NH, Pandey KK, Bera S, Bohl TE, Kurniawan F, Orellana K, Zhang W, Grandgenett DP, Harris RS, Sundborger-Lunna AC, Aihara H (2020) "Structural basis of host protein hijacking in human T-cell leukemia virus integration." Nat Commun, 11, 3121. doi: 10.1038/s41467-020-16963-6. cryo-EM structure of htlv-1 instasome. SNAP output
6vpc DNA binding protein-DNA-RNA cryo-EM (3.2 Å) Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E, Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA (2020) "DNA capture by a CRISPR-Cas9-guided adenine base editor." Science, 369, 566-571. doi: 10.1126/science.abb1390. Structure of the spcas9 DNA adenine base editor - abe8e. SNAP output
6vrd hydrolase-RNA X-ray (1.299 Å) Cho Y-J, Butler D "Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level." Crystal structure of rnase h-RNA-ps-aso complex at an atomic level. SNAP output
6vtx DNA binding protein-DNA X-ray (2.14 Å) Sharma R, Choi KJ, Quan MD, Sharma S, Sankaran B, Park H, LaGrone A, Kim JJ, MacKenzie KR, Ferreon ACM, Kim C, Ferreon JC (2021) "Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization." Nat Commun, 12, 5579. doi: 10.1038/s41467-021-25761-7. Crystal structure of human klf4 zinc finger DNA binding domain in complex with nanog DNA. SNAP output
6vug protein binding X-ray (3.0 Å) Chesterman C, Arnold E (2021) "Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry." Structure, 29, 598-605.e3. doi: 10.1016/j.str.2021.02.001. Diabody bound to a reverse transcriptase aptamer complex. SNAP output
6vvs transcription,transferase-DNA-antibiotic X-ray (3.112 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with antibiotic sorangicin. SNAP output
6vvt transcription,transferase-DNA-antibiotic X-ray (2.901 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Crystal structure of a mycobacterium smegmatis transcription initiation complex with rifampicin-resistant RNA polymerase and antibiotic sorangicin. SNAP output
6vvv transcription,transferase-DNA X-ray (3.2 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Crystal structure of a mycobacterium smegmatis transcription initiation complex with rifampicin-resistant RNA polymerase. SNAP output
6vvx transcription,transferase-DNA-antibiotic cryo-EM (3.39 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Mycobacterium tuberculosis wt rnap transcription initiation intermediate structure with sorangicin. SNAP output
6vvy transcription,transferase-DNA-antibiotic cryo-EM (3.42 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Mycobacterium tuberculosis wt rnap transcription open promoter complex with sorangicin. SNAP output
6vvz transcription,transferase-DNA-antibiotic cryo-EM (3.72 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Mycobacterium tuberculosis rnap s456l mutant transcription initiation intermediate structure with sorangicin. SNAP output
6vw0 transcription,transferase-DNA cryo-EM (3.59 Å) Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA (2020) "The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase." Proc.Natl.Acad.Sci.USA, 117, 30423-30432. doi: 10.1073/pnas.2013706117. Mycobacterium tuberculosis rnap s456l mutant open promoter complex. SNAP output
6vyp nuclear protein-DNA X-ray (4.99 Å) Kim SA, Zhu J, Yennawar N, Eek P, Tan S (2020) "Crystal Structure of the LSD1/CoREST Histone Demethylase Bound to Its Nucleosome Substrate." Mol.Cell, 78, 903. doi: 10.1016/j.molcel.2020.04.019. Crystal structure of the lsd1-corest histone demethylase bound to its nucleosome substrate. SNAP output
6vz4 motor protein cryo-EM (3.9 Å) Baker RW, Reimer JM, Carman PJ, Turegun B, Arakawa T, Dominguez R, Leschziner AE (2021) "Structural insights into assembly and function of the RSC chromatin remodeling complex." Nat.Struct.Mol.Biol., 28, 71-80. doi: 10.1038/s41594-020-00528-8. cryo-EM structure of sth1-arp7-arp9-rtt102 bound to the nucleosome in adp beryllium fluoride state. SNAP output
6w0m lyase-DNA X-ray (2.37 Å) Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL (2020) "The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase." Nat Commun, 11, 4437. doi: 10.1038/s41467-020-18290-2. Human 8-oxoguanine glycosylase crosslinked with oxog lesion containing DNA. SNAP output
6w0q DNA binding protein-DNA X-ray (1.89 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 endonuclease product complex d148e. SNAP output
6w0r lyase-DNA X-ray (2.35 Å) Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL (2020) "The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase." Nat Commun, 11, 4437. doi: 10.1038/s41467-020-18290-2. Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA. SNAP output
6w13 lyase-DNA X-ray (2.38 Å) Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL (2020) "The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase." Nat Commun, 11, 4437. doi: 10.1038/s41467-020-18290-2. Human 8-oxoguanine glycosylase interrogating fully intrahelical oxog lesion DNA. SNAP output
6w1a DNA binding protein-DNA X-ray (2.8 Å) Capodagli GC, Tylor KM, Kaelber JT, Petrou VI, Federle MJ, Neiditch MB (2020) "Structure-function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay." Proc.Natl.Acad.Sci.USA, 117, 24494-24502. doi: 10.1073/pnas.2008427117. Crystal structure of streptococcus dysgalactiae shp pheromone receptor rgg2 bound to DNA. SNAP output
6w1f DNA binding protein-DNA X-ray (3.2 Å) Capodagli GC, Tylor KM, Kaelber JT, Petrou VI, Federle MJ, Neiditch MB (2020) "Structure-function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay." Proc.Natl.Acad.Sci.USA, 117, 24494-24502. doi: 10.1073/pnas.2008427117. Crystal structure of streptococcus thermophilus shp pheromone receptor rgg3 bound to DNA. SNAP output
6w2m transferase-DNA X-ray (1.998 Å) Batra VK, Wilson SH (2020) "Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus." Commun Biol, 3, 348. doi: 10.1038/s42003-020-1080-4. Abortive ternary complex crystal structure of DNA polymerase beta with 8og-dc base pair at the primer terminus and flipped out da. SNAP output
6w2p DNA binding protein-DNA X-ray (1.94 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 endonuclease product complex l104r. SNAP output
6w3l DNA binding protein-DNA X-ray (2.59 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 exonuclease substrate complex wild-type. SNAP output
6w3n DNA binding protein-DNA X-ray (2.69 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 exonuclease substrate complex d148e. SNAP output
6w3q DNA binding protein-DNA X-ray (2.49 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 exonuclease substrate complex l104r. SNAP output
6w3u DNA binding protein-DNA X-ray (2.4 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 exonuclease substrate complex r237c. SNAP output
6w43 DNA binding protein-DNA X-ray (1.99 Å) Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD (2020) "Molecular and structural characterization of disease-associated APE1 polymorphisms." DNA Repair (Amst.), 91-92, 102867. doi: 10.1016/j.dnarep.2020.102867. Ape1 ap-endonuclease product complex r237c. SNAP output
6w4i lyase-DNA X-ray (2.2 Å) Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal PK, Van Houten B, Freudenthal BD (2020) "AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop." Nucleic Acids Res., 48, 7345-7355. doi: 10.1093/nar/gkaa496. Ape1 y269a product complex with abasic DNA. SNAP output
6w4t lyase-DNA X-ray (2.77 Å) Hoitsma NM, Whitaker AM, Beckwitt EC, Jang S, Agarwal PK, Van Houten B, Freudenthal BD (2020) "AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop." Nucleic Acids Res., 48, 7345-7355. doi: 10.1093/nar/gkaa496. Ape1 y269a phosphorothioate substrate complex with abasic DNA. SNAP output
6w5c hydrolase-DNA-RNA cryo-EM (2.9 Å) Zhang H, Li Z, Xiao R, Chang L (2020) "Mechanisms for target recognition and cleavage by the Cas12i RNA-guided endonuclease." Nat.Struct.Mol.Biol., 27, 1069-1076. doi: 10.1038/s41594-020-0499-0. cryo-EM structure of cas12i(e894a)-crrna-dsDNA complex. SNAP output
6w5i transferase-structural protein-DNA cryo-EM (6.9 Å) Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y (2021) "Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin." Nat Commun, 12, 2953. doi: 10.1038/s41467-021-23268-9. cryo-EM structure of mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (class01). SNAP output
6w5m transferase-structural protein-DNA cryo-EM (4.6 Å) Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y (2021) "Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin." Nat Commun, 12, 2953. doi: 10.1038/s41467-021-23268-9. cryo-EM structure of mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (class02). SNAP output
6w5n transferase-structural protein-DNA cryo-EM (6.0 Å) Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y (2021) "Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin." Nat Commun, 12, 2953. doi: 10.1038/s41467-021-23268-9. cryo-EM structure of mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (class05). SNAP output
6w5x DNA binding protein-DNA X-ray (2.59 Å) Jung H, Lee S "Crystal structure of human polymerase eta complexed with N7-benzylguanine and dCTP*." Crystal structure of human polymerase eta complexed with n7-benzylguanine and dctp*. SNAP output
6w64 hydrolase-DNA-RNA cryo-EM (3.9 Å) Zhang H, Li Z, Xiao R, Chang L (2020) "Mechanisms for target recognition and cleavage by the Cas12i RNA-guided endonuclease." Nat.Struct.Mol.Biol., 27, 1069-1076. doi: 10.1038/s41594-020-0499-0. cryo-EM structure of cas12i-crrna-dsDNA complex in i1 state. SNAP output
6w6w structural protein-DNA cryo-EM (3.0 Å) Lim CJ, Barbour AT, Zaug AJ, Goodrich KJ, McKay AE, Wuttke DS, Cech TR (2020) "The structure of human CST reveals a decameric assembly bound to telomeric DNA." Science, 368, 1081-1085. doi: 10.1126/science.aaz9649. cryo-EM structure of cst bound to telomeric single-stranded DNA. SNAP output
6w7a viral protein-DNA X-ray (2.09 Å) Kumar G, Cuypers M, Webby RR, Webb TR, White SW (2021) "Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism." Nucleic Acids Res., 49, 1609-1618. doi: 10.1093/nar/gkaa1294. The crystal structure of the 2009-h1n1-california pa endonuclease mutant e119d bound to DNA oligomer tagcat (uncleaved, 5mm overnight DNA soak). SNAP output
6w89 transferase-DNA X-ray (2.499 Å) Anteneh H, Fang J, Song J (2020) "Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation." Nat Commun, 11, 2294. doi: 10.1038/s41467-020-16213-9. Structure of dnmt3a (r882h) in complex with cga DNA. SNAP output
6w8b transferase-DNA X-ray (2.4 Å) Anteneh H, Fang J, Song J (2020) "Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation." Nat Commun, 11, 2294. doi: 10.1038/s41467-020-16213-9. Structure of dnmt3a in complex with cga DNA. SNAP output
6w8d transferase-DNA X-ray (2.598 Å) Anteneh H, Fang J, Song J (2020) "Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation." Nat Commun, 11, 2294. doi: 10.1038/s41467-020-16213-9. Structure of dnmt3a (r882h) in complex with cgt DNA. SNAP output
6w8j transferase-DNA X-ray (2.445 Å) Anteneh H, Fang J, Song J (2020) "Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation." Nat Commun, 11, 2294. doi: 10.1038/s41467-020-16213-9. Structure of dnmt3a (r882h) in complex with cag DNA. SNAP output
6w8v transferase-DNA X-ray (3.12 Å) Adam S, Anteneh H, Hornisch M, Wagner V, Lu J, Radde NE, Bashtrykov P, Song J, Jeltsch A (2020) "DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context." Nat Commun. Crystal structure of mouse dnmt1 in complex with acg DNA. SNAP output
6w8w transferase-DNA X-ray (3.0 Å) Adam S, Anteneh H, Hornisch M, Wagner V, Lu J, Radde NE, Bashtrykov P, Song J, Jeltsch A (2020) "DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context." Nat Commun. Crystal structure of mouse dnmt1 in complex with ccg DNA. SNAP output
6waa isomerase-DNA-isomerase inhibitor X-ray (3.2 Å) Skepper CK, Armstrong D, Balibar CJ, Bauer D, Bellamacina C, Benton BM, Bussiere D, De Pascale G, De Vicente J, Dean CR, Dhumale B, Fisher LM, Fuller J, Fulsunder M, Holder LM, Hu C, Kantariya B, Lapointe G, Leeds JA, Li X, Lu P, Lvov A, Ma S, Madhavan S, Malekar S, McKenney D, Mergo W, Metzger L, Moser HE, Mutnick D, Noeske J, Osborne C, Patel A, Patel D, Patel T, Prajapati K, Prosen KR, Reck F, Richie DL, Rico A, Sanderson MR, Satasia S, Sawyer WS, Selvarajah J, Shah N, Shanghavi K, Shu W, Thompson KV, Traebert M, Vala A, Vala L, Veselkov DA, Vo J, Wang M, Widya M, Williams SL, Xu Y, Yue Q, Zang R, Zhou B, Rivkin A (2020) "Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria." J.Med.Chem., 63, 7773-7816. doi: 10.1021/acs.jmedchem.0c00347. K. pneumoniae topoisomerase iv (pare-parc) in complex with DNA and compound 34 (7-[(1s,5r)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1h)-one). SNAP output
6waz viral protein-RNA cryo-EM (4.1 Å) Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV (2020) "Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription." J.Mol.Biol., 432, 4499-4522. doi: 10.1016/j.jmb.2020.06.003. +1 extended hiv-1 reverse transcriptase initiation complex core (pre-translocation state). SNAP output
6wb0 viral protein-RNA cryo-EM (4.2 Å) Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV (2020) "Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription." J.Mol.Biol., 432, 4499-4522. doi: 10.1016/j.jmb.2020.06.003. +3 extended hiv-1 reverse transcriptase initiation complex core (pre-translocation state). SNAP output
6wb1 viral protein-RNA cryo-EM (4.7 Å) Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV (2020) "Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription." J.Mol.Biol., 432, 4499-4522. doi: 10.1016/j.jmb.2020.06.003. +3 extended hiv-1 reverse transcriptase initiation complex core (intermediate state). SNAP output
6wb2 viral protein-RNA cryo-EM (4.5 Å) Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV (2020) "Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription." J.Mol.Biol., 432, 4499-4522. doi: 10.1016/j.jmb.2020.06.003. +3 extended hiv-1 reverse transcriptase initiation complex core (displaced state). SNAP output
6wbr RNA binding protein-DNA-RNA X-ray (2.91 Å) Das A, Hand TH, Smith CL, Wickline E, Zawrotny M, Li H (2020) "The molecular basis for recognition of 5'-NNNCC-3' PAM and its methylation state by Acidothermus cellulolyticus Cas9." Nat Commun, 11, 6346. doi: 10.1038/s41467-020-20204-1. Crystal structure of acecas9 bound with guide RNA and DNA with 5'-nnncc-3' pam. SNAP output
6wc0 RNA binding protein-RNA-DNA X-ray (3.61 Å) Das A, Hand TH, Smith CL, Wickline E, Zawrotny M, Li H (2020) "The molecular basis for recognition of 5'-NNNCC-3' PAM and its methylation state by Acidothermus cellulolyticus Cas9." Nat Commun, 11, 6346. doi: 10.1038/s41467-020-20204-1. Crystal structure of acecas9 bound with guide RNA and DNA with 5'-nnntc-3' pam. SNAP output
6wc2 transcription X-ray (2.1 Å) Lei X, Zhao J, Sagendorf JM, Rajashekar N, Xu J, Dantas Machado AC, Sen C, Rohs R, Feng P, Chen L (2020) "Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface." J.Mol.Biol., 432, 5499-5508. doi: 10.1016/j.jmb.2020.07.004. Crystal structure of a ternary mef2 chimera-nkx2-5-myocardin enhancer DNA complex. SNAP output
6wc5 transcription X-ray (2.9 Å) Lei X, Zhao J, Sagendorf JM, Rajashekar N, Xu J, Dantas Machado AC, Sen C, Rohs R, Feng P, Chen L (2020) "Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface." J.Mol.Biol., 432, 5499-5508. doi: 10.1016/j.jmb.2020.07.004. Crystal structure of a ternary mef2b-nkx2-5-myocardin enhancer DNA complex. SNAP output
6wdz replication-DNA X-ray (2.03 Å) Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limon-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR (2021) "Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering." Nucleic Acids Res., 49, 1046-1064. doi: 10.1093/nar/gkaa1248. Porcine circovirus 2 rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site. SNAP output
6we0 replication-DNA X-ray (1.8 Å) Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limon-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR (2021) "Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering." Nucleic Acids Res., 49, 1046-1064. doi: 10.1093/nar/gkaa1248. Wheat dwarf virus rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site. SNAP output
6we1 replication-DNA X-ray (2.612 Å) Tompkins KJ, Houtti M, Litzau LA, Aird EJ, Everett BA, Nelson AT, Pornschloegl L, Limon-Swanson LK, Evans RL, Evans K, Shi K, Aihara H, Gordon WR (2021) "Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering." Nucleic Acids Res., 49, 1046-1064. doi: 10.1093/nar/gkaa1248. Wheat dwarf virus rep domain complexed with a single-stranded DNA 8-mer comprising the cleavage site. SNAP output
6we9 DNA binding protein-DNA X-ray (1.59 Å) Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X (2020) "Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA." Nucleic Acids Res., 48, 10329-10341. doi: 10.1093/nar/gkaa604. Yth domain of human ythdc1 with 11mer ssDNA containing n6ma. SNAP output
6wea DNA binding protein-DNA X-ray (1.8 Å) Woodcock CB, Horton JR, Zhou J, Bedford MT, Blumenthal RM, Zhang X, Cheng X (2020) "Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA." Nucleic Acids Res., 48, 10329-10341. doi: 10.1093/nar/gkaa604. Yth domain of human ythdc1 with a 10mer oligo containing n6ma. SNAP output
6wfq gene regulation cryo-EM (3.9 Å) Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ (2021) "Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism." Nat Commun, 12, 1988. doi: 10.1038/s41467-021-22253-6. Nanr dimer-DNA hetero-complex. SNAP output
6wg3 cell cycle-DNA cryo-EM (5.3 Å) Shi Z, Gao H, Bai XC, Yu H (2020) "Cryo-EM structure of the human cohesin-NIPBL-DNA complex." Science, 368, 1454-1459. doi: 10.1126/science.abb0981. cryo-EM structure of human cohesin-nipbl-DNA complex. SNAP output
6wg6 cell cycle-DNA X-ray (3.54 Å) Shi Z, Gao H, Bai XC, Yu H (2020) "Cryo-EM structure of the human cohesin-NIPBL-DNA complex." Science, 368, 1454-1459. doi: 10.1126/science.abb0981. Crystal structure of human smc1-smc3 hinge domain heterodimer in north-open conformation. SNAP output
6wg7 gene regulation cryo-EM (8.3 Å) Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ (2021) "Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism." Nat Commun, 12, 1988. doi: 10.1038/s41467-021-22253-6. Coordinates of nanr dimer fitted in hexameric nanr-DNA hetero-complex cryo-EM map. SNAP output
6wgc replication-DNA cryo-EM (4.3 Å) Yuan Z, Schneider S, Dodd T, Riera A, Bai L, Yan C, Magdalou I, Ivanov I, Stillman B, Li H, Speck C (2020) "Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6." Proc.Natl.Acad.Sci.USA, 117, 17747-17756. doi: 10.1073/pnas.2006231117. Atomic model of semi-attached mutant occm-DNA complex (orc-cdc6-cdt1-mcm2-7 with mcm6 whd truncation). SNAP output
6wge cell cycle-DNA cryo-EM (3.9 Å) Shi Z, Gao H, Bai XC, Yu H (2020) "Cryo-EM structure of the human cohesin-NIPBL-DNA complex." Science, 368, 1454-1459. doi: 10.1126/science.abb0981. cryo-EM structure of human cohesin-nipbl-DNA complex without stag1. SNAP output
6wgg replication-DNA cryo-EM (8.1 Å) Yuan Z, Schneider S, Dodd T, Riera A, Bai L, Yan C, Magdalou I, Ivanov I, Stillman B, Li H, Speck C (2020) "Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6." Proc.Natl.Acad.Sci.USA, 117, 17747-17756. doi: 10.1073/pnas.2006231117. Atomic model of pre-insertion mutant occm-DNA complex(orc-cdc6-cdt1-mcm2-7 with mcm6 whd truncation). SNAP output
6wgi replication-DNA cryo-EM (10.0 Å) Yuan Z, Schneider S, Dodd T, Riera A, Bai L, Yan C, Magdalou I, Ivanov I, Stillman B, Li H, Speck C (2020) "Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6." Proc.Natl.Acad.Sci.USA, 117, 17747-17756. doi: 10.1073/pnas.2006231117. Atomic model of the mutant occm (orc-cdc6-cdt1-mcm2-7 with mcm6 whd truncation) loaded on DNA at 10.5 Å resolution. SNAP output
6whi immune system-DNA-RNA cryo-EM (4.2 Å) Hirschi M, Lu WT, Santiago-Frangos A, Wilkinson R, Golden SM, Davidson AR, Lander GC, Wiedenheft B (2020) "AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex." Nat Commun, 11, 2730. doi: 10.1038/s41467-020-16512-1. Cryo-electron microscopy structure of the type i-f crispr RNA-guided surveillance complex bound to the anti-crispr acrif9. SNAP output
6whm viral protein-DNA X-ray (1.92 Å) Kumar G, Cuypers M, Webby RR, Webb TR, White SW (2021) "Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism." Nucleic Acids Res., 49, 1609-1618. doi: 10.1093/nar/gkaa1294. The crystal structure of the 2009-h1n1-california pa endonuclease wild type bound to DNA oligomer tagc (cleaved ttagcatt, 5mm overnight DNA soak). SNAP output
6wic transferase-DNA X-ray (1.55 Å) Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K (2020) "Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break." Nat Commun, 11, 4784. doi: 10.1038/s41467-020-18506-5. Pre-catalytic quaternary complex of human polymerase mu on a complementary DNA double-strand break substrate. SNAP output
6wid transferase-DNA X-ray (1.5 Å) Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K (2020) "Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break." Nat Commun, 11, 4784. doi: 10.1038/s41467-020-18506-5. Nucleotide incorporation intermediate into quaternary complex of human polymerase mu on a complementary DNA double-strand break substrate. SNAP output
6wie transferase-DNA X-ray (1.5 Å) Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K (2020) "Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break." Nat Commun, 11, 4784. doi: 10.1038/s41467-020-18506-5. Post-catalytic nicked complex of human polymerase mu on a complementary DNA double-strand break substrate. SNAP output
6wig plant protein-DNA X-ray (2.1 Å) Pathak PK, Zhang F, Peng S, Niu L, Chaturvedi J, Elliott J, Xiang Y, Tadege M, Deng J (2021) "Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA." Acta Crystallogr D Struct Biol, 77, 1050-1063. doi: 10.1107/S205979832100632X. Structure of stenofolia protein hd domain bound with DNA. SNAP output
6wk6 DNA binding protein X-ray (2.35 Å) Jung H, Hawkins M, Lee S (2020) "Structural insights into the bypass of the major deaminated purines by translesion synthesis DNA polymerase." Biochem.J., 477, 4797-4810. doi: 10.1042/BCJ20200800. Crystal structure of human polymerase eta complexed with xanthine containing DNA. SNAP output
6wkr gene regulation-DNA cryo-EM (3.5 Å) Kasinath V, Beck C, Sauer P, Poepsel S, Kosmatka J, Faini M, Toso D, Aebersold R, Nogales E (2021) "JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications." Science, 371. doi: 10.1126/science.abc3393. Prc2-aebp2-jarid2 bound to h2ak119ub1 nucleosome. SNAP output
6wma hydrolase-DNA X-ray (2.5 Å) Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H (2020) "Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains." J.Mol.Biol., 432, 6042-6060. doi: 10.1016/j.jmb.2020.10.020. Crystal structure of a soluble variant of full-length human apobec3g (ph 7.6). SNAP output
6wmb hydrolase-DNA X-ray (3.02 Å) Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H (2020) "Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains." J.Mol.Biol., 432, 6042-6060. doi: 10.1016/j.jmb.2020.10.020. Crystal structure of a soluble variant of full-length human apobec3g (ph 8.0). SNAP output
6wmc hydrolase-DNA X-ray (3.49 Å) Maiti A, Myint W, Delviks-Frankenberry KA, Hou S, Kanai T, Balachandran V, Sierra Rodriguez C, Tripathi R, Kurt Yilmaz N, Pathak VK, Schiffer CA, Matsuo H (2020) "Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains." J.Mol.Biol., 432, 6042-6060. doi: 10.1016/j.jmb.2020.10.020. Crystal structure of a soluble variant of full-length human apobec3g (ph 9.0). SNAP output
6wmi transcription-DNA X-ray (2.75 Å) Lan X, Ren R, Feng R, Ly LC, Lan Y, Zhang Z, Aboreden N, Qin K, Horton JR, Grevet JD, Mayuranathan T, Abdulmalik O, Keller CA, Giardine B, Hardison RC, Crossley M, Weiss MJ, Cheng X, Shi J, Blobel GA (2021) "ZNF410 Uniquely Activates the NuRD Component CHD4 to Silence Fetal Hemoglobin Expression." Mol.Cell, 81, 239-254.e8. doi: 10.1016/j.molcel.2020.11.006. Znf410 zinc fingers 1-5 with 17 mer blunt DNA oligonucleotide. SNAP output
6wmp transcription cryo-EM (2.98 Å) Travis BA, Ramsey KM, Prezioso SM, Tallo T, Wandzilak JM, Hsu A, Borgnia M, Bartesaghi A, Dove SL, Brennan RG, Schumacher MA (2021) "Structural Basis for Virulence Activation of Francisella tularensis." Mol.Cell, 81, 139. doi: 10.1016/j.molcel.2020.10.035. F. tularensis rnaps70-igla DNA complex. SNAP output
6wmr transcription cryo-EM (3.46 Å) Travis BA, Ramsey KM, Prezioso SM, Tallo T, Wandzilak JM, Hsu A, Borgnia M, Bartesaghi A, Dove SL, Brennan RG, Schumacher MA (2021) "Structural Basis for Virulence Activation of Francisella tularensis." Mol.Cell, 81, 139. doi: 10.1016/j.molcel.2020.10.035. F. tularensis rnaps70-(mgla-sspa)-igla DNA complex. SNAP output
6wmt transcription cryo-EM (4.43 Å) Travis BA, Ramsey KM, Prezioso SM, Tallo T, Wandzilak JM, Hsu A, Borgnia M, Bartesaghi A, Dove SL, Brennan RG, Schumacher MA (2021) "Structural Basis for Virulence Activation of Francisella tularensis." Mol.Cell, 81, 139. doi: 10.1016/j.molcel.2020.10.035. F. tularensis rnaps70-(mgla-sspa)-ppgpp-pigr-igla DNA complex. SNAP output
6wmu transcription cryo-EM (3.18 Å) Travis BA, Ramsey KM, Prezioso SM, Tallo T, Wandzilak JM, Hsu A, Borgnia M, Bartesaghi A, Dove SL, Brennan RG, Schumacher MA (2021) "Structural Basis for Virulence Activation of Francisella tularensis." Mol.Cell, 81, 139. doi: 10.1016/j.molcel.2020.10.035. E. coli rnaps70-sspa-gada DNA complex. SNAP output
6wox transcription-DNA-RNA X-ray (3.14 Å) Makinen JJ, Shin Y, Vieras E, Virta P, Metsa-Ketela M, Murakami KS, Belogurov GA (2021) "The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases." Nat Commun, 12, 796. doi: 10.1038/s41467-021-21005-w. Thermus thermophilus RNA polymerase initially transcribing complex with 2'dctp. SNAP output
6woy transcription-DNA-RNA X-ray (3.0 Å) Makinen JJ, Shin Y, Vieras E, Virta P, Metsa-Ketela M, Murakami KS, Belogurov GA (2021) "The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases." Nat Commun, 12, 796. doi: 10.1038/s41467-021-21005-w. Thermus thermophilus RNA polymerase initially transcribing complex with 3'dctp. SNAP output
6wpa DNA binding protein-DNA X-ray (3.09 Å) Kapoor I, Olivares P, Nair SK (2020) "Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones." Elife, 9. doi: 10.7554/eLife.57824. Structure of avar1 bound to DNA half-site. SNAP output
6wpf transferase-DNA X-ray (2.53 Å) Bertoletti N, Chan AH, Schinazi RF, Anderson KS (2020) "Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance." Molecules, 25. doi: 10.3390/molecules25204868. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and d4t. SNAP output
6wph transferase-DNA X-ray (2.72 Å) Bertoletti N, Chan AH, Schinazi RF, Anderson KS (2020) "Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance." Molecules, 25. doi: 10.3390/molecules25204868. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and (-)-ftc. SNAP output
6wpj transferase-DNA X-ray (2.73 Å) Bertoletti N, Chan AH, Schinazi RF, Anderson KS (2020) "Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance." Molecules, 25. doi: 10.3390/molecules25204868. Structure of hiv-1 reverse transcriptase (rt) in complex with dsDNA and d4t. SNAP output
6wq0 virus cryo-EM (2.8 Å) Wang F, Baquero DP, Beltran LC, Su Z, Osinski T, Zheng W, Prangishvili D, Krupovic M, Egelman EH (2020) "Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments." Proc.Natl.Acad.Sci.USA, 117, 19643-19652. doi: 10.1073/pnas.2011125117. cryo-EM of the s. solfataricus rod-shaped virus, ssrv1. SNAP output
6wq2 virus cryo-EM (4.0 Å) Wang F, Baquero DP, Beltran LC, Su Z, Osinski T, Zheng W, Prangishvili D, Krupovic M, Egelman EH (2020) "Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments." Proc.Natl.Acad.Sci.USA, 117, 19643-19652. doi: 10.1073/pnas.2011125117. cryo-EM of the s. islandicus filamentous virus, sifv. SNAP output
6wqu transcription-signaling protein-DNA X-ray (2.41 Å) Landor SKJ, Santio NM, Eccleshall WB, Paramonov VM, Gagliani EK, Hall D, Jin SB, Dahlstrom KM, Salminen TA, Rivero-Muller A, Lendahl U, Kovall RA, Koskinen PJ, Sahlgren C (2021) "PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion." J.Biol.Chem., 296, 100593. doi: 10.1016/j.jbc.2021.100593. Csl (rbpj) bound to notch3 ram and DNA. SNAP output
6ws3 viral protein-DNA X-ray (2.2 Å) Kumar G, Cuypers M, Webby RR, Webb TR, White SW (2021) "Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism." Nucleic Acids Res., 49, 1609-1618. doi: 10.1093/nar/gkaa1294. The crystal structure of the 2009-h1n1-california pa endonuclease wild type bound to DNA oligomers tg and agca (from cleaved gtgagcagtg). SNAP output
6wvj transcription-DNA-RNA cryo-EM (3.36 Å) Newing TP, Oakley AJ, Miller M, Dawson CJ, Brown SHJ, Bouwer JC, Tolun G, Lewis PJ (2020) "Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD." Nat Commun, 11, 6420. doi: 10.1038/s41467-020-20157-5. cryo-EM structure of bacillus subtilis RNA polymerase elongation complex. SNAP output
6wya transferase-DNA X-ray (2.41 Å) Choi WS, He P, Pothukuchy A, Gollihar J, Ellington AD, Yang W (2020) "How a B family DNA polymerase has been evolved to copy RNA." Proc.Natl.Acad.Sci.USA, 117, 21274-21280. doi: 10.1073/pnas.2009415117. Rtx (reverse transcription xenopolymerase) in complex with a DNA duplex and dampnpp. SNAP output
6wyb transferase-RNA-DNA X-ray (2.5 Å) Choi WS, He P, Pothukuchy A, Gollihar J, Ellington AD, Yang W (2020) "How a B family DNA polymerase has been evolved to copy RNA." Proc.Natl.Acad.Sci.USA, 117, 21274-21280. doi: 10.1073/pnas.2009415117. Rtx (reverse transcription xenopolymerase) in complex with an RNA-DNA hybrid. SNAP output
6wz5 gene regulation cryo-EM (2.2 Å) Bilokapic S, Suskiewicz MJ, Ahel I, Halic M (2020) "Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin." Nature, 585, 609-613. doi: 10.1038/s41586-020-2725-7. Bridging of double-strand DNA break activates parp2-hpf1 to modify chromatin. SNAP output
6wz9 gene regulation cryo-EM (2.8 Å) Bilokapic S, Suskiewicz MJ, Ahel I, Halic M (2020) "Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin." Nature, 585, 609-613. doi: 10.1038/s41586-020-2725-7. Bridging of double-strand DNA break activates parp2-hpf1 to modify chromatin. SNAP output
6x0l gene regulation cryo-EM (3.9 Å) Bilokapic S, Suskiewicz MJ, Ahel I, Halic M (2020) "Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin." Nature, 585, 609-613. doi: 10.1038/s41586-020-2725-7. Bridging of double-strand DNA break activates parp2-hpf1 to modify chromatin. SNAP output
6x0m gene regulation cryo-EM (6.3 Å) Bilokapic S, Suskiewicz MJ, Ahel I, Halic M (2020) "Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin." Nature, 585, 609-613. doi: 10.1038/s41586-020-2725-7. Bridging of double-strand DNA break activates parp2-hpf1 to modify chromatin. SNAP output
6x0n gene regulation cryo-EM (10.0 Å) Bilokapic S, Suskiewicz MJ, Ahel I, Halic M (2020) "Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin." Nature, 585, 609-613. doi: 10.1038/s41586-020-2725-7. Bridging of double-strand DNA break activates parp2-hpf1 to modify chromatin. SNAP output
6x1j hydrolase X-ray (1.945 Å) Nawimanage RR, Yuan Z, Casares M, Joshi R, Lohman JR, Gimble FS (2022) "Structure-Function Studies of Two Yeast Homing Endonucleases that Evolved to Cleave Identical Targets with Dissimilar Rates and Specificities." J.Mol.Biol., 434, 167550. doi: 10.1016/j.jmb.2022.167550. The homing endonuclease i-wcai bound to its DNA recognition sequence. SNAP output
6x26 transcription-RNA-DNA cryo-EM (4.1 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - l1 state. SNAP output
6x2f transcription-RNA-DNA cryo-EM (4.0 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - l2 state. SNAP output
6x2n transcription-RNA-DNA cryo-EM (3.9 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - i state. SNAP output
6x43 transcription cryo-EM (3.6 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - ii state. SNAP output
6x4w transcription-RNA-DNA cryo-EM (3.8 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - iii state. SNAP output
6x4y transcription-RNA-DNA cryo-EM (3.6 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - iv state. SNAP output
6x50 transcription-RNA-DNA cryo-EM (3.3 Å) Kang JY, Llewellyn E, Chen J, Olinares PDB, Brewer J, Chait BT, Campbell EA, Darst SA (2021) "Structural basis for transcription complex disruption by the Mfd translocase." Elife, 10. doi: 10.7554/eLife.62117. Mfd-bound e.coli RNA polymerase elongation complex - v state. SNAP output
6x59 DNA binding protein-DNA-transferase cryo-EM (2.98 Å) Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P (2020) "The molecular basis of tight nuclear tethering and inactivation of cGAS." Nature, 587, 673-677. doi: 10.1038/s41586-020-2749-z. The mouse cgas catalytic domain binding to human assembled nucleosome. SNAP output
6x5a DNA binding protein-DNA-transferase cryo-EM (4.36 Å) Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P (2020) "The molecular basis of tight nuclear tethering and inactivation of cGAS." Nature, 587, 673-677. doi: 10.1038/s41586-020-2749-z. The mouse cgas catalytic domain binding to human nucleosome that purified from hek293t cells. SNAP output
6x67 DNA binding protein-DNA cryo-EM (3.47 Å) Chen Q, Luo W, Veach RA, Hickman AB, Wilson MH, Dyda F (2020) "Structural basis of seamless excision and specific targeting by piggyBac transposase." Nat Commun, 11, 3446. doi: 10.1038/s41467-020-17128-1. cryo-EM structure of piggybac transposase strand transfer complex (stc). SNAP output
6x68 DNA binding protein-DNA cryo-EM (3.66 Å) Chen Q, Luo W, Veach RA, Hickman AB, Wilson MH, Dyda F (2020) "Structural basis of seamless excision and specific targeting by piggyBac transposase." Nat Commun, 11, 3446. doi: 10.1038/s41467-020-17128-1. cryo-EM structure of piggybac transposase synaptic complex with hairpin DNA (snhp). SNAP output
6x6d DNA-DNA binding protein X-ray (2.48 Å) Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA (2021) "Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element." Nucleic Acids Res., 49, 8923-8933. doi: 10.1093/nar/gkab605. Glucocorticoid receptor DNA binding domain in complex with unmodified precursor for a modern recognition element (pre-gbs). SNAP output
6x6e DNA binding protein X-ray (2.0 Å) Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA (2021) "Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element." Nucleic Acids Res., 49, 8923-8933. doi: 10.1093/nar/gkab605. Glucocorticoid receptor DNA binding domain in complex with methylated precursor for a modern recognition element (methylated pre-gbs). SNAP output
6x6z replication-DNA X-ray (1.4 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 ternary complex with dctp and ca2+. SNAP output
6x70 replication-DNA X-ray (2.05 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1-DNA binary complex. SNAP output
6x71 replication-DNA X-ray (1.78 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 mg2+-facilitated intermediate complex with reactant dctp and product dcmp. SNAP output
6x72 replication-DNA X-ray (2.19 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 mg2+-facilitated product complex with two monophosphates. SNAP output
6x73 replication-DNA X-ray (2.05 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 mg2+-facilitated product complex with one monophosphate. SNAP output
6x74 replication-DNA X-ray (1.69 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 mg2+-facilitated product complex with no monophosphates. SNAP output
6x75 replication-DNA X-ray (1.95 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 mn2+-facilitated product complex with second dctp bound. SNAP output
6x76 replication-DNA X-ray (2.53 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 l325g mn2+-facilitated product complex with second dctp bound. SNAP output
6x77 replication-DNA X-ray (1.64 Å) Weaver TM, Cortez LM, Khoang TH, Washington MT, Agarwal PK, Freudenthal BD (2020) "Visualizing Rev1 catalyze protein-template DNA synthesis." Proc.Natl.Acad.Sci.USA, 117, 25494-25504. doi: 10.1073/pnas.2010484117. Rev1 r518a ternary complex with dctp and ca2+. SNAP output
6x9i transferase X-ray (2.2 Å) Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) "Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia." Nat Cancer, 2, 1002-1017. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA. SNAP output
6x9j transferase-transferase inhibitor-DNA X-ray (1.79 Å) Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) "Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia." Nat Cancer, 2, 1002-1017. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3830052. SNAP output
6x9k transferase-transferase inhibitor-DNA X-ray (2.65 Å) Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) "Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia." Nat Cancer, 2, 1002-1017. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3685032a. SNAP output
6xas transcription cryo-EM (3.8 Å) Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E (2021) "Pre-termination Transcription Complex: Structure and Function." Mol.Cell, 81, 281. doi: 10.1016/j.molcel.2020.11.013. Cryoem structure of e. coli rho-dependent transcription pre-termination complex. SNAP output
6xav transcription cryo-EM (7.7 Å) Hao Z, Epshtein V, Kim KH, Proshkin S, Svetlov V, Kamarthapu V, Bharati B, Mironov A, Walz T, Nudler E (2021) "Pre-termination Transcription Complex: Structure and Function." Mol.Cell, 81, 281. doi: 10.1016/j.molcel.2020.11.013. Cryoem structure of e. coli rho-dependent transcription pre-termination complex bound with nusg. SNAP output
6xb8 viral protein X-ray (3.3 Å) Santosh V, Musayev FN, Jaiswal R, Zarate-Perez F, Vandewinkel B, Dierckx C, Endicott M, Sharifi K, Dryden K, Henckaerts E, Escalante CR (2020) "The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states." Nucleic Acids Res., 48, 12983-12999. doi: 10.1093/nar/gkaa1133. Adeno-associated virus origin binding domain in complex with ssDNA. SNAP output
6xbu DNA binding protein-DNA-RNA X-ray (3.29 Å) Chandramouly G, Zhao J, McDevitt S, Rusanov T, Hoang T, Borisonnik N, Treddinick T, Lopezcolorado FW, Kent T, Siddique LA, Mallon J, Huhn J, Shoda Z, Kashkina E, Brambati A, Stark JM, Chen XS, Pomerantz RT (2021) "Pol theta reverse transcribes RNA and promotes RNA-templated DNA repair." Sci Adv, 7. doi: 10.1126/sciadv.abf1771. Polymerase domain of polymerase-theta. SNAP output
6xeo DNA binding protein, hydrolase-DNA cryo-EM (5.5 Å) Brugger C, Zhang C, Suhanovsky MM, Kim DD, Sinclair AN, Lyumkis D, Deaconescu AM (2020) "Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd." Nat Commun, 11, 3740. doi: 10.1038/s41467-020-17457-1. Structure of mfd bound to dsDNA. SNAP output
6xg8 recombination X-ray (3.5 Å) Kosek D, Hickman AB, Ghirlando R, He S, Dyda F (2021) "Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition." Embo J., 40, e105666. doi: 10.15252/embj.2020105666. Iscth4 transposase, pre-cleaved complex, pcc. SNAP output
6xgw recombination X-ray (3.5 Å) Kosek D, Hickman AB, Ghirlando R, He S, Dyda F (2021) "Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition." Embo J., 40, e105666. doi: 10.15252/embj.2020105666. Iscth4 transposase, pre-reaction complex, prc. SNAP output
6xgx recombination X-ray (3.5 Å) Kosek D, Hickman AB, Ghirlando R, He S, Dyda F (2021) "Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition." Embo J., 40, e105666. doi: 10.15252/embj.2020105666. Iscth4 transposase, strand transfer complex 1, stc1. SNAP output
6xh7 transcription-DNA cryo-EM (3.9 Å) Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B (2021) "Structural basis of copper-efflux-regulator-dependent transcription activation." Iscience, 24, 102449. doi: 10.1016/j.isci.2021.102449. Cuer-tac without RNA. SNAP output
6xh8 transcription-DNA-RNA cryo-EM (4.1 Å) Shi W, Zhang B, Jiang Y, Liu C, Zhou W, Chen M, Yang Y, Hu Y, Liu B (2021) "Structural basis of copper-efflux-regulator-dependent transcription activation." Iscience, 24, 102449. doi: 10.1016/j.isci.2021.102449. Cuer-transcription activation complex with RNA transcript. SNAP output
6xjd immune system-DNA cryo-EM (6.8 Å) Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P (2020) "The molecular basis of tight nuclear tethering and inactivation of cGAS." Nature, 587, 673-677. doi: 10.1038/s41586-020-2749-z. Two mouse cgas catalytic domain binding to human assembled nucleosome. SNAP output
6xl5 transcription, transferase-DNA cryo-EM (2.5 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of ecmrr-rnap-promoter open complex (ecmrr-rpo). SNAP output
6xl6 transcription cryo-EM (3.0 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of ecmrr-DNA complex in ecmrr-rpo. SNAP output
6xl9 transcription, transferase-DNA cryo-EM (2.5 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of ecmrr-rnap-promoter initial transcribing complex with 3-nt RNA transcript (ecmrr-rpitc-3nt). SNAP output
6xla transcription cryo-EM (3.1 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of ecmrr-DNA complex in ecmrr-rpitc-3nt. SNAP output
6xlj transcription, transferase-DNA cryo-EM (2.7 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of ecmrr-rnap-promoter initial transcribing complex with 4-nt RNA transcript (ecmrr-rpitc-4nt). SNAP output
6xlk transcription cryo-EM (3.3 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of ecmrr-DNA complex in ecmrr-rpitc-4nt. SNAP output
6xll transcription, transferase-DNA cryo-EM (2.7 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of e. coli rnap-promoter initial transcribing complex with 5-nt RNA transcript (rpitc-5nt). SNAP output
6xlm transcription, transferase-DNA cryo-EM (3.2 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of e.coli rnap-DNA elongation complex 1 (rde1) in ecmrr-dependent transcription. SNAP output
6xln transcription, transferase-DNA cryo-EM (2.8 Å) Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B (2021) "Structural visualization of transcription activated by a multidrug-sensing MerR family regulator." Nat Commun, 12, 2702. doi: 10.1038/s41467-021-22990-8. cryo-EM structure of e. coli rnap-DNA elongation complex 2 (rde2) in ecmrr-dependent transcription. SNAP output
6xlv RNA binding protein-splicing X-ray (1.4 Å) Maji D, Glasser E, Henderson S, Galardi J, Pulvino MJ, Jenkins JL, Kielkopf CL (2020) "Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing." J.Biol.Chem., 295, 17148-17157. doi: 10.1074/jbc.RA120.015339. Crystal structure of leukemia-associated n196k mutant of u2af65 bound to adml splice site. SNAP output
6xlw RNA binding protein-splicing X-ray (1.5 Å) Maji D, Glasser E, Henderson S, Galardi J, Pulvino MJ, Jenkins JL, Kielkopf CL (2020) "Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing." J.Biol.Chem., 295, 17148-17157. doi: 10.1074/jbc.RA120.015339. Crystal structure of u2af65 bound to adml splice site sequence. SNAP output
6xlx RNA binding protein-splicing X-ray (1.7 Å) Maji D, Glasser E, Henderson S, Galardi J, Pulvino MJ, Jenkins JL, Kielkopf CL (2020) "Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing." J.Biol.Chem., 295, 17148-17157. doi: 10.1074/jbc.RA120.015339. Crystal structure of cancer-associated g301d mutant of u2af65 bound to adml splice site. SNAP output
6xnx recombination cryo-EM (2.7 Å) Zhang Y, Corbett E, Wu S, Schatz DG (2020) "Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase." Embo J., 39, e105857. doi: 10.15252/embj.2020105857. Structure of rag1 (r848m-e649v)-rag2-DNA strand transfer complex (dynamic-form). SNAP output
6xny recombination cryo-EM (2.9 Å) Zhang Y, Corbett E, Wu S, Schatz DG (2020) "Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase." Embo J., 39, e105857. doi: 10.15252/embj.2020105857. Structure of rag1 (r848m-e649v)-rag2-DNA strand transfer complex (paired-form). SNAP output
6xnz recombination cryo-EM (3.8 Å) Zhang Y, Corbett E, Wu S, Schatz DG (2020) "Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase." Embo J., 39, e105857. doi: 10.15252/embj.2020105857. Structure of rag1 (r848m-e649v)-rag2-DNA target capture complex. SNAP output
6xtx replication cryo-EM (3.29 Å) Rzechorzek NJ, Hardwick SW, Jatikusumo VA, Chirgadze DY, Pellegrini L (2020) "CryoEM structures of human CMG-ATP gamma S-DNA and CMG-AND-1 complexes." Nucleic Acids Res., 48, 6980-6995. doi: 10.1093/nar/gkaa429. Cryoem structure of human cmg bound to atpgammas and DNA. SNAP output
6xu0 DNA binding protein X-ray (1.9 Å) Golovinas E, Manakova E, Sasnauskas G, Zaremba M "Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT." Archaeoglobus fulgidus argonaute protein with DNA oligoduplex 5'-patcgtggccacgat. SNAP output
6xup DNA binding protein X-ray (1.9 Å) Golovinas E, Manakova E, Sasnauskas G, Zaremba M "Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT." Archaeoglobus fulgidus argonaute protein with DNA oligoduplex 5'-patcgtggccacgat. SNAP output
6xwg transcription X-ray (2.4 Å) Osz J, McEwen AG, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mely Y, Cianferani S, Jeffries CM, Svergun DI, Rochel N (2020) "Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR." Nucleic Acids Res., 48, 9969-9985. doi: 10.1093/nar/gkaa697. Crystal structure of the human rxr-rar DNA-binding domain heterodimer bound to the human rarb2 dr5 response element. SNAP output
6xwh transcription X-ray (2.1 Å) Osz J, McEwen AG, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mely Y, Cianferani S, Jeffries CM, Svergun DI, Rochel N (2020) "Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR." Nucleic Acids Res., 48, 9969-9985. doi: 10.1093/nar/gkaa697. Crystal structure of the human rxr DNA-binding domain homodimer bound to the human hoxb13 dr0 response element. SNAP output
6y35 transcription X-ray (2.6 Å) Hortschansky P, Misslinger M, Morl J, Gsaller F, Bromley MJ, Brakhage AA, Groll M, Haas H, Huber EM (2020) "Structural basis of HapE P88L -linked antifungal triazole resistance in Aspergillus fumigatus ." Life Sci Alliance, 3. doi: 10.26508/lsa.202000729. Ccaat-binding complex from aspergillus fumigatus with cyca DNA. SNAP output
6y36 transcription X-ray (2.3 Å) Hortschansky P, Misslinger M, Morl J, Gsaller F, Bromley MJ, Brakhage AA, Groll M, Haas H, Huber EM (2020) "Structural basis of HapE P88L -linked antifungal triazole resistance in Aspergillus fumigatus ." Life Sci Alliance, 3. doi: 10.26508/lsa.202000729. Ccaat-binding complex from aspergillus fumigatus with ccca DNA. SNAP output
6y37 transcription X-ray (2.2 Å) Hortschansky P, Misslinger M, Morl J, Gsaller F, Bromley MJ, Brakhage AA, Groll M, Haas H, Huber EM (2020) "Structural basis of HapE P88L -linked antifungal triazole resistance in Aspergillus fumigatus ." Life Sci Alliance, 3. doi: 10.26508/lsa.202000729. Ccaat-binding complex from aspergillus nidulans with ccca DNA. SNAP output
6y39 transcription X-ray (2.3 Å) Hortschansky P, Misslinger M, Morl J, Gsaller F, Bromley MJ, Brakhage AA, Groll M, Haas H, Huber EM (2020) "Structural basis of HapE P88L -linked antifungal triazole resistance in Aspergillus fumigatus ." Life Sci Alliance, 3. doi: 10.26508/lsa.202000729. Hape-p88l mutant ccaat-binding complex from aspergillus nidulans with cyca DNA. SNAP output
6y42 transcription X-ray (4.3 Å) Crack JC, Amara P, Volbeda A, Mouesca JM, Rohac R, Pellicer Martinez MT, Huang CY, Gigarel O, Rinaldi C, Le Brun NE, Fontecilla-Camps JC (2020) "Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR." J.Am.Chem.Soc., 142, 5104-5116. doi: 10.1021/jacs.9b12250. Crystal structure of rsrr complexed to a 39 basepair DNA fragment of the rsrr promoter. SNAP output
6y5d immune system cryo-EM (4.1 Å) Pathare GR, Decout A, Gluck S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thoma NH, Ablasser A (2020) "Structural mechanism of cGAS inhibition by the nucleosome." Nature, 587, 668-672. doi: 10.1038/s41586-020-2750-6. Structure of human cgas (k394e) bound to the nucleosome. SNAP output
6y5e immune system cryo-EM (3.15 Å) Pathare GR, Decout A, Gluck S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thoma NH, Ablasser A (2020) "Structural mechanism of cGAS inhibition by the nucleosome." Nature, 587, 668-672. doi: 10.1038/s41586-020-2750-6. Structure of human cgas (k394e) bound to the nucleosome (focused refinement of cgas-ncp subcomplex). SNAP output
6y93 DNA binding protein X-ray (2.23 Å) Jalal ASB, Tran NT, Stevenson CE, Chan EW, Lo R, Tan X, Noy A, Lawson DM, Le TBK (2020) "Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family." Cell Rep, 32, 107928. doi: 10.1016/j.celrep.2020.107928. Crystal structure of the DNA-binding domain of the nucleoid occlusion factor (noc) complexed to the noc-binding site (nbs). SNAP output
6ybw translation cryo-EM (3.1 Å) Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V (2020) "Structure of a human 48Stranslational initiation complex." Science, 369, 1220-1227. doi: 10.1126/science.aba4904. Structure of a human 48s translational initiation complex - 40s body. SNAP output
6ycq transcription X-ray (1.65 Å) Freire-Rios A, Tanaka K, Crespo I, van der Wijk E, Sizentsova Y, Levitsky V, Lindhoud S, Fontana M, Hohlbein J, Boer DR, Mironova V, Weijers D (2020) "Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis ." Proc.Natl.Acad.Sci.USA, 117, 24557-24566. doi: 10.1073/pnas.2009554117. Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (atarf1) in complex with high affinity DNA. SNAP output
6ycs transcription X-ray (3.05 Å) Hyjek-Skladanowska M, Vickers TA, Napiorkowska A, Anderson BA, Tanowitz M, Crooke ST, Liang XH, Seth PP, Nowotny M (2020) "Origins of the Increased Affinity of Phosphorothioate-Modified Therapeutic Nucleic Acids for Proteins." J.Am.Chem.Soc., 142, 7456-7468. doi: 10.1021/jacs.9b13524. Human transcription cofactor pc4 DNA-binding domain in complex with full phosphorothioate 5-10-5 2'-o-methyl DNA gapmer antisense oligonucleotide.. SNAP output
6yjb hydrolase X-ray (1.55 Å) Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M (2021) "Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA." Nucleic Acids Res., 49, 1708-1723. doi: 10.1093/nar/gkaa1218. Vcam4i restriction endonuclease 5hmc-ssDNA complex. SNAP output
6ykf hydrolase X-ray (1.48 Å) Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M (2021) "Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA." Nucleic Acids Res., 49, 1708-1723. doi: 10.1093/nar/gkaa1218. Vcam4i restriction endonuclease in the presence of 5mc-modified ssDNA. SNAP output
6yl2 DNA binding protein X-ray (3.15 Å) Pritchard JE, Sula A, Cole AR, Kendall SL, Keep NH "Structural and DNA binding studies of the transcriptional repressor Rv2506 (BkaR) from Mycobacterium tuberculosis supports a role in L-Leucine catabolism." Structural and DNA binding studies of the transcriptional repressor rv2506 (bkar) from mycobacterium tuberculosis supports a role in l-leucine catabolism. SNAP output
6ymg hydrolase X-ray (3.14 Å) Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M (2021) "Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA." Nucleic Acids Res., 49, 1708-1723. doi: 10.1093/nar/gkaa1218. Vcam4i restriction endonuclease in complex with 5mc-modified dsDNA. SNAP output
6ymv transcription cryo-EM (3.1 Å) De Wijngaert B, Sultana S, Singh A, Dharia C, Vanbuel H, Shen J, Vasilchuk D, Martinez SE, Kandiah E, Patel SS, Das K (2021) "Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase." Mol.Cell, 81, 268. doi: 10.1016/j.molcel.2020.11.016. cryo-EM structure of yeast mitochondrial RNA polymerase partially-melted transcription initiation complex (pmic). SNAP output
6ymw transcription cryo-EM (3.71 Å) De Wijngaert B, Sultana S, Singh A, Dharia C, Vanbuel H, Shen J, Vasilchuk D, Martinez SE, Kandiah E, Patel SS, Das K (2021) "Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase." Mol.Cell, 81, 268. doi: 10.1016/j.molcel.2020.11.016. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex. SNAP output
6yov transcription cryo-EM (3.42 Å) Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH (2020) "Mechanisms of OCT4-SOX2 motif readout on nucleosomes." Science, 368, 1460-1465. doi: 10.1126/science.abb0074. Oct4-sox2-bound nucleosome - shl+6. SNAP output
6yrb viral protein X-ray (2.351 Å) Serris A, Stass R, Bignon EA, Muena NA, Manuguerra JC, Jangra RK, Li S, Chandran K, Tischler ND, Huiskonen JT, Rey FA, Guardado-Calvo P (2020) "The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism." Cell, 183, 442. doi: 10.1016/j.cell.2020.08.023. Crystal structure of the tetramerization domain of the glycoprotein gn (andes virus) at ph 7.5. SNAP output
6yuf DNA binding protein cryo-EM (3.94 Å) Higashi TL, Eickhoff P, Sousa JS, Locke J, Nans A, Flynn HR, Snijders AP, Papageorgiou G, O'Reilly N, Chen ZA, O'Reilly FJ, Rappsilber J, Costa A, Uhlmann F (2020) "A Structure-Based Mechanism for DNA Entry into the Cohesin Ring." Mol.Cell, 79, 917. doi: 10.1016/j.molcel.2020.07.013. Cohesin complex with loader gripping DNA. SNAP output
6yww DNA binding protein X-ray (2.102 Å) Ibrahim A, Papin C, Mohideen-Abdul K, Le Gras S, Stoll I, Bronner C, Dimitrov S, Klaholz BP, Hamiche A (2021) "MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion." Science, 372. doi: 10.1126/science.abd5581. Mecp2 is a microsatellite binding protein that protects ca repeats from nucleosome invasion. SNAP output
6z1a isomerase X-ray (2.3 Å) Kolaric A, Germe T, Hrast M, Stevenson CEM, Lawson DM, Burton NP, Voros J, Maxwell A, Minovski N, Anderluh M (2021) "Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds." Nat Commun, 12, 150. doi: 10.1038/s41467-020-20405-8. Ternary complex of staphylococcus aureus DNA gyrase with amk12 and DNA. SNAP output
6z6p gene regulation cryo-EM (4.43 Å) Lee JH, Bollschweiler D, Schafer T, Huber R (2021) "Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies." Sci Adv, 7. doi: 10.1126/sciadv.abd4413. Hdac-pc-nuc. SNAP output
6z8v hydrolase X-ray (1.58 Å) Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E (2021) "Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12." Mol Ther Nucleic Acids, 23, 863-871. doi: 10.1016/j.omtn.2021.01.004. X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (tba-3l), which contains 1-beta-d-lactopyranosyl residue in the side chain of thy3 at n3.. SNAP output
6z8w hydrolase X-ray (1.73 Å) Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E (2021) "Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12." Mol Ther Nucleic Acids, 23, 863-871. doi: 10.1016/j.omtn.2021.01.004. X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (tba-3g), which contains 1-beta-d-glucopyranosyl residue in the side chain of thy3 at n3.. SNAP output
6z8x hydrolase X-ray (2.53 Å) Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E (2021) "Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12." Mol Ther Nucleic Acids, 23, 863-871. doi: 10.1016/j.omtn.2021.01.004. X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (tba-3leu), which contains leucyl amide in the side chain of thy3 at n3.. SNAP output
6z9p transcription cryo-EM (3.9 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 1. SNAP output
6z9q transcription cryo-EM (5.7 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 2. SNAP output
6z9r transcription cryo-EM (4.1 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 3. SNAP output
6z9s transcription cryo-EM (4.4 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 4. SNAP output
6z9t transcription cryo-EM (4.1 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 5. SNAP output
6za3 transcription X-ray (2.05 Å) Vigouroux A, Meyer T, Naretto A, Legrand P, Aumont-Nicaise M, Di Cicco A, Renoud S, Dore J, Levy D, Vial L, Lavire C, Morera S (2021) "Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum." Nucleic Acids Res., 49, 529-546. doi: 10.1093/nar/gkaa1181. Structure of the transcriptional repressor atu1419 (vanr) from agrobacterium fabrum in complex a palindromic DNA (c2221 space group). SNAP output
6zab transcription X-ray (2.8 Å) Vigouroux A, Meyer T, Naretto A, Legrand P, Aumont-Nicaise M, Di Cicco A, Renoud S, Dore J, Levy D, Vial L, Lavire C, Morera S (2021) "Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum." Nucleic Acids Res., 49, 529-546. doi: 10.1093/nar/gkaa1181. Structure of the transcriptional repressor atu1419 (vanr) from agrobacterium fabrum in complex a palindromic DNA (p6422 space group). SNAP output
6zh8 DNA binding protein cryo-EM (4.14 Å) Chaplin AK, Hardwick SW, Liang S, Kefala Stavridi A, Hnizda A, Cooper LR, De Oliveira TM, Chirgadze DY, Blundell TL (2021) "Dimers of DNA-PK create a stage for DNA double-strand break repair." Nat.Struct.Mol.Biol., 28, 13-19. doi: 10.1038/s41594-020-00517-x. cryo-EM structure of DNA-pkcs:DNA. SNAP output
6zha DNA binding protein cryo-EM (3.91 Å) Chaplin AK, Hardwick SW, Liang S, Kefala Stavridi A, Hnizda A, Cooper LR, De Oliveira TM, Chirgadze DY, Blundell TL (2021) "Dimers of DNA-PK create a stage for DNA double-strand break repair." Nat.Struct.Mol.Biol., 28, 13-19. doi: 10.1038/s41594-020-00517-x. cryo-EM structure of DNA-pk monomer. SNAP output
6zhe DNA binding protein cryo-EM (7.24 Å) Chaplin AK, Hardwick SW, Liang S, Kefala Stavridi A, Hnizda A, Cooper LR, De Oliveira TM, Chirgadze DY, Blundell TL (2021) "Dimers of DNA-PK create a stage for DNA double-strand break repair." Nat.Struct.Mol.Biol., 28, 13-19. doi: 10.1038/s41594-020-00517-x. cryo-EM structure of DNA-pk dimer. SNAP output
6zhx DNA binding protein cryo-EM (2.5 Å) Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S (2020) "Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch." Cell Rep, 33, 108529. doi: 10.1016/j.celrep.2020.108529. cryo-EM structure of the regulatory linker of alc1 bound to the nucleosome's acidic patch: nucleosome class.. SNAP output
6zhy DNA binding protein cryo-EM (3.0 Å) Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S (2020) "Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch." Cell Rep, 33, 108529. doi: 10.1016/j.celrep.2020.108529. cryo-EM structure of the regulatory linker of alc1 bound to the nucleosome's acidic patch: hexasome class.. SNAP output
6zix DNA binding protein X-ray (3.4 Å) Huesa J, Giner-Lamia J, Pucciarelli MG, Paredes-Martinez F, Portillo FG, Marina A, Casino P (2021) "Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon." Nucleic Acids Res., 49, 2357-2374. doi: 10.1093/nar/gkab060. Structure of rcsb from salmonella enterica serovar typhimurium bound to promoter p1flhdc in the presence of phosphomimetic bef3-. SNAP output
6zj2 DNA binding protein X-ray (3.38 Å) Huesa J, Giner-Lamia J, Pucciarelli MG, Paredes-Martinez F, Portillo FG, Marina A, Casino P (2021) "Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon." Nucleic Acids Res., 49, 2357-2374. doi: 10.1093/nar/gkab060. Structure of rcsb from salmonella enterica serovar typhimurium bound to promoter rpra in the presence of phosphomimetic bef3-. SNAP output
6zmn signaling protein X-ray (2.333 Å) Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C, Freier R, Baginski B, Martin-Malpartida P, de Martin Garrido N, Marquez JA, Cordeiro TN, Pluta R, Macias MJ (2021) "Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes." Comput Struct Biotechnol J, 19, 632-646. doi: 10.1016/j.csbj.2020.12.044. Crystal structure of the smad3-smad5 mh1 domain chimera bound to the ggcgc site. SNAP output
6znc transcription X-ray (1.64 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human wild-type p53dbd bound to DNA and mq: wt-DNA-mq (i). SNAP output
6znp hydrolase X-ray (3.16 Å) Roske JJ, Liu S, Loll B, Neu U, Wahl MC (2021) "A skipping rope translocation mechanism in a widespread family of DNA repair helicases." Nucleic Acids Res., 49, 504-518. doi: 10.1093/nar/gkaa1174. Crystal structure of duf1998 helicase mrfa bound to DNA. SNAP output
6znq hydrolase X-ray (3.34 Å) Roske JJ, Liu S, Loll B, Neu U, Wahl MC (2021) "A skipping rope translocation mechanism in a widespread family of DNA repair helicases." Nucleic Acids Res., 49, 504-518. doi: 10.1093/nar/gkaa1174. Crystal structure of duf1998 helicase mrfa bound to DNA and amppnp. SNAP output
6zvh ribosome cryo-EM (2.9 Å) Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper W, Bennett EJ, Beckmann R, Green R (2020) "EDF1 coordinates cellular responses to ribosome collisions." Elife, 9. doi: 10.7554/eLife.58828. Edf1-ribosome complex. SNAP output
6zy5 isomerase cryo-EM (3.6 Å) Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V (2021) "Structural basis for allosteric regulation of Human Topoisomerase II alpha." Nat Commun, 12, 2962. doi: 10.1038/s41467-021-23136-6. cryo-EM structure of the human topoisomerase ii alpha DNA-binding-cleavage domain in state 1. SNAP output
6zy6 isomerase cryo-EM (4.1 Å) Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V (2021) "Structural basis for allosteric regulation of Human Topoisomerase II alpha." Nat Commun, 12, 2962. doi: 10.1038/s41467-021-23136-6. cryo-EM structure of the human topoisomerase ii alpha DNA-binding-cleavage domain in state 2. SNAP output
6zy7 isomerase cryo-EM (4.64 Å) Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V (2021) "Structural basis for allosteric regulation of Human Topoisomerase II alpha." Nat Commun, 12, 2962. doi: 10.1038/s41467-021-23136-6. cryo-EM structure of the entire human topoisomerase ii alpha in state 1. SNAP output
6zy8 isomerase cryo-EM (7.4 Å) Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V (2021) "Structural basis for allosteric regulation of Human Topoisomerase II alpha." Nat Commun, 12, 2962. doi: 10.1038/s41467-021-23136-6. cryo-EM structure of the entire human topoisomerase ii alpha in state 2. SNAP output
6zz6 cell cycle cryo-EM (3.4 Å) Collier JE, Lee BG, Roig MB, Yatskevich S, Petela NJ, Metson J, Voulgaris M, Gonzalez Llamazares A, Lowe J, Nasmyth KA (2020) "Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3." Elife, 9. doi: 10.7554/eLife.59560. cryo-EM structure of s.cerevisiae cohesin-scc2-DNA complex. SNAP output
7a08 transferase cryo-EM (3.11 Å) Michalski S, de Oliveira Mann CC, Stafford CA, Witte G, Bartho J, Lammens K, Hornung V, Hopfner KP (2020) "Structural basis for sequestration and autoinhibition of cGAS by chromatin." Nature, 587, 678-682. doi: 10.1038/s41586-020-2748-0. Cryoem structure of cgas nucleosome complex. SNAP output
7abs lyase X-ray (1.97 Å) Yosaatmadja Y, Baddock HT, Newman JA, Bielinski M, Gavard AE, Mukhopadhyay SMM, Dannerfjord AA, Schofield CJ, McHugh PJ, Gileadi O (2021) "Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition." Nucleic Acids Res., 49, 9310-9326. doi: 10.1093/nar/gkab693. Structure of human dclre1c-artemis in complex with DNA - re-evaluation of 6wo0. SNAP output
7ad8 DNA binding protein cryo-EM (3.5 Å) Barnett JT, Kuper J, Koelmel W, Kisker C, Kad NM (2020) "The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair." Nucleic Acids Res., 48, 12689-12696. doi: 10.1093/nar/gkaa973. Core tfiih-xpa-DNA complex with modelled p62 subunit. SNAP output
7adb transcription cryo-EM (4.4 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 1 delta nusg. SNAP output
7adc transcription cryo-EM (4.0 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex 3 delta nusg. SNAP output
7add transcription cryo-EM (4.3 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination intermediate complex iiia. SNAP output
7ade transcription cryo-EM (4.2 Å) Said N, Hilal T, Sunday ND, Khatri A, Burger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) "Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho." Science, 371. doi: 10.1126/science.abd1673. Transcription termination complex iva. SNAP output
7adu viral protein X-ray (2.62 Å) Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke Jr TR, Hughes SH (2021) "HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants." Acs Infect Dis., 7, 1469-1482. doi: 10.1021/acsinfecdis.0c00819. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz440 (compound 5j). SNAP output
7adv viral protein X-ray (2.65 Å) Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke Jr TR, Hughes SH (2021) "HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants." Acs Infect Dis., 7, 1469-1482. doi: 10.1021/acsinfecdis.0c00819. Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and the insti xz447 (compound 6v). SNAP output
7ae1 transcription cryo-EM (2.8 Å) Girbig M, Misiaszek AD, Vorlander MK, Lafita A, Grotsch H, Baudin F, Bateman A, Muller CW (2021) "Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states." Nat.Struct.Mol.Biol., 28, 210-219. doi: 10.1038/s41594-020-00555-5. cryo-EM structure of human RNA polymerase iii elongation complex 1. SNAP output
7ae3 transcription cryo-EM (3.1 Å) Girbig M, Misiaszek AD, Vorlander MK, Lafita A, Grotsch H, Baudin F, Bateman A, Muller CW (2021) "Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states." Nat.Struct.Mol.Biol., 28, 210-219. doi: 10.1038/s41594-020-00555-5. cryo-EM structure of human RNA polymerase iii elongation complex 3. SNAP output
7aea transcription cryo-EM (3.4 Å) Girbig M, Misiaszek AD, Vorlander MK, Lafita A, Grotsch H, Baudin F, Bateman A, Muller CW (2021) "Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states." Nat.Struct.Mol.Biol., 28, 210-219. doi: 10.1038/s41594-020-00555-5. cryo-EM structure of human RNA polymerase iii elongation complex 2. SNAP output
7aeo DNA binding protein X-ray (2.8 Å) Obaji E, Maksimainen MM, Galera-Prat A, Lehtio L (2021) "Activation of PARP2/ARTD2 by DNA damage induces conformational changes relieving enzyme autoinhibition." Nat Commun, 12, 3479. doi: 10.1038/s41467-021-23800-x. Human artd2 in complex with DNA oligonucleotides. SNAP output
7ahx transferase X-ray (2.73 Å) Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K (2021) "Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues." J.Med.Chem., 64, 782-796. doi: 10.1021/acs.jmedchem.0c01747. Hiv-1 reverse transcriptase complex with DNA and d-aspartate tenofovir with bound manganese. SNAP output
7ai5 DNA binding protein cryo-EM (4.4 Å) Fernandez-Leiro R, Bhairosing-Kok D, Kunetsky V, Laffeber C, Winterwerp HH, Groothuizen F, Fish A, Lebbink JHG, Friedhoff P, Sixma TK, Lamers MH (2021) "The selection process of licensing a DNA mismatch for repair." Nat.Struct.Mol.Biol., 28, 373-381. doi: 10.1038/s41594-021-00577-7. Muts in scanning state. SNAP output
7ai6 DNA binding protein cryo-EM (6.9 Å) Fernandez-Leiro R, Bhairosing-Kok D, Kunetsky V, Laffeber C, Winterwerp HH, Groothuizen F, Fish A, Lebbink JHG, Friedhoff P, Sixma TK, Lamers MH (2021) "The selection process of licensing a DNA mismatch for repair." Nat.Struct.Mol.Biol., 28, 373-381. doi: 10.1038/s41594-021-00577-7. Muts in mismatch bound state. SNAP output
7ai7 DNA binding protein cryo-EM (3.9 Å) Fernandez-Leiro R, Bhairosing-Kok D, Kunetsky V, Laffeber C, Winterwerp HH, Groothuizen F, Fish A, Lebbink JHG, Friedhoff P, Sixma TK, Lamers MH (2021) "The selection process of licensing a DNA mismatch for repair." Nat.Struct.Mol.Biol., 28, 373-381. doi: 10.1038/s41594-021-00577-7. Muts in intermediate state. SNAP output
7aib DNA binding protein cryo-EM (4.7 Å) Fernandez-Leiro R, Bhairosing-Kok D, Kunetsky V, Laffeber C, Winterwerp HH, Groothuizen F, Fish A, Lebbink JHG, Friedhoff P, Sixma TK, Lamers MH (2021) "The selection process of licensing a DNA mismatch for repair." Nat.Struct.Mol.Biol., 28, 373-381. doi: 10.1038/s41594-021-00577-7. Muts-mutl in clamp state. SNAP output
7aic DNA binding protein cryo-EM (5.0 Å) Fernandez-Leiro R, Bhairosing-Kok D, Kunetsky V, Laffeber C, Winterwerp HH, Groothuizen F, Fish A, Lebbink JHG, Friedhoff P, Sixma TK, Lamers MH (2021) "The selection process of licensing a DNA mismatch for repair." Nat.Struct.Mol.Biol., 28, 373-381. doi: 10.1038/s41594-021-00577-7. Muts-mutl in clamp state (kinked clamp domain). SNAP output
7aid transferase X-ray (3.15 Å) Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K (2021) "Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues." J.Med.Chem., 64, 782-796. doi: 10.1021/acs.jmedchem.0c01747. Hiv-1 reverse transcriptase complex with DNA and d-aspartate tenofovir. SNAP output
7aif transferase X-ray (2.75 Å) Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K (2021) "Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues." J.Med.Chem., 64, 782-796. doi: 10.1021/acs.jmedchem.0c01747. Hiv-1 reverse transcriptase complex with DNA and l-glutamate tenofovir with bound manganese. SNAP output
7aig transferase X-ray (2.95 Å) Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K (2021) "Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues." J.Med.Chem., 64, 782-796. doi: 10.1021/acs.jmedchem.0c01747. Hiv-1 reverse transcriptase complex with DNA and l-glutamate tenofovir. SNAP output
7aii transferase X-ray (2.62 Å) Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K (2021) "Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues." J.Med.Chem., 64, 782-796. doi: 10.1021/acs.jmedchem.0c01747. Hiv-1 reverse transcriptase complex with DNA and l-methionine tenofovir with bound manganese. SNAP output
7aij transferase X-ray (2.95 Å) Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K (2021) "Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues." J.Med.Chem., 64, 782-796. doi: 10.1021/acs.jmedchem.0c01747. Hiv-1 reverse transcriptase complex with DNA and l-methionine tenofovir. SNAP output
7amn transcription X-ray (2.3 Å) Zhang J, Liu B, Gu D, Hao Y, Chen M, Ma Y, Zhou X, Reverter D, Zhang Y, Wang Q (2021) "Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression." Nucleic Acids Res., 49, 3274-3293. doi: 10.1093/nar/gkab150. Structure of luxr with DNA (repression). SNAP output
7amt transcription X-ray (2.6 Å) Zhang J, Liu B, Gu D, Hao Y, Chen M, Ma Y, Zhou X, Reverter D, Zhang Y, Wang Q (2021) "Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression." Nucleic Acids Res., 49, 3274-3293. doi: 10.1093/nar/gkab150. Structure of luxr with DNA (activation). SNAP output
7amv transcription cryo-EM (2.8 Å) Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U (2021) "Structural basis of the complete poxvirus transcription initiation process." Nat.Struct.Mol.Biol., 28, 779-788. doi: 10.1038/s41594-021-00655-w. Atomic structure of the poxvirus transcription pre-initiation complex in the initially melted state. SNAP output
7aoe transcription cryo-EM (3.9 Å) Heiss FB, Daiss JL, Becker P, Engel C (2021) "Conserved strategies of RNA polymerase I hibernation and activation." Nat Commun, 12, 758. doi: 10.1038/s41467-021-21031-8. Schizosaccharomyces pombe RNA polymerase i (elongation complex). SNAP output
7aoh transcription cryo-EM (2.7 Å) Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U (2021) "Structural basis of the complete poxvirus transcription initiation process." Nat.Struct.Mol.Biol., 28, 779-788. doi: 10.1038/s41594-021-00655-w. Atomic structure of the poxvirus late initially transcribing complex. SNAP output
7aoz transcription cryo-EM (2.85 Å) Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U (2021) "Structural basis of the complete poxvirus transcription initiation process." Nat.Struct.Mol.Biol., 28, 779-788. doi: 10.1038/s41594-021-00655-w. Atomic structure of the poxvirus transcription initiation complex in conformation 1. SNAP output
7ap8 transcription cryo-EM (3.15 Å) Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U (2021) "Structural basis of the complete poxvirus transcription initiation process." Nat.Struct.Mol.Biol., 28, 779-788. doi: 10.1038/s41594-021-00655-w. Atomic structure of the poxvirus initially transcribing complex in conformation 2. SNAP output
7ap9 transcription cryo-EM (3.01 Å) Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U (2021) "Structural basis of the complete poxvirus transcription initiation process." Nat.Struct.Mol.Biol., 28, 779-788. doi: 10.1038/s41594-021-00655-w. Atomic structure of the poxvirus initially transcribing complex in conformation 3. SNAP output
7apd DNA binding protein cryo-EM (3.9 Å) Javed A, Major B, Stead JA, Sanders CM, Orlova EV (2021) "Unwinding of a DNA replication fork by a hexameric viral helicase." Nat Commun, 12, 5535. doi: 10.1038/s41467-021-25843-6. Bovine papillomavirus e1 DNA helicase-replication fork complex. SNAP output
7at8 gene regulation cryo-EM (4.4 Å) Finogenova K, Bonnet J, Poepsel S, Schafer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Muller J (2020) "Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3." Elife, 9. doi: 10.7554/eLife.61964. Histone h3 recognition by nucleosome-bound prc2 subunit ezh2.. SNAP output
7aud nuclear protein X-ray (2.96 Å) Chen X, Ali YI, Fisher CE, Arribas-Bosacoma R, Rajasekaran MB, Williams G, Walker S, Booth JR, Hudson JJ, Roe SM, Pearl LH, Ward SE, Pearl FM, Oliver AW (2021) "Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein." Elife, 10. doi: 10.7554/eLife.65339. Structure of an engineered helicase domain construct for human bloom syndrome protein (blm). SNAP output
7aw7 transcription X-ray (3.4 Å) Huber EM, Hortschansky P, Scheven MT, Misslinger M, Haas H, Brakhage AA, Groll M (2022) "Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX." Structure, 30, 934. doi: 10.1016/j.str.2022.04.001. Ccaat-binding complex and hapx bound to aspergillus nidulans ccca DNA. SNAP output
7aw9 transcription X-ray (3.5 Å) Huber EM, Hortschansky P, Scheven MT, Misslinger M, Haas H, Brakhage AA, Groll M (2022) "Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX." Structure, 30, 934. doi: 10.1016/j.str.2022.04.001. Ccaat-binding complex and hapx bound to aspergillus fumigatus ccca DNA. SNAP output
7b0c DNA binding protein X-ray (3.0 Å) Rohac R, Crack JC, de Rosny E, Gigarel O, Le Brun NE, Fontecilla-Camps JC, Volbeda A (2022) "Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors." Commun Biol, 5, 769. doi: 10.1038/s42003-022-03745-7. [4fe-4s]-nsrr complexed to 23-bp hmpa1 operator fragment. SNAP output
7b0f DNA binding protein X-ray (2.797 Å) Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdwijn P, Delarue M (2020) "Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution." Biomolecules, 10. doi: 10.3390/biom10121647. Tgot_6g12 binary complex. SNAP output
7b0g DNA binding protein X-ray (3.0 Å) Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdwijn P, Delarue M (2020) "Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution." Biomolecules, 10. doi: 10.3390/biom10121647. Tgot_6g12 binary with 2 hctps. SNAP output
7b0h DNA binding protein X-ray (3.15 Å) Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdwijn P, Delarue M (2020) "Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution." Biomolecules, 10. doi: 10.3390/biom10121647. Tgot_6g12 ternary complex. SNAP output
7b0y splicing cryo-EM (3.6 Å) Zhang S, Aibara S, Vos SM, Agafonov DE, Luhrmann R, Cramer P (2021) "Structure of a transcribing RNA polymerase II-U1 snRNP complex." Science, 371, 305-309. doi: 10.1126/science.abf1870. Structure of a transcribing RNA polymerase ii-u1 snrnp complex. SNAP output
7b46 transcription X-ray (2.02 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human wild-type p53dbd bound to DNA and mq: wt-DNA-mq (p1). SNAP output
7b49 transcription X-ray (1.42 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human p53dbd-r273h mutant bound to DNA and mq: r273h-DNA-mq. SNAP output
7b4a transcription X-ray (1.9 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human p53dbd-r273h mutant bound to DNA: r273h-DNA. SNAP output
7b4d transcription X-ray (1.85 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human p53dbd-r273c-s240r double mutant bound to DNA and mq: r273c-s240r-DNA-mq. SNAP output
7b4e transcription X-ray (1.58 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human p53dbd-r282w mutant bound to DNA and mq: r282w-DNA-mq. SNAP output
7b4f transcription X-ray (1.78 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human p53dbd-r282w mutant bound to DNA: r282w-mq (i). SNAP output
7b4g transcription X-ray (1.86 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human p53dbd-r282w mutant bound to DNA: r282w-mq (ii). SNAP output
7b4h transcription X-ray (1.39 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human wild-type p53dbd bound to DNA and mq: wt-DNA-mq (iii). SNAP output
7b4n transcription X-ray (1.32 Å) Degtjarik O, Golovenko D, Diskin-Posner Y, Abrahmsen L, Rozenberg H, Shakked Z (2021) "Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (MQ)." Nat Commun, 12, 7057. doi: 10.1038/s41467-021-27142-6. Structural basis of reactivation of oncogenic p53 mutants by a small molecule: methylene quinuclidinone (mq). human wild-type p53dbd bound to DNA and mq: wt-DNA-mq (ii). SNAP output
7b5y DNA binding protein cryo-EM (7.1 Å) Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwarzer J, Hopfner KP, Witte G (2021) "BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture." Nucleic Acids Res., 49, 10166-10177. doi: 10.1093/nar/gkab736. S. agalactiae busr in complex with its busab-promotor DNA. SNAP output
7bca DNA binding protein X-ray (2.8 Å) Fernandez-Lopez R, Ruiz R, Del Campo I, Gonzalez-Montes L, Boer DR, de la Cruz F, Moncalian G (2022) "Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors." Nucleic Acids Res., 50, 11938-11947. doi: 10.1093/nar/gkac1024. Crystal structure of the hth DNA binding protein ardk from r388 plasmid bound to a direct-repeat DNA element. SNAP output
7bcb DNA binding protein X-ray (2.8 Å) Fernandez-Lopez R, Ruiz R, Del Campo I, Gonzalez-Montes L, Boer DR, de la Cruz F, Moncalian G (2022) "Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors." Nucleic Acids Res., 50, 11938-11947. doi: 10.1093/nar/gkac1024. Crystal structure of the hth DNA binding protein ardk from r388 plasmid bound to ir3 DNA. SNAP output
7bef transcription cryo-EM (4.5 Å) Hao M, Ye F, Jovanovic M, Kotta-Loizou I, Xu Q, Qin X, Buck M, Zhang X, Wang M (2022) "Structures of Class I and Class II Transcription Complexes Reveal the Molecular Basis of RamA-Dependent Transcription Activation." Adv Sci, 9, e2103669. doi: 10.1002/advs.202103669. Structures of class ii bacterial transcription complexes. SNAP output
7beg transcription cryo-EM (4.2 Å) Hao M, Ye F, Jovanovic M, Kotta-Loizou I, Xu Q, Qin X, Buck M, Zhang X, Wang M (2022) "Structures of Class I and Class II Transcription Complexes Reveal the Molecular Basis of RamA-Dependent Transcription Activation." Adv Sci, 9, e2103669. doi: 10.1002/advs.202103669. Structures of class i bacterial transcription complexes. SNAP output
7bg9 RNA binding protein cryo-EM (3.8 Å) Ghanim GE, Fountain AJ, van Roon AM, Rangan R, Das R, Collins K, Nguyen THD (2021) "Structure of human telomerase holoenzyme with bound telomeric DNA." Nature, 593, 449-453. doi: 10.1038/s41586-021-03415-4. The catalytic core lobe of human telomerase in complex with a telomeric DNA substrate. SNAP output
7bhy DNA binding protein X-ray (2.3 Å) Soltysova M, Sieglova I, Fabry M, Brynda J, Skerlova J, Rezacova P (2021) "Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family." Acta Crystallogr D Struct Biol, 77, 1411-1424. doi: 10.1107/S2059798321009633. DNA-binding domain of deor in complex with the DNA operator. SNAP output
7bil hydrolase X-ray (2.21 Å) Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG (2021) "Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition." Nucleic Acids Res., 49, 4129-4143. doi: 10.1093/nar/gkab188. Crystal structure of helicase pif1 from thermus oshimai in complex with oligo ggtttggtttggtt. SNAP output
7bjq DNA binding protein X-ray (2.7 Å) De March M, Onesti S "Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus." Crystal structure of recjcdc45 from methanothermobacter thermoautotroficus in complex with ssDNA. SNAP output
7btq immune system cryo-EM (4.54 Å) Gao Y, Cao D, Zhu J, Feng H, Luo X, Liu S, Yan XX, Zhang X, Gao P (2020) "Structural insights into assembly, operation and inhibition of a type I restriction-modification system." Nat Microbiol, 5, 1107-1118. doi: 10.1038/s41564-020-0731-z. Ecor124i-DNA in the restriction-alleviation state. SNAP output
7bwd translation cryo-EM (4.32 Å) Liu L, Lou ZY, Ai HS, Cao L "Structure of the Dot1L-H2BK34ub Nucleosome Complex Reveals an Unprecedented Crosstalk Activation Mechanism through Nucleosome Shape Distortion." Structure of dot1l-h2bk34ub nucleosome complex. SNAP output
7bxt cell cycle-DNA cryo-EM (4.2 Å) Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T (2021) "Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C." Embo J., 40, e105671. doi: 10.15252/embj.2020105671. The cryo-EM structure of cenp-a nucleosome in complex with cenp-c peptide and cenp-n n-terminal domain. SNAP output
7by0 cell cycle cryo-EM (4.5 Å) Ariyoshi M, Makino F, Watanabe R, Nakagawa R, Kato T, Namba K, Arimura Y, Fujita R, Kurumizaka H, Okumura EI, Hara M, Fukagawa T (2021) "Cryo-EM structure of the CENP-A nucleosome in complex with phosphorylated CENP-C." Embo J., 40, e105671. doi: 10.15252/embj.2020105671. The cryo-EM structure of cenp-a nucleosome in complex with the phosphorylated cenp-c. SNAP output
7bzg DNA binding protein X-ray (2.9 Å) Zhu R, Zhang G, Jing M, Han Y, Li J, Zhao J, Li Y, Chen PR (2021) "Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction." Nat Commun, 12, 581. doi: 10.1038/s41467-020-20754-4. Structure of bacillus subtilis hxlr, wild type in complex with formaldehyde and DNA. SNAP output
7c0g transcription X-ray (2.4 Å) Liu YH, Zhang LS, Wu BX, Huang HD "Aca1 in complex with 14bp palindromic DNA target." Aca1 in complex with 14bp palindromic DNA target. SNAP output
7c0i DNA binding protein X-ray (2.4 Å) Park C, Zheng X, Park CY, Kim J, Lee SK, Won H, Choi J, Kim YG, Choi HJ (2020) "Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process." Nucleic Acids Res., 48, 12957-12971. doi: 10.1093/nar/gkaa1115. Crystal structure of chimeric mutant of e3l in complex with z-DNA. SNAP output
7c0j DNA binding protein-DNA X-ray (2.75 Å) Park C, Zheng X, Park CY, Kim J, Lee SK, Won H, Choi J, Kim YG, Choi HJ (2020) "Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process." Nucleic Acids Res., 48, 12957-12971. doi: 10.1093/nar/gkaa1115. Crystal structure of chimeric mutant of gh5 in complex with z-DNA. SNAP output
7c0m DNA binding protein-DNA cryo-EM (3.9 Å) Kujirai T, Zierhut C, Takizawa Y, Kim R, Negishi L, Uruma N, Hirai S, Funabiki H, Kurumizaka H (2020) "Structural basis for the inhibition of cGAS by nucleosomes." Science, 370, 455-458. doi: 10.1126/science.abd0237. Human cgas-nucleosome complex. SNAP output
7c17 transcription cryo-EM (4.22 Å) Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O'Halloran TV, Zhang Y (2021) "CueR activates transcription through a DNA distortion mechanism." Nat.Chem.Biol., 17, 57-64. doi: 10.1038/s41589-020-00653-x. The cryo-EM structure of e. coli cuer transcription activation complex with fully duplex promoter DNA. SNAP output
7c4p DNA binding protein X-ray (1.995 Å) Jin Z, Park JH, Yun JH, Park SY, Lee W "Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA." Crystal structure of dbd plasma treated zebrafish trf2 myb-domain complexed with DNA. SNAP output
7c4q DNA binding protein X-ray (2.5 Å) Jin Y, Park JH, Yun JH, Park SY, Lee W "Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA." Crystal structure of dbd plasma treated zebrafish trf2 myb-domain complexed with DNA. SNAP output
7c4r DNA binding protein X-ray (2.44 Å) Jin Z, Park JH, Yun JH, Park SY, Lee W "Crystal structure of hydrogen peroxide treated zebrafish TRF2 myb-domain complexed with DNA." Crystal structure of hydrogen peroxide treated zebrafish trf2 complexed with DNA. SNAP output
7c7l RNA binding protein-RNA-DNA cryo-EM (3.3 Å) Takeda SN, Nakagawa R, Okazaki S, Hirano H, Kobayashi K, Kusakizako T, Nishizawa T, Yamashita K, Nishimasu H, Nureki O (2021) "Structure of the miniature type V-F CRISPR-Cas effector enzyme." Mol.Cell, 81, 558-570.e3. doi: 10.1016/j.molcel.2020.11.035. cryo-EM structure of the cas12f1-sgrna-target DNA complex. SNAP output
7c97 transferase-DNA cryo-EM (3.68 Å) Wei L, Yu F (2020) "Structural basis for transcription inhibition by E. coli SspA." Nucleic Acids Res. cryo-EM structure of an escherichia coli rnap-promoter open complex (rpo) with sspa. SNAP output
7c98 recombination-DNA cryo-EM (3.47 Å) Luo SC, Yeh HY, Lan WH, Wu YM, Yang CH, Chang HY, Su GC, Lee CY, Wu WJ, Li HW, Ho MC, Chi P, Tsai MD (2021) "Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures." Nat Commun, 12, 115. doi: 10.1038/s41467-020-20258-1. Human dmc1 post-synaptic complexes. SNAP output
7c99 recombination-DNA cryo-EM (3.36 Å) Luo SC, Yeh HY, Lan WH, Wu YM, Yang CH, Chang HY, Su GC, Lee CY, Wu WJ, Li HW, Ho MC, Chi P, Tsai MD (2021) "Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures." Nat Commun, 12, 115. doi: 10.1038/s41467-020-20258-1. Human dmc1 post-synaptic complexes with mismatched dsDNA. SNAP output
7c9a recombination cryo-EM (3.43 Å) Luo SC, Yeh HY, Lan WH, Wu YM, Yang CH, Chang HY, Su GC, Lee CY, Wu WJ, Li HW, Ho MC, Chi P, Tsai MD (2021) "Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures." Nat Commun, 12, 115. doi: 10.1038/s41467-020-20258-1. Human rad51 post-synaptic complexes mutant (v273p, d274g). SNAP output
7c9c recombination-DNA cryo-EM (3.33 Å) Luo SC, Yeh HY, Lan WH, Wu YM, Yang CH, Chang HY, Su GC, Lee CY, Wu WJ, Li HW, Ho MC, Chi P, Tsai MD (2021) "Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures." Nat Commun, 12, 115. doi: 10.1038/s41467-020-20258-1. Human dmc1 pre-synaptic complexes. SNAP output
7c9o transcription X-ray (2.55 Å) Shen C, Liu H, Guan Z, Yan J, Zheng T, Yan W, Wu C, Zhang Q, Yin P, Xing Y (2020) "Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering." Plant Cell, 32, 3469-3484. doi: 10.1105/tpc.20.00067. Crystal structure of DNA-bound cct-nf-yb-yc complex (hd1cct-ghd8-osnf-yc2). SNAP output
7cby transcription X-ray (1.646 Å) Dai S, Li J, Zhang H, Chen X, Guo M, Chen Z, Chen Y (2020) "Structural Basis for DNA Recognition by FOXG1 and the Characterization of Disease-causing FOXG1 Mutations." J.Mol.Biol., 432, 6146-6156. doi: 10.1016/j.jmb.2020.10.007. Structure of foxg1 DNA binding domain bound to dbe2 DNA site. SNAP output
7cc9 DNA binding protein-DNA X-ray (2.063 Å) Yu H, Li J, Liu G, Zhao G, Wang Y, Hu W, Deng Z, Wu G, Gan J, Zhao YL, He X (2020) "DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses." Nucleic Acids Res., 48, 8755-8766. doi: 10.1093/nar/gkaa574. Sulfur binding domain of sprmcra complexed with phosphorothioated DNA. SNAP output
7ccd DNA binding protein-DNA X-ray (2.42 Å) Yu H, Li J, Liu G, Zhao G, Wang Y, Hu W, Deng Z, Wu G, Gan J, Zhao YL, He X (2020) "DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses." Nucleic Acids Res., 48, 8755-8766. doi: 10.1093/nar/gkaa574. Sulfur binding domain of sprmcra complexed with phosphorothioated DNA. SNAP output
7ccj DNA binding protein-DNA X-ray (3.3 Å) Yu H, Li J, Liu G, Zhao G, Wang Y, Hu W, Deng Z, Wu G, Gan J, Zhao YL, He X (2020) "DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses." Nucleic Acids Res., 48, 8755-8766. doi: 10.1093/nar/gkaa574. Sulfur binding domain of sprmcra complexed with phosphorothioated DNA. SNAP output
7ccq structural protein-transferase-DNA cryo-EM (3.8 Å) Cao D, Han X, Fan X, Xu RM, Zhang X (2020) "Structural basis for nucleosome-mediated inhibition of cGAS activity." Cell Res., 30, 1088-1097. doi: 10.1038/s41422-020-00422-4. Structure of the 1:1 cgas-nucleosome complex. SNAP output
7ccr structural protein-transferase-DNA cryo-EM (4.9 Å) Cao D, Han X, Fan X, Xu RM, Zhang X (2020) "Structural basis for nucleosome-mediated inhibition of cGAS activity." Cell Res., 30, 1088-1097. doi: 10.1038/s41422-020-00422-4. Structure of the 2:2 cgas-nucleosome complex. SNAP output
7cd5 hydrolase-DNA X-ray (2.7 Å) Liu TC, Lin CT, Chang KC, Guo KW, Wang S, Chu JW, Hsiao YY (2021) "APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling." Nat Commun, 12, 601. doi: 10.1038/s41467-020-20853-2. Mape1-blunt-ended dsDNA product complex. SNAP output
7cd6 hydrolase-DNA X-ray (2.701 Å) Liu TC, Lin CT, Chang KC, Guo KW, Wang S, Chu JW, Hsiao YY (2021) "APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling." Nat Commun, 12, 601. doi: 10.1038/s41467-020-20853-2. Mape1-recessed dsDNA product complex. SNAP output
7ce1 transcription X-ray (3.2 Å) Ye F, Wang C, Fu Q, Yan XF, Bharath SR, Casanas A, Wang M, Song H, Zhang LH, Gao YG (2020) "Structural basis of a novel repressor, SghR, controllingAgrobacteriuminfection by cross-talking to plants." J.Biol.Chem., 295, 12290-12304. doi: 10.1074/jbc.RA120.012908. Complex structure of transcription factor sghr with its cognate DNA. SNAP output
7chw transcription-DNA cryo-EM (3.58 Å) Wei L, Yu F (2020) "Structural basis for transcription inhibition by E. coli SspA." Nucleic Acids Res. cryo-EM structure of an escherichia coli rnap-promoter open complex (rpo). SNAP output
7ckq transcription cryo-EM (4.4 Å) Fang C, Li L, Zhao Y, Wu X, Philips SJ, You L, Zhong M, Shi X, O'Halloran TV, Li Q, Zhang Y (2020) "The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription." Nat Commun, 11, 6284. doi: 10.1038/s41467-020-20134-y. The cryo-EM structure of b. subtilis bmrr transcription activation complex. SNAP output
7cli DNA binding protein X-ray (3.0 Å) Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VY (2023) "Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation." Elife, 12. doi: 10.7554/eLife.86258. Structure of nf-kb p52 homodimer bound to p-selectin kb DNA fragment. SNAP output
7co6 hydrolase-DNA X-ray (1.9 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Binary complex of DNA polymerase mu with 1-nt gapped DNA (templating thymine). SNAP output
7co8 hydrolase-DNA X-ray (1.697 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Ternary complex of DNA polymerase mu with 2-nt gapped DNA (t:dgmpnpp). SNAP output
7co9 hydrolase-DNA X-ray (1.599 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Ternary complex of DNA polymerase mu with 1-nt gapped DNA (t:dgmpnpp) and mg. SNAP output
7coa hydrolase-DNA X-ray (1.698 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Ternary complex of DNA polymerase mu with 1-nt gapped DNA (t:dgmpnpp) and mn. SNAP output
7cob hydrolase-DNA X-ray (1.797 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Ternary complex of DNA polymerase mu (q441a) with 1-nt gapped DNA (t:dgmpnpp). SNAP output
7coc hydrolase-DNA X-ray (1.9 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Ternary complex of DNA polymerase mu (k438a-q441a) with 1-nt gapped DNA (t:dgmpnpp). SNAP output
7cod hydrolase-DNA X-ray (1.8 Å) Guo M, Wang Y, Tang Y, Chen Z, Hou J, Dai J, Wang Y, Wang L, Xu H, Tian B, Hua Y, Zhao Y (2021) "Mechanism of genome instability mediated by human DNA polymerase mu misincorporation." Nat Commun, 12, 3759. doi: 10.1038/s41467-021-24096-7. Post insertion complex of DNA polymerase mu (k438a-q441a) with 1-nt gapped DNA. SNAP output
7cow DNA binding protein X-ray (2.86 Å) Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA (2021) "Engineering nucleosomes for generating diverse chromatin assemblies." Nucleic Acids Res., 49, e52. doi: 10.1093/nar/gkab070. 353 bp di-nucleosome harboring cohesive DNA termini with linker histone h1.0. SNAP output
7cpw transferase-DNA X-ray (2.849 Å) Liu H, Mao S, Sheng J, Gan J (2022) "Crystallization and Structural Determination of 8-17 DNAzyme." Methods Mol.Biol., 2439, 117-130. doi: 10.1007/978-1-0716-2047-2_9. Complex structure of DNA with self-catalyzed depurination activity. SNAP output
7cq4 hydrolase X-ray (3.294 Å) Xu X, Wang M, Sun J, Yu Z, Li G, Yang N, Xu RM (2021) "Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex." Nucleic Acids Res., 49, 7740-7752. doi: 10.1093/nar/gkab542. Crystal structure of slx1-slx4 in complex with 5'flap DNA. SNAP output
7cr6 immune system-DNA X-ray (3.72 Å) Wu C, Tang D, Cheng J, Hu D, Yang Z, Ma X, He H, Yao S, Fu TM, Yu Y, Chen Q (2021) "Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis." Nucleic Acids Res., 49, 2973-2984. doi: 10.1093/nar/gkab105. Synechocystis cas1-cas2-prespacer binary complex. SNAP output
7cre DNA binding protein-DNA X-ray (3.0 Å) Yao J, Tu Y, Shen C, Zhou Q, Xiao H, Jia D, Sun Q (2021) "Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN." Cell.Mol.Life Sci., 78, 7617-7633. doi: 10.1007/s00018-021-03992-7. Hnrnpk kh3 domain in complex with a ssDNA fragment from the sirloin element. SNAP output
7cro gene regulation cryo-EM (3.75 Å) Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z (2021) "Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases." Nature, 590, 498-503. doi: 10.1038/s41586-020-03069-8. Nsd2 bearing e1099k-t1150a dual mutation in complex with 187-bp ncp. SNAP output
7crp gene regulation cryo-EM (3.2 Å) Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z (2021) "Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases." Nature, 590, 498-503. doi: 10.1038/s41586-020-03069-8. Nsd3 bearing e1181k-t1232a dual mutation in complex with 187-bp ncp (1:1 binding mode). SNAP output
7crq gene regulation cryo-EM (3.15 Å) Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z (2021) "Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases." Nature, 590, 498-503. doi: 10.1038/s41586-020-03069-8. Nsd3 bearing e1181k-t1232a dual mutation in complex with 187-bp ncp (2:1 binding mode). SNAP output
7crr gene regulation cryo-EM (3.48 Å) Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z (2021) "Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases." Nature, 590, 498-503. doi: 10.1038/s41586-020-03069-8. Native nsd3 bound to 187-bp nucleosome. SNAP output
7csw antitoxin-DNA X-ray (1.97 Å) Song Y, Luo G, Zhu Y, Li T, Li C, He L, Zhao N, Zhao C, Yang J, Huang Q, Mu X, Tang X, Kang M, Wu S, He Y, Bao R (2021) "Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs." Environ.Microbiol., 23, 1541-1558. doi: 10.1111/1462-2920.15365. Pseudomonas aeruginosa antitoxin higa with pa2440 promoter. SNAP output
7csy antitoxin-DNA X-ray (2.29 Å) Song Y, Luo G, Zhu Y, Li T, Li C, He L, Zhao N, Zhao C, Yang J, Huang Q, Mu X, Tang X, Kang M, Wu S, He Y, Bao R (2021) "Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs." Environ.Microbiol., 23, 1541-1558. doi: 10.1111/1462-2920.15365. Pseudomonas aeruginosa antitoxin higa with higba promoter. SNAP output
7csz RNA binding protein-DNA X-ray (1.8 Å) Chen X, Yang Z, Wang W, Qian K, Liu M, Wang J, Wang M (2021) "Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45." Nucleic Acids Res., 49, 2946-2958. doi: 10.1093/nar/gkab075. Crystal structure of the n-terminal tandem rrm domains of rbm45 in complex with single-stranded DNA. SNAP output
7cuh DNA binding protein X-ray (3.0 Å) Sun H, Wu Z, Zhou Y, Lu Y, Lu H, Chen H, Shi S, Zeng Z, Wu J, Lei M (2022) "Structural insights into Pot1-ssDNA, Pot1-Tpz1 and Tpz1-Ccq1 Interactions within fission yeast shelterin complex." Plos Genet., 18, e1010308. doi: 10.1371/journal.pgen.1010308. Crystal structure of fission yeast pot1 and ssDNA. SNAP output
7cvo DNA binding protein-DNA X-ray (2.6 Å) Lv X, Zeng X, Hu H, Chen L, Zhang F, Liu R, Liu Y, Zhou X, Wang C, Wu Z, Kim C, He Y, Du J (2021) "Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex." Plant Cell, 33, 1182-1195. doi: 10.1093/plcell/koab016. Crystal structure of arabidopsis co cct domain in complex with nf-yb3-yc4 and ft core2 DNA. SNAP output
7cvq DNA binding protein-DNA X-ray (3.3 Å) Lv X, Zeng X, Hu H, Chen L, Zhang F, Liu R, Liu Y, Zhou X, Wang C, Wu Z, Kim C, He Y, Du J (2021) "Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex." Plant Cell, 33, 1182-1195. doi: 10.1093/plcell/koab016. Crystal structure of arabidopsis co cct domain in complex with nf-yb2-yc3 and ft core1 DNA. SNAP output
7cy6 transferase X-ray (2.1 Å) Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J (2021) "Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1." Nat Commun, 12, 744. doi: 10.1038/s41467-021-21061-2. Crystal structure of cmd1 in complex with 5mc-DNA. SNAP output
7cy7 transferase X-ray (2.15 Å) Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J (2021) "Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1." Nat Commun, 12, 744. doi: 10.1038/s41467-021-21061-2. Crystal structure of cmd1 in complex with DNA. SNAP output
7cy8 transferase X-ray (2.4 Å) Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J (2021) "Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1." Nat Commun, 12, 744. doi: 10.1038/s41467-021-21061-2. Crystal structure of cmd1 in complex with 5mc-DNA and vitamin c. SNAP output
7d1z nuclear protein cryo-EM (3.15 Å) Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H (2021) "Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase." Life Sci Alliance, 4. doi: 10.26508/lsa.202000919. cryo-EM structure of set8-nucleosome complex. SNAP output
7d20 nuclear protein cryo-EM (3.0 Å) Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H (2021) "Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase." Life Sci Alliance, 4. doi: 10.26508/lsa.202000919. cryo-EM structure of set8-cenp-a-nucleosome complex. SNAP output
7d2l RNA binding protein X-ray (2.75 Å) Zhang B, Luo D, Li Y, Perculija V, Chen J, Lin J, Ye Y, Ouyang S (2021) "Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1." Nat Commun, 12, 3476. doi: 10.1038/s41467-021-23876-5. Crystal structure of the cas12i1 r-loop complex before target DNA cleavage. SNAP output
7d3j RNA binding protein X-ray (2.45 Å) Zhang B, Luo D, Li Y, Perculija V, Chen J, Lin J, Ye Y, Ouyang S (2021) "Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1." Nat Commun, 12, 3476. doi: 10.1038/s41467-021-23876-5. Crystal structure of the cas12i1 r-loop complex after target DNA cleavage. SNAP output
7d3t DNA binding protein-DNA X-ray (2.7 Å) Guan Z, Zhang Q, Zhang Z, Zuo J, Chen J, Liu R, Savarin J, Broger L, Cheng P, Wang Q, Pei K, Zhang D, Zou T, Yan J, Yin P, Hothorn M, Liu Z (2022) "Mechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 - PHR2 complex." Nat Commun, 13, 1581. doi: 10.1038/s41467-022-29275-8. Crystal structure of osphr2 in complex with DNA. SNAP output
7d3v DNA binding protein-DNA NMR Liu YP, Lan WX, Wang CX, Cao CY "Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by APOBEC3." Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by apobec3a. SNAP output
7d3w DNA binding protein-DNA NMR Liu Y, Lan W, Wang C, Cao C (2022) "Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance." Protein Sci., 31, 443-453. doi: 10.1002/pro.4242. Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by apobec3a. SNAP output
7d3x DNA binding protein-DNA NMR Liu Y, Lan W, Wang C, Cao C (2022) "Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance." Protein Sci., 31, 443-453. doi: 10.1002/pro.4242. Non-specific and specific interactions work cooperatively to promote cytidine deamination catalyzed by apobec3a. SNAP output
7d58 transcription cryo-EM (2.9 Å) Wang Q, Li S, Wan F, Xu Y, Wu Z, Cao M, Lan P, Lei M, Wu J (2021) "Structural insights into transcriptional regulation of human RNA polymerase III." Nat.Struct.Mol.Biol., 28, 220-227. doi: 10.1038/s41594-021-00557-x. cryo-EM structure of human RNA polymerase iii in elongating state. SNAP output
7d69 nuclear protein cryo-EM (3.57 Å) Sato S, Takizawa Y, Hoshikawa F, Dacher M, Tanaka H, Tachiwana H, Kujirai T, Iikura Y, Ho CH, Adachi N, Patwal I, Flaus A, Kurumizaka H (2021) "Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones." Nucleic Acids Res., 49, 8934-8946. doi: 10.1093/nar/gkab644. cryo-EM structure of the nucleosome containing giardia histones. SNAP output
7d7c transcription cryo-EM (3.6 Å) Shi J, Wen A, Jin S, Gao B, Huang Y, Feng Y (2021) "Transcription activation by a sliding clamp." Nat Commun, 12, 1131. doi: 10.1038/s41467-021-21392-0. Cryoem structure of gp55-dependent RNA polymerase-promoter open complex. SNAP output
7d7d transcription cryo-EM (4.5 Å) Shi J, Wen A, Jin S, Gao B, Huang Y, Feng Y (2021) "Transcription activation by a sliding clamp." Nat Commun, 12, 1131. doi: 10.1038/s41467-021-21392-0. Cryoem structure of gp45-dependent transcription activation complex. SNAP output
7d8t transcription-DNA X-ray (3.201 Å) Liu Z, Chen K, Dai J, Xu P, Sun W, Liu W, Zhao Z, Bennett SP, Li P, Ma T, Lin Y, Kawakami A, Yu J, Wang F, Wang C, Li M, Chase P, Hodder P, Spicer TP, Scampavia L, Cao C, Pan L, Dong J, Chen Y, Yu B, Guo M, Fang P, Fisher DE, Wang J (2023) "A unique hyperdynamic dimer interface permits small molecule perturbation of the melanoma oncoprotein MITF for melanoma therapy." Cell Res., 33, 55-70. doi: 10.1038/s41422-022-00744-5. Mitf bhlhlz complex with m-box DNA. SNAP output
7d98 DNA binding protein-DNA X-ray (3.6 Å) Giannopoulou EA, Senda M, Koentjoro MP, Adachi N, Ogawa N, Senda T (2021) "Crystal structure of the full-length LysR-type transcription regulator CbnR in complex with promoter DNA." Febs J., 288, 4560-4575. doi: 10.1111/febs.15764. Crystal structure of full-length cbnr complexed with the target DNA complex. SNAP output
7dbh DNA binding protein cryo-EM (3.6 Å) Hirai S, Tomimatsu K, Miyawaki-Kuwakado A, Takizawa Y, Komatsu T, Tachibana T, Fukushima Y, Takeda Y, Negishi L, Kujirai T, Koyama M, Ohkawa Y, Kurumizaka H (2022) "Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant." Nucleic Acids Res., 50, 72-91. doi: 10.1093/nar/gkab1137. The mouse nucleosome structure containing h3mm18. SNAP output
7dbm transferase-DNA X-ray (2.43 Å) Nakajima S, Watashi K, Kato T, Muramatsu M, Wakita T, Tamura N, Hattori SI, Maeda K, Mitsuya H, Yasutake Y, Toyoda T (2021) "Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations." J.Virol., 95, e0240120. doi: 10.1128/JVI.02401-20. Hiv-1 reverse transcriptase mutant q151m-y115f-f116y-m184v:DNA:dgtp ternary complex. SNAP output
7dbn transferase-DNA X-ray (2.67 Å) Nakajima S, Watashi K, Kato T, Muramatsu M, Wakita T, Tamura N, Hattori SI, Maeda K, Mitsuya H, Yasutake Y, Toyoda T (2021) "Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations." J.Virol., 95, e0240120. doi: 10.1128/JVI.02401-20. Hiv-1 reverse transcriptase mutant q151m-y115f-f116y-m184v-f160m:DNA:dctp ternary complex. SNAP output
7dbp structural protein cryo-EM (4.5 Å) Wang S, Vogirala VK, Soman A, Berezhnoy NV, Liu ZB, Wong ASW, Korolev N, Su CJ, Sandin S, Nordenskiold L (2021) "Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome." Sci Rep, 11, 380. doi: 10.1038/s41598-020-79654-8. Linker histone defines structure and self-association behaviour of the 177 bp human chromosome. SNAP output
7dci DNA binding protein-DNA X-ray (1.7 Å) Wei L, Wei L "Crystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation." Crystal structure of hsf2 DNA-binding domain in complex with 2-site hse DNA in the head-to-head orientation. SNAP output
7dcj DNA binding protein-DNA X-ray (2.004 Å) Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W (2021) "Structures of heat shock factor trimers bound to DNA." Iscience, 24, 102951. doi: 10.1016/j.isci.2021.102951. Crystal structure of hsf1 DNA-binding domain in complex with 2-site hse DNA in the head-to-head orientation. SNAP output
7dcs DNA binding protein-DNA X-ray (2.4 Å) Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W (2021) "Structures of heat shock factor trimers bound to DNA." Iscience, 24, 102951. doi: 10.1016/j.isci.2021.102951. Crystal structure of hsf1 DNA-binding domain in complex with 3-site hse DNA (23 bp). SNAP output
7dct DNA binding protein-DNA X-ray (2.36 Å) Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W (2021) "Structures of heat shock factor trimers bound to DNA." Iscience, 24, 102951. doi: 10.1016/j.isci.2021.102951. Crystal structure of hsf1 DNA-binding domain in complex with 3-site hse DNA (24 bp). SNAP output
7dcu DNA binding protein-DNA X-ray (1.75 Å) Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W (2021) "Structures of heat shock factor trimers bound to DNA." Iscience, 24, 102951. doi: 10.1016/j.isci.2021.102951. Crystal structure of hsf2 DNA-binding domain in complex with 3-site hse DNA (21 bp). SNAP output
7dn3 transcription cryo-EM (3.5 Å) Li L, Yu Z, Zhao D, Ren Y, Hou H, Xu Y (2021) "Structure of human RNA polymerase III elongation complex." Cell Res., 31, 791-800. doi: 10.1038/s41422-021-00472-2. Structure of human RNA polymerase iii elongation complex. SNAP output
7dpe transferase-DNA X-ray (2.751 Å) Luo Q, Ma JB "Structure of RNA m6A methyltransferase METTL4 in complex with DNA at 2.75 Angstroms resolutioon." RNA methyltransferase mettl4. SNAP output
7dq0 antibiotic-DNA X-ray (2.0 Å) Satange R, Chang CC, Li LY, Lin SH, Neidle S, Hou MH (2023) "Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects." Nucleic Acids Res. doi: 10.1093/nar/gkad156. Crystal structure of actinomycin d-echinomycin-d(acgtgct-agctcgt) complex. SNAP output
7dq8 antibiotic-DNA X-ray (2.4 Å) Satange R, Chang CC, Li LY, Lin SH, Neidle S, Hou MH (2023) "Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects." Nucleic Acids Res. doi: 10.1093/nar/gkad156. Crystal structure of actinomycin d-echinomycin-d(acgcgct-agctcgt) complex. SNAP output
7dta DNA binding protein NMR Duan B, Fu D, Zhang C, Ding P, Dong X, Xia B (2021) "Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains." J.Am.Chem.Soc., 143, 7688-7697. doi: 10.1021/jacs.1c00599. Solution structure of the c-clamp domain from human hdbp1 in complex with DNA. SNAP output
7du2 transcription cryo-EM (3.35 Å) Li L, Yu Z, Zhao D, Ren Y, Hou H, Xu Y (2021) "Structure of human RNA polymerase III elongation complex." Cell Res., 31, 791-800. doi: 10.1038/s41422-021-00472-2. RNA polymerase iii ec complex in post-translocation state. SNAP output
7dv2 DNA binding protein X-ray (3.1 Å) Yen CY, Lin MG, Chen BW, Ng IW, Read N, Kabli AF, Wu CT, Shen YY, Chen CH, Barilla D, Sun YJ, Hsiao CD (2021) "Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly." Nucleic Acids Res., 49, 13150-13164. doi: 10.1093/nar/gkab1155. Structure of sulfolobus solfataricus segb-DNA complex. SNAP output
7dvv transcription X-ray (2.49 Å) Nishinaga M, Sugimoto H, Nishitani Y, Nagai S, Nagatoishi S, Muraki N, Tosha T, Tsumoto K, Aono S, Shiro Y, Sawai H (2021) "Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival." Commun Biol, 4, 467. doi: 10.1038/s42003-021-01987-5. Heme sensor protein pefr from streptococcus agalactiae bound to operator DNA (28-mer). SNAP output
7dw5 DNA binding protein-DNA X-ray (2.83 Å) Zhang H, Cheng N, Li Z, Bai L, Fang C, Li Y, Zhang W, Dong X, Jiang M, Liang Y, Zhang S, Mi J, Zhu J, Zhang Y, Chen SJ, Zhao Y, Weng XQ, Hu W, Chen Z, Huang J, Meng G (2021) "DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia." Cancer Commun (Lond), 41, 1116-1136. doi: 10.1002/cac2.12234. Crystal structure of dux4 hd1-hd2 domain complexed with erg sites. SNAP output
7dwr DNA binding protein X-ray (2.8 Å) Yen CY, Lin MG, Chen BW, Ng IW, Read N, Kabli AF, Wu CT, Shen YY, Chen CH, Barilla D, Sun YJ, Hsiao CD (2021) "Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly." Nucleic Acids Res., 49, 13150-13164. doi: 10.1093/nar/gkab1155. Structure of sulfolobus solfataricus sega-adp complex bound to DNA. SNAP output
7dy6 transcription cryo-EM (3.68 Å) Wang F, Feng Y, Shang Z, Lin W (2021) "A unique binding between SspA and RNAP beta' NTH across low-GC Gram-negative bacteria facilitates SspA-mediated transcription regulation." Biochem.Biophys.Res.Commun., 583, 86-92. doi: 10.1016/j.bbrc.2021.10.048. A refined cryo-EM structure of an escherichia coli rnap-promoter open complex (rpo) with sspa. SNAP output
7e1b DNA binding protein X-ray (4.587 Å) Hong S, Guo J, Zhang X, Zhou X, Zhang P, Yu F (2023) "Structural basis of phosphorylation-induced activation of the response regulator VbrR." Acta Biochim.Biophys.Sin. doi: 10.3724/abbs.2022200. Crystal structure of vbrr-DNA complex. SNAP output
7e8d gene regulation cryo-EM (2.8 Å) Sato K, Kumar A, Hamada K, Okada C, Oguni A, Machiyama A, Sakuraba S, Nishizawa T, Nureki O, Kono H, Ogata K, Sengoku T (2021) "Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2." Nat Commun, 12, 6605. doi: 10.1038/s41467-021-26913-5. Nsd2 e1099k mutant bound to nucleosome. SNAP output
7e8i nuclear protein cryo-EM (3.1 Å) Dai L, Dai Y, Han J, Huang Y, Wang L, Huang J, Zhou Z (2021) "Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin." Mol.Cell, 81, 2765-2777.e6. doi: 10.1016/j.molcel.2021.05.010. Structural insight into brca1-bard1 complex recruitment to damaged chromatin. SNAP output
7e9c structural protein cryo-EM (3.5 Å) Jiang H, Yu C, Liu CP, Han X, Yu Z, Xu RM "Nucleosome binding relinquishes the association of the BAH domain of Orc1 with Sir1." cryo-EM structure of the 1:1 orc1 bah domain in complex with nucleosome. SNAP output
7e9f structural protein cryo-EM (4.0 Å) Jiang H, Yu C, Liu CP, Han X, Yu Z, Xu RM "Nucleosome binding relinquishes the association of the BAH domain of Orc1 with Sir1." cryo-EM structure of the 2:1 orc1 bah domain in complex with nucleosome. SNAP output
7ea5 gene regulation cryo-EM (3.3 Å) Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J (2021) "Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations." Cell Discov, 7, 32. doi: 10.1038/s41421-021-00261-6. Yeast set2 bound to a nucleosome containing oncohistone mutations. SNAP output
7ea8 gene regulation cryo-EM (3.1 Å) Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J (2021) "Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations." Cell Discov, 7, 32. doi: 10.1038/s41421-021-00261-6. Human setd2 bound to a nucleosome containing oncohistone mutations. SNAP output
7ecw immune system-RNA-DNA cryo-EM (3.1 Å) Liu X, Zhang L, Xiu Y, Gao T, Huang L, Xie Y, Yang L, Wang W, Wang P, Zhang Y, Yang M, Feng Y (2021) "Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR-Cas surveillance complex." Nucleic Acids Res., 49, 10178-10191. doi: 10.1093/nar/gkab738. The csy-acrif14-dsDNA complex. SNAP output
7edb DNA binding protein X-ray (2.39 Å) Kita K, Mikami B "Structural analysis of EcoT38I restriction endonuclease." Ecot38i restriction endonuclease complexed with DNA. SNAP output
7eds transcription X-ray (1.77 Å) Xing YF, Lu M "Arsenic-bound p53 Hotspot mutant M133T in complex with the natural PIG3 p53-response element." Human p53 core domain with germline hot spot mutation m133t in complex with the natural pig3 p53-response element and arsenic. SNAP output
7edx transcription cryo-EM (4.5 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. P53-bound tfiid-based core pic on hdm2 promoter. SNAP output
7eeu transcription X-ray (2.9 Å) Xing YF, Lu M "Human p53 core domain with hot spot mutation R282W in complex with the natural CDKN1A(p21) p53-response element and Arsenic." Human p53 core domain with hot spot mutation r282w in complex with the natural cdkn1a(p21) p53-response element and arsenic. SNAP output
7ef8 DNA binding protein-DNA X-ray (2.45 Å) Nakamura T, Okabe K, Hirayama S, Chirifu M, Ikemizu S, Morioka H, Nakabeppu Y, Yamagata Y (2021) "Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer." Nucleic Acids Res., 49, 7154-7163. doi: 10.1093/nar/gkab492. Crystal structure of mouse mutyh in complex with DNA containing ap site analogue:8-oxog (form i). SNAP output
7ef9 DNA binding protein-DNA X-ray (1.97 Å) Nakamura T, Okabe K, Hirayama S, Chirifu M, Ikemizu S, Morioka H, Nakabeppu Y, Yamagata Y (2021) "Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer." Nucleic Acids Res., 49, 7154-7163. doi: 10.1093/nar/gkab492. Crystal structure of mouse mutyh in complex with DNA containing ap site analogue:8-oxog (form ii). SNAP output
7eg6 DNA binding protein-DNA cryo-EM (3.1 Å) He ZY, Chen KJ, Ye YP, Chen ZC (2021) "Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity." Cell Discov, 7, 28. doi: 10.1038/s41421-021-00262-5. Snf5 finger helix bound to the nucleosome. SNAP output
7eg7 transcription cryo-EM (6.2 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Tfiid-based core pic on scp promoter. SNAP output
7eg8 transcription cryo-EM (7.4 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Tfiid-based core pic on puma promoter. SNAP output
7eg9 transcription cryo-EM (3.7 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Tfiid-based intermediate pic on scp promoter. SNAP output
7ega transcription cryo-EM (4.1 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Tfiid-based intermediate pic on puma promoter. SNAP output
7egd transcription cryo-EM (6.75 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Scp promoter-bound tfiid-tfiia in initial tbp-loading state. SNAP output
7egh transcription cryo-EM (3.04 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Tfiid lobe c subcomplex. SNAP output
7egj transcription cryo-EM (8.64 Å) Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y (2021) "Structural insights into preinitiation complex assembly on core promoters." Science, 372. doi: 10.1126/science.aba8490. Scp promoter-bound tfiid-tfiia in post tbp-loading state. SNAP output
7egp DNA binding protein cryo-EM (6.9 Å) He ZY, Chen KJ, Ye YP, Chen ZC (2021) "Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity." Cell Discov, 7, 28. doi: 10.1038/s41421-021-00262-5. The structure of swi-snf-nucleosome complex. SNAP output
7eh0 transcription-DNA-RNA X-ray (2.808 Å) Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE (2021) "Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli ." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2106388118. Thermus thermophilus RNA polymerase transcription initiation complex containing a template-strand purine at position tss-2, upa RNA primer and cmpcpp. SNAP output
7eh1 transcription-DNA-RNA X-ray (2.9 Å) Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE (2021) "Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli ." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2106388118. Thermus thermophilus transcription initiation complex containing a template-strand purine at position tss-2, gpg RNA primer, and cmpcpp. SNAP output
7eh2 transcription-DNA-RNA X-ray (3.34 Å) Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE (2021) "Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli ." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2106388118. Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position tss-2 and gpg RNA primer. SNAP output
7ej6 DNA binding protein-DNA cryo-EM (3.21 Å) Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW (2021) "Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination." Nucleic Acids Res., 49, 13135-13149. doi: 10.1093/nar/gkab1141. Yeast dmc1 presynaptic complex. SNAP output
7ej7 DNA binding protein-DNA cryo-EM (3.41 Å) Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW (2021) "Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination." Nucleic Acids Res., 49, 13135-13149. doi: 10.1093/nar/gkab1141. Yeast dmc1 post-synaptic complex. SNAP output
7ejc DNA binding protein-DNA cryo-EM (2.97 Å) Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW (2021) "Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination." Nucleic Acids Res., 49, 13135-13149. doi: 10.1093/nar/gkab1141. Human rad51 presynaptic complex. SNAP output
7eje DNA binding protein-DNA cryo-EM (3.98 Å) Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW (2021) "Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination." Nucleic Acids Res., 49, 13135-13149. doi: 10.1093/nar/gkab1141. Human rad51 post-synaptic complex. SNAP output
7el1 unknown function X-ray (2.22 Å) Liu H, Zhu Y, Lu Z, Huang Z (2021) "Structural basis of Staphylococcus aureus Cas9 inhibition by AcrIIA14." Nucleic Acids Res., 49, 6587-6595. doi: 10.1093/nar/gkab487. Structure of a protein from bacteria. SNAP output
7el3 DNA binding protein X-ray (1.7 Å) Permsirivisarn P, Yuenyao A, Pramanpol N, Charoenwattanasatien R, Suginta W, Chaiyen P, Pakotiprapha D (2022) "Mechanism of transcription regulation by Acinetobacter baumannii HpaR in the catabolism of p-hydroxyphenylacetate." Febs J., 289, 3217-3240. doi: 10.1111/febs.16340. Crystal structure of hpar-DNA complex from acinetobacter baumannii. SNAP output
7eln immune system-RNA-DNA cryo-EM (3.0 Å) Yang L, Zhang L, Yin P, Ding H, Xiao Y, Zeng J, Wang W, Zhou H, Wang Q, Zhang Y, Chen Z, Yang M, Feng Y (2022) "Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24." Nat Commun, 13, 1931. doi: 10.1038/s41467-022-29581-1. Structure of csy-acrif24-dsDNA. SNAP output
7enn DNA binding protein cryo-EM (2.8 Å) Wang L, Chen K, Chen Z (2021) "Structural basis of ALC1/CHD1L autoinhibition and the mechanism of activation by the nucleosome." Nat Commun, 12, 4057. doi: 10.1038/s41467-021-24320-4. The structure of alc1 bound to the nucleosome. SNAP output
7eof DNA binding protein-DNA X-ray (2.733 Å) Liu YR "Structure of CCDC25-DNA complex." Structure of ccdc25-DNA complex. SNAP output
7eqg immune system-RNA-DNA cryo-EM (3.2 Å) Xie Y, Zhang L, Gao Z, Yin P, Wang H, Li H, Chen Z, Zhang Y, Yang M, Feng Y (2022) "AcrIF5 specifically targets DNA-bound CRISPR-Cas surveillance complex for inhibition." Nat.Chem.Biol., 18, 670-677. doi: 10.1038/s41589-022-00995-8. Structure of csy-acrif5. SNAP output
7et4 DNA binding protein-DNA X-ray (2.7 Å) Hu H, Tian S, Xie G, Liu R, Wang N, Li S, He Y, Du J (2021) "TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103895118. Crystal structure of arabidopsis tem1 ap2 domain. SNAP output
7et6 DNA binding protein-DNA X-ray (2.7 Å) Hu H, Tian S, Xie G, Liu R, Wang N, Li S, He Y, Du J (2021) "TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103895118. Crystal structure of arabidopsis tem1 b3-DNA complex. SNAP output
7eu0 transcription cryo-EM (3.16 Å) Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y (2021) "Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA." Science, 374, 1579-1586. doi: 10.1126/science.abj9184. The cryo-EM structure of a. thaliana pol iv-rdr2 backtracked complex. SNAP output
7eu9 RNA binding protein X-ray (2.35 Å) Zhang B, Luo D, Li Y, Perculija V, Chen J, Lin J, Ye Y, Ouyang S (2021) "Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1." Nat Commun, 12, 3476. doi: 10.1038/s41467-021-23876-5. Crystal structure of the selenomethionine(semet)-derived cas12i1 r-loop complex before target DNA cleavage. SNAP output
7eyi structural protein X-ray (2.401 Å) Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X (2021) "Structural basis for human ZBTB7A action at the fetal globin promoter." Cell Rep, 36, 109759. doi: 10.1016/j.celrep.2021.109759. Crystal structure of zbtb7a in complex with gamma-globin -200 sequence element with c-194a mutation. SNAP output
7ezj DNA binding protein-DNA X-ray (2.9 Å) Koley T, Roy Chowdhury S, Kushwaha T, Kumar M, Inampudi KK, Kaur P, Singh TP, Viadiu H, Ethayathulla AS (2022) "Deciphering the mechanism of p73 recognition of p53 response elements using the crystal structure of p73-DNA complexes and computational studies." Int.J.Biol.Macromol., 206, 40-50. doi: 10.1016/j.ijbiomac.2022.02.108. Crystal structure of p73 DNA binding domain complex bound with 1 bp and 2 bp spacer DNA response elements.. SNAP output
7f0r transcription-DNA cryo-EM (5.8 Å) He D, You L, Wu X, Shi J, Wen A, Yan Z, Mu W, Fang C, Feng Y, Zhang Y (2022) "Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding." Nat Commun, 13, 4204. doi: 10.1038/s41467-022-31871-7. cryo-EM structure of pseudomonas aeruginosa suta transcription activation complex. SNAP output
7f2f transcription X-ray (2.55 Å) Gui W, Xue L, Yue J, Kuang Z, Jin Y, Niu L (2021) "Crystal structure of the complex of DNA with the C-terminal domain of TYE7 from Saccharomyces cerevisiae." Acta Crystallogr.,Sect.F, 77, 341-347. doi: 10.1107/S2053230X21009250. The complex of DNA with the c-terminal domain of tye7 from saccharomyces cerevisiae.. SNAP output
7f4y transferase-DNA X-ray (2.2 Å) Park J, Youn HS, An JY, Lee Y, Eom SH, Wang J (2021) "Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69." Front Mol Biosci, 8, 704813. doi: 10.3389/fmolb.2021.704813. Crystal structure of replisomal dimer of DNA polymerase from bacteriophage rb69 with DNA duplexes. SNAP output
7f75 transcription-DNA cryo-EM (4.2 Å) Shi J, Li F, Wen A, Yu L, Wang L, Wang F, Jin Y, Jin S, Feng Y, Lin W (2021) "Structural basis of transcription activation by the global regulator Spx." Nucleic Acids Res., 49, 10756-10769. doi: 10.1093/nar/gkab790. cryo-EM structure of spx-dependent transcription activation complex. SNAP output
7f9h DNA binding protein X-ray (1.78 Å) Ma R, Liu Y, Gan J, Qiao H, Ma J, Zhang Y, Bu Y, Shao S, Zhang Y, Wang Q (2022) "Xenogeneic nucleoid-associated EnrR thwarts H-NS silencing of bacterial virulence with unique DNA binding." Nucleic Acids Res., 50, 3777-3798. doi: 10.1093/nar/gkac180. Complex structure of enrr-DNA. SNAP output
7fef DNA binding protein-DNA X-ray (2.39 Å) Wu Z, Chen S, Zhou M, Jia L, Li Z, Zhang X, Min J, Liu K (2022) "Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs." J.Mol.Biol., 434, 167404. doi: 10.1016/j.jmb.2021.167404. Crystal structure of atmbd6 with DNA. SNAP output
7fgi viral protein-RNA cryo-EM (2.51 Å) Zhang K, Law MCY, Nguyen TM, Tan YB, Wirawan M, Law YS, Jeong LS, Luo D (2022) "Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1." Cell Rep, 40, 111133. doi: 10.1016/j.celrep.2022.111133. cryo-EM structure of chikungunya virus nonstructural protein 1 with m7gppp-au. SNAP output
7fhj DNA binding protein-DNA X-ray (2.28 Å) Chen S, Zhou M, Dong A, Loppnau P, Wang M, Min J, Liu K (2021) "Structural basis of the TAM domain of BAZ2A in binding to DNA or RNA independent of methylation status." J.Biol.Chem., 297, 101351. doi: 10.1016/j.jbc.2021.101351. Crystal structure of baz2a with DNA. SNAP output
7fj2 transcription X-ray (3.098 Å) Zhang H, Dai S, Liang X, Li J, Chen Y (2021) "Mechanistic Insights into the Preference for Tandem Binding Sites in DNA Recognition by FOXM1." J.Mol.Biol., 434, 167426. doi: 10.1016/j.jmb.2021.167426. Structure of foxm1 homodimer bound to a palindromic DNA site. SNAP output
7fji transcription-RNA-DNA cryo-EM (3.6 Å) Hou H, Li Y, Wang M, Liu A, Yu Z, Chen K, Zhao D, Xu Y (2021) "Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine." Nat Commun, 12, 6135. doi: 10.1038/s41467-021-26402-9. Human pol iii elongation complex. SNAP output
7fjj transcription-RNA-DNA cryo-EM (3.6 Å) Hou H, Li Y, Wang M, Liu A, Yu Z, Chen K, Zhao D, Xu Y (2021) "Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine." Nat Commun, 12, 6135. doi: 10.1038/s41467-021-26402-9. Human pol iii pre-termination complex. SNAP output
7ftn transferase-DNA X-ray (2.001 Å) Groebke-Zbinden K, Vandemeulebroucke A, Hilbert M, Rudolph MG "Crystal Structure of a human cyclic GMP-AMP synthase complex." Crystal structure of human cyclic gmp-amp synthase in complex with propanedioic acid. SNAP output
7fvs isomerase X-ray (2.16 Å) Cumming JG, Kreis L, Kuhne H, Wermuth R, Vercruysse M, Kramer C, Rudolph MG, Xu Z (2023) "Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens." Acs Med.Chem.Lett., 14, 993-998. doi: 10.1021/acsmedchemlett.3c00187. Crystal structure of s. aureus gyrase in complex with 4-[[1-[(1-chloro-6,7-dihydro-5h-cyclopenta[c]pyridin-6-yl)methyl]azetidin-3-yl]methylamino]-6-fluorochromen-2-one. SNAP output
7fvt isomerase X-ray (2.081 Å) Cumming JG, Kreis L, Kuhne H, Wermuth R, Vercruysse M, Kramer C, Rudolph MG, Xu Z (2023) "Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens." Acs Med.Chem.Lett., 14, 993-998. doi: 10.1021/acsmedchemlett.3c00187. Crystal structure of s. aureus gyrase in complex with 6-[5-[2-[(4-chloro-2,3-dihydro-1h-inden-2-yl)methylamino]ethyl]-2-oxo-1,3-oxazolidin-3-yl]-4h-pyrido[3,2-b][1,4]oxazin-3-one. SNAP output
7gat transcription-DNA NMR Starich MR, Wikstrom M, Schumacher S, Arst Jr HN, Gronenborn AM, Clore GM (1998) "The solution structure of the Leu22-->Val mutant AREA DNA binding domain complexed with a TGATAG core element defines a role for hydrophobic packing in the determination of specificity." J.Mol.Biol., 277, 621-634. doi: 10.1006/jmbi.1997.1626. Solution NMR structure of the l22v mutant DNA binding domain of area complexed to a 13 bp DNA containing a tgata site, 34 structures. SNAP output
7ice transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of cacl2. SNAP output
7icf transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of cdcl2 (0.1 millimolar) (four-day soak). SNAP output
7icg transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of cdcl2. SNAP output
7ich transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of cocl2. SNAP output
7ici transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of crcl3 (0.1 millimolar). SNAP output
7icj transferase-DNA X-ray (3.5 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of cucl2 (0.1 millimolar). SNAP output
7ick transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of mgcl2. SNAP output
7icl transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of mncl2 (0.1 millimolar). SNAP output
7icm transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of mncl2 (1.0 millimolar). SNAP output
7icn transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of nicl2. SNAP output
7ico transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of zncl2. SNAP output
7icp transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of zncl2 (0.01 millimolar). SNAP output
7icq transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of zncl2. SNAP output
7icr transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of zncl2. SNAP output
7ics transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of zncl2. SNAP output
7ict transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of zncl2 and mgcl2. SNAP output
7icu transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of cdcl2 (0.1 millimolar). SNAP output
7icv transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of mncl2 (0.1 millimolar) and in the absence of nacl. SNAP output
7jgr replication cryo-EM (3.9 Å) Schmidt JM, Bleichert F (2020) "Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6." Nat Commun, 11, 4263. doi: 10.1038/s41467-020-18067-7. Structure of drosophila orc bound to DNA (84 bp) and cdc6. SNAP output
7jgs replication cryo-EM (3.2 Å) Schmidt JM, Bleichert F (2020) "Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6." Nat Commun, 11, 4263. doi: 10.1038/s41467-020-18067-7. Structure of drosophila orc bound to poly(da-dt) DNA and cdc6 (conformation 2). SNAP output
7jk1 transferase-DNA X-ray (2.62 Å) Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK (2021) "Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase." Nat Commun, 12, 4020. doi: 10.1038/s41467-021-24317-z. Human primpol inserting correct dctp opposite the 8-oxoguanine lesion. SNAP output
7jk2 replication-DNA cryo-EM (3.2 Å) Schmidt JM, Bleichert F (2020) "Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6." Nat Commun, 11, 4263. doi: 10.1038/s41467-020-18067-7. Structure of drosophila orc bound to poly(da-dt) DNA and cdc6 (conformation 1). SNAP output
7jk3 replication-DNA cryo-EM (3.4 Å) Schmidt JM, Bleichert F (2020) "Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6." Nat Commun, 11, 4263. doi: 10.1038/s41467-020-18067-7. Structure of drosophila orc bound to gc-rich DNA and cdc6. SNAP output
7jk4 replication-DNA cryo-EM (3.4 Å) Schmidt JM, Bleichert F (2020) "Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6." Nat Commun, 11, 4263. doi: 10.1038/s41467-020-18067-7. Structure of drosophila orc bound to at-rich DNA and cdc6. SNAP output
7jk5 replication-DNA cryo-EM (3.9 Å) Schmidt JM, Bleichert F (2020) "Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6." Nat Commun, 11, 4263. doi: 10.1038/s41467-020-18067-7. Structure of drosophila orc bound to DNA. SNAP output
7jkl transferase-DNA X-ray (2.384 Å) Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK (2021) "Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase." Nat Commun, 12, 4020. doi: 10.1038/s41467-021-24317-z. Human primpol misinserting datp opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated).. SNAP output
7jkp transferase-DNA X-ray (2.592 Å) Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK (2021) "Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase." Nat Commun, 12, 4020. doi: 10.1038/s41467-021-24317-z. Human primpol misinserting datp opposite the 8-oxoguanine lesion. SNAP output
7jl8 transferase-DNA X-ray (2.1 Å) Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK (2021) "Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase." Nat Commun, 12, 4020. doi: 10.1038/s41467-021-24317-z. Human primpol extending from the correct primer base c opposite the 8-oxoguanine lesion. SNAP output
7jlg transferase-DNA X-ray (2.07 Å) Rechkoblit O, Johnson RE, Gupta YK, Prakash L, Prakash S, Aggarwal AK (2021) "Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase." Nat Commun, 12, 4020. doi: 10.1038/s41467-021-24317-z. Human primpol extending from the erroneous primer base a opposite the 8-oxoguanine lesion. SNAP output
7jm4 transcription X-ray (2.95 Å) Sundararaj S, Seneviratne S, Williams SJ, Enders A, Casarotto MG (2021) "Structural determinants of the IRF4/DNA homodimeric complex." Nucleic Acids Res., 49, 2255-2265. doi: 10.1093/nar/gkaa1287. Irf transcription factor. SNAP output
7jn3 hydrolase-DNA-inhibitor cryo-EM (3.21 Å) Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP (2021) "Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome." Commun Biol, 4, 330. doi: 10.1038/s42003-021-01855-2. cryo-EM structure of rous sarcoma virus cleaved synaptic complex (csc) with hiv-1 integrase strand transfer inhibitor mk-2048. SNAP output
7jnp DNA binding protein X-ray (2.6 Å) Beggs GA, Ayala JC, Kavanaugh LG, Read TD, Hooks GM, Schumacher MA, Shafer WM, Brennan RG (2021) "Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations." Nucleic Acids Res., 49, 4155-4170. doi: 10.1093/nar/gkab213. Mtrr bound to the rpoh operator from neisseria gonorrhoeae. SNAP output
7jo9 DNA binding protein-DNA-transferase cryo-EM (3.3 Å) Boyer JA, Spangler CJ, Strauss JD, Cesmat AP, Liu P, McGinty RK, Zhang Q (2020) "Structural basis of nucleosome-dependent cGAS inhibition." Science, 370, 450-454. doi: 10.1126/science.abd0609. 1:1 cgas-nucleosome complex. SNAP output
7joa DNA binding protein-DNA-transferase cryo-EM (3.3 Å) Boyer JA, Spangler CJ, Strauss JD, Cesmat AP, Liu P, McGinty RK, Zhang Q (2020) "Structural basis of nucleosome-dependent cGAS inhibition." Science, 370, 450-454. doi: 10.1126/science.abd0609. 2:1 cgas-nucleosome complex. SNAP output
7jps replication-DNA cryo-EM (4.4 Å) Jaremko MJ, On KF, Thomas DR, Stillman B, Joshua-Tor L (2020) "The dynamic nature of the human Origin Recognition Complex revealed through five cryoEM structures." Elife, 9. doi: 10.7554/eLife.58622. Orc-DNA: human origin recognition complex (orc) with DNA bound in the core. SNAP output
7jqq motor protein cryo-EM (4.1 Å) Woodson M, Pajak J, Mahler BP, Zhao W, Zhang W, Arya G, White MA, Jardine PJ, Morais MC (2021) "A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA." Sci Adv, 7. doi: 10.1126/sciadv.abc1955. The bacteriophage phi-29 viral genome packaging motor assembly. SNAP output
7jsa DNA binding protein-DNA X-ray (2.85 Å) Hou C, McCown C, Ivanov DN, Tsodikov OV (2020) "Structural Insight into the DNA Binding Function of Transcription Factor ERF." Biochemistry. doi: 10.1021/acs.biochem.0c00774. Crystal structure of the DNA binding domain of human transcription factor erf in the reduced form, in complex with double-stranded DNA accggaagtg. SNAP output
7jse viral protein-DNA cryo-EM (4.6 Å) Santosh V, Musayev FN, Jaiswal R, Zarate-Perez F, Vandewinkel B, Dierckx C, Endicott M, Sharifi K, Dryden K, Henckaerts E, Escalante CR (2020) "The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states." Nucleic Acids Res., 48, 12983-12999. doi: 10.1093/nar/gkaa1133. Adeno-associated virus origin binding domain in complex with ssDNA. SNAP output
7jsf viral protein cryo-EM (6.7 Å) Santosh V, Musayev FN, Jaiswal R, Zarate-Perez F, Vandewinkel B, Dierckx C, Endicott M, Sharifi K, Dryden K, Henckaerts E, Escalante CR (2020) "The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states." Nucleic Acids Res., 48, 12983-12999. doi: 10.1093/nar/gkaa1133. Adeno-associated virus helicase domain heptamer with ssDNA. SNAP output
7jsg viral protein-DNA cryo-EM (5.2 Å) Santosh V, Musayev FN, Jaiswal R, Zarate-Perez F, Vandewinkel B, Dierckx C, Endicott M, Sharifi K, Dryden K, Henckaerts E, Escalante CR (2020) "The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states." Nucleic Acids Res., 48, 12983-12999. doi: 10.1093/nar/gkaa1133. Adeno-associated virus 2 rep68 hd-heptamer-ssDNA with atpgs. SNAP output
7jsh viral protein-DNA cryo-EM (4.4 Å) Santosh V, Musayev FN, Jaiswal R, Zarate-Perez F, Vandewinkel B, Dierckx C, Endicott M, Sharifi K, Dryden K, Henckaerts E, Escalante CR (2020) "The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states." Nucleic Acids Res., 48, 12983-12999. doi: 10.1093/nar/gkaa1133. Adeno-associated virus 2 rep68 hd heptamer-ssaavs1 with atpgs. SNAP output
7jsi viral protein cryo-EM (5.01 Å) Santosh V, Musayev FN, Jaiswal R, Zarate-Perez F, Vandewinkel B, Dierckx C, Endicott M, Sharifi K, Dryden K, Henckaerts E, Escalante CR (2020) "The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states." Nucleic Acids Res., 48, 12983-12999. doi: 10.1093/nar/gkaa1133. Adeno-associated virus 2 rep68 hd hexamer-ssDNA with atpgs. SNAP output
7jsl DNA binding protein-DNA X-ray (4.51 Å) Hou C, McCown C, Ivanov DN, Tsodikov OV (2020) "Structural Insight into the DNA Binding Function of Transcription Factor ERF." Biochemistry. doi: 10.1021/acs.biochem.0c00774. Crystal structure of the DNA binding domain of human transcription factor erf in the oxidized form, in complex with double-stranded DNA accggaagtg. SNAP output
7jtn immune system-DNA X-ray (3.1 Å) Xu X, Zhang C, Denton DT, O'Connell D, Drolet DW, Geisbrecht BV (2021) "Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B." J Immunol., 206, 861-873. doi: 10.4049/jimmunol.2001260. Human complement factor b inhibited by a slow off-rate modified aptamer of 29 bases. SNAP output
7jtq immune system-DNA X-ray (3.5 Å) Xu X, Zhang C, Denton DT, O'Connell D, Drolet DW, Geisbrecht BV (2021) "Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B." J Immunol., 206, 861-873. doi: 10.4049/jimmunol.2001260. Human complement factor b inhibited by a slow off-rate modified aptamer of 31 bases. SNAP output
7ju3 DNA binding protein X-ray (2.7 Å) Beggs GA, Ayala JC, Kavanaugh LG, Read TD, Hooks GM, Schumacher MA, Shafer WM, Brennan RG (2021) "Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations." Nucleic Acids Res., 49, 4155-4170. doi: 10.1093/nar/gkab213. Mtrr bound to the mtrcde operator from neisseria gonorrhoeae. SNAP output
7jvt gene regulation-DNA X-ray (3.16 Å) Truong JQ, Pukala T, Bruning JB, Shearwin KS "Crystal structure of a hybrid lambda-186 repressor." Crystal structure of a lambda-186 hybrid repressor. SNAP output
7jy6 DNA binding protein-DNA cryo-EM (2.5 Å) Yang H, Zhou C, Dhar A, Pavletich NP (2020) "Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures." Nature, 586, 801-806. doi: 10.1038/s41586-020-2820-9. Analysis of a strand exchange reaction with a mini filament of 9-reca, oligo(dt)27 primary ssDNA, non-homologous 120 bp dsDNA and atpgammas. SNAP output
7jy7 DNA binding protein-DNA cryo-EM (2.9 Å) Yang H, Zhou C, Dhar A, Pavletich NP (2020) "Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures." Nature, 586, 801-806. doi: 10.1038/s41586-020-2820-9. Structure of a 12 base pair reca-d loop complex. SNAP output
7jy8 DNA binding protein-DNA cryo-EM (2.4 Å) Yang H, Zhou C, Dhar A, Pavletich NP (2020) "Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures." Nature, 586, 801-806. doi: 10.1038/s41586-020-2820-9. Analysis of a strand exchange reaction with a mini filament of 9-reca, 27-mer ssDNA, partially-homologous 67 bp dsDNA and atpgammas. SNAP output
7jy9 DNA binding protein-DNA cryo-EM (2.7 Å) Yang H, Zhou C, Dhar A, Pavletich NP (2020) "Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures." Nature, 586, 801-806. doi: 10.1038/s41586-020-2820-9. Structure of a 9 base pair reca-d loop complex. SNAP output
7jzv ligase-DNA cryo-EM (3.9 Å) Witus SR, Burrell AL, Farrell DP, Kang J, Wang M, Hansen JM, Pravat A, Tuttle LM, Stewart MD, Brzovic PS, Chatterjee C, Zhao W, DiMaio F, Kollman JM, Klevit RE (2021) "BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1." Nat.Struct.Mol.Biol., 28, 268-277. doi: 10.1038/s41594-020-00556-4. cryo-EM structure of the brca1-ubch5c-bard1 e3-e2 module bound to a nucleosome. SNAP output
7k04 nuclear protein-DNA cryo-EM (9.25 Å) van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K (2021) "Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair." Nat Commun, 12, 3338. doi: 10.1038/s41467-021-23684-x. Structure of tfiih-rad4-rad23-rad33-DNA in DNA opening. SNAP output
7k0y DNA binding protein-DNA cryo-EM (3.7 Å) Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W (2021) "Structure of an activated DNA-PK and its implications for NHEJ." Mol.Cell, 81, 801-810.e3. doi: 10.1016/j.molcel.2020.12.015. cryo-EM structure of activated-form DNA-pk (complex vi). SNAP output
7k19 DNA binding protein-DNA cryo-EM (4.3 Å) Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W (2021) "Structure of an activated DNA-PK and its implications for NHEJ." Mol.Cell, 81, 801-810.e3. doi: 10.1016/j.molcel.2020.12.015. Cryoem structure of DNA-pk catalytic subunit complexed with DNA (complex i). SNAP output
7k1b DNA binding protein-DNA cryo-EM (4.3 Å) Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W (2021) "Structure of an activated DNA-PK and its implications for NHEJ." Mol.Cell, 81, 801-810.e3. doi: 10.1016/j.molcel.2020.12.015. Cryoem structure of DNA-pk catalytic subunit complexed with DNA (complex ii). SNAP output
7k1j DNA binding protein-DNA cryo-EM (3.9 Å) Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W (2021) "Structure of an activated DNA-PK and its implications for NHEJ." Mol.Cell, 81, 801-810.e3. doi: 10.1016/j.molcel.2020.12.015. Cryoem structure of inactivated-form DNA-pk (complex iii). SNAP output
7k1k DNA binding protein-DNA cryo-EM (4.1 Å) Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W (2021) "Structure of an activated DNA-PK and its implications for NHEJ." Mol.Cell, 81, 801-810.e3. doi: 10.1016/j.molcel.2020.12.015. Cryoem structure of inactivated-form DNA-pk (complex iv). SNAP output
7k1n DNA binding protein-DNA cryo-EM (3.9 Å) Chen X, Xu X, Chen Y, Cheung JC, Wang H, Jiang J, de Val N, Fox T, Gellert M, Yang W (2021) "Structure of an activated DNA-PK and its implications for NHEJ." Mol.Cell, 81, 801-810.e3. doi: 10.1016/j.molcel.2020.12.015. Cryoem structure of inactivated-form DNA-pk (complex v). SNAP output
7k30 hydrolase-DNA X-ray (2.34 Å) Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, Aihara H (2021) "Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2021120118. Crystal structure of endonuclease q complex with 27-mer duplex substrate with du at the active site. SNAP output
7k31 hydrolase-DNA X-ray (2.88 Å) Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, Aihara H (2021) "Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2021120118. Crystal structure of endonuclease q complex with 27-mer duplex substrate with di at the active site. SNAP output
7k32 hydrolase-DNA X-ray (3.11 Å) Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, Aihara H (2021) "Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2021120118. Crystal structure of endonuclease q complex with 27-mer duplex substrate with an abasic lesion at the active site. SNAP output
7k33 hydrolase-DNA X-ray (3.11 Å) Shi K, Moeller NH, Banerjee S, McCann JL, Carpenter MA, Yin L, Moorthy R, Orellana K, Harki DA, Harris RS, Aihara H (2021) "Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2021120118. Crystal structure of endonuclease q complex with 27-mer duplex substrate with an abasic lesion at the active site. SNAP output
7k5d viral protein X-ray (1.78 Å) Landeras-Bueno S, Wasserman H, Oliveira G, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen K, Saphire EO (2021) "Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form." Cell Rep, 35, 108986. doi: 10.1016/j.celrep.2021.108986. Ebola virus vp40 octameric ring generated by a DNA oligonucleotide. SNAP output
7k5o transferase-DNA X-ray (2.16 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 1 min post datp addition. SNAP output
7k5p transferase X-ray (1.97 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 4 min post datp addition. SNAP output
7k5q transferase-DNA X-ray (2.0 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 8 min post datp addition. SNAP output
7k5r transferase-DNA X-ray (2.3 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 120 min post datp addition. SNAP output
7k5s transferase-DNA X-ray (1.67 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 4 hr post datp and dctp addition. SNAP output
7k5t transferase-DNA X-ray (2.3 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 25.5 hr post datp and dctp addition. SNAP output
7k5u transferase-DNA X-ray (2.0 Å) Chim N, Meza RA, Trinh AM, Yang K, Chaput JC (2021) "Following replicative DNA synthesis by time-resolved X-ray crystallography." Nat Commun, 12, 2641. doi: 10.1038/s41467-021-22937-z. Bst DNA polymerase i time-resolved structure, 48 hr post datp and dctp addition. SNAP output
7k5x nuclear protein-DNA cryo-EM (2.93 Å) Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y (2021) "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms." Mol.Cell, 81, 166-182.e6. doi: 10.1016/j.molcel.2020.10.038. cryo-EM structure of a chromatosome containing human linker histone h1.0. SNAP output
7k5y nuclear protein-DNA cryo-EM (2.76 Å) Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y (2021) "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms." Mol.Cell, 81, 166-182.e6. doi: 10.1016/j.molcel.2020.10.038. cryo-EM structure of a chromatosome containing human linker histone h1.4. SNAP output
7k60 nuclear protein-DNA cryo-EM (3.12 Å) Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y (2021) "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms." Mol.Cell, 81, 166-182.e6. doi: 10.1016/j.molcel.2020.10.038. cryo-EM structure of a chromatosome containing human linker histone h1.10. SNAP output
7k61 nuclear protein-DNA cryo-EM (2.85 Å) Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y (2021) "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms." Mol.Cell, 81, 166-182.e6. doi: 10.1016/j.molcel.2020.10.038. cryo-EM structure of 197bp nucleosome aided by scfv. SNAP output
7k63 nuclear protein-DNA cryo-EM (3.03 Å) Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y (2021) "Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms." Mol.Cell, 81, 166-182.e6. doi: 10.1016/j.molcel.2020.10.038. cryo-EM structure of a chromatosome containing chimeric linker histone gh1.10-nch1.4. SNAP output
7k6p structural protein-DNA-transferase cryo-EM (3.2 Å) Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ (2021) "Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation." Science, 371. doi: 10.1126/science.abc6663. Active state dot1 bound to the unacetylated h4 nucleosome. SNAP output
7k6q structural protein-DNA-transferase cryo-EM (3.1 Å) Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ (2021) "Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation." Science, 371. doi: 10.1126/science.abc6663. Active state dot1 bound to the h4k16ac nucleosome. SNAP output
7k78 DNA binding protein-DNA cryo-EM (3.1 Å) Guan R, Lian T, Zhou BR, He E, Wu C, Singleton M, Bai Y (2021) "Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation." Nat Commun, 12, 1763. doi: 10.1038/s41467-021-21985-9. Antibody and nucleosome complex. SNAP output
7k7g DNA binding protein-DNA cryo-EM (4.2 Å) Guan R, Lian T, Zhou BR, He E, Wu C, Singleton M, Bai Y (2021) "Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation." Nat Commun, 12, 1763. doi: 10.1038/s41467-021-21985-9. Nucleosome and gal4 complex. SNAP output
7k96 transferase-DNA X-ray (2.1 Å) Varela FA, Freudenthal BD (2021) "Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta." Biochemistry, 60, 373-380. doi: 10.1021/acs.biochem.0c00847. Human DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate. SNAP output
7k97 transferase-DNA X-ray (2.4 Å) Varela FA, Freudenthal BD (2021) "Mechanism of Deoxyguanosine Diphosphate Insertion by Human DNA Polymerase beta." Biochemistry, 60, 373-380. doi: 10.1021/acs.biochem.0c00847. Human DNA polymerase beta dgdp product complex with mn2+. SNAP output
7k9y RNA binding protein-RNA-DNA X-ray (3.2 Å) Lentzsch AM, Stamos JL, Yao J, Russell R, Lambowitz AM (2021) "Structural basis for template switching by a group II intron-encoded non-LTR-retroelement reverse transcriptase." J.Biol.Chem., 297, 100971. doi: 10.1016/j.jbc.2021.100971. Gsi-iic rt template-switching complex (twinned). SNAP output
7kbd structural protein-DNA cryo-EM (3.38 Å) Arimura Y, Shih RM, Froom R, Funabiki H (2021) "Structural features of nucleosomes in interphase and metaphase chromosomes." Mol.Cell, 81, 4377. doi: 10.1016/j.molcel.2021.08.010. Nucleosome in interphase chromosome formed in xenopus egg extract (oligo fraction). SNAP output
7kbe DNA binding protein-DNA cryo-EM (3.5 Å) Arimura Y, Shih RM, Froom R, Funabiki H (2021) "Structural features of nucleosomes in interphase and metaphase chromosomes." Mol.Cell, 81, 4377. doi: 10.1016/j.molcel.2021.08.010. Nucleosome isolated from metaphase chromosome formed in xenopus egg extract (oligo fraction). SNAP output
7kbf DNA binding protein cryo-EM (4.42 Å) Arimura Y, Shih RM, Froom R, Funabiki H (2021) "Structural features of nucleosomes in interphase and metaphase chromosomes." Mol.Cell, 81, 4377. doi: 10.1016/j.molcel.2021.08.010. H1.8 bound nucleosome isolated from metaphase chromosome in xenopus egg extract (oligo fraction). SNAP output
7kc0 replication cryo-EM (3.2 Å) Zheng F, Georgescu RE, Li H, O'Donnell ME (2020) "Structure of eukaryotic DNA polymerase delta bound to the PCNA clamp while encircling DNA." Proc.Natl.Acad.Sci.USA, 117, 30344-30353. doi: 10.1073/pnas.2017637117. Structure of the saccharomyces cerevisiae replicative polymerase delta in complex with a primer-template and the pcna clamp. SNAP output
7ked transcription-DNA-RNA X-ray (3.6 Å) Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D (2021) "Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II." Nat.Chem.Biol., 17, 906-914. doi: 10.1038/s41589-021-00817-3. RNA polymerase ii elongation complex with unnatural base dtpt3. SNAP output
7kee transcription-DNA-RNA X-ray (3.45 Å) Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D (2021) "Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II." Nat.Chem.Biol., 17, 906-914. doi: 10.1038/s41589-021-00817-3. RNA polymerase ii elongation complex with unnatural base dtpt3, rnamtp bound to e-site. SNAP output
7kef transcription-DNA-RNA X-ray (3.89 Å) Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D (2021) "Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II." Nat.Chem.Biol., 17, 906-914. doi: 10.1038/s41589-021-00817-3. RNA polymerase ii elongation complex with unnatural base dtpt3, rnam in swing state. SNAP output
7khb transcription-DNA cryo-EM (3.53 Å) Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS (2021) "Structural basis of ribosomal RNA transcription regulation." Nat Commun, 12, 528. doi: 10.1038/s41467-020-20776-y. Escherichia coli RNA polymerase and rrnbp1 promoter open complex. SNAP output
7khc transcription-DNA cryo-EM (4.14 Å) Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS (2021) "Structural basis of ribosomal RNA transcription regulation." Nat Commun, 12, 528. doi: 10.1038/s41467-020-20776-y. Escherichia coli RNA polymerase and rrnbp1 promoter closed complex. SNAP output
7khe transcription-DNA cryo-EM (3.58 Å) Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS (2021) "Structural basis of ribosomal RNA transcription regulation." Nat Commun, 12, 528. doi: 10.1038/s41467-020-20776-y. Escherichia coli RNA polymerase and rrnbp1 promoter pre-open complex with dksa-ppgpp. SNAP output
7khi transcription-DNA cryo-EM (3.62 Å) Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS (2021) "Structural basis of ribosomal RNA transcription regulation." Nat Commun, 12, 528. doi: 10.1038/s41467-020-20776-y. Escherichia coli RNA polymerase and rrnbp1 promoter complex with dksa-ppgpp. SNAP output
7kif transcription, transferase-DNA cryo-EM (2.94 Å) Lilic M, Darst SA, Campbell EA (2021) "Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7." Mol.Cell, 81, 2875-2886.e5. doi: 10.1016/j.molcel.2021.05.017. Mycobacterium tuberculosis wt rnap transcription open promoter complex with whib7 transcription factor. SNAP output
7kii replication-DNA X-ray (1.3 Å) Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans 3rd RL, Shi K, Aihara H, Gordon WR (2023) "Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases." Mbio, 14, e0258722. doi: 10.1128/mbio.02587-22. Muscovy duck circovirus rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and mn2+. SNAP output
7kij replication-DNA X-ray (1.69 Å) Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans 3rd RL, Shi K, Aihara H, Gordon WR (2023) "Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases." Mbio, 14, e0258722. doi: 10.1128/mbio.02587-22. Muscovy duck circovirus rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site. SNAP output
7kik replication-DNA X-ray (1.73 Å) Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans 3rd RL, Shi K, Aihara H, Gordon WR (2023) "Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases." Mbio, 14, e0258722. doi: 10.1128/mbio.02587-22. Wheat dwarf virus rep domain circular permutation complexed with a single-stranded DNA 10-mer comprising the cleavage site and mn2+. SNAP output
7kim transcription, transferase-DNA cryo-EM (3.38 Å) Lilic M, Darst SA, Campbell EA (2021) "Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7." Mol.Cell, 81, 2875-2886.e5. doi: 10.1016/j.molcel.2021.05.017. Mycobacterium tuberculosis wt rnap transcription closed promoter complex with whib7 transcription factor. SNAP output
7kin transcription, transferase-DNA cryo-EM (2.74 Å) Lilic M, Darst SA, Campbell EA (2021) "Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7." Mol.Cell, 81, 2875-2886.e5. doi: 10.1016/j.molcel.2021.05.017. Mycobacterium tuberculosis wt rnap transcription open promoter complex with whib7 promoter. SNAP output
7kle DNA binding protein X-ray (3.003 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP." Ternary structure of dpo4 bound to n7mg in the template base paired with incoming dctp. SNAP output
7klf DNA binding protein X-ray (2.301 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP." Ternary structure of dpo4 bound to g in the template base paired with incoming dctp. SNAP output
7kqm transferase-RNA-DNA X-ray (2.73 Å) Choi WS, Weng PJ, Yang W (2022) "Flexibility of telomerase in binding the RNA template and DNA telomeric repeat." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2116159118. Binary complex of tert (telomerase reverse transcriptase) with RNA-telomeric DNA hybrid. SNAP output
7kqn transferase-RNA-DNA X-ray (2.02 Å) Choi WS, Weng PJ, Yang W (2022) "Flexibility of telomerase in binding the RNA template and DNA telomeric repeat." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2116159118. Ternary complex of tert (telomerase reverse transcriptase) with RNA template, DNA primer, an incoming dgtp and a downstream hybrid duplex. SNAP output
7kr3 ligase-DNA X-ray (2.778 Å) Williams JS, Tumbale PP, Arana ME, Rana JA, Williams RS, Kunkel TA (2021) "High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication." Nat Commun, 12, 482. doi: 10.1038/s41467-020-20800-1. Human DNA ligase 1(e346a-e592a) bound to a bulged DNA substrate. SNAP output
7kr4 ligase-DNA X-ray (2.2 Å) Williams JS, Tumbale PP, Arana ME, Rana JA, Williams RS, Kunkel TA (2021) "High-fidelity DNA ligation enforces accurate Okazaki fragment maturation during DNA replication." Nat Commun, 12, 482. doi: 10.1038/s41467-020-20800-1. Human DNA ligase 1(e346a-e592a) bound to a nicked DNA substrate control duplex. SNAP output
7ksp DNA binding protein-DNA X-ray (2.8 Å) Peng S, Meng X, Zhang F, Pathak PK, Chaturvedi J, Coronado J, Morales M, Mao Y, Qian SB, Deng J, Xiang Y (2022) "Structure and function of an effector domain in antiviral factors and tumor suppressors SAMD9 and SAMD9L." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2116550119. Crystal structure of hsamd9_dbd with DNA. SNAP output
7kss replication X-ray (1.503 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct pre-catalytic ground state ternary complex, 10 mm ca2+ (20min). SNAP output
7kst replication-DNA X-ray (1.599 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct reaction state ternary complex, 10 mm mn2+ (2min). SNAP output
7ksu replication-DNA X-ray (1.65 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct product state ternary complex, 10 mm mn2+ (4min). SNAP output
7ksv replication-DNA X-ray (1.64 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct product state ternary complex, 10 mm mn2+ (960min). SNAP output
7ksw replication-DNA X-ray (1.49 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct reaction state ternary complex, 10 mm mg2+ (10min). SNAP output
7ksx replication-DNA X-ray (1.57 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct product state ternary complex, 10 mm mg2+ (30min). SNAP output
7ksy replication-DNA X-ray (1.577 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:ct product state ternary complex, 10 mm mg2+ (960min). SNAP output
7ksz replication-DNA X-ray (1.417 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:at pre-catalytic ground state ternary complex, 10 mm ca2+ (960min). SNAP output
7kt0 replication-DNA X-ray (1.36 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:at ground state ternary complex, 50 mm mg2+ (60min). SNAP output
7kt1 replication-DNA X-ray (1.665 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:at reaction state ternary complex, 50 mm mn2+ (180min). SNAP output
7kt2 replication-DNA X-ray (1.499 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, dgtp:at product state ternary complex, 50 mm mn2+ (225min). SNAP output
7kt3 replication X-ray (1.879 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at pre-catalytic ground state ternary complex, 20 mm ca2+ (120min). SNAP output
7kt4 replication X-ray (1.922 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at reaction state ternary complex, 10 mm mn2+ (30min). SNAP output
7kt5 replication X-ray (1.46 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at product state ternary complex, 10 mm mn2+ (120min). SNAP output
7kt6 replication X-ray (1.87 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at product state ternary complex, 10 mm mn2+ (960min). SNAP output
7kt7 replication X-ray (1.76 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at reaction state ternary complex, 50 mm mg2+ (60min). SNAP output
7kt8 replication X-ray (1.701 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at product state ternary complex, 50 mm mg2+ (180min). SNAP output
7kt9 replication X-ray (1.482 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at product state ternary complex, 50 mm mg2+ (960min). SNAP output
7kta replication X-ray (1.844 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct pre-catalytic ground state ternary complex, 20 mm ca2+ (120min). SNAP output
7ktb replication X-ray (1.576 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct reaction state ternary complex, 10 mm mn2+ (40min). SNAP output
7ktc replication X-ray (1.653 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct product state ternary complex, 10 mm mn2+ (120min). SNAP output
7ktd replication X-ray (1.551 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct product state ternary complex, 10 mm mn2+ (960min). SNAP output
7kte replication X-ray (1.479 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct reaction state ternary complex, 50 mm mg2+ (90min). SNAP output
7ktf replication X-ray (1.489 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct product state ternary complex, 50 mm mg2+ (180min). SNAP output
7ktg replication X-ray (1.445 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct product state ternary complex, 50 mm mg2+ (960min). SNAP output
7kth replication X-ray (1.476 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct product state ternary complex, 10 mm mg2+ (2160min). SNAP output
7kti replication X-ray (1.57 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:ct product state ternary complex, 20 um mn2+ (120min). SNAP output
7ktj replication X-ray (1.452 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu (k438d), 8-oxodgtp:ct pre-catalytic ground state ternary complex, 20 mm ca2+ (120min). SNAP output
7ktk replication X-ray (1.419 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu (k438d), 8-oxodgtp:ct ground state ternary complex, 50 mm mg2+ (90min). SNAP output
7ktl replication X-ray (1.421 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu (k438d), 8-oxodgtp:ct product state ternary complex, 50 mm mn2+ (90min). SNAP output
7ktm replication X-ray (1.528 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu (k438d), 8-oxodgtp:ct reaction state ternary complex, 50 mm mn2+ (30min). SNAP output
7ktn replication X-ray (1.33 Å) Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson SH (2021) "Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide." Nat Commun, 12, 2059. doi: 10.1038/s41467-021-21354-6. DNA polymerase mu, 8-oxodgtp:at product state ternary complex, 10 mm mg2+ (2160min). SNAP output
7ktq gene regulation-DNA cryo-EM (3.3 Å) Grau D, Zhang Y, Lee CH, Valencia-Sanchez M, Zhang J, Wang M, Holder M, Svetlov V, Tan D, Nudler E, Reinberg D, Walz T, Armache KJ (2021) "Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction." Nat Commun, 12, 714. doi: 10.1038/s41467-020-20775-z. Nucleosome from a dimeric prc2 bound to a nucleosome. SNAP output
7ku7 hydrolase-DNA-inhibitor cryo-EM (3.4 Å) Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP (2021) "Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome." Commun Biol, 4, 330. doi: 10.1038/s42003-021-01855-2. cryo-EM structure of rous sarcoma virus cleaved synaptic complex (csc) with hiv-1 integrase strand transfer inhibitor mk-2048. cluster identified by 3-dimensional variability analysis in cryosparc.. SNAP output
7kuf transcription X-ray (2.6 Å) Wan T, Horova M, Beltran DG, Li S, Wong HX, Zhang LM (2021) "Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis." Mol.Cell, 81, 2887. doi: 10.1016/j.molcel.2021.06.002. Transcription activation subcomplex with whib7 bound to sigmaar4-rnap beta flap tip chimera and DNA. SNAP output
7kui viral protein cryo-EM (3.4 Å) Pandey KK, Bera S, Shi K, Rau MJ, Oleru AV, Fitzpatrick JAJ, Engelman AN, Aihara H, Grandgenett DP (2021) "Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome." Commun Biol, 4, 330. doi: 10.1038/s42003-021-01855-2. cryo-EM structure of rous sarcoma virus cleaved synaptic complex (csc) with hiv-1 integrase strand transfer inhibitor mk-2048. cic region of a cluster identified by 3-dimensional variability analysis in cryosparc.. SNAP output
7kz0 hydrolase-DNA X-ray (1.57 Å) Pidugu LS, Bright H, Lin WJ, Majumdar C, Van Ostrand RP, David SS, Pozharski E, Drohat AC (2021) "Structural Insights into the Mechanism of Base Excision by MBD4." J.Mol.Biol., 433, 167097. doi: 10.1016/j.jmb.2021.167097. Human mbd4 glycosylase domain bound to DNA containing substrate analog 2'-deoxy-pseudouridine. SNAP output
7kz1 hydrolase-DNA X-ray (1.62 Å) Pidugu LS, Bright H, Lin WJ, Majumdar C, Van Ostrand RP, David SS, Pozharski E, Drohat AC (2021) "Structural Insights into the Mechanism of Base Excision by MBD4." J.Mol.Biol., 433, 167097. doi: 10.1016/j.jmb.2021.167097. Human mbd4 glycosylase domain bound to DNA containing an abasic site. SNAP output
7kzg hydrolase-DNA X-ray (1.68 Å) Pidugu LS, Bright H, Lin WJ, Majumdar C, Van Ostrand RP, David SS, Pozharski E, Drohat AC (2021) "Structural Insights into the Mechanism of Base Excision by MBD4." J.Mol.Biol., 433, 167097. doi: 10.1016/j.jmb.2021.167097. Human mbd4 glycosylase domain bound to DNA containing oxacarbenium-ion analog 1-aza-2'-deoxyribose. SNAP output
7l34 ligase-DNA X-ray (1.901 Å) Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS, O'Brien PJ (2021) "LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency." Nucleic Acids Res., 49, 1619-1630. doi: 10.1093/nar/gkaa1297. Human DNA ligase 1 - r641l nicked DNA complex. SNAP output
7l35 ligase-DNA X-ray (2.0 Å) Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS, O'Brien PJ (2021) "LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency." Nucleic Acids Res., 49, 1619-1630. doi: 10.1093/nar/gkaa1297. Human DNA ligase 1 - r771w nicked DNA complex. SNAP output
7l49 RNA binding protein-RNA-DNA cryo-EM (3.1 Å) Xiao R, Li Z, Wang S, Han R, Chang L (2021) "Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR-Cas12f nuclease." Nucleic Acids Res., 49, 4120-4128. doi: 10.1093/nar/gkab179. cryo-EM structure of crispr-cas12f ternary complex. SNAP output
7l4c DNA binding protein-DNA X-ray (2.11 Å) Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J (2021) "Substrate deformation regulates DRM2-mediated DNA methylation in plants." Sci Adv, 7. doi: 10.1126/sciadv.abd9224. Crystal structure of the drm2-ctt DNA complex. SNAP output
7l4f DNA binding protein-DNA X-ray (2.55 Å) Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J (2021) "Substrate deformation regulates DRM2-mediated DNA methylation in plants." Sci Adv, 7. doi: 10.1126/sciadv.abd9224. Crystal structure of the drm2-cat DNA complex. SNAP output
7l4h DNA binding protein-DNA X-ray (2.56 Å) Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J (2021) "Substrate deformation regulates DRM2-mediated DNA methylation in plants." Sci Adv, 7. doi: 10.1126/sciadv.abd9224. Crystal structure of the drm2-ctg DNA complex. SNAP output
7l4k DNA binding protein-DNA X-ray (2.61 Å) Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J (2021) "Substrate deformation regulates DRM2-mediated DNA methylation in plants." Sci Adv, 7. doi: 10.1126/sciadv.abd9224. Crystal structure of the drm2-ccg DNA complex. SNAP output
7l4m DNA binding protein-DNA X-ray (2.805 Å) Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J (2021) "Substrate deformation regulates DRM2-mediated DNA methylation in plants." Sci Adv, 7. doi: 10.1126/sciadv.abd9224. Crystal structure of the drm2-cct DNA complex. SNAP output
7l4n DNA binding protein-DNA X-ray (2.247 Å) Fang J, Leichter SM, Jiang J, Biswal M, Lu J, Zhang ZM, Ren W, Zhai J, Cui Q, Zhong X, Song J (2021) "Substrate deformation regulates DRM2-mediated DNA methylation in plants." Sci Adv, 7. doi: 10.1126/sciadv.abd9224. Crystal structure of the drm2 (c397r)-ccg DNA complex. SNAP output
7l4v transcription-DNA X-ray (1.75 Å) Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X (2021) "Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations." Nucleic Acids Res., 49, 5084-5094. doi: 10.1093/nar/gkab276. C-terminal bzip domain of human c-ebpbeta bound to DNA with consensus recognition with gt mismatch. SNAP output
7l4x DNA binding protein-DNA X-ray (1.79 Å) Yu D, Horton JR, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X (2021) "Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions." Nucleic Acids Res., 49, 11629-11642. doi: 10.1093/nar/gkab460. Yth domain of human ythdc1 with dsDNA comprising single n6ma joined by two six-bp DNA duplexes in p3221 crystal. SNAP output
7l4y DNA binding protein-DNA X-ray (1.79 Å) Yu D, Horton JR, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X (2021) "Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions." Nucleic Acids Res., 49, 11629-11642. doi: 10.1093/nar/gkab460. Yth domain of human ythdc1 with dsDNA comprising single n6ma joined by two six-bp DNA duplexes in p212121 crystal. SNAP output
7l69 replication X-ray (1.91 Å) Jung H, Lee S "Crystal structure of human polymerase eta complexed with syn N7-benzylguanine." Crystal structure of human polymerase eta complexed with syn n7-benzylguanine. SNAP output
7lar replication, hydrolase-DNA cryo-EM (3.8 Å) Tarasova E, Dhindwal S, Popp M, Hussain S, Khayat R (2021) "Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus." Mbio, 12, e0076321. doi: 10.1128/mBio.00763-21. cryo-EM structure of pcv2 replicase bound to ssDNA. SNAP output
7las replication, hydrolase-DNA cryo-EM (4.4 Å) Tarasova E, Dhindwal S, Popp M, Hussain S, Khayat R (2021) "Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus." Mbio, 12, e0076321. doi: 10.1128/mBio.00763-21. cryo-EM structure of pcv2 replicase bound to ssDNA. SNAP output
7lbw transcription-DNA X-ray (2.84 Å) Choi WS, Garcia-Diaz M (2022) "A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)." Nucleic Acids Res., 50, 322-332. doi: 10.1093/nar/gkab1230. Crystal structure of tfam (mitochondrial transcription factor a) bridging two non-sequence specific DNA substrates. SNAP output
7lbx transcription-DNA X-ray (2.7 Å) Choi WS, Garcia-Diaz M (2022) "A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)." Nucleic Acids Res., 50, 322-332. doi: 10.1093/nar/gkab1230. Crystal structure of tfam (mitochondrial transcription factor a) in complex with lsp. SNAP output
7lcc recombination cryo-EM (3.66 Å) Kosek D, Grabundzija I, Lei H, Bilic I, Wang H, Jin Y, Peaslee GF, Hickman AB, Dyda F (2021) "The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end." Mol.Cell, 81, 4271-4286.e4. doi: 10.1016/j.molcel.2021.07.028. Helitron transposase bound to lts. SNAP output
7lcd DNA binding protein-DNA X-ray (1.98 Å) Jung H, Lee S "Crystal structure of human polymerase eta complexed with syn N7-acetophenoneguanine." Crystal structure of human polymerase eta complexed with syn n7-acetophenoneguanine. SNAP output
7lfq ligase-DNA X-ray (2.7 Å) Banerjee A, Goldgur Y, Shuman S (2021) "Structure of 3'-PO 4 /5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide." Rna, 27, 584-590. doi: 10.1261/rna.078692.121. Pyrococcus RNA ligase. SNAP output
7lh9 DNA binding protein-DNA X-ray (2.6 Å) Zhang M, Lei M, Qin S, Dong A, Yang A, Li Y, Loppnau P, Hughes TR, Min J, Liu Y (2021) "Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains." Biochim Biophys Acta Gene Regul Mech, 1864, 194688. doi: 10.1016/j.bbagrm.2021.194688. Crystal structure of brpf2 pwwp domain in complex with DNA. SNAP output
7lhz isomerase-DNA-inhibitor X-ray (3.3 Å) Lapointe G, Skepper CK, Holder LM, Armstrong D, Bellamacina C, Blais J, Bussiere D, Bian J, Cepura C, Chan H, Dean CR, De Pascale G, Dhumale B, Fisher LM, Fulsunder M, Kantariya B, Kim J, King S, Kossy L, Kulkarni U, Lakshman J, Leeds JA, Ling X, Lvov A, Ma S, Malekar S, McKenney D, Mergo W, Metzger L, Mhaske K, Moser HE, Mostafavi M, Namballa S, Noeske J, Osborne C, Patel A, Patel D, Patel T, Piechon P, Polyakov V, Prajapati K, Prosen KR, Reck F, Richie DL, Sanderson MR, Satasia S, Savani B, Selvarajah J, Sethuraman V, Shu W, Tashiro K, Thompson KV, Vaarla K, Vala L, Veselkov DA, Vo J, Vora B, Wagner T, Wedel L, Williams SL, Yendluri S, Yue Q, Yifru A, Zhang Y, Rivkin A (2021) "Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria." J.Med.Chem., 64, 6329-6357. doi: 10.1021/acs.jmedchem.1c00375. K. pneumoniae topoisomerase iv (pare-parc) in complex with DNA and (3s)-10-[(3r)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5h-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid (compound 25). SNAP output
7liu RNA-binding protein-DNA,RNA X-ray (3.001 Å) Enemark EJ, Yu S "DDX3X bound to ATP analog and remodeled RNA:DNA hybrid." Ddx3x bound to atp analog and remodeled RNA:DNA hybrid. SNAP output
7lma replication-RNA-DNA cryo-EM (3.3 Å) He Y, Wang Y, Liu B, Helmling C, Susac L, Cheng R, Zhou ZH, Feigon J (2021) "Structures of telomerase at several steps of telomere repeat synthesis." Nature, 593, 454-459. doi: 10.1038/s41586-021-03529-9. Tetrahymena telomerase t3d2 structure at 3.3 angstrom. SNAP output
7lmb replication-RNA-DNA cryo-EM (3.8 Å) He Y, Wang Y, Liu B, Helmling C, Susac L, Cheng R, Zhou ZH, Feigon J (2021) "Structures of telomerase at several steps of telomere repeat synthesis." Nature, 593, 454-459. doi: 10.1038/s41586-021-03529-9. Tetrahymena telomerase t5d5 structure at 3.8 angstrom. SNAP output
7lni transferase-DNA X-ray (2.68 Å) Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X (2021) "Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix." Nat Commun, 12, 3436. doi: 10.1038/s41467-021-23693-w. Semet cama adenine methyltransferase complexed to cognate substrate DNA. SNAP output
7lnj transferase-DNA X-ray (2.68 Å) Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X (2021) "Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix." Nat Commun, 12, 3436. doi: 10.1038/s41467-021-23693-w. Cama adenine methyltransferase complexed to cognate substrate DNA. SNAP output
7lo5 hydrolase-DNA cryo-EM (2.86 Å) Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL (2021) "Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM." Structure, 29, 521-530.e5. doi: 10.1016/j.str.2021.03.012. Cryoem structure drdv-DNA complex. SNAP output
7lpg lyase-DNA X-ray (2.08 Å) Hoitsma NM, Click TH, Agarwal PK, Freudenthal BD (2021) "Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker." Comput Struct Biotechnol J, 19, 3293-3302. doi: 10.1016/j.csbj.2021.05.035. Ape1 product complex with abasic ribonucleotide DNA. SNAP output
7lph lyase-DNA X-ray (1.99 Å) Hoitsma NM, Click TH, Agarwal PK, Freudenthal BD (2021) "Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker." Comput Struct Biotechnol J, 19, 3293-3302. doi: 10.1016/j.csbj.2021.05.035. Ape1 mn-bound product complex with abasic ribonucleotide DNA. SNAP output
7lpi lyase-DNA X-ray (2.05 Å) Hoitsma NM, Click TH, Agarwal PK, Freudenthal BD (2021) "Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker." Comput Struct Biotechnol J, 19, 3293-3302. doi: 10.1016/j.csbj.2021.05.035. Ape1 phosphorothioate substrate complex with abasic ribonucleotide DNA. SNAP output
7lpj lyase-DNA X-ray (2.56 Å) Hoitsma NM, Click TH, Agarwal PK, Freudenthal BD (2021) "Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker." Comput Struct Biotechnol J, 19, 3293-3302. doi: 10.1016/j.csbj.2021.05.035. Ape1 mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA. SNAP output
7lri transferase-DNA X-ray (3.05 Å) Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E (2022) "Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing." Drug Discov Today, 27, 1832-1846. doi: 10.1016/j.drudis.2022.02.016. Structure of hiv-1 reverse transcriptase in complex with DNA, dttp, and ca(2+) ion. SNAP output
7lrm transferase-DNA X-ray (3.14 Å) Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E (2022) "Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing." Drug Discov Today, 27, 1832-1846. doi: 10.1016/j.drudis.2022.02.016. Structure of hiv-1 reverse transcriptase in complex with DNA, dctp, and ca(2+) ion. SNAP output
7lrx transferase-DNA X-ray (2.9 Å) Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E (2022) "Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing." Drug Discov Today, 27, 1832-1846. doi: 10.1016/j.drudis.2022.02.016. Structure of hiv-1 reverse transcriptase in complex with DNA, l-dctp, and ca(2+) ion. SNAP output
7lry transferase-DNA X-ray (2.45 Å) Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E (2022) "Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing." Drug Discov Today, 27, 1832-1846. doi: 10.1016/j.drudis.2022.02.016. Structure of hiv-1 reverse transcriptase in complex with DNA, (-)ftc-tp, and ca(2+) ion. SNAP output
7lsk transferase-DNA X-ray (2.7 Å) Ruiz FX, Hoang A, Dilmore CR, DeStefano JJ, Arnold E (2022) "Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing." Drug Discov Today, 27, 1832-1846. doi: 10.1016/j.drudis.2022.02.016. Structure of hiv-1 reverse transcriptase in complex with DNA, l-dttp, and ca(2+) ion. SNAP output
7lsy DNA binding protein-DNA cryo-EM (8.4 Å) Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y (2021) "Structural basis of long-range to short-range synaptic transition in NHEJ." Nature, 593, 294-298. doi: 10.1038/s41586-021-03458-7. Nhej short-range synaptic complex. SNAP output
7lt3 DNA binding protein-DNA cryo-EM (4.6 Å) Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, He Y (2021) "Structural basis of long-range to short-range synaptic transition in NHEJ." Nature, 593, 294-298. doi: 10.1038/s41586-021-03458-7. Nhej long-range synaptic complex. SNAP output
7lt5 transferase-DNA X-ray (2.54 Å) Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X (2021) "Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix." Nat Commun, 12, 3436. doi: 10.1038/s41467-021-23693-w. Cama adenine methyltransferase complexed to cognate substrate DNA and cofactor sah. SNAP output
7luf transferase-DNA X-ray (3.5 Å) Hayes RP, Heo MR, Mason M, Reid J, Burlein C, Armacost KA, Tellers DM, Raheem I, Shaw AW, Murray E, McKenna PM, Abeywickrema P, Sharma S, Soisson SM, Klein D (2021) "Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase." Nat Commun, 12, 3040. doi: 10.1038/s41467-021-23312-8. Hsv1 polymerase ternary complex with dsDNA and pnu-183792. SNAP output
7lv8 structural protein-DNA cryo-EM (3.4 Å) Valencia-Sanchez MI, Abini-Agbomson S, Wang M, Lee R, Vasilyev N, Zhang J, De Ioannes P, La Scola B, Talbert P, Henikoff S, Nudler E, Erives A, Armache KJ (2021) "The structure of a virus-encoded nucleosome." Nat.Struct.Mol.Biol., 28, 413-417. doi: 10.1038/s41594-021-00585-7. Structure of the marseillevirus nucleosome. SNAP output
7lv9 structural protein-DNA cryo-EM (4.5 Å) Valencia-Sanchez MI, Abini-Agbomson S, Wang M, Lee R, Vasilyev N, Zhang J, De Ioannes P, La Scola B, Talbert P, Henikoff S, Nudler E, Erives A, Armache KJ (2021) "The structure of a virus-encoded nucleosome." Nat.Struct.Mol.Biol., 28, 413-417. doi: 10.1038/s41594-021-00585-7. Marseillevirus heterotrimeric (hexameric) nucleosome. SNAP output
7lvv hydrolase-DNA cryo-EM (3.25 Å) Shen BW, Quispe JD, Luyten Y, McGough BE, Morgan RD, Stoddard BL (2021) "Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM." Structure, 29, 521-530.e5. doi: 10.1016/j.str.2021.03.012. Cryoem structure drdv-DNA complex. SNAP output
7lw8 hydrolase-DNA X-ray (2.88 Å) Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, Tainer JA (2021) "EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart." Mol.Cell, 81, 2989. doi: 10.1016/j.molcel.2021.05.027. Human exonuclease 5 crystal structure in complex with a ssDNA. SNAP output
7lw9 hydrolase-DNA X-ray (2.71 Å) Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, Tainer JA (2021) "EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart." Mol.Cell, 81, 2989. doi: 10.1016/j.molcel.2021.05.027. Human exonuclease 5 crystal structure in complex with ssDNA, sm, and na. SNAP output
7lwa hydrolase-DNA X-ray (2.85 Å) Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, Tainer JA (2021) "EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart." Mol.Cell, 81, 2989. doi: 10.1016/j.molcel.2021.05.027. Human exonuclease 5 crystal structure (t88e) in complex with ssDNA and mg. SNAP output
7lxh hydrolase-DNA-antibiotic X-ray (1.667 Å) Mullins EA, Dorival J, Tang GL, Boger DL, Eichman BF (2021) "Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites." Nat Commun, 12, 6942. doi: 10.1038/s41467-021-27284-7. Bacillus cereus DNA glycosylase alkd bound to a cc1065-adenine nucleobase adduct and DNA containing an abasic site. SNAP output
7lxj hydrolase-DNA-antibiotic X-ray (1.93 Å) Mullins EA, Dorival J, Tang GL, Boger DL, Eichman BF (2021) "Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites." Nat Commun, 12, 6942. doi: 10.1038/s41467-021-27284-7. Bacillus cereus DNA glycosylase alkd bound to a duocarmycin sa-adenine nucleobase adduct and DNA containing an abasic site. SNAP output
7lya structural protein-DNA cryo-EM (2.91 Å) Hu Q, Botuyan MV, Zhao D, Cui G, Mer E, Mer G (2021) "Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation." Nature, 596, 438-443. doi: 10.1038/s41586-021-03716-8. cryo-EM structure of the human nucleosome core particle with linked histone proteins h2a and h2b. SNAP output
7lyb structural protein-DNA cryo-EM (3.28 Å) Hu Q, Botuyan MV, Zhao D, Cui G, Mer E, Mer G (2021) "Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation." Nature, 596, 438-443. doi: 10.1038/s41586-021-03716-8. cryo-EM structure of the human nucleosome core particle in complex with brca1-bard1-ubch5c. SNAP output
7lyc structural protein-DNA cryo-EM (2.94 Å) Hu Q, Botuyan MV, Zhao D, Cui G, Mer E, Mer G (2021) "Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation." Nature, 596, 438-443. doi: 10.1038/s41586-021-03716-8. cryo-EM structure of the human nucleosome core particle ubiquitylated at histone h2a lys13 and lys15 in complex with bard1 (residues 415-777). SNAP output
7lys viral protein-RNA-DNA cryo-EM (3.05 Å) Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA (2021) "DNA interference states of the hypercompact CRISPR-Cas Phi effector." Nat.Struct.Mol.Biol., 28, 652-661. doi: 10.1038/s41594-021-00632-3. cryo-EM structure of casphi-2 (cas12j) bound to crrna and DNA. SNAP output
7lyt viral protein-RNA-DNA cryo-EM (2.9 Å) Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA (2021) "DNA interference states of the hypercompact CRISPR-Cas Phi effector." Nat.Struct.Mol.Biol., 28, 652-661. doi: 10.1038/s41594-021-00632-3. cryo-EM structure of casphi-2 (cas12j) bound to crrna and phosphorothioate-DNA. SNAP output
7m07 transferase X-ray (1.57 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2022) "Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining." Nat Commun, 13, 3806. doi: 10.1038/s41467-022-31278-4. Pre-catalytic ternary complex of DNA polymerase lambda with bound 1-nt gapped ssb substrate and incoming dumpnpp. SNAP output
7m08 transferase X-ray (1.7 Å) Kaminski AM, Bebenek K, Kunkel TA, Pedersen LC "Comprehensive structural survey of DNA double-strand break synapsis by DNA Polymerase Lambda." Not Published. Post-catalytic nicked complex of DNA polymerase lambda with bound 1-nt gapped ssb substrate and incoming dumpnpp. SNAP output
7m09 transferase X-ray (1.65 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2022) "Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining." Nat Commun, 13, 3806. doi: 10.1038/s41467-022-31278-4. Pre-catalytic quaternary complex of DNA polymerase lambda with blunt-ended dsb substrate and incoming dumpnpp. SNAP output
7m0a transferase X-ray (1.83 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2022) "Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining." Nat Commun, 13, 3806. doi: 10.1038/s41467-022-31278-4. Incomplete in crystallo incorporation by DNA polymerase lambda bound to blunt-ended dsb substrate and incoming dttp. SNAP output
7m0b transferase X-ray (2.0 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2022) "Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining." Nat Commun, 13, 3806. doi: 10.1038/s41467-022-31278-4. Pre-catalytic quaternary complex of DNA polymerase lambda with bound mismatched dsb and incoming dumpnpp. SNAP output
7m0c transferase X-ray (2.65 Å) Kaminski AM, Bebenek K, Kunkel TA, Pedersen LC "Comprehensive structural survey of DNA double-strand break synapsis by DNA Polymerase Lambda." Not Published. Post-catalytic nicked complex of DNA polymerase lambda with bound mismatched dsb substrate. SNAP output
7m0d transferase X-ray (1.8 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2022) "Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining." Nat Commun, 13, 3806. doi: 10.1038/s41467-022-31278-4. Pre-catalytic quaternary complex of DNA polymerase lambda with bound complementary dsb substrate and incoming dumpnpp. SNAP output
7m0e transferase X-ray (2.25 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2022) "Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining." Nat Commun, 13, 3806. doi: 10.1038/s41467-022-31278-4. Pre-catalytic synaptic complex of DNA polymerase lambda with gapped dsb substrate and incoming dumpnpp. SNAP output
7m1x DNA binding protein-DNA cryo-EM (3.7 Å) Lewis TS, Sokolova V, Jung H, Ng H, Tan D (2021) "Structural basis of chromatin regulation by histone variant H2A.Z." Nucleic Acids Res., 49, 11379-11391. doi: 10.1093/nar/gkab907. cryo-EM structure of nucleosome containing mouse histone variant h2a.z. SNAP output
7m2u nuclear protein-DNA cryo-EM (8.2 Å) van Eeuwen T, Shim Y, Kim HJ, Zhao T, Basu S, Garcia BA, Kaplan CD, Min JH, Murakami K (2021) "Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair." Nat Commun, 12, 3338. doi: 10.1038/s41467-021-23684-x. Nucleotide excision repair complex tfiih rad4-33. SNAP output
7m43 replication X-ray (1.978 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at ca2+ ground state ternary complex. SNAP output
7m44 replication X-ray (1.901 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mg2+ reaction state ternary complex, 90 sec. SNAP output
7m45 replication X-ray (1.889 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mg2+ reaction state ternary complex, 120 sec. SNAP output
7m46 replication X-ray (1.92 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mg2+ product state ternary complex, 5 min. SNAP output
7m47 replication X-ray (1.648 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mg2+ product state ternary complex, 60 min. SNAP output
7m48 replication X-ray (1.93 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mg2+ product state ternary complex, 960 min. SNAP output
7m49 replication X-ray (1.6 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mn2+ reaction state ternary complex, 5 min. SNAP output
7m4a replication X-ray (1.868 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mn2+ product state ternary complex, 20 min. SNAP output
7m4b replication X-ray (1.66 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mn2+ product state ternary complex, 60 min. SNAP output
7m4c replication X-ray (1.95 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttp:at mn2+ product state ternary complex, 960 min. SNAP output
7m4d replication X-ray (1.817 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at ca2+ ground state ternary complex. SNAP output
7m4e replication X-ray (1.903 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at mg2+ reaction state ternary complex, 120 min. SNAP output
7m4f replication X-ray (1.947 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at mg2+ product state ternary complex, 300 min. SNAP output
7m4g replication X-ray (1.88 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at mg2+ product state ternary complex, 960 min. SNAP output
7m4h replication X-ray (1.923 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at mn2+ reaction state ternary complex, 225 min. SNAP output
7m4i replication X-ray (2.005 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at mn2+ product state ternary complex, 420 min. SNAP output
7m4j replication X-ray (2.377 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, dctp:at mn2+ product state ternary complex, 960 min. SNAP output
7m4k replication X-ray (1.719 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttpas:at ca2+ ground state ternary complex. SNAP output
7m4l replication X-ray (1.701 Å) Jamsen JA, Shock DD, Wilson SH (2022) "Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints." Nat Commun, 13, 3193. doi: 10.1038/s41467-022-30141-w. DNA polymerase lambda, ttpas:at mn2+ product state ternary complex, 60 min. SNAP output
7m5w DNA binding protein-DNA X-ray (2.95 Å) Webb J, Gnann AD, Liew JJ, Patterson M, Paul S, Fores M, Jimenez G, Veraksa A, Dowling DP (2022) "Molecular basis of DNA recognition by the HMG-box-C1 module of Capicua." Biorxiv. doi: 10.1101/2022.03.28.485992. Crystal structure of the hmg-c1 domain of human capicua bound to DNA. SNAP output
7m7l transferase-DNA X-ray (1.58 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with da-ended primer and dampnpp. SNAP output
7m7m transferase-DNA X-ray (1.46 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with ra-ended primer and dampnpp. SNAP output
7m7n transferase-DNA X-ray (1.31 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with 2'-fa-ended primer and dampnpp. SNAP output
7m7o transferase-DNA X-ray (1.8 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with dt-ended primer and 0.1 mm dampnpp. SNAP output
7m7p transferase-DNA X-ray (1.8 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and dampnpp. SNAP output
7m7q transferase-DNA X-ray (2.27 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with dt-ended primer and dampnpp. SNAP output
7m7r transferase-DNA X-ray (1.81 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with ra-ended primer and dampnpp. SNAP output
7m7s transferase-DNA X-ray (1.85 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with dt-ended primer and 0.1 mm dampnpp. SNAP output
7m7t transferase-DNA X-ray (1.46 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with dt-ended primer and datp: in crystallo reaction for 0 s. SNAP output
7m7u transferase-DNA X-ray (1.94 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with dt-ended primer and datp: in crystallo reaction for 480s. SNAP output
7m7y DNA binding protein-DNA X-ray (1.8 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with da-ended primer and datp: in crystallo reaction for 0 s. SNAP output
7m7z transferase-DNA X-ray (1.82 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with da-ended primer and datp: in crystallo reaction for 40 s. SNAP output
7m80 transferase-DNA X-ray (1.98 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with da-ended primer and datp: in crystallo reaction for 100 s. SNAP output
7m81 transferase-DNA X-ray (2.05 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with da-ended primer and datp: in crystallo reaction for 100 s. SNAP output
7m82 transferase-DNA X-ray (2.07 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta with da-ended primer and datp: in crystallo reaction for 300 s. SNAP output
7m83 transferase-DNA X-ray (1.55 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and datp: in crystallo reaction for 0 s. SNAP output
7m84 transferase-DNA X-ray (1.47 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and datp: in crystallo reaction for 40 s. SNAP output
7m85 transferase-DNA X-ray (1.75 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and datp: in crystallo reaction for 80 s. SNAP output
7m86 transferase-DNA X-ray (1.55 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and datp: in crystallo reaction for 140 s. SNAP output
7m87 transferase-DNA X-ray (1.85 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and datp: in crystallo reaction for 230 s. SNAP output
7m88 transferase-DNA X-ray (1.66 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with da-ended primer and datp: in crystallo reaction for 300 s. SNAP output
7m89 transferase-DNA X-ray (1.83 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with ra-ended primer and datp: in crystallo reaction for 0 s. SNAP output
7m8a transferase-DNA X-ray (1.91 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with ra-ended primer and datp: in crystallo reaction for 40 s. SNAP output
7m8b transferase-DNA X-ray (1.85 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with ra-ended primer and datp: in crystallo reaction for 140 s. SNAP output
7m8c transferase-DNA X-ray (1.85 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with ra-ended primer and datp: in crystallo reaction for 230 s. SNAP output
7m8d transferase-DNA X-ray (1.92 Å) Gregory MT, Gao Y, Cui Q, Yang W (2021) "Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2103990118. Human DNA pol eta s113a with ra-ended primer and datp: in crystallo reaction for 300 s. SNAP output
7m8e transferase-hydrolase-DNA-RNA cryo-EM (3.4 Å) Shi W, Zhou W, Chen M, Yang Y, Hu Y, Liu B (2021) "Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase." Nucleic Acids Res., 49, 10707-10716. doi: 10.1093/nar/gkab744. E.coli rnap-rapa elongation complex. SNAP output
7m99 DNA binding protein-DNA cryo-EM (3.2 Å) Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH (2021) "Structural basis for target site selection in RNA-guided DNA transposition systems." Science, 373, 768-774. doi: 10.1126/science.abi8976. Atpgs bound tnsc filament from shcast system. SNAP output
7m9a DNA binding protein-DNA cryo-EM (3.9 Å) Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH (2021) "Structural basis for target site selection in RNA-guided DNA transposition systems." Science, 373, 768-774. doi: 10.1126/science.abi8976. Adp-alf3 bound tnsc structure from shcast system. SNAP output
7m9b DNA binding protein-DNA cryo-EM (3.8 Å) Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH (2021) "Structural basis for target site selection in RNA-guided DNA transposition systems." Science, 373, 768-774. doi: 10.1126/science.abi8976. Adp-alf3 bound tnsc structure in closed form. SNAP output
7m9c DNA binding protein cryo-EM (4.2 Å) Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH (2021) "Structural basis for target site selection in RNA-guided DNA transposition systems." Science, 373, 768-774. doi: 10.1126/science.abi8976. Adp-alf3 bound tnsc structure in open form. SNAP output
7mbm transferase-DNA binding protein-DNA cryo-EM Ayoub A, Park SH, Lee YT, Cho US, Dou Y (2022) "Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes." Biochemistry, 61, 1-9. doi: 10.1021/acs.biochem.1c00603. cryo-EM structure of mll1-ncp (h3k4m) complex, mode01. SNAP output
7mbn transferase-DNA binding protein-DNA cryo-EM Ayoub A, Park SH, Lee YT, Cho US, Dou Y (2022) "Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes." Biochemistry, 61, 1-9. doi: 10.1021/acs.biochem.1c00603. cryo-EM structure of mll1-ncp (h3k4m) complex, mode02. SNAP output
7mca replication cryo-EM (3.6 Å) Feng X, Noguchi Y, Barbon M, Stillman B, Speck C, Li H (2021) "The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6." Nat Commun, 12, 3883. doi: 10.1038/s41467-021-24199-1. Structure of the s. cerevisiae origin recognition complex bound to the replication initiator cdc6 and the ars1 origin DNA.. SNAP output
7mcs DNA binding protein-DNA cryo-EM (3.56 Å) Shen Y, Gomez-Blanco J, Petassi MT, Peters JE, Ortega J, Guarne A (2022) "Structural basis for DNA targeting by the Tn7 transposon." Nat.Struct.Mol.Biol., 29, 143-151. doi: 10.1038/s41594-022-00724-8. Cryo-electron microscopy structure of tnsc(1-503)a225v bound to DNA. SNAP output
7mei transcription cryo-EM (3.54 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. Composite structure of ec+ec. SNAP output
7mg5 sugar binding protein-DNA X-ray (2.1 Å) Partridge BE, Winegar PH, Han Z, Mirkin CA (2021) "Redefining Protein Interfaces within Protein Single Crystals with DNA." J.Am.Chem.Soc., 143, 8925-8934. doi: 10.1021/jacs.1c04191. Concanavalin a bound to a DNA glycoconjugate, man-atat. SNAP output
7mg6 sugar binding protein-DNA X-ray (1.7 Å) Partridge BE, Winegar PH, Han Z, Mirkin CA (2021) "Redefining Protein Interfaces within Protein Single Crystals with DNA." J.Am.Chem.Soc., 143, 8925-8934. doi: 10.1021/jacs.1c04191. Concanavalin a bound to a DNA glycoconjugate, man-agct. SNAP output
7mg7 sugar binding protein-DNA X-ray (1.75 Å) Partridge BE, Winegar PH, Han Z, Mirkin CA (2021) "Redefining Protein Interfaces within Protein Single Crystals with DNA." J.Am.Chem.Soc., 143, 8925-8934. doi: 10.1021/jacs.1c04191. Concanavalin a bound to a DNA glycoconjugate, man-gtac. SNAP output
7mg8 sugar binding protein-DNA X-ray (3.0 Å) Partridge BE, Winegar PH, Han Z, Mirkin CA (2021) "Redefining Protein Interfaces within Protein Single Crystals with DNA." J.Am.Chem.Soc., 143, 8925-8934. doi: 10.1021/jacs.1c04191. Concanavalin a bound to a DNA glycoconjugate, man-cgcg. SNAP output
7mg9 sugar binding protein-DNA X-ray (2.55 Å) Partridge BE, Winegar PH, Han Z, Mirkin CA (2021) "Redefining Protein Interfaces within Protein Single Crystals with DNA." J.Am.Chem.Soc., 143, 8925-8934. doi: 10.1021/jacs.1c04191. Concanavalin a bound to DNA glycoconjugates, man-tttt and man-aaaa. SNAP output
7mga sugar binding protein-DNA X-ray (2.0 Å) Partridge BE, Winegar PH, Han Z, Mirkin CA (2021) "Redefining Protein Interfaces within Protein Single Crystals with DNA." J.Am.Chem.Soc., 143, 8925-8934. doi: 10.1021/jacs.1c04191. Concanavalin a bound to a DNA glycoconjugate, man-aaattt. SNAP output
7mht transferase-DNA X-ray (2.87 Å) O'Gara M, Horton JR, Roberts RJ, Cheng X (1998) "Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base." Nat.Struct.Biol., 5, 872-877. doi: 10.1038/2312. Cytosine-specific methyltransferase hhai-DNA complex. SNAP output
7mi4 hydrolase-DNA cryo-EM (3.2 Å) Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A (2021) "Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas." Nature, 598, 515-520. doi: 10.1038/s41586-021-03951-z. Symmetrical pam-pam prespacer bound cas4-cas1-cas2 complex. SNAP output
7mi5 hydrolase-DNA cryo-EM (3.57 Å) Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A (2021) "Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas." Nature, 598, 515-520. doi: 10.1038/s41586-021-03951-z. Asymmetrical pam-non pam prespacer bound cas4-cas1-cas2 complex. SNAP output
7mi9 hydrolase-DNA cryo-EM (3.89 Å) Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A (2021) "Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas." Nature, 598, 515-520. doi: 10.1038/s41586-021-03951-z. Full integration complex of cas1-cas2 from cas4-containing system. SNAP output
7mib hydrolase-DNA cryo-EM (5.8 Å) Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A (2021) "Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas." Nature, 598, 515-520. doi: 10.1038/s41586-021-03951-z. Half integration complex of cas4-cas1-cas2 with cas4 still on the non-pam side. SNAP output
7mid hydrolase-DNA cryo-EM (3.56 Å) Hu C, Almendros C, Nam KH, Costa AR, Vink JNA, Haagsma AC, Bagde SR, Brouns SJJ, Ke A (2021) "Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas." Nature, 598, 515-520. doi: 10.1038/s41586-021-03951-z. Sub-complex of cas4-cas1-cas2 bound pam containing DNA. SNAP output
7mk1 immune system-DNA X-ray (1.9 Å) Ren X, Gelinas AD, Linehan M, Iwasaki A, Wang W, Janjic N, Pyle AM (2021) "Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA." J.Mol.Biol., 433, 167227. doi: 10.1016/j.jmb.2021.167227. Structure of a protein-modified aptamer complex. SNAP output
7mk9 transcription cryo-EM (3.54 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. Complex structure of trailing ec of ec+ec (trailing ec-focused). SNAP output
7mka transcription cryo-EM (3.54 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. Structure of ec+ec (leading ec-focused). SNAP output
7mkd transcription-DNA cryo-EM (3.2 Å) Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA (2021) "Structural origins of Escherichia coli RNA polymerase open promoter complex stability." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2112877118. cryo-EM structure of escherichia coli RNA polymerase bound to lambda pr promoter DNA (class 1). SNAP output
7mke transcription-DNA cryo-EM (3.7 Å) Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA (2021) "Structural origins of Escherichia coli RNA polymerase open promoter complex stability." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2112877118. cryo-EM structure of escherichia coli RNA polymerase bound to lambda pr promoter DNA (class 2). SNAP output
7mki transcription-DNA cryo-EM (3.5 Å) Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA (2021) "Structural origins of Escherichia coli RNA polymerase open promoter complex stability." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2112877118. cryo-EM structure of escherichia coli RNA polymerase bound to lambda pr (-5g to c) promoter DNA. SNAP output
7mkj transcription-DNA cryo-EM (2.9 Å) Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA (2021) "Structural origins of Escherichia coli RNA polymerase open promoter complex stability." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2112877118. cryo-EM structure of escherichia coli RNA polymerase bound to t7a1 promoter DNA. SNAP output
7mkn transcription-DNA-RNA cryo-EM (3.3 Å) Qayyum MZ, Molodtsov V, Renda A, Murakami KS (2021) "Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli." J.Biol.Chem., 297, 101404. doi: 10.1016/j.jbc.2021.101404. Escherichia coli RNA polymerase and rapa elongation complex. SNAP output
7mko transcription-DNA-RNA cryo-EM (3.15 Å) Qayyum MZ, Molodtsov V, Renda A, Murakami KS (2021) "Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli." J.Biol.Chem., 297, 101404. doi: 10.1016/j.jbc.2021.101404. Escherichia coli RNA polymerase elongation complex. SNAP output
7ml0 transcription cryo-EM (3.0 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. RNA polymerase ii pre-initiation complex (pic1). SNAP output
7ml1 transcription cryo-EM (4.0 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. RNA polymerase ii pre-initiation complex (pic2). SNAP output
7ml2 transcription cryo-EM (3.4 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. RNA polymerase ii pre-initiation complex (pic3). SNAP output
7ml3 transcription cryo-EM (7.6 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. General transcription factor tfiih (weak binding). SNAP output
7ml4 transcription cryo-EM (3.1 Å) Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colon JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K (2022) "Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II." Mol.Cell, 82, 660-676.e9. doi: 10.1016/j.molcel.2021.12.020. RNA polymerase ii initially transcribing complex (itc). SNAP output
7mlb transcription X-ray (3.6 Å) Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH (2022) "Structural and mechanistic basis of reiterative transcription initiation." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2115746119. Crystal structure of thermus thermophilus transcription initiation complex with 5nt RNA. SNAP output
7mli transcription X-ray (3.6 Å) Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH (2022) "Structural and mechanistic basis of reiterative transcription initiation." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2115746119. Crystal structure of thermus thermophilus reiterative transcription complex with 5nt oligo-c RNA. SNAP output
7mlj transcription X-ray (3.75 Å) Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH (2022) "Structural and mechanistic basis of reiterative transcription initiation." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2115746119. Crystal structure of thermus thermophilus reiterative transcription complex with 4nt oligo-g RNA. SNAP output
7mr3 hydrolase-DNA cryo-EM (3.6 Å) Hao L, Zhang R, Lohman TM (2021) "Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting." J.Mol.Biol., 433, 167147. doi: 10.1016/j.jmb.2021.167147. cryo-EM structure of recbcd-DNA complex with docked recbnuc and stabilized recd. SNAP output
7mr4 hydrolase-DNA cryo-EM (4.5 Å) Hao L, Zhang R, Lohman TM (2021) "Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting." J.Mol.Biol., 433, 167147. doi: 10.1016/j.jmb.2021.167147. cryo-EM structure of recbcd-DNA complex with undocked recbnuc and flexible recd. SNAP output
7mtl DNA binding protein-DNA X-ray (2.446 Å) Tripathi P, Bruner SD (2021) "Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA." Biochemistry, 60, 1619-1625. doi: 10.1021/acs.biochem.1c00201. Crystal structure of colibactin self-resistance protein clbs in complex with a dsDNA. SNAP output
7mvs isomerase-DNA-antibiotic X-ray (2.6 Å) Lu Y, Vibhute S, Li L, Okumu A, Ratigan SC, Nolan S, Papa JL, Mann CA, English A, Chen A, Seffernick JT, Koci B, Duncan LR, Roth B, Cummings JE, Slayden RA, Lindert S, McElroy CA, Wozniak DJ, Yalowich J, Mitton-Fry MJ (2021) "Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA." J.Med.Chem., 64, 15214-15249. doi: 10.1021/acs.jmedchem.1c01250. DNA gyrase complexed with uncleaved DNA and compound 7 to 2.6a resolution. SNAP output
7mwh DNA binding protein-DNA X-ray (2.28 Å) Feng Y, Chen S, Zhou M, Zhang J, Min J, Liu K (2022) "Crystal structure of the BAZ2B TAM domain." Heliyon, 8, e09873. doi: 10.1016/j.heliyon.2022.e09873. Crystal structure of baz2a with DNA. SNAP output
7mwk DNA binding protein-DNA X-ray (2.453 Å) Liu K, Dong A, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "Crystal structure of MBD2 with DNA." Crystal structure of mbd2 with DNA. SNAP output
7mwl DNA binding protein-DNA X-ray (1.84 Å) Liu K, Dong A, Li Y, Loppnau P, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "The TAM domain of BAZ2A in complex with a 12mer mCG DNA." The tam domain of baz2a in complex with a 12mer mcg DNA. SNAP output
7mwm DNA binding protein-DNA X-ray (1.601 Å) Liu K, Dong A, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "Crystal structure of MBD2 with DNA." Crystal structure of mbd2 with DNA. SNAP output
7mxq hydrolase-DNA X-ray (3.23 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (r-1). SNAP output
7mxr hydrolase-DNA X-ray (3.101 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (r-2). SNAP output
7mxs hydrolase-DNA X-ray (2.798 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (cr). SNAP output
7mxt hydrolase-DNA X-ray (3.048 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (cmr). SNAP output
7mxu hydrolase-DNA X-ray (3.042 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' flap DNA (cf2). SNAP output
7mxv hydrolase-DNA X-ray (2.211 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' recessed-end DNA (ur). SNAP output
7mxw hydrolase-DNA X-ray (2.836 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (wt) in complex with 5' flap DNA (uf1). SNAP output
7mxx hydrolase-DNA X-ray (2.85 Å) Shi Y, Hellinga HW, Beese LS "Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities." Crystal structure of human exonuclease 1 exo1 (r92a) in complex with 5' flap DNA (uf4). SNAP output
7mz0 transferase-DNA X-ray (2.021 Å) Koag M-C, Lee S "Structure Of Human Dna Polymerase Beta Complexed With dzA As The Template Base In A 1-Nucleotide Gapped Dna." Structure of human DNA polymerase beta complexed with dza as the template base in a 1-nucleotide gapped DNA. SNAP output
7mz1 transferase-DNA X-ray (2.175 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with dzA in the template base paired with incoming non-hydrolyzable TTP." Structure of human DNA polymerase beta complexed with dza in the template base paired with incoming non-hydrolyzable ttp. SNAP output
7mz2 transferase-DNA X-ray (2.088 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP." Structure of human DNA polymerase beta complexed with dza at n-1 of the template base paired with incoming dttp. SNAP output
7mz3 transferase-DNA X-ray (2.418 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA." Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dmea) as the template base in a 1-nucleotide gapped DNA. SNAP output
7mz4 transferase-DNA X-ray (2.076 Å) Koag M-C, Lee S "Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP." Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dmea) in the template base paired with incoming dttp. SNAP output
7mz8 transferase-DNA X-ray (2.6 Å) Koag M-C, Lee S "Structure Of Human Dna Polymerase Beta Complexed With 8Oa As The Template Base In A 1-Nucleotide Gapped Dna." Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dmea) at n-1 of the template base paired with incoming dttp. SNAP output
7n06 viral protein, hydrolase-RNA cryo-EM (2.2 Å) Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE (2021) "Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U." Nucleic Acids Res., 49, 10136-10149. doi: 10.1093/nar/gkab719. Sars-cov-2 nsp15 endoribonuclease post-cleavage state. SNAP output
7n2m transferase-DNA-RNA X-ray (2.9 Å) Baranovskiy AG, Babayeva ND, Lisova AE, Morstadt LM, Tahirov TH (2022) "Structural and functional insight into mismatch extension by human DNA polymerase alpha." Proc.Natl.Acad.Sci.USA, 119, e2111744119. doi: 10.1073/pnas.2111744119. Crystal structure of DNA polymerase alpha catalytic core in complex with dctp and template-primer having t-c mismatch at the post-insertion site. SNAP output
7n33 viral protein-RNA cryo-EM (2.5 Å) Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE (2021) "Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U." Nucleic Acids Res., 49, 10136-10149. doi: 10.1093/nar/gkab719. Sars-cov-2 nsp15 endoribonuclease pre-cleavage state. SNAP output
7n3p RNA binding protein-RNA-DNA cryo-EM (3.65 Å) Xiao R, Wang S, Han R, Li Z, Gabel C, Mukherjee IA, Chang L (2021) "Structural basis of target DNA recognition by CRISPR-Cas12k for RNA-guided DNA transposition." Mol.Cell, 81, 4457-4466.e5. doi: 10.1016/j.molcel.2021.07.043. cryo-EM structure of the cas12k-sgrna-dsDNA complex. SNAP output
7n3y hydrolase-DNA X-ray (2.73 Å) Williams JS, Wojtaszek JL, Appel DC, Krahn J, Wallace BD, Walsh E, Kunkel TA, Williams RS (2022) "Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2." Cell Rep, 41, 111448. doi: 10.1016/j.celrep.2022.111448. Crystal structure of saccharomyces cerevisiae apn2 catalytic domain e59q-d222n mutant in complex with DNA. SNAP output
7n4e transferase-DNA-RNA cryo-EM (3.8 Å) Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE (2022) "Structural and mechanistic basis of sigma-dependent transcriptional pausing." Proc.Natl.Acad.Sci.USA, 119, e2201301119. doi: 10.1073/pnas.2201301119. Escherichia coli sigma 70-dependent paused transcription elongation complex. SNAP output
7n5s DNA binding protein-DNA X-ray (2.86 Å) Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X (2021) "Structural basis for human ZBTB7A action at the fetal globin promoter." Cell Rep, 36, 109759. doi: 10.1016/j.celrep.2021.109759. Zbtb7a zinc finger domain bound to -200 site of fetal globin promoter (oligo 6). SNAP output
7n5t DNA binding protein-DNA X-ray (2.9 Å) Yang Y, Ren R, Ly LC, Horton JR, Li F, Quinlan KGR, Crossley M, Shi Y, Cheng X (2021) "Structural basis for human ZBTB7A action at the fetal globin promoter." Cell Rep, 36, 109759. doi: 10.1016/j.celrep.2021.109759. Zbtb7a zinc finger domain bound to -200 site of fetal globin promoter (oligo 5). SNAP output
7n5u DNA binding protein-DNA X-ray (2.86 Å) Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X (2023) "Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia." J.Biol.Chem., 299, 102885. doi: 10.1016/j.jbc.2023.102885. Zbtb7a zinc finger domain bound to DNA duplex containing ggaccc (oligo 21). SNAP output
7n5v DNA binding protein-DNA X-ray (3.08 Å) Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X (2023) "Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia." J.Biol.Chem., 299, 102885. doi: 10.1016/j.jbc.2023.102885. Zbtb7a zinc finger domain bound to DNA duplex containing ggaccc (oligo 20). SNAP output
7n5w DNA binding protein-DNA X-ray (2.24 Å) Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X (2023) "Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia." J.Biol.Chem., 299, 102885. doi: 10.1016/j.jbc.2023.102885. Zbtb7a zinc finger domain bound to DNA duplex containing ggaccc (oligo 23). SNAP output
7n6i DNA binding protein-DNA cryo-EM (3.9 Å) Park JU, Tsai AW, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH (2021) "Structural basis for target site selection in RNA-guided DNA transposition systems." Science, 373, 768-774. doi: 10.1126/science.abi8976. Atp-bound tnsc-tniq complex from shcast system. SNAP output
7n8n DNA binding protein-DNA cryo-EM (3.89 Å) Liu Y, Bisio H, Toner CM, Jeudy S, Philippe N, Zhou K, Bowerman S, White A, Edwards G, Abergel C, Luger K (2021) "Virus-encoded histone doublets are essential and form nucleosome-like structures." Cell, 184, 4237-4250.e19. doi: 10.1016/j.cell.2021.06.032. Melbournevirus nucleosome like particle. SNAP output
7n8s hydrolase-DNA X-ray (2.79 Å) Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S (2021) "Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease." Nucleic Acids Res., 49, 11350-11366. doi: 10.1093/nar/gkab826. Line-1 endonuclease domain complex with DNA. SNAP output
7n94 hydrolase-DNA X-ray (2.85 Å) Miller I, Totrov M, Korotchkina L, Kazyulkin DN, Gudkov AV, Korolev S (2021) "Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease." Nucleic Acids Res., 49, 11350-11366. doi: 10.1093/nar/gkab826. Line-1 endonuclease domain complex with DNA. SNAP output
7ne3 oxidoreductase X-ray (2.26 Å) Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Razew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP (2022) "Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function." Sci Adv, 8, eabm2427. doi: 10.1126/sciadv.abm2427. Human tet2 in complex with favourable DNA substrate.. SNAP output
7ne6 oxidoreductase X-ray (2.3 Å) Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Razew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP (2022) "Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function." Sci Adv, 8, eabm2427. doi: 10.1126/sciadv.abm2427. Human tet2 in complex with unfavourable DNA substrate.. SNAP output
7nfc DNA binding protein cryo-EM (4.14 Å) Chaplin AK, Hardwick SW, Stavridi AK, Buehl CJ, Goff NJ, Ropars V, Liang S, De Oliveira TM, Chirgadze DY, Meek K, Charbonnier JB, Blundell TL (2021) "Cryo-EM of NHEJ supercomplexes provides insights into DNA repair." Mol.Cell, 81, 3400-3409. doi: 10.1016/j.molcel.2021.07.005. cryo-EM structure of nhej super-complex (dimer). SNAP output
7nfe DNA binding protein cryo-EM (4.29 Å) Chaplin AK, Hardwick SW, Stavridi AK, Buehl CJ, Goff NJ, Ropars V, Liang S, De Oliveira TM, Chirgadze DY, Meek K, Charbonnier JB, Blundell TL (2021) "Cryo-EM of NHEJ supercomplexes provides insights into DNA repair." Mol.Cell, 81, 3400-3409. doi: 10.1016/j.molcel.2021.07.005. cryo-EM structure of nhej super-complex (monomer). SNAP output
7nkx transcription cryo-EM (2.9 Å) Farnung L, Ochmann M, Engeholm M, Cramer P (2021) "Structural basis of nucleosome transcription mediated by Chd1 and FACT." Nat.Struct.Mol.Biol., 28, 382-387. doi: 10.1038/s41594-021-00578-6. RNA polymerase ii-spt4-5-nucleosome-chd1 structure. SNAP output
7nky transcription cryo-EM (3.2 Å) Farnung L, Ochmann M, Engeholm M, Cramer P (2021) "Structural basis of nucleosome transcription mediated by Chd1 and FACT." Nat.Struct.Mol.Biol., 28, 382-387. doi: 10.1038/s41594-021-00578-6. RNA polymerase ii-spt4-5-nucleosome-fact structure. SNAP output
7nl0 gene regulation cryo-EM (3.5 Å) Roberts GA, Ozkan B, Gachulincova I, O'Dwyer MR, Hall-Ponsele E, Saxena M, Robinson PJ, Soufi A (2021) "Dissecting OCT4 defines the role of nucleosome binding in pluripotency." Nat.Cell Biol., 23, 834-845. doi: 10.1038/s41556-021-00727-5. cryo-EM structure of the lin28b nucleosome core particle. SNAP output
7npf DNA binding protein cryo-EM (4.5 Å) Parker AV, Mann D, Tzokov SB, Hwang LC, Bergeron JRC (2021) "The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding." Nat Commun, 12, 5166. doi: 10.1038/s41467-021-25429-2. Vibrio cholerae para2-atpys-DNA filament. SNAP output
7nqf transferase X-ray (2.02 Å) Li AWH, Zabrady K, Bainbridge LJ, Zabrady M, Naseem-Khan S, Berger MB, Kolesar P, Cisneros GA, Doherty AJ (2022) "Molecular basis for the initiation of DNA primer synthesis." Nature, 605, 767-773. doi: 10.1038/s41586-022-04695-0. Prim-pol domain of crispr-associated prim-pol (capp) from marinitoga sp. 1137 with dsDNA. SNAP output
7ntu hydrolase X-ray (3.1 Å) Troisi R, Balasco N, Santamaria A, Vitagliano L, Sica F (2021) "Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human alpha-thrombin." Int.J.Biol.Macromol., 181, 858-867. doi: 10.1016/j.ijbiomac.2021.04.076. X-ray structure of the complex between human alpha thrombin and two duplex-quadruplex aptamers: nu172 and hd22_27mer. SNAP output
7nv0 replication cryo-EM (3.4 Å) Lancey C, Tehseen M, Bakshi S, Percival M, Takahashi M, Sobhy MA, Raducanu VS, Blair K, Muskett FW, Ragan TJ, Crehuet R, Hamdan SM, De Biasio A (2021) "Cryo-EM structure of human Pol kappa bound to DNA and mono-ubiquitylated PCNA." Nat Commun, 12, 6095. doi: 10.1038/s41467-021-26251-6. Human pol kappa holoenzyme with wt pcna. SNAP output
7nv1 replication cryo-EM (6.4 Å) Lancey C, Tehseen M, Bakshi S, Percival M, Takahashi M, Sobhy MA, Raducanu VS, Blair K, Muskett FW, Ragan TJ, Crehuet R, Hamdan SM, De Biasio A (2021) "Cryo-EM structure of human Pol kappa bound to DNA and mono-ubiquitylated PCNA." Nat Commun, 12, 6095. doi: 10.1038/s41467-021-26251-6. Human pol kappa holoenzyme with ub-pcna. SNAP output
7nvr transcription cryo-EM (4.5 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. Human mediator with RNA polymerase ii pre-initiation complex. SNAP output
7nvs transcription cryo-EM (2.8 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. RNA polymerase ii core pre-initiation complex with closed promoter DNA in proximal position. SNAP output
7nvt transcription cryo-EM (2.9 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. RNA polymerase ii core pre-initiation complex with closed promoter DNA in distal position. SNAP output
7nvu transcription cryo-EM (2.5 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. RNA polymerase ii core pre-initiation complex with open promoter DNA. SNAP output
7nvv transcription cryo-EM (2.9 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. Xpb-containing part of tfiih in a post-translocated state (with adp-bef3). SNAP output
7nvw transcription cryo-EM (4.3 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. Tfiih in a pre-translocated state (without adp-bef3). SNAP output
7nvx transcription cryo-EM (3.9 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. Tfiih in a post-translocated state (with adp-bef3). SNAP output
7nvy transcription cryo-EM (7.3 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. RNA polymerase ii pre-initiation complex with closed promoter DNA in proximal position. SNAP output
7nvz transcription cryo-EM (7.2 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. RNA polymerase ii pre-initiation complex with closed promoter DNA in distal position. SNAP output
7nw0 transcription cryo-EM (6.6 Å) Aibara S, Schilbach S, Cramer P (2021) "Structures of mammalian RNA polymerase II pre-initiation complexes." Nature, 594, 124-128. doi: 10.1038/s41586-021-03554-8. RNA polymerase ii pre-initiation complex with open promoter DNA. SNAP output
7nx5 viral protein X-ray (2.5 Å) Bernaudat F, Gustems M, Gunther J, Oliva MF, Buschle A, Gobel C, Pagniez P, Lupo J, Signor L, Muller CW, Morand P, Sattler M, Hammerschmidt W, Petosa C (2022) "Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1." Nucleic Acids Res., 50, 490-511. doi: 10.1093/nar/gkab1183. Crystal structure of the epstein-barr virus protein zebra (bzlf1, zta) bound to a methylated DNA duplex. SNAP output
7nyw DNA binding protein cryo-EM (3.1 Å) Burmann F, Funke LFH, Chin JW, Lowe J (2021) "Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites." Mol.Cell, 81, 4891-4906.e8. doi: 10.1016/j.molcel.2021.10.011. cryo-EM structure of the mukbef-matp-DNA head module. SNAP output
7nyx DNA binding protein cryo-EM (4.6 Å) Burmann F, Funke LFH, Chin JW, Lowe J (2021) "Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites." Mol.Cell, 81, 4891-4906.e8. doi: 10.1016/j.molcel.2021.10.011. cryo-EM structure of the mukbef-matp-DNA monomer (closed conformation). SNAP output
7nyz DNA binding protein cryo-EM (6.5 Å) Burmann F, Funke LFH, Chin JW, Lowe J (2021) "Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites." Mol.Cell, 81, 4891-4906.e8. doi: 10.1016/j.molcel.2021.10.011. cryo-EM structure of the mukbef-matp-DNA monomer (partially open conformation). SNAP output
7nz0 DNA binding protein cryo-EM (6.3 Å) Burmann F, Funke LFH, Chin JW, Lowe J (2021) "Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites." Mol.Cell, 81, 4891-4906.e8. doi: 10.1016/j.molcel.2021.10.011. cryo-EM structure of the mukbef-matp-DNA monomer (open conformation). SNAP output
7o0g viral protein X-ray (3.1 Å) Nowacka M, Nowak E, Czarnocki-Cieciura M, Jackiewicz J, Skowronek K, Szczepanowski RH, Wohrl BM, Nowotny M (2021) "Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase." J.Virol., 95, e0084821. doi: 10.1128/JVI.00848-21. Structure of the foamy viral protease-reverse transcriptase in complex with RNA-DNA hybrid.. SNAP output
7o0h viral protein X-ray (3.09 Å) Nowacka M, Nowak E, Czarnocki-Cieciura M, Jackiewicz J, Skowronek K, Szczepanowski RH, Wohrl BM, Nowotny M (2021) "Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase." J.Virol., 95, e0084821. doi: 10.1128/JVI.00848-21. Structure of the foamy viral protease-reverse transcriptase drh in complex with ds DNA.. SNAP output
7o24 viral protein cryo-EM (4.8 Å) Nowacka M, Nowak E, Czarnocki-Cieciura M, Jackiewicz J, Skowronek K, Szczepanowski RH, Wohrl BM, Nowotny M (2021) "Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase." J.Virol., 95, e0084821. doi: 10.1128/JVI.00848-21. Structure of the foamy viral protease-reverse transcriptase in complex with dsDNA.. SNAP output
7o4i transcription cryo-EM (3.2 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast RNA polymerase ii transcription pre-initiation complex with initial transcription bubble. SNAP output
7o4j transcription cryo-EM (2.9 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast RNA polymerase ii transcription pre-initiation complex (consensus). SNAP output
7o4k transcription cryo-EM (3.6 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast tfiih in the contracted state within the pre-initiation complex. SNAP output
7o4l transcription cryo-EM (3.4 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast tfiih in the expanded state within the pre-initiation complex. SNAP output
7o56 DNA binding protein X-ray (2.6 Å) Agnarelli A, El Omari K, Duman R, Wagner A, Mancini EJ (2021) "Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4." Acta Crystallogr.,Sect.F, 77, 202-207. doi: 10.1107/S2053230X21006506. X-ray structure of interferon regulatory factor 4 DNA binding domain bound to an interferon-stimulated response element solved by phosphorus and sulphur sad methods. SNAP output
7o72 transcription cryo-EM (3.4 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast RNA polymerase ii transcription pre-initiation complex with closed promoter DNA. SNAP output
7o73 transcription cryo-EM (3.4 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast RNA polymerase ii transcription pre-initiation complex with closed distorted promoter DNA. SNAP output
7o75 transcription cryo-EM (3.2 Å) Schilbach S, Aibara S, Dienemann C, Grabbe F, Cramer P (2021) "Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening." Cell, 184, 4064-4072.e28. doi: 10.1016/j.cell.2021.05.012. Yeast RNA polymerase ii transcription pre-initiation complex with open promoter DNA. SNAP output
7oa5 DNA binding protein X-ray (2.378 Å) Roe SM, Pearl LH (1998) "Crystal structure of an octameric RuvA-Holliday junction complex." Molecular Cell, 2, 361-372. Ruva complexed to a holliday junction.. SNAP output
7oar hydrolase X-ray (2.58 Å) Dai YX, Guo HL, Liu NN, Chen WF, Ai X, Li HH, Sun B, Hou XM, Rety S, Xi XG (2022) "Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding." Embo Rep., 23, e53874. doi: 10.15252/embr.202153874. Crystal structure of helicase pif1 from thermus oshimai in complex with parallel g-quadruplex. SNAP output
7ob9 transcription cryo-EM (2.7 Å) Misiaszek AD, Girbig M, Grotsch H, Baudin F, Murciano B, Lafita A, Muller CW (2021) "Cryo-EM structures of human RNA polymerase I." Nat.Struct.Mol.Biol., 28, 997-1008. doi: 10.1038/s41594-021-00693-4. cryo-EM structure of human RNA polymerase i in elongation state. SNAP output
7obb transcription cryo-EM (3.3 Å) Misiaszek AD, Girbig M, Grotsch H, Baudin F, Murciano B, Lafita A, Muller CW (2021) "Cryo-EM structures of human RNA polymerase I." Nat.Struct.Mol.Biol., 28, 997-1008. doi: 10.1038/s41594-021-00693-4. cryo-EM structure of human RNA polymerase i open complex. SNAP output
7obn DNA binding protein X-ray (2.45 Å) Pan J, Lian K, Sarre A, Leiros HS, Williamson A (2021) "Bacteriophage origin of some minimal ATP-dependent DNA ligases: a new structure from Burkholderia pseudomallei with striking similarity to Chlorella virus ligase." Sci Rep, 11, 18693. doi: 10.1038/s41598-021-98155-w. Structural investigations of a new l3 DNA ligase: structure-function analysis. SNAP output
7odf RNA binding protein cryo-EM (2.66 Å) Carabias A, Fuglsang A, Temperini P, Pape T, Sofos N, Stella S, Erlendsson S, Montoya G (2021) "Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3." Nat Commun, 12, 4476. doi: 10.1038/s41467-021-24707-3. Structure of the mini-RNA-guided endonuclease crispr-cas_phi3. SNAP output
7ogs DNA binding protein X-ray (2.37 Å) Agnarelli A, El Omari K, Alt AO, Mancini EJ "X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to interferon-stimulated response element." X-ray structure of interferon regulatory factor 4 DNA binding domain bound to an interferon-stimulated response element. SNAP output
7oh9 transcription cryo-EM (3.0 Å) Wang H, Xiong L, Cramer P (2021) "Structures and implications of TBP-nucleosome complexes." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2108859118. Nucleosome with tbp and tfiia bound at shl -6. SNAP output
7oha transcription cryo-EM (2.9 Å) Wang H, Xiong L, Cramer P (2021) "Structures and implications of TBP-nucleosome complexes." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2108859118. Nucleosome with tbp and tfiia bound at shl +2. SNAP output
7ohb transcription cryo-EM (3.4 Å) Wang H, Xiong L, Cramer P (2021) "Structures and implications of TBP-nucleosome complexes." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2108859118. Tbp-nucleosome complex. SNAP output
7ohc nuclear protein cryo-EM (2.5 Å) Wang H, Xiong L, Cramer P (2021) "Structures and implications of TBP-nucleosome complexes." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2108859118. cryo-EM structure of nucleosome core particle composed of the widom 601 DNA sequence. SNAP output
7okx transcription cryo-EM (3.3 Å) Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P (2021) "Allosteric transcription stimulation by RNA polymerase II super elongation complex." Mol.Cell, 81, 3386-3399.e10. doi: 10.1016/j.molcel.2021.06.019. Structure of active transcription elongation complex pol ii-dsif (spt5-kow5)-ell2-eaf1 (composite structure). SNAP output
7oky transcription cryo-EM (4.14 Å) Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P (2021) "Allosteric transcription stimulation by RNA polymerase II super elongation complex." Mol.Cell, 81, 3386-3399.e10. doi: 10.1016/j.molcel.2021.06.019. Structure of active transcription elongation complex pol ii-dsif-ell2-eaf1(composite structure). SNAP output
7ol0 transcription cryo-EM (3.0 Å) Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P (2021) "Allosteric transcription stimulation by RNA polymerase II super elongation complex." Mol.Cell, 81, 3386-3399.e10. doi: 10.1016/j.molcel.2021.06.019. Structure of active transcription elongation complex pol ii-dsif (spt5-kow5). SNAP output
7ol9 DNA binding protein X-ray (2.9 Å) Sukhoverkov KV, Jalal ASB, Ault JR, Sobott F, Lawson DM, Le TBK (2023) "The CTP-binding domain is disengaged from the DNA-binding domain in a cocrystal structure of Bacillus subtilis Noc-DNA complex." J.Biol.Chem., 299, 103063. doi: 10.1016/j.jbc.2023.103063. Crystal structure of c-terminally truncated bacillus subtilis nucleoid occlusion protein (noc) complexed to the noc-binding site (nbs). SNAP output
7om3 replication X-ray (1.92 Å) Kropp HM, Ludmann S, Diederichs K, Betz K, Marx A (2021) "Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase." Chembiochem, 22, 3060-3066. doi: 10.1002/cbic.202100306. Crystal structure of kod DNA polymerase in a binary complex with hypoxanthine containing template. SNAP output
7omb replication X-ray (2.01 Å) Kropp HM, Ludmann S, Diederichs K, Betz K, Marx A (2021) "Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase." Chembiochem, 22, 3060-3066. doi: 10.1002/cbic.202100306. Crystal structure of kod DNA polymerase in a ternary complex with a p-t duplex containing an extended 5' single stranded template overhang. SNAP output
7omg replication X-ray (2.1 Å) Kropp HM, Ludmann S, Diederichs K, Betz K, Marx A (2021) "Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase." Chembiochem, 22, 3060-3066. doi: 10.1002/cbic.202100306. Crystal structure of kod DNA polymerase in a ternary complex with an uracil containing template. SNAP output
7on1 cell cycle cryo-EM (3.35 Å) Yan K, Yang J, Zhang Z, Barford D "Cenp-A nucleosome in complex with Cenp-C." Cenp-a nucleosome in complex with cenp-c. SNAP output
7oo3 transcription cryo-EM (2.8 Å) Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P (2021) "Structural basis of human transcription-DNA repair coupling." Nature, 598, 368-372. doi: 10.1038/s41586-021-03906-4. Pol ii-csb-csa-ddb1-uvssa (structure1). SNAP output
7oob transcription cryo-EM (2.7 Å) Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P (2021) "Structural basis of human transcription-DNA repair coupling." Nature, 598, 368-372. doi: 10.1038/s41586-021-03906-4. Pol ii-csb-csa-ddb1-uvssa-adpbef3 (structure2). SNAP output
7oop transcription cryo-EM (2.9 Å) Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P (2021) "Structural basis of human transcription-DNA repair coupling." Nature, 598, 368-372. doi: 10.1038/s41586-021-03906-4. Pol ii-csb-csa-ddb1-uvssa-paf-spt6 (structure 3). SNAP output
7oot DNA binding protein X-ray (2.25 Å) Agnarelli A, El Omari K, Alt AO, Mancini EJ "X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to interferon-stimulated response element." X-ray structure of interferon regulatory factor 4 DNA binding domain bound to an interferon-stimulated response element. SNAP output
7opc transcription cryo-EM (3.0 Å) Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P (2021) "Structural basis of human transcription-DNA repair coupling." Nature, 598, 368-372. doi: 10.1038/s41586-021-03906-4. Pol ii-csb-crl4csa-uvssa-spt6-paf (structure 4). SNAP output
7opd transcription cryo-EM (3.0 Å) Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P (2021) "Structural basis of human transcription-DNA repair coupling." Nature, 598, 368-372. doi: 10.1038/s41586-021-03906-4. Pol ii-csb-crl4csa-uvssa-spt6-paf (structure 5). SNAP output
7ot6 transferase X-ray (3.2 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-282. SNAP output
7ota transferase X-ray (3.0 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-230. SNAP output
7otj hydrolase X-ray (2.58 Å) Lu KY, Xin BG, Zhang T, Liu NN, Li D, Rety S, Xi XG (2021) "Structural study of the function of Candida Albicans Pif1." Biochem.Biophys.Res.Commun., 567, 190-194. doi: 10.1016/j.bbrc.2021.06.050. Crystal structure of pif1 helicase from candida albicans. SNAP output
7otk transferase X-ray (2.95 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-233. SNAP output
7otn transferase X-ray (3.4 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-247. SNAP output
7otq DNA binding protein cryo-EM (4.8 Å) Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton S, Deindl S, Workman JL (2021) "Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome." Elife, 10. doi: 10.7554/eLife.71420. cryo-EM structure of alc1-chd1l bound to a parylated nucleosome. SNAP output
7otx transferase X-ray (3.45 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-257. SNAP output
7otz transferase X-ray (3.1 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-259. SNAP output
7oue hydrolase X-ray (2.04 Å) Franck C, Stephane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C (2022) "Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing." Nucleic Acids Res., 50, 11072-11092. doi: 10.1093/nar/gkac932. Crystal structure of a trapped pab-agog-single-standed DNA covalent intermediate. SNAP output
7ouf viral protein cryo-EM (3.0 Å) Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN (2021) "Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures." Nat Commun, 12, 4996. doi: 10.1038/s41467-021-25284-1. Structure of the stlv intasome:b56 complex bound to the strand-transfer inhibitor xz450. SNAP output
7oug viral protein cryo-EM (3.1 Å) Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN (2021) "Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures." Nat Commun, 12, 4996. doi: 10.1038/s41467-021-25284-1. Stlv-1 intasome:b56 in complex with the strand-transfer inhibitor raltegravir. SNAP output
7ouh viral protein cryo-EM (3.5 Å) Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke Jr TR, Cherepanov P, Maertens GN (2021) "Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures." Nat Commun, 12, 4996. doi: 10.1038/s41467-021-25284-1. Structure of the stlv intasome:b56 complex bound to the strand-transfer inhibitor bictegravir. SNAP output
7out transferase X-ray (3.2 Å) Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S (2021) "Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design." Eur.J.Med.Chem., 225, 113785. doi: 10.1016/j.ejmech.2021.113785. Hiv-1 reverse transcriptase complex with DNA and inhibitor rmc-264. SNAP output
7owf transferase X-ray (1.91 Å) Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG (2022) "Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases." J.Am.Chem.Soc., 144, 10556-10569. doi: 10.1021/jacs.2c03454. Klentaq DNA polymerase in a ternary complex with primer-template and the fluorescent nucleotide analog bfdutp. SNAP output
7ox7 hydrolase X-ray (2.6 Å) Donohoue PD, Pacesa M, Lau E, Vidal B, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Gibson J, Kohrs B, Baek K, Owen ALG, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P (2021) "Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells." Mol.Cell, 81, 3637-3649.e5. doi: 10.1016/j.molcel.2021.07.035. Target-bound spcas9 complex with trac chimeric RNA-DNA guide. SNAP output
7ox8 hydrolase X-ray (2.75 Å) Donohoue PD, Pacesa M, Lau E, Vidal B, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Gibson J, Kohrs B, Baek K, Owen ALG, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P (2021) "Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells." Mol.Cell, 81, 3637-3649.e5. doi: 10.1016/j.molcel.2021.07.035. Target-bound spcas9 complex with trac full RNA guide. SNAP output
7ox9 hydrolase X-ray (2.45 Å) Donohoue PD, Pacesa M, Lau E, Vidal B, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Gibson J, Kohrs B, Baek K, Owen ALG, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P (2021) "Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells." Mol.Cell, 81, 3637-3649.e5. doi: 10.1016/j.molcel.2021.07.035. Target-bound spcas9 complex with aavs1 all-RNA guide. SNAP output
7oxa hydrolase X-ray (2.15 Å) Donohoue PD, Pacesa M, Lau E, Vidal B, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Gibson J, Kohrs B, Baek K, Owen ALG, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P (2021) "Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells." Mol.Cell, 81, 3637-3649.e5. doi: 10.1016/j.molcel.2021.07.035. Target-bound spcas9 complex with aavs1 chimeric RNA-DNA guide. SNAP output
7oxq transferase X-ray (3.3 Å) Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K (2021) "Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening." Nat Commun, 12, 7127. doi: 10.1038/s41467-021-27409-y. Crystal structure of hiv-1 reverse transcriptase with a double stranded DNA in complex with fragment 048 at the transient p-pocket.. SNAP output
7oy7 hydrolase X-ray (1.7 Å) Franck C, Stephane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C (2022) "Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing." Nucleic Acids Res., 50, 11072-11092. doi: 10.1093/nar/gkac932. Crystal structure of a trapped pab-agog-double-standed DNA covalent intermediate (DNA containing cytosine opposite to lesion). SNAP output
7oz2 transferase X-ray (2.85 Å) Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K (2021) "Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening." Nat Commun, 12, 7127. doi: 10.1038/s41467-021-27409-y. Crystal structure of hiv-1 reverse transcriptase with a double stranded DNA showing a transient p-pocket. SNAP output
7oz3 DNA binding protein cryo-EM (4.46 Å) Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwarzer J, Hopfner KP, Witte G (2021) "BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture." Nucleic Acids Res., 49, 10166-10177. doi: 10.1093/nar/gkab736. S. agalactiae busr in complex with its busa-promotor DNA. SNAP output
7oz5 transferase X-ray (3.37 Å) Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K (2021) "Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening." Nat Commun, 12, 7127. doi: 10.1038/s41467-021-27409-y. Crystal structure of hiv-1 reverse transcriptase with a double stranded DNA in complex with fragment 166 at the transient p-pocket.. SNAP output
7ozw transferase cryo-EM (3.38 Å) Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K (2021) "Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening." Nat Commun, 12, 7127. doi: 10.1038/s41467-021-27409-y. cryo-EM structure of hiv-1 reverse transcriptase with a DNA aptamer in complex with fragment 166 at the transient p-pocket. SNAP output
7p0w hydrolase X-ray (1.12 Å) Franck C, Stephane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C (2022) "Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing." Nucleic Acids Res., 50, 11072-11092. doi: 10.1093/nar/gkac932. Crystal structure of a trapped pab-agog-double-standed DNA covalent intermediate (DNA containing thymine opposite to lesion). SNAP output
7p15 transferase cryo-EM (3.58 Å) Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K (2021) "Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening." Nat Commun, 12, 7127. doi: 10.1038/s41467-021-27409-y. cryo-EM structure of hiv-1 reverse transcriptase with a DNA aptamer in complex with fragment f04 at the transient p-pocket. SNAP output
7p3f DNA binding protein cryo-EM (3.31 Å) Rozman Grinberg I, Martinez-Carranza M, Bimai O, Nouairia G, Shahid S, Lundin D, Logan DT, Sjoberg BM, Stenmark P (2022) "A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases." Nat Commun, 13, 2700. doi: 10.1038/s41467-022-30328-1. Streptomyces coelicolor datp-atp-loaded nrdr in complex with its cognate DNA. SNAP output
7p8l hydrolase X-ray (1.25 Å) Franck C, Stephane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C (2022) "Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing." Nucleic Acids Res., 50, 11072-11092. doi: 10.1093/nar/gkac932. Crystal structure of pyrococcus abyssi 8-oxoguanine DNA glycosylase (pabagog) in complex with dsDNA containing cytosine opposite to 8-oxog. SNAP output
7p8v DNA binding protein cryo-EM (3.6 Å) Borsellini A, Lebbink JHG, Lamers MH (2022) "MutL binds to 3' resected DNA ends and blocks DNA polymerase access." Nucleic Acids Res., 50, 6224-6234. doi: 10.1093/nar/gkac432. The structure of e. coli mutl bound to a 3' resected DNA end. SNAP output
7p9j transferase X-ray (1.9 Å) Li AWH, Zabrady K, Bainbridge LJ, Zabrady M, Naseem-Khan S, Berger MB, Kolesar P, Cisneros GA, Doherty AJ (2022) "Molecular basis for the initiation of DNA primer synthesis." Nature, 605, 767-773. doi: 10.1038/s41586-022-04695-0. Prim-pol domain of crispr-associated prim-pol (capp) from marinitoga sp. 1137 - primer initiation complex. SNAP output
7p9z hydrolase X-ray (1.33 Å) Franck C, Stephane G, Julien C, Virginie G, Martine G, Norbert G, Fabrice C, Didier F, Josef SM, Bertrand C (2022) "Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing." Nucleic Acids Res., 50, 11072-11092. doi: 10.1093/nar/gkac932. Crystal structure of a trapped pab-agog-double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion). SNAP output
7pbl hydrolase cryo-EM (3.2 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s1 [t2 dataset]. SNAP output
7pbm hydrolase cryo-EM (3.2 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s2 [t2 dataset]. SNAP output
7pbn hydrolase cryo-EM (3.2 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s3 [t2 dataset]. SNAP output
7pbo hydrolase cryo-EM (2.9 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s4 [t2 dataset]. SNAP output
7pbp hydrolase cryo-EM (3.2 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s5 [t2 dataset]. SNAP output
7pbq hydrolase cryo-EM (3.1 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s0+a [t2 dataset]. SNAP output
7pbr hydrolase cryo-EM (3.0 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s0-a [t2 dataset]. SNAP output
7pbs hydrolase cryo-EM (3.3 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s0+a [t1 dataset]. SNAP output
7pbt hydrolase cryo-EM (3.3 Å) Wald J, Fahrenkamp D, Goessweiner-Mohr N, Lugmayr W, Ciccarelli L, Vesper O, Marlovits TC (2022) "Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration." Nature, 609, 630-639. doi: 10.1038/s41586-022-05121-1. Ruvab branch migration motor complexed to the holliday junction - ruvb aaa+ state s1 [t1 dataset]. SNAP output
7pds replication cryo-EM (3.14 Å) Qiao C, Debiasi-Anders G, Mir-Sanchis I (2022) "Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility." Nucleic Acids Res., 50, 8349-8362. doi: 10.1093/nar/gkac625. The structure of prirep1 with dsDNA. SNAP output
7pel viral protein cryo-EM (3.34 Å) Barski MS, Minnell JJ, Hodakova Z, Pye VE, Nans A, Cherepanov P, Maertens GN (2020) "Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56gamma." Nat Commun, 11, 5043. doi: 10.1038/s41467-020-18874-y. Cryoem structure of simian t-cell lymphotropic virus intasome in complex with pp2a regulatory subunit b56 gamma. SNAP output
7pet DNA binding protein cryo-EM (9.5 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. The 4x177 nucleosome array containing h1. SNAP output
7peu DNA binding protein cryo-EM (7.2 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Trinucleosome of the 4x177 nucleosome array containing h1. SNAP output
7pev DNA binding protein cryo-EM (6.0 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome stack of the 4x177 nucleosome array containing h1. SNAP output
7pew DNA binding protein cryo-EM (4.6 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 1 of the 4x177 nucleosome array containing h1. SNAP output
7pex DNA binding protein cryo-EM (5.1 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 2 of the 4x177 nucleosome array containing h1. SNAP output
7pey DNA binding protein cryo-EM (4.5 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 3 of the 4x177 nucleosome array containing h1. SNAP output
7pez DNA binding protein cryo-EM (7.9 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 4 of the 4x177 nucleosome array containing h1. SNAP output
7pf0 DNA binding protein cryo-EM (11.0 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Trinucleosome of the 4x177 nucleosome array containing h1. SNAP output
7pf2 DNA binding protein cryo-EM (5.1 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome stack of the 4x187 nucleosome array containing h1. SNAP output
7pf3 DNA binding protein cryo-EM (4.0 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 4 of the 4x187 nucleosome array containing h1. SNAP output
7pf4 DNA binding protein cryo-EM (4.0 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 3 of the 4x187 nucleosome array containing h1. SNAP output
7pf5 DNA binding protein cryo-EM (3.8 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 2 of the 4x187 nucleosome array containing h1. SNAP output
7pf6 DNA binding protein cryo-EM (4.0 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 1 of the 4x187 nucleosome array containing h1. SNAP output
7pfa DNA binding protein cryo-EM (9.7 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Trinucleosome of the 4x197 nucleosome array containing h1. SNAP output
7pfc DNA binding protein cryo-EM (6.4 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome stack of the 4x197 nucleosome array containing h1. SNAP output
7pfd DNA binding protein cryo-EM (4.4 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 1 of the 4x197 nucleosome array containing h1. SNAP output
7pfe DNA binding protein cryo-EM (4.4 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 2 of the 4x197 nucleosome array containing h1. SNAP output
7pff DNA binding protein cryo-EM (4.3 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 3 of the 4x197 nucleosome array containing h1. SNAP output
7pft DNA binding protein cryo-EM (9.8 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Trinucleosome of the 4x207 nucleosome array containing h1. SNAP output
7pfu DNA binding protein cryo-EM (5.0 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome stack of the 4x207 nucleosome array containing h1. SNAP output
7pfv DNA binding protein cryo-EM (4.4 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 1 of the 4x207 nucleosome array containing h1. SNAP output
7pfw DNA binding protein cryo-EM (5.2 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 2 of the 4x207 nucleosome array containing h1. SNAP output
7pfx DNA binding protein cryo-EM (4.3 Å) Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P (2022) "Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory." Nat.Struct.Mol.Biol., 29, 493-501. doi: 10.1038/s41594-022-00768-w. Nucleosome 3 of the 4x207 nucleosome array containing h1. SNAP output
7pii cell cycle cryo-EM (2.68 Å) Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D (2022) "Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome." Science, 376, 844-852. doi: 10.1126/science.abn3810. Structure of the human ccan cenp-a alpha-satellite complex. SNAP output
7pik DNA binding protein cryo-EM (2.68 Å) Kaczmarska Z, Czarnocki-Cieciura M, Gorecka-Minakowska KM, Wingo RJ, Jackiewicz J, Zajko W, Poznanski JT, Rawski M, Grant T, Peters JE, Nowotny M (2022) "Structural basis of transposon end recognition explains central features of Tn7 transposition systems." Mol.Cell, 82, 2618. doi: 10.1016/j.molcel.2022.05.005. cryo-EM structure of e. coli tnsb in complex with right end fragment of tn7 transposon. SNAP output
7pla DNA binding protein cryo-EM (3.04 Å) Querques I, Schmitz M, Oberli S, Chanez C, Jinek M (2021) "Target site selection and remodelling by type V CRISPR-transposon systems." Nature, 599, 497-502. doi: 10.1038/s41586-021-04030-z. cryo-EM structure of shcas12k in complex with a sgrna and a dsDNA target. SNAP output
7plh DNA binding protein cryo-EM (3.57 Å) Querques I, Schmitz M, Oberli S, Chanez C, Jinek M (2021) "Target site selection and remodelling by type V CRISPR-transposon systems." Nature, 599, 497-502. doi: 10.1038/s41586-021-04030-z. Scytonema hofmannii tnsc bound to amppnp and DNA. SNAP output
7pli RNA binding protein X-ray (2.5 Å) Wurm JP (2023) "Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA." Rna, 29, 1339-1354. doi: 10.1261/rna.079582.123. Dead-box helicase dbpa bound to single stranded RNA and adp-bef3. SNAP output
7prv signaling protein X-ray (2.7 Å) Postel S, Wissler L, Johansson CA, Gunnarsson A, Gordon E, Collins B, Castaldo M, Kohler C, Oling D, Johansson P, Froderberg Roth L, Beinsteiner B, Dainty I, Delaney S, Klaholz BP, Billas IML, Edman K (2023) "Quaternary glucocorticoid receptor structure highlights allosteric interdomain communication." Nat.Struct.Mol.Biol., 30, 286-295. doi: 10.1038/s41594-022-00914-4. The glucocorticoid receptor in complex with fluticasone furoate, a pgc1a coactivator fragment and sgk 23bp. SNAP output
7prw signaling protein X-ray (2.502 Å) Postel S, Wissler L, Johansson CA, Gunnarsson A, Gordon E, Collins B, Castaldo M, Kohler C, Oling D, Johansson P, Froderberg Roth L, Beinsteiner B, Dainty I, Delaney S, Klaholz BP, Billas IML, Edman K (2023) "Quaternary glucocorticoid receptor structure highlights allosteric interdomain communication." Nat.Struct.Mol.Biol., 30, 286-295. doi: 10.1038/s41594-022-00914-4. The glucocorticoid receptor in complex with velsecorat, a pgc1a coactivator fragment and sgk 23bp. SNAP output
7psx DNA binding protein X-ray (2.0 Å) Morgunova E, Popov A, Yin Y, Taipale J "Structure of HOXB13 bound to hydroxymethylated DNA." Structure of hoxb13 bound to hydroxymethylated DNA. SNAP output
7pu7 replication cryo-EM (2.9 Å) Chengalroyen MD, Mason MK, Borsellini A, Tassoni R, Abrahams GL, Lynch S, Ahn YM, Ambler J, Young K, Crowley BM, Olsen DB, Warner DF, Barry Iii CE, Boshoff HIM, Lamers MH, Mizrahi V (2022) "DNA-Dependent Binding of Nargenicin to DnaE1 Inhibits Replication in Mycobacterium tuberculosis." Acs Infect Dis., 8, 612-625. doi: 10.1021/acsinfecdis.1c00643. DNA polymerase from m. tuberculosis. SNAP output
7py0 transcription cryo-EM (4.5 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusg (nusg-ec in more-swiveled conformation). SNAP output
7py1 transcription cryo-EM (3.8 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusg (the consensus nusg-ec). SNAP output
7py3 transcription cryo-EM (3.8 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusa (the consensus nusa-ec). SNAP output
7py5 transcription cryo-EM (3.9 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusa and nusg (the consensus nusa-nusg-ec). SNAP output
7py6 transcription cryo-EM (4.1 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusa and nusg (nusa and nusg elongation complex in less-swiveled conformation). SNAP output
7py7 transcription cryo-EM (4.1 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusa and nusg (nusa and nusg elongation complex in more-swiveled conformation). SNAP output
7py8 transcription cryo-EM (3.8 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusg (nusg-ec in less-swiveled conformation). SNAP output
7pyj transcription cryo-EM (4.2 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusa (nusa elongation complex in less-swiveled conformation). SNAP output
7pyk transcription cryo-EM (4.1 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. Cryoem structure of e.coli RNA polymerase elongation complex bound to nusa (nusa elongation complex in more-swiveled conformation). SNAP output
7pza signaling protein X-ray (2.72 Å) Werel L, Farmani N, Krol E, Serrania J, Essen LO, Becker A (2023) "Structural Basis of Dual Specificity of Sinorhizobium meliloti Clr, a cAMP and cGMP Receptor Protein." Mbio, 14, e0302822. doi: 10.1128/mbio.03028-22. Structure of the clr-camp-DNA complex. SNAP output
7pzb signaling protein X-ray (3.12 Å) Werel L, Farmani N, Krol E, Serrania J, Essen LO, Becker A (2023) "Structural Basis of Dual Specificity of Sinorhizobium meliloti Clr, a cAMP and cGMP Receptor Protein." Mbio, 14, e0302822. doi: 10.1128/mbio.03028-22. Structure of the clr-camp-DNA complex. SNAP output
7q0j transcription cryo-EM (4.3 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. RNA polymerase elongation complex in more-swiveled conformation. SNAP output
7q0k transcription cryo-EM (4.0 Å) Zhu C, Guo X, Dumas P, Takacs M, Abdelkareem M, Vanden Broeck A, Saint-Andre C, Papai G, Crucifix C, Ortiz J, Weixlbaumer A (2022) "Transcription factors modulate RNA polymerase conformational equilibrium." Nat Commun, 13, 1546. doi: 10.1038/s41467-022-29148-0. RNA polymerase elongation complex in less-swiveled conformation. SNAP output
7q0n DNA binding protein X-ray (2.5 Å) Gallego Del Sol F, Quiles-Puchalt N, Brady A, Penades JR, Marina A (2022) "Insights into the mechanism of action of the arbitrium communication system in SPbeta phages." Nat Commun, 13, 3627. doi: 10.1038/s41467-022-31144-3. Arbitrium receptor from katmira phage. SNAP output
7q2x cell cycle cryo-EM (3.0 Å) Lee BG, Rhodes J, Lowe J (2022) "Clamping of DNA shuts the condensin neck gate." Proc.Natl.Acad.Sci.USA, 119, e2120006119. doi: 10.1073/pnas.2120006119. cryo-EM structure of clamped s.cerevisiae condensin-DNA complex (form i). SNAP output
7q2y cell cycle cryo-EM (3.0 Å) Lee BG, Rhodes J, Lowe J (2022) "Clamping of DNA shuts the condensin neck gate." Proc.Natl.Acad.Sci.USA, 119, e2120006119. doi: 10.1073/pnas.2120006119. cryo-EM structure of clamped s.cerevisiae condensin-DNA complex (form ii). SNAP output
7q2z cell cycle cryo-EM (3.2 Å) Lee BG, Rhodes J, Lowe J (2022) "Clamping of DNA shuts the condensin neck gate." Proc.Natl.Acad.Sci.USA, 119, e2120006119. doi: 10.1073/pnas.2120006119. cryo-EM structure of s.cerevisiae condensin ycg1-brn1-DNA complex. SNAP output
7q3o transcription X-ray (2.78 Å) Morgunova E, Yin Y, Popov A, Taipale J "Structure of CDX1 bound to hydroxymethylated DNA." Structure of cdx1 bound to hydroxymethylated DNA. SNAP output
7q4n transcription X-ray (3.2 Å) Morgunova E, Yin Y, Popov A, Taipale J "transcription factor CDX2 bound to hydroxymethylated DNA." Transcription factor cdx2 bound to hydroxymethylated DNA. SNAP output
7q5b DNA binding protein cryo-EM (3.98 Å) Abascal-Palacios G, Jochem L, Pla-Prats C, Beuron F, Vannini A (2021) "Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes." Nat Commun, 12, 6992. doi: 10.1038/s41467-021-27338-w. cryo-EM structure of ty3 retrotransposon targeting a tfiiib-bound trna gene. SNAP output
7q8a transcription X-ray (2.05 Å) Ni X, Joerger AC, Chaikuad A, Knapp S, Structural Genomics Consortium (SGC) "Crystal structure of tandem domain RRM1-2 of FIR bound to FUSE ssDNA fragment." Crystal structure of tandem domain rrm1-2 of fubp-interacting repressor (fir) bound to fuse ssDNA fragment. SNAP output
7q94 transcription X-ray (4.3 Å) Minazzato G, Gasparrini M, Heroux A, Sernova NV, Rodionov DA, Cianci M, Sorci L, Raffaelli N (2022) "Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis." J.Struct.Biol., 214, 107917. doi: 10.1016/j.jsb.2022.107917. Crystal structure of agrobacterium tumefaciens nadq, DNA complex.. SNAP output
7qaz transferase X-ray (2.11 Å) Li AWH, Zabrady K, Bainbridge LJ, Zabrady M, Naseem-Khan S, Berger MB, Kolesar P, Cisneros GA, Doherty AJ (2022) "Molecular basis for the initiation of DNA primer synthesis." Nature, 605, 767-773. doi: 10.1038/s41586-022-04695-0. Prim-pol domain of crispr-associated prim-pol (capp) from marinitoga sp. 1137 - primer initiation complex. SNAP output
7qd4 recombination cryo-EM (2.9 Å) Shkumatov AV, Aryanpour N, Oger CA, Goossens G, Hallet BF, Efremov RG (2022) "Structural insight into Tn3 family transposition mechanism." Nat Commun, 13, 6155. doi: 10.1038/s41467-022-33871-z. cryo-EM structure of tn4430 tnpa transposase from tn3 family in complex with 100 bp long transposon end DNA. SNAP output
7qd5 recombination cryo-EM (3.1 Å) Shkumatov AV, Aryanpour N, Oger CA, Goossens G, Hallet BF, Efremov RG (2022) "Structural insight into Tn3 family transposition mechanism." Nat Commun, 13, 6155. doi: 10.1038/s41467-022-33871-z. cryo-EM structure of tn4430 tnpa transposase from tn3 family in complex with 48 bp long transposon end DNA. SNAP output
7qd6 recombination cryo-EM (3.0 Å) Shkumatov AV, Aryanpour N, Oger CA, Goossens G, Hallet BF, Efremov RG (2022) "Structural insight into Tn3 family transposition mechanism." Nat Commun, 13, 6155. doi: 10.1038/s41467-022-33871-z. cryo-EM structure of tn4430 tnpa transposase from tn3 family in complex with strand-transfer like DNA product. SNAP output
7qen DNA binding protein cryo-EM (3.46 Å) Shaltiel IA, Datta S, Lecomte L, Hassler M, Kschonsak M, Bravo S, Stober C, Ormanns J, Eustermann S, Haering CH (2022) "A hold-and-feed mechanism drives directional DNA loop extrusion by condensin." Science, 376, 1087-1094. doi: 10.1126/science.abm4012. S.c. condensin core in DNA- and atp-bound state. SNAP output
7qfw DNA binding protein cryo-EM (3.86 Å) Shaltiel IA, Datta S, Lecomte L, Hassler M, Kschonsak M, Bravo S, Stober C, Ormanns J, Eustermann S, Haering CH (2022) "A hold-and-feed mechanism drives directional DNA loop extrusion by condensin." Science, 376, 1087-1094. doi: 10.1126/science.abm4012. S.c. condensin peripheral ycg1 subcomplex bound to DNA. SNAP output
7qnz replication cryo-EM (4.58 Å) Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Creuhet R, Hamdan SM, De Biasio A (2022) "Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing." Nat Commun, 13, 7833. doi: 10.1038/s41467-022-35475-z. Human lig1-DNA-pcna complex reconstituted in absence of atp. SNAP output
7qo1 replication cryo-EM (4.4 Å) Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Creuhet R, Hamdan SM, De Biasio A (2022) "Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing." Nat Commun, 13, 7833. doi: 10.1038/s41467-022-35475-z. Complex of DNA ligase i and fen1 on pcna and DNA. SNAP output
7qqd DNA binding protein X-ray (2.7 Å) Lapi M, Chaves-Sanjuan A, Gourlay LJ, Tiberi M, Polentarutti M, Demitri N, Bais G, Nardini M "Nuclear factor one X - NFIX in P41212." Nuclear factor one x - nfix in p21. SNAP output
7qqo hydrolase X-ray (3.0 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to aavs1 off-target1 DNA substrate. SNAP output
7qqp hydrolase X-ray (2.6 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to aavs1 off-target3 DNA substrate. SNAP output
7qqq hydrolase X-ray (2.65 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to aavs1 off-target4 DNA substrate. SNAP output
7qqr hydrolase X-ray (2.75 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to aavs1 off-target5 DNA substrate. SNAP output
7qqs hydrolase X-ray (2.4 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf on-target DNA substrate. SNAP output
7qqt hydrolase X-ray (2.5 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target1 DNA substrate. SNAP output
7qqu hydrolase X-ray (2.45 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target2 DNA substrate. SNAP output
7qqv hydrolase X-ray (2.25 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target3 DNA substrate. SNAP output
7qqw hydrolase X-ray (3.1 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target4 DNA substrate. SNAP output
7qqx hydrolase X-ray (2.4 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target5 DNA substrate. SNAP output
7qqz hydrolase X-ray (2.25 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target7 DNA substrate. SNAP output
7qr0 hydrolase X-ray (2.3 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to trac off-target1 DNA substrate. SNAP output
7qr1 hydrolase X-ray (2.6 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to trac off-target2 DNA substrate. SNAP output
7qr5 hydrolase X-ray (3.3 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to fancf off-target6 DNA substrate. SNAP output
7qr7 hydrolase X-ray (3.0 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to aavs1 off-target2 DNA substrate. SNAP output
7qr8 hydrolase X-ray (2.75 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to ptprc off-target1 DNA substrate. SNAP output
7qv9 transcription cryo-EM (3.5 Å) Ye F, Gao F, Liu X, Buck M, Zhang X (2022) "Mechanisms of DNA opening revealed in AAA+ transcription complex structures." Sci Adv, 8, eadd3479. doi: 10.1126/sciadv.add3479. Cryoem structure of bacterial transcription intermediate complex mediated by activator pspf. SNAP output
7qw5 transferase X-ray (2.3 Å) Mitsikas DA, Kouyianou K, Kotsifaki D, Providaki M, Bouriotis V, Glykos NM, Kokkinidis M "Structure of M.BseCI DNA methyltransferase from Geobacillus stearothermophilus." Adenine-specific DNA methyltransferase m.bseci complexed with adohcy and cognate unmethylated DNA duplex. SNAP output
7qw6 transferase X-ray (2.4 Å) Mitsikas DA, Kouyianou K, Kotsifaki D, Providaki M, Bouriotis V, Glykos NM, Kokkinidis M "Structure of M.BseCI DNA methyltransferase from Geobacillus stearothermophilus." Adenine-specific DNA methyltransferase m.bseci complexed with adohcy and cognate hemimethylated DNA duplex. SNAP output
7qw7 transferase X-ray (2.6 Å) Mitsikas DA, Kouyianou K, Kotsifaki D, Providaki M, Bouriotis V, Glykos NM, Kokkinidis M "Structure of M.BseCI DNA methyltransferase from Geobacillus stearothermophilus." Adenine-specific DNA methyltransferase m.bseci complexed with adohcy and cognate fully methylated DNA duplex. SNAP output
7qwp transcription cryo-EM (3.4 Å) Ye F, Gao F, Liu X, Buck M, Zhang X (2022) "Mechanisms of DNA opening revealed in AAA+ transcription complex structures." Sci Adv, 8, eadd3479. doi: 10.1126/sciadv.add3479. Cryoem structure of bacterial transcription close complex (rpc). SNAP output
7qxa RNA binding protein cryo-EM (3.2 Å) Sekne Z, Ghanim GE, van Roon AM, Nguyen THD (2022) "Structural basis of human telomerase recruitment by TPP1-POT1." Science, 375, 1173-1176. doi: 10.1126/science.abn6840. cryo-EM map of human telomerase-DNA-tpp1 complex (sharpened). SNAP output
7qxb RNA binding protein cryo-EM (3.9 Å) Sekne Z, Ghanim GE, van Roon AM, Nguyen THD (2022) "Structural basis of human telomerase recruitment by TPP1-POT1." Science, 375, 1173-1176. doi: 10.1126/science.abn6840. cryo-EM map of human telomerase-DNA-tpp1-pot1 complex (sharpened map). SNAP output
7qxi transcription cryo-EM (3.4 Å) Ye F, Gao F, Liu X, Buck M, Zhang X (2022) "Mechanisms of DNA opening revealed in AAA+ transcription complex structures." Sci Adv, 8, eadd3479. doi: 10.1126/sciadv.add3479. cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex. SNAP output
7qxs RNA binding protein cryo-EM (3.9 Å) Sekne Z, Ghanim GE, van Roon AM, Nguyen THD (2022) "Structural basis of human telomerase recruitment by TPP1-POT1." Science, 375, 1173-1176. doi: 10.1126/science.abn6840. cryo-EM structure of human telomerase-DNA-tpp1-pot1 complex (with pot1 side chains). SNAP output
7r06 antiviral protein cryo-EM (2.27 Å) Figiel M, Gapinska M, Czarnocki-Cieciura M, Zajko W, Sroka M, Skowronek K, Nowotny M (2022) "Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases." Nucleic Acids Res., 50, 10026-10040. doi: 10.1093/nar/gkac772. Abortive infection DNA polymerase abik from lactococcus lactis. SNAP output
7r07 antiviral protein X-ray (3.1 Å) Figiel M, Gapinska M, Czarnocki-Cieciura M, Zajko W, Sroka M, Skowronek K, Nowotny M (2022) "Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases." Nucleic Acids Res., 50, 10026-10040. doi: 10.1093/nar/gkac772. Abortive infection DNA polymerase abik from lactococcus lactis. SNAP output
7r3x DNA binding protein X-ray (2.46 Å) Barbari SR, Beach AK, Markgren JG, Parkash V, Moore EA, Johansson E, Shcherbakova PV (2022) "Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels." Nucleic Acids Res., 50, 8023-8040. doi: 10.1093/nar/gkac602. The crystal structure of the l439v variant of pol2core in complex with DNA and an incoming nucleotide. SNAP output
7r3y DNA binding protein X-ray (2.6 Å) Barbari SR, Beach AK, Markgren JG, Parkash V, Moore EA, Johansson E, Shcherbakova PV (2022) "Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ε variants at low dNTP levels." Nucleic Acids Res., 50, 8023-8040. doi: 10.1093/nar/gkac602. The crystal structure of the v426l variant of pol2core in complex with DNA and an incoming nucleotide. SNAP output
7r5r cell cycle cryo-EM (2.44 Å) Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D (2022) "Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome." Science, 376, 844-852. doi: 10.1126/science.abn3810. Structure of the human ccan cenp-a alpha-satellite complex. SNAP output
7r5s cell cycle cryo-EM (2.83 Å) Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D (2022) "Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome." Science, 376, 844-852. doi: 10.1126/science.abn3810. Structure of the human ccan bound to alpha satellite DNA. SNAP output
7r5v cell cycle cryo-EM (4.55 Å) Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D (2022) "Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome." Science, 376, 844-852. doi: 10.1126/science.abn3810. Structure of the human ccan cenp-a alpha-satellite complex. SNAP output
7r6r gene regulation-DNA X-ray (3.13 Å) McGinnis RJ, Brambley CA, Stamey B, Green WC, Gragg KN, Cafferty ER, Terwilliger TC, Hammel M, Hollis TJ, Miller JM, Gainey MD, Wallen JR (2022) "A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence." Nat Commun, 13, 4105. doi: 10.1038/s41467-022-31678-6. Crystal structure of a mycobacteriophage cluster a2 immunity repressor:DNA complex. SNAP output
7r6t DNA binding protein-DNA X-ray (2.9 Å) Szymanski MR, Yin YW "Human EXOG possesses strong AP hydrolysis activity." Human exog complexed with drp-containing DNA. SNAP output
7r6v DNA binding protein-DNA X-ray (2.16 Å) Szymanski MR, Yin YW "Human EXOG possesses strong AP hydrolysis activity." Human exog complexed with drp-containing DNA. SNAP output
7r77 transferase-DNA cryo-EM (3.0 Å) Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ (2022) "Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance." Mol.Cell, 82, 1186-1198.e6. doi: 10.1016/j.molcel.2022.01.028. cryo-EM structure of dnmt5 binary complex with hemimethylated DNA. SNAP output
7r78 transferase-DNA cryo-EM (3.5 Å) Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ (2022) "Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance." Mol.Cell, 82, 1186-1198.e6. doi: 10.1016/j.molcel.2022.01.028. cryo-EM structure of dnmt5 quaternary complex with hemimethylated DNA, amp-pnp and sah. SNAP output
7r8g hydrolase-DNA X-ray (2.5 Å) Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A (2022) "Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity." Nat Commun, 13, 4624. doi: 10.1038/s41467-022-32079-5. Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' oh guide DNA. SNAP output
7r8h hydrolase-DNA X-ray (2.54 Å) Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A (2022) "Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity." Nat Commun, 13, 4624. doi: 10.1038/s41467-022-32079-5. Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' p guide DNA. SNAP output
7r8i hydrolase-DNA X-ray (2.4 Å) Shin Y, Murakami KS "Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA in the presence of Mg2+." Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' oh guide DNA in the presence of mg2+. SNAP output
7r8j hydrolase-DNA X-ray (2.7 Å) Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A (2022) "Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity." Nat Commun, 13, 4624. doi: 10.1038/s41467-022-32079-5. Crystal structure of pseudooceanicola lipolyticus argonaute bound to 5' p guide DNA in the presence of mg2+. SNAP output
7ray DNA binding protein-DNA X-ray (1.78 Å) Liu K, Dong A, Loppnau P, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "Crystal structure of MBD2 with DNA." Crystal structure of mbd2 with DNA. SNAP output
7rbe transferase-DNA X-ray (1.89 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked binary complex - a. SNAP output
7rbf transferase-DNA X-ray (1.84 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked binary complex - b. SNAP output
7rbg transferase-DNA X-ray (1.9 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked ternary complex 1. SNAP output
7rbh transferase-DNA X-ray (1.75 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked ternary complex 2. SNAP output
7rbi transferase-DNA X-ray (1.93 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 20 s ca to mg exchange. SNAP output
7rbj transferase-DNA X-ray (1.91 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 30 s ca to mg exchange. SNAP output
7rbk transferase-DNA X-ray (2.2 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 40 s ca to mg exchange. SNAP output
7rbl transferase-DNA X-ray (1.98 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 60 s ca to mg exchange. SNAP output
7rbm transferase-DNA X-ray (2.21 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 60 s ca to mn exchange. SNAP output
7rbn transferase-DNA X-ray (2.9 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 20 min ca to mg exchange. SNAP output
7rbo transferase-DNA X-ray (2.96 Å) Kumar A, Reed AJ, Zahurancik WJ, Daskalova SM, Hecht SM, Suo Z (2022) "Interlocking activities of DNA polymerase beta in the base excision repair pathway." Proc.Natl.Acad.Sci.USA, 119, e2118940119. doi: 10.1073/pnas.2118940119. Human DNA polymerase beta crosslinked complex, 60 min ca to mg exchange. SNAP output
7rcc DNA binding protein-DNA X-ray (2.45 Å) Werther RA, Ubilla-Rodriguez NC, Smiley AT, Havens K, Lambert AR, Stoddard BL "Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease." First stage engineered variant of i-onui after initial reassembly. SNAP output
7rcd DNA binding protein-DNA X-ray (2.448 Å) Werther RA, Ubilla-Rodriguez NC, Smiley AT, Havens K, Lambert AR, Stoddard BL "Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease." Second stage reengineered variant of i-onui targeting human pd1 gene with activity enhancing substitutions. SNAP output
7rce DNA binding protein-DNA X-ray (2.42 Å) Werther RA, Ubilla-Rodriguez NC, Smiley AT, Havens K, Lambert AR, Stoddard BL "Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease." Third stage reengineered variant of i-onui with specificity enhancing substitutions. SNAP output
7rcf DNA binding protein-DNA X-ray (2.233 Å) Werther RA, Ubilla-Rodriguez NC, Smiley AT, Havens K, Lambert AR, Stoddard BL "Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease." Fourth stage reengineered variant of i-onui with stability enhancing substitutions. SNAP output
7rcg DNA binding protein-DNA X-ray (2.368 Å) Werther RA, Ubilla-Rodriguez NC, Smiley AT, Havens K, Lambert AR, Stoddard BL "Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease." I-onui_e-hpd1-f final stage reengineered variant of i-onui. SNAP output
7rcu transcription X-ray (2.69 Å) Speltz TE, Qiao Z, Swenson CS, Shangguan X, Coukos JS, Lee CW, Thomas DM, Santana J, Fanning SW, Greene GL, Moellering RE (2023) "Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains." Nat.Biotechnol., 41, 541-551. doi: 10.1038/s41587-022-01504-x. Synthetic max homodimer mimic in complex with DNA. SNAP output
7rdq transcription cryo-EM (3.0 Å) Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH (2022) "Structural and mechanistic basis of reiterative transcription initiation." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2115746119. cryo-EM structure of thermus thermophilus reiterative transcription complex with 11nt oligo-g RNA. SNAP output
7rfk DNA binding protein-DNA X-ray (2.05 Å) Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X (2022) "Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA." Epigenetics, 17, 970-981. doi: 10.1080/15592294.2021.1976910. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor sinefungin. SNAP output
7rfl DNA binding protein-DNA X-ray (2.38 Å) Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X (2022) "Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA." Epigenetics, 17, 970-981. doi: 10.1080/15592294.2021.1976910. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor sgc0946. SNAP output
7rfm DNA binding protein-DNA X-ray (2.68 Å) Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X (2022) "Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA." Epigenetics, 17, 970-981. doi: 10.1080/15592294.2021.1976910. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor epz004777. SNAP output
7rfn DNA binding protein-DNA X-ray (2.5 Å) Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X (2022) "Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA." Epigenetics, 17, 970-981. doi: 10.1080/15592294.2021.1976910. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor sgc8158. SNAP output
7rh2 transcription X-ray (2.47 Å) Sundararaj S, Seneviratne S, Williams SJ, Enders A, Casarotto MG (2022) "The molecular basis for the development of adult T-cell leukemia/lymphoma in patients with an IRF4 K59R mutation." Protein Sci., 31, 787-796. doi: 10.1002/pro.4260. Irf4 transcription factor mutant -k59r. SNAP output
7rhx recombination-DNA cryo-EM (3.23 Å) Stachowski K, Norris AS, Potter D, Wysocki VH, Foster MP (2022) "Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM." Nucleic Acids Res., 50, 1753-1769. doi: 10.1093/nar/gkac032. cryo-EM structure of precleavage cre tetrameric complex. SNAP output
7rhy recombination-DNA cryo-EM (3.91 Å) Stachowski K, Norris AS, Potter D, Wysocki VH, Foster MP (2022) "Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM." Nucleic Acids Res., 50, 1753-1769. doi: 10.1093/nar/gkac032. Cre recombinase mutant (d33a-a36v-r192a) in complex with loxa DNA hairpin. SNAP output
7rhz recombination-DNA cryo-EM (4.48 Å) Stachowski K, Norris AS, Potter D, Wysocki VH, Foster MP (2022) "Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM." Nucleic Acids Res., 50, 1753-1769. doi: 10.1093/nar/gkac032. Heterodimer of cre recombinase mutants d33a-a36v-r192a and r72e-l115d-r119d in complex with loxp DNA.. SNAP output
7rim DNA binding protein-DNA-RNA X-ray (2.9 Å) Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D (2022) "RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2114065119. RNA polymerase ii elongation complex with hairpin polyamide py-im 1, scaffold 1. SNAP output
7rip DNA binding protein-DNA-RNA X-ray (3.3 Å) Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D (2022) "RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2114065119. RNA polymerase ii elongation complex with hairpin polyamide py-im 1, scaffold 1 soaked with ctp. SNAP output
7riq DNA binding protein-DNA-RNA X-ray (3.0 Å) Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D (2022) "RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2114065119. RNA polymerase ii elongation complex scaffold 1 without polyamide. SNAP output
7riw DNA binding protein-DNA-RNA X-ray (3.2 Å) Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D (2022) "RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2114065119. RNA polymerase ii elongation complex scaffold 2, without polyamide. SNAP output
7rix DNA binding protein-DNA-RNA X-ray (3.4 Å) Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D (2022) "RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2114065119. RNA polymerase ii elongation complex with hairpin polyamide py-im 1, scaffold 2. SNAP output
7riy DNA binding protein-DNA-RNA X-ray (3.7 Å) Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D (2022) "RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder." Proc.Natl.Acad.Sci.USA, 119. doi: 10.1073/pnas.2114065119. RNA polymerase ii elongation complex with hairpin polyamide py-im 1, scaffold 2 soaked with utp. SNAP output
7rpo ligase-DNA cryo-EM (4.16 Å) Sverzhinsky A, Tomkinson AE, Pascal JM (2022) "Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase." Structure, 30, 371. doi: 10.1016/j.str.2021.11.002. Archaeal DNA ligase and heterotrimeric pcna in complex with non-ligatable DNA. SNAP output
7rpw ligase-DNA cryo-EM (4.38 Å) Sverzhinsky A, Tomkinson AE, Pascal JM (2022) "Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase." Structure, 30, 371. doi: 10.1016/j.str.2021.11.002. Archaeal DNA ligase and heterotrimeric pcna in complex with adenylated DNA. SNAP output
7rpx ligase-DNA cryo-EM (4.2 Å) Sverzhinsky A, Tomkinson AE, Pascal JM (2022) "Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase." Structure, 30, 371. doi: 10.1016/j.str.2021.11.002. Archaeal DNA ligase and heterotrimeric pcna in complex with end-joined DNA. SNAP output
7rsr transferase-DNA X-ray (1.98 Å) Hajjar M, Chim N, Liu C, Herdewijn P, Chaput JC (2022) "Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid." Nucleic Acids Res., 50, 9663-9674. doi: 10.1093/nar/gkac792. Kod-ri incorporating pmt, n+2. SNAP output
7rss transferase-DNA X-ray (2.71 Å) Hajjar M, Chim N, Liu C, Herdewijn P, Chaput JC (2022) "Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid." Nucleic Acids Res., 50, 9663-9674. doi: 10.1093/nar/gkac792. Kod-ri incorporating DNA, n+2. SNAP output
7rsu transferase-DNA X-ray (2.1 Å) Li Q, Maola VA, Chim N, Hussain J, Lozoya-Colinas A, Chaput JC (2021) "Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities." J.Am.Chem.Soc., 143, 17761-17768. doi: 10.1021/jacs.1c08649. Tna polymerase, n+2 product. SNAP output
7rva DNA binding protein-DNA X-ray (1.89 Å) Ward AR, Dmytriw S, Vajapayajula A, Snow CD (2022) "Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA." Crystals, 12. doi: 10.3390/cryst12010049. Updated crystal structure of replication initiator protein repe54.. SNAP output
7rwi transcription-inhibitor X-ray (3.7 Å) Ma Z, He S, Yuan Y, Zhuang Z, Liu Y, Wang H, Chen J, Xu X, Ding C, Molodtsov V, Lin W, Robertson GT, Weiss WJ, Pulse M, Nguyen P, Duncan L, Doyle T, Ebright RH, Lynch AS (2022) "Design, Synthesis, and Characterization of TNP-2198, a Dual-Targeted Rifamycin-Nitroimidazole Conjugate with Potent Activity against Microaerophilic and Anaerobic Bacterial Pathogens." J.Med.Chem., 65, 4481-4495. doi: 10.1021/acs.jmedchem.1c02045. Mycobacterium tuberculosis RNA polymerase sigma l holoenzyme open promoter complex containing tnp-2198. SNAP output
7s01 transcription-DNA X-ray (3.4 Å) Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG (2022) "Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase." Nat Commun, 13, 3526. doi: 10.1038/s41467-022-31214-6. X-ray structure of the phage ar9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the p077 promoter. SNAP output
7s03 DNA binding protein-DNA X-ray (2.37 Å) Chen Q, Bates AM, Hanquier JN, Simpson E, Rusch DB, Podicheti R, Liu Y, Wek RC, Cornett EM, Georgiadis MM (2022) "Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing." J.Biol.Chem., 298, 101894. doi: 10.1016/j.jbc.2022.101894. DNA-binding domain of human setmar in complex with hsmar1 terminal inverted repeat (tir) DNA. SNAP output
7s0t DNA binding protein-DNA cryo-EM (3.05 Å) Malik R, Johnson RE, Prakash L, Prakash S, Ubarretxena-Belandia I, Aggarwal AK (2022) "Cryo-EM structure of translesion DNA synthesis polymerase zeta with a base pair mismatch." Nat Commun, 13, 1050. doi: 10.1038/s41467-022-28644-7. Structure of DNA polymerase zeta with mismatched DNA. SNAP output
7s36 hydrolase-RNA-DNA cryo-EM (3.2 Å) Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA (2022) "CRISPR-Cas9 bends and twists DNA to read its sequence." Nat.Struct.Mol.Biol., 29, 395-402. doi: 10.1038/s41594-022-00756-0. Cas9:sgrna:DNA (s. pyogenes) with 0 RNA:DNA base pairs, closed-protein-bent-DNA conformation. SNAP output
7s38 hydrolase-RNA-DNA cryo-EM (3.3 Å) Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA (2022) "CRISPR-Cas9 bends and twists DNA to read its sequence." Nat.Struct.Mol.Biol., 29, 395-402. doi: 10.1038/s41594-022-00756-0. Cas9:sgrna:DNA (s. pyogenes) forming a 3-base-pair r-loop. SNAP output
7s3a RNA binding protein-RNA-DNA X-ray (1.48 Å) Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL (2022) "Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal." Nucleic Acids Res., 50, 5299-5312. doi: 10.1093/nar/gkac287. Crystal structure of intact u2af65 rrm-region bound to adml-c5 oligonucleotide. SNAP output
7s3b RNA binding protein-RNA-DNA X-ray (1.89 Å) Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL (2022) "Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal." Nucleic Acids Res., 50, 5299-5312. doi: 10.1093/nar/gkac287. Crystal structure of intact u2af65 rrm-region bound to adml-g5 oligonucleotide. SNAP output
7s3c RNA binding protein-RNA-DNA X-ray (1.51 Å) Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL (2022) "Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal." Nucleic Acids Res., 50, 5299-5312. doi: 10.1093/nar/gkac287. Crystal structure of intact u2af65 rrm-region bound to adml-a5 oligonucleotide. SNAP output
7s3h hydrolase-RNA-DNA cryo-EM (2.5 Å) Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA (2022) "CRISPR-Cas9 bends and twists DNA to read its sequence." Nat.Struct.Mol.Biol., 29, 395-402. doi: 10.1038/s41594-022-00756-0. Cas9:sgrna:DNA (s. pyogenes) with 0 RNA:DNA base pairs, open-protein-linear-DNA conformation. SNAP output
7s4u immune system-DNA-RNA cryo-EM (3.56 Å) Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW (2022) "Structural basis for mismatch surveillance by CRISPR-Cas9." Nature, 603, 343-347. doi: 10.1038/s41586-022-04470-1. cryo-EM structure of cas9 in complex with 12-14mm DNA substrate, 5 minute time-point. SNAP output
7s4v immune system-DNA-RNA cryo-EM (3.28 Å) Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW (2022) "Structural basis for mismatch surveillance by CRISPR-Cas9." Nature, 603, 343-347. doi: 10.1038/s41586-022-04470-1. Cas9 bound to 12-14mm DNA, 60 min time-point, kinked conformation. SNAP output
7s4x immune system-DNA-RNA cryo-EM (2.76 Å) Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW (2022) "Structural basis for mismatch surveillance by CRISPR-Cas9." Nature, 603, 343-347. doi: 10.1038/s41586-022-04470-1. Cas9:grna in complex with 18-20mm DNA, 1 minute time-point, kinked active conformation. SNAP output
7s68 DNA binding protein-DNA X-ray (3.3 Å) Rouleau-Turcotte E, Krastev DB, Pettitt SJ, Lord CJ, Pascal JM (2022) "Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery." Mol.Cell, 82, 2939-2951.e5. doi: 10.1016/j.molcel.2022.06.011. Structure of human parp1 domains (zn1, zn3, wgr and hd) bound to a DNA double strand break.. SNAP output
7s6h DNA binding protein-DNA X-ray (3.1 Å) Rouleau-Turcotte E, Krastev DB, Pettitt SJ, Lord CJ, Pascal JM (2022) "Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery." Mol.Cell, 82, 2939-2951.e5. doi: 10.1016/j.molcel.2022.06.011. Human parp1 deltav687-e688 bound to nad+ analog eb-47 and to a DNA double strand break.. SNAP output
7s6m DNA binding protein-DNA X-ray (3.2 Å) Rouleau-Turcotte E, Krastev DB, Pettitt SJ, Lord CJ, Pascal JM (2022) "Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery." Mol.Cell, 82, 2939-2951.e5. doi: 10.1016/j.molcel.2022.06.011. Human parp1 deltav687-e688 bound to a DNA double strand break.. SNAP output
7s81 DNA binding protein X-ray (3.6 Å) Rouleau-Turcotte E, Krastev DB, Pettitt SJ, Lord CJ, Pascal JM (2022) "Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery." Mol.Cell, 82, 2939-2951.e5. doi: 10.1016/j.molcel.2022.06.011. Structure of human parp1 domains (zn1, zn3, wgr, hd) bound to a DNA double strand break.. SNAP output
7s9j DNA bnding protein-DNA X-ray (1.91 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Crystal structure of DNA polymerase beta with fapy-dg base-paired with a dc. SNAP output
7s9k DNA binding protein-DNA X-ray (1.97 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Crystal structure of DNA polymerase beta with fapy-dg base-paired with a da. SNAP output
7s9l DNA binding protein-DNA X-ray (2.05 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Crystal structure of DNA polymerase beta with ring open intermediate fapy-dg base-paired with a dc. SNAP output
7s9m DNA binding-DNA X-ray (2.31 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Crystal structure of DNA polymerase beta with ring open intermediate fapy-dg base-paired with a da. SNAP output
7s9n DNA binding protein-DNA X-ray (1.71 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Binary complex of DNA polymerase beta with fapy-dg in the template position. SNAP output
7s9o DNA binding protein-DNA X-ray (2.23 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Binary complex of DNA polymerase beta with ring open intermediate fapy-dg in the template position. SNAP output
7s9p DNA binding protein-DNA X-ray (1.86 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Ternary complex of DNA polymerase beta with template fapy-dg and an incoming dctp analog. SNAP output
7s9q DNA binding protein-DNA X-ray (1.9 Å) Ryan BJ, Yang H, Bacurio JHT, Smith MR, Basu AK, Greenberg MM, Freudenthal BD (2022) "Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication." J.Am.Chem.Soc., 144, 8054-8065. doi: 10.1021/jacs.2c00193. Ternary complex of DNA polymerase beta with template fapy-dg and an incoming datp analog. SNAP output
7s9w immune system cryo-EM (3.4 Å) Bravo JPK, Aparicio-Maldonado C, Nobrega FL, Brouns SJJ, Taylor DW (2022) "Structural basis for broad anti-phage immunity by DISARM." Nat Commun, 13, 2987. doi: 10.1038/s41467-022-30673-1. Structure of drmab:adp:DNA complex. SNAP output
7sba DNA binding protein-DNA-RNA cryo-EM (2.9 Å) Schwartz EA, McBride TM, Bravo JPK, Wrapp D, Fineran PC, Fagerlund RD, Taylor DW (2022) "Structural rearrangements allow nucleic acid discrimination by type I-D Cascade." Nat Commun, 13, 2829. doi: 10.1038/s41467-022-30402-8. Structure of type i-d cascade bound to a dsDNA target. SNAP output
7scy DNA binding protein-DNA cryo-EM (4.1 Å) Rudolph J, Muthurajan UM, Palacio M, Mahadevan J, Roberts G, Erbse AH, Dyer PN, Luger K (2021) "The BRCT domain of PARP1 binds intact DNA and mediates intrastrand transfer." Mol.Cell, 81, 4994-5006.e5. doi: 10.1016/j.molcel.2021.11.014. Nuc147 bound to single brct. SNAP output
7scz DNA binding protein-DNA cryo-EM (3.5 Å) Rudolph J, Muthurajan UM, Palacio M, Mahadevan J, Roberts G, Erbse AH, Dyer PN, Luger K (2021) "The BRCT domain of PARP1 binds intact DNA and mediates intrastrand transfer." Mol.Cell, 81, 4994-5006.e5. doi: 10.1016/j.molcel.2021.11.014. Nuc147 bound to multiple brcts. SNAP output
7sdp DNA binding protein-DNA X-ray (3.01 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Replication initiator protein repe54 and cognate DNA sequence with terminal three prime phosphates.. SNAP output
7sfc transferase-transferase inhibitor X-ray (1.97 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3735967a. SNAP output
7sfe transferase-transferase inhibitor X-ray (2.55 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3830334a. SNAP output
7sff transferase-transferase inhibitor X-ray (2.05 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3852279b. SNAP output
7sfg transferase-transferase inhibitor X-ray (2.43 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and cofactor sam. SNAP output
7sgc DNA binding protein-DNA X-ray (2.7 Å) Ward AR, Dmytriw S, Vajapayajula A, Snow CD (2022) "Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA." Crystals, 12. doi: 10.3390/cryst12010049. Replication initiator protein repe54 and cognate DNA sequence with terminal five prime phosphates.. SNAP output
7sgl DNA binding protein-DNA cryo-EM (3.0 Å) Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M (2022) "Autophosphorylation transforms DNA-PK from protecting to processing DNA ends." Mol.Cell, 82, 177. doi: 10.1016/j.molcel.2021.11.025. DNA-pk complex of DNA end processing. SNAP output
7sgz DNA binding protein-DNA cryo-EM (3.17 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2022) "DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp." Nat.Struct.Mol.Biol., 29, 376-385. doi: 10.1038/s41594-022-00742-6. Structure of the yeast rad24-rfc loader bound to DNA and the closed 9-1-1 clamp. SNAP output
7sh2 DNA binding protein-DNA cryo-EM (3.23 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2022) "DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp." Nat.Struct.Mol.Biol., 29, 376-385. doi: 10.1038/s41594-022-00742-6. Structure of the yeast rad24-rfc loader bound to DNA and the open 9-1-1 clamp. SNAP output
7sjr DNA binding protein-DNA cryo-EM (3.8 Å) Warren GM, Meir A, Wang J, Patel DJ, Greene EC, Shuman S (2022) "Structure-activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB." Nucleic Acids Res., 50, 952-961. doi: 10.1093/nar/gkab1270. cryo-EM structure of aDNA-adnb(w325a) in complex with DNA and amppnp. SNAP output
7soz DNA binding protein-DNA X-ray (3.14 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Replication initiator protein repe54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (5 mg-ml edc, 12 hours).. SNAP output
7spm DNA binding protein-DNA X-ray (3.28 Å) Orun AR, Dmytriw S, Vajapayajula A, Snow CD (2022) "Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA." Crystals, 12. doi: 10.3390/cryst12010049. Replication initiator protein repe54 and cognate DNA sequence with terminal three prime phosphates chemically crosslinked (30 mg-ml edc, 12 hours, 2 doses).. SNAP output
7sr6 replication X-ray (2.62 Å) Baldwin ET, Gotte M, Tchesnokov EP, Arnold E, Hagel M, Nichols C, Dossang P, Lamers M, Wan P, Steinbacher S, Romero DL (2022) "Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition." Proc.Natl.Acad.Sci.USA, 119, e2200260119. doi: 10.1073/pnas.2200260119. Human endogenous retrovirus (herv-k) reverse transcriptase ternary complex with dsDNA template primer and dntp. SNAP output
7ss5 hydrolase-DNA cryo-EM (2.7 Å) Shan Z, Ghadirian N, Lyumkis D, Horton NC (2022) "Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity." J.Biol.Chem., 298, 101760. doi: 10.1016/j.jbc.2022.101760. Activated sgrai endonuclease DNA-bound dimer with ca2+ and intact primary site DNA. SNAP output
7ssa gene regulation cryo-EM (3.2 Å) Donovan BT, Chen H, Eek P, Meng Z, Jipa C, Tan S, Bai L, Poirier MG (2023) "Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions." Mol.Cell, 83, 1251-1263.e6. doi: 10.1016/j.molcel.2023.03.006. cryo-EM structure of pioneer factor cbf1 bound to the nucleosome. SNAP output
7ssg DNA binding protein-DNA cryo-EM (5.2 Å) Paudel BP, Xu ZQ, Jergic S, Oakley AJ, Sharma N, Brown SHJ, Bouwer JC, Lewis PJ, Dixon NE, van Oijen AM, Ghodke H (2022) "Mechanism of transcription modulation by the transcription-repair coupling factor." Nucleic Acids Res., 50, 5688-5712. doi: 10.1093/nar/gkac449. Mfd DNA complex. SNAP output
7st9 replication-DNA cryo-EM (2.2 Å) Castaneda JC, Schrecker M, Remus D, Hite RK (2022) "Mechanisms of loading and release of the 9-1-1 checkpoint clamp." Nat.Struct.Mol.Biol., 29, 369-375. doi: 10.1038/s41594-022-00741-7. Open state of rad24-rfc:9-1-1 bound to a 5' ss-dsDNA junction. SNAP output
7stb replication-DNA cryo-EM (2.72 Å) Castaneda JC, Schrecker M, Remus D, Hite RK (2022) "Mechanisms of loading and release of the 9-1-1 checkpoint clamp." Nat.Struct.Mol.Biol., 29, 369-375. doi: 10.1038/s41594-022-00741-7. Closed state of rad24-rfc:9-1-1 bound to a 5' ss-dsDNA junction. SNAP output
7su3 DNA binding protein-DNA cryo-EM (3.3 Å) Liu L, Chen X, Li J, Wang H, Buehl CJ, Goff NJ, Meek K, Yang W, Gellert M (2022) "Autophosphorylation transforms DNA-PK from protecting to processing DNA ends." Mol.Cell, 82, 177. doi: 10.1016/j.molcel.2021.11.025. Cryoem structure of DNA-pk complex vii. SNAP output
7sum ligase-DNA X-ray (2.9 Å) Tang Q, Gulkis M, McKenna R, Caglayan M (2022) "Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair." Nat Commun, 13, 3860. doi: 10.1038/s41467-022-31585-w. Crystal structure of human ligase i with nick duplexes containing cognate a:t. SNAP output
7suv hydrolase-DNA X-ray (1.99 Å) Whitaker AM, Stark WJ, Freudenthal BD (2022) "Processing oxidatively damaged bases at DNA strand breaks by APE1." Nucleic Acids Res., 50, 9521-9533. doi: 10.1093/nar/gkac695. Ape1 exonuclease substrate complex with 8oxog opposite a. SNAP output
7svb hydrolase-DNA X-ray (2.24 Å) Whitaker AM, Stark WJ, Freudenthal BD (2022) "Processing oxidatively damaged bases at DNA strand breaks by APE1." Nucleic Acids Res., 50, 9521-9533. doi: 10.1093/nar/gkac695. Ape1 exonuclease substrate complex with 8oxog opposite c. SNAP output
7svu DNA binding protein-DNA cryo-EM (3.5 Å) Park J, Tsai AWT, Rizo AN, Truong VH, Wellner TX, Schargel RD, Kellogg EH (2023) "Structures of the holo CRISPR RNA-guided transposon integration complex." Nature, 613, 775-782. doi: 10.1038/s41586-022-05573-5. Tnsbctd-tnsc-tniq complex. SNAP output
7svv DNA binding protein-DNA cryo-EM (3.54 Å) Park JU, Tsai AW, Chen TH, Peters JE, Kellogg EH (2022) "Mechanistic details of CRISPR-associated transposon recruitment and integration revealed by cryo-EM." Proc.Natl.Acad.Sci.USA, 119, e2202590119. doi: 10.1073/pnas.2202590119. Tnsbctd-tnsc complex. SNAP output
7svw DNA binding protein-DNA cryo-EM (3.69 Å) Park JU, Tsai AW, Chen TH, Peters JE, Kellogg EH (2022) "Mechanistic details of CRISPR-associated transposon recruitment and integration revealed by cryo-EM." Proc.Natl.Acad.Sci.USA, 119, e2202590119. doi: 10.1073/pnas.2202590119. Strand-transfer complex of tnsb from shcast. SNAP output
7swy DNA binding protein-DNA cryo-EM (2.6 Å) Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP (2022) "Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state." Nat.Struct.Mol.Biol., 29, 121-129. doi: 10.1038/s41594-021-00719-x. 2.6 a structure of a 40-601[ta-rich+1]-40 nucleosome. SNAP output
7sx5 ligase X-ray (2.8 Å) Tang Q, Gulkis M, McKenna R, Caglayan M (2022) "Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair." Nat Commun, 13, 3860. doi: 10.1038/s41467-022-31585-w. Crystal structure of ligase i with nick duplexes containing mismatch a:c. SNAP output
7sxe ligase-DNA X-ray (3.0 Å) Tang Q, Gulkis M, McKenna R, Caglayan M (2022) "Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair." Nat Commun, 13, 3860. doi: 10.1038/s41467-022-31585-w. Crystal structure of ligase i with nick duplexes containing cognate g:t. SNAP output
7szj transferase-DNA-antibiotic cryo-EM (3.11 Å) Rajeswaran W, Ashkar SR, Lee PH, Yeomans L, Shin Y, Franzblau SG, Murakami KS, Showalter HD, Garcia GA (2022) "Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis." Acs Infect Dis., 8, 1422-1438. doi: 10.1021/acsinfecdis.1c00636. cryo-EM structure of rifamycin bound to e. coli rnap and rrnbp1 promoter complex. SNAP output
7szk transferase-DNA-antibiotic cryo-EM (2.94 Å) Rajeswaran W, Ashkar SR, Lee PH, Yeomans L, Shin Y, Franzblau SG, Murakami KS, Showalter HD, Garcia GA (2022) "Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis." Acs Infect Dis., 8, 1422-1438. doi: 10.1021/acsinfecdis.1c00636. cryo-EM structure of 27a bound to e. coli rnap and rrnbp1 promoter complex. SNAP output
7t02 transferase-DNA cryo-EM (3.8 Å) Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ (2022) "Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance." Mol.Cell, 82, 1186-1198.e6. doi: 10.1016/j.molcel.2022.01.028. cryo-EM structure of dnmt5 pseudo-ternary complex solved by incubation with hemimethylated DNA and sam. SNAP output
7t18 transferase-DNA X-ray (1.7 Å) Weaver TM, Click TH, Khoang TH, Todd Washington M, Agarwal PK, Freudenthal BD (2022) "Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1." Nat Commun, 13, 2876. doi: 10.1038/s41467-022-30577-0. Rev1 ternary complex with dttp and ca2+. SNAP output
7t19 transferase-DNA X-ray (2.01 Å) Weaver TM, Click TH, Khoang TH, Todd Washington M, Agarwal PK, Freudenthal BD (2022) "Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1." Nat Commun, 13, 2876. doi: 10.1038/s41467-022-30577-0. Rev1 ternary complex with dgtp and ca2+. SNAP output
7t1a transferase-DNA X-ray (1.81 Å) Weaver TM, Click TH, Khoang TH, Todd Washington M, Agarwal PK, Freudenthal BD (2022) "Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1." Nat Commun, 13, 2876. doi: 10.1038/s41467-022-30577-0. Rev1 ternary complex with datp and ca2+. SNAP output
7t1b transferase-DNA X-ray (1.75 Å) Weaver TM, Click TH, Khoang TH, Todd Washington M, Agarwal PK, Freudenthal BD (2022) "Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1." Nat Commun, 13, 2876. doi: 10.1038/s41467-022-30577-0. Rev1 ternary complex with rctp and ca2+. SNAP output
7t20 replication-DNA cryo-EM (4.7 Å) Oakley AJ, Xu ZQ "Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli." E. coli dnab bound to ssDNA and amppnp. SNAP output
7t21 replication-DNA cryo-EM (5.4 Å) Oakley AJ, Xu ZQ "Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli." E. coli dnab bound to ssDNA and adp-alf4. SNAP output
7t22 replication-DNA cryo-EM (4.2 Å) Oakley AJ, Xu ZQ "Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli." E. coli dnab bound to three dnag c-terminal domains, ssDNA, adp and alf4. SNAP output
7t23 replication-DNA cryo-EM (4.2 Å) Oakley AJ, Xu ZQ "Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli." E. coli dnab bound to two dnag c-terminal domains, ssDNA, adp and alf4. SNAP output
7t3l hydrolase-RNA-DNA cryo-EM (3.6 Å) Mukherjee IA, Gabel C, Noinaj N, Bondy-Denomy J, Chang L (2022) "Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor." Nat.Chem.Biol., 18, 1417-1424. doi: 10.1038/s41589-022-01137-w. cryo-EM structure of csy-acrif24-DNA dimer. SNAP output
7t8k DNA binding protein-DNA X-ray (2.3 Å) Luyten YA, Hausman DE, Young JC, Doyle LA, Higashi KM, Ubilla-Rodriguez NC, Lambert AR, Arroyo CS, Forsberg KJ, Morgan RD, Stoddard BL, Kaiser BK (2022) "Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system." Nucleic Acids Res., 50, 5171-5190. doi: 10.1093/nar/gkac311. Brxr from acinetobacter brex type i phage restriction system bound to DNA. SNAP output
7tan structural protein-DNA-transferase cryo-EM (3.0 Å) Budziszewski GR, Zhao Y, Spangler CJ, Kedziora KM, Williams MR, Azzam DN, Skrajna A, Koyama Y, Cesmat AP, Simmons HC, Arteaga EC, Strauss JD, Kireev D, McGinty RK (2022) "Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity." Nucleic Acids Res., 50, 4355-4371. doi: 10.1093/nar/gkac198. Structure of vrk1 c-terminal tail bound to nucleosome core particle. SNAP output
7taw hydrolase-RNA-DNA cryo-EM (2.7 Å) Mukherjee IA, Gabel C, Noinaj N, Bondy-Denomy J, Chang L (2022) "Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor." Nat.Chem.Biol., 18, 1417-1424. doi: 10.1038/s41589-022-01137-w. cryo-EM structure of the csy-acrif24-promoter DNA dimer. SNAP output
7tax hydrolase-RNA-DNA cryo-EM (2.8 Å) Mukherjee IA, Gabel C, Noinaj N, Bondy-Denomy J, Chang L (2022) "Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor." Nat.Chem.Biol., 18, 1417-1424. doi: 10.1038/s41589-022-01137-w. cryo-EM structure of the csy-acrif24-promoter DNA complex. SNAP output
7tdw transcription-DNA X-ray (4.0 Å) Leng F, Zhang W, Ramirez RN, Leon J, Zhong Y, Hou L, Yuki K, van der Veeken J, Rudensky AY, Benoist C, Hur S (2022) "The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis." Immunity, 55, 1354. doi: 10.1016/j.immuni.2022.07.002. Structure of foxp3-DNA complex. SNAP output
7tdx transcription-DNA X-ray (3.1 Å) Leng F, Zhang W, Ramirez RN, Leon J, Zhong Y, Hou L, Yuki K, van der Veeken J, Rudensky AY, Benoist C, Hur S (2022) "The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis." Immunity, 55, 1354. doi: 10.1016/j.immuni.2022.07.002. Structure of foxp3-DNA complex. SNAP output
7tea DNA binding protein-DNA X-ray (2.35 Å) Travis BA, Peck JV, Salinas R, Dopkins B, Lent N, Nguyen VD, Borgnia MJ, Brennan RG, Schumacher MA (2022) "Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria." Nat Commun, 13, 3793. doi: 10.1038/s41467-022-31573-0. Crystal structure of s. aureus glnr-DNA complex. SNAP output
7tec DNA binding protein-DNA X-ray (3.45 Å) Travis BA, Peck JV, Salinas R, Dopkins B, Lent N, Nguyen VD, Borgnia MJ, Brennan RG, Schumacher MA (2022) "Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria." Nat Commun, 13, 3793. doi: 10.1038/s41467-022-31573-0. Structure of the listeria monocytogenes glnr-DNA complex to 3.45 angstrom. SNAP output
7tfh DNA binding protein-DNA cryo-EM (3.09 Å) Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME (2022) "Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair." Elife, 11. doi: 10.7554/eLife.77469. Atomic model of the s. cerevisiae clamp-clamp loader complex pcna-rfc bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end. SNAP output
7tfi DNA binding protein-DNA cryo-EM (3.41 Å) Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME (2022) "Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair." Elife, 11. doi: 10.7554/eLife.77469. Atomic model of the s. cerevisiae clamp-clamp loader complex pcna-rfc bound to DNA with an open clamp. SNAP output
7tfj DNA binding protein-DNA cryo-EM (3.3 Å) Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME (2022) "Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair." Elife, 11. doi: 10.7554/eLife.77469. Atomic model of s. cerevisiae clamp-clamp loader complex pcna-rfc bound to DNA with a closed clamp ring. SNAP output
7tfk DNA binding protein-DNA cryo-EM (3.25 Å) Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME (2022) "Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair." Elife, 11. doi: 10.7554/eLife.77469. Atomic model of s. cerevisiae clamp loader rfc bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end. SNAP output
7tfl DNA binding protein-DNA cryo-EM (3.33 Å) Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME (2022) "Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair." Elife, 11. doi: 10.7554/eLife.77469. Atomic model of s. cerevisiae clamp loader rfc bound to DNA. SNAP output
7tib replication-DNA cryo-EM (3.4 Å) Gaubitz C, Liu X, Pajak J, Stone NP, Hayes JA, Demo G, Kelch PhD BA (2022) "Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader." Elife, 11. doi: 10.7554/eLife.74175. Structure of the yeast clamp loader (replication factor c rfc) bound to the open sliding clamp (proliferating cell nuclear antigen pcna) and primer-template DNA. SNAP output
7tid replication-DNA cryo-EM (3.3 Å) Gaubitz C, Liu X, Pajak J, Stone NP, Hayes JA, Demo G, Kelch PhD BA (2022) "Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader." Elife, 11. doi: 10.7554/eLife.74175. Structure of the yeast clamp loader (replication factor c rfc) bound to the sliding clamp (proliferating cell nuclear antigen pcna) and primer-template DNA. SNAP output
7tjf replication-DNA cryo-EM (2.6 Å) Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) "A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6." Nat Commun, 13, 1059. doi: 10.1038/s41467-022-28695-w. S. cerevisiae orc bound to 84 bp ars1 DNA. SNAP output
7tjh replication-DNA cryo-EM (2.5 Å) Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) "A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6." Nat Commun, 13, 1059. doi: 10.1038/s41467-022-28695-w. S. cerevisiae orc bound to 84 bp ars1 DNA and cdc6 (state 1) with flexible orc6 n-terminal domain. SNAP output
7tji replication-DNA cryo-EM (2.7 Å) Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) "A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6." Nat Commun, 13, 1059. doi: 10.1038/s41467-022-28695-w. S. cerevisiae orc bound to 84 bp ars1 DNA and cdc6 (state 2) with flexible orc6 n-terminal domain. SNAP output
7tjj replication-DNA cryo-EM (2.7 Å) Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) "A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6." Nat Commun, 13, 1059. doi: 10.1038/s41467-022-28695-w. S. cerevisiae orc bound to 84 bp ars1 DNA and cdc6 (state 1) with docked orc6 n-terminal domain. SNAP output
7tjk replication-DNA cryo-EM (2.7 Å) Schmidt JM, Yang R, Kumar A, Hunker O, Seebacher J, Bleichert F (2022) "A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6." Nat Commun, 13, 1059. doi: 10.1038/s41467-022-28695-w. S. cerevisiae orc bound to 84 bp ars1 DNA and cdc6 (state 2) with docked orc6 n-terminal domain. SNAP output
7tn2 DNA binding protein cryo-EM (2.3 Å) Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP (2022) "Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state." Nat.Struct.Mol.Biol., 29, 121-129. doi: 10.1038/s41594-021-00719-x. Composite model of a chd1-nucleosome complex in the nucleotide-free state derived from 2.3a and 2.7a cryo-EM maps. SNAP output
7tqb immune system-DNA-RNA hybrid X-ray (3.1 Å) Bou-Nader C, Bothra A, Garboczi DN, Leppla SH, Zhang J (2022) "Structural basis of R-loop recognition by the S9.6 monoclonal antibody." Nat Commun, 13, 1641. doi: 10.1038/s41467-022-29187-7. Crystal structure of monoclonal s9.6 fab bound to DNA-RNA hybrid. SNAP output
7tqq hydrolase-DNA X-ray (2.2 Å) Zhou W, Richmond-Buccola D, Wang Q, Kranzusch PJ (2022) "Structural basis of human TREX1 DNA degradation and autoimmune disease." Nat Commun, 13, 4277. doi: 10.1038/s41467-022-32055-z. Structure of human trex1-DNA complex. SNAP output
7tqw transferase-DNA X-ray (3.01 Å) Hajjar M, Chim N, Liu C, Herdewijn P, Chaput JC (2022) "Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid." Nucleic Acids Res., 50, 9663-9674. doi: 10.1093/nar/gkac792. Kod rsga incorporating pmt, n+2. SNAP output
7tr7 lyase-DNA X-ray (2.0 Å) Hoitsma NM, Norris J, Khoang TH, Kaushik V, Chadda R, Antony E, Hedglin M, Freudenthal BD (2023) "Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics." Nucleic Acids Res., 51, 6738-6753. doi: 10.1093/nar/gkad481. Ape1 product complex with abasic ssDNA. SNAP output
7trd replication cryo-EM (3.3 Å) Liu B, He Y, Wang Y, Song H, Zhou ZH, Feigon J (2022) "Structure of active human telomerase with telomere shelterin protein TPP1." Nature, 604, 578-583. doi: 10.1038/s41586-022-04582-8. Human telomerase catalytic core structure at 3.3 angstrom. SNAP output
7tre replication cryo-EM (3.5 Å) Liu B, He Y, Wang Y, Song H, Zhou ZH, Feigon J (2022) "Structure of active human telomerase with telomere shelterin protein TPP1." Nature, 604, 578-583. doi: 10.1038/s41586-022-04582-8. Human telomerase catalytic core with shelterin protein tpp1. SNAP output
7trf replication cryo-EM (3.7 Å) Liu B, He Y, Wang Y, Song H, Zhou ZH, Feigon J (2022) "Structure of active human telomerase with telomere shelterin protein TPP1." Nature, 604, 578-583. doi: 10.1038/s41586-022-04582-8. Human telomerase catalytic core rnp with h2a-h2b. SNAP output
7tve DNA binding protein-DNA cryo-EM (3.8 Å) Yu Y, Li S, Ser Z, Kuang H, Than T, Guan D, Zhao X, Patel DJ (2022) "Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes." Proc.Natl.Acad.Sci.USA, 119, e2202799119. doi: 10.1073/pnas.2202799119. Atp and DNA bound smc5-6 core complex. SNAP output
7txc DNA binding protein-DNA X-ray (3.04 Å) Huang P, Peslak SA, Ren R, Khandros E, Qin K, Keller CA, Giardine B, Bell HW, Lan X, Sharma M, Horton JR, Abdulmalik O, Chou ST, Shi J, Crossley M, Hardison RC, Cheng X, Blobel GA (2022) "HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription." Nat.Genet., 54, 1417-1426. doi: 10.1038/s41588-022-01152-6. Hic2 zinc finger domain in complex with the DNA binding motif-2 of the bcl11a enhancer. SNAP output
7txj virus cryo-EM (3.9 Å) Wang F, Cvirkaite-Krupovic V, Krupovic M, Egelman EH "Cryo-EM of AFV6." cryo-EM of afv6. SNAP output
7tz1 gene regulation-DNA X-ray (2.79 Å) McGinnis RJ, Brambley CA, Stamey B, Green WC, Gragg KN, Cafferty ER, Terwilliger TC, Hammel M, Hollis TJ, Miller JM, Gainey MD, Wallen JR (2022) "A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence." Nat Commun, 13, 4105. doi: 10.1038/s41467-022-31678-6. Crystal structure of a mycobacteriophage cluster a2 immunity repressor:DNA complex. SNAP output
7tzv transcription X-ray (1.65 Å) Gozzi K, Salinas R, Nguyen VD, Laub MT, Schumacher MA (2022) "ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD." Genes Dev., 36, 618-633. doi: 10.1101/gad.349541.122. Structure of drid c-domain bound to 9mer ssDNA. SNAP output
7u02 transcription X-ray (2.48 Å) Gozzi K, Salinas R, Nguyen VD, Laub MT, Schumacher MA (2022) "ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD." Genes Dev., 36, 618-633. doi: 10.1101/gad.349541.122. Structure of the c. crescentus drid c-domain bound to ssDNA. SNAP output
7u0g transcription-DNA cryo-EM (2.6 Å) Guan R, Lian T, Zhou BR, Wheeler D, Bai Y (2023) "Structural mechanism of LIN28B nucleosome targeting by OCT4." Mol.Cell, 83, 1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. Structure of lin28b nucleosome bound 3 oct4. SNAP output
7u0i transcription-DNA cryo-EM (2.6 Å) Guan R, Lian T, Zhou BR, Wheeler D, Bai Y (2023) "Structural mechanism of LIN28B nucleosome targeting by OCT4." Mol.Cell, 83, 1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. Structure of lin28b nucleosome bound 2 oct4. SNAP output
7u0j transcription-DNA cryo-EM (2.7 Å) Guan R, Lian T, Zhou BR, Wheeler D, Bai Y (2023) "Structural mechanism of LIN28B nucleosome targeting by OCT4." Mol.Cell, 83, 1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. Structure of 162bp lin28b nucleosome. SNAP output
7u19 replication cryo-EM (3.7 Å) Liu X, Gaubitz C, Pajak J, Kelch BA (2022) "A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA." Elife, 11. doi: 10.7554/eLife.77483. Rfc:pcna bound to nicked DNA. SNAP output
7u1a replication-DNA cryo-EM (3.3 Å) Liu X, Gaubitz C, Pajak J, Kelch BA (2022) "A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA." Elife, 11. doi: 10.7554/eLife.77483. Rfc:pcna bound to dsDNA with a ssDNA gap of six nucleotides. SNAP output
7u1p replication-DNA cryo-EM (3.0 Å) Liu X, Gaubitz C, Pajak J, Kelch BA (2022) "A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA." Elife, 11. doi: 10.7554/eLife.77483. Rfc:pcna bound to DNA with a ssDNA gap of five nucleotides. SNAP output
7u1t viral protein-DNA cryo-EM (3.3 Å) Mei Y, Lieberman P "EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element." Ebna1 DNA binding domain (401-641) binds to half dyad symmetry element. SNAP output
7u22 antibiotic X-ray (3.87 Å) Lan T, Ganapathy US, Sharma S, Ahn YM, Zimmerman M, Molodtsov V, Hegde P, Gengenbacher M, Ebright RH, Dartois V, Freundlich JS, Dick T, Aldrich CC (2022) "Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance." Angew.Chem.Int.Ed.Engl., 61, e202211498. doi: 10.1002/anie.202211498. Mycobacterium tuberculosis RNA polymerase sigma a holoenzyme open promoter complex containing umn-7. SNAP output
7u32 viral protein-DNA cryo-EM (3.46 Å) Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P (2022) "Multivalent interactions essential for lentiviral integrase function." Nat Commun, 13, 2416. doi: 10.1038/s41467-022-29928-8. Mvv cleaved synaptic complex (csc) intasome at 3.4 Å resolution. SNAP output
7u46 DNA binding protein-DNA cryo-EM (2.68 Å) Zhou K, Gebala M, Woods D, Sundararajan K, Edwards G, Krzizike D, Wereszczynski J, Straight AF, Luger K (2022) "CENP-N promotes the compaction of centromeric chromatin." Nat.Struct.Mol.Biol., 29, 403-413. doi: 10.1038/s41594-022-00758-y. cryo-EM structure of cenp-a nucleosome (palindromic alpha satellite DNA) in complex with cenp-n. SNAP output
7u47 DNA binding protein-DNA cryo-EM (7.5 Å) Zhou K, Gebala M, Woods D, Sundararajan K, Edwards G, Krzizike D, Wereszczynski J, Straight AF, Luger K (2022) "CENP-N promotes the compaction of centromeric chromatin." Nat.Struct.Mol.Biol., 29, 403-413. doi: 10.1038/s41594-022-00758-y. Cryoem structure of cenp-n promoted nucleosome stacks with cenp-a and palindromic alpha satellite DNA sequence. SNAP output
7u4d DNA binding protein-DNA cryo-EM (8.1 Å) Zhou K, Gebala M, Woods D, Sundararajan K, Edwards G, Krzizike D, Wereszczynski J, Straight AF, Luger K (2022) "CENP-N promotes the compaction of centromeric chromatin." Nat.Struct.Mol.Biol., 29, 403-413. doi: 10.1038/s41594-022-00758-y. Cryoem structure of cenp-n promoted nucleosome stacks with cenp-a and 601 DNA sequence. SNAP output
7u50 DNA binding protein-DNA cryo-EM (3.4 Å) Weaver TM, Hoitsma NM, Spencer JJ, Gakhar L, Schnicker NJ, Freudenthal BD (2022) "Structural basis for APE1 processing DNA damage in the nucleosome." Nat Commun, 13, 5390. doi: 10.1038/s41467-022-33057-7. Ape1 bound to a nucleosome core particle with ap-site at shl-6. SNAP output
7u51 DNA binding protein-DNA cryo-EM (3.1 Å) Weaver TM, Hoitsma NM, Spencer JJ, Gakhar L, Schnicker NJ, Freudenthal BD (2022) "Structural basis for APE1 processing DNA damage in the nucleosome." Nat Commun, 13, 5390. doi: 10.1038/s41467-022-33057-7. Nucleosome core particle with ap-site at shl-6. SNAP output
7u52 DNA binding protein-DNA cryo-EM (3.4 Å) Weaver TM, Hoitsma NM, Spencer JJ, Gakhar L, Schnicker NJ, Freudenthal BD (2022) "Structural basis for APE1 processing DNA damage in the nucleosome." Nat Commun, 13, 5390. doi: 10.1038/s41467-022-33057-7. Nucleosome core particle with ap-site at shl-6.5. SNAP output
7u53 DNA binding protein-DNA cryo-EM (4.0 Å) Weaver TM, Hoitsma NM, Spencer JJ, Gakhar L, Schnicker NJ, Freudenthal BD (2022) "Structural basis for APE1 processing DNA damage in the nucleosome." Nat Commun, 13, 5390. doi: 10.1038/s41467-022-33057-7. Nucleosome core particle with ap-site at shl0. SNAP output
7u5c DNA binding protein-DNA cryo-EM (4.6 Å) Cai SW, Zinder JC, Svetlov V, Bush MW, Nudler E, Walz T, de Lange T (2022) "Cryo-EM structure of the human CST-Pol alpha /primase complex in a recruitment state." Nat.Struct.Mol.Biol., 29, 813-819. doi: 10.1038/s41594-022-00766-y. cryo-EM structure of human cst bound to DNA polymerase alpha-primase in a recruitment state. SNAP output
7u5d DNA binding protein-DNA-RNA cryo-EM (3.52 Å) Park JU, Petassi MT, Hsieh SC, Mehrotra E, Schuler G, Budhathoki J, Truong VH, Thyme SB, Ke A, Kellogg EH, Peters JE (2023) "Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition." Mol.Cell, 83, 1827-1838.e6. doi: 10.1016/j.molcel.2023.05.005. I-f3b cascade-tniq full r-loop complex. SNAP output
7u5e DNA binding protein-DNA-RNA cryo-EM (4.03 Å) Park JU, Petassi MT, Hsieh SC, Mehrotra E, Schuler G, Budhathoki J, Truong VH, Thyme SB, Ke A, Kellogg EH, Peters JE (2023) "Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition." Mol.Cell, 83, 1827-1838.e6. doi: 10.1016/j.molcel.2023.05.005. I-f3b cascade-tniq partial r-loop complex. SNAP output
7u6k DNA binding protein-DNA X-ray (2.38 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence.. SNAP output
7u72 transferase-DNA X-ray (1.53 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:ground state at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
7u73 transferase-DNA X-ray (1.56 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 0.5 mm mn2+ for 1800s. SNAP output
7u74 transferase-DNA X-ray (1.52 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 0.5 mm mn2+ for 1800s then with 10 mm mn2+ for 30s. SNAP output
7u75 transferase-DNA X-ray (1.55 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 0.5 mm mn2+ for 1800s then with 10 mm mn2+ for 90s. SNAP output
7u76 transferase-DNA X-ray (1.69 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 0.5 mm mn2+ for 1800s then with 10 mm mn2+ for 300s. SNAP output
7u77 transferase-DNA X-ray (1.58 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 40s. SNAP output
7u78 transferase-DNA X-ray (1.61 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 80s. SNAP output
7u79 transferase-DNA X-ray (1.69 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 140s. SNAP output
7u7a transferase-DNA X-ray (1.58 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 200s. SNAP output
7u7b transferase-DNA X-ray (1.58 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 250s. SNAP output
7u7c transferase-DNA X-ray (1.55 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 300s. SNAP output
7u7d transferase-DNA X-ray (1.57 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 30s. SNAP output
7u7e transferase-DNA X-ray (1.58 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 60s. SNAP output
7u7f transferase-DNA X-ray (1.65 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 90s. SNAP output
7u7g transferase-DNA X-ray (1.77 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 120s. SNAP output
7u7i transferase-DNA X-ray (1.57 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 180s. SNAP output
7u7j transferase-DNA X-ray (1.58 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 300s. SNAP output
7u7k transferase-DNA X-ray (1.67 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mm mn2+ for 600s. SNAP output
7u7l transferase-DNA X-ray (1.47 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mm mg2+ for 300s with flipped-out product. SNAP output
7u7o DNA binding protein-DNA X-ray (2.97 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional t-a rich sequence.. SNAP output
7u7r transferase-DNA X-ray (1.64 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex:no me2+ soaking. SNAP output
7u7s transferase-DNA X-ray (1.6 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.025 mm mg2+ for 600s. SNAP output
7u7t transferase-DNA X-ray (1.55 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.05 mm mg2+ for 600s. SNAP output
7u7u transferase-DNA X-ray (1.54 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.1 mm mg2+ for 600s. SNAP output
7u7v transferase-DNA X-ray (1.65 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.4 mm mg2+ for 600s. SNAP output
7u7w transferase-DNA X-ray (1.66 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 1.0 mm mg2+ for 600s. SNAP output
7u7x transferase-DNA X-ray (1.65 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 2.0 mm mg2+ for 600s. SNAP output
7u7y transferase-DNA X-ray (1.78 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.06 mm mn2+ for 600s. SNAP output
7u7z transferase-DNA X-ray (1.67 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.12 mm mn2+ for 600s. SNAP output
7u80 transferase-DNA X-ray (1.83 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.25 mm mn2+ for 600s. SNAP output
7u81 transferase-DNA X-ray (1.6 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 0.5 mm mn2+ for 600s. SNAP output
7u82 transferase-DNA X-ray (1.55 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 1.0 mm mn2+ for 600s. SNAP output
7u83 transferase-DNA X-ray (1.55 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 3.0 mm mn2+ for 600s. SNAP output
7u84 transferase-DNA X-ray (1.71 Å) Chang C, Lee Luo C, Gao Y (2022) "In crystallo observation of three metal ion promoted DNA polymerase misincorporation." Nat Commun, 13, 2346. doi: 10.1038/s41467-022-30005-3. Human DNA polymerase eta-DNA-dgmpnpp ternary mismatch complex in 6.0 mm mn2+ for 600s. SNAP output
7ub2 DNA binding protein-DNA cryo-EM (3.4 Å) Caldwell BJ, Norris AS, Karbowski CF, Wiegand AM, Wysocki VH, Bell CE (2022) "Structure of a RecT/Red beta family recombinase in complex with a duplex intermediate of DNA annealing." Nat Commun, 13, 7855. doi: 10.1038/s41467-022-35572-z. Structure of rect protein from listeria innoccua phage a118 in complex with 83-mer annealed duplex. SNAP output
7ubl gene regulation-DNA X-ray (2.177 Å) Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH (2022) "In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel." Proc.Natl.Acad.Sci.USA, 119, e2205278119. doi: 10.1073/pnas.2205278119. Transcription antitermination factor qlambda in complex with q-lambda-binding-element DNA. SNAP output
7ubm gene regulation, transferase-DNA-RNA cryo-EM (3.13 Å) Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH (2022) "In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel." Proc.Natl.Acad.Sci.USA, 119, e2205278119. doi: 10.1073/pnas.2205278119. Transcription antitermination complex: "pre-engaged" qlambda-loading complex. SNAP output
7ubn gene regulation, transferase-DNA-RNA cryo-EM (3.36 Å) Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH (2022) "In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel." Proc.Natl.Acad.Sci.USA, 119, e2205278119. doi: 10.1073/pnas.2205278119. Transcription antitermination complex: nusa-containing "engaged" qlambda-loading complex. SNAP output
7ubu transferase-DNA X-ray (2.39 Å) Fang J, Jiang J, Leichter SM, Liu J, Biswal M, Khudaverdyan N, Zhong X, Song J (2022) "Mechanistic basis for maintenance of CHG DNA methylation in plants." Nat Commun, 13, 3877. doi: 10.1038/s41467-022-31627-3. Crystal structure of zmet2 in complex with hemimethylated cag DNA and a histone h3kc9me2 peptide. SNAP output
7ud5 DNA binding protein cryo-EM (4.25 Å) Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C (2022) "Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome." Proc.Natl.Acad.Sci.USA, 119, e2205691119. doi: 10.1073/pnas.2205691119. Complex between mll1-wrad and an h2b-ubiquitinated nucleosome. SNAP output
7ufi DNA binding protein-DNA cryo-EM (3.4 Å) Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernandez IS, Sternberg SH (2022) "Selective TnsC recruitment enhances the fidelity of RNA-guided transposition." Nature, 609, 384-393. doi: 10.1038/s41586-022-05059-4. Vchtnsc aaa+ atpase with DNA, single heptamer. SNAP output
7ufm DNA binding protein-DNA cryo-EM (3.9 Å) Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernandez IS, Sternberg SH (2022) "Selective TnsC recruitment enhances the fidelity of RNA-guided transposition." Nature, 609, 384-393. doi: 10.1038/s41586-022-05059-4. Vchtnsc aaa+ with DNA (double heptamer). SNAP output
7ufx DNA binding protein X-ray (2.8 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate repe54 sequence and an additional g-c rich sequence, respectively.. SNAP output
7ugw isomerase-antibiotic-DNA X-ray (3.0 Å) Imai Y, Hauk G, Quigley J, Liang L, Son S, Ghiglieri M, Gates MF, Morrissette M, Shahsavari N, Niles S, Baldisseri D, Honrao C, Ma X, Guo JJ, Berger JM, Lewis K (2022) "Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis." Nat.Chem.Biol., 18, 1236-1244. doi: 10.1038/s41589-022-01102-7. M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin. SNAP output
7uik transcription cryo-EM (7.7 Å) Gorbea Colon JJ, Palao 3rd L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K (2023) "Structural basis of a transcription pre-initiation complex on a divergent promoter." Mol.Cell, 83, 574. doi: 10.1016/j.molcel.2023.01.011. Mediator-pic early (tail a + upstream DNA & activator). SNAP output
7uin RNA binding protein-RNA-DNA cryo-EM (2.8 Å) Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM (2022) "Structures of a mobile intron retroelement poised to attack its structured DNA target." Science, 378, 627-634. doi: 10.1126/science.abq2844. Cryoem structure of an group ii intron retroelement. SNAP output
7ujl recombination-DNA cryo-EM (3.3 Å) Newing TP, Brewster JL, Fitschen LJ, Bouwer JC, Johnston NP, Yu H, Tolun G (2022) "Red beta 177 annealase structure reveals details of oligomerization and lambda Red-mediated homologous DNA recombination." Nat Commun, 13, 5649. doi: 10.1038/s41467-022-33090-6. Bacteriophage lambda red-beta n-terminal domain helical assembly in complex with dsDNA. SNAP output
7um0 transcription cryo-EM (3.8 Å) Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG (2022) "Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase." Nat Commun, 13, 3526. doi: 10.1038/s41467-022-31214-6. Structure of the phage ar9 non-virion RNA polymerase holoenzyme in complex with two DNA oligonucleotides containing the ar9 p077 promoter as determined by cryo-EM. SNAP output
7un7 replication X-ray (2.04 Å) Chandramouly G, Jamsen J, Borisonnik N, Tyagi M, Calbert ML, Tredinnick T, Ozdemir AY, Kent T, Demidova EV, Arora S, Wilson SH, Pomerantz RT (2023) "Pol lambda promotes microhomology-mediated end-joining." Nat.Struct.Mol.Biol., 30, 107-114. doi: 10.1038/s41594-022-00895-4. DNA polymerase lambda in complex with a 1nt microhomology substrate. SNAP output
7uog DNA binding protein-DNA X-ray (2.63 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and asymmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence.. SNAP output
7upz DNA binding protein-DNA X-ray (2.487 Å) Lountos GT, Cherry S, Tropea JE, Wlodawer A, Miller M (2022) "Structural basis for cell type specific DNA binding of C/EBP beta : The case of cell cycle inhibitor p15INK4b promoter." J.Struct.Biol., 214, 107918. doi: 10.1016/j.jsb.2022.107918. Structural basis for cell type specific DNA binding of c-ebpbeta: the case of cell cycle inhibitor p15ink4b promoter. SNAP output
7ur0 DNA binding protein-DNA X-ray (3.3 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and scaffold-insert duplexes (21mer and 10mer) containing the cognate repe54 sequence and an additional t-a rich sequence, respectively.. SNAP output
7usf hydrolase-DNA cryo-EM (3.5 Å) Jozwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman AN, Lyumkis D (2022) "B-to-A transition in target DNA during retroviral integration." Nucleic Acids Res., 50, 8898-8918. doi: 10.1093/nar/gkac644. Mouse mammary tumor virus strand transfer complex intasome. SNAP output
7ut1 hydrolase-DNA cryo-EM (3.8 Å) Jozwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman AN, Lyumkis D (2022) "B-to-A transition in target DNA during retroviral integration." Nucleic Acids Res., 50, 8898-8918. doi: 10.1093/nar/gkac644. Higher-order assembly of multiple mmtv strand transfer complex intasomes. SNAP output
7utn RNA binding protein-RNA-DNA cryo-EM (2.74 Å) Schuler G, Hu C, Ke A (2022) "Structural basis for RNA-guided DNA cleavage by IscB-omega RNA and mechanistic comparison with Cas9." Science, 376, 1476-1481. doi: 10.1126/science.abq7220. Iscb and wrna bound to target DNA. SNAP output
7utt transferase-DNA X-ray (2.04 Å) Wu S, Gabelli SB, Sohn JS "Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination." Structure of non-hydrolyzable atp (apcpp) binds to cyclic gmp amp synthase (cgas) through mn coordination. SNAP output
7uux transferase-DNA X-ray (2.26 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Atp binds to cyclic gmp amp synthase (cgas) through mg coordination. SNAP output
7uv6 DNA binding protein-DNA X-ray (2.72 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and scaffold duplex (21mer) containing the cognate repe54 sequence and an insert duplex (10mer) with guest tamra-labelled thymine and g-c rich sequence.. SNAP output
7uv7 DNA binding protein-DNA X-ray (3.02 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and scaffold duplex (21mer) containing the cognate repe54 sequence and an insert duplex (10mer) with guest tamra-labelled thymine and t-a rich sequence.. SNAP output
7uv9 gene regulation-DNA cryo-EM (3.2 Å) Spangler CJ, Skrajna A, Foley CA, Nguyen A, Budziszewski GR, Azzam DN, Arteaga EC, Simmons HC, Smith CB, Wesley NA, Wilkerson EM, McPherson JE, Kireev D, James LI, Frye SV, Goldfarb D, McGinty RK (2023) "Structural basis of paralog-specific KDM2A/B nucleosome recognition." Nat.Chem.Biol., 19, 624-632. doi: 10.1038/s41589-023-01256-y. Kdm2a-nucleosome structure stabilized by h3k36c-unc8015 covalent conjugate. SNAP output
7uwe transferase-hydrolase-DNA-RNA cryo-EM (2.9 Å) Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E (2023) "RNA polymerase drives ribonucleotide excision DNA repair in E. coli." Cell, 186, 2425. doi: 10.1016/j.cell.2023.04.029. Cryoem structure of e. coli transcription-coupled ribonucleotide excision repair (tc-rer) complex. SNAP output
7uwh transferase-hydrolase-DNA-RNA cryo-EM (3.1 Å) Hao Z, Gowder M, Proshkin S, Bharati BK, Epshtein V, Svetlov V, Shamovsky I, Nudler E (2023) "RNA polymerase drives ribonucleotide excision DNA repair in E. coli." Cell, 186, 2425. doi: 10.1016/j.cell.2023.04.029. Cryoem structure of e. coli transcription-coupled ribonucleotide excision repair (tc-rer) complex bound to ribonucleotide substrate. SNAP output
7ux9 gene regulation cryo-EM (3.2 Å) Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA (2023) "Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation." Cell, 186, 4100. doi: 10.1016/j.cell.2023.08.001. Arabidopsis ddm1 bound to nucleosome (h2a.w, h2b, h3.3, h4, with 147 bp DNA). SNAP output
7uxd hydrolase-DNA X-ray (1.5 Å) Maiti A, Hedger AK, Myint W, Balachandran V, Watts JK, Schiffer CA, Matsuo H (2022) "Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state." Nat Commun, 13, 7117. doi: 10.1038/s41467-022-34752-1. Crystal structure of apobec3g catalytic domain complex with ssDNA containing 2'-deoxy zebularine.. SNAP output
7uxw transferase-DNA X-ray (2.57 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of atp and gtp bind to cyclic gmp amp synthase (cgas) through mg coordination. SNAP output
7uxy DNA binding protein-DNA X-ray (3.15 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of protein variant replication initiator protein repe54 (l53g,q54g,e55g) and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence.. SNAP output
7uy5 replication cryo-EM (3.5 Å) He Y, Song H, Chan H, Liu B, Wang Y, Susac L, Zhou ZH, Feigon J (2022) "Structure of Tetrahymena telomerase-bound CST with polymerase alpha-primase." Nature, 608, 813-818. doi: 10.1038/s41586-022-04931-7. Tetrahymena telomerase with cst. SNAP output
7uy6 replication cryo-EM (2.9 Å) He Y, Song H, Chan H, Liu B, Wang Y, Susac L, Zhou ZH, Feigon J (2022) "Structure of Tetrahymena telomerase-bound CST with polymerase alpha-primase." Nature, 608, 813-818. doi: 10.1038/s41586-022-04931-7. Tetrahymena telomerase at 2.9 angstrom resolution. SNAP output
7uy7 replication cryo-EM (4.2 Å) He Y, Song H, Chan H, Liu B, Wang Y, Susac L, Zhou ZH, Feigon J (2022) "Structure of Tetrahymena telomerase-bound CST with polymerase alpha-primase." Nature, 608, 813-818. doi: 10.1038/s41586-022-04931-7. Tetrahymena cst with polymerase alpha-primase. SNAP output
7uyn DNA binding protein-DNA X-ray (1.65 Å) Shukla MS, Hoshika S, Benner SA, Georgiadis MM (2023) "Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form." Philos.Trans.R.Soc.Lond.B Biol.Sci., 378, 20220028. doi: 10.1098/rstb.2022.0028. Crystal structure of b-form alien DNA 5'-cttbppbbsszzsaag in a host-guest complex with the n-terminal fragment of moloney murine leukemia virus reverse transcriptase. SNAP output
7uyo DNA binding protein-DNA X-ray (1.65 Å) Shukla MS, Hoshika S, Benner SA, Georgiadis MM (2023) "Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form." Philos.Trans.R.Soc.Lond.B Biol.Sci., 378, 20220028. doi: 10.1098/rstb.2022.0028. Crystal structure of b-form alien DNA 5'-cttsspbzpszbbaag in a host-guest complex with the n-terminal fragment of moloney murine leukemia virus reverse transcriptase. SNAP output
7uyp DNA binding protein-DNA X-ray (1.5 Å) Shukla MS, Hoshika S, Benner SA, Georgiadis MM (2023) "Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form." Philos.Trans.R.Soc.Lond.B Biol.Sci., 378, 20220028. doi: 10.1098/rstb.2022.0028. Crystal structure of b-form alien DNA 5'-cttzzpbsbszppaag in a host-guest complex with the n-terminal fragment of moloney murine leukemia virus reverse transcriptase. SNAP output
7uyq transferase-DNA X-ray (2.57 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of gtp binds to cyclic gmp amp synthase (cgas) through mg coordination. SNAP output
7uyz transferase-DNA X-ray (2.49 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound 5 -pppg(2 ,5 )pg. SNAP output
7uzr transferase-DNA X-ray (2.7 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound 5 -pppg(2 ,5 )pg. SNAP output
7v0c transferase-DNA X-ray (2.57 Å) Wu S, Gabelli SB, Sohn JS "Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -pppG(2 ,5 )pG." Structure of ternary complex of cgas with dsDNA and bound 5 -pppg(2 ,5 )pg. SNAP output
7v0r transferase-DNA X-ray (2.51 Å) Wu S, Gabelli SB, Sohn JS "Structure of Ternary Complex of cGAS with dsDNA and Bound 5 -ppcpG(2 ,5 )pA." Structure of ternary complex of cgas with dsDNA and bound 5 -ppcpg(2 ,5 )pa. SNAP output
7v0w transferase-DNA X-ray (2.66 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound 5 -pppg(2,5 )pa. SNAP output
7v59 RNA binding protein-RNA-DNA cryo-EM (5.26 Å) Yang M, Sun R, Deng P, Yang Y, Wang W, Liu JG, Chen C (2021) "Nonspecific interactions between SpCas9 and dsDNA sites located downstream of the PAM mediate facilitated diffusion to accelerate target search." Chem Sci, 12, 12776-12784. doi: 10.1039/d1sc02633j. cryo-EM structure of spycas9-sgrna-DNA dimer. SNAP output
7v5n immune system-DNA X-ray (1.7 Å) Saito T, Shimizu Y, Tsukakoshi K, Abe K, Lee J, Ueno K, Asano R, Jones BV, Yamada T, Nakano T, Tong J, Hishiki A, Hara K, Hashimoto H, Sode K, Toyo'oka T, Todoroki K, Ikebukuro K (2022) "Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection." Biosens.Bioelectron., 203, 114027. doi: 10.1016/j.bios.2022.114027. Crystal structure of fab fragment of bevacizumab bound to DNA aptamer. SNAP output
7v6w DNA binding protein-antitoxin-DNA X-ray (2.55 Å) Xue L, Khan MH, Yue J, Zhu Z, Niu L (2022) "The two paralogous copies of the YoeB-YefM toxin-antitoxin module in Staphylococcus aureus differ in DNA binding and recognition patterns." J.Biol.Chem., 298, 101457. doi: 10.1016/j.jbc.2021.101457. Crystal structure of heterohexameric sa2yoeb-sa2yefm complex bound to 26bp-DNA. SNAP output
7v90 DNA binding protein-DNA cryo-EM (3.5 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric mononucleosome. SNAP output
7v94 RNA binding protein-RNA-DNA cryo-EM (2.7 Å) Kurihara N, Nakagawa R, Hirano H, Okazaki S, Tomita A, Kobayashi K, Kusakizako T, Nishizawa T, Yamashita K, Scott DA, Nishimasu H, Nureki O (2022) "Structure of the type V-C CRISPR-Cas effector enzyme." Mol.Cell, 82, 1865-1877.e4. doi: 10.1016/j.molcel.2022.03.006. cryo-EM structure of the cas12c2-sgrna-target DNA ternary complex. SNAP output
7v96 DNA binding protein-DNA cryo-EM (3.92 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric dinucleosome. SNAP output
7v99 replication cryo-EM (3.54 Å) Wan F, Ding Y, Zhang Y, Wu Z, Li S, Yang L, Yan X, Lan P, Li G, Wu J, Lei M (2021) "Zipper head mechanism of telomere synthesis by human telomerase." Cell Res., 31, 1275-1290. doi: 10.1038/s41422-021-00586-7. Catalytic core of human telomerase holoenzyme. SNAP output
7v9c DNA binding protein-DNA cryo-EM (4.5 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric dinucleosome in open state. SNAP output
7v9f DNA binding protein-DNA X-ray (2.5 Å) Zhang J, Zhang Y, You Q, Huang C, Zhang T, Wang M, Zhang T, Yang X, Xiong J, Li Y, Liu CP, Zhang Z, Xu RM, Zhu B (2022) "Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation." Science, 375, 1053-1058. doi: 10.1126/science.abm0730. Selenomethionine mutant (l740sem) of ben4 domain of protein bend3 with DNA. SNAP output
7v9g DNA binding protein-DNA X-ray (3.5 Å) Zhang J, Zhang Y, You Q, Huang C, Zhang T, Wang M, Zhang T, Yang X, Xiong J, Li Y, Liu CP, Zhang Z, Xu RM, Zhu B (2022) "Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation." Science, 375, 1053-1058. doi: 10.1126/science.abm0730. Native ben4 domain of protein bend3 with DNA. SNAP output
7v9i DNA binding protein-DNA X-ray (3.5 Å) Zhang J, Zhang Y, You Q, Huang C, Zhang T, Wang M, Zhang T, Yang X, Xiong J, Li Y, Liu CP, Zhang Z, Xu RM, Zhu B (2022) "Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation." Science, 375, 1053-1058. doi: 10.1126/science.abm0730. The monomer mutant of ben4 domain of protein bend3 with DNA. SNAP output
7v9j DNA binding protein-DNA cryo-EM (8.0 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric trinucleosome. SNAP output
7v9k DNA binding protein-DNA cryo-EM (8.1 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric tetranucleosome. SNAP output
7v9s DNA binding protein-DNA cryo-EM (11.0 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric trinucleosome in open state. SNAP output
7v9u transferase-DNA-RNA cryo-EM (3.12 Å) Wang Y, Guan Z, Wang C, Nie Y, Chen Y, Qian Z, Cui Y, Xu H, Wang Q, Zhao F, Zhang D, Tao P, Sun M, Yin P, Jin S, Wu S, Zou T (2022) "Cryo-EM structures of Escherichia coli Ec86 retron complexes reveal architecture and defence mechanism." Nat Microbiol, 7, 1480-1489. doi: 10.1038/s41564-022-01197-7. cryo-EM structure of e.coli retron-ec86 (rt-msDNA-RNA) at 3.2 angstrom. SNAP output
7v9x transferase-RNA binding protein-DNA-RNA cryo-EM (2.82 Å) Wang TJ, Guan ZY, Zou TT "Structural insight into anti-phage Retron-Ec86 complex." cryo-EM structure of e.coli retron-ec86 in complex with its effector at 2.8 angstrom. SNAP output
7va4 DNA binding protein-DNA cryo-EM (14.0 Å) Soman A, Wong SY, Korolev N, Surya W, Lattmann S, Vogirala VK, Chen Q, Berezhnoy NV, van Noort J, Rhodes D, Nordenskiold L (2022) "Columnar structure of human telomeric chromatin." Nature, 609, 1048-1055. doi: 10.1038/s41586-022-05236-5. Telomeric tetranucleosome in open state. SNAP output
7vbm DNA binding protein cryo-EM (3.4 Å) Hirai S, Tomimatsu K, Miyawaki-Kuwakado A, Takizawa Y, Komatsu T, Tachibana T, Fukushima Y, Takeda Y, Negishi L, Kujirai T, Koyama M, Ohkawa Y, Kurumizaka H (2022) "Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant." Nucleic Acids Res., 50, 72-91. doi: 10.1093/nar/gkab1137. The mouse nucleosome structure containing h3mm18 aided by pl2-6 scfv. SNAP output
7vdt DNA binding protein cryo-EM (2.8 Å) Yuan JJ, Chen KJ, Zhang WB, Chen ZC (2022) "Structure of human chromatin-remodelling PBAF complex bound to a nucleosome." Nature, 605, 166-171. doi: 10.1038/s41586-022-04658-5. The motor-nucleosome module of human chromatin remodeling pbaf-nucleosome complex. SNAP output
7vdv DNA binding protein cryo-EM (3.4 Å) Yuan JJ, Chen KJ, Zhang WB, Chen ZC (2022) "Structure of human chromatin-remodelling PBAF complex bound to a nucleosome." Nature, 605, 166-171. doi: 10.1038/s41586-022-04658-5. The overall structure of human chromatin remodeling pbaf-nucleosome complex. SNAP output
7ve5 DNA binding protein-DNA X-ray (2.0 Å) Kumar JV, Tseng TS, Lou YC, Wei SY, Wu TH, Tang HC, Chiu YC, Hsu CH, Chen C (2022) "Structural insights into DNA binding domain of vancomycin-resistance-associated response regulator in complex with its promoter DNA from Staphylococcus aureus." Protein Sci., 31, e4286. doi: 10.1002/pro.4286. C-terminal domain of vrar. SNAP output
7vg8 viral protein X-ray (2.04 Å) Zhang SY, Wang CN "structure of TYLCV Rep complexed with ssDNA." Tylcv rep-DNA. SNAP output
7vjm transcription-DNA X-ray (3.0 Å) Liu Y, Zhang L, Guo M, Chen L, Wu B, Huang H (2021) "Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2." J.Biol.Chem., 297, 101357. doi: 10.1016/j.jbc.2021.101357. Aca1 in complex with 19bp palindromic DNA substrate. SNAP output
7vjq transcription-DNA X-ray (2.79 Å) Liu Y, Zhang L, Guo M, Chen L, Wu B, Huang H (2021) "Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2." J.Biol.Chem., 297, 101357. doi: 10.1016/j.jbc.2021.101357. Pectobacterium phage zf40 apo-aca2 complexed with 26bp DNA substrate. SNAP output
7vn2 transcription X-ray (2.42 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning atcacgtgat. SNAP output
7vn3 transcription X-ray (1.94 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning cacacgtgtg. SNAP output
7vn4 transcription X-ray (2.1 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning tccacgtgga. SNAP output
7vn5 transcription X-ray (1.95 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning ttcacgtgaa. SNAP output
7vn6 transcription X-ray (2.79 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning cgcacgtgcg. SNAP output
7vn7 transcription X-ray (2.11 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning gacacgtgtc. SNAP output
7vn8 transcription X-ray (2.04 Å) Nosaki S, Mitsuda N, Sakamoto S, Kusubayashi K, Yamagami A, Xu Y, Bui TBC, Terada T, Miura K, Nakano T, Tanokura M, Miyakawa T (2022) "Brassinosteroid-induced gene repression requires specific and tight promoter binding of BIL1/BZR1 via DNA shape readout." Nat.Plants, 8, 1440-1452. doi: 10.1038/s41477-022-01289-6. Crystal structure of mbp-fused bil1-bzr1 (21-90) in complex with double-stranded DNA contaning gtcacgtgac. SNAP output
7vo0 DNA binding protein cryo-EM (3.4 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (trimer of dimers). SNAP output
7vo9 DNA binding protein cryo-EM (3.8 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. Streptomyces coelicolor zinc uptake regulator complexed with zinc and DNA (dimer of dimers). SNAP output
7vou transcription-DNA X-ray (3.1 Å) Choi Y, Luo Y, Lee S, Jin H, Yoon HJ, Hahn Y, Bae J, Lee HH (2022) "FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations." Nucleic Acids Res., 50, 8929-8946. doi: 10.1093/nar/gkac673. The crystal structure of human forkhead box protein in complex with DNA 1. SNAP output
7vov transcription-DNA X-ray (3.15 Å) Choi Y, Luo Y, Lee S, Jin H, Yoon HJ, Hahn Y, Bae J, Lee HH (2022) "FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations." Nucleic Acids Res., 50, 8929-8946. doi: 10.1093/nar/gkac673. The crystal structure of human forkhead box protein in complex with DNA 2. SNAP output
7vox transcription-DNA X-ray (2.1 Å) Choi Y, Luo Y, Lee S, Jin H, Yoon HJ, Hahn Y, Bae J, Lee HH (2022) "FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations." Nucleic Acids Res., 50, 8929-8946. doi: 10.1093/nar/gkac673. The crystal structure of human forkhead box protein a in complex with DNA 2. SNAP output
7vp1 DNA binding protein X-ray (2.902 Å) Zhang Y, Xu YP, Wang B, Su XD "Structural basis for DNA recognition by TCP transcription factors." Structure of a transcription factor and DNA complex. SNAP output
7vp2 DNA binding protein X-ray (1.92 Å) Zhang Y, Xu YP, Wang B, Su XD "Structural basis for DNA recognition by TCP transcription factors." Structure of a transcription factor and DNA complex. SNAP output
7vp3 DNA binding protein X-ray (3.003 Å) Zhang Y, Xu YP, Wang B, Su XD "Structural basis for DNA recognition by TCP transcription factors." Structure of a transcription factor and DNA complex. SNAP output
7vp4 DNA binding protein X-ray (3.04 Å) Zhang Y, Xu YP, Wang B, Su XD "Structural basis for DNA recognition by TCP transcription factors." Structure of a transcription factor and DNA complex. SNAP output
7vp5 DNA binding protein X-ray (2.992 Å) Zhang Y, Xu YP, Wang B, Su XD "Structural basis for DNA recognition by TCP transcription factors." Structure of a transcription factor and DNA complex. SNAP output
7vp7 DNA binding protein X-ray (2.653 Å) Zhang Y, Xu YP, Wang B, Su XD "Structural basis for DNA recognition by TCP transcription factors." Structure of a transcription factor and DNA complex. SNAP output
7vpd DNA binding protein cryo-EM (3.77 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. cryo-EM structure of streptomyces coelicolor rnap-promoter open complex with one zur dimers. SNAP output
7vpz DNA binding protein cryo-EM (4.14 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. cryo-EM structure of streptomyces coelicolor transcription initial complex with one zur dimer. SNAP output
7vru transferase-DNA X-ray (2.4 Å) Zhu J, Gao Y, Wang Y, Zhan Q, Feng H, Luo X, Li P, Liu S, Hou H, Gao P (2022) "Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems." Nat Commun, 13, 6391. doi: 10.1038/s41467-022-34085-z. Crystal structure of pacii_m1m2s-DNA-sah complex. SNAP output
7vs4 transferase-DNA X-ray (2.55 Å) Zhu J, Gao Y, Wang Y, Zhan Q, Feng H, Luo X, Li P, Liu S, Hou H, Gao P (2022) "Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems." Nat Commun, 13, 6391. doi: 10.1038/s41467-022-34085-z. Crystal structure of pacii_m1m2s-DNA(m6a)-sah complex. SNAP output
7vup DNA binding protein-DNA X-ray (3.4 Å) Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VY (2023) "Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation." Elife, 12. doi: 10.7554/eLife.86258. Structure of nf-kb p52 homodimer bound to +1--1 swap p-selectin kb DNA fragment. SNAP output
7vuq DNA binding protein-DNA X-ray (3.1 Å) Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VY (2023) "Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation." Elife, 12. doi: 10.7554/eLife.86258. Structure of nf-kb p52 homodimer bound to a-t-centric p-selectin kb DNA fragment. SNAP output
7vvu DNA binding protein-DNA cryo-EM (3.4 Å) Qu K, Chen K, Wang H, Li X, Chen Z (2022) "Structure of the NuA4 acetyltransferase complex bound to the nucleosome." Nature, 610, 569-574. doi: 10.1038/s41586-022-05303-x. Nua4 hat module bound to the nucleosome. SNAP output
7vvz DNA binding protein-DNA cryo-EM (8.8 Å) Qu K, Chen K, Wang H, Li X, Chen Z (2022) "Structure of the NuA4 acetyltransferase complex bound to the nucleosome." Nature, 610, 569-574. doi: 10.1038/s41586-022-05303-x. Nua4 bound to the nucleosome. SNAP output
7vw3 DNA binding protein-RNA-DNA cryo-EM (3.8 Å) Du W, Zhu H, Qian J, Xue D, Zheng S, Huang Q (2023) "Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State." Int J Mol Sci, 24. doi: 10.3390/ijms24021204. cryo-EM structure of sacas9-sgrna-DNA ternary complex. SNAP output
7vwz transcription-DNA cryo-EM (4.0 Å) Shi J, Wang F, Li F, Wang L, Xiong Y, Wen A, Jin Y, Jin S, Gao F, Feng Z, Li J, Zhang Y, Shang Z, Wang S, Feng Y, Lin W (2022) "Structural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator." Nucleic Acids Res., 50, 5974-5987. doi: 10.1093/nar/gkac433. cryo-EM structure of rob-dependent transcription activation complex in a unique conformation. SNAP output
7vyx RNA binding protein-RNA-DNA X-ray (3.2 Å) Zhang B, Lin J, Perculija V, Li Y, Lu Q, Chen J, Ouyang S (2022) "Structural insights into target DNA recognition and cleavage by the CRISPR-Cas12c1 system." Nucleic Acids Res., 50, 11820-11833. doi: 10.1093/nar/gkac987. Crystal structure of the selenomethionine(semet)-derived cas12c1 (d969a) ternary complex. SNAP output
7vz4 nuclear protein-DNA cryo-EM (1.89 Å) Takizawa Y, Ho CH, Sato S, Danev R, Kurumizaka H "Methods for High Resolution Cryo-EM Analyses of Nucleosomes." cryo-EM structure of human nucleosome core particle composed of the widom 601l DNA sequence. SNAP output
7w1m DNA binding protein-DNA cryo-EM (6.5 Å) Zhang H, Shi Z, Banigan EJ, Kim Y, Yu H, Bai XC, Finkelstein IJ (2023) "CTCF and R-loops are boundaries of cohesin-mediated DNA looping." Mol.Cell, 83, 2856-2871.e8. doi: 10.1016/j.molcel.2023.07.006. cryo-EM structure of human cohesin-ctcf-DNA complex. SNAP output
7w27 DNA binding protein-DNA X-ray (1.49 Å) Zheng L, Liu J, Niu L, Kamran M, Yang AWH, Jolma A, Dai Q, Hughes TR, Patel DJ, Zhang L, Prasanth SG, Yu Y, Ren A, Lai EC (2022) "Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins." Genes Dev., 36, 225-240. doi: 10.1101/gad.348993.121. Crystal structure of bend3-ben4-DNA complex. SNAP output
7w5p DNA binding protein-DNA X-ray (2.3 Å) Mu Y, Zhang L, Hu J, Zhou J, Lin HW, He C, Chen HZ, Zhang L (2022) "A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA." Nat.Chem.Biol., 18, 733-741. doi: 10.1038/s41589-022-01041-3. Crystal structure of the dioxygenase cctet from coprinopsis cinereain bound to 12bp n6-methyldeoxyadenine (6ma) containing duplex DNA. SNAP output
7w5w transcription-DNA cryo-EM (4.55 Å) Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W (2022) "Structural basis of three different transcription activation strategies adopted by a single regulator SoxS." Nucleic Acids Res., 50, 11359-11373. doi: 10.1093/nar/gkac898. cryo-EM structure of soxs-dependent transcription activation complex with micf promoter DNA. SNAP output
7w5x transcription-DNA cryo-EM (3.4 Å) Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W (2022) "Structural basis of three different transcription activation strategies adopted by a single regulator SoxS." Nucleic Acids Res., 50, 11359-11373. doi: 10.1093/nar/gkac898. cryo-EM structure of soxs-dependent transcription activation complex with zwf promoter DNA. SNAP output
7w5y transcription-DNA cryo-EM (4.2 Å) Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W (2022) "Structural basis of three different transcription activation strategies adopted by a single regulator SoxS." Nucleic Acids Res., 50, 11359-11373. doi: 10.1093/nar/gkac898. cryo-EM structure of soxs-dependent transcription activation complex with fpr promoter DNA. SNAP output
7w7l DNA binding protein-DNA-DNA X-ray (3.0 Å) Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VY (2023) "Structures of NF-kappa B p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation." Elife, 12. doi: 10.7554/eLife.86258. Structure of nf-kb p52 homodimer bound to 13-mer a-t-centric p-selectin kb DNA fragment. SNAP output
7w9v gene regulation cryo-EM (3.95 Å) Hatazawa S, Liu J, Takizawa Y, Zandian M, Negishi L, Kutateladze TG, Kurumizaka H (2022) "Structural basis for binding diversity of acetyltransferase p300 to the nucleosome." Iscience, 25, 104563. doi: 10.1016/j.isci.2022.104563. cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex i). SNAP output
7way RNA binding protein-RNA-DNA cryo-EM (2.9 Å) Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG (2022) "Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity." Mol.Cell, 82, 1199-1209.e6. doi: 10.1016/j.molcel.2022.02.002. Plmcasx-sgrnav1-dsDNA ternary complex at nts loading state. SNAP output
7waz RNA binding protein-DNA-RNA cryo-EM (3.4 Å) Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG (2022) "Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity." Mol.Cell, 82, 1199-1209.e6. doi: 10.1016/j.molcel.2022.02.002. Plmcasx-sgrnav1-dsDNA ternary complex at ts loading state. SNAP output
7wb0 RNA binding protein-RNA-DNA cryo-EM (3.2 Å) Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG (2022) "Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity." Mol.Cell, 82, 1199-1209.e6. doi: 10.1016/j.molcel.2022.02.002. Plmcasx-sgrnav1-dsDNA ternary complex at nts loading state with flexible h2 domain. SNAP output
7wb1 RNA binding protein-RNA-DNA cryo-EM (3.7 Å) Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG (2022) "Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity." Mol.Cell, 82, 1199-1209.e6. doi: 10.1016/j.molcel.2022.02.002. Plmcasx-sgrnav2-dsDNA ternary complex at nts loading state. SNAP output
7wb3 gene regulation-DNA X-ray (2.401 Å) Jeong KH, Lee HJ, Park YW, Lee JY (2022) "Structural Basis of Redox-Sensing Transcriptional Repressor Rex with Cofactor NAD + and Operator DNA." Int J Mol Sci, 23. doi: 10.3390/ijms23031578. Crystal structure of t. maritima rex in ternary complex. SNAP output
7wbv transcription cryo-EM (4.1 Å) Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H (2023) "Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome." J.Mol.Biol., 435, 168130. doi: 10.1016/j.jmb.2023.168130. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-4) of the nucleosome. SNAP output
7wbw transcription cryo-EM (7.1 Å) Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H (2023) "Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome." J.Mol.Biol., 435, 168130. doi: 10.1016/j.jmb.2023.168130. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-3.5) of the nucleosome. SNAP output
7wbx transcription cryo-EM (4.0 Å) Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H (2023) "Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome." J.Mol.Biol., 435, 168130. doi: 10.1016/j.jmb.2023.168130. RNA polymerase ii elongation complex bound with elf1 and spt4-5, stalled at shl(-3) of the nucleosome. SNAP output
7we6 viral protein cryo-EM (3.2 Å) Yang L, Zhang L, Yin P, Ding H, Xiao Y, Zeng J, Wang W, Zhou H, Wang Q, Zhang Y, Chen Z, Yang M, Feng Y (2022) "Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24." Nat Commun, 13, 1931. doi: 10.1038/s41467-022-29581-1. Structure of csy-acrif24-dsDNA. SNAP output
7wju RNA binding protein-RNA-DNA cryo-EM (2.69 Å) Wu Z, Liu D, Pan D, Shen H, Ji Q "Structure-directed functional evolution of the miniature CRISPR-AsCas12f1 system." cryo-EM structure of the ascas12f1-sgrnav1-dsDNA ternary complex. SNAP output
7wlr gene regulation-DNA cryo-EM (3.54 Å) Fukushima Y, Hatazawa S, Hirai S, Kujirai T, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H (2022) "Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones." J.Biochem., 172, 79-88. doi: 10.1093/jb/mvac043. cryo-EM structure of the nucleosome containing komagataella pastoris histones. SNAP output
7wm3 DNA binding protein-DNA X-ray (1.62 Å) Liu Y, Abula A, Xiao H, Guo H, Li T, Zheng L, Chen B, Nguyen HC, Ji X (2022) "Structural Insight Into hnRNP A2/B1 Homodimerization and DNA Recognition." J.Mol.Biol., 435, 167920. doi: 10.1016/j.jmb.2022.167920. Hnrnp a2-b1 rrms in complex with single-stranded DNA. SNAP output
7wnh transcription X-ray (3.1 Å) Zhao M, Wang N, Guo Y, Li J, Yin Y, Dong Y, Zhu J, Peng C, Xu T, Liu J (2022) "Integrative analysis reveals structural basis for transcription activation of Nurr1 and Nurr1-RXR alpha heterodimer." Proc.Natl.Acad.Sci.USA, 119, e2206737119. doi: 10.1073/pnas.2206737119. Crystal structure of nurr1 binding to nbre. SNAP output
7wnr antitoxin-DNA NMR Kumari K, Sarma SP (2022) "Structural and mutational analysis of MazE6-operator DNA complex provide insights into autoregulation of toxin-antitoxin systems." Commun Biol, 5, 963. doi: 10.1038/s42003-022-03933-5. Data-driven haddock model of mycobacterial nmaze6-operator DNA complex. SNAP output
7wq5 DNA binding protein X-ray (2.35 Å) Qiao Z, Kong Q, Tee WT, Lim ARQ, Teo MX, Olieric V, Low PM, Yang Y, Qian G, Ma W, Gao YG (2022) "Molecular basis of the key regulator WRINKLED1 in plant oil biosynthesis." Sci Adv, 8, eabq1211. doi: 10.1126/sciadv.abq1211. Crystal structure of arabidopsis transcriptional factor wrinkled1 with dsDNA. SNAP output
7wwv RNA binding protein-RNA-DNA cryo-EM (3.2 Å) Zhang M, Peng R, Peng Q, Liu S, Li Z, Zhang Y, Song H, Yang J, Xing X, Wang P, Qi J, Gao GF (2023) "Mechanistic insights into DNA binding and cleavage by a compact type I-F CRISPR-Cas system in bacteriophage." Proc.Natl.Acad.Sci.USA, 120, e2215098120. doi: 10.1073/pnas.2215098120. DNA bound-icp1 csy complex. SNAP output
7x1n transcription-DNA X-ray (3.315 Å) Zhang M, Zhang H, Li Z, Bai L, Wang Q, Li J, Jiang M, Xue Q, Cheng N, Zhang W, Mao D, Chen Z, Huang J, Meng G, Chen Z, Chen SJ (2022) "Functional, structural, and molecular characterizations of the leukemogenic driver MEF2D-HNRNPUL1 fusion." Blood, 140, 1390-1407. doi: 10.1182/blood.2022016241. Crystal structure of mef2d-mre complex. SNAP output
7x3t protein binding cryo-EM (5.4 Å) Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z (2024) "Structure of the ISW1a complex bound to the dinucleosome." Nat.Struct.Mol.Biol., 31, 266-274. doi: 10.1038/s41594-023-01174-6. cryo-EM structure of isw1a-dinucleosome. SNAP output
7x3v protein binding-DNA cryo-EM (3.09 Å) Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z (2024) "Structure of the ISW1a complex bound to the dinucleosome." Nat.Struct.Mol.Biol., 31, 266-274. doi: 10.1038/s41594-023-01174-6. cryo-EM structure of ioc3-n2 nucleosome. SNAP output
7x3w protein binding cryo-EM (3.1 Å) Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z (2024) "Structure of the ISW1a complex bound to the dinucleosome." Nat.Struct.Mol.Biol., 31, 266-274. doi: 10.1038/s41594-023-01174-6. cryo-EM structure of isw1-n1 nucleosome. SNAP output
7x3x protein binding-DNA cryo-EM (3.2 Å) Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z (2024) "Structure of the ISW1a complex bound to the dinucleosome." Nat.Struct.Mol.Biol., 31, 266-274. doi: 10.1038/s41594-023-01174-6. cryo-EM structure of n1 nucleosome-ra. SNAP output
7x57 DNA binding protein-DNA cryo-EM (3.63 Å) Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H (2022) "Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B." Proc.Natl.Acad.Sci.USA, 119, e2206542119. doi: 10.1073/pnas.2206542119. cryo-EM structure of human subnucleosome (closed form). SNAP output
7x58 DNA binding protein-DNA cryo-EM (3.93 Å) Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H (2022) "Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B." Proc.Natl.Acad.Sci.USA, 119, e2206542119. doi: 10.1073/pnas.2206542119. cryo-EM structure of human subnucleosome (open form). SNAP output
7x5e transcription-DNA X-ray (2.3 Å) Sengoku T, Shiina M, Suzuki K, Hamada K, Sato K, Uchiyama A, Kobayashi S, Oguni A, Itaya H, Kasahara K, Moriwaki H, Watanabe C, Honma T, Okada C, Baba S, Ohta T, Motohashi H, Yamamoto M, Ogata K (2022) "Structural basis of transcription regulation by CNC family transcription factor, Nrf2." Nucleic Acids Res., 50, 12543-12557. doi: 10.1093/nar/gkac1102. Nrf2-mafg heterodimer bound with csmbe1. SNAP output
7x5f transcription-DNA X-ray (2.6 Å) Sengoku T, Shiina M, Suzuki K, Hamada K, Sato K, Uchiyama A, Kobayashi S, Oguni A, Itaya H, Kasahara K, Moriwaki H, Watanabe C, Honma T, Okada C, Baba S, Ohta T, Motohashi H, Yamamoto M, Ogata K (2022) "Structural basis of transcription regulation by CNC family transcription factor, Nrf2." Nucleic Acids Res., 50, 12543-12557. doi: 10.1093/nar/gkac1102. Nrf2-mafg heterodimer bound with csmbe2. SNAP output
7x5g transcription X-ray (2.3 Å) Sengoku T, Shiina M, Suzuki K, Hamada K, Sato K, Uchiyama A, Kobayashi S, Oguni A, Itaya H, Kasahara K, Moriwaki H, Watanabe C, Honma T, Okada C, Baba S, Ohta T, Motohashi H, Yamamoto M, Ogata K (2022) "Structural basis of transcription regulation by CNC family transcription factor, Nrf2." Nucleic Acids Res., 50, 12543-12557. doi: 10.1093/nar/gkac1102. Nrf2 (a510y)-mafg heterodimer bound with csmbe2. SNAP output
7x5k hydrolase-DNA cryo-EM (3.8 Å) Yu D, Song W, Tan EYJ, Liu L, Cao Y, Jirschitzka J, Li E, Logemann E, Xu C, Huang S, Jia A, Chang X, Han Z, Wu B, Schulze-Lefert P, Chai J (2022) "TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death." Cell, 185, 2370-2386.e18. doi: 10.1016/j.cell.2022.04.032. Tir-dsDNA complex, the initial binding state. SNAP output
7x5l hydrolase-DNA cryo-EM (3.51 Å) Yu D, Song W, Tan EYJ, Liu L, Cao Y, Jirschitzka J, Li E, Logemann E, Xu C, Huang S, Jia A, Chang X, Han Z, Wu B, Schulze-Lefert P, Chai J (2022) "TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death." Cell, 185, 2370-2386.e18. doi: 10.1016/j.cell.2022.04.032. Tir-dsDNA complex, the initial binding state. SNAP output
7x5m hydrolase-DNA cryo-EM (3.42 Å) Yu D, Song W, Tan EYJ, Liu L, Cao Y, Jirschitzka J, Li E, Logemann E, Xu C, Huang S, Jia A, Chang X, Han Z, Wu B, Schulze-Lefert P, Chai J (2022) "TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death." Cell, 185, 2370-2386.e18. doi: 10.1016/j.cell.2022.04.032. Tir-dsDNA complex, the initial binding state. SNAP output
7x6r DNA-antibiotic X-ray (1.89 Å) Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH (2022) "Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism." Nucleic Acids Res., 50, 8867-8881. doi: 10.1093/nar/gkac629. Crystal structure of actinomycin d-echinomycin-d(agcacgt-acgggct) complex. SNAP output
7x74 DNA binding protein cryo-EM (3.7 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. cryo-EM structure of streptomyces coelicolor transcription initial complex with two zur dimers.. SNAP output
7x75 gene regulation cryo-EM (3.45 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. cryo-EM structure of streptomyces coelicolor rnap-promoter open complex with three zur dimers. SNAP output
7x76 DNA binding protein cryo-EM (3.67 Å) Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J (2022) "Structural basis of Streptomyces transcription activation by zinc uptake regulator." Nucleic Acids Res., 50, 8363-8376. doi: 10.1093/nar/gkac627. cryo-EM structure of streptomyces coelicolor rnap-promoter open complex with two zur dimers. SNAP output
7x7p motor protein-DNA cryo-EM (7.02 Å) Zhang X, Zhou Z, Dai L, Chao Y, Liu Z, Huang M, Qu Q, Lin Z (2023) "Cryo-EM structure of the RuvAB-Holliday junction intermediate complex from Pseudomonas aeruginosa." Front Plant Sci, 14, 1139106. doi: 10.3389/fpls.2023.1139106. Cryoem structure of dsDNA-ruvb-ruva domain3 complex. SNAP output
7x97 DNA-antibiotic X-ray (1.95 Å) Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH (2022) "Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism." Nucleic Acids Res., 50, 8867-8881. doi: 10.1093/nar/gkac629. Crystal structure of actinomycin d-echinomycin-d(agcccgt-acgggct) complex. SNAP output
7x9f DNA-antibiotic X-ray (2.96 Å) Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH (2022) "Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism." Nucleic Acids Res., 50, 8867-8881. doi: 10.1093/nar/gkac629. Crystal structure of actinomycin d-echinomycin-d(agcgcgt-acgcgct) complex. SNAP output
7xaq transcription cryo-EM (3.59 Å) Zhu YB, Luo BN, Song YJ, Su ZM, Bao R "The Pseudomonas aeruginosa regulator PvrA binds cooperatively to multiple pseudo-palindromic sites to efficiently stimulate target gene." cryo-EM structure of pvra-DNA complex. SNAP output
7xcr nuclear protein cryo-EM (2.57 Å) Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L (2022) "H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity." Nat.Chem.Biol., 18, 972-980. doi: 10.1038/s41589-022-01067-7. cryo-EM structure of dot1l and h2bk34ub-h3k79nle nucleosome 1:1 complex. SNAP output
7xct nuclear protein cryo-EM (2.72 Å) Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L (2022) "H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity." Nat.Chem.Biol., 18, 972-980. doi: 10.1038/s41589-022-01067-7. cryo-EM structure of dot1l and h2bk34ub-h3k79nle nucleosome 2:1 complex. SNAP output
7xd0 nuclear protein cryo-EM (3.48 Å) Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L (2022) "H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity." Nat.Chem.Biol., 18, 972-980. doi: 10.1038/s41589-022-01067-7. cryo-EM structure of h2bk34ub nucleosome. SNAP output
7xd1 nuclear protein cryo-EM (3.2 Å) Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L (2022) "H2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity." Nat.Chem.Biol., 18, 972-980. doi: 10.1038/s41589-022-01067-7. cryo-EM structure of unmodified nucleosome. SNAP output
7xdj DNA-antibiotic X-ray (2.435 Å) Satange R, Kao SH, Chien CM, Chou SH, Lin CC, Neidle S, Hou MH (2022) "Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism." Nucleic Acids Res., 50, 8867-8881. doi: 10.1093/nar/gkac629. Crystal structure of actinomycin d-echinomycin-d(agcgcgt-acgagct) complex. SNAP output
7xf1 structural protein-DNA X-ray (3.2 Å) Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N (2023) "Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment." Mol.Cell, 83, 2493-2508.e5. doi: 10.1016/j.molcel.2023.05.036. Crystal strucutre of apocasding in complex with ssDNA. SNAP output
7xfc DNA binding protein-DNA cryo-EM (2.9 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-di complex (-30i, apo state). SNAP output
7xfh DNA binding protein-DNA cryo-EM (2.9 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-aag complex (a-30i, post-catalytic state). SNAP output
7xfi DNA binding protein-DNA cryo-EM (2.9 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-di complex (-50i, apo state). SNAP output
7xfj DNA binding protein-DNA cryo-EM (3.0 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-aag complex (t-50i, post-catalytic state). SNAP output
7xfl DNA binding protein-DNA cryo-EM (2.8 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-aag complex (a-53i, free state). SNAP output
7xfm DNA binding protein-DNA cryo-EM (3.1 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-aag complex (a-53i, post-catalytic state). SNAP output
7xfn DNA binding protein-DNA cryo-EM (2.8 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-di complex (-55i, apo state). SNAP output
7xfz structural protein-RNA-DNA cryo-EM (3.0 Å) Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N (2023) "Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment." Mol.Cell, 83, 2493-2508.e5. doi: 10.1016/j.molcel.2023.05.036. Cryoem structure of type iv-a csf-crrnasp14-dsDNA ternary complex. SNAP output
7xg0 structural protein-RNA-DNA cryo-EM (2.6 Å) Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N (2023) "Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment." Mol.Cell, 83, 2493-2508.e5. doi: 10.1016/j.molcel.2023.05.036. Cryoem structure of type iv-a csf-crrna-dsDNA ternary complex. SNAP output
7xg2 structural protein-RNA-DNA cryo-EM (2.8 Å) Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N (2023) "Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment." Mol.Cell, 83, 2493-2508.e5. doi: 10.1016/j.molcel.2023.05.036. Cryoem structure of type iv-a nts-nicked dsDNA bound csf-crrna ternary complex. SNAP output
7xg3 structural protein-RNA-DNA cryo-EM (3.0 Å) Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N (2023) "Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment." Mol.Cell, 83, 2493-2508.e5. doi: 10.1016/j.molcel.2023.05.036. Cryoem structure of type iv-a casding bound nts-nicked csf-crrna-dsDNA quaternary complex. SNAP output
7xg4 structural protein-RNA-DNA cryo-EM (3.7 Å) Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N (2023) "Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment." Mol.Cell, 83, 2493-2508.e5. doi: 10.1016/j.molcel.2023.05.036. Cryoem structure of type iv-a casding bound nts-nicked csf-crrna-dsDNA quaternary complex in a second state. SNAP output
7xhn cell cycle cryo-EM (3.71 Å) Tian T, Chen L, Dou Z, Yang Z, Gao X, Yuan X, Wang C, Liu R, Shen Z, Gui P, Teng M, Meng X, Hill DL, Li L, Zhang X, Liu X, Sun L, Zang J, Yao X (2022) "Structural insights into human CCAN complex assembled onto DNA." Cell Discov, 8, 90. doi: 10.1038/s41421-022-00439-6. Structure of human inner kinetochore ccan-DNA complex. SNAP output
7xht RNA binding protein-RNA-DNA cryo-EM (2.55 Å) Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H (2022) "Structure of the IscB-omega RNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9." Nat Commun, 13, 6719. doi: 10.1038/s41467-022-34378-3. Structure of the ogeuiscb-omega RNA-target DNA complex. SNAP output
7xhv transcription-DNA X-ray (3.996 Å) Sun X, Jing L, Li F, Zhang M, Diao X, Zhuang J, Rastinejad F, Wu D (2022) "Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family." Proc.Natl.Acad.Sci.USA, 119, e2208804119. doi: 10.1073/pnas.2208804119. Crystal structure of the npas4-arnt heterodimer in complex with DNA. SNAP output
7xi3 transcription-DNA X-ray (4.274 Å) Sun X, Jing L, Li F, Zhang M, Diao X, Zhuang J, Rastinejad F, Wu D (2022) "Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family." Proc.Natl.Acad.Sci.USA, 119, e2208804119. doi: 10.1073/pnas.2208804119. Crystal structure of the npas4-arnt2 heterodimer in complex with DNA. SNAP output
7xi4 transcription X-ray (4.707 Å) Sun X, Jing L, Li F, Zhang M, Diao X, Zhuang J, Rastinejad F, Wu D (2022) "Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family." Proc.Natl.Acad.Sci.USA, 119, e2208804119. doi: 10.1073/pnas.2208804119. Crystal structure of the npas4-arnt heterodimer in complex with DNA. SNAP output
7xjg RNA binding protein-DNA-RNA cryo-EM (2.51 Å) Wang Y, Guan Z, Wang C, Nie Y, Chen Y, Qian Z, Cui Y, Xu H, Wang Q, Zhao F, Zhang D, Tao P, Sun M, Yin P, Jin S, Wu S, Zou T (2022) "Cryo-EM structures of Escherichia coli Ec86 retron complexes reveal architecture and defence mechanism." Nat Microbiol, 7, 1480-1489. doi: 10.1038/s41564-022-01197-7. cryo-EM structure of e.coli retron-ec86 in complex with its effector at 2.5 angstrom. SNAP output
7xlt DNA-RNA hybrid cryo-EM (4.4 Å) Li Q, Lin C, Luo Z, Li H, Li X, Sun Q (2022) "Cryo-EM structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids." J Genet Genomics, 49, 677-680. doi: 10.1016/j.jgg.2022.04.011. cryo-EM structure of r-loop monoclonal antibody s9.6 in recognizing RNA:DNA hybrids. SNAP output
7xm0 DNA binding protein-DNA X-ray (2.6 Å) Liu Y, Xu C, Zhou H, Wang W, Liu B, Li Y, Hu X, Yu F, He J (2023) "The crystal structures of Sau3AI with and without bound DNA suggest a self-activation-based DNA cleavage mechanism." Structure, 31, 1463-1472.e2. doi: 10.1016/j.str.2023.08.005. Crystal structure of sau3ai-c and DNA substrate complex. SNAP output
7xnp DNA binding protein-DNA cryo-EM (2.9 Å) Zheng L, Tsai B, Gao N (2023) "Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome." Cell Discov, 9, 62. doi: 10.1038/s41421-023-00560-0. Structure of nucleosome-aag complex (a-55i, post-catalytic state). SNAP output
7xp3 transcription X-ray (3.25 Å) Chun I, Kim HJ, Hong S, Kim YG, Kim MS (2023) "Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence." Plant Commun., 4, 100510. doi: 10.1016/j.xplc.2022.100510. DNA complex form of oresara1(anac092) nac domain. SNAP output
7xpx nuclear protein-DNA cryo-EM (3.2 Å) Shi L, Huang L, Long H, Song A, Zhou Z (2022) "Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8." Faseb J., 36, e22338. doi: 10.1096/fj.202101821R. cryo-EM structure of the histone methyltransferase set8 bound to h4k20ecx-nucleosome. SNAP output
7xq5 transcription X-ray (2.25 Å) Khan MH, Xue L, Yue J, Schuller HJ, Zhu Z, Niu L (2022) "Structural Analysis of Ino2p/Ino4p Mutual Interactions and Their Binding Interface with Promoter DNA." Int J Mol Sci, 23. doi: 10.3390/ijms23147600. Crystal structure of scino2p-scino4p bound promoter DNA. SNAP output
7xrc transcription-DNA X-ray (1.89 Å) Tan DS, Cheung SL, Gao Y, Weinbuch M, Hu H, Shi L, Ti SC, Hutchins AP, Cojocaru V, Jauch R (2023) "The homeodomain of Oct4 is a dimeric binder of methylated CpG elements." Nucleic Acids Res., 51, 1120-1138. doi: 10.1093/nar/gkac1262. Crystal structure of the dimeric brn2 (pou3f2) pou domain bound to palindromic more DNA. SNAP output
7xue transcription cryo-EM (3.17 Å) Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY (2022) "Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA." Nat Commun, 13, 4668. doi: 10.1038/s41467-022-32315-y. cryo-EM structure of hk022 putrna-associated e.coli RNA polymerase elongation complex. SNAP output
7xug transcription cryo-EM (3.57 Å) Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY (2022) "Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA." Nat Commun, 13, 4668. doi: 10.1038/s41467-022-32315-y. cryo-EM structure of hk022 putrna-less e.coli RNA polymerase elongation complex. SNAP output
7xui transcription cryo-EM (3.61 Å) Hwang S, Olinares PDB, Lee J, Kim J, Chait BT, King RA, Kang JY (2022) "Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA." Nat Commun, 13, 4668. doi: 10.1038/s41467-022-32315-y. cryo-EM structure of sigma70 bound hk022 putrna-associated e.coli RNA polymerase elongation complex. SNAP output
7xur transcription-DNA cryo-EM (3.49 Å) Sun J, Li X, Hou X, Cao S, Cao W, Zhang Y, Song J, Wang M, Wang H, Yan X, Li Z, Roeder RG, Wang W (2022) "Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter." Nat Commun, 13, 6871. doi: 10.1038/s41467-022-34639-1. The cryo-EM structure of human mini-snapc in complex with hu6-1 pse. SNAP output
7xuz transcription X-ray (3.591 Å) Dai S, Guo L, Dey R, Guo M, Zhang X, Bates D, Cayford J, Jiang L, Wei H, Chen Z, Zhang Y, Chen L, Chen Y (2024) "Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation." Nucleic Acids Res., 52, 2711-2723. doi: 10.1093/nar/gkae036. Crystal structure of a hdac4-mef2a-DNA ternary complex. SNAP output
7xv6 DNA binding protein-DNA X-ray (2.3 Å) Liu Y, Ma L, Li M, Tian Z, Yang M, Wu X, Wang X, Shang G, Xie M, Chen Y, Liu X, Jiang L, Wu W, Xu C, Xia L, Li G, Dai S, Chen Z (2023) "Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation." Nucleic Acids Res., 51, 1443-1457. doi: 10.1093/nar/gkac1259. Crystal structure of the human tr4 DNA-binding domain with c-terminal extension (dbd-cte) homodimer bound to dr1 response element. SNAP output
7xv8 DNA binding protein-DNA X-ray (3.199 Å) Liu Y, Ma L, Li M, Tian Z, Yang M, Wu X, Wang X, Shang G, Xie M, Chen Y, Liu X, Jiang L, Wu W, Xu C, Xia L, Li G, Dai S, Chen Z (2023) "Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation." Nucleic Acids Res., 51, 1443-1457. doi: 10.1093/nar/gkac1259. Crystal structure of the human tr4 DNA-binding domain homodimer bound to dr1 response element. SNAP output
7xvl DNA binding protein-DNA X-ray (3.506 Å) Adhireksan Z, Sharma D, Qiuye B, Lee PL, Padavattan S, Davey CA "Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)." Crystal structure of nucleosome-h1.0 linker histone assembly (sticky-169an DNA fragment). SNAP output
7xvm DNA binding protein-DNA X-ray (2.84 Å) Adhireksan Z, Qiuye B, Lee PL, Sharma D, Padavattan S, Davey CA "Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)." Crystal structure of nucleosome-h5 linker histone assembly (sticky-169a DNA fragment). SNAP output
7xvn DNA binding protein-DNA X-ray (2.302 Å) Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y (2024) "Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma." Structure, 32, 467-475.e3. doi: 10.1016/j.str.2024.01.004. Structural basis for DNA recognition feature of retinoid-related orphan receptors. SNAP output
7xx5 DNA binding protein-DNA X-ray (3.19 Å) Adhireksan Z, Qiuye B, Lee PL, Sharma D, Padavattan S, Davey CA "Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)." Crystal structure of nucleosome-h1.3 linker histone assembly (sticky-169a DNA fragment). SNAP output
7xx6 DNA binding protein-DNA X-ray (3.39 Å) Adhireksan Z, Qiuye B, Lee PL, Sharma D, Padavattan S, Davey CA "Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)." Crystal structure of nucleosome-h1.0 linker histone assembly (sticky-169a DNA fragment). SNAP output
7xya transcription cryo-EM (3.3 Å) Wen A, Zhao M, Jin S, Lu YQ, Feng Y (2022) "Structural basis of AlpA-dependent transcription antitermination." Nucleic Acids Res., 50, 8321-8330. doi: 10.1093/nar/gkac608. The cryo-EM structure of an alpa-loading complex. SNAP output
7xyb transcription cryo-EM (3.7 Å) Wen A, Zhao M, Jin S, Lu YQ, Feng Y (2022) "Structural basis of AlpA-dependent transcription antitermination." Nucleic Acids Res., 50, 8321-8330. doi: 10.1093/nar/gkac608. The cryo-EM structure of an alpa-loaded complex. SNAP output
7xyf DNA binding protein cryo-EM (3.8 Å) Nan Z, Tao J, Yangao H "Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome (Class I Fft3-nucleosome complex)." cryo-EM structure of fft3-nucleosome complex with fft3 bound to shl+2 position of the nucleosome. SNAP output
7xyg DNA binding protein cryo-EM (4.2 Å) Nan Z, Tao J, Yangao H "Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome (Class II Fft3-nucleosome complex)." cryo-EM structure of fft3-nucleosome complex with fft3 bound to shl+3 position of the nucleosome. SNAP output
7xzx gene reguration-DNA cryo-EM (4.53 Å) Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H (2022) "Structural basis for p53 binding to its nucleosomal target DNA sequence." Pnas Nexus, 1, pgac177. doi: 10.1093/pnasnexus/pgac177. cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain. SNAP output
7xzy gene reguration-DNA cryo-EM (3.97 Å) Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H (2022) "Structural basis for p53 binding to its nucleosomal target DNA sequence." Pnas Nexus, 1, pgac177. doi: 10.1093/pnasnexus/pgac177. cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence. SNAP output
7xzz gene regulation-DNA cryo-EM (4.07 Å) Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H (2022) "Structural basis for p53 binding to its nucleosomal target DNA sequence." Pnas Nexus, 1, pgac177. doi: 10.1093/pnasnexus/pgac177. cryo-EM structure of the nucleosome in complex with p53. SNAP output
7y00 gene regulation-DNA cryo-EM (3.96 Å) Nishimura M, Takizawa Y, Nozawa K, Kurumizaka H (2022) "Structural basis for p53 binding to its nucleosomal target DNA sequence." Pnas Nexus, 1, pgac177. doi: 10.1093/pnasnexus/pgac177. cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence. SNAP output
7y01 plant protein-DNA X-ray (2.8 Å) Zhao X, Wang J, Jin D, Cheng J, Chen H, Li Z, Wang Y, Lou H, Zhu JK, Du X, Gong Z (2023) "AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis." J Integr Plant Biol, 65, 203-222. doi: 10.1111/jipb.13438. Crystal structure of zmmcm10 in complex with 16nt ssDNA at 2.8. angstrom resolution. SNAP output
7y3i DNA-DNA binding protein X-ray (2.45 Å) Ru W, Koga T, Wang X, Guo Q, Gearhart MD, Zhao S, Murphy M, Kawakami H, Corcoran D, Zhang J, Zhu Z, Yao X, Kawakami Y, Xu C (2022) "Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif." J.Biol.Chem., 298, 102607. doi: 10.1016/j.jbc.2022.102607. Structure of DNA bound sall4. SNAP output
7y3k DNA binding protein-DNA X-ray (2.501 Å) Ru W, Koga T, Wang X, Guo Q, Gearhart MD, Zhao S, Murphy M, Kawakami H, Corcoran D, Zhang J, Zhu Z, Yao X, Kawakami Y, Xu C (2022) "Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif." J.Biol.Chem., 298, 102607. doi: 10.1016/j.jbc.2022.102607. Structure of sall4 zfc4 bound with 16 bp at-rich dsDNA. SNAP output
7y3l DNA binding protein-DNA X-ray (2.5 Å) Ru W, Koga T, Wang X, Guo Q, Gearhart MD, Zhao S, Murphy M, Kawakami H, Corcoran D, Zhang J, Zhu Z, Yao X, Kawakami Y, Xu C (2022) "Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif." J.Biol.Chem., 298, 102607. doi: 10.1016/j.jbc.2022.102607. Structure of sall3 zfc4 bound with 12 bp at-rich dsDNA. SNAP output
7y3m DNA-DNA binding protein X-ray (2.723 Å) Ru W, Koga T, Wang X, Guo Q, Gearhart MD, Zhao S, Murphy M, Kawakami H, Corcoran D, Zhang J, Zhu Z, Yao X, Kawakami Y, Xu C (2022) "Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif." J.Biol.Chem., 298, 102607. doi: 10.1016/j.jbc.2022.102607. Structure of sall4 zfc1 bound with 16 bp at-rich dsDNA. SNAP output
7y43 DNA binding protein-DNA X-ray (1.5 Å) Weber LM, Jia Y, Stielow B, Gisselbrecht SS, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forne I, Nist A, Stiewe T, Bulyk ML, Wang Z, Liefke R (2023) "The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain." Nucleic Acids Res., 51, 574-594. doi: 10.1093/nar/gkac1188. Crystal structure of the kat6a wh domain and its bound double stranded DNA. SNAP output
7y5w DNA binding protein-DNA cryo-EM (3.5 Å) Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM (2023) "Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1." Science, 381, eadd8673. doi: 10.1126/science.add8673. cryo-EM structure of the left-handed di-tetrasome. SNAP output
7y60 replication cryo-EM (3.8 Å) Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM (2023) "Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1." Science, 381, eadd8673. doi: 10.1126/science.add8673. cryo-EM structure of human caf1lc bound right-handed di-tetrasome. SNAP output
7y61 replication-DNA cryo-EM (5.6 Å) Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM (2023) "Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1." Science, 381, eadd8673. doi: 10.1126/science.add8673. cryo-EM structure of the two caf1lcs bound right-handed di-tetrasome. SNAP output
7y7i nuclear protein-DNA cryo-EM (3.42 Å) Jiang H, Ariyoshi M, Watanabe R, Makino F, Namba K, Fukagawa T (2022) "The cryo-EM structure of the CENP-A nucleosome in complex with ggKNL2." Biorxiv. doi: 10.1101/2022.06.24.497480. Chicken knl2 in complex with the cenp-a nucleosome. SNAP output
7y7r RNA binding protein X-ray (2.1 Å) Cui R, Li H, Zhao J, Li X, Gan J, Ma J (2022) "Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1." Nucleic Acids Res., 50, 10169-10186. doi: 10.1093/nar/gkac727. Qde-1 in complex with DNA template, RNA primer and 3'-dgtp. SNAP output
7y7s RNA binding protein X-ray (2.7 Å) Cui R, Li H, Zhao J, Li X, Gan J, Ma J (2022) "Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1." Nucleic Acids Res., 50, 10169-10186. doi: 10.1093/nar/gkac727. Qde-1 in complex with DNA template, RNA primer and ampnpp. SNAP output
7y7t RNA binding protein X-ray (2.5 Å) Cui R, Li H, Zhao J, Li X, Gan J, Ma J (2022) "Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1." Nucleic Acids Res., 50, 10169-10186. doi: 10.1093/nar/gkac727. Qde-1 in complex with 12nt DNA template, atp and 3'-dgtp. SNAP output
7y8r DNA binding protein-DNA cryo-EM (4.4 Å) Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y (2022) "Structure of nucleosome-bound human PBAF complex." Nat Commun, 13, 7644. doi: 10.1038/s41467-022-34859-5. The nucleosome-bound human pbaf complex. SNAP output
7yc7 DNA binding protein X-ray (1.95 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Dark, fully reduced structure of the mmcpdii-DNA complex as produced at swissfel. SNAP output
7ycm DNA binding protein X-ray (2.0 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 100 ps snapshot. includes 100ps, dark, and extrapolated structure factors. SNAP output
7ycp DNA binding protein X-ray (2.08 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 250 ps snapshot. includes 250 ps, dark, and extrapolated structure factors. SNAP output
7ycr DNA binding protein X-ray (2.15 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 450 ps snapshot. includes 450ps, dark, and extrapolated structure factors. SNAP output
7yd6 DNA binding protein X-ray (2.15 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 650 ps snapshot. includes 650ps, dark, and extrapolated structure factors. SNAP output
7yd7 DNA binding protein X-ray (2.25 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 1 ns snapshot. includes 1 ns, dark, and extrapolated structure factors. SNAP output
7yd8 DNA binding protein X-ray (2.15 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 2 ns snapshot. includes 2 ns, dark, and extrapolated structure factors. SNAP output
7ydw DNA binding protein X-ray (2.47 Å) Yang M, Li X, Tian Z, Ma L, Ma J, Liu Y, Shang G, Liang A, Wu W, Chen Z (2023) "Structures of MPND Reveal the Molecular Recognition of Nucleosomes." Int J Mol Sci, 24. doi: 10.3390/ijms24043368. Crystal structure of the mpnd-DNA complex. SNAP output
7ydz DNA binding protein X-ray (2.23 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: dark state as collected in sacla. SNAP output
7ye0 DNA binding protein X-ray (2.75 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Df-sfx mmcpdii-DNA complex: steady state oxidized complex. SNAP output
7ye1 transcription cryo-EM (3.7 Å) Wu XX, Zhang Y (2023) "Cryo-EM structures of Caulobacter crescentus transcription activation complex with an essential cell cycle regulator GcrA." Nucleic Acids Res. The cryo-EM structure of c. crescentus gcra-tacup. SNAP output
7ye2 transcription cryo-EM (3.8 Å) Wu XX, Zhang Y (2023) "Cryo-EM structures of Caulobacter crescentus transcription activation complex with an essential cell cycle regulator GcrA." Nucleic Acids Res. The cryo-EM structure of c. crescentus gcra-tacdown. SNAP output
7yeb DNA binding protein X-ray (2.2 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 3.35 ns snapshot. includes 3.35 ns, dark, and extrapolated structure factors. SNAP output
7yec DNA binding protein X-ray (2.2 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 6 ns snapshot. includes 6 ns, dark, and extrapolated structure factors. SNAP output
7yee DNA binding protein X-ray (2.15 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 10 ns snapshot. includes 10 ns, dark, and extrapolated structure factors. collected at swissfel. SNAP output
7yei DNA binding protein X-ray (2.7 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 10 ns time-point collected in sacla. includes 10 ns, dark, and extrapolated structure factors. SNAP output
7yej DNA binding protein X-ray (2.55 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 100 ns time-point collected in sacla. includes 100 ns, dark, and extrapolated structure factors. SNAP output
7yek DNA binding protein X-ray (2.4 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 500 ns time-point collected in sacla. includes 500 ns, dark, and extrapolated structure factors. SNAP output
7yel DNA binding protein X-ray (2.5 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 25 us time-point collected in sacla. includes 25 us, dark, and extrapolated structure factors. SNAP output
7yem DNA binding protein X-ray (2.6 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Tr-sfx mmcpdii-DNA complex: 200 us time-point collected in sacla. includes 200 us, dark, and extrapolated structure factors. SNAP output
7yho DNA binding protein-DNA cryo-EM (3.3 Å) Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J (2023) "Molecular basis of the plant ROS1-mediated active DNA demethylation." Nat.Plants, 9, 271-279. doi: 10.1038/s41477-022-01322-8. Cryoem structure of arabidopsis ros1 in complex with tg mismatch dsDNA at 3.3 angstroms resolution. SNAP output
7yhp DNA binding protein-DNA cryo-EM (3.1 Å) Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J (2023) "Molecular basis of the plant ROS1-mediated active DNA demethylation." Nat.Plants, 9, 271-279. doi: 10.1038/s41477-022-01322-8. Cryoem structure of arabidopsis ros1 in complex with 5mc-dsDNA at 3.1 angstroms resolution. SNAP output
7yhq DNA binding protein-DNA cryo-EM (3.9 Å) Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J (2023) "Molecular basis of the plant ROS1-mediated active DNA demethylation." Nat.Plants, 9, 271-279. doi: 10.1038/s41477-022-01322-8. Cryoem structure of arabidopsis ros1 in complex with a covalent-linked reaction intermediate at 3.9 angstroms resolution. SNAP output
7yhs immune system-RNA-DNA cryo-EM (3.37 Å) Gao Z, Zhang L, Ge Z, Wang H, Yue Y, Jiang Z, Wang X, Xu C, Zhang Y, Yang M, Feng Y (2022) "Anti-CRISPR protein AcrIF4 inhibits the type I-F CRISPR-Cas surveillance complex by blocking nuclease recruitment and DNA cleavage." J.Biol.Chem., 298, 102575. doi: 10.1016/j.jbc.2022.102575. Structure of csy-acrif4-dsDNA. SNAP output
7yi1 gene regulation cryo-EM (2.8 Å) Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H (2023) "Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S." Nature, 620, 669-675. doi: 10.1038/s41586-023-06349-1. cryo-EM structure of eaf3 chd bound to h3k36me3 nucleosome. SNAP output
7yi2 gene regulation cryo-EM (3.4 Å) Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H (2023) "Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S." Nature, 620, 669-675. doi: 10.1038/s41586-023-06349-1. cryo-EM structure of rpd3s in loose-state rpd3s-ncp complex. SNAP output
7yi4 gene regulation cryo-EM (3.96 Å) Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H (2023) "Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S." Nature, 620, 669-675. doi: 10.1038/s41586-023-06349-1. cryo-EM structure of rpd3s complex bound to h3k36me3 nucleosome in close state. SNAP output
7yi5 gene regulation cryo-EM (3.96 Å) Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H (2023) "Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S." Nature, 620, 669-675. doi: 10.1038/s41586-023-06349-1. cryo-EM structure of rpd3s complex bound to h3k36me3 nucleosome in loose state. SNAP output
7yoj RNA binding protein-DNA-RNA cryo-EM (3.36 Å) Sun A, Li CP, Chen Z, Zhang S, Li DY, Yang Y, Li LQ, Zhao Y, Wang K, Li Z, Liu J, Liu S, Wang J, Liu JG (2023) "The compact Cas pi (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation." Cell Res., 33, 229-244. doi: 10.1038/s41422-022-00771-2. Structure of caspi with guide RNA and target DNA. SNAP output
7yoz DNA binding protein-DNA cryo-EM (4.3 Å) Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H (2022) "Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B." Proc.Natl.Acad.Sci.USA, 119, e2206542119. doi: 10.1073/pnas.2206542119. cryo-EM structure of human subnucleosome (intermediate form). SNAP output
7yp9 transcription-DNA-RNA cryo-EM (3.58 Å) You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y (2023) "Structural basis for intrinsic transcription termination." Nature, 613, 783-789. doi: 10.1038/s41586-022-05604-1. cryo-EM structure of escherichia coli paused complex of transcription termination (ttc-pause). SNAP output
7ypa transcription-DNA-RNA cryo-EM (3.05 Å) You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y (2023) "Structural basis for intrinsic transcription termination." Nature, 613, 783-789. doi: 10.1038/s41586-022-05604-1. cryo-EM structure of escherichia coli hairpin-nucleation complex of transcription termination (ttc-hairpin). SNAP output
7ypb transcription--DNA-RNA cryo-EM (3.48 Å) You L, Omollo EO, Yu C, Mooney RA, Shi J, Shen L, Wu X, Wen A, He D, Zeng Y, Feng Y, Landick R, Zhang Y (2023) "Structural basis for intrinsic transcription termination." Nature, 613, 783-789. doi: 10.1038/s41586-022-05604-1. cryo-EM structure of escherichia coli release complex of transcription termination (ttc-release). SNAP output
7ypo DNA binding protein cryo-EM (3.5 Å) Yin J, Fu Y, Rao G, Li Z, Tian K, Chong T, Kuang K, Wang M, Hu Z, Cao S (2022) "Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA." Nucleic Acids Res., 50, 13100-13113. doi: 10.1093/nar/gkac1142. cryo-EM structure of baculovirus lef-3 in complex with ssDNA. SNAP output
7ypq DNA binding protein cryo-EM (3.1 Å) Yin J, Fu Y, Rao G, Li Z, Tian K, Chong T, Kuang K, Wang M, Hu Z, Cao S (2022) "Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA." Nucleic Acids Res., 50, 13100-13113. doi: 10.1093/nar/gkac1142. cryo-EM structure of one baculovirus lef-3 molecule in complex with ssDNA. SNAP output
7yq3 structural protein cryo-EM (3.6 Å) Kim J, Yunn NO, Park M, Kim J, Park S, Kim Y, Noh J, Ryu SH, Cho Y (2022) "Functional selectivity of insulin receptor revealed by aptamer-trapped receptor structures." Nat Commun, 13, 6500. doi: 10.1038/s41467-022-34292-8. Human insulin receptor bound with a43 DNA aptamer and insulin. SNAP output
7yq4 structural protein cryo-EM (3.95 Å) Kim J, Yunn NO, Park M, Kim J, Park S, Kim Y, Noh J, Ryu SH, Cho Y (2022) "Functional selectivity of insulin receptor revealed by aptamer-trapped receptor structures." Nat Commun, 13, 6500. doi: 10.1038/s41467-022-34292-8. Human insulin receptor bound with a62 DNA aptamer and insulin - locally refined. SNAP output
7yq5 structural protein cryo-EM (4.27 Å) Kim J, Yunn NO, Park M, Kim J, Park S, Kim Y, Noh J, Ryu SH, Cho Y (2022) "Functional selectivity of insulin receptor revealed by aptamer-trapped receptor structures." Nat Commun, 13, 6500. doi: 10.1038/s41467-022-34292-8. Human insulin receptor bound with a62 DNA aptamer and insulin. SNAP output
7yq6 structural protein cryo-EM (4.18 Å) Kim J, Yunn NO, Park M, Kim J, Park S, Kim Y, Noh J, Ryu SH, Cho Y (2022) "Functional selectivity of insulin receptor revealed by aptamer-trapped receptor structures." Nat Commun, 13, 6500. doi: 10.1038/s41467-022-34292-8. Human insulin receptor bound with a62 DNA aptamer. SNAP output
7yq8 isomerase-DNA cryo-EM (3.9 Å) Bunch H, Kim D, Naganuma M, Nakagawa R, Cong A, Jeong J, Ehara H, Vu H, Chang JH, Schellenberg MJ, Sekine SI (2023) "ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes." Nat Commun, 14, 8341. doi: 10.1038/s41467-023-44089-y. cryo-EM structure of human topoisomerase ii beta in complex with DNA and etoposide. SNAP output
7yqk nuclear protein cryo-EM (3.38 Å) Ai H, Chu GC, Gong Q, Tong ZB, Deng Z, Liu X, Yang F, Xu Z, Li JB, Tian C, Liu L (2022) "Chemical Synthesis of Post-Translationally Modified H2AX Reveals Redundancy in Interplay between Histone Phosphorylation, Ubiquitination, and Methylation on the Binding of 53BP1 with Nucleosomes." J.Am.Chem.Soc., 144, 18329-18337. doi: 10.1021/jacs.2c06156. cryo-EM structure of gammah2axk15ub-h4k20me2 nucleosome bound to 53bp1. SNAP output
7yrd gene regulation cryo-EM (3.2 Å) Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z (2023) "Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1." Mol.Cell, 83, 2884-2895.e7. doi: 10.1016/j.molcel.2023.07.001. Histone methyltransferase. SNAP output
7yrg gene regulation cryo-EM (4.2 Å) Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z (2023) "Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1." Mol.Cell, 83, 2884-2895.e7. doi: 10.1016/j.molcel.2023.07.001. Histone methyltransferase. SNAP output
7ysf transferase-DNA X-ray (2.4 Å) Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F, Kappei D (2023) "ZNF524 directly interacts with telomeric DNA and supports telomere integrity." Nat Commun, 14, 8252. doi: 10.1038/s41467-023-43397-7. Crystal structure of znf524 zf1-4 in complex with telomeric DNA. SNAP output
7yuk DNA binding protein X-ray (2.11 Å) Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J (2023) "Structural insights into DNA recognition by the BEN domain of the transcription factor BANP." J.Biol.Chem., 299, 104734. doi: 10.1016/j.jbc.2023.104734. Complex structure of banp ben domain bound to DNA. SNAP output
7yul DNA binding protein X-ray (1.82 Å) Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J (2023) "Structural insights into DNA recognition by the BEN domain of the transcription factor BANP." J.Biol.Chem., 299, 104734. doi: 10.1016/j.jbc.2023.104734. Crystal structure of human bend6 ben domain in complex with DNA. SNAP output
7yun DNA binding protein X-ray (2.13 Å) Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J (2023) "Structural insights into DNA recognition by the BEN domain of the transcription factor BANP." J.Biol.Chem., 299, 104734. doi: 10.1016/j.jbc.2023.104734. Crystal structure of human bend6 ben domain in complex with methylated DNA. SNAP output
7ywa DNA binding protein-DNA cryo-EM (3.26 Å) Gao B, Liang L, Su L, Wen A, Zhou C, Feng Y (2023) "Structural basis for regulation of SOS response in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2217493120. doi: 10.1073/pnas.2217493120. Structure of dini in complex with reca filament. SNAP output
7ywx cell cycle cryo-EM (12.0 Å) Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D (2022) "Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome." Science, 376, 844-852. doi: 10.1126/science.abn3810. Structure of the human ccan cenp-a alpha-satellite complex. SNAP output
7yyh cell cycle cryo-EM (8.9 Å) Yatskevich S, Muir KW, Bellini D, Zhang Z, Yang J, Tischer T, Predin M, Dendooven T, McLaughlin SH, Barford D (2022) "Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome." Science, 376, 844-852. doi: 10.1126/science.abn3810. Structure of the human ccandeltat cenp-a alpha-satellite complex. SNAP output
7yz7 DNA binding protein X-ray (0.98 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the zebrafish foxh1 bound to the tgtggatt site. SNAP output
7yza DNA binding protein X-ray (1.18 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the zebrafish foxh1 bound to the tgtgtatt site. SNAP output
7yzb DNA binding protein X-ray (1.47 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the human foxh1 bound to the tgtggatt site. SNAP output
7yzc DNA binding protein X-ray (2.17 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the zebrafish foxh1 bound to the tgtttatt site. SNAP output
7yzd DNA binding protein X-ray (2.13 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the zebrafish foxh1 bound to the tgtttact site (fkh motif gtaaaca). SNAP output
7yze DNA binding protein X-ray (1.99 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the human foxa2 bound to the tgtttact site (forkhead motif gtaaaca). SNAP output
7yzf DNA binding protein X-ray (2.18 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the human foxa2 bound to the tgtttatt site (forkhead motif ataaaca). SNAP output
7yzg DNA binding protein X-ray (2.82 Å) Pluta R, Aragon E, Prescott NA, Ruiz L, Mees RA, Baginski B, Flood JR, Martin-Malpartida P, Massague J, David Y, Macias MJ (2022) "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1." Nat Commun, 13, 7279. doi: 10.1038/s41467-022-34925-y. Crystal structure of the xenopus foxh1 bound to the tgtggatt site. SNAP output
7yzo DNA binding protein cryo-EM (3.4 Å) Gut F, Kashammer L, Lammens K, Bartho JD, Boggusch AM, van de Logt E, Kessler B, Hopfner KP (2022) "Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50." Mol.Cell, 82, 3513-3522.e6. doi: 10.1016/j.molcel.2022.07.019. Endonuclease state of the e. coli mre11-rad50 (sbccd) head complex bound to adp and dsDNA. SNAP output
7yzp DNA binding protein cryo-EM (4.0 Å) Gut F, Kashammer L, Lammens K, Bartho JD, Boggusch AM, van de Logt E, Kessler B, Hopfner KP (2022) "Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50." Mol.Cell, 82, 3513-3522.e6. doi: 10.1016/j.molcel.2022.07.019. Hairpin-bound state of the e. coli mre11-rad50 (sbccd) head complex bound to adp and a DNA hairpin. SNAP output
7z03 DNA binding protein cryo-EM (3.7 Å) Gut F, Kashammer L, Lammens K, Bartho JD, Boggusch AM, van de Logt E, Kessler B, Hopfner KP (2022) "Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50." Mol.Cell, 82, 3513-3522.e6. doi: 10.1016/j.molcel.2022.07.019. Endonuclease state of the e. coli mre11-rad50 (sbccd) head complex bound to adp and extended dsDNA. SNAP output
7z0o transcription cryo-EM (2.8 Å) Baudin F, Murciano B, Fung HKH, Fromm SA, Mattei S, Mahamid J, Muller CW (2022) "Mechanism of RNA polymerase I selection by transcription factor UAF." Sci Adv, 8, eabn5725. doi: 10.1126/sciadv.abn5725. Structure of transcription factor uaf in complex with tbp and 35s rrna promoter DNA. SNAP output
7z0u transcription X-ray (2.85 Å) Grzechowiak M, Ruszkowska A, Sliwiak J, Urbanowicz A, Jaskolski M, Ruszkowski M (2022) "New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain." Int.J.Biol.Macromol., 213, 589-601. doi: 10.1016/j.ijbiomac.2022.05.186. Crystal structure of atwrky18 DNA-binding domain in complex with w-box DNA. SNAP output
7z1n transcription cryo-EM (3.9 Å) Girbig M, Xie J, Grotsch H, Libri D, Porrua O, Muller CW (2022) "Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals." Cell Rep, 40, 111316. doi: 10.1016/j.celrep.2022.111316. Structure of yeast RNA polymerase iii delta c53-c37-c11. SNAP output
7z1z viral protein cryo-EM (3.5 Å) Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P (2022) "Multivalent interactions essential for lentiviral integrase function." Nat Commun, 13, 2416. doi: 10.1038/s41467-022-29928-8. Mvv strand transfer complex (stc) intasome in complex with ledgf-p75 at 3.5 Å resolution. SNAP output
7z24 transferase cryo-EM (3.32 Å) Singh AK, De Wijngaert B, Bijnens M, Uyttersprot K, Nguyen H, Martinez SE, Schols D, Herdewijn P, Pannecouque C, Arnold E, Das K (2022) "Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine." Proc.Natl.Acad.Sci.USA, 119, e2203660119. doi: 10.1073/pnas.2203660119. cryo-EM structure of hiv-1 reverse transcriptase with a DNA aptamer in complex with nevirapine. SNAP output
7z29 transferase cryo-EM (3.38 Å) Singh AK, De Wijngaert B, Bijnens M, Uyttersprot K, Nguyen H, Martinez SE, Schols D, Herdewijn P, Pannecouque C, Arnold E, Das K (2022) "Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine." Proc.Natl.Acad.Sci.USA, 119, e2203660119. doi: 10.1073/pnas.2203660119. cryo-EM structure of nnrti resistant m184i-e138k mutant hiv-1 reverse transcriptase with a DNA aptamer in complex with nevirapine. SNAP output
7z2d transferase cryo-EM (3.38 Å) Singh AK, De Wijngaert B, Bijnens M, Uyttersprot K, Nguyen H, Martinez SE, Schols D, Herdewijn P, Pannecouque C, Arnold E, Das K (2022) "Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine." Proc.Natl.Acad.Sci.USA, 119, e2203660119. doi: 10.1073/pnas.2203660119. cryo-EM structure of hiv-1 reverse transcriptase with a DNA aptamer in complex with rilpivirine. SNAP output
7z2e transferase cryo-EM (3.45 Å) Singh AK, De Wijngaert B, Bijnens M, Uyttersprot K, Nguyen H, Martinez SE, Schols D, Herdewijn P, Pannecouque C, Arnold E, Das K (2022) "Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine." Proc.Natl.Acad.Sci.USA, 119, e2203660119. doi: 10.1073/pnas.2203660119. cryo-EM structure of nnrti resistant m184i-e138k mutant hiv-1 reverse transcriptase with a DNA aptamer in complex with rilpivirine. SNAP output
7z2g transferase cryo-EM (3.65 Å) Singh AK, De Wijngaert B, Bijnens M, Uyttersprot K, Nguyen H, Martinez SE, Schols D, Herdewijn P, Pannecouque C, Arnold E, Das K (2022) "Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine." Proc.Natl.Acad.Sci.USA, 119, e2203660119. doi: 10.1073/pnas.2203660119. cryo-EM structure of hiv-1 reverse transcriptase with a DNA aptamer in complex with doravirine. SNAP output
7z2h transferase cryo-EM (3.58 Å) Singh AK, De Wijngaert B, Bijnens M, Uyttersprot K, Nguyen H, Martinez SE, Schols D, Herdewijn P, Pannecouque C, Arnold E, Das K (2022) "Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine." Proc.Natl.Acad.Sci.USA, 119, e2203660119. doi: 10.1073/pnas.2203660119. cryo-EM structure of nnrti resistant m184i-e138k mutant hiv-1 reverse transcriptase with a DNA aptamer in complex with doravirine. SNAP output
7z3x DNA binding protein X-ray (1.65 Å) Ni X, Chaikuad A, Knapp S "Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA." Crystal structure of fir rrm1-2 y115f mutant bound to fuse ssDNA. SNAP output
7z4c hydrolase cryo-EM (3.87 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 6 nucleotide complementary DNA substrate. SNAP output
7z4d hydrolase X-ray (3.1 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Crystal structure of spcas9 bound to a 10 nucleotide complementary DNA substrate. SNAP output
7z4e hydrolase cryo-EM (4.14 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 8-nucleotide complementary DNA substrate. SNAP output
7z4g hydrolase cryo-EM (3.64 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 12-nucleotide complementary DNA substrate. SNAP output
7z4h hydrolase cryo-EM (3.49 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 14-nucleotide complementary DNA substrate. SNAP output
7z4i hydrolase cryo-EM (3.12 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 16-nucleotide complementary DNA substrate. SNAP output
7z4j hydrolase cryo-EM (2.99 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 18-nucleotide complementary DNA substrate in the catalytic state. SNAP output
7z4k hydrolase cryo-EM (3.81 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 10-nucleotide complementary DNA substrate. SNAP output
7z4l hydrolase cryo-EM (2.54 Å) Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M (2022) "R-loop formation and conformational activation mechanisms of Cas9." Nature, 609, 191-196. doi: 10.1038/s41586-022-05114-0. Spcas9 bound to 18-nucleotide complementary DNA substrate in the checkpoint state. SNAP output
7z5a DNA binding protein X-ray (2.28 Å) Huskova A, Dinesh DC, Srb P, Boura E, Veverka V, Silhan J (2022) "Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model." Nucleic Acids Res., 50, 10436-10448. doi: 10.1093/nar/gkac793. Crystal structure of the trapped complex of mouse endonuclease viii-like 3 (mneil3) and hairpin DNA with 5'overhang. SNAP output
7z5i transcription X-ray (3.0 Å) Morgunova E, Popov A, Yin Y, Taipale J "Transcription factor MYF5 bound to symmetrical site." Transcription factor myf5 bound to symmetrical site. SNAP output
7z5k transcription X-ray (2.28 Å) Morgunova E, Popov A, Yin Y, Taipale J "Transcription factor MYF5 bound to non-symmetrical site." Transcription factor myf5 bound to non-symmetrical site. SNAP output
7z5y transferase X-ray (1.71 Å) Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchene D, Iannazzo L, Patin D, Touze T, van Tilbeurgh H, Herdewijn P, Etheve-Quelquejeu M, Fonvielle M (2022) "Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis." Nucleic Acids Res., 50, 11415-11425. doi: 10.1093/nar/gkac1023. Crystal structure of weissella viridescens femxvv non-ribosomal amino acid transferase in complex with a peptidyl-xna conjugate. SNAP output
7z5z transferase X-ray (1.49 Å) Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchene D, Iannazzo L, Patin D, Touze T, van Tilbeurgh H, Herdewijn P, Etheve-Quelquejeu M, Fonvielle M (2022) "Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis." Nucleic Acids Res., 50, 11415-11425. doi: 10.1093/nar/gkac1023. Crystal structure of weissella viridescens femxvv non-ribosomal amino acid transferase in complex with a peptidyl-xna conjugate. SNAP output
7z6h DNA binding protein cryo-EM (3.59 Å) Day M, Oliver AW, Pearl LH (2022) "Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction." Nucleic Acids Res., 50, 8279-8289. doi: 10.1093/nar/gkac588. Structure of DNA-bound human rad17-rfc clamp loader and 9-1-1 checkpoint clamp. SNAP output
7z6o DNA binding protein X-ray (3.7 Å) Kefala Stavridi A, Gontier A, Morin V, Frit P, Ropars V, Barboule N, Racca C, Jonchhe S, Morten MJ, Andreani J, Rak A, Legrand P, Bourand-Plantefol A, Hardwick SW, Chirgadze DY, Davey P, De Oliveira TM, Rothenberg E, Britton S, Calsou P, Blundell TL, Varela PF, Chaplin AK, Charbonnier JB (2023) "Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction." Nucleic Acids Res., 51, 11732-11747. doi: 10.1093/nar/gkad863. X-ray studies of ku70-80 reveal the binding site for ip6. SNAP output
7z7n transcription cryo-EM (5.1 Å) Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP (2023) "Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1." Nat.Struct.Mol.Biol., 30, 640-649. doi: 10.1038/s41594-023-00966-0. Mot1e1434q:tbp:DNA - substrate recognition state. SNAP output
7z87 DNA binding protein cryo-EM (2.91 Å) Liang S, Blundell TL (2023) "Human DNA-dependent protein kinase activation mechanism." Nat.Struct.Mol.Biol., 30, 140-147. doi: 10.1038/s41594-022-00881-w. DNA-pk in the active state. SNAP output
7z88 DNA binding protein cryo-EM (3.33 Å) Liang S, Blundell TL (2023) "Human DNA-dependent protein kinase activation mechanism." Nat.Struct.Mol.Biol., 30, 140-147. doi: 10.1038/s41594-022-00881-w. DNA-pk in the intermediate state. SNAP output
7z8s transcription cryo-EM (3.9 Å) Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP (2023) "Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1." Nat.Struct.Mol.Biol., 30, 640-649. doi: 10.1038/s41594-023-00966-0. Mot1:tbp:DNA - post hydrolysis state. SNAP output
7z9c isomerase cryo-EM (3.06 Å) Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D (2023) "Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin." Nat Catal, 6, 52-67. doi: 10.1038/s41929-022-00904-1. E.coli gyrase holocomplex with 217 bp DNA and albicidin. SNAP output
7z9g isomerase cryo-EM (3.25 Å) Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D (2023) "Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin." Nat Catal, 6, 52-67. doi: 10.1038/s41929-022-00904-1. E.coli gyrase holocomplex with 217 bp DNA and albi-2. SNAP output
7z9k isomerase cryo-EM (3.25 Å) Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D (2023) "Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin." Nat Catal, 6, 52-67. doi: 10.1038/s41929-022-00904-1. E.coli gyrase holocomplex with 217 bp DNA and albi-1 (site tg). SNAP output
7z9m isomerase cryo-EM (3.3 Å) Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D (2023) "Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin." Nat Catal, 6, 52-67. doi: 10.1038/s41929-022-00904-1. E.coli gyrase holocomplex with 217 bp DNA and albi-1 (site aa). SNAP output
7zb5 transcription cryo-EM (2.8 Å) Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP (2023) "Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1." Nat.Struct.Mol.Biol., 30, 640-649. doi: 10.1038/s41594-023-00966-0. Mot1(1-1836):tbp:DNA - post-hydrolysis complex dimer. SNAP output
7zes hydrolase cryo-EM (3.1 Å) Metzner FJ, Wenzl SJ, Kugler M, Krebs S, Hopfner KP, Lammens K (2022) "Mechanistic understanding of human SLFN11." Nat Commun, 13, 5464. doi: 10.1038/s41467-022-33123-0. Human slfn11 dimer bound to ssDNA. SNAP output
7zf1 DNA binding protein cryo-EM (4.14 Å) Lemonidis K, Rennie ML, Arkinson C, Chaugule VK, Clarke M, Streetley J, Walden H (2023) "Structural and biochemical basis of interdependent FANCI-FANCD2 ubiquitination." Embo J., 42, e111898. doi: 10.15252/embj.2022111898. Structure of ubiquitinated fanci in complex with fancd2 and double-stranded DNA. SNAP output
7zg5 toxin X-ray (2.0 Å) Grabe GJ, Giorgio RT, Wieczor M, Gollan B, Sargen M, Orozco M, Hare SA, Helaine S (2024) "Molecular stripping underpins derepression of a toxin-antitoxin system." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01253-2. The crystal structure of salmonella tacat3-DNA complex. SNAP output
7zie DNA binding protein multiple methods: x-ray diffraction, solution scattering Tarres-Sole A, Ruiz-Lopez E, Lyonnais S, Sola M (2023) "Gcf1p tetramerizes upon DNA binding, revealing a novel compaction method for mitochondrial DNA in Candida albicans." Nucleic Acids Res. doi: 10.1093/nar/gkad39. Gcf1p, multimerizes and bridges the mitochondrial DNA from candida albicans by a specific mechanism.. SNAP output
7zke transcription cryo-EM (3.6 Å) Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP (2023) "Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1." Nat.Struct.Mol.Biol., 30, 640-649. doi: 10.1038/s41594-023-00966-0. Mot1:tbp:DNA - pre-hydrolysis state. SNAP output
7zkl hydrolase X-ray (3.18 Å) Troisi R, Riccardi C, Perez de Carvasal K, Smietana M, Morvan F, Del Vecchio P, Montesarchio D, Sica F (2022) "A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers." Mol Ther Nucleic Acids, 30, 585-594. doi: 10.1016/j.omtn.2022.11.007. X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (tba-nnp-ddp) - crystal form alpha. SNAP output
7zkm hydrolase X-ray (2.0 Å) Troisi R, Riccardi C, Perez de Carvasal K, Smietana M, Morvan F, Del Vecchio P, Montesarchio D, Sica F (2022) "A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers." Mol Ther Nucleic Acids, 30, 585-594. doi: 10.1016/j.omtn.2022.11.007. X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (tba-nnp-ddp) - crystal form beta. SNAP output
7zkn hydrolase X-ray (3.03 Å) Troisi R, Riccardi C, Perez de Carvasal K, Smietana M, Morvan F, Del Vecchio P, Montesarchio D, Sica F (2022) "A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers." Mol Ther Nucleic Acids, 30, 585-594. doi: 10.1016/j.omtn.2022.11.007. X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (tba-nnp-ddp) - crystal form gamma. SNAP output
7zko hydrolase X-ray (2.5 Å) Troisi R, Riccardi C, Perez de Carvasal K, Smietana M, Morvan F, Del Vecchio P, Montesarchio D, Sica F (2022) "A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers." Mol Ther Nucleic Acids, 30, 585-594. doi: 10.1016/j.omtn.2022.11.007. X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (tba-nnp-ddp) - crystal form delta. SNAP output
7zla DNA binding protein cryo-EM (3.99 Å) Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega MV, Isupov MN, Harmer NJ, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo ML, Contestabile R, Vallone B, Tramonti A, Montemiglio LC (2023) "Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR." Nucleic Acids Res., 51, 8237-8254. doi: 10.1093/nar/gkad552. cryo-EM structure of holo-pdxr from bacillus clausii bound to its target DNA in the half-closed conformation. SNAP output
7zn5 DNA binding protein cryo-EM (3.7 Å) Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega MV, Isupov MN, Harmer NJ, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo ML, Contestabile R, Vallone B, Tramonti A, Montemiglio LC (2023) "Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR." Nucleic Acids Res., 51, 8237-8254. doi: 10.1093/nar/gkad552. cryo-EM structure of holo-pdxr from bacillus clausii bound to its target DNA in the closed conformation, c2 symmetry.. SNAP output
7zo1 hydrolase X-ray (2.4 Å) Pacesa M, Lin CH, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M (2022) "Structural basis for Cas9 off-target activity." Cell, 185, 4067-4081.e21. doi: 10.1016/j.cell.2022.09.026. Spcas9 bound to cd34 off-target9 DNA substrate. SNAP output
7zpa DNA binding protein cryo-EM (3.9 Å) Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega MV, Isupov MN, Harmer NJ, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo ML, Contestabile R, Vallone B, Tramonti A, Montemiglio LC (2023) "Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR." Nucleic Acids Res., 51, 8237-8254. doi: 10.1093/nar/gkad552. cryo-EM structure of holo-pdxr from bacillus clausii bound to its target DNA in the closed conformation, c1 symmetry. SNAP output
7zpp viral protein cryo-EM (4.5 Å) Ballandras-Colas A, Maskell DP, Serrao E, Locke J, Swuec P, Jonsson SR, Kotecha A, Cook NJ, Pye VE, Taylor IA, Andresdottir V, Engelman AN, Costa A, Cherepanov P (2017) "A supramolecular assembly mediates lentiviral DNA integration." Science, 355, 93-95. doi: 10.1126/science.aah7002. cryo-EM structure of the mvv csc intasome at 4.5a resolution. SNAP output
7zqs membrane protein cryo-EM (2.54 Å) Cheng EL, Cardle II, Kacherovsky N, Bansia H, Wang T, Zhou Y, Raman J, Yen A, Gutierrez D, Salipante SJ, des Georges A, Jensen MC, Pun SH (2022) "Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing." J.Am.Chem.Soc., 144, 13851-13864. doi: 10.1021/jacs.2c05349. cryo-EM structure of human transferrin receptor 1 bound to DNA aptamer. SNAP output
7zs9 transcription cryo-EM (3.1 Å) Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P (2023) "Structures of transcription preinitiation complex engaged with the +1 nucleosome." Nat.Struct.Mol.Biol., 30, 226-232. doi: 10.1038/s41594-022-00865-w. Yeast RNA polymerase ii transcription pre-initiation complex with the +1 nucleosome (complex a). SNAP output
7zsa transcription cryo-EM (4.0 Å) Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P (2023) "Structures of transcription preinitiation complex engaged with the +1 nucleosome." Nat.Struct.Mol.Biol., 30, 226-232. doi: 10.1038/s41594-022-00865-w. Yeast RNA polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp (complex b). SNAP output
7zsb transcription cryo-EM (6.6 Å) Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P (2023) "Structures of transcription preinitiation complex engaged with the +1 nucleosome." Nat.Struct.Mol.Biol., 30, 226-232. doi: 10.1038/s41594-022-00865-w. Yeast RNA polymerase ii transcription pre-initiation complex with the +1 nucleosome and ntp, complex c. SNAP output
7zth DNA binding protein cryo-EM (4.0 Å) Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega MV, Isupov MN, Harmer NJ, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo ML, Contestabile R, Vallone B, Tramonti A, Montemiglio LC (2023) "Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR." Nucleic Acids Res., 51, 8237-8254. doi: 10.1093/nar/gkad552. cryo-EM structure of holo-pdxr from bacillus clausii bound to its target DNA in the open conformation. SNAP output
7zvn lipid binding protein X-ray (1.87 Å) Hyjek-Skladanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznanski JT, Skowronek K, Seth P, Nowotny M (2023) "Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding." Nucleic Acids Res., 51, 1409-1423. doi: 10.1093/nar/gkac774. Crystal structure of human annexin a2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 1.87 Å resolution. SNAP output
7zvt DNA binding protein cryo-EM (2.74 Å) Kefala Stavridi A, Gontier A, Morin V, Frit P, Ropars V, Barboule N, Racca C, Jonchhe S, Morten MJ, Andreani J, Rak A, Legrand P, Bourand-Plantefol A, Hardwick SW, Chirgadze DY, Davey P, De Oliveira TM, Rothenberg E, Britton S, Calsou P, Blundell TL, Varela PF, Chaplin AK, Charbonnier JB (2023) "Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction." Nucleic Acids Res., 51, 11732-11747. doi: 10.1093/nar/gkad863. Cryoem structure of ku heterodimer bound to DNA. SNAP output
7zvx lipid binding protein X-ray (2.4 Å) Hyjek-Skladanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznanski JT, Skowronek K, Seth P, Nowotny M (2023) "Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding." Nucleic Acids Res., 51, 1409-1423. doi: 10.1093/nar/gkac774. Crystal structure of human annexin a2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 2.4 Å resolution. SNAP output
7zwa DNA binding protein cryo-EM (2.8 Å) Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK (2023) "PAXX binding to the NHEJ machinery explains functional redundancy with XLF." Sci Adv, 9, eadg2834. doi: 10.1126/sciadv.adg2834. Cryoem structure of ku heterodimer bound to DNA and paxx. SNAP output
7zwc transcription cryo-EM (3.2 Å) Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P (2022) "Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II." Nat.Struct.Mol.Biol., 29, 1159-1169. doi: 10.1038/s41594-022-00857-w. Structure of snapc:tbp-tfiia-tfiib sub-complex bound to u5 snrna promoter. SNAP output
7zxe transcription cryo-EM (3.5 Å) Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P (2022) "Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II." Nat.Struct.Mol.Biol., 29, 1159-1169. doi: 10.1038/s41594-022-00857-w. Structure of snapc containing pol ii pre-initiation complex bound to u1 snrna promoter (oc). SNAP output
7zyg DNA binding protein cryo-EM (2.68 Å) Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK (2023) "PAXX binding to the NHEJ machinery explains functional redundancy with XLF." Sci Adv, 9, eadg2834. doi: 10.1126/sciadv.adg2834. Cryoem structure of ku heterodimer bound to DNA, paxx and xlf. SNAP output
8a0w DNA binding protein X-ray (2.334 Å) Hadzi S, Zivic Z, Kovacic M, Zavrtanik U, Haeserts S, Charlier D, Plavec J, Volkov AN, Lah J, Loris R (2024) "Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae." Nat Commun, 15, 3105. doi: 10.1038/s41467-024-47296-3. Crystal structure of the higa2 antitoxin in complex with operator DNA. SNAP output
8a0x DNA binding protein X-ray (3.296 Å) Hadzi S, Loris R "Fuzzy DNA recognition by a prokaryotic transcription factor." Crystal structure of the higb2-higa2 tetramer in complex with operator DNA. SNAP output
8a1c DNA binding protein X-ray (2.1 Å) Breidenstein A, Ter Beek J, Berntsson RP (2023) "Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing." Life Sci Alliance, 6. doi: 10.26508/lsa.202201775. Trai trans-esterase domain from pkm101 (DNA bound). SNAP output
8a40 transcription cryo-EM (3.0 Å) Farnung L, Ochmann M, Garg G, Vos SM, Cramer P (2022) "Structure of a backtracked hexasomal intermediate of nucleosome transcription." Mol.Cell, 82, 3126-3134.e7. doi: 10.1016/j.molcel.2022.06.027. Structure of mammalian pol ii-tfiis elongation complex. SNAP output
8a4i DNA binding protein X-ray (2.76 Å) Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG (2023) "Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome." Life Sci Alliance, 6. doi: 10.26508/lsa.202201588. Crystal structure of sall4 zinc finger cluster 4 with at-rich DNA. SNAP output
8a5p DNA binding protein cryo-EM (3.4 Å) Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP (2022) "Structural mechanism of extranucleosomal DNA readout by the INO80 complex." Sci Adv, 8, eadd3189. doi: 10.1126/sciadv.add3189. Structure of arp4-ies4-n-actin-arp8-ino80hsa subcomplex (a-module) of chaetomium thermophilum ino80 on curved DNA. SNAP output
8a5q DNA binding protein cryo-EM (3.3 Å) Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP (2022) "Structural mechanism of extranucleosomal DNA readout by the INO80 complex." Sci Adv, 8, eadd3189. doi: 10.1126/sciadv.add3189. Structure of arp4-ies4-n-actin-arp8-ino80hsa subcomplex (a-module) of chaetomium thermophilum ino80 on straight DNA. SNAP output
8a8j DNA binding protein cryo-EM (3.1 Å) Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M (2023) "Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination." Nat.Struct.Mol.Biol., 30, 650-660. doi: 10.1038/s41594-023-00967-z. Complex of recf and DNA from thermus thermophilus.. SNAP output
8a93 DNA binding protein cryo-EM (3.05 Å) Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M (2023) "Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination." Nat.Struct.Mol.Biol., 30, 650-660. doi: 10.1038/s41594-023-00967-z. Complex of recf-recr-DNA from thermus thermophilus.. SNAP output
8aag gene regulation cryo-EM (10.0 Å) Louro JA, Boopathi R, Beinsteiner B, Mohideen Patel AK, Cheng TC, Angelov D, Hamiche A, Bendar J, Kale S, Klaholz BP, Dimitrov S (2023) "Nucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms." Structure, 31, 201. doi: 10.1016/j.str.2022.12.005. H1-bound palindromic nucleosome, state 1. SNAP output
8aan DNA binding protein X-ray (2.19 Å) Wegrzyn K, Oliwa M, Nowacka M, Zabrocka E, Bury K, Purzycki P, Czaplewska P, Pipka J, Giraldo R, Konieczny I (2023) "Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation." Nucleic Acids Res., 51, 10551-10567. doi: 10.1093/nar/gkad740. The nucleoprotein complex of rep protein with iteron containing dsDNA and due ssDNA.. SNAP output
8aas DNA binding protein X-ray (3.2 Å) Madru C, Martinez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L (2023) "DNA-binding mechanism and evolution of replication protein A." Nat Commun, 14, 2326. doi: 10.1038/s41467-023-38048-w. Crystal structure of the pyrococcus abyssi rpa trimerization core bound to poly-dt20 ssDNA. SNAP output
8ab0 DNA binding protein cryo-EM (6.09 Å) Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M (2023) "Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination." Nat.Struct.Mol.Biol., 30, 650-660. doi: 10.1038/s41594-023-00967-z. Complex of reco-recr-DNA from thermus thermophilus.. SNAP output
8aby transcription cryo-EM (3.7 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase bound to purified in vitro transcribed regulatory RNA putl - pause prone, closed clamp state. SNAP output
8abz transcription cryo-EM (3.4 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase at u-rich pause bound to non-regulatory RNA - pause prone, closed clamp state. SNAP output
8ac0 transcription cryo-EM (4.1 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase at u-rich pause bound to regulatory RNA putl - active, closed clamp state. SNAP output
8ac1 transcription cryo-EM (4.06 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase at u-rich pause bound to non-regulatory RNA - inactive, open clamp state. SNAP output
8ac2 transcription cryo-EM (3.7 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase- post-terminated, open clamp state. SNAP output
8ac8 DNA binding protein X-ray (1.6 Å) Wegrzyn K, Oliwa M, Nowacka M, Zabrocka E, Bury K, Purzycki P, Czaplewska P, Pipka J, Giraldo R, Konieczny I (2023) "Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation." Nucleic Acids Res., 51, 10551-10567. doi: 10.1093/nar/gkad740. The nucleoprotein complex of rep protein with due ssDNA. SNAP output
8acp transcription cryo-EM (4.5 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase at u-rich pause bound to regulatory RNA putl - inactive, open clamp state. SNAP output
8ad1 transcription cryo-EM (4.1 Å) Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-Andre C, Weixlbaumer A (2022) "Structural insights into RNA-mediated transcription regulation in bacteria." Mol.Cell, 82, 3885. doi: 10.1016/j.molcel.2022.09.020. RNA polymerase at u-rich pause bound to RNA putl triple mutant - pause prone, closed clamp state. SNAP output
8ag6 DNA binding protein cryo-EM (2.8 Å) Bruekner SR, Pieters W, Fish A, Liaci AM, Scheffers S, Rayner E, Kaldenbach D, Drost L, Dekker M, van Hees-Stuivenberg S, Delzenne-Goette E, de Konink C, Houlleberghs H, Dubbink HJ, AlSaegh A, de Wind N, Forster F, Te Riele H, Sixma TK (2023) "Unexpected moves: a conformational change in MutS alpha enables high-affinity DNA mismatch binding." Nucleic Acids Res., 51, 1173-1188. doi: 10.1093/nar/gkad015. Human mutsalpha (msh2-msh6) binding to DNA with a gt mismatch. SNAP output
8amd recombination cryo-EM (3.9 Å) Hertzog M, Perry TN, Dupaigne P, Serres S, Morales V, Soulet AL, Bell JC, Margeat E, Kowalczykowski SC, Le Cam E, Fronzes R, Polard P (2023) "Assembly mechanism and cryoEM structure of RecA recombination nucleofilaments from Streptococcus pneumoniae." Nucleic Acids Res., 51, 2800-2817. doi: 10.1093/nar/gkad080. cryo-EM structure of the reca presynaptic filament from s.pneumoniae. SNAP output
8amf recombination cryo-EM (3.8 Å) Hertzog M, Perry TN, Dupaigne P, Serres S, Morales V, Soulet AL, Bell JC, Margeat E, Kowalczykowski SC, Le Cam E, Fronzes R, Polard P (2023) "Assembly mechanism and cryoEM structure of RecA recombination nucleofilaments from Streptococcus pneumoniae." Nucleic Acids Res., 51, 2800-2817. doi: 10.1093/nar/gkad080. cryo-EM structure of the reca postsynaptic filament from s. pneumoniae. SNAP output
8amu replication X-ray (3.0 Å) Machon C, Ruiz-Maso JA, Amodio J, Boer DR, Bordanaba-Ruiseco L, Bury K, Konieczny I, Del Solar G, Coll M (2023) "Structures of pMV158 replication initiator RepB with and without DNA reveal a flexible dual-function protein." Nucleic Acids Res., 51, 1458-1472. doi: 10.1093/nar/gkac1271. Repb pmv158 obd domain bound to ddr region. SNAP output
8ap1 transcription cryo-EM (3.47 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with two gtp molecules poised for de novo initiation (ic2). SNAP output
8apm viral protein cryo-EM (6.6 Å) Hutin S, Ling WL, Tarbouriech N, Schoehn G, Grimm C, Fischer U, Burmeister WP (2022) "The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction." Viruses, 14. doi: 10.3390/v14102206. Vaccinia virus DNA helicase d5 residues 323-785 hexamer with bound DNA processed in c1. SNAP output
8asc DNA binding protein X-ray (2.95 Å) Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK (2023) "PAXX binding to the NHEJ machinery explains functional redundancy with XLF." Sci Adv, 9, eadg2834. doi: 10.1126/sciadv.adg2834. Ku70-80 binds to the ku-binding motif of paxx. SNAP output
8atf DNA binding protein cryo-EM (3.45 Å) Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP (2022) "Structural mechanism of extranucleosomal DNA readout by the INO80 complex." Sci Adv, 8, eadd3189. doi: 10.1126/sciadv.add3189. Nucleosome-bound ino80 atpase. SNAP output
8att transcription cryo-EM (3.44 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 4-mer RNA, pppgpgpupa (ic4). SNAP output
8atv transcription cryo-EM (3.39 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 5-mer RNA, pppgpgpapapa (ic5). SNAP output
8atw transcription cryo-EM (3.62 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 6-mer RNA, pppgpgpapapapu (ic6). SNAP output
8av6 DNA binding protein cryo-EM (4.68 Å) Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP (2022) "Structural mechanism of extranucleosomal DNA readout by the INO80 complex." Sci Adv, 8, eadd3189. doi: 10.1126/sciadv.add3189. Cryoem structure of ino80 core nucleosome complex in closed grappler conformation. SNAP output
8axa DNA binding protein cryo-EM (2.96 Å) Tenjo-Castano F, Sofos N, Stutzke LS, Temperini P, Fuglsang A, Pape T, Mesa P, Montoya G (2024) "Conformational landscape of the type V-K CRISPR-associated transposon integration assembly." Mol.Cell, 84, 2353-2367.e5. doi: 10.1016/j.molcel.2024.05.005. cryo-EM structure of shcas12k-sgrna-dsDNA ternary complex (type v-k crispr-associated transposon). SNAP output
8b0a DNA binding protein cryo-EM (3.0 Å) Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S (2024) "Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1." Nat Commun, 15, 1000. doi: 10.1038/s41467-024-45237-8. cryo-EM structure of alc1 bound to an asymmetric, site-specifically parylated nucleosome. SNAP output
8b1t DNA binding protein cryo-EM (3.4 Å) Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS (2022) "Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub." Elife, 11. doi: 10.7554/eLife.83409. Recbcd-DNA in complex with the phage protein abc2. SNAP output
8b1u DNA binding protein cryo-EM (3.8 Å) Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS (2022) "Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub." Elife, 11. doi: 10.7554/eLife.83409. Recbcd-DNA in complex with the phage protein abc2 and host ppib. SNAP output
8b3d transcription cryo-EM (2.6 Å) Kokic G, Cramer P "Structure of the Pol II-TCR-ELOF1 complex." Structure of the pol ii-tcr-elof1 complex.. SNAP output
8b3f transcription cryo-EM (3.1 Å) Kokic G, Cramer P "Pol II-CSB-CSA-DDB1-ELOF1 structure." Pol ii-csb-csa-ddb1-elof1. SNAP output
8b4b DNA binding protein X-ray (1.75 Å) Canals A, Pieretti S, Muriel-Masanes M, El Yaman N, Plecha SC, Thomson JJ, Fabrega-Ferrer M, Perez-Luque R, Krukonis ES, Coll M (2023) "ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites." Proc.Natl.Acad.Sci.USA, 120, e2304378120. doi: 10.1073/pnas.2304378120. Toxr bacterial transcriptional regulator bound to 19 bp ompu promoter DNA. SNAP output
8b4c DNA binding protein X-ray (2.07 Å) Canals A, Pieretti S, Muriel-Masanes M, El Yaman N, Plecha SC, Thomson JJ, Fabrega-Ferrer M, Perez-Luque R, Krukonis ES, Coll M (2023) "ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites." Proc.Natl.Acad.Sci.USA, 120, e2304378120. doi: 10.1073/pnas.2304378120. Toxr bacterial transcriptional regulator bound to 20 bp toxt promoter DNA. SNAP output
8b4d DNA binding protein X-ray (2.64 Å) Canals A, Pieretti S, Muriel-Masanes M, El Yaman N, Plecha SC, Thomson JJ, Fabrega-Ferrer M, Perez-Luque R, Krukonis ES, Coll M (2023) "ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites." Proc.Natl.Acad.Sci.USA, 120, e2304378120. doi: 10.1073/pnas.2304378120. Toxr bacterial transcriptional regulator bound to 40 bp toxt promoter DNA. SNAP output
8b4e DNA binding protein X-ray (3.25 Å) Canals A, Pieretti S, Muriel-Masanes M, El Yaman N, Plecha SC, Thomson JJ, Fabrega-Ferrer M, Perez-Luque R, Krukonis ES, Coll M (2023) "ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites." Proc.Natl.Acad.Sci.USA, 120, e2304378120. doi: 10.1073/pnas.2304378120. Toxr bacterial transcriptional regulator bound to 25 bp toxt promoter DNA. SNAP output
8b4h DNA binding protein cryo-EM (3.35 Å) Spinola-Amilibia M, Araujo-Bazan L, de la Gandara A, Berger JM, Arias-Palomo E (2023) "IS21 family transposase cleaved donor complex traps two right-handed superhelical crossings." Nat Commun, 14, 2335. doi: 10.1038/s41467-023-38071-x. Ista transposase cleaved donor complex. SNAP output
8b67 DNA binding protein X-ray (2.6 Å) Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E (2023) "A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides." Nucleic Acids Res. doi: 10.1093/nar/gkad817. The crystal structure of m644g variant of DNA pol epsilon containing ctp in the polymerase active site. SNAP output
8b6k DNA binding protein X-ray (2.5 Å) Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E (2023) "A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides." Nucleic Acids Res. doi: 10.1093/nar/gkad817. The crystal structure of m644g variant of DNA pol epsilon containing dctp in the polymerase active site. SNAP output
8b76 DNA binding protein X-ray (2.6 Å) Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E (2023) "A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides." Nucleic Acids Res. doi: 10.1093/nar/gkad817. The crystal structure of m644g variant of DNA pol epsilon containing dttp in the polymerase active site. SNAP output
8b77 DNA binding protein X-ray (2.7 Å) Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E (2023) "A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides." Nucleic Acids Res. doi: 10.1093/nar/gkad817. The crystal structure of n828v variant of DNA pol epsilon containing datp in the polymerase active site. SNAP output
8b79 DNA binding protein X-ray (2.65 Å) Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E (2023) "A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides." Nucleic Acids Res. doi: 10.1093/nar/gkad817. The crystal structure of m644g variant of DNA pol epsilon containing utp in the polymerase active site. SNAP output
8b7e DNA binding protein X-ray (2.6 Å) Parkash V, Kulkarni Y, Bylund GO, Osterman P, Kamerlin SCL, Johansson E (2023) "A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides." Nucleic Acids Res. doi: 10.1093/nar/gkad817. The crystal structure of n828v variant of DNA pol epsilon containing utp in the polymerase active site. SNAP output
8b9n DNA binding protein X-ray (2.0 Å) Klima M, Boura E, Silhan J "Crystal structure of NEI domain of mouse NEIL3 trapped in covalent complex with ssDNA with abasic site." Crystal structure of nei domain of mouse neil3 trapped in covalent complex with ssDNA with abasic site. SNAP output
8bar toxin X-ray (1.63 Å) Schuller M, Raggiaschi R, Mikolcevic P, Rack JGM, Ariza A, Zhang Y, Ledermann R, Tang C, Mikoc A, Ahel I (2023) "Molecular basis for the reversible ADP-ribosylation of guanosine bases." Mol.Cell, 83, 2303. doi: 10.1016/j.molcel.2023.06.013. E. coli c7 dart1 in complex with adp-ribosylated ssDNA and nicotinamide. SNAP output
8bas toxin X-ray (1.92 Å) Schuller M, Raggiaschi R, Mikolcevic P, Rack JGM, Ariza A, Zhang Y, Ledermann R, Tang C, Mikoc A, Ahel I (2023) "Molecular basis for the reversible ADP-ribosylation of guanosine bases." Mol.Cell, 83, 2303. doi: 10.1016/j.molcel.2023.06.013. E. coli c7 dart1 in complex with carba-nad and DNA. SNAP output
8bd4 DNA binding protein cryo-EM (3.44 Å) Schmitz M, Querques I, Oberli S, Chanez C, Jinek M (2022) "Structural basis for the assembly of the type V CRISPR-associated transposon complex." Cell, 185, 4999. doi: 10.1016/j.cell.2022.11.009. Tniq-capped tns-atp-dsDNA complex. SNAP output
8bd5 RNA binding protein cryo-EM (3.3 Å) Schmitz M, Querques I, Oberli S, Chanez C, Jinek M (2022) "Structural basis for the assembly of the type V CRISPR-associated transposon complex." Cell, 185, 4999. doi: 10.1016/j.cell.2022.11.009. Cas12k-sgrna-dsDNA-s15-tniq-tnsc transposon recruitment complex. SNAP output
8bd6 RNA binding protein cryo-EM (4.1 Å) Schmitz M, Querques I, Oberli S, Chanez C, Jinek M (2022) "Structural basis for the assembly of the type V CRISPR-associated transposon complex." Cell, 185, 4999. doi: 10.1016/j.cell.2022.11.009. Cas12k-sgrna-dsDNA-tnsc non-productive complex.. SNAP output
8bh3 DNA binding protein cryo-EM (4.55 Å) Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK (2023) "PAXX binding to the NHEJ machinery explains functional redundancy with XLF." Sci Adv, 9, eadg2834. doi: 10.1126/sciadv.adg2834. DNA-pk ku80 mediated dimer bound to paxx. SNAP output
8bhv DNA binding protein cryo-EM (4.51 Å) Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK (2023) "PAXX binding to the NHEJ machinery explains functional redundancy with XLF." Sci Adv, 9, eadg2834. doi: 10.1126/sciadv.adg2834. DNA-pk xlf mediated dimer bound to paxx. SNAP output
8bhy DNA binding protein cryo-EM (5.33 Å) Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK (2023) "PAXX binding to the NHEJ machinery explains functional redundancy with XLF." Sci Adv, 9, eadg2834. doi: 10.1126/sciadv.adg2834. DNA-pk ku80 mediated dimer bound to paxx and xlf. SNAP output
8bpr DNA binding protein cryo-EM (3.65 Å) Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M (2023) "Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination." Nat.Struct.Mol.Biol., 30, 650-660. doi: 10.1038/s41594-023-00967-z. Complex of recf-reco-recr-DNA from thermus thermophilus (low resolution reconstruction).. SNAP output
8bq2 DNA binding protein cryo-EM (3.8 Å) Appleby R, Bollschweiler D, Chirgadze DY, Joudeh L, Pellegrini L (2023) "A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly." Iscience, 26, 106689. doi: 10.1016/j.isci.2023.106689. Cryoem structure of the pre-synaptic rad51 nucleoprotein filament in the presence of atp and ca2+. SNAP output
8br2 DNA binding protein cryo-EM (2.9 Å) Appleby R, Bollschweiler D, Chirgadze DY, Joudeh L, Pellegrini L (2023) "A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly." Iscience, 26, 106689. doi: 10.1016/j.isci.2023.106689. Cryoem structure of the post-synaptic rad51 nucleoprotein filament in the presence of atp and ca2+. SNAP output
8btg replication cryo-EM (3.2 Å) Pelliciari S, Bodet-Lefevre S, Fenyk S, Stevens D, Winterhalter C, Schramm FD, Pintar S, Burnham DR, Merces G, Richardson TT, Tashiro Y, Hubbard J, Yardimci H, Ilangovan A, Murray H (2023) "The bacterial replication origin BUS promotes nucleobase capture." Nat Commun, 14, 8339. doi: 10.1093/nar/gkac1060. cryo-EM structure of the bacterial replication origin opening basal unwinding system. SNAP output
8bw5 hydrolase X-ray (2.8 Å) Troisi R, Napolitano V, Rossitto E, Osman W, Nagano M, Wakui K, Popowicz GM, Yoshimoto K, Sica F (2023) "Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide." Nucleic Acids Res., 51, 8880-8890. doi: 10.1093/nar/gkad634. X-ray structure of the complex between human alpha thrombin and the duplex-quadruplex aptamer m08s-1_41mer. SNAP output
8bws transcription cryo-EM (3.2 Å) Nguyen PQ, Huecas S, Asif-Laidin A, Plaza-Pegueroles A, Capuzzi B, Palmic N, Conesa C, Acker J, Reguera J, Lesage P, Fernandez-Tornero C (2023) "Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration." Nat Commun, 14, 1729. doi: 10.1038/s41467-023-37109-4. Structure of yeast RNA polymerase iii elongation complex at 3.3 a. SNAP output
8bx1 transcription X-ray (2.5 Å) Chojnowski G, Wilmanns M, Round E "Crystal structure of Oct4-Soc2-HoxB1 complex." Oct4-sox2 protein:DNA complex. SNAP output
8bx2 transcription X-ray (3.14 Å) Chojnowski G, Wilmanns M, Round E "Crystal structure of Oct4-Soc2-UTF1 complex." Oct4-sox2 protein:DNA complex. SNAP output
8byx transcription X-ray (3.0 Å) Morgunova E, Popov A, Yin Y, Taipale J "HOXB13-homodimer bound to DNA." Hoxb13-homodimer bound to DNA. SNAP output
8bzm transcription X-ray (2.69 Å) Morgunova E, Popov A, Yin Y, Taipale J "FOXK1-ELF1_heterodimer bound to DNA." Foxk1-elf1-heterodimer bound to DNA. SNAP output
8c41 isomerase X-ray (2.393 Å) Najmudin S, Pan XS, Wang B, Chayen NE, Fisher LM, Sanderson MR "The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin." High resolution structure of the streptococcus pneumoniae topoisomerase iv-DNA complex with the novel fluoroquinolone delafloxacin. SNAP output
8c56 transferase X-ray (2.4 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mz) and 5-methylcytosine containing dsDNA. SNAP output
8c57 transferase X-ray (1.95 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhac) and 5-methylcytosine containing dsDNA. SNAP output
8c58 transferase X-ray (1.85 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 5-hydroxycytosine and 5-methylcytosine containing dsDNA. SNAP output
8c59 transferase X-ray (1.7 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 5-bromocytosine (converted to 5mc) and 5-methylcytosine containing dsDNA. SNAP output
8c5s transcription cryo-EM (3.75 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 7-mer RNA, pppgpgpupapapapu (ic7). SNAP output
8c5u transcription cryo-EM (3.62 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppgpgpupapapapupg (ic8). SNAP output
8c7s transcription X-ray (3.05 Å) Hainzl T, Bonde M, Almqvist F, Johansson J, Sauer-Eriksson AE (2023) "Structural insights into CodY activation and DNA recognition." Nucleic Acids Res., 51, 7631-7648. doi: 10.1093/nar/gkad512. Transcriptional pleiotropic repressor cody from staphylococcus aureus in complex with ile, gtp, and a 30-bp DNA fragment encompassing two overlapping binding sites. SNAP output
8c7u transcription X-ray (3.15 Å) Hainzl T, Bonde M, Almqvist F, Johansson J, Sauer-Eriksson AE (2023) "Structural insights into CodY activation and DNA recognition." Nucleic Acids Res., 51, 7631-7648. doi: 10.1093/nar/gkad512. Transcriptional pleiotropic repressor cody from enterococcus faecalis in complex with leu and a 30-bp DNA fragment encompassing two overlapping binding sites. SNAP output
8c84 transcription X-ray (1.9 Å) Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A (2024) "Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA." J.Mol.Biol., 436, 168541. doi: 10.1016/j.jmb.2024.168541. Crystal structure of mads-box-mef2d n-terminal domain complex. SNAP output
8c8j replication X-ray (2.1 Å) Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS (2024) "Structures, functions and adaptations of the human LINE-1 ORF2 protein." Nature, 626, 194-206. doi: 10.1038/s41586-023-06947-z. Long interspersed nuclear element 1 (line-1) reverse transcriptase ternary complex with hybrid duplex and dttp. SNAP output
8cbn transcription cryo-EM (3.34 Å) Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V (2023) "Multivalency of nucleosome recognition by LEDGF." Nucleic Acids Res., 51, 10011-10025. doi: 10.1093/nar/gkad674. Structure of ledgf-p75 pwwp domain bound to the h3k36 trimethylated dinucleosome. SNAP output
8cbq DNA binding protein cryo-EM (4.0 Å) Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V (2023) "Multivalency of nucleosome recognition by LEDGF." Nucleic Acids Res., 51, 10011-10025. doi: 10.1093/nar/gkad674. Structure of ledgf-p75 pwwp domain bound to the h3k36 trimethylated dinucleosome. SNAP output
8cdn transcription X-ray (2.55 Å) Newman JA, Gavard AE, von Delft F, Gileadi O, Bountra C "Crystal structure of human Brachyury in complex with a single T box binding element DNA." Crystal structure of human brachyury in complex with a single t box binding element DNA. SNAP output
8cef hormone X-ray (2.486 Å) Patel AKM, Vilela P, Shaik TB, McEwen AG, Hazemann I, Brillet K, Ennifar E, Hamiche A, Markov GV, Laudet V, Moras D, Klaholz BP, Billas IML (2023) "Asymmetric dimerization in a transcription factor superfamily is promoted by allosteric interactions with DNA." Nucleic Acids Res., 51, 8864-8879. doi: 10.1093/nar/gkad632. Asymmetric dimerization in a transcription factor superfamily is promoted by allosteric interactions with DNA. SNAP output
8cli transcription cryo-EM (3.2 Å) Seifert-Davila W, Girbig M, Hauptmann L, Hoffmann T, Eustermann S, Muller CW (2023) "Structural insights into human TFIIIC promoter recognition." Sci Adv, 9, eadh2019. doi: 10.1126/sciadv.adh2019. Tfiiic taub-DNA monomer. SNAP output
8clj transcription cryo-EM (3.2 Å) Seifert-Davila W, Girbig M, Hauptmann L, Hoffmann T, Eustermann S, Muller CW (2023) "Structural insights into human TFIIIC promoter recognition." Sci Adv, 9, eadh2019. doi: 10.1126/sciadv.adh2019. Tfiiic taub-DNA dimer. SNAP output
8com DNA binding protein cryo-EM (3.3 Å) Deak G, Wapenaar H, Sandoval G, Chen R, Taylor MRD, Burdett H, Watson JA, Tuijtel MW, Webb S, Wilson MD (2023) "Histone divergence in trypanosomes results in unique alterations to nucleosome structure." Nucleic Acids Res., 51, 7882-7899. doi: 10.1093/nar/gkad577. Structure of the nucleosome core particle from trypanosoma brucei. SNAP output
8cpg DNA binding protein X-ray (1.4 Å) Nue-Martinez JJ, Maturana M, Lagartera L, Rodriguez-Gutierrez JA, Boer R, Campos JL, Saperas N, Dardonville C (2024) "Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs." Sci Rep, 14, 26173. doi: 10.1038/s41598-024-77522-3. Structure of the at-hook 1 peptide from the mammalian hmga protein in complex with DNA. SNAP output
8cro transcription cryo-EM (3.1 Å) Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D (2024) "Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment." Nucleic Acids Res., 52, 6017-6035. doi: 10.1093/nar/gkae282. cryo-EM structure of pyrococcus furiosus transcription elongation complex. SNAP output
8cs0 DNA binding protein-DNA X-ray (1.65 Å) Georgiadis MM, Hoshika S, Shukla M, Benner SA "Alien DNA visualized at high resolution in A- and B-forms." Crystal structure of alien DNA ctszzpbsbszppbag in a host-guest complex with the n-terminal fragment of moloney murine leukemia virus reverse transcriptase. SNAP output
8csh DNA binding protein-DNA X-ray (2.25 Å) Chan HY, Jensen SO, LeBard RJ, Figgett WA, Lai E, Simpson AE, Brzoska AJ, Davies DS, Connolly AM, Cordwell SJ, Travis BA, Salinas R, Skurray RA, Firth N, Schumacher MA (2022) "Molecular Analysis of pSK1 par: A Novel Plasmid Partitioning System Encoded by Staphylococcal Multiresistance Plasmids." J.Mol.Biol., 434, 167770. doi: 10.1016/j.jmb.2022.167770. Structure of the DNA binding domain of psk1 par partition protein bound to centromere DNA. SNAP output
8csz RNA binding protein-RNA-DNA cryo-EM (3.2 Å) Schuler G, Hu C, Ke A (2022) "Structural basis for RNA-guided DNA cleavage by IscB-omega RNA and mechanistic comparison with Cas9." Science, 376, 1476-1481. doi: 10.1126/science.abq7220. Iscb and wrna bound to target DNA. SNAP output
8ctl RNA binding protein-RNA-DNA cryo-EM (3.1 Å) Schuler G, Hu C, Ke A (2022) "Structural basis for RNA-guided DNA cleavage by IscB-omega RNA and mechanistic comparison with Cas9." Science, 376, 1476-1481. doi: 10.1126/science.abq7220. Iscb and wrna bound to target DNA (locked state). SNAP output
8cty DNA X-ray (2.3 Å) Kellum Jr AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M (2022) "Conformation and Pairing Properties of an O 6 -Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA." Chem.Res.Toxicol., 35, 1903-1913. doi: 10.1021/acs.chemrestox.2c00165. 12-mer DNA structure of exbim bound to rnase-h. SNAP output
8ctz DNA X-ray (2.32 Å) Kellum Jr AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M (2022) "Conformation and Pairing Properties of an O 6 -Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA." Chem.Res.Toxicol., 35, 1903-1913. doi: 10.1021/acs.chemrestox.2c00165. 12-mer DNA structure of exbim & o6me-g bound to rnase-h. SNAP output
8cu0 DNA X-ray (1.74 Å) Kellum Jr AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M (2022) "Conformation and Pairing Properties of an O 6 -Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA." Chem.Res.Toxicol., 35, 1903-1913. doi: 10.1021/acs.chemrestox.2c00165. 12-mer DNA structure of exbim bound to rnaseh -modified ddd. SNAP output
8cuc transcription-DNA X-ray (2.09 Å) Seo HS, Dhe-Paganon S "Crystal Structure Analysis of SALL4 Zinc Finger domain in complex with DNA." Crystal structure analysis of sall4 zinc finger domain in complex with DNA. SNAP output
8cww DNA binding protein-DNA cryo-EM (2.74 Å) Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A (2024) "Chromatin binding by HORMAD proteins regulates meiotic recombination initiation." Embo J., 43, 836-867. doi: 10.1038/s44318-024-00034-3. Structure of s. cerevisiae hop1 cbr bound to a nucleosome. SNAP output
8cxs DNA binding protein-DNA X-ray (2.49 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor mta. SNAP output
8cxt DNA binding protein-DNA X-ray (2.61 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor n6-benzyladenosine (compound 1). SNAP output
8cxu DNA binding protein-DNA X-ray (2.28 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 2. SNAP output
8cxv DNA binding protein-DNA X-ray (2.26 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 3. SNAP output
8cxw DNA binding protein-DNA X-ray (2.78 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor piclidenoson (compound 4). SNAP output
8cxx DNA binding protein-DNA X-ray (2.34 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 6. SNAP output
8cxy DNA binding protein-DNA X-ray (2.19 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor n6-(2-phenethyl)adenosine (compound 8). SNAP output
8cxz DNA binding protein-DNA X-ray (2.35 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor n6-(3-phenylpropyl)adenosine (compound 14). SNAP output
8cy0 DNA binding protein-DNA X-ray (2.65 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor mc4756 (compound 178). SNAP output
8cy1 DNA binding protein-DNA X-ray (2.38 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 19. SNAP output
8cy2 DNA binding protein-DNA X-ray (2.81 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor apnea (compound 9). SNAP output
8cy3 DNA binding protein-DNA X-ray (2.65 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 15. SNAP output
8cy4 DNA binding protein-DNA X-ray (2.34 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 16. SNAP output
8cy5 DNA binding protein-DNA X-ray (2.5 Å) Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Huben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X (2023) "Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence." J.Med.Chem., 66, 934-950. doi: 10.1021/acs.jmedchem.2c01789. Cama adenine methyltransferase complexed to cognate substrate DNA and compound 39. SNAP output
8cyf transcription-DNA-transferase X-ray (2.44 Å) Wan T, Horova M, Khetrapal V, Li S, Jones C, Schacht A, Sun X, Zhang L (2023) "Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis." J.Biol.Chem., 299, 104777. doi: 10.1016/j.jbc.2023.104777. Whib3 bound to sigmaar4-rnap beta flap tip chimera and DNA. SNAP output
8cze DNA binding protein-DNA cryo-EM (2.58 Å) Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A (2024) "Chromatin binding by HORMAD proteins regulates meiotic recombination initiation." Embo J., 43, 836-867. doi: 10.1038/s44318-024-00034-3. Structure of a xenopus nucleosome with widom 601 DNA. SNAP output
8czq isomerase-DNA X-ray (2.78 Å) Ferdous S, Dasgupta T, Annamalai T, Tan K, Tse-Dinh YC (2023) "The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments." Nucleic Acids Res., 51, 349-364. doi: 10.1093/nar/gkac1205. The crystal structure of mtbtop1 in complex with both g- and t-segments. SNAP output
8d0b replication-DNA cryo-EM (3.43 Å) He Q, Lin X, Chavez BL, Agrawal S, Lusk BL, Lim CJ (2022) "Structures of the human CST-Pol alpha-primase complex bound to telomere templates." Nature, 608, 826-832. doi: 10.1038/s41586-022-05040-1. Human cst-DNA polymerase alpha-primase preinitiation complex bound to 4xtel-foldback template. SNAP output
8d0k replication-DNA cryo-EM (4.27 Å) He Q, Lin X, Chavez BL, Agrawal S, Lusk BL, Lim CJ (2022) "Structures of the human CST-Pol alpha-primase complex bound to telomere templates." Nature, 608, 826-832. doi: 10.1038/s41586-022-05040-1. Human cst-DNA polymerase alpha-primase preinitiation complex bound to 4xtel-foldback template - prim2c advanced pic. SNAP output
8d2k RNA binding protein-DNA-RNA cryo-EM (2.43 Å) Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H (2023) "Coupled catalytic states and the role of metal coordination in Cas9." Nat Catal, 6, 969-977. doi: 10.1038/s41929-023-01031-1. Structure of acidothermus cellulolyticus cas9 ternary complex (cleavage intermediate 2). SNAP output
8d2l RNA binding protein-DNA-RNA cryo-EM (2.21 Å) Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H (2023) "Coupled catalytic states and the role of metal coordination in Cas9." Nat Catal, 6, 969-977. doi: 10.1038/s41929-023-01031-1. Structure of acidothermus cellulolyticus cas9 ternary complex (cleavage intermediate 1). SNAP output
8d2m DNA binding protein-DNA X-ray (1.821 Å) Paulin KA, Cortez D, Eichman BF (2022) "The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA-protein cross-link." J.Biol.Chem., 298, 102307. doi: 10.1016/j.jbc.2022.102307. Covalent schiff base complex of yedk c2a and abasic DNA. SNAP output
8d2n RNA binding protein-DNA-RNA cryo-EM (2.88 Å) Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H (2023) "Coupled catalytic states and the role of metal coordination in Cas9." Nat Catal, 6, 969-977. doi: 10.1038/s41929-023-01031-1. Structure of acidothermus cellulolyticus cas9 ternary complex (pre-cleavage). SNAP output
8d2o RNA binding protein-DNA-RNA cryo-EM (2.66 Å) Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H (2023) "Coupled catalytic states and the role of metal coordination in Cas9." Nat Catal, 6, 969-977. doi: 10.1038/s41929-023-01031-1. Structure of acidothermus cellulolyticus cas9 ternary complex (post-cleavage 2). SNAP output
8d2p RNA binding protein-DNA-RNA cryo-EM (2.78 Å) Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H (2023) "Coupled catalytic states and the role of metal coordination in Cas9." Nat Catal, 6, 969-977. doi: 10.1038/s41929-023-01031-1. Structure of acidothermus cellulolyticus cas9 ternary complex (target bound). SNAP output
8d2q RNA binding protein-DNA-RNA cryo-EM (2.58 Å) Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H (2023) "Coupled catalytic states and the role of metal coordination in Cas9." Nat Catal, 6, 969-977. doi: 10.1038/s41929-023-01031-1. Structure of acidothermus cellulolyticus cas9 ternary complex (post-cleavage 1). SNAP output
8d33 transferase-DNA cryo-EM (2.46 Å) Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW (2023) "Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity." Nat.Struct.Mol.Biol., 30, 812-823. doi: 10.1038/s41594-023-00980-2. Human mitochondrial DNA polymerase gamma ternary complex with gc basepair. SNAP output
8d37 transferase-DNA cryo-EM (2.65 Å) Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW (2023) "Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity." Nat.Struct.Mol.Biol., 30, 812-823. doi: 10.1038/s41594-023-00980-2. Human mitochondrial DNA polymerase gamma ternary complex with gt basepair in replication conformer. SNAP output
8d3l hydrolase-DNA cryo-EM (3.49 Å) Dhingra Y, Suresh SK, Juneja P, Sashital DG (2022) "PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation." Mol.Cell, 82, 4353. doi: 10.1016/j.molcel.2022.09.030. Type i-c cas4-cas1-cas2 complex bound to a pam-pam prespacer. SNAP output
8d3m hydrolase-DNA cryo-EM (3.41 Å) Dhingra Y, Suresh SK, Juneja P, Sashital DG (2022) "PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation." Mol.Cell, 82, 4353. doi: 10.1016/j.molcel.2022.09.030. Type i-c cas4-cas1-cas2 complex bound to a pam-processed prespacer. SNAP output
8d3p hydrolase-DNA cryo-EM (4.26 Å) Dhingra Y, Suresh SK, Juneja P, Sashital DG (2022) "PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation." Mol.Cell, 82, 4353. doi: 10.1016/j.molcel.2022.09.030. Type i-c cas4-cas1-cas2 complex bound to half-site integration intermediate (hsi). SNAP output
8d3q hydrolase-DNA cryo-EM (3.9 Å) Dhingra Y, Suresh SK, Juneja P, Sashital DG (2022) "PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation." Mol.Cell, 82, 4353. doi: 10.1016/j.molcel.2022.09.030. Type i-c cas4-cas1-cas2 complex bound to a pam-nopam prespacer. SNAP output
8d3r transferase-DNA cryo-EM (3.04 Å) Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW (2023) "Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity." Nat.Struct.Mol.Biol., 30, 812-823. doi: 10.1038/s41594-023-00980-2. Human mitochondrial DNA polymerase gamma ternary complex with gt basepair in intermediate conformer. SNAP output
8d42 transferase-DNA cryo-EM (2.91 Å) Park J, Herrmann GK, Mitchell PG, Sherman MB, Yin YW (2023) "Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity." Nat.Struct.Mol.Biol., 30, 812-823. doi: 10.1038/s41594-023-00980-2. Human mitochondrial DNA polymerase gamma ternary complex with gt basepair in editing conformer (composite). SNAP output
8d4a DNA binding protein-RNA-DNA cryo-EM (2.74 Å) Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW (2023) "RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2." Nature, 613, 582-587. doi: 10.1038/s41586-022-05560-w. Cas12a2 quaternary complex. SNAP output
8d86 DNA binding protein-DNA X-ray (3.12 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD (2023) "Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds." Acs Nano, 17, 13110-13120. doi: 10.1021/acsnano.2c07282. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence co-crystallized with a guest small molecule, netropsin.. SNAP output
8d8m DNA binding protein-DNA X-ray (3.1 Å) Orun AR, Shields ET, Dmytriw S, Vajapayajula A, Snow CD "Designed crystalline assemblies of protein and DNA enable site-specific installation of a guest protein, DNA, and small molecule." Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence grown in a calcium chloride crystallization solution.. SNAP output
8d94 hydrolase-DNA X-ray (2.44 Å) Hollis TJ, Batalis SM "SAMHD1-DNA complex." Samhd1-DNA complex. SNAP output
8d96 replication cryo-EM (3.35 Å) He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH (2023) "Structures of human primosome elongation complexes." Nat.Struct.Mol.Biol., 30, 579-583. doi: 10.1038/s41594-023-00971-3. Human DNA polymerase alpha-primase elongation complex i bound to primer-template. SNAP output
8d9d replication cryo-EM (3.59 Å) He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH (2023) "Structures of human primosome elongation complexes." Nat.Struct.Mol.Biol., 30, 579-583. doi: 10.1038/s41594-023-00971-3. Human DNA polymerase-alpha-primase elongation complex ii bound to primer-template. SNAP output
8d9j hydrolase-DNA X-ray (2.82 Å) Simermeyer TL, Batalis S, Rogers LC, Zalesak OJ, Hollis T (2023) "Protein oxidation increases SAMHD1 binding ssDNA via its regulatory site." Nucleic Acids Res., 51, 7014-7024. doi: 10.1093/nar/gkad447. Samhd1-DNA complex. SNAP output
8dc2 RNA binding protein-RNA-DNA cryo-EM (2.99 Å) Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA (2022) "Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors." Cell, 185, 4574-4586.e16. doi: 10.1016/j.cell.2022.10.020. cryo-EM structure of caslambda (cas12l) bound to crrna and DNA. SNAP output
8dej DNA binding protein-DNA-RNA cryo-EM (2.86 Å) O'Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW (2023) "Structural snapshots of R-loop formation by a type I-C CRISPR Cascade." Mol.Cell, 83, 746. doi: 10.1016/j.molcel.2023.01.024. D. vulgaris type i-c cascade bound to dsDNA target. SNAP output
8df7 DNA binding protein-DNA X-ray (3.52 Å) Osterman A, Mondragon A (2022) "Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism." Elife, 11. doi: 10.7554/eLife.72702. Structure of m. kandleri topoisomerase v in complex with DNA. 38 base pair symmetric DNA complex. SNAP output
8df8 DNA binding protein-DNA X-ray (2.92 Å) Osterman A, Mondragon A (2022) "Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism." Elife, 11. doi: 10.7554/eLife.72702. Structure of m. kandleri topoisomerase v in complex with DNA. 40 base pair symmetric DNA complex. SNAP output
8df9 DNA binding protein-DNA X-ray (3.24 Å) Osterman A, Mondragon A (2022) "Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism." Elife, 11. doi: 10.7554/eLife.72702. Structure of m. kandleri topoisomerase v in complex with DNA. 38 base pair asymmetric DNA complex. SNAP output
8dfa DNA binding protein-DNA-RNA cryo-EM (2.8 Å) O'Brien RE, Bravo JPK, Ramos D, Hibshman GN, Wright JT, Taylor DW (2023) "Structural snapshots of R-loop formation by a type I-C CRISPR Cascade." Mol.Cell, 83, 746. doi: 10.1016/j.molcel.2023.01.024. Type i-c cascade bound to ssDNA target. SNAP output
8dfb DNA binding protein-DNA X-ray (3.17 Å) Osterman A, Mondragon A (2022) "Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism." Elife, 11. doi: 10.7554/eLife.72702. Structure of m. kandleri topoisomerase v in complex with DNA. 39 base pair symmetric DNA complex. SNAP output
8dh0 transferase-DNA-RNA X-ray (2.9 Å) Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D (2023) "Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase." Nat Commun, 14, 195. doi: 10.1038/s41467-022-35755-8. T7 RNA polymerase elongation complex with unnatural base dds. SNAP output
8dh1 transferase-DNA-RNA X-ray (2.65 Å) Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D (2023) "Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase." Nat Commun, 14, 195. doi: 10.1038/s41467-022-35755-8. T7 RNA polymerase elongation complex with unnatural base dds-patp pair. SNAP output
8dh2 transferase-DNA-RNA X-ray (2.9 Å) Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D (2023) "Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase." Nat Commun, 14, 195. doi: 10.1038/s41467-022-35755-8. T7 RNA polymerase elongation complex with unnatural base dds-atp mismatch. SNAP output
8dh3 transferase-DNA-RNA X-ray (3.0 Å) Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D (2023) "Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase." Nat Commun, 14, 195. doi: 10.1038/s41467-022-35755-8. T7 RNA polymerase elongation complex with unnatural base dpa. SNAP output
8dh4 transferase-DNA-RNA X-ray (2.8 Å) Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D (2023) "Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase." Nat Commun, 14, 195. doi: 10.1038/s41467-022-35755-8. T7 RNA polymerase elongation complex with unnatural base dpa-dstp pair. SNAP output
8dh5 transferase-DNA-RNA X-ray (2.85 Å) Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D (2023) "Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase." Nat Commun, 14, 195. doi: 10.1038/s41467-022-35755-8. T7 RNA polymerase elongation complex with unnatural base dpa-atp mismatch. SNAP output
8dk2 DNA binding protein-DNA cryo-EM (4.1 Å) Deep A, Gu Y, Gao YQ, Ego KM, Herzik Jr MA, Zhou H, Corbett KD (2022) "The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA." Mol.Cell, 82, 4145. doi: 10.1016/j.molcel.2022.09.008. Cryoem structure of pseudomonas aeruginosa pa14 jetabc in an unclamped state trapped in atp dependent dimeric form. SNAP output
8dk3 DNA binding protein-DNA cryo-EM (3.28 Å) Deep A, Gu Y, Gao YQ, Ego KM, Herzik Jr MA, Zhou H, Corbett KD (2022) "The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA." Mol.Cell, 82, 4145. doi: 10.1016/j.molcel.2022.09.008. Cryoem structure of pseudomonas aeruginosa pa14 jetc atpase domain bound to DNA and cwhd domain of jeta. SNAP output
8dk5 transcription-DNA cryo-EM (2.71 Å) Guan R, Lian T, Zhou BR, Wheeler D, Bai Y (2023) "Structural mechanism of LIN28B nucleosome targeting by OCT4." Mol.Cell, 83, 1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. Structure of 187bp lin28b nucleosome with site 0 mutation. SNAP output
8dlf viral protein-DNA cryo-EM (3.23 Å) Mei Y, Messick TE, Dheekollu J, Kim HJ, Molugu S, Munoz LJC, Moiskeenkova-Bell V, Murakami K, Lieberman PM (2022) "Cryo-EM Structure and Functional Studies of EBNA1 Binding to the Family of Repeats and Dyad Symmetry Elements of Epstein-Barr Virus oriP." J.Virol., 96, e0094922. doi: 10.1128/jvi.00949-22. Ebna1 DNA binding domain (dbd) (458-617)+2 repeats of family repeat (fr) region. SNAP output
8dmb RNA binding protein-RNA-DNA cryo-EM (3.1 Å) Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F (2022) "Structure of the OMEGA nickase IsrB in complex with omega RNA and target DNA." Nature, 610, 575-581. doi: 10.1038/s41586-022-05324-6. Structure of desulfovirgula thermocuniculi isrb (dtisrb) in complex with omega RNA and target DNA. SNAP output
8dq1 transcription-DNA cryo-EM (4.1 Å) Feathers JR, Richael EK, Simanek KA, Fromme JC, Paczkowski JE (2022) "Structure of the RhlR-PqsE complex from Pseudomonas aeruginosa reveals mechanistic insights into quorum-sensing gene regulation." Structure, 30, 1626. doi: 10.1016/j.str.2022.10.008. Quorum-sensing receptor rhlr bound to pqse. SNAP output
8dqw replication-DNA cryo-EM (2.1 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Open state of rad24-rfc:9-1-1 bound to a 5' ss-dsDNA junction. SNAP output
8dqx replication-DNA cryo-EM (2.1 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Open state of rfc:pcna bound to a 3' ss-dsDNA junction. SNAP output
8dqz replication-DNA cryo-EM (2.92 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Intermediate state of rfc:pcna bound to a 3' ss-dsDNA junction. SNAP output
8dr0 replication-DNA cryo-EM (2.42 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Closed state of rfc:pcna bound to a 3' ss-dsDNA junction. SNAP output
8dr1 replication-DNA cryo-EM (2.14 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Consensus closed state of rfc:pcna bound to a 3' ss-dsDNA junction (dna2). SNAP output
8dr3 replication-DNA cryo-EM (2.2 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Closed state of rfc:pcna bound to a 3' ss-dsDNA junction (dna2) with ntd. SNAP output
8dr4 replication-DNA cryo-EM (2.45 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Open state of rfc:pcna bound to a 3' ss-dsDNA junction (dna2) without ntd. SNAP output
8dr5 replication-DNA cryo-EM (2.76 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Open state of rfc:pcna bound to a 3' ss-dsDNA junction (dna2) with ntd. SNAP output
8dr6 replication-DNA cryo-EM (2.39 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Closed state of rfc:pcna bound to a nicked dsDNA. SNAP output
8dr7 replication-DNA cryo-EM (2.7 Å) Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK (2022) "Multistep loading of a DNA sliding clamp onto DNA by replication factor C." Elife, 11. doi: 10.7554/eLife.78253. Open state of rfc:pcna bound to a nicked dsDNA. SNAP output
8dtp replication-DNA-RNA cryo-EM (2.7 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. Close state of t4 bacteriophage gp41 hexamer bound with single strand DNA. SNAP output
8du4 DNA binding protein cryo-EM (3.55 Å) Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C (2022) "Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome." Proc.Natl.Acad.Sci.USA, 119, e2205691119. doi: 10.1073/pnas.2205691119. Complex between rbbp5-wdr5 and an h2b-ubiquitinated nucleosome. SNAP output
8due replication-DNA-RNA cryo-EM (2.9 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. Open state of t4 bacteriophage gp41 hexamer bound with single strand DNA. SNAP output
8dvf replication-DNA-RNA cryo-EM (3.3 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. T4 bacteriophage primosome with single strand DNA, state 1. SNAP output
8dvi replication-DNA-RNA cryo-EM (3.2 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. T4 bacteriophage primosome with single strand DNA, state 2. SNAP output
8dvp hydrolase-DNA X-ray (1.54 Å) Demir M, Russelburg LP, Lin WJ, Trasvina-Arenas CH, Huang B, Yuen PK, Horvath MP, David SS (2023) "Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism." Nucleic Acids Res., 51, 1034-1049. doi: 10.1093/nar/gkac1246. Glycosylase muty variant n146s in complex with DNA containing d(8-oxo-g) paired with substrate purine. SNAP output
8dvy hydrolase-DNA X-ray (2.36 Å) Demir M, Russelburg LP, Lin WJ, Trasvina-Arenas CH, Huang B, Yuen PK, Horvath MP, David SS (2023) "Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism." Nucleic Acids Res., 51, 1034-1049. doi: 10.1093/nar/gkac1246. DNA glycosylase muty variant n146s in complex with DNA containing d(8-oxo-g) paired with an enzyme-generated abasic site product (ap) and crystalized with calcium acetate. SNAP output
8dw0 hydrolase-DNA X-ray (1.68 Å) Demir M, Russelburg LP, Lin WJ, Trasvina-Arenas CH, Huang B, Yuen PK, Horvath MP, David SS (2023) "Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism." Nucleic Acids Res., 51, 1034-1049. doi: 10.1093/nar/gkac1246. Glycosylase muty variant n146s in complex with DNA containing d(8-oxo-g) paired with an enzyme-generated abasic site (ap) product and crystallized with sodium acetate. SNAP output
8dw1 DNA binding protein-DNA X-ray (1.849 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2023) "Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites." Bioorg.Med.Chem., 77, 117113. doi: 10.1016/j.bmc.2022.117113. Crystal structure of a host-guest complex with 5'-cttagttataactaag-3'. SNAP output
8dw4 hydrolase-DNA X-ray (2.49 Å) Demir M, Russelburg LP, Lin WJ, Trasvina-Arenas CH, Huang B, Yuen PK, Horvath MP, David SS (2023) "Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism." Nucleic Acids Res., 51, 1034-1049. doi: 10.1093/nar/gkac1246. Glycosylase muty variant n146s in complex with DNA containing d(8-oxo-g) paired with an abasic site product (ap) generated by the enzyme in crystals by removal of calcium. SNAP output
8dw6 replication-DNA-RNA cryo-EM (3.5 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. T4 bacteriophage primosome with single-strand DNA, state 3. SNAP output
8dw7 hydrolase-DNA X-ray (1.96 Å) Demir M, Russelburg LP, Lin WJ, Trasvina-Arenas CH, Huang B, Yuen PK, Horvath MP, David SS (2023) "Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism." Nucleic Acids Res., 51, 1034-1049. doi: 10.1093/nar/gkac1246. DNA glycosylase muty variant n146s in complex with DNA containing the transition state analog 1n paired with d(8-oxo-g). SNAP output
8dw8 DNA binding protein-DNA X-ray (2.58 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2023) "Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites." Bioorg.Med.Chem., 77, 117113. doi: 10.1016/j.bmc.2022.117113. Host-guest structure of blma2 partially bound to 5'-attagttataactaat-3'. SNAP output
8dwd hydrolase-DNA X-ray (1.68 Å) Russelburg LP, Demir M, Cedeno K, David SS, Horvath MP "Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY." Adenine glycosylase muty variant e43s in complex with DNA containing d(8-oxo-g) paired with an ap site generated by the enzyme acting on purine. SNAP output
8dwe hydrolase-DNA X-ray (2.2 Å) Russelburg LP, Demir M, Cedeno K, David SS, Horvath MP "Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY." Adenine glycosylase muty variant e43q in complex with DNA containing d(8-oxo-g) paired with substrate purine. SNAP output
8dwf hydrolase-DNA X-ray (2.6 Å) Russelburg LP, Demir M, Cedeno K, David SS, Horvath MP "Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY." Glycosylase muty variant e43s in complex with DNA containing d(8-oxo-g) paired with substrate adenine. SNAP output
8dwj replication-DNA-RNA cryo-EM (3.9 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. Primase of mutant bacteriophage t4 primosome with single strand DNA-RNA primer hybrid in primer exiting state. SNAP output
8dwm DNA binding protein-DNA X-ray (2.99 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2023) "Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites." Bioorg.Med.Chem., 77, 117113. doi: 10.1016/j.bmc.2022.117113. Host-guest complex of bleomycin a2 fully bound to cttagttataactaag. SNAP output
8dy7 transcription-transferase-DNA cryo-EM (3.18 Å) Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA (2023) "Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB." Proc.Natl.Acad.Sci.USA, 120, e2220785120. doi: 10.1073/pnas.2220785120. Streptomyces venezuelae rnap transcription open promoter complex with whia and whib transcription factors. SNAP output
8dy9 transcription-transferase-DNA cryo-EM (3.12 Å) Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA (2023) "Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB." Proc.Natl.Acad.Sci.USA, 120, e2220785120. doi: 10.1073/pnas.2220785120. Streptomyces venezuelae rnap unconstrained open promoter complex with whia and whib transcription factors. SNAP output
8dzj RNA binding protein-RNA-DNA cryo-EM (2.9 Å) Wu T, Liu C, Zou S, Lyu R, Yang B, Yan H, Zhao M, Tang W (2023) "An engineered hypercompact CRISPR-Cas12f system with boosted gene-editing activity." Nat.Chem.Biol., 19, 1384-1393. doi: 10.1038/s41589-023-01380-9. cryo-EM structure of acidibacillus sulfuroxidans cas12f in complex with sgrna and target DNA. SNAP output
8e14 viral protein-DNA cryo-EM (3.36 Å) Bera S, Shi K, Aihara H, Grandgenett DP, Pandey KK (2023) "Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration." J.Biol.Chem., 299, 104730. doi: 10.1016/j.jbc.2023.104730. cryo-EM structure of rous sarcoma virus strand transfer complex. SNAP output
8e23 DNA binding protein-DNA X-ray (2.59 Å) Bubenik M, Mader P, Mochirian P, Vallee F, Clark J, Truchon JF, Perryman AL, Pau V, Kurinov I, Zahn KE, Leclaire ME, Papp R, Mathieu MC, Hamel M, Duffy NM, Godbout C, Casas-Selves M, Falgueyret JP, Baruah PS, Nicolas O, Stocco R, Poirier H, Martino G, Fortin AB, Roulston A, Chefson A, Dorich S, St-Onge M, Patel P, Pellerin C, Ciblat S, Pinter T, Barabe F, El Bakkouri M, Parikh P, Gervais C, Sfeir A, Mamane Y, Morris SJ, Black WC, Sicheri F, Gallant M (2022) "Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta." J.Med.Chem., 65, 13198-13215. doi: 10.1021/acs.jmedchem.2c00998. Human DNA polymerase theta in complex with allosteric inhibitor. SNAP output
8e24 DNA binding protein-DNA X-ray (2.34 Å) Bubenik M, Mader P, Mochirian P, Vallee F, Clark J, Truchon JF, Perryman AL, Pau V, Kurinov I, Zahn KE, Leclaire ME, Papp R, Mathieu MC, Hamel M, Duffy NM, Godbout C, Casas-Selves M, Falgueyret JP, Baruah PS, Nicolas O, Stocco R, Poirier H, Martino G, Fortin AB, Roulston A, Chefson A, Dorich S, St-Onge M, Patel P, Pellerin C, Ciblat S, Pinter T, Barabe F, El Bakkouri M, Parikh P, Gervais C, Sfeir A, Mamane Y, Morris SJ, Black WC, Sicheri F, Gallant M (2022) "Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta." J.Med.Chem., 65, 13198-13215. doi: 10.1021/acs.jmedchem.2c00998. Human DNA polymerase theta in complex with allosteric inhibitor. SNAP output
8e2l replication-DNA cryo-EM (3.51 Å) Li Z, Kaur P, Lo CY, Chopra N, Smith J, Wang H, Gao Y (2022) "Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase." Nucleic Acids Res., 50, 11965-11978. doi: 10.1093/nar/gkac1089. Structure of lates calcarifer twinkle helicase with atp and DNA. SNAP output
8e2p DNA binding protein-DNA X-ray (2.72 Å) Lam DK, Feliciano PR, Arif A, Bohnuud T, Fernandez TP, Gehrke JM, Grayson P, Lee KD, Ortega MA, Sawyer C, Schwaegerle ND, Peraro L, Young L, Lee SJ, Ciaramella G, Gaudelli NM (2023) "Improved cytosine base editors generated from TadA variants." Nat.Biotechnol., 41, 686-697. doi: 10.1038/s41587-022-01611-9. Crystal structure of tada*8.20 in a complex with ssDNA. SNAP output
8e2q DNA binding protein-DNA X-ray (2.34 Å) Lam DK, Feliciano PR, Arif A, Bohnuud T, Fernandez TP, Gehrke JM, Grayson P, Lee KD, Ortega MA, Sawyer C, Schwaegerle ND, Peraro L, Young L, Lee SJ, Ciaramella G, Gaudelli NM (2023) "Improved cytosine base editors generated from TadA variants." Nat.Biotechnol., 41, 686-697. doi: 10.1038/s41587-022-01611-9. Crystal structure of tadac-1.17 in a complex with ssDNA. SNAP output
8e3d DNA binding protein-DNA X-ray (2.62 Å) Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X (2023) "Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia." J.Biol.Chem., 299, 102885. doi: 10.1016/j.jbc.2023.102885. Zbtb7a zinc finger domain bound to DNA duplex containing cast sequence (#11). SNAP output
8e3e DNA binding protein-DNA X-ray (2.99 Å) Ren R, Horton JR, Chen Q, Yang J, Liu B, Huang Y, Blumenthal RM, Zhang X, Cheng X (2023) "Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia." J.Biol.Chem., 299, 102885. doi: 10.1016/j.jbc.2023.102885. Zbtb7a zinc finger domain bound to DNA duplex containing cast sequence (#10). SNAP output
8e3f transcription, transferase-DNA-RNA cryo-EM (6.5 Å) Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023) "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1. Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, mg-adp-bef3, and nusg; tec part. SNAP output
8e3k transcription-DNA X-ray (1.28 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg). SNAP output
8e3r transcription-DNA X-ray (1.45 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaaaggaagtggg). SNAP output
8e4h transcription-DNA X-ray (1.39 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagaggaagtggg). SNAP output
8e5d toxin-DNA X-ray (2.39 Å) Yin L, Shi K, Aihara H (2023) "Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA." Nat.Struct.Mol.Biol., 30, 1153-1159. doi: 10.1038/s41594-023-01034-3. Crystal structure of double-stranded DNA deaminase toxin ddda in complex with DNA with the target cytosine parked in the major groove. SNAP output
8e5e toxin-DNA X-ray (2.62 Å) Yin L, Shi K, Aihara H (2023) "Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA." Nat.Struct.Mol.Biol., 30, 1153-1159. doi: 10.1038/s41594-023-01034-3. Crystal structure of double-stranded DNA deaminase toxin ddda in complex with DNA with the target cytosine flipped into the active site. SNAP output
8e5k transcription, transferase-DNA-RNA cryo-EM (4.2 Å) Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023) "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1. Escherichia coli rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, mg-adp-bef3, and nusg; tec part. SNAP output
8e5o transcription, transferase-DNA-RNA cryo-EM (4.4 Å) Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023) "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1. Escherichia coli rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, mg-adp-bef3, and nusg; tec part. SNAP output
8e5y transcription-DNA X-ray (1.32 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain bound to d(aataagcggaagtggg) acetate free at ph 5.4. SNAP output
8e66 DNA binding protein-DNA X-ray (2.35 Å) Scheu K, Chan AC, Murphy ME, McIntosh LP "The functional role of histidine within the ETV6 ETS domain." Etv6 h396y variant bound to DNA containing the sequence ggaa. SNAP output
8e67 DNA binding protein-DNA X-ray (2.3 Å) Scheu K, Chan AC, Murphy ME, McIntosh LP "The functional role of histidine within the ETV6 ETS domain." Etv6 h396y variant bound to DNA containing the sequence ggat. SNAP output
8e6x transcription, transferase-DNA-RNA cryo-EM (4.27 Å) Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023) "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1. Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, lambda-tr1 rut RNA, mg-adp-bef3, and nusg; tec part. SNAP output
8e6z transcription, transferase-DNA-RNA cryo-EM (4.1 Å) Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023) "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1. Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, dc75 rut mimic RNA, mg-adp-bef3, and nusg; tec part. SNAP output
8e70 transcription-RNA cryo-EM (4.1 Å) Molodtsov V, Wang C, Firlar E, Kaelber JT, Ebright RH (2023) "Structural basis of Rho-dependent transcription termination." Nature, 614, 367-374. doi: 10.1038/s41586-022-05658-1. Escherichia coli rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, dc75 rut mimic RNA, mg-adp-bef3, and nusg; rho hexamer part. SNAP output
8e74 transcription-DNA-RNA cryo-EM (2.94 Å) Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R (2023) "Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis." Mol.Cell, 83, 1474-1488.e8. doi: 10.1016/j.molcel.2023.04.007. Mycobacterium tuberculosis rnap paused elongation complex with nusg transcription factor. SNAP output
8e79 transcription-DNA-RNA cryo-EM (3.71 Å) Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R (2023) "Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis." Mol.Cell, 83, 1474-1488.e8. doi: 10.1016/j.molcel.2023.04.007. Mycobacterium tuberculosis rnap paused elongation complex with escherichia coli nusg transcription factor. SNAP output
8e82 transcription-DNA-RNA cryo-EM (3.03 Å) Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R (2023) "Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis." Mol.Cell, 83, 1474-1488.e8. doi: 10.1016/j.molcel.2023.04.007. Mycobacterium tuberculosis rnap elongation complex with nusg transcription factor. SNAP output
8e85 transferase-DNA X-ray (1.72 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-rg-ended primer-dgmpnpp ternary mismatch complex with mn2+. SNAP output
8e86 transferase-DNA X-ray (1.78 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-rc-ended primer-dgmpnpp ternary mismatch complex with mn2+. SNAP output
8e87 transferase-DNA X-ray (2.19 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ra-ended primer-dgmpnpp ternary mismatch complex with mg2+. SNAP output
8e88 transferase-DNA X-ray (2.4 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer-dgmpnpp ternary mismatch complex with mg2+. SNAP output
8e89 transferase-DNA X-ray (2.2 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer-binary complex. SNAP output
8e8a transferase-DNA X-ray (1.8 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-dt-ended primer binary complex. SNAP output
8e8b transferase-DNA X-ray (2.2 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:ground state at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
8e8c transferase-DNA X-ray (2.25 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:reaction with 10 mm mn2+ for 30s. SNAP output
8e8d transferase-DNA X-ray (2.09 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:reaction with 10 mm mn2+ for 60s. SNAP output
8e8e transferase-DNA X-ray (2.05 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:reaction with 10 mm mn2+ for 90s. SNAP output
8e8f transferase-DNA X-ray (2.14 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:reaction with 10 mm mn2+ for 120s. SNAP output
8e8g transferase-DNA X-ray (2.13 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:reaction with 10 mm mn2+ for 180s. SNAP output
8e8h transferase-DNA X-ray (2.13 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-ru-ended primer ternary mismatch complex:reaction with 10 mm mn2+ for 300s. SNAP output
8e8j transferase-DNA X-ray (2.4 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-rg-ended primer-dgmpnpp ternary mismatch complex with mg2+. SNAP output
8e8k transferase-DNA X-ray (2.4 Å) Chang C, Lee Luo C, Eleraky S, Lin A, Zhou G, Gao Y (2023) "Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity." J.Biol.Chem., 299, 102938. doi: 10.1016/j.jbc.2023.102938. Human DNA polymerase eta-DNA-rc-ended primer-dgmpnpp ternary mismatch complex with mg2+. SNAP output
8e8m transcription-DNA-RNA cryo-EM (3.13 Å) Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R (2023) "Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis." Mol.Cell, 83, 1474-1488.e8. doi: 10.1016/j.molcel.2023.04.007. Mycobacterium tuberculosis rnap paused elongation complex. SNAP output
8e95 transcription, transferase-DNA-RNA cryo-EM (2.9 Å) Delbeau M, Omollo EO, Froom R, Koh S, Mooney RA, Lilic M, Brewer JJ, Rock J, Darst SA, Campbell EA, Landick R (2023) "Structural and functional basis of the universal transcription factor NusG pro-pausing activity in Mycobacterium tuberculosis." Mol.Cell, 83, 1474-1488.e8. doi: 10.1016/j.molcel.2023.04.007. Mycobacterium tuberculosis rnap elongation complex. SNAP output
8e9a transferase-DNA X-ray (2.69 Å) Cramer ER, Starcovic SA, Avey RM, Kaya AI, Robart AR (2023) "Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation." Commun Chem, 6, 119. doi: 10.1038/s42004-023-00924-3. Crystal structure of asfvpolx in complex with 10-23 dnazyme and mg. SNAP output
8ea3 DNA binding protein-DNA-RNA cryo-EM (3.7 Å) Park JU, Tsai AW, Rizo AN, Truong VH, Wellner TX, Schargel RD, Kellogg EH (2023) "Structures of the holo CRISPR RNA-guided transposon integration complex." Nature, 613, 775-782. doi: 10.1038/s41586-022-05573-5. V-k cast transpososome from scytonema hofmanni, major configuration. SNAP output
8ea4 DNA binding protein-RNA-DNA cryo-EM (3.0 Å) Park JU, Tsai AW, Rizo AN, Truong VH, Wellner TX, Schargel RD, Kellogg EH (2023) "Structures of the holo CRISPR RNA-guided transposon integration complex." Nature, 613, 775-782. doi: 10.1038/s41586-022-05573-5. V-k cast transpososome from scytonema hofmanni, minor configuration. SNAP output
8eae transferase-DNA X-ray (2.56 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound 5-pppg(2,5)pi. SNAP output
8eb5 DNA binding protein-DNA X-ray (2.5 Å) Lannes L, Furman CM, Hickman AB, Dyda F (2023) "Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding." Nat Commun, 14, 4470. doi: 10.1038/s41467-023-40210-3. Tandem of hermes transposase bed domain in complex with the quasi palindrome of its transposon left-end. SNAP output
8ebh transcription-DNA X-ray (1.33 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaatgggg). SNAP output
8ebs DNA binding protein-DNA cryo-EM (4.0 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Initial DNA-lesion (cy5) binding by xpc and tfiih. SNAP output
8ebt DNA binding protein-DNA cryo-EM (3.9 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Xpa repositioning core7 of tfiih relative to xpc-DNA lesion (cy5). SNAP output
8ebu DNA binding protein-DNA cryo-EM (3.3 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Xpc release from core7-xpa-DNA (cy5). SNAP output
8ebv DNA binding protein-DNA cryo-EM (7.1 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Initial DNA-lesion (ap) binding by xpc and tfiih complex 1. SNAP output
8ebw DNA binding protein-DNA cryo-EM (5.6 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Initial DNA-lesion (ap) binding by xpc and tfiih complex2. SNAP output
8ebx DNA binding protein-DNA cryo-EM (3.6 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Xpa repositioning core7 of tfiih relative to xpc-DNA lesion (ap). SNAP output
8eby DNA binding protein-DNA cryo-EM (3.6 Å) Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W (2023) "Lesion recognition by XPC, TFIIH and XPA in DNA excision repair." Nature, 617, 170-175. doi: 10.1038/s41586-023-05959-z. Xpc release from core7-xpa-DNA (ap). SNAP output
8ecc transferase-DNA X-ray (2.44 Å) Wu S, Sohn J "Structure of Ternary Complex of cGAS with dsDNA and Bound 5-pppI(2,5)pA." Structure of ternary complex of cgas with dsDNA and bound 5-pppi(2,5)pa. SNAP output
8edg recombination-DNA cryo-EM (4.64 Å) Lannes L, Furman CM, Hickman AB, Dyda F (2023) "Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding." Nat Commun, 14, 4470. doi: 10.1038/s41467-023-40210-3. cryo-EM structure of the hermes transposase bound to two left-ends of its DNA transposon. SNAP output
8ee9 transcription-DNA X-ray (1.22 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaaaggaatgggg). SNAP output
8ef9 DNA binding protein-DNA cryo-EM (2.4 Å) Li C, Zhu H, Jin S, Maksoud LM, Jain N, Sun J, Gao Y (2023) "Structural basis of DNA polymerase theta mediated DNA end joining." Nucleic Acids Res., 51, 463-474. doi: 10.1093/nar/gkac1201. Structure of lates calcarifer DNA polymerase theta polymerase domain with long duplex DNA, complex ia. SNAP output
8efc DNA binding protein cryo-EM (2.8 Å) Li C, Zhu H, Jin S, Maksoud LM, Jain N, Sun J, Gao Y (2023) "Structural basis of DNA polymerase theta mediated DNA end joining." Nucleic Acids Res., 51, 463-474. doi: 10.1093/nar/gkac1201. Structure of lates calcarifer DNA polymerase theta polymerase domain with long duplex DNA, complex ia. SNAP output
8efk DNA binding protein-DNA cryo-EM (3.0 Å) Li C, Zhu H, Jin S, Maksoud LM, Jain N, Sun J, Gao Y (2023) "Structural basis of DNA polymerase theta mediated DNA end joining." Nucleic Acids Res., 51, 463-474. doi: 10.1093/nar/gkac1201. Structure of lates calcarifer DNA polymerase theta polymerase domain with hairpin DNA. SNAP output
8efv structural protein cryo-EM (2.97 Å) Shen ZF, Rish AD, Fu TM "Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor." Structure of single homo-hexameric holliday junction atp-dependent DNA helicase ruvb motor. SNAP output
8efy structural protein cryo-EM (3.16 Å) Rish AD, Shen ZF, Fu TM "Structure of double homo-hexameric AAA+ ATPase RuvB motor binding with DNA substrate." Structure of double homo-hexameric aaa+ atpase ruvb motors. SNAP output
8eg7 transcription, transferase-DNA-RNA cryo-EM (3.2 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of pre-consensus elemental paused elongation complex. SNAP output
8eg8 transcription, transferase-DNA-RNA cryo-EM (3.3 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of consensus elemental paused elongation complex with a folded tl. SNAP output
8egb transcription, transferase-DNA-RNA cryo-EM (3.8 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of consensus elemental paused elongation complex with an unfolded tl. SNAP output
8eh8 transcription, transferase-DNA-RNA cryo-EM (3.4 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of his-elemental paused elongation complex with a folded tl and a rotated rh-fl (1). SNAP output
8eh9 transcription, transferase-DNA-RNA cryo-EM (3.9 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of his-elemental paused elongation complex with a folded tl and a rotated rh-fl (2). SNAP output
8eha transcription, transferase-DNA-RNA cryo-EM (3.7 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of his-elemental paused elongation complex with a folded tl and a rotated rh-fl (out). SNAP output
8ehf transcription, transferase-DNA-RNA cryo-EM (3.3 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of his-elemental paused elongation complex with an unfolded tl (1). SNAP output
8ehi transcription, transferase-DNA-RNA cryo-EM (5.5 Å) Kang JY, Mishanina TV, Bao Y, Chen J, Llewellyn E, Liu J, Darst SA, Landick R (2023) "An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options." Proc.Natl.Acad.Sci.USA, 120, e2215945120. doi: 10.1073/pnas.2215945120. cryo-EM structure of his-elemental paused elongation complex with an unfolded tl (2). SNAP output
8ehq transcription cryo-EM (3.0 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. Mycobacterium tuberculosis paused transcription complex with bacillus subtilis nusg. SNAP output
8ej3 transcription cryo-EM (3.13 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. M. tuberculosis rnap pause escaped complex with bacillus subtilis nusg and gmpcpp. SNAP output
8ej6 transcription-DNA X-ray (1.39 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagaggaatgggg). SNAP output
8ej8 transcription-DNA X-ray (1.45 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) q226e mutant bound to d(aataaaaggaagtggg). SNAP output
8ejo DNA binding protein-DNA X-ray (2.67 Å) Bosnakovski D, Toso EA, Ener ET, Gearhart MD, Yin L, Luttmann FF, Magli A, Shi K, Kim J, Aihara H, Kyba M (2023) "Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein." Iscience, 26, 107823. doi: 10.1016/j.isci.2023.107823. Crystal structure of the homeodomain of platypus sdux in complex with DNA. SNAP output
8ejp DNA binding protein-DNA X-ray (2.174 Å) Bosnakovski D, Toso EA, Ener ET, Gearhart MD, Yin L, Luttmann FF, Magli A, Shi K, Kim J, Aihara H, Kyba M (2023) "Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein." Iscience, 26, 107823. doi: 10.1016/j.isci.2023.107823. Crystal structure of the homeodomain of platypus sdux in complex with DNA containing 5-bromouracil. SNAP output
8ek3 transcription-DNA X-ray (1.38 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) q226e mutant bound to d(aataagcggaatgggg). SNAP output
8ek8 transcription-DNA X-ray (2.63 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaaaggagaaggg). SNAP output
8ekj transcription-DNA X-ray (1.54 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaatggaagtggg). SNAP output
8eku transcription-DNA X-ray (1.52 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaatggaatgggg). SNAP output
8ekv transcription-DNA X-ray (1.62 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggatgtggg). SNAP output
8ekz transcription-DNA X-ray (1.42 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaggagaagtagg). SNAP output
8em9 transcription-DNA X-ray (2.341 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataggagaagtaggg). SNAP output
8emd transcription-DNA X-ray (1.55 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) q226e mutant bound to d(aataagcggaagtggg). SNAP output
8emh antimicrobial protein cryo-EM (3.63 Å) Shen BW, Doyle LA, Werther R, Westburg AA, Bies DP, Walter SI, Luyten YA, Morgan RD, Stoddard BL, Kaiser BK (2023) "Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor." Nucleic Acids Res., 51, 3513-3528. doi: 10.1093/nar/gkad083. Cryoem characterization of a unique aaa+ brxl phage restriction factor. SNAP output
8eml transcription-DNA X-ray (2.21 Å) Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky AE, Schoch E, Gagliani EK, Herr AB, Gebelein B, Kovall RA (2024) "Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface." Nucleic Acids Res., 52, 7987-8002. doi: 10.1093/nar/gkae522. Crystal structure of gsx2 homeodomain in complex with DNA. SNAP output
8eng transcription-DNA X-ray (1.25 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg) with hemi-methylated cpg (forward strand). SNAP output
8eo1 transcription-DNA X-ray (1.28 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg) with hemi-methylated cpg (reverse strand). SNAP output
8eo4 transcription-DNA X-ray (1.24 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg) with di-methylated cpg sites. SNAP output
8eoe transcription cryo-EM (3.2 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. Mycobacterium tuberculosis transcription elongation complex with bacillus subtilis nusg (ec_lg). SNAP output
8eof transcription cryo-EM (3.3 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. Mycobacterium tuberculosis transcription elongation complex with bacillus subtilis nusg (ec_pg). SNAP output
8eos transcription cryo-EM (3.1 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. M. tuberculosis rnap elongation complex with nusg and cmpcpp. SNAP output
8eot transcription cryo-EM (3.3 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. M. tuberculosis rnap elongation complex with nusg. SNAP output
8epx DNA binding protein cryo-EM (3.15 Å) Kennedy MA, Hosford CJ, Azumaya CM, Luyten YA, Chen M, Morgan RD, Stoddard BL (2023) "Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI." Nucleic Acids Res., 51, 4467-4487. doi: 10.1093/nar/gkad228. Type iis restriction endonuclease paqci, DNA bound. SNAP output
8eqg transcription-DNA X-ray (1.39 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaa(du)ggaagtggg). SNAP output
8eqk transcription-DNA X-ray (1.45 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataaccggaagtggg). SNAP output
8eql transcription-DNA X-ray (1.52 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) q226e mutant bound to d(aataaccggaagtggg). SNAP output
8er8 virus-DNA cryo-EM (2.3 Å) Penzes JJ, Pham HT, Chipman P, Smith EW, McKenna R, Tijssen P (2023) "Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus." Nat Commun, 14, 3515. doi: 10.1038/s41467-023-38875-x. Acheta domesticus segmented densovirus, mature virion capsid structure. SNAP output
8ett structural protein-DNA cryo-EM (6.68 Å) Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y (2023) "Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility." Science, 381, 319-324. doi: 10.1126/science.adf4197. Class1 of the ino80-hexasome complex. SNAP output
8etv motor protein-DNA cryo-EM (3.16 Å) Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y (2023) "Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility." Science, 381, 319-324. doi: 10.1126/science.adf4197. Class2 of the ino80-hexasome complex. SNAP output
8eu2 structural protein-DNA cryo-EM (2.93 Å) Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y (2023) "Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility." Science, 381, 319-324. doi: 10.1126/science.adf4197. Class3 of the ino80-hexasome complex. SNAP output
8eue DNA binding protein-DNA cryo-EM (3.48 Å) Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y (2023) "Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility." Science, 381, 319-324. doi: 10.1126/science.adf4197. Class1 of the ino80-nucleosome complex. SNAP output
8euj DNA binding protein-DNA cryo-EM (3.36 Å) Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y (2023) "Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility." Science, 381, 319-324. doi: 10.1126/science.adf4197. Class2 of the ino80-nucleosome complex. SNAP output
8eve replication,transferase-DNA X-ray (2.35 Å) Richie-Jannetta R, Pallan P, Kingsley PJ, Kamdar N, Egli M, Marnett LJ (2023) "The peroxidation-derived DNA adduct, 6-oxo-M 1 dG, is a strong block to replication by human DNA polymerase eta." J.Biol.Chem., 299, 105067. doi: 10.1016/j.jbc.2023.105067. Human DNA polymerase eta insertion complex. SNAP output
8evf replication,transferase-DNA X-ray (2.87 Å) Richie-Jannetta R, Pallan P, Kingsley PJ, Kamdar N, Egli M, Marnett LJ (2023) "The peroxidation-derived DNA adduct, 6-oxo-M 1 dG, is a strong block to replication by human DNA polymerase eta." J.Biol.Chem., 299, 105067. doi: 10.1016/j.jbc.2023.105067. Human DNA polymerase eta extension complex with an incoming dctp. SNAP output
8evg transcription-DNA cryo-EM (2.75 Å) Tengfei L, Ruifang G, Yawen B "Structural basis of cooperative targeting of the CX3CR1 nucleosome." 162bp cx3cr1 nucleosome (further classified with better nucleosome end). SNAP output
8evh transcription-DNA cryo-EM (2.85 Å) Lian T, Guan R, Zhou BR, Bai Y (2024) "Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP alpha." Nat.Struct.Mol.Biol., 31, 633-643. doi: 10.1038/s41594-023-01189-z. Cx3cr1 nucleosome and wild type pu.1 complex. SNAP output
8evi transcription-DNA cryo-EM (2.64 Å) Lian T, Guan R, Zhou BR, Bai Y (2024) "Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP alpha." Nat.Struct.Mol.Biol., 31, 633-643. doi: 10.1038/s41594-023-01189-z. Cx3cr1 nucleosome and pu.1 complex containing disulfide bond mutations. SNAP output
8evj transcription-DNA cryo-EM (4.1 Å) Lian T, Guan R, Zhou BR, Bai Y (2024) "Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP alpha." Nat.Struct.Mol.Biol., 31, 633-643. doi: 10.1038/s41594-023-01189-z. Cx3cr1 nucleosome bound pu.1 and c-ebpa. SNAP output
8ex9 RNA binding protein cryo-EM (2.96 Å) Sasnauskas G, Tamulaitiene G, Druteika G, Carabias A, Silanskas A, Kazlauskas D, Venclovas C, Montoya G, Karvelis T, Siksnys V (2023) "TnpB structure reveals minimal functional core of Cas12 nuclease family." Nature, 616, 384-389. doi: 10.1038/s41586-023-05826-x. Isdra2 tnpb in complex with rerna and cognate DNA, conformation 2 (ruvc domain unresolved). SNAP output
8exa RNA binding protein cryo-EM (3.14 Å) Sasnauskas G, Tamulaitiene G, Druteika G, Carabias A, Silanskas A, Kazlauskas D, Venclovas C, Montoya G, Karvelis T, Siksnys V (2023) "TnpB structure reveals minimal functional core of Cas12 nuclease family." Nature, 616, 384-389. doi: 10.1038/s41586-023-05826-x. Isdra2 tnpb in complex with rerna and cognate DNA, conformation 1 (ruvc domain resolved). SNAP output
8exx viral protein-DNA cryo-EM (3.3 Å) Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J (2024) "Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance." Cell, 187, 5572-5586.e15. doi: 10.1016/j.cell.2024.07.048. Herpes simplex virus 1 polymerase holoenzyme bound to DNA and foscarnet (pre-translocation state). SNAP output
8exy transcription cryo-EM (3.2 Å) Vishwakarma RK, Qayyum MZ, Babitzke P, Murakami KS (2023) "Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase." Proc.Natl.Acad.Sci.USA, 120, e2218516120. doi: 10.1073/pnas.2218516120. M. tuberculosis rnap paused complex with b. subtilis nusg and gmpcpp. SNAP output
8eza DNA binding protein-DNA cryo-EM (4.39 Å) Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y (2023) "Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ." Sci Adv, 9, eadg2838. doi: 10.1126/sciadv.adg2838. Nhej long-range complex with paxx. SNAP output
8ezb DNA binding protein-DNA cryo-EM (8.9 Å) Chen S, Vogt A, Lee L, Naila T, McKeown R, Tomkinson AE, Lees-Miller SP, He Y (2023) "Cryo-EM visualization of DNA-PKcs structural intermediates in NHEJ." Sci Adv, 9, eadg2838. doi: 10.1126/sciadv.adg2838. Nhej long-range complex with atp. SNAP output
8f1i transcription-DNA cryo-EM (3.0 Å) Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA (2023) "A general mechanism for transcription bubble nucleation in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2220874120. doi: 10.1073/pnas.2220874120. Sign RNA polymerase early-melted intermediate bound to mismatch fragment dhsu36mm1 (-12t). SNAP output
8f1j transcription-DNA cryo-EM (2.6 Å) Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA (2023) "A general mechanism for transcription bubble nucleation in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2220874120. doi: 10.1073/pnas.2220874120. Sign RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsu36mm2 (-12a). SNAP output
8f1k transcription-DNA cryo-EM (2.8 Å) Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA (2023) "A general mechanism for transcription bubble nucleation in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2220874120. doi: 10.1073/pnas.2220874120. Sign RNA polymerase early-melted intermediate bound to full duplex DNA fragment dhsu36 (-12t). SNAP output
8f3c transcription cryo-EM (3.4 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM consensus structure of escherichia coli que-pec (paused elongation complex) RNA polymerase minus preq1 ligand. SNAP output
8f69 DNA binding protein-DNA X-ray (2.2 Å) Wojtaszek JL, Hoff KE, Longley MJ, Kaur P, Andres SN, Wang H, Williams RS, Copeland WC (2023) "Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA." Nucleic Acids Res., 51, 9716-9732. doi: 10.1093/nar/gkad679. Crystal structure of murine polg2 dimer bound to DNA. SNAP output
8f6b DNA binding protein-DNA X-ray (2.75 Å) Wojtaszek JL, Hoff KE, Longley MJ, Kaur P, Andres SN, Wang H, Williams RS, Copeland WC (2023) "Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA." Nucleic Acids Res., 51, 9716-9732. doi: 10.1093/nar/gkad679. Crystal structure of murine polg2 hexamer bound to DNA. SNAP output
8f86 gene regulation cryo-EM (3.1 Å) Wang ZA, Markert JW, Whedon SD, Yapa Abeywardana M, Lee K, Jiang H, Suarez C, Lin H, Farnung L, Cole PA (2023) "Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation." J.Am.Chem.Soc., 145, 6811-6822. doi: 10.1021/jacs.2c13512. Sirt6 bound to an h3k9ac nucleosome. SNAP output
8fay hydrolase-DNA X-ray (1.91 Å) Trasvina-Arenas CH "Human MUTYH adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)." Human mutyh adenine glycosylase bound to DNA containing a transition state analog (1n) paired with d(8-oxo-g). SNAP output
8fcj DNA binding protein cryo-EM (2.83 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of cascade-DNA (p23) complex in type i-b cast system. SNAP output
8fcu DNA binding protein cryo-EM (3.19 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of cascade-DNA-tniq-tnsc complex in type i-b cast system. SNAP output
8fcv DNA binding protein cryo-EM (2.95 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of tnsc-tniq-DNA complex in type i-b cast system. SNAP output
8fcw DNA binding protein cryo-EM (2.87 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of tnsc-DNA complex in type i-b cast system. SNAP output
8fd3 DNA binding protein cryo-EM (3.12 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of cascade-pam complex in type i-b cast system. SNAP output
8ff4 DNA binding protein cryo-EM (3.6 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of cascade-DNA-tniq-tnsc complex (composite) in type i-b cast system. SNAP output
8ff5 DNA binding protein cryo-EM (3.13 Å) Wang S, Gabel C, Siddique R, Klose T, Chang L (2023) "Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector." Cell, 186, 4204-4215.e19. doi: 10.1016/j.cell.2023.07.010. cryo-EM structure of cascade-DNA-fullrloop in type i-b cast system. SNAP output
8ffi immune system cryo-EM (2.7 Å) Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM (2023) "Oligomerization-mediated activation of a short prokaryotic Argonaute." Nature, 621, 154-161. doi: 10.1038/s41586-023-06456-z. Structure of tetramerized mapsparta upon guide RNA-mediated target DNA binding. SNAP output
8ffz transcription-DNA cryo-EM (3.8 Å) Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y (2023) "Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation." Mol.Cell, 83, 2641. doi: 10.1016/j.molcel.2023.06.015. Tfiiia-tfiiic-brf1-tbp complex bound to 5s rrna gene. SNAP output
8fii DNA binding protein X-ray (2.94 Å) Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB (2023) "Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A." Nat Commun, 14, 6382. doi: 10.1038/s41467-023-42174-w. Wild type apobec3a in complex with tt(fdz)-hairpin inhibitor (crystal form 1). SNAP output
8fij DNA binding protein X-ray (2.799 Å) Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB (2023) "Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A." Nat Commun, 14, 6382. doi: 10.1038/s41467-023-42174-w. Wild type apobec3a in complex with tt(fdz)-hairpin inhibitor (crystal form 2). SNAP output
8fik DNA binding protein-DNA X-ray (1.912 Å) Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB (2023) "Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A." Nat Commun, 14, 6382. doi: 10.1038/s41467-023-42174-w. Apobec3a e72a inactive mutant in complex with attc-hairpin DNA substrate. SNAP output
8fil DNA binding protein X-ray (2.01 Å) Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB (2023) "Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A." Nat Commun, 14, 6382. doi: 10.1038/s41467-023-42174-w. Zinc-free apobec3a (inactive e72a mutant) in complex with ttc-hairpin DNA substrate. SNAP output
8fim DNA binding protein X-ray (2.22 Å) Harjes S, Kurup HM, Rieffer AE, Bayarjargal M, Filitcheva J, Su Y, Hale TK, Filichev VV, Harjes E, Harris RS, Jameson GB (2023) "Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A." Nat Commun, 14, 6382. doi: 10.1038/s41467-023-42174-w. Structure of apobec3a (e72a inactive mutant) in complex with ttc-hairpin DNA substrate. SNAP output
8fix transcription cryo-EM (3.9 Å) Wee LM, Tong AB, Florez Ariza AJ, Canari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ (2023) "A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery." Cell, 186, 1244-1262.e34. doi: 10.1016/j.cell.2023.02.008. cryo-EM structure of e. coli RNA polymerase backtracked elongation complex harboring a terminal mismatch. SNAP output
8fiy transcription-DNA-RNA cryo-EM (7.3 Å) Wee LM, Tong AB, Florez Ariza AJ, Canari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ (2023) "A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery." Cell, 186, 1244-1262.e34. doi: 10.1016/j.cell.2023.02.008. cryo-EM structure of e. coli RNA polymerase elongation complex in the transcription-translation complex (rnap in an anti-swiveled conformation). SNAP output
8flj recombination, DNA binding protein, hydrolase-DNA cryo-EM (3.48 Å) Santiago-Frangos A, Henriques WS, Wiegand T, Gauvin CC, Buyukyoruk M, Graham AB, Wilkinson RA, Triem L, Neselu K, Eng ET, Lander GC, Wiedenheft B (2023) "Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays." Nat.Struct.Mol.Biol., 30, 1675-1685. doi: 10.1038/s41594-023-01097-2. Cas1-cas2-3 integrase and ihf bound to crispr leader, repeat and foreign DNA. SNAP output
8fn3 transferase-DNA X-ray (2.17 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating dITP across dC." Crystal structure of human DNA polymerase eta incorporating ditp across dc. SNAP output
8fn7 viral protein-DNA-inhibitor cryo-EM (2.8 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of wt hiv-1 intasome bound to dolutegravir. SNAP output
8fnd viral protein-DNA-inhibitor cryo-EM (3.0 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k hiv-1 intasome with dolutegravir bound. SNAP output
8fng viral protein-DNA-inhibitor cryo-EM (2.2 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k hiv-1 intasome with dolutegravir bound. SNAP output
8fnh viral protein-DNA-inhibitor cryo-EM (2.5 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of q148k hiv-1 intasome with dolutegravir bound. SNAP output
8fnj viral protein-DNA-inhibitor cryo-EM (2.4 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k-g140a hiv-1 intasome with dolutegravir bound. SNAP output
8fnl viral protein-DNA-inhibitor cryo-EM (2.8 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k-q148k hiv-1 intasome with dolutegravir bound. SNAP output
8fnm viral protein-DNA-inhibitor cryo-EM (2.8 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of g140a-q148k hiv-1 intasome with dolutegravir bound. SNAP output
8fnn viral protein-DNA-inhibitor cryo-EM (2.7 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k-g140a-q148k hiv-1 intasome with dolutegravir bound. SNAP output
8fno viral protein-DNA-inhibitor cryo-EM (2.5 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k-g140a-q148r hiv-1 intasome with dolutegravir bound. SNAP output
8fnp viral protein-DNA-inhibitor cryo-EM (2.2 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k-g140s-q148h hiv-1 intasome with dolutegravir bound. SNAP output
8fnq viral protein-DNA-inhibitor cryo-EM (2.8 Å) Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke Jr TR, Levy RM, Hughes SH, Craigie R, Lyumkis D (2023) "Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants." Sci Adv, 9, eadg5953. doi: 10.1126/sciadv.adg5953. Structure of e138k-g140a-q148k hiv-1 intasome with 4d bound. SNAP output
8fog transferase-DNA X-ray (2.29 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating dITP across dT." Crystal structure of human DNA polymerase eta incorporating ditp across dt. SNAP output
8foh DNA binding protein cryo-EM (4.6 Å) Yuan Z, Georgescu R, Li H, O'Donnell ME (2023) "Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase." Nat Commun, 14, 3697. doi: 10.1038/s41467-023-39441-1. cryo-EM structure of s. cerevisiae DNA polymerase alpha-primase complex in the RNA synthesis state. SNAP output
8foj DNA binding protein cryo-EM (4.8 Å) Yuan Z, Georgescu R, Li H, O'Donnell ME (2023) "Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase." Nat Commun, 14, 3697. doi: 10.1038/s41467-023-39441-1. cryo-EM structure of s. cerevisiae DNA polymerase alpha-primase complex in the post RNA handoff state. SNAP output
8fok DNA binding protein cryo-EM (3.56 Å) Yuan Z, Georgescu R, Li H, O'Donnell ME (2023) "Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase." Nat Commun, 14, 3697. doi: 10.1038/s41467-023-39441-1. cryo-EM structure of s. cerevisiae DNA polymerase alpha-primase complex in the DNA elongation state. SNAP output
8fs1 transferase-DNA-inhibitor X-ray (2.74 Å) Zhou J, Deng Y, Iyamu ID, Horton JR, Yu D, Hajian T, Vedadi M, Rotili D, Mai A, Blumenthal RM, Zhang X, Huang R, Cheng X (2023) "Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile- Specific DNA Adenine Methyltransferase." Acs Chem.Biol., 18, 734-745. doi: 10.1021/acschembio.3c00035. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor 11a (yd905). SNAP output
8fs2 transferase-DNA-inhibitor X-ray (2.59 Å) Zhou J, Deng Y, Iyamu ID, Horton JR, Yu D, Hajian T, Vedadi M, Rotili D, Mai A, Blumenthal RM, Zhang X, Huang R, Cheng X (2023) "Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile- Specific DNA Adenine Methyltransferase." Acs Chem.Biol., 18, 734-745. doi: 10.1021/acschembio.3c00035. Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor 11b (yd907). SNAP output
8fs3 cell cycle-DNA cryo-EM (2.93 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2023) "Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology." Biorxiv. doi: 10.1101/2023.05.03.539266. Structure of s. cerevisiae rad24-rfc loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 1 (open 9-1-1 and shoulder bound DNA only). SNAP output
8fs4 cell cycle-DNA cryo-EM (2.94 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2023) "Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology." Biorxiv. doi: 10.1101/2023.05.03.539266. Structure of s. cerevisiae rad24-rfc loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 2 (open 9-1-1 ring and flexibly bound chamber DNA). SNAP output
8fs5 cell cycle-DNA cryo-EM (2.76 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2023) "Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology." Biorxiv. doi: 10.1101/2023.05.03.539266. Structure of s. cerevisiae rad24-rfc loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 3 (open 9-1-1 and stably bound chamber DNA). SNAP output
8fs6 cell cycle-DNA cryo-EM (2.9 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2023) "Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology." Biorxiv. doi: 10.1101/2023.05.03.539266. Structure of s. cerevisiae rad24-rfc loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 4 (partially closed 9-1-1 and stably bound chamber DNA). SNAP output
8fs7 cell cycle-DNA cryo-EM (2.85 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2023) "Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology." Biorxiv. doi: 10.1101/2023.05.03.539266. Structure of s. cerevisiae rad24-rfc loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 5 (closed 9-1-1 and stably bound chamber DNA). SNAP output
8fs8 cell cycle-DNA cryo-EM (3.04 Å) Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H (2023) "Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology." Biorxiv. doi: 10.1101/2023.05.03.539266. Structure of s. cerevisiae rad24-rfc loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA). SNAP output
8ftd transcription, transferase-DNA cryo-EM (2.76 Å) Vasilyev N, Liu MMJ, Epshtein V, Shamovsky I, Nudler E (2024) "General transcription factor from Escherichia coli with a distinct mechanism of action." Nat.Struct.Mol.Biol., 31, 141-149. doi: 10.1038/s41594-023-01154-w. Structure of escherichia coli ceda in complex with transcription initiation complex. SNAP output
8ftj DNA binding protein-DNA X-ray (2.3 Å) Tomar R, Minko IG, Sharma P, Kellum AH, Lei L, Harp JM, Iverson TM, Lloyd RS, Egli M, Stone MP (2023) "Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase." Nucleic Acids Res., 51, 3754-3769. doi: 10.1093/nar/gkad164. Crystal structure of human neil1 (p2g (242k) c(delta)100) glycosylase bound to DNA duplex containing urea. SNAP output
8ftm transcription-RNA X-ray (3.01 Å) Appel CD, Bermek O, Dandey VP, Wood M, Viverette E, Williams JG, Bouvette J, Riccio AA, Krahn JM, Borgnia MJ, Williams RS (2023) "Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2." Mol.Cell, 83, 3692. doi: 10.1016/j.molcel.2023.09.024. Setx-ssrna-adp-so4 complex. SNAP output
8fvr transcription-DNA-RNA cryo-EM (2.42 Å) Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, Afanaseva E, Mironov A, Serganov A, Nudler E (2023) "Control of transcription elongation and DNA repair by alarmone ppGpp." Nat.Struct.Mol.Biol., 30, 600-607. doi: 10.1038/s41594-023-00948-2. Cryoem structure of e.coli transcription elongation complex. SNAP output
8fvw transcription-DNA-RNA cryo-EM (2.1 Å) Weaver JW, Proshkin S, Duan W, Epshtein V, Gowder M, Bharati BK, Afanaseva E, Mironov A, Serganov A, Nudler E (2023) "Control of transcription elongation and DNA repair by alarmone ppGpp." Nat.Struct.Mol.Biol., 30, 600-607. doi: 10.1038/s41594-023-00948-2. Cryoem structure of e.coli transcription elongation complex bound to ppgpp. SNAP output
8fw7 DNA binding protein-DNA X-ray (2.0 Å) Hocher A, Laursen SP, Radford P, Tyson J, Lambert C, Stevens KM, Montoya A, Shliaha PV, Picardeau M, Sockett RE, Luger K, Warnecke T (2023) "Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus." Nat Microbiol, 8, 2006-2019. doi: 10.1038/s41564-023-01492-x. Histone from bdellovibrio bacteriovorus bound to dsDNA. SNAP output
8fy9 DNA binding protein-DNA cryo-EM (3.1 Å) Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA (2023) "Genome expansion by a CRISPR trimmer-integrase." Nature, 618, 855-861. doi: 10.1038/s41586-023-06178-2. cryo-EM structure of cas1:cas2-deddh:pam-deficient prespacer complex. SNAP output
8fya DNA binding protein-DNA cryo-EM (2.91 Å) Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA (2023) "Genome expansion by a CRISPR trimmer-integrase." Nature, 618, 855-861. doi: 10.1038/s41586-023-06178-2. cryo-EM structure of cas1:cas2-deddh:pam-containing prespacer complex. SNAP output
8fyb DNA binding protein-DNA cryo-EM (3.1 Å) Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA (2023) "Genome expansion by a CRISPR trimmer-integrase." Nature, 618, 855-861. doi: 10.1038/s41586-023-06178-2. cryo-EM structure of cas1:cas2-deddh:half-site integration complex. SNAP output
8fyc DNA binding protein-DNA cryo-EM (4.1 Å) Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA (2023) "Genome expansion by a CRISPR trimmer-integrase." Nature, 618, 855-861. doi: 10.1038/s41586-023-06178-2. cryo-EM structure of cas1:cas2-deddh:half-site integration complex linear crispr repeat conformation. SNAP output
8fyd DNA binding protein-DNA cryo-EM (3.9 Å) Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA (2023) "Genome expansion by a CRISPR trimmer-integrase." Nature, 618, 855-861. doi: 10.1038/s41586-023-06178-2. cryo-EM structure of cas1:cas2-deddh:half-site integration complex bent crispr repeat conformation. SNAP output
8fzt hydrolase cryo-EM (3.03 Å) Korolev S, Gagnon K "SpCas9 with dual-guide RNA and target DNA." Spcas9 with dual-guide RNA and target DNA. SNAP output
8g00 transcription cryo-EM (3.4 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM structure of 3dva component 0 of escherichia coli que-pec (paused elongation complex) RNA polymerase minus preq1 ligand. SNAP output
8g0h DNA binding protein-DNA X-ray (3.8 Å) Velagapudi UK, Rouleau-Turcotte E, Billur R, Shao X, Patil M, Black BE, Pascal JM, Talele TT (2024) "Novel modifications of PARP inhibitor veliparib increase PARP1 binding to DNA breaks." Biochem.J., 481, 437-460. doi: 10.1042/BCJ20230406. Human parp1 deltav687-e688 bound to uktt5 (compound 10) and to a DNA double strand break.. SNAP output
8g0z replication cryo-EM (3.61 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. Mutant bacteriophage t4 gp41 helicase hexamer bound with single strand DNA and atpgammas in the stalled primosome. SNAP output
8g10 transferase-DNA X-ray (2.47 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound itp and gtp. SNAP output
8g1i hydrolase cryo-EM (3.12 Å) Korolev S, Gagnon K "SpCas9 with sgRNA and target DNA." Spcas9 with sgrna and target DNA. SNAP output
8g1j transferase-DNA X-ray (2.3 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound atp and itp. SNAP output
8g1s transcription cryo-EM (3.7 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM structure of 3dva component 1 of escherichia coli que-pec (paused elongation complex) RNA polymerase minus preq1 ligand. SNAP output
8g23 immune system-DNA X-ray (2.71 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound pppipa. SNAP output
8g2p transferase-DNA X-ray (2.521 Å) Wu S, Sohn J "Structure of Ternary Complex of cGAS with dsDNA and Bound ATP and GTP." Structure of ternary complex of cgas with dsDNA and bound atp and gtp. SNAP output
8g2q transferase-DNA X-ray (2.37 Å) Wu S, Sohn J "Structure of Ternary Complex of mouse cGAS with dsDNA and Bound GTP." Structure of ternary complex of mouse cgas with dsDNA and bound gtp. SNAP output
8g2w transcription cryo-EM (3.7 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM structure of 3dva component 2 of escherichia coli que-pec (paused elongation complex) RNA polymerase minus preq1 ligand. SNAP output
8g4w transcription cryo-EM (3.8 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM consensus structure of escherichia coli que-pec (paused elongation complex) RNA polymerase plus preq1 ligand. SNAP output
8g57 transferase-DNA cryo-EM (3.07 Å) Chio US, Rechiche O, Bryll AR, Zhu J, Leith EM, Feldman JL, Peterson CL, Tan S, Armache JP (2023) "Cryo-EM structure of the human Sirtuin 6-nucleosome complex." Sci Adv, 9, eadf7586. doi: 10.1126/sciadv.adf7586. Structure of nucleosome-bound sirtuin 6 deacetylase. SNAP output
8g5i replication-DNA cryo-EM (2.75 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the mismatch sensing complex (i) of human mitochondrial DNA polymerase gamma. SNAP output
8g5j replication-DNA cryo-EM (2.63 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the mismatch uncoupling complex (ii) of human mitochondrial DNA polymerase gamma. SNAP output
8g5k replication-DNA cryo-EM (2.9 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the wedge alignment complex (viii) of human mitochondrial DNA polymerase gamma. SNAP output
8g5l replication-DNA cryo-EM (3.0 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the primer separation complex (ix) of human mitochondrial DNA polymerase gamma. SNAP output
8g5m replication-DNA-RNA cryo-EM (2.58 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the mismatch locking complex (iii) of human mitochondrial DNA polymerase gamma. SNAP output
8g5n replication-DNA-RNA cryo-EM (2.73 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the guide loop engagement complex (vi) of human mitochondrial DNA polymerase gamma. SNAP output
8g5o replication-DNA-RNA cryo-EM (2.61 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the guide loop engagement complex (iv) of human mitochondrial DNA polymerase gamma. SNAP output
8g5p replication-DNA cryo-EM (2.78 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the guide loop engagement complex (v) of human mitochondrial DNA polymerase gamma. SNAP output
8g6g DNA binding protein-DNA cryo-EM (2.93 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2bk120ub+h3k79me2-modified nucleosome ubiquitin position 5. SNAP output
8g6h DNA binding protein-DNA cryo-EM (3.06 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2bk120ub+h3k79me2-modified nucleosome ubiquitin position 6. SNAP output
8g6q DNA binding protein-DNA cryo-EM (3.41 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2ak119ub-modified nucleosome ubiquitin position 1. SNAP output
8g6s DNA binding protein-DNA cryo-EM (3.47 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2ak119ub-modified nucleosome ubiquitin position 2. SNAP output
8g7e transcription cryo-EM (3.9 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM structure of 3dva component 0 of escherichia coli que-pec (paused elongation complex) RNA polymerase plus preq1 ligand. SNAP output
8g86 DNA binding protein-DNA cryo-EM (2.3 Å) Sinha KK, Bilokapic S, Du Y, Malik D, Halic M (2023) "Histone modifications regulate pioneer transcription factor cooperativity." Nature, 619, 378-384. doi: 10.1038/s41586-023-06112-6. Human oct4 bound to nucleosome with human nmatn1 sequence (focused refinement of nucleosome). SNAP output
8g87 DNA binding protein-DNA cryo-EM (8.1 Å) Sinha KK, Bilokapic S, Du Y, Malik D, Halic M (2023) "Histone modifications regulate pioneer transcription factor cooperativity." Nature, 619, 378-384. doi: 10.1038/s41586-023-06112-6. Human oct4 bound to nucleosome with human nmatn1 sequence (focused refinement of oct4 bound region). SNAP output
8g88 DNA binding protein-DNA cryo-EM (2.3 Å) Sinha KK, Bilokapic S, Du Y, Malik D, Halic M (2023) "Histone modifications regulate pioneer transcription factor cooperativity." Nature, 619, 378-384. doi: 10.1038/s41586-023-06112-6. Human oct4 bound to nucleosome with human nmatn1 sequence. SNAP output
8g8b DNA binding protein-DNA cryo-EM (4.3 Å) Sinha KK, Bilokapic S, Du Y, Malik D, Halic M (2023) "Histone modifications regulate pioneer transcription factor cooperativity." Nature, 619, 378-384. doi: 10.1038/s41586-023-06112-6. Nucleosome with human nmatn1 sequence in complex with human oct4. SNAP output
8g8e DNA binding protein-DNA cryo-EM (3.9 Å) Sinha KK, Bilokapic S, Du Y, Malik D, Halic M (2023) "Histone modifications regulate pioneer transcription factor cooperativity." Nature, 619, 378-384. doi: 10.1038/s41586-023-06112-6. Human oct4 bound to nucleosome with human lin28b sequence. SNAP output
8g8g DNA binding protein-DNA cryo-EM (3.2 Å) Sinha KK, Bilokapic S, Du Y, Malik D, Halic M (2023) "Histone modifications regulate pioneer transcription factor cooperativity." Nature, 619, 378-384. doi: 10.1038/s41586-023-06112-6. Interaction of h3 tail in lin28b nucleosome with oct4. SNAP output
8g8h transferase-DNA X-ray (1.64 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating ITP across dC." Crystal structure of human DNA polymerase eta incorporating itp across dc. SNAP output
8g8j transferase-DNA X-ray (1.74 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating ITP across dT." Crystal structure of human DNA polymerase eta incorporating itp across dt. SNAP output
8g8z transcription cryo-EM (4.3 Å) Chauvier A, Porta JC, Deb I, Ellinger E, Meze K, Frank AT, Ohi MD, Walter NG (2023) "Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand." Nat.Struct.Mol.Biol., 30, 902-913. doi: 10.1038/s41594-023-01002-x. cryo-EM structure of 3dva component 1 of escherichia coli que-pec (paused elongation complex) RNA polymerase plus preq1 ligand. SNAP output
8g9l replication, transferase-DNA-RNA cryo-EM (3.3 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. DNA initiation subcomplex of xenopus laevis DNA polymerase alpha-primase. SNAP output
8g9n replication, transferase-DNA-RNA cryo-EM (3.5 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. Partial DNA elongation subcomplex of xenopus laevis DNA polymerase alpha-primase. SNAP output
8g9o replication, transferase-DNA-RNA cryo-EM (4.4 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. Complete DNA elongation subcomplex of xenopus laevis DNA polymerase alpha-primase. SNAP output
8g9u DNA binding protein cryo-EM (3.0 Å) Hu C, Myers MT, Zhou X, Hou Z, Lozen ML, Nam KH, Zhang Y, Ke A (2024) "Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications." Mol.Cell, 84, 463-475.e5. doi: 10.1016/j.molcel.2023.12.034. Exploiting activation and inactivation mechanisms in type i-c crispr-cas3 for genome editing applications. SNAP output
8g9z transferase-RNA X-ray (2.07 Å) Puppala AK, Castillo Suchkou J, French RL, Kiernan KA, Simonovic M (2023) "Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans." Nucleic Acids Res., 51, 4012-4026. doi: 10.1093/nar/gkad182. High-resolution crystal structure of the human selenomethionine-derived sepsecs-trnasec complex. SNAP output
8gam hydrolase-RNA-DNA cryo-EM (3.46 Å) Hu C, Myers MT, Zhou X, Hou Z, Lozen ML, Nam KH, Zhang Y, Ke A (2024) "Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications." Mol.Cell, 84, 463-475.e5. doi: 10.1016/j.molcel.2023.12.034. Exploiting activation and inactivation mechanisms in type i-c crispr-cas3 for genome editing applications. SNAP output
8gan hydrolase-RNA-DNA cryo-EM (3.26 Å) Hu C, Myers MT, Zhou X, Hou Z, Lozen ML, Nam KH, Zhang Y, Ke A (2024) "Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications." Mol.Cell, 84, 463-475.e5. doi: 10.1016/j.molcel.2023.12.034. Exploiting activation and inactivation mechanisms in type i-c crispr-cas3 for genome editing applications. SNAP output
8gao replication cryo-EM (4.1 Å) Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H (2023) "Structural basis of the T4 bacteriophage primosome assembly and primer synthesis." Nat Commun, 14, 4396. doi: 10.1038/s41467-023-40106-2. Bacteriophage t4 stalled primosome with mutant gp41-e227q. SNAP output
8gap RNA binding protein cryo-EM (3.8 Å) Wang Y, He Y, Wang Y, Yang Y, Singh M, Eichhorn CD, Cheng X, Jiang YX, Zhou ZH, Feigon J (2023) "Structure of LARP7 Protein p65-telomerase RNA Complex in Telomerase Revealed by Cryo-EM and NMR." J.Mol.Biol., 435, 168044. doi: 10.1016/j.jmb.2023.168044. Structure of larp7 protein p65-telomerase RNA complex in telomerase. SNAP output
8gbf transferase-DNA X-ray (2.11 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating syn-ITP across dT." Crystal structure of human DNA polymerase eta incorporating syn-itp across dt. SNAP output
8gbj recombination cryo-EM (3.11 Å) Rawal Y, Jia L, Meir A, Zhou S, Kaur H, Ruben EA, Kwon Y, Bernstein KA, Jasin M, Taylor AB, Burma S, Hromas R, Mazin AV, Zhao W, Zhou D, Wasmuth EV, Greene EC, Sung P, Olsen SK (2023) "Structural insights into BCDX2 complex function in homologous recombination." Nature, 619, 640-649. doi: 10.1038/s41586-023-06219-w. cryo-EM structure of a human bcdx2-ssDNA complex. SNAP output
8gcc isomerase cryo-EM (2.94 Å) Rao SPS, Gould MK, Noeske J, Saldivia M, Jumani RS, Ng PS, Rene O, Chen YL, Kaiser M, Ritchie R, Francisco AF, Johnson N, Patra D, Cheung H, Deniston C, Schenk AD, Cortopassi WA, Schmidt RS, Wiedemar N, Thomas B, Palkar R, Ghafar NA, Manoharan V, Luu C, Gable JE, Wan KF, Myburgh E, Mottram JC, Barnes W, Walker J, Wartchow C, Aziz N, Osborne C, Wagner J, Sarko C, Kelly JM, Manjunatha UH, Maeser P, Jiricek J, Lakshminarayana SB, Barrett MP, Diagana TT (2023) "Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections." Science, 380, 1349-1356. doi: 10.1126/science.adh0614. T. cruzi topoisomerase ii alpha bound to dsDNA and the covalent inhibitor ct1. SNAP output
8gd7 DNA binding protein-DNA X-ray (3.24 Å) Fried W, Tyagi M, Minakhin L, Chandramouly G, Tredinnick T, Ramanjulu M, Auerbacher W, Calbert M, Rusanov T, Hoang T, Borisonnik N, Betsch R, Krais JJ, Wang Y, Vekariya UM, Gordon J, Morton G, Kent T, Skorski T, Johnson N, Childers W, Chen XS, Pomerantz RT (2024) "Discovery of a small-molecule inhibitor that traps Pol theta on DNA and synergizes with PARP inhibitors." Nat Commun, 15, 2862. doi: 10.1038/s41467-024-46593-1. Loop deleted DNA polymerase theta polymerase domain in complex with double strand DNA overhang and inhibitor. SNAP output
8gh6 RNA binding protein-RNA-DNA cryo-EM (3.08 Å) Wilkinson ME, Frangieh CJ, Macrae RK, Zhang F (2023) "Structure of the R2 non-LTR retrotransposon initiating target-primed reverse transcription." Science, 380, 301-308. doi: 10.1126/science.adg7883. Bombyx mori r2 retrotransposon initiating target-primed reverse transcription. SNAP output
8gh8 DNA binding protein-DNA cryo-EM (4.3 Å) Rish AD, Fu T "RuvA Holliday junction DNA complex." Ruva holliday junction DNA complex. SNAP output
8gim immune system-DNA X-ray (2.63 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+. SNAP output
8gin immune system-DNA X-ray (2.75 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+ and 0.015mm mn2+. SNAP output
8gio immune system,transferase-DNA X-ray (2.67 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+ and 0.1mm mn2+. SNAP output
8gip immune system-DNA X-ray (2.7 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+ and 0.040mm mn2+. SNAP output
8gir immune system,transferase-DNA X-ray (2.5 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+ and 0.2mm mn2+. SNAP output
8gis immune system,transferase-DNA X-ray (2.46 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+ and 0.5mm mn2+. SNAP output
8git immune system,transferase-DNA X-ray (2.72 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp: with 10mm mg2+ and 1mm mn2+. SNAP output
8gj0 DNA binding protein-DNA cryo-EM (2.9 Å) Xu ZQ, Jergic S, Lo ATY, Pradhan AC, Brown SHJ, Bouwer JC, Ghodke H, Lewis PJ, Tolun G, Oakley AJ, Dixon NE (2024) "Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli." Nat Commun, 15, 8372. doi: 10.1038/s41467-024-52623-9. E. coli clamp loader with open clamp on primed template DNA (form 1). SNAP output
8gj2 DNA binding protein-DNA cryo-EM (2.6 Å) Xu ZQ, Jergic S, Lo ATY, Pradhan AC, Brown SHJ, Bouwer JC, Ghodke H, Lewis PJ, Tolun G, Oakley AJ, Dixon NE (2024) "Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli." Nat Commun, 15, 8372. doi: 10.1038/s41467-024-52623-9. E. coli clamp loader with closed clamp on primed template DNA. SNAP output
8gj3 DNA binding protein-DNA cryo-EM (2.8 Å) Xu ZQ, Jergic S, Lo ATY, Pradhan AC, Brown SHJ, Bouwer JC, Ghodke H, Lewis PJ, Tolun G, Oakley AJ, Dixon NE (2024) "Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli." Nat Commun, 15, 8372. doi: 10.1038/s41467-024-52623-9. E. coli clamp loader on primed template DNA. SNAP output
8gkh RNA binding protein-RNA-DNA cryo-EM (2.7 Å) Saito M, Xu P, Faure G, Maguire S, Kannan S, Altae-Tran H, Vo S, Desimone A, Macrae RK, Zhang F (2023) "Fanzor is a eukaryotic programmable RNA-guided endonuclease." Nature, 620, 660-668. doi: 10.1038/s41586-023-06356-2. Structure of the spizellomyces punctatus fanzor (spufz) in complex with omega RNA and target DNA. SNAP output
8gkr transferase-DNA X-ray (2.784 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA." Crystal structure of human DNA polymerase eta incorporating 5f-dutp across da. SNAP output
8glw DNA binding protein-DNA cryo-EM (3.51 Å) Shen Y, Krishnan SS, Petassi MT, Hancock MA, Peters JE, Guarne A (2024) "Assembly of the Tn7 targeting complex by a regulated stepwise process." Mol.Cell, 84, 2368-2381.e6. doi: 10.1016/j.molcel.2024.05.012. Cryoem structure of the tnsc(1-503)-tnsd(1-318)-DNA complex in a 7:2:1 stoichiometry from e. coli tn7. SNAP output
8glx DNA binding protein-DNA cryo-EM (3.88 Å) Shen Y, Krishnan SS, Petassi MT, Hancock MA, Peters JE, Guarne A (2024) "Assembly of the Tn7 targeting complex by a regulated stepwise process." Mol.Cell, 84, 2368-2381.e6. doi: 10.1016/j.molcel.2024.05.012. Cryoem structure of the tnsc(1-503)-tnsd(1-318)-DNA complex in a 6:2:1 stoichiometry from e. coli tn7. SNAP output
8gme DNA binding protein-DNA X-ray (4.98 Å) He X, Yun MK, White SW "Crystal structure of the gp32-Dda-dT17 complex." Crystal structure of the gp32-dda-dt17 complex. SNAP output
8gml transferase-DNA X-ray (2.567 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA." Crystal structure of human DNA polymerase eta incorporating 5f-dutp across dg. SNAP output
8gmt DNA binding protein-DNA cryo-EM (3.31 Å) Gao B, Liang L, Su L, Wen A, Zhou C, Feng Y (2023) "Structural basis for regulation of SOS response in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2217493120. doi: 10.1073/pnas.2217493120. Structure of umud in complex with reca filament. SNAP output
8gmu DNA binding protein-DNA cryo-EM (2.78 Å) Gao B, Liang L, Su L, Wen A, Zhou C, Feng Y (2023) "Structural basis for regulation of SOS response in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2217493120. doi: 10.1073/pnas.2217493120. Structure of lambda repressor in complex with reca filament. SNAP output
8gn3 DNA binding protein-DNA X-ray (1.8 Å) Wang S, Xu Z, Li M, Lv M, Shen S, Shi Y, Li F (2023) "Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-a-brac - zinc finger protein ZBTB10." J.Biol.Chem., 299, 102918. doi: 10.1016/j.jbc.2023.102918. The crystal structure of zbtb10 zf1-2 in complex with telomeric vairant repeat ttgggg. SNAP output
8gn4 DNA binding protein-DNA X-ray (1.9 Å) Wang S, Xu Z, Li M, Lv M, Shen S, Shi Y, Li F (2023) "Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-a-brac - zinc finger protein ZBTB10." J.Biol.Chem., 299, 102918. doi: 10.1016/j.jbc.2023.102918. The crystal structure of zbtb10 zf1-2 r767q in complex with telomeric DNA ttaggg. SNAP output
8gpn gene regulation cryo-EM (3.2 Å) Lin J, Wu Y, Tian G, Yu D, Yang E, Lam WH, Liu Z, Jing Y, Dang S, Bao X, Wong JWH, Zhai Y, Li XD (2023) "Menin "reads" H3K79me2 mark in a nucleosomal context." Science, 379, 717-723. doi: 10.1126/science.adc9318. Human menin in complex with h3k79me2 nucleosome. SNAP output
8grm nuclear protein cryo-EM (3.05 Å) Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L (2023) "Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination." Chem. doi: 10.1016/j.chempr.2023.01.012. cryo-EM structure of prc1 bound to h2ak119-ubch5b-ub nucleosome. SNAP output
8grq nuclear protein cryo-EM (3.87 Å) Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L (2023) "Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination." Chem. doi: 10.1016/j.chempr.2023.01.012. cryo-EM structure of brca1-bard1 bound to h2ak127-ubch5c-ub nucleosome. SNAP output
8gui gene regulation-DNA cryo-EM (2.81 Å) Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T (2024) "Structure of the human Bre1 complex bound to the nucleosome." Nat Commun, 15, 2580. doi: 10.1038/s41467-024-46910-8. Bre1-nucleosome complex (model i). SNAP output
8guj gene regulation-DNA cryo-EM (2.8 Å) Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T (2024) "Structure of the human Bre1 complex bound to the nucleosome." Nat Commun, 15, 2580. doi: 10.1038/s41467-024-46910-8. Bre1-nucleosome complex (model ii). SNAP output
8guk gene regulation-DNA cryo-EM (2.51 Å) Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T (2024) "Structure of the human Bre1 complex bound to the nucleosome." Nat Commun, 15, 2580. doi: 10.1038/s41467-024-46910-8. Human nucleosome core particle (free form). SNAP output
8gzg transcription-DNA-RNA cryo-EM (3.13 Å) Shen L, Lai G, You L, Shi J, Wu X, Puiu M, Gu Z, Feng Y, Yuzenkova Y, Zhang Y (2023) "An SI3-sigma arch stabilizes cyanobacteria transcription initiation complex." Proc.Natl.Acad.Sci.USA, 120, e2219290120. doi: 10.1073/pnas.2219290120. cryo-EM structure of synechocystis sp. pcc 6803 rpitc. SNAP output
8gzh transcription-DNA-RNA cryo-EM (2.96 Å) Shen L, Lai G, You L, Shi J, Wu X, Puiu M, Gu Z, Feng Y, Yuzenkova Y, Zhang Y (2023) "An SI3-sigma arch stabilizes cyanobacteria transcription initiation complex." Proc.Natl.Acad.Sci.USA, 120, e2219290120. doi: 10.1073/pnas.2219290120. cryo-EM structure of synechocystis sp. pcc 6803 ctp-bound rpitc. SNAP output
8h0l DNA binding protein-DNA X-ray (1.8 Å) Hu W, Yang B, Xiao Q, Wang Y, Shuai Y, Zhao G, Zhang L, Deng Z, He X, Liu G (2023) "Characterization of a promiscuous DNA sulfur binding domain and application in site-directed RNA base editing." Nucleic Acids Res., 51, 10782-10794. doi: 10.1093/nar/gkad743. Sulfur binding domain of hga complexed with phosphorothioated DNA. SNAP output
8h0v transcription cryo-EM (3.8 Å) Hirano R, Ehara H, Kujirai T, Uejima T, Takizawa Y, Sekine SI, Kurumizaka H (2022) "Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1." Nat Commun, 13, 7287. doi: 10.1038/s41467-022-35003-z. RNA polymerase ii transcribing a chromatosome (type i). SNAP output
8h0w transcription cryo-EM (4.6 Å) Hirano R, Ehara H, Kujirai T, Uejima T, Takizawa Y, Sekine SI, Kurumizaka H (2022) "Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1." Nat Commun, 13, 7287. doi: 10.1038/s41467-022-35003-z. RNA polymerase ii transcribing a chromatosome (type ii). SNAP output
8h1j RNA binding protein cryo-EM (3.1 Å) Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O (2023) "Cryo-EM structure of the transposon-associated TnpB enzyme." Nature, 616, 390-397. doi: 10.1038/s41586-023-05933-9. cryo-EM structure of the tnpb-omegarna-target DNA ternary complex. SNAP output
8h1t gene regulation cryo-EM (3.0 Å) Ge W, Yu C, Li J, Yu Z, Li X, Zhang Y, Liu CP, Li Y, Tian C, Zhang X, Li G, Zhu B, Xu RM (2023) "Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase." Nature, 616, 176-182. doi: 10.1038/s41586-023-05841-y. cryo-EM structure of bap1-asxl1 bound to chromatosome. SNAP output
8h3v transcription cryo-EM (4.5 Å) Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ (2024) "DNA looping mediates cooperative transcription activation." Nat.Struct.Mol.Biol., 31, 293-299. doi: 10.1038/s41594-023-01149-7. cryo-EM structure of the full transcription activation complex ntca-ntcb-tac. SNAP output
8h40 transcription cryo-EM (3.6 Å) Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ (2024) "DNA looping mediates cooperative transcription activation." Nat.Struct.Mol.Biol., 31, 293-299. doi: 10.1038/s41594-023-01149-7. cryo-EM structure of the transcription activation complex ntca-tac. SNAP output
8h67 RNA binding protein cryo-EM (3.8 Å) Lu M, Yu C, Zhang Y, Ju W, Ye Z, Hua C, Mao J, Hu C, Yang Z, Xiao Y (2024) "Structure and genome editing of type I-B CRISPR-Cas." Nat Commun, 15, 4126. doi: 10.1038/s41467-024-48598-2. Type i-b cascade bound to a pam-containing dsDNA target at 3.8 angstrom resolution.. SNAP output
8h7a DNA binding protein-DNA X-ray (1.92 Å) Weber LM, Jia Y, Stielow B, Gisselbrecht SS, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forne I, Nist A, Stiewe T, Bulyk ML, Wang Z, Liefke R (2023) "The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain." Nucleic Acids Res., 51, 574-594. doi: 10.1093/nar/gkac1188. Crystal structure of the dimer form kat6a wh domain with its bound double stranded DNA. SNAP output
8h7q RNA binding protein cryo-EM (3.8 Å) Xiao Y, Lu M, Yu C, Zhang Y "Cryo-EM structure of Synechocystis sp. PCC6714 Cascade at 3.8 angstrom resolution." cryo-EM structure of synechocystis sp. pcc6714 cascade at 3.8 angstrom resolution. SNAP output
8h9h DNA binding protein X-ray (2.2 Å) Yang Y, Xiao L, Xue Y, Idris MO, Liu J, Pei D, Shi Y, Liao B, Li F (2023) "ZBTB7A regulates primed-to-naive transition of pluripotent stem cells via recognition of the PNT-associated sequence by zinc fingers 1-2 and recognition of gamma-globin -200 gene element by zinc fingers 1-4." Febs J., 290, 3896-3909. doi: 10.1111/febs.16789. Crystal structure of zbtb7a in complex with gaccc-containing sequence. SNAP output
8hag transferase-DNA cryo-EM (3.2 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the p300 catalytic core bound to the h4k12ack16ac nucleosome, class 1 (3.2 angstrom resolution). SNAP output
8hah transferase-DNA cryo-EM (3.9 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the p300 catalytic core bound to the h4k12ack16ac nucleosome, class 2 (3.9 angstrom resolution). SNAP output
8hai transferase-DNA cryo-EM (4.7 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the p300 catalytic core bound to the h4k12ack16ac nucleosome, class 1 (4.7 angstrom resolution). SNAP output
8haj transferase-DNA cryo-EM (4.8 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the p300 catalytic core bound to the h4k12ack16ac nucleosome, class 2 (4.8 angstrom resolution). SNAP output
8hak transferase-DNA cryo-EM (4.5 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the p300 catalytic core bound to the h4k12ack16ac nucleosome, class 4 (4.5 angstrom resolution). SNAP output
8hal transferase-DNA cryo-EM (4.4 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the cbp catalytic core bound to the h4k12ack16ac nucleosome, class 1. SNAP output
8ham transferase-DNA cryo-EM (4.5 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the cbp catalytic core bound to the h4k12ack16ac nucleosome, class 2. SNAP output
8han transferase-DNA cryo-EM (4.2 Å) Kikuchi M, Morita S, Wakamori M, Sato S, Uchikubo-Kamo T, Suzuki T, Dohmae N, Shirouzu M, Umehara T (2023) "Epigenetic mechanisms to propagate histone acetylation by p300/CBP." Nat Commun, 14, 4103. doi: 10.1038/s41467-023-39735-4. cryo-EM structure of the cbp catalytic core bound to the h4k12ack16ac nucleosome, class 3. SNAP output
8hbm DNA binding protein-DNA X-ray (3.3 Å) Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y (2023) "Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA." Comput Struct Biotechnol J, 21, 3149-3157. doi: 10.1016/j.csbj.2023.05.026. Structural basis of the farnesoid x receptor-retinoid x receptor heterodimer on inverted repeat DNA. SNAP output
8hcl DNA binding protein-DNA X-ray (1.99 Å) Wang ZX, Liu B, Xie H, Liu X, Li X, Shi F, Ouyang S, Zhang YA (2024) "Crystal Structures of DNA-bound Fish IRF10 and IRF11 Reveal the Determinants of IFN Regulation." J Immunol., 213, 743-752. doi: 10.4049/jimmunol.2300414. Zebrafish irf-10 dbd complex with DNA. SNAP output
8hcm DNA binding protein-DNA X-ray (2.59 Å) Wang ZX, Liu B, Xie H, Liu X, Li X, Shi F, Ouyang S, Zhang YA (2024) "Crystal Structures of DNA-bound Fish IRF10 and IRF11 Reveal the Determinants of IFN Regulation." J Immunol., 213, 743-752. doi: 10.4049/jimmunol.2300414. Zebrafish irf-11 dbd complex with DNA. SNAP output
8he5 transcription cryo-EM (6.95 Å) Osumi K, Kujirai T, Ehara H, Ogasawara M, Kinoshita C, Saotome M, Kagawa W, Sekine SI, Takizawa Y, Kurumizaka H (2023) "Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome." J.Mol.Biol., 435, 168130. doi: 10.1016/j.jmb.2023.168130. RNA polymerase ii elongation complex bound with rad26 and elf1, stalled at shl(-3.5) of the nucleosome. SNAP output
8hg1 replication-DNA cryo-EM (2.8 Å) Peng Q, Xie Y, Kuai L, Wang H, Qi J, Gao GF, Shi Y (2023) "Structure of monkeypox virus DNA polymerase holoenzyme." Science, 379, 100-105. doi: 10.1126/science.ade6360. The structure of mpxv polymerase holoenzyme in replicating state. SNAP output
8hhl RNA binding protein cryo-EM (2.87 Å) Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O (2023) "Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme." Nat.Struct.Mol.Biol., 30, 1172-1182. doi: 10.1038/s41594-023-01042-3. cryo-EM structure of the cas12m2-crrna-target DNA full r-loop complex. SNAP output
8hhm RNA binding protein cryo-EM (3.08 Å) Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O (2023) "Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme." Nat.Struct.Mol.Biol., 30, 1172-1182. doi: 10.1038/s41594-023-01042-3. cryo-EM structure of the cas12m2-crrna-target DNA ternary complex intermediate state. SNAP output
8hi1 immune system cryo-EM (3.09 Å) Tang D, Jia T, Luo Y, Mou B, Cheng J, Qi S, Yao S, Su Z, Yu Y, Chen Q (2023) "DnaQ mediates directional spacer acquisition in the CRISPR-Cas system by a time-dependent mechanism." Innovation (N Y), 4, 100495. doi: 10.1016/j.xinn.2023.100495. Streptococcus thermophilus cas1-cas2- prespacer ternary complex. SNAP output
8hig transcription-DNA X-ray (2.329 Å) Lin W, Xu JC, Zhang Y "Co-crystal structure of C-terminal DNA binding domain of Saccharopolyspora erythraea GlnR in complex with its cognate promoter DNA." Co-crystal structure of c-terminal DNA binding domain of saccharopolyspora erythraea glnr in complex with its cognate promoter DNA. SNAP output
8hih transcription-DNA cryo-EM (3.66 Å) Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W (2023) "Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria." Proc.Natl.Acad.Sci.USA, 120, e2300282120. doi: 10.1073/pnas.2300282120. cryo-EM structure of mycobacterium tuberculosis transcription initiation complex with transcription factor glnr. SNAP output
8him transcription cryo-EM (2.8 Å) Xie G, Du X, Hu H, Li S, Cao X, Jacobsen SE, Du J (2023) "Structure and mechanism of the plant RNA polymerase V." Science, 379, 1209-1213. doi: 10.1126/science.adf8231. A cryo-EM structure of b. oleracea RNA polymerase v elongation complex at 2.73 angstrom. SNAP output
8hkc transcription-DNA cryo-EM (2.49 Å) Lu Q, Chen T, Wang J, Wang F, Ye W, Ma L, Wu S (2023) "Structural Insight into the Mechanism of sigma 32-Mediated Transcription Initiation of Bacterial RNA Polymerase." Biomolecules, 13. doi: 10.3390/biom13050738. cryo-EM structure of e. coli rnap sigma32 complex. SNAP output
8hml transferase-DNA X-ray (2.95 Å) Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W (2023) "Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria." Proc.Natl.Acad.Sci.USA, 120, e2300282120. doi: 10.1073/pnas.2300282120. Co-crystal structure of the c terminal DNA binding domain of saccharopolyspora erythraea glnr in complex with its conserved promoter DNA in 2.95 angstrom resolution. SNAP output
8hni DNA binding protein X-ray (2.644 Å) Liu Y, Abula A, Xiao H, Guo H, Li T, Zheng L, Chen B, Nguyen HC, Ji X (2023) "Structural Insight Into hnRNP A2/B1 Homodimerization and DNA Recognition." J.Mol.Biol., 435, 167920. doi: 10.1016/j.jmb.2022.167920. Hnrnp a2-b1 rrms in complex with telomeric DNA. SNAP output
8hnv antimicrobial protein cryo-EM (3.1 Å) Sun W, Cheng Z, Wang J, Yang J, Li X, Wang J, Chen M, Yang X, Sheng G, Lou J, Wang Y (2023) "AcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation." Proc.Natl.Acad.Sci.USA, 120, e2303675120. doi: 10.1073/pnas.2303675120. Cryoem structure of hpacas9-sgrna-dsDNA in the presence of acriic4. SNAP output
8hnw immune system X-ray (3.41 Å) Sun W, Cheng Z, Wang J, Yang J, Li X, Wang J, Chen M, Yang X, Sheng G, Lou J, Wang Y (2023) "AcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation." Proc.Natl.Acad.Sci.USA, 120, e2303675120. doi: 10.1073/pnas.2303675120. Crystal structure of hpacas9-sgrna surveillance complex bound to double-stranded DNA. SNAP output
8hov DNA binding protein-DNA X-ray (2.77 Å) Khan MH "Crystal structure of Hms1p from Saccharomyces cerevisiae." Crystal structure of hms1p from saccharomyces cerevisiae. SNAP output
8hpa viral protein cryo-EM (3.01 Å) Xu Y, Wu Y, Zhang Y, Fan R, Yang Y, Li D, Zhu S, Yang B, Zhang Z, Dong C (2023) "Cryo-EM structures of human monkeypox viral replication complexes with and without DNA duplex." Cell Res., 33, 479-482. doi: 10.1038/s41422-023-00796-1. Monkeypox virus DNA replication holoenzyme f8, a22 and e4 complex in a DNA binding form. SNAP output
8hqy structural protein cryo-EM (3.05 Å) Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L (2024) "Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes." Nat.Struct.Mol.Biol., 31, 300-310. doi: 10.1038/s41594-023-01141-1. cryo-EM structure of ssx1 bound to the h2ak119ub nucleosome at a resolution of 3.05 angstrom. SNAP output
8hr1 structural protein cryo-EM (3.02 Å) Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L (2024) "Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes." Nat.Struct.Mol.Biol., 31, 300-310. doi: 10.1038/s41594-023-01141-1. cryo-EM structure of ssx1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom. SNAP output
8hr5 RNA binding protein-RNA-DNA cryo-EM (3.73 Å) Li F, Ji Q "Structure and engineering of miniature Clostridium novyi CRISPR-Cas12f1 with rare C-rich PAM specificity." cryo-EM structure of the cncas12f1-sgrna-DNA complex. SNAP output
8hsg transcription cryo-EM (3.2 Å) Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI (2023) "Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus." Sci Adv, 9, eade7093. doi: 10.1126/sciadv.ade7093. Thermus thermophilus RNA polymerase elongation complex. SNAP output
8hsr transcription cryo-EM (4.0 Å) Murayama Y, Ehara H, Aoki M, Goto M, Yokoyama T, Sekine SI (2023) "Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus." Sci Adv, 9, eade7093. doi: 10.1126/sciadv.ade7093. Thermus thermophilus rho-engaged rnap elongation complex (composite structure). SNAP output
8ht7 DNA binding protein NMR Geng Y, Liu C, Xu N, Shi X, Suen MC, Zhou B, Yan B, Wu C, Li H, Song Y, Chen X, Wang Z, Cai Q, Zhu G (2024) "The N-terminal region of Cdc6 specifically recognizes human DNA G-quadruplex." Int.J.Biol.Macromol., 260, 129487. doi: 10.1016/j.ijbiomac.2024.129487. The n-terminal region of cdc6 specifically recognizes human DNA g-quadruplex. SNAP output
8htx DNA binding protein X-ray (2.8 Å) Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J (2023) "Structural insights into DNA recognition by the BEN domain of the transcription factor BANP." J.Biol.Chem., 299, 104734. doi: 10.1016/j.jbc.2023.104734. Crystal structure of banp in complex with methylated DNA. SNAP output
8hud RNA binding protein-RNA-DNA cryo-EM (3.43 Å) Tang N, Wu Z, Gao Y, Chen W, Wang Z, Su M, Ji W, Ji Q (2024) "Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System." Acs Synth Biol, 13, 269-281. doi: 10.1021/acssynbio.3c00501. cryo-EM structure of the evcas9-sgrna-target DNA ternary complex. SNAP output
8hvr gene regulation cryo-EM (3.35 Å) Wang Y, Yang X, Yu F, Deng Z, Lin S, Zheng J (2024) "Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces." Plos Biol., 22, e3002528. doi: 10.1371/journal.pbio.3002528. cryo-EM structure of afsr-dependent transcription activation complex with afss promoter. SNAP output
8hwa viral protein cryo-EM (3.7 Å) Li Y, Zhu J, Guo Y, Yan R (2024) "Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus." Nat.Struct.Mol.Biol., 31, 68-81. doi: 10.1038/s41594-023-01142-0. D5 atp-adp-apo-ssDNA is1. SNAP output
8hwb viral protein cryo-EM (3.9 Å) Li Y, Zhu J, Guo Y, Yan R (2024) "Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus." Nat.Struct.Mol.Biol., 31, 68-81. doi: 10.1038/s41594-023-01142-0. D5 atp-adp-apo-ssDNA is2. SNAP output
8hwf viral protein cryo-EM (3.3 Å) Li Y, Zhu J, Guo Y, Yan R (2024) "Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus." Nat.Struct.Mol.Biol., 31, 68-81. doi: 10.1038/s41594-023-01142-0. cryo-EM structure of d5 adp-ssDNA form. SNAP output
8hwg viral protein cryo-EM (3.0 Å) Li Y, Zhu J, Guo Y, Yan R (2024) "Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus." Nat.Struct.Mol.Biol., 31, 68-81. doi: 10.1038/s41594-023-01142-0. D5 atprs-adp-ssDNA form. SNAP output
8hwh viral protein cryo-EM (3.6 Å) Li Y, Zhu J, Guo Y, Yan R (2024) "Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus." Nat.Struct.Mol.Biol., 31, 68-81. doi: 10.1038/s41594-023-01142-0. cryo-EM structure of d5 apo-ssDNA form. SNAP output
8hxy gene regulation cryo-EM (3.1 Å) Li W, Cui H, Lu Z, Wang H (2023) "Structure of histone deacetylase complex Rpd3S bound to nucleosome." Nat.Struct.Mol.Biol., 30, 1893-1901. doi: 10.1038/s41594-023-01121-5. cryo-EM structure of the histone deacetylase complex rpd3s in complex with nucleosome. SNAP output
8hxz gene regulation cryo-EM (3.4 Å) Li W, Cui H, Lu Z, Wang H (2023) "Structure of histone deacetylase complex Rpd3S bound to nucleosome." Nat.Struct.Mol.Biol., 30, 1893-1901. doi: 10.1038/s41594-023-01121-5. cryo-EM structure of eaf3 chd in complex with nucleosome. SNAP output
8hy0 gene regulation cryo-EM (3.1 Å) Li W, Cui H, Lu Z, Wang H (2023) "Structure of histone deacetylase complex Rpd3S bound to nucleosome." Nat.Struct.Mol.Biol., 30, 1893-1901. doi: 10.1038/s41594-023-01121-5. Composite cryo-EM structure of the histone deacetylase complex rpd3s in complex with nucleosome. SNAP output
8hyj transcription cryo-EM (4.3 Å) Zhang HW, Huang K, Gu ZX, Wu XX, Wang JW, Zhang Y (2023) "A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex." Nat Commun, 14, 3118. doi: 10.1038/s41467-023-38619-x. A cryo-EM structure of ktf1-bound polymerase v transcription elongation complex. SNAP output
8i23 transcription-DNA cryo-EM (3.03 Å) Li J, Zhang H, Li D, Liu YJ, Bayer EA, Cui Q, Feng Y, Zhu P (2023) "Structure of the transcription open complex of distinct sigma I factors." Nat Commun, 14, 6455. doi: 10.1038/s41467-023-41796-4. Clostridium thermocellum RNA polymerase transcription open complex with sigi1 and its promoter. SNAP output
8i24 transcription cryo-EM (3.36 Å) Li J, Zhang H, Li D, Liu YJ, Bayer EA, Cui Q, Feng Y, Zhu P (2023) "Structure of the transcription open complex of distinct sigma I factors." Nat Commun, 14, 6455. doi: 10.1038/s41467-023-41796-4. Clostridium thermocellum RNA polymerase transcription open complex with sigi6 and its promoter. SNAP output
8i54 antimicrobial protein cryo-EM (3.95 Å) Jianwei L, Jobichen C, Machida S, Meng S, Read RJ, Hongying C, Jian S, Yuan YA, Sivaraman J (2023) "Structures of apo Cas12a and its complex with crRNA and DNA reveal the dynamics of ternary complex formation and target DNA cleavage." Plos Biol., 21, e3002023. doi: 10.1371/journal.pbio.3002023. Lb2cas12a RNA DNA complex. SNAP output
8i6k DNA binding protein-DNA X-ray (2.4 Å) Li Y, Zhang C, Samad A, Zheng P, Li Y, Chen F, Jin T (2023) "Structural mechanism of dsDNA recognition by the hMNDA HIN domain: New insights into the DNA-binding model of a PYHIN protein." Int.J.Biol.Macromol., 245, 125461. doi: 10.1016/j.ijbiomac.2023.125461. Structure of hmnda hin with dsDNA. SNAP output
8i87 antiviral protein cryo-EM (3.1 Å) Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H (2023) "Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity." Cell Res., 33, 699-711. doi: 10.1038/s41422-023-00839-7. cryo-EM structure of tir-apaz-ago-grna-DNA complex. SNAP output
8ia3 transcription-DNA X-ray (3.5 Å) Huang C, Xia M, Qiao H, Liu Z, Lin Y, Sun H, Yu B, Fang P, Wang J (2023) "Tetramerization of upstream stimulating factor USF2 requires the elongated bent leucine zipper of the bHLH-LZ domain." J.Biol.Chem., 299, 105240. doi: 10.1016/j.jbc.2023.105240. Crystal structure of human usf2 bhlhlz domain in complex with DNA. SNAP output
8iaz RNA binding protein-RNA-DNA cryo-EM (3.0 Å) Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z (2024) "Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs." Cell Res., 34, 370-385. doi: 10.1038/s41422-024-00952-1. cryo-EM structure of the isfba1 tnpb-rerna-dsDNA complex. SNAP output
8ibw RNA binding protein-RNA-DNA cryo-EM (3.6 Å) Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG (2023) "Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon." Cell, 186, 2865-2879.e20. doi: 10.1016/j.cell.2023.05.032. Structure of r2 with 3'utr and DNA in binding state. SNAP output
8ibx RNA binding protein-RNA-DNA cryo-EM (3.74 Å) Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JG (2023) "Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon." Cell, 186, 2865-2879.e20. doi: 10.1016/j.cell.2023.05.032. Structure of r2 with 3'utr and DNA in unwinding state. SNAP output
8ica transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and cacl2 (5 millimolar). SNAP output
8icb transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of artificial mother liquor. SNAP output
8icc transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA (no 5'-phosphate). SNAP output
8ice transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and cdcl2 (1 millimolar). SNAP output
8icf transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (10 millimolar) and mgcl2 (50 millimolar). SNAP output
8icg transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and mgcl2 (5 millimolar). SNAP output
8ich transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dctp (1 millimolar) and mgcl2 (5 millimolar). SNAP output
8ici transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dgtp (1 millimolar) and mgcl2 (5 millimolar). SNAP output
8icj transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + thymidine-5'-triphosphate, soaked in the presence of dttp and mgcl2. SNAP output
8ick transferase-DNA X-ray (2.7 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar), mgcl2 (5 millimolar), and mncl2 (5 millimolar). SNAP output
8icl transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and nicl2 (5 millimolar). SNAP output
8icm transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar), mncl2 (5 millimolar), and ammonium sulfate (75 millimolar). SNAP output
8icn transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of atp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8ico transferase-DNA X-ray (2.7 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of azt-tp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icp transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icq transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of of datp (0.1 millimolar) and mncl2 (0.5 millimolar). SNAP output
8icr transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8ics transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dctp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8ict transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dctp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icu transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of ddatp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icv transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dgtp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icw transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dttp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icx transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dttp (1 millimolar) and mncl2 (5 millimolar). SNAP output
8icy transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + thymidine-5'-triphosphate, soaked in the presence of dttp and mncl2. SNAP output
8icz transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of of datp (1 millimolar), mncl2 (5 millimolar), and lithium sulfate (75 millimolar). SNAP output
8ieg nuclear protein cryo-EM (3.44 Å) Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L (2023) "Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A." Mol.Cell, 83, 3080-3094.e14. doi: 10.1016/j.molcel.2023.08.001. Bre1(mrbd-ring)-rad6-ub-nucleosome complex. SNAP output
8iej nuclear protein cryo-EM (3.12 Å) Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L (2023) "Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A." Mol.Cell, 83, 3080-3094.e14. doi: 10.1016/j.molcel.2023.08.001. Rnf20-rnf40-hrad6a-ub-nucleosome complex. SNAP output
8iew RNA binding protein-RNA-DNA cryo-EM (3.1 Å) Zhang X, Duan ZQ, Zhu JK "Cryo-EM structure of Cas005-crRNA-DNA complex at 3.1 Angstroms resolution." Cas005-crrna-DNA complex. SNAP output
8ifk RNA binding protein-RNA-DNA cryo-EM (2.54 Å) Zhang JT, Wei XY, Cui N, Tian R, Jia N (2024) "Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system." Nat.Chem.Biol., 20, 503-511. doi: 10.1038/s41589-023-01479-z. cryo-EM structure of monomeric sparta grna-ssDNA target complex. SNAP output
8ifl RNA binding protein-RNA-DNA cryo-EM (3.11 Å) Zhang JT, Wei XY, Cui N, Tian R, Jia N (2024) "Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system." Nat.Chem.Biol., 20, 503-511. doi: 10.1038/s41589-023-01479-z. cryo-EM structure of tetrameric sparta grna-ssDNA target complex in state 1. SNAP output
8ifm RNA binding protein-RNA-DNA cryo-EM (2.92 Å) Zhang JT, Wei XY, Cui N, Tian R, Jia N (2024) "Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system." Nat.Chem.Biol., 20, 503-511. doi: 10.1038/s41589-023-01479-z. cryo-EM structure of tetrameric sparta grna-ssDNA target complex in state 2. SNAP output
8ifo transcription X-ray (2.2 Å) Zhen X, Gan Q, Qu L, Dong Y, Pan C, Liu J, Wang N, Xu T (2023) "ERR gamma-DBD undergoes dimerization and conformational rearrangement upon binding to the downstream site of the DR1 element." Biochem.Biophys.Res.Commun., 656, 16-22. doi: 10.1016/j.bbrc.2023.03.038. Crystal structure of estrogen related receptor-gamma DNA binding domain complexed with pla2g12b promoter. SNAP output
8igr transcription cryo-EM (3.1 Å) Zhao M, Gao B, Wen A, Feng Y, Lu YQ (2023) "Structural basis of lambda CII-dependent transcription activation." Structure, 31, 968. doi: 10.1016/j.str.2023.05.008. cryo-EM structure of cii-dependent transcription activation complex. SNAP output
8igs transcription cryo-EM (3.4 Å) Zhao M, Gao B, Wen A, Feng Y, Lu YQ (2023) "Structural basis of lambda CII-dependent transcription activation." Structure, 31, 968. doi: 10.1016/j.str.2023.05.008. cryo-EM structure of rnap-promoter open complex at lambda promoter pre. SNAP output
8ihl nuclear protein-DNA cryo-EM (7.64 Å) Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H (2024) "Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties." Commun Biol, 7, 61. doi: 10.1038/s42003-023-05694-1. Overlapping tri-nucleosome. SNAP output
8ihm transcription cryo-EM (3.58 Å) Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X (2023) "Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme." Cell Res., 33, 971-974. doi: 10.1038/s41422-023-00884-2. Eaf3 chd domain bound to the nucleosome. SNAP output
8iht transcription cryo-EM (3.72 Å) Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X (2023) "Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme." Cell Res., 33, 971-974. doi: 10.1038/s41422-023-00884-2. Rpd3s bound to the nucleosome. SNAP output
8ijo DNA binding protein X-ray (1.65 Å) Adhav VA, Saikrishnan K "Structural basis of target recognition by the DNA binding domain of McrBC." Structure of DNA binding domain of mcrbc endonuclease bound to DNA: y41f-l68f double mutant. SNAP output
8ijp DNA binding protein X-ray (1.55 Å) Adhav VA, Saikrishnan K "Structural basis of target recognition by the DNA binding domain of McrBC." Structure of DNA binding domain of mcrbc endonuclease bound to DNA: l68y mutant. SNAP output
8ik4 DNA binding protein X-ray (2.1 Å) Adhav VA, Saikrishnan K "Structural basis of target recognition by the DNA binding domain of McrBC." Structure of DNA binding domain of mcrbc endonuclease bound to hemimethylated DNA: l68f mutant. SNAP output
8ik5 DNA binding protein-DNA X-ray (1.989 Å) Lv MQ, Lin LQ (2024) "Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain." Febs J. Transcription factor lmx1a homeobox domain in complex with wnt1 promoter. SNAP output
8ik8 DNA binding protein X-ray (1.8 Å) Adhav VA, Saikrishnan K "Structural basis of target recognition by the DNA binding domain of McrBC." Structure of DNA binding domain of mcrbc endonuclease bound to DNA: l68f mutant. SNAP output
8ikd DNA binding protein X-ray (2.1 Å) Adhav VA, Saikrishnan K "Structural basis of target recognition by the DNA binding domain of McrBC." Structure of DNA binding domain of mcrbc endonuclease bound to DNA: y41f-l68y double mutant. SNAP output
8ike DNA binding protein-DNA X-ray (2.6 Å) Lv MQ, Lin LQ (2024) "Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain." Febs J. Transcription factors lmx1a mutant-r199a homeobox domain complex with wnt1 promoter. SNAP output
8ild replication-DNA X-ray (2.25 Å) Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z (2023) "Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom." Int J Mol Sci, 24. doi: 10.3390/ijms242115758. The crystal structure of native dgtp:dnapre-i:pol x substrate ternary complex. SNAP output
8ile replication-DNA X-ray (3.0 Å) Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z (2023) "Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom." Int J Mol Sci, 24. doi: 10.3390/ijms242115758. The crystal structure of dgtpalphase-rp:dnapre-ii:pol x substrate ternary complex. SNAP output
8ilf replication-DNA X-ray (2.3 Å) Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z (2023) "Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom." Int J Mol Sci, 24. doi: 10.3390/ijms242115758. The crystal structure of dgtpalphase-sp:dnapre-ii:pol x substrate ternary complex. SNAP output
8ilg replication-DNA X-ray (1.805 Å) Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z (2023) "Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom." Int J Mol Sci, 24. doi: 10.3390/ijms242115758. The crystal structure of dg-DNA:pol x product binary complex. SNAP output
8ilh replication-DNA X-ray (2.1 Å) Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z (2023) "Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom." Int J Mol Sci, 24. doi: 10.3390/ijms242115758. The crystal structure of dg(se-sp)-DNA:pol x product binary complex. SNAP output
8ili replication-DNA X-ray (1.9 Å) Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z (2023) "Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom." Int J Mol Sci, 24. doi: 10.3390/ijms242115758. The crystal structure of dg(se-rp)-DNA:pol x product binary complex. SNAP output
8ilw DNA binding protein-DNA X-ray (2.712 Å) Lv MQ, Lin LQ (2024) "Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain." Febs J. Transcription factor lmx1a homeobox domain in complex with pitx3 promoter. SNAP output
8in8 antiviral protein cryo-EM (3.0 Å) Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H (2023) "Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity." Cell Res., 33, 699-711. doi: 10.1038/s41422-023-00839-7. cryo-EM structure of the target ssDNA-bound sir2-apaz-ago-grna quaternary complex. SNAP output
8inb RNA binding protein-RNA-DNA cryo-EM (3.1 Å) Duan Z, Zhang X, Zhang JT, Li S, Liu R, Sun J, Zhao Q, Jia N, Jia N, Zhu JK (2023) "Molecular basis for DNA cleavage by the hypercompact Cas12j-SF05." Cell Discov, 9, 117. doi: 10.1038/s41421-023-00612-5. cryo-EM structure of cas12j-sf05-crrna-dsDNA complex. SNAP output
8ip0 RNA binding protein-RNA-DNA cryo-EM (3.6 Å) Lu M, Yu C, Zhang Y, Ju W, Ye Z, Hua C, Mao J, Hu C, Yang Z, Xiao Y (2024) "Structure and genome editing of type I-B CRISPR-Cas." Nat Commun, 15, 4126. doi: 10.1038/s41467-024-48598-2. cryo-EM structure of type i-b cascade bound to a pam-containing dsDNA target at 3.6 angstrom resolution. SNAP output
8ipp DNA binding protein-DNA X-ray (2.007 Å) Ngo KH, Liew CW, Heddi B, Phan AT (2024) "Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein." J.Am.Chem.Soc., 146, 13709-13713. doi: 10.1021/jacs.4c01971. Crystal structure of the complex between an ankyrin and a parallel g-quadruplex. SNAP output
8iqi DNA binding protein cryo-EM (3.32 Å) Shao Z, Su S, Yang J, Zhang W, Gao Y, Zhao X, Zhang Y, Shao Q, Cao C, Li H, Liu H, Zhang J, Lin J, Ma J, Gan J (2023) "Structures and implications of the C962R protein of African swine fever virus." Nucleic Acids Res., 51, 9475-9490. doi: 10.1093/nar/gkad677. Structure of full-length asfvprimpol in complex-form. SNAP output
8isz DNA binding protein-DNA-RNA cryo-EM (3.27 Å) Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S (2024) "Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute." Nature, 625, 822-831. doi: 10.1038/s41586-023-06665-6. cryo-EM structure of crt-sparta-grna-tDNA monomer. SNAP output
8it0 DNA binding protein-DNA-RNA cryo-EM (3.5 Å) Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S (2024) "Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute." Nature, 625, 822-831. doi: 10.1038/s41586-023-06665-6. cryo-EM structure of crt-sparta-grna-tDNA dimer (conformation-2). SNAP output
8it1 DNA binding protein-DNA-RNA cryo-EM (3.41 Å) Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S (2024) "Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute." Nature, 625, 822-831. doi: 10.1038/s41586-023-06665-6. cryo-EM structure of crt-sparta-grna-tDNA tetramer (nadase active form). SNAP output
8ity transcription cryo-EM (3.9 Å) Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y (2023) "Structure of the SNAPc-bound RNA polymerase III preinitiation complex." Cell Res., 33, 565-568. doi: 10.1038/s41422-023-00819-x. Human RNA polymerase iii pre-initiation complex closed DNA 1. SNAP output
8iue transcription cryo-EM (4.1 Å) Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y (2023) "Structure of the SNAPc-bound RNA polymerase III preinitiation complex." Cell Res., 33, 565-568. doi: 10.1038/s41422-023-00819-x. RNA polymerase iii pre-initiation complex melting complex 1. SNAP output
8iuh transcription cryo-EM (3.4 Å) Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y (2023) "Structure of the SNAPc-bound RNA polymerase III preinitiation complex." Cell Res., 33, 565-568. doi: 10.1038/s41422-023-00819-x. RNA polymerase iii pre-initiation complex open complex 1. SNAP output
8iyq DNA binding protein-DNA-RNA cryo-EM (2.46 Å) Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG (2024) "Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity." Nature, 630, 484-492. doi: 10.1038/s41586-024-07486-x. Structure of cbcas9 bound to 20-nucleotide complementary DNA substrate. SNAP output
8j0k DNA binding protein-DNA X-ray (2.1 Å) Liu K, Xiao Y, Gan L, Li W, Zhang J, Min J (2023) "Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors." Nucleic Acids Res., 51, 8270-8282. doi: 10.1093/nar/gkad583. Crystal structure of human tfap2a in complex with DNA. SNAP output
8j0r DNA binding protein-DNA X-ray (2.1 Å) Liu K, Xiao Y, Gan L, Li W, Zhang J, Min J (2023) "Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors." Nucleic Acids Res., 51, 8270-8282. doi: 10.1093/nar/gkad583. Structure of human tfap2a in complex with DNA. SNAP output
8j12 RNA binding protein-DNA-RNA cryo-EM (3.08 Å) Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O (2023) "An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis." Cell, 186, 4920-4935.e23. doi: 10.1016/j.cell.2023.08.031. cryo-EM structure of the ascas12f-sgrna-target DNA ternary complex. SNAP output
8j1j RNA binding protein-DNA-RNA cryo-EM (2.91 Å) Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O (2023) "An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis." Cell, 186, 4920-4935.e23. doi: 10.1016/j.cell.2023.08.031. cryo-EM structure of the ascas12f-yham-sgrnas3-5v7-target DNA. SNAP output
8j1q viral protein-immune system-DNA cryo-EM (3.3 Å) Rahman MS, Han MJ, Kim SW, Kang SM, Kim BR, Kim H, Lee CJ, Noh JE, Kim H, Lee JO, Jang SK (2023) "Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection." Molecules, 28. doi: 10.3390/molecules28124645. Cryoem structure of sars cov-2 rbd and aptamer complex. SNAP output
8j26 viral protein-immune system-DNA cryo-EM (3.4 Å) Rahman MS, Han MJ, Kim SW, Kang SM, Kim BR, Kim H, Lee CJ, Noh JE, Kim H, Lee JO, Jang SK (2023) "Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection." Molecules, 28. doi: 10.3390/molecules28124645. Cryoem structure of sars cov-2 rbd and aptamer complex. SNAP output
8j3r RNA binding protein-DNA-RNA cryo-EM (2.95 Å) Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O (2023) "An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis." Cell, 186, 4920-4935.e23. doi: 10.1016/j.cell.2023.08.031. cryo-EM structure of the ascas12f-hkra-sgrnas3-5v7-target DNA. SNAP output
8j54 DNA-DNA binding protein X-ray (2.72 Å) Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y (2024) "Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma." Structure, 32, 467-475.e3. doi: 10.1016/j.str.2024.01.004. Crystal structure of rxr-dr2 complex. SNAP output
8j6s replication-DNA cryo-EM (3.8 Å) Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM (2023) "Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1." Science, 381, eadd8673. doi: 10.1126/science.add8673. cryo-EM structure of the single caf-1 bound right-handed di-tetrasome. SNAP output
8j6t replication-DNA cryo-EM (6.6 Å) Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM (2023) "Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1." Science, 381, eadd8673. doi: 10.1126/science.add8673. cryo-EM structure of the double caf-1 bound right-handed di-tetrasome. SNAP output
8j70 DNA binding protein-DNA X-ray (1.85 Å) Li HT, Liu WQ "Molecular basis for Speckled protein SP140 bivalent recognition of histone H3 and DNA." Native sand domain of protein sp140 with DNA. SNAP output
8j71 DNA binding protein-DNA X-ray (1.85 Å) Li HT, Liu WQ "Molecular basis for Speckled protein SP140 bivalent recognition of histone H3 and DNA." Selenomethionine mutant (l601sem-l654sem) of sand domain of protein sp140 with DNA. SNAP output
8j86 viral protein cryo-EM (3.22 Å) Xu Y, Wu Y, Wu X, Zhang Y, Yang Y, Li D, Yang B, Gao K, Zhang Z, Dong C (2024) "Structural basis of human mpox viral DNA replication inhibition by brincidofovir and cidofovir." Int.J.Biol.Macromol., 270, 132231. doi: 10.1016/j.ijbiomac.2024.132231. Monkeypox virus DNA replication holoenzyme f8, a22 and e4 complex in a DNA binding form. SNAP output
8j8f viral protein cryo-EM (2.98 Å) Xu Y, Wu Y, Wu X, Zhang Y, Yang Y, Li D, Yang B, Gao K, Zhang Z, Dong C (2024) "Structural basis of human mpox viral DNA replication inhibition by brincidofovir and cidofovir." Int.J.Biol.Macromol., 270, 132231. doi: 10.1016/j.ijbiomac.2024.132231. Monkeypox virus DNA replication holoenzyme f8, a22 and e4 in complex with a DNA duplex and dctp. SNAP output
8j8g viral protein cryo-EM (2.79 Å) Xu Y, Wu Y, Wu X, Zhang Y, Yang Y, Li D, Yang B, Gao K, Zhang Z, Dong C (2024) "Structural basis of human mpox viral DNA replication inhibition by brincidofovir and cidofovir." Int.J.Biol.Macromol., 270, 132231. doi: 10.1016/j.ijbiomac.2024.132231. Monkeypox virus DNA replication holoenzyme f8, a22 and e4 in complex with a DNA duplex and cidofovir diphosphate. SNAP output
8j8h DNA binding protein-DNA-RNA cryo-EM (3.4 Å) Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y (2024) "Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system." Nat.Chem.Biol., 20, 512-520. doi: 10.1038/s41589-023-01478-0. Sparta monomer bound with guide-target, state 2. SNAP output
8j90 nuclear protein cryo-EM (4.71 Å) Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H (2024) "Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1." Nat Commun, 15, 5187. doi: 10.1038/s41467-024-49465-w. cryo-EM structure of ddm1-nucleosome complex. SNAP output
8j91 nuclear protein cryo-EM (2.9 Å) Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H (2024) "Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1." Nat Commun, 15, 5187. doi: 10.1038/s41467-024-49465-w. cryo-EM structure of nucleosome containing arabidopsis thaliana histones. SNAP output
8j92 nuclear protein cryo-EM (2.9 Å) Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H (2024) "Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1." Nat Commun, 15, 5187. doi: 10.1038/s41467-024-49465-w. cryo-EM structure of nucleosome containing arabidopsis thaliana h2a.w. SNAP output
8j9g DNA binding protein-DNA-RNA cryo-EM (3.5 Å) Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y (2024) "Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system." Nat.Chem.Biol., 20, 512-520. doi: 10.1038/s41589-023-01478-0. Crtsparta hetero-dimer bound with guide-target, state 1. SNAP output
8j9p DNA binding protein-RNA-DNA cryo-EM (3.4 Å) Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y (2024) "Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system." Nat.Chem.Biol., 20, 512-520. doi: 10.1038/s41589-023-01478-0. Sparta dimer bound with guide-target. SNAP output
8j9v isomerase-DNA cryo-EM (2.71 Å) Chang CM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD (2024) "A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase." Commun Chem, 7, 45. doi: 10.1038/s42004-024-01129-y. cryo-EM structure of the african swine fever virus topoisomerase 2 complexed with cut02aDNA and etoposide (edi-1). SNAP output
8j9w isomerase-DNA cryo-EM (2.76 Å) Chang CM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD (2024) "A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase." Commun Chem, 7, 45. doi: 10.1038/s42004-024-01129-y. cryo-EM structure of the african swine fever virus topoisomerase 2 complexed with cut02bDNA and etoposide (edi-2). SNAP output
8j9x isomerase-DNA cryo-EM (3.0 Å) Chang CM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD (2024) "A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase." Commun Chem, 7, 45. doi: 10.1038/s42004-024-01129-y. cryo-EM structure of the african swine fever virus topoisomerase 2 complexed with cut02aDNA and m-amsa (edi-3). SNAP output
8jay DNA binding protein-DNA-RNA cryo-EM (4.2 Å) Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y (2024) "Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system." Nat.Chem.Biol., 20, 512-520. doi: 10.1038/s41589-023-01478-0. Crtsparta octamer bound with guide-target. SNAP output
8jbx DNA binding protein-DNA cryo-EM (3.35 Å) Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T (2024) "Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions." Nucleic Acids Res., 52, 11612-11625. doi: 10.1093/nar/gkae825. Human canonical 601 DNA nucleosome. SNAP output
8jcc DNA binding protein-DNA cryo-EM (3.42 Å) Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T (2024) "Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions." Nucleic Acids Res., 52, 11612-11625. doi: 10.1093/nar/gkae825. Human histone h2b variant h2bfwt cryo-EM structure with 601 DNA sequence. SNAP output
8jcd DNA binding protein-DNA cryo-EM (3.14 Å) Ding D, Pang MYH, Deng M, Nguyen TT, Liu Y, Sun X, Xu Z, Zhang Y, Zhai Y, Yan Y, Ishibashi T (2024) "Testis-specific H2B.W1 disrupts nucleosome integrity by reducing DNA-histone interactions." Nucleic Acids Res., 52, 11612-11625. doi: 10.1093/nar/gkae825. Human h2bfwth100r nucleosome with 601 DNA. SNAP output
8jch transcription cryo-EM (2.7 Å) Zeng Y, Zhang HW, Wu XX, Zhang Y (2024) "Structural basis of exoribonuclease-mediated mRNA transcription termination." Nature, 628, 887-893. doi: 10.1038/s41586-024-07240-3. cryo-EM structure of yeast rat1-bound pol ii pre-termination transcription complex 1 (pol ii rat1-pttc1). SNAP output
8jfr viral protein X-ray (3.1 Å) Deng X, Sun W, Li X, Wang J, Cheng Z, Sheng G, Wang Y (2024) "An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding." Nat Commun, 15, 1806. doi: 10.1038/s41467-024-45987-5. N-terminal domain of acriia15 in complex with palindromic DNA substrate. SNAP output
8jfu viral protein X-ray (3.15 Å) Deng X, Sun W, Li X, Wang J, Cheng Z, Sheng G, Wang Y (2024) "An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding." Nat Commun, 15, 1806. doi: 10.1038/s41467-024-45987-5. Acriia15 in complex with palindromic DNA substrate. SNAP output
8jg9 viral protein cryo-EM (3.82 Å) Deng X, Sun W, Li X, Wang J, Cheng Z, Sheng G, Wang Y (2024) "An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding." Nat Commun, 15, 1806. doi: 10.1038/s41467-024-45987-5. cryo-EM structure of the sacas9-sgrna-acriia15-promoter DNA dimer. SNAP output
8jh2 transcription-DNA-RNA cryo-EM (5.7 Å) Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H (2023) "Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA." J.Biol.Chem., 299, 105477. doi: 10.1016/j.jbc.2023.105477. RNA polymerase ii elongation complex bound with elf1, spt4-5 and foreign DNA, stalled at shl(-1) of the nucleosome. SNAP output
8jh3 transcription-DNA-RNA cryo-EM (3.7 Å) Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H (2023) "Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA." J.Biol.Chem., 299, 105477. doi: 10.1016/j.jbc.2023.105477. RNA polymerase ii elongation complex containing 40 bp upstream DNA loop, stalled at shl(-1) of the nucleosome. SNAP output
8jh4 transcription-DNA-RNA cryo-EM (3.2 Å) Akatsu M, Ehara H, Kujirai T, Fujita R, Ito T, Osumi K, Ogasawara M, Takizawa Y, Sekine SI, Kurumizaka H (2023) "Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA." J.Biol.Chem., 299, 105477. doi: 10.1016/j.jbc.2023.105477. RNA polymerase ii elongation complex containing 60 bp upstream DNA loop, stalled at shl(-1) of the nucleosome. SNAP output
8jhf gene regulation-DNA cryo-EM (3.68 Å) Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W (2023) "Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase." Cell Discov, 9, 120. doi: 10.1038/s41421-023-00620-5. Native suv420h1 bound to 167-bp nucleosome. SNAP output
8jhg gene regulation-DNA cryo-EM (3.58 Å) Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W (2023) "Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase." Cell Discov, 9, 120. doi: 10.1038/s41421-023-00620-5. Native suv420h1 bound to 167-bp nucleosome. SNAP output
8jho gene regulation cryo-EM (7.6 Å) Li W, Cui H, Lu Z, Wang H (2023) "Structure of histone deacetylase complex Rpd3S bound to nucleosome." Nat.Struct.Mol.Biol., 30, 1893-1901. doi: 10.1038/s41594-023-01121-5. cryo-EM structure of the histone deacetylase complex rpd3s in complex with di-nucleosome. SNAP output
8jke gene regulation-DNA cryo-EM (3.67 Å) Wang Y, Yang X, Yu F, Deng Z, Lin S, Zheng J (2024) "Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces." Plos Biol., 22, e3002528. doi: 10.1371/journal.pbio.3002528. Afsr(t337a) transcription activation complex. SNAP output
8jkk DNA binding protein-DNA X-ray (2.3 Å) Zhang L, Mu Y, Li T, Hu J, Lin H, Zhang L (2024) "Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation." Nucleic Acids Res., 52, 3886-3895. doi: 10.1093/nar/gkae066. Crystal structure of the dioxygenase cctet from coprinopsis cinerea bound to 12bp 5-methylcytosine (5mc) containing duplex DNA. SNAP output
8jkl transcription X-ray (2.94 Å) Wang G, Feng X, Ding J (2023) "Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency." Structure, 31, 1441. doi: 10.1016/j.str.2023.08.013. Irf4 DNA-binding domain bound to an DNA containing gata motif. SNAP output
8jkn transcription X-ray (2.92 Å) Wang G, Feng X, Ding J (2023) "Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency." Structure, 31, 1441. doi: 10.1016/j.str.2023.08.013. T95r mutant irf4 DNA-binding domain bound to an DNA containing gaaa motif. SNAP output
8jko transcription X-ray (2.95 Å) Wang G, Feng X, Ding J (2023) "Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency." Structure, 31, 1441. doi: 10.1016/j.str.2023.08.013. T95r mutant irf4 DNA-binding domain bound to an DNA containing gata motif. SNAP output
8jkq transcription X-ray (3.09 Å) Wang G, Feng X, Ding J (2023) "Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency." Structure, 31, 1441. doi: 10.1016/j.str.2023.08.013. T95r mutant irf4 DNA-binding domain bound to an DNA containing gaca motif. SNAP output
8jks transcription X-ray (3.3 Å) Wang G, Feng X, Ding J (2023) "Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency." Structure, 31, 1441. doi: 10.1016/j.str.2023.08.013. T95r mutant irf4 DNA-binding domain bound to an DNA containing gaga motif. SNAP output
8jl0 antiviral protein-DNA-RNA cryo-EM (3.1 Å) Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S (2024) "Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system." Nat Commun, 15, 450. doi: 10.1038/s41467-023-44660-7. cryo-EM structure of the prokaryotic sparsa system complex. SNAP output
8jl9 gene regulation-DNA cryo-EM (2.65 Å) Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H (2023) "Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II." Nucleic Acids Res., 51, 10364-10374. doi: 10.1093/nar/gkad754. cryo-EM structure of the human nucleosome with scfv. SNAP output
8jla gene regulation-DNA cryo-EM (3.44 Å) Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H (2023) "Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II." Nucleic Acids Res., 51, 10364-10374. doi: 10.1093/nar/gkad754. cryo-EM structure of the human nucleosome lacking n-terminal region of h2a, h2b, h3, and h4. SNAP output
8jlb gene regulation-DNA cryo-EM (2.36 Å) Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H (2023) "Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II." Nucleic Acids Res., 51, 10364-10374. doi: 10.1093/nar/gkad754. cryo-EM structure of the 145 bp human nucleosome containing h3.2 c110a mutant. SNAP output
8jld gene regulation-DNA cryo-EM (2.48 Å) Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H (2023) "Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II." Nucleic Acids Res., 51, 10364-10374. doi: 10.1093/nar/gkad754. cryo-EM structure of the 145 bp human nucleosome containing acetylated h3 tail. SNAP output
8jmj DNA binding protein X-ray (2.57 Å) Chu CH, Wu CT, Lin MG, Yen CY, Wu YZ, Hsiao CD, Sun YJ (2024) "Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB." Nucleic Acids Res., 52, 7321-7336. doi: 10.1093/nar/gkae450. Structure of helicobacter pylori soj-DNA-spo0j complex. SNAP output
8jmk DNA binding protein X-ray (2.7 Å) Chu CH, Wu CT, Lin MG, Yen CY, Wu YZ, Hsiao CD, Sun YJ (2024) "Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB." Nucleic Acids Res., 52, 7321-7336. doi: 10.1093/nar/gkae450. Structure of helicobacter pylori soj mutant, d41a bound to DNA. SNAP output
8jnd DNA binding protein-DNA cryo-EM (3.66 Å) Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H (2024) "Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site." Nature, 628, 212-220. doi: 10.1038/s41586-024-07196-4. The cryo-EM structure of the nonameric rad51 ring bound to the nucleosome with the linker DNA binding. SNAP output
8jne DNA binding protein-DNA cryo-EM (4.68 Å) Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H (2024) "Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site." Nature, 628, 212-220. doi: 10.1038/s41586-024-07196-4. The cryo-EM structure of the decameric rad51 ring bound to the nucleosome without the linker DNA binding. SNAP output
8jnk RNA binding protein X-ray (2.69 Å) Zhang L, Duan HC, Paduch M, Hu J, Zhang C, Mu Y, Lin H, He C, Kossiakoff AA, Jia G, Zhang L (2024) "The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation." Angew.Chem.Int.Ed.Engl., 63, e202313900. doi: 10.1002/anie.202313900. Crystal structure of human alkbh3 bound to ssDNA through active site crosslink. SNAP output
8jnr DNA binding protein-DNA X-ray (3.66 Å) Zhang L, Duan HC, Paduch M, Hu J, Zhang C, Mu Y, Lin H, He C, Kossiakoff AA, Jia G, Zhang L (2024) "The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation." Angew.Chem.Int.Ed.Engl., 63. doi: 10.1002/anie.202313900. Crystal structure of human alkbh3 bound to 3mc containing ssDNA through distal crosslink. SNAP output
8jo2 transcription cryo-EM (2.74 Å) Lou YC, Huang HY, Yeh HH, Chiang WH, Chen C, Wu KP (2023) "Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA." Nucleic Acids Res., 51, 10049-10058. doi: 10.1093/nar/gkad724. Structural basis of transcriptional activation by the ompr-phob-family response regulator pmra. SNAP output
8jpx gene regulation cryo-EM (2.9 Å) Wang L, Chen W, Zhang C, Xie X, Huang F, Chen M, Mao W, Yu N, Wei Q, Ma L, Li Z (2024) "Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute." Mol.Cell, 84, 675-686.e4. doi: 10.1016/j.molcel.2024.01.004. cryo-EM structure of pfago-guide DNA-target DNA complex. SNAP output
8jr8 DNA binding protein-DNA-RNA cryo-EM (3.48 Å) Huang PP, Guo LJ, Li ZX, Yan PR, Chen MR, Xiao YB "Cryo-EM Structure of MapSPARTA." Mapsparta dimer bound with guide-target. SNAP output
8jsi DNA binding protein-DNA cryo-EM (2.9 Å) Li Z "Cryo-EM structure of a DNA-protein complex." cryo-EM structure of a DNA-protein complex. SNAP output
8jtj DNA binding protein-RNA-DNA cryo-EM (3.08 Å) Shen PP, Liu BB, Li X, Zhang LL, Chen C-C, Guo R-T "Cryo-EM structure of GeoCas9-sgRNA-DNA ternary complex." cryo-EM structure of geocas9-sgrna-dsDNA ternary complex. SNAP output
8k21 antibiotic-RNA binding protein-DNA cryo-EM (3.8 Å) Zhang LX, Feng Y "Structure of csy complex with short DNA." Cas1-cas2-dsDNA subregion in icp1 csy-DNA-cas1-2-3 complex. SNAP output
8k27 RNA binding protein-DNA-RNA cryo-EM (3.6 Å) Zhang LX, Feng Y "Structure of csy complex with short DNA." Icp1 csy-dsDNA complex (partial duplex). SNAP output
8k28 RNA binding protein-DNA-RNA cryo-EM (3.54 Å) Zhang LX, Feng Y "Structure of csy complex with long DNA State1." Icp1 csy-dsDNA complex (form 1). SNAP output
8k29 RNA binding protein-DNA-RNA cryo-EM (3.18 Å) Zhang LX, Feng Y "Structure of csy complex with long DNA State2." Icp1 csy-dsDNA complex (form 2). SNAP output
8k3d DNA binding protein-DNA X-ray (2.3 Å) Liu K, Li W, Xiao Y, Lei M, Zhang M, Min J (2024) "Molecular mechanism of specific DNA sequence recognition by NRF1." Nucleic Acids Res., 52, 953-966. doi: 10.1093/nar/gkad1162. Crystal structure of nrf1 dbd bound to DNA. SNAP output
8k4l DNA binding protein-DNA X-ray (2.1 Å) Liu K, Li W, Xiao Y, Lei M, Zhang M, Min J (2024) "Molecular mechanism of specific DNA sequence recognition by NRF1." Nucleic Acids Res., 52, 953-966. doi: 10.1093/nar/gkad1162. Crystal structure of nrf1 homodimer in complex with DNA. SNAP output
8k58 transcription-DNA-RNA cryo-EM (3.15 Å) Zhang KN, Liu Y, Chen M, Wang Y, Lin W, Li M, Zhang X, Gao Y, Gong Q, Chen H, Steve M, Li S, Zhang K, Liu B "TIEA inhibits Sigma70-dependent transcriptions, accelerates elongation speed and elevates transcription error." The cryo-EM map of close tiea-tec complex. SNAP output
8k59 transcription-DNA-RNA cryo-EM (3.5 Å) Zhang KN, Liu Y, Chen M, Wang Y, Lin W, Li M, Zhang X, Gao Y, Gong Q, Chen H, Steve M, Li S, Zhang K, Liu B "TIEA inhibits sigma70-dependent transcriptions, accelerates elongation speed and elevates transcription error." The cryo-EM map of tic-tiea complex. SNAP output
8k5a transcription-DNA-RNA cryo-EM (3.3 Å) Zhang KN, Liu Y, Chen M, Wang Y, Lin W, Li M, Zhang X, Gao Y, Gong Q, Chen H, Steve M, Li S, Zhang K, Liu B "TIEA inhibits sigma70-dependent transcriptions, accelerates elongation speed and elevates transcription error." The cryo-EM map of open tiea-tec complex. SNAP output
8k5p transcription cryo-EM (2.8 Å) Zeng Y, Zhang HW, Wu XX, Zhang Y (2024) "Structural basis of exoribonuclease-mediated mRNA transcription termination." Nature, 628, 887-893. doi: 10.1038/s41586-024-07240-3. cryo-EM structure of yeast rat1-bound pol ii pre-termination transcription complex 2 (pol ii rat1-pttc2). SNAP output
8k60 gene regulation cryo-EM (3.4 Å) Shi J, Ye Z, Feng Z, Wen A, Wang L, Zhang Z, Xu L, Song Q, Wang F, Liu T, Wang S, Feng Y, Lin W (2024) "Structural insights into transcription activation of the Streptomyces antibiotic regulatory protein, AfsR." Iscience, 27, 110421. doi: 10.1016/j.isci.2024.110421. cryo-EM structure of streptomyces coelicolor transcription initiation complex with the global transcription factor afsr. SNAP output
8k86 DNA binding protein-DNA X-ray (2.06 Å) Chen S, Lei M, Liu K, Min J (2024) "Structural basis for specific DNA sequence recognition by the transcription factor NFIL3." J.Biol.Chem., 300, 105776. doi: 10.1016/j.jbc.2024.105776. Crystal structure of nfil3 in complex with ttatgtaa DNA. SNAP output
8k87 DNA-RNA-cell invasion cryo-EM (2.9 Å) Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S (2024) "Nucleic acid-induced NADase activation of a short Sir2-associated prokaryotic Argonaute system." Cell Rep, 43, 114391. doi: 10.1016/j.celrep.2024.114391. Dimer structure of procaryotic ago. SNAP output
8k88 DNA-RNA-cell invasion cryo-EM (2.6 Å) Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S (2024) "Nucleic acid-induced NADase activation of a short Sir2-associated prokaryotic Argonaute system." Cell Rep, 43, 114391. doi: 10.1016/j.celrep.2024.114391. Structure of procaryotic ago. SNAP output
8k8a DNA binding protein-DNA X-ray (2.07 Å) Chen S, Lei M, Liu K, Min J (2024) "Structural basis for specific DNA sequence recognition by the transcription factor NFIL3." J.Biol.Chem., 300, 105776. doi: 10.1016/j.jbc.2024.105776. Crystal structure of nfil3 in complex with ttacgtaa DNA. SNAP output
8k8c DNA binding protein-DNA X-ray (2.06 Å) Chen S, Lei M, Liu K, Min J (2024) "Structural basis for specific DNA sequence recognition by the transcription factor NFIL3." J.Biol.Chem., 300, 105776. doi: 10.1016/j.jbc.2024.105776. Crystal structure of c-ebpalpha bzip domain bound to a high affinity DNA. SNAP output
8k8d DNA binding protein-DNA X-ray (2.2 Å) Chen S, Lei M, Liu K, Min J (2024) "Structural basis for specific DNA sequence recognition by the transcription factor NFIL3." J.Biol.Chem., 300, 105776. doi: 10.1016/j.jbc.2024.105776. Crystal structure of c-ebpbeta bzip domain bound to a high affinity DNA. SNAP output
8k8s viral protein-DNA cryo-EM (3.06 Å) Shen Y, Li Y, Yan R (2024) "Structural basis for the inhibition mechanism of the DNA polymerase holoenzyme from mpox virus." Structure, 32, 654-661.e3. doi: 10.1016/j.str.2024.03.004. F8-a22-e4 complex of mpxv in complex with DNA and ara-ctp. SNAP output
8k8u viral protein-DNA cryo-EM (3.05 Å) Shen Y, Li Y, Yan R (2024) "Structural basis for the inhibition mechanism of the DNA polymerase holoenzyme from mpox virus." Structure, 32, 654-661.e3. doi: 10.1016/j.str.2024.03.004. F8-a22-e4 complex of mpxv in complex with DNA and dctp. SNAP output
8k9g DNA-RNA-cell invasion cryo-EM (3.49 Å) Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S (2024) "Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute." Nature, 625, 822-831. doi: 10.1038/s41586-023-06665-6. cryo-EM structure of crt-sparta-grna-tDNA dimer (conformation-1). SNAP output
8ka3 hydrolase-DNA X-ray (3.0 Å) Guo W, Wu W, Wen Y, Gao Y, Zhuang S, Meng C, Chen H, Zhao Z, Hu K, Wu B (2024) "Structural insights into the catalytic mechanism of the AP endonuclease AtARP." Structure, 32, 780-794.e5. doi: 10.1016/j.str.2024.02.014. Arabidopsis ap endonuclease arp complex with 22bp thf-containing DNA. SNAP output
8ka5 hydrolase-DNA X-ray (2.8 Å) Guo W, Wu W, Wen Y, Gao Y, Zhuang S, Meng C, Chen H, Zhao Z, Hu K, Wu B (2024) "Structural insights into the catalytic mechanism of the AP endonuclease AtARP." Structure, 32, 780-794.e5. doi: 10.1016/j.str.2024.02.014. Arabidopsis ap endonuclease arp complex with 20bp thf-containing DNA. SNAP output
8kah RNA binding protein-RNA-DNA X-ray (3.36 Å) Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L (2024) "Trans-nuclease activity of Cas9 activated by DNA or RNA target binding." Nat.Biotechnol. doi: 10.1038/s41587-024-02255-7. Crystal structure of spycas9-crrna-tracrrna complex bound to 18nt target DNA. SNAP output
8kai RNA binding protein-RNA-DNA X-ray (3.49 Å) Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L (2024) "Trans-nuclease activity of Cas9 activated by DNA or RNA target binding." Nat.Biotechnol. doi: 10.1038/s41587-024-02255-7. Crystal structure of spycas9-crrna-tracrrna complex bound to 17nt target DNA. SNAP output
8kaj RNA binding protein-RNA-DNA X-ray (3.42 Å) Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L (2024) "Trans-nuclease activity of Cas9 activated by DNA or RNA target binding." Nat.Biotechnol. doi: 10.1038/s41587-024-02255-7. Crystal structure of spycas9-crrna-tracrrna complex bound to 16nt target DNA. SNAP output
8kak RNA binding protein-RNA-DNA X-ray (3.6 Å) Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L (2024) "Trans-nuclease activity of Cas9 activated by DNA or RNA target binding." Nat.Biotechnol. doi: 10.1038/s41587-024-02255-7. Crystal structure of spycas9 in complex with sgrna and 18nt target DNA. SNAP output
8kal RNA binding protein-RNA-DNA X-ray (3.16 Å) Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L (2024) "Trans-nuclease activity of Cas9 activated by DNA or RNA target binding." Nat.Biotechnol. doi: 10.1038/s41587-024-02255-7. Crystal structure of spycas9 in complex with sgrna and 17nt target DNA. SNAP output
8kam RNA binding protein-RNA-DNA X-ray (3.91 Å) Chen J, Chen Y, Huang L, Lin X, Chen H, Xiang W, Liu L (2024) "Trans-nuclease activity of Cas9 activated by DNA or RNA target binding." Nat.Biotechnol. doi: 10.1038/s41587-024-02255-7. Crystal structure of spycas9 in complex with sgrna and 16nt target DNA. SNAP output
8kb5 DNA binding protein cryo-EM (2.26 Å) Hirai S, Kujirai T, Akatsu M, Ogasawara M, Ehara H, Sekine SI, Ohkawa Y, Takizawa Y, Kurumizaka H (2023) "Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8." J.Biochem., 174, 549-559. doi: 10.1093/jb/mvad069. cryo-EM structure of the human nucleosome containing h3.8. SNAP output
8kcb structural protein cryo-EM (3.17 Å) Zhang H, Gu Z, Zeng Y, Zhang Y (2024) "Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures." Structure, 32, 1222-1230.e4. doi: 10.1016/j.str.2024.05.013. Complex of ddm1-nucleosome(h2a) complex with ddm1 bound to shl2. SNAP output
8kcc structural protein cryo-EM (3.1 Å) Zhang H, Gu Z, Zeng Y, Zhang Y (2024) "Mechanism of heterochromatin remodeling revealed by the DDM1 bound nucleosome structures." Structure, 32, 1222-1230.e4. doi: 10.1016/j.str.2024.05.013. Complex of ddm1-nucleosome(h2a.w) complex with ddm1 bound to shl2. SNAP output
8kcm DNA binding protein X-ray (2.5 Å) Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Muller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD (2023) "Visualizing the DNA repair process by a photolyase at atomic resolution." Science, 382, eadd7795. doi: 10.1126/science.add7795. Mmcpdii-DNA complex containing low-dosage, light induced repaired DNA.. SNAP output
8kd2 transcription cryo-EM (3.02 Å) Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J (2023) "Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex." Cell Res., 33, 790-801. doi: 10.1038/s41422-023-00869-1. Rpd3s in complex with 187bp nucleosome. SNAP output
8kd4 transcription cryo-EM (2.93 Å) Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J (2023) "Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex." Cell Res., 33, 790-801. doi: 10.1038/s41422-023-00869-1. Rpd3s in complex with nucleosome with h3k36mla modification and 187bp DNA, class1. SNAP output
8kd5 transcription cryo-EM (2.9 Å) Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J (2023) "Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex." Cell Res., 33, 790-801. doi: 10.1038/s41422-023-00869-1. Rpd3s in complex with nucleosome with h3k36mla modification and 187bp DNA, class2. SNAP output
8kd6 transcription cryo-EM (3.07 Å) Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J (2023) "Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex." Cell Res., 33, 790-801. doi: 10.1038/s41422-023-00869-1. Rpd3s in complex with nucleosome with h3k36mla modification and 187bp DNA, class3. SNAP output
8kd7 transcription cryo-EM (3.09 Å) Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J (2023) "Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex." Cell Res., 33, 790-801. doi: 10.1038/s41422-023-00869-1. Rpd3s in complex with nucleosome with h3k36mla modification and 167bp DNA. SNAP output
8kfr hydrolase X-ray (2.1 Å) Zhang D, Xu S, Luo Z, Lin Z (2024) "MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions." Nat Commun, 15, 5140. doi: 10.1038/s41467-024-49490-9. Crystal structure of zmmoc1-nicked holliday junction-ca2+ complex. SNAP output
8kfs hydrolase X-ray (2.15 Å) Zhang D, Xu S, Luo Z, Lin Z (2024) "MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions." Nat Commun, 15, 5140. doi: 10.1038/s41467-024-49490-9. Crystal structure of zmmoc1-nicked holliday junction complex at ground state. SNAP output
8kft hydrolase X-ray (2.43 Å) Zhang D, Xu S, Luo Z, Lin Z (2024) "MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions." Nat Commun, 15, 5140. doi: 10.1038/s41467-024-49490-9. Crystal structure of zmmoc1 in complex with a nicked holliday junction soaked in mn2+ for 15 seconds. SNAP output
8kfu hydrolase X-ray (2.3 Å) Zhang D, Xu S, Luo Z, Lin Z (2024) "MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions." Nat Commun, 15, 5140. doi: 10.1038/s41467-024-49490-9. Crystal structure of zmmoc1 in complex with a nicked holliday junction soaked in mn2+ for 180 seconds. SNAP output
8kfv hydrolase X-ray (2.19 Å) Zhang D, Xu S, Luo Z, Lin Z (2024) "MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions." Nat Commun, 15, 5140. doi: 10.1038/s41467-024-49490-9. Crystal structure of zmmoc1 k229a in complex with a nicked holliday junction soaked in mn2+ for 180 seconds. SNAP output
8kfw DNA binding protein X-ray (2.3 Å) Zhang D, Xu S, Luo Z, Lin Z (2024) "MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions." Nat Commun, 15, 5140. doi: 10.1038/s41467-024-49490-9. Crystal structure of zmmoc1 k229a in complex with a nicked holliday junction soaked in mn2+ for 600 seconds. SNAP output
8kg9 replication cryo-EM (4.52 Å) Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y (2023) "Synergism between CMG helicase and leading strand DNA polymerase at replication fork." Nat Commun, 14, 5849. doi: 10.1038/s41467-023-41506-0. Yeast replisome in state iii. SNAP output
8kgm viral protein-DNA cryo-EM (4.8 Å) Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y (2024) "Structural insights into the DNA topoisomerase II of the African swine fever virus." Nat Commun, 15, 4607. doi: 10.1038/s41467-024-49047-w. Structure of african swine fever virus topoisomerase ii in complex with dsDNA. SNAP output
8kgn viral protein-DNA cryo-EM (5.9 Å) Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y (2024) "Structural insights into the DNA topoisomerase II of the African swine fever virus." Nat Commun, 15, 4607. doi: 10.1038/s41467-024-49047-w. Structure of african swine fever virus topoisomerase ii in complex with dsDNA. SNAP output
8kgq viral protein-DNA cryo-EM (5.6 Å) Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y (2024) "Structural insights into the DNA topoisomerase II of the African swine fever virus." Nat Commun, 15, 4607. doi: 10.1038/s41467-024-49047-w. Structure of african swine fever virus topoisomerase ii in complex with dsDNA. SNAP output
8kgr viral protein-DNA cryo-EM (3.2 Å) Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y (2024) "Structural insights into the DNA topoisomerase II of the African swine fever virus." Nat Commun, 15, 4607. doi: 10.1038/s41467-024-49047-w. Structure of african swine fever virus topoisomerase ii in complex with dsDNA. SNAP output
8mht transferase-DNA X-ray (2.76 Å) O'Gara M, Horton JR, Roberts RJ, Cheng X (1998) "Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base." Nat.Struct.Biol., 5, 872-877. doi: 10.1038/2312. Cytosine-specific methyltransferase hhai-DNA complex. SNAP output
8oej DNA binding protein cryo-EM (7.96 Å) Madru C, Martinez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L (2023) "DNA-binding mechanism and evolution of replication protein A." Nat Commun, 14, 2326. doi: 10.1038/s41467-023-38048-w. Extended rpa-DNA nucleoprotein filament. SNAP output
8oel DNA binding protein cryo-EM (8.2 Å) Madru C, Martinez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L (2023) "DNA-binding mechanism and evolution of replication protein A." Nat Commun, 14, 2326. doi: 10.1038/s41467-023-38048-w. Condensed rpa-DNA nucleoprotein filament. SNAP output
8oet lyase X-ray (2.11 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Sfx structure of the class ii photolyase complexed with a thymine dimer. SNAP output
8oeu transcription cryo-EM (3.04 Å) Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P (2023) "Structure of the transcribing RNA polymerase II-Elongin complex." Nat.Struct.Mol.Biol., 30, 1925-1935. doi: 10.1038/s41594-023-01138-w. Structure of the mammalian pol ii-spt6 complex (composite structure, structure 4). SNAP output
8oev transcription cryo-EM (2.86 Å) Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P (2023) "Structure of the transcribing RNA polymerase II-Elongin complex." Nat.Struct.Mol.Biol., 30, 1925-1935. doi: 10.1038/s41594-023-01138-w. Structure of the mammalian pol ii-spt6-elongin complex, lacking eloa latch (composite structure, structure 3). SNAP output
8oew transcription cryo-EM (2.8 Å) Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P (2023) "Structure of the transcribing RNA polymerase II-Elongin complex." Nat.Struct.Mol.Biol., 30, 1925-1935. doi: 10.1038/s41594-023-01138-w. Structure of the mammalian pol ii-elongin complex, lacking the eloa latch (composite structure, structure 2). SNAP output
8of0 transcription cryo-EM (3.05 Å) Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P (2023) "Structure of the transcribing RNA polymerase II-Elongin complex." Nat.Struct.Mol.Biol., 30, 1925-1935. doi: 10.1038/s41594-023-01138-w. Structure of the mammalian pol ii-spt6-elongin complex, structure 1. SNAP output
8of4 gene regulation cryo-EM (2.94 Å) Smirnova E, Bignon E, Schultz P, Papai G, Ben Shem A (2024) "Binding to nucleosome poises human SIRT6 for histone H3 deacetylation." Elife, 12. doi: 10.7554/eLife.87989. Nucleosome bound human sirt6 (composite). SNAP output
8oj1 transcription X-ray (2.57 Å) Crespo I, Weijers D, Boer DR "Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with High Affinity DNA." Crystal structure of the DNA binding domain of m. polymorpha auxin response factor 2 (mparf2) in complex with high affinity DNA. SNAP output
8oj2 transcription X-ray (2.56 Å) Crespo I, Weijers D, Boer DR "Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with protomor-like sequence IR7." Crystal structure of the DNA binding domain of m. polymorpha auxin response factor 2 (mparf2) in complex with protomor-like sequence ir7. SNAP output
8oj6 transferase cryo-EM (2.41 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase-processivity factor complex in pre-translocation state. SNAP output
8oj7 transferase cryo-EM (2.46 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase-processivity factor complex in halted elongation state. SNAP output
8oja transferase cryo-EM (1.87 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase-processivity factor complex in exonuclease state. SNAP output
8ojb transferase cryo-EM (1.9 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase-processivity factor complex in exonuclease state active site. SNAP output
8ojc transferase cryo-EM (2.08 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase active site in alternative exonuclease state. SNAP output
8ojd transferase cryo-EM (2.46 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase beta-hairpin loop. SNAP output
8ok9 RNA binding protein X-ray (2.5 Å) Manakova E, Golovinas E, Poceviciute R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaite E, Jurgelaitis E, Grybauskas A, Venclovas C, Zaremba M (2024) "The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein." Nucleic Acids Res., 52, 2530-2545. doi: 10.1093/nar/gkad1241. Heterodimeric complex of archaeoglobus fulgidus argonaute protein af1318 (afago) with DNA and afago-n protein containing n-l1-l2 domains. SNAP output
8oki transcription cryo-EM (3.45 Å) Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D (2024) "Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment." Nucleic Acids Res., 52, 6017-6035. doi: 10.1093/nar/gkae282. cryo-EM structure of pyrococcus furiosus transcription elongation complex bound to spt4-5. SNAP output
8ol1 immune system cryo-EM (3.5 Å) Xu P, Liu Y, Liu C, Guey B, Li L, Melenec P, Ricci J, Ablasser A (2024) "The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation." Nature, 627, 873-879. doi: 10.1038/s41586-024-07112-w. Cgas-nucleosome in complex with spsb3-elobc (composite structure). SNAP output
8olx DNA binding protein cryo-EM (3.1 Å) Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC "MutSbeta bound to (CAG)2 DNA (canonical form)." Mutsbeta bound to (cag)2 DNA (canonical form). SNAP output
8om9 DNA binding protein cryo-EM (3.32 Å) Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC "MutSbeta bound to (CAG)2 DNA (open form)." Mutsbeta bound to (cag)2 DNA (open form). SNAP output
8oma DNA binding protein cryo-EM (3.29 Å) Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC "MutSbeta bound to 61bp homoduplex DNA." Mutsbeta bound to 61bp homoduplex DNA. SNAP output
8oo6 DNA binding protein cryo-EM (4.3 Å) Botto MM, Borsellini A, Lamers MH (2023) "A four-point molecular handover during Okazaki maturation." Nat.Struct.Mol.Biol., 30, 1505-1515. doi: 10.1038/s41594-023-01071-y. Pol i bound to extended and displaced DNA section - closed conformation. SNAP output
8oo9 DNA binding protein cryo-EM (3.2 Å) Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S (2023) "Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling." Science, 381, 313-319. doi: 10.1126/science.adf6287. Cryoem structure ino80core hexasome complex atpase-DNA refinement state1. SNAP output
8ooa DNA binding protein cryo-EM (3.18 Å) Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S (2023) "Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling." Science, 381, 313-319. doi: 10.1126/science.adf6287. Cryoem structure ino80core hexasome complex hexasome refinement state1. SNAP output
8oos DNA binding protein cryo-EM (3.29 Å) Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S (2023) "Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling." Science, 381, 313-319. doi: 10.1126/science.adf6287. Cryoem structure ino80core hexasome complex atpase-hexasome refinement state 2. SNAP output
8ooy DNA binding protein cryo-EM (4.0 Å) Botto MM, Borsellini A, Lamers MH (2023) "A four-point molecular handover during Okazaki maturation." Nat.Struct.Mol.Biol., 30, 1505-1515. doi: 10.1038/s41594-023-01071-y. Pol i bound to extended and displaced DNA section - open conformation. SNAP output
8osb transcription X-ray (2.9 Å) Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J (2024) "DNA-guided transcription factor cooperativity shapes face and limb mesenchyme." Cell, 187, 692. doi: 10.1016/j.cell.2023.12.032. Twist1-tcf4-alx4 complex on specific DNA. SNAP output
8osj gene regulation cryo-EM (6.2 Å) Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH (2023) "Cooperation between bHLH transcription factors and histones for DNA access." Nature, 619, 385-393. doi: 10.1038/s41586-023-06282-3. cryo-EM structure of clock-bmal1 bound to a nucleosomal e-box at position shl-6.2 (DNA conformation 1). SNAP output
8osk gene regulation cryo-EM (3.6 Å) Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH (2023) "Cooperation between bHLH transcription factors and histones for DNA access." Nature, 619, 385-393. doi: 10.1038/s41586-023-06282-3. cryo-EM structure of clock-bmal1 bound to a nucleosomal e-box at position shl+5.8 (composite map). SNAP output
8osl gene regulation cryo-EM (4.9 Å) Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH (2023) "Cooperation between bHLH transcription factors and histones for DNA access." Nature, 619, 385-393. doi: 10.1038/s41586-023-06282-3. cryo-EM structure of clock-bmal1 bound to the native por enhancer nucleosome (map 2, additional 3d classification and flexible refinement). SNAP output
8ots transcription cryo-EM (3.3 Å) Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH (2023) "Cooperation between bHLH transcription factors and histones for DNA access." Nature, 619, 385-393. doi: 10.1038/s41586-023-06282-3. Oct4 and myc-max co-bound to a nucleosome. SNAP output
8ott transcription cryo-EM (3.3 Å) Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH (2023) "Cooperation between bHLH transcription factors and histones for DNA access." Nature, 619, 385-393. doi: 10.1038/s41586-023-06282-3. Myc-max bound to a nucleosome at shl+5.8. SNAP output
8ovw cell cycle cryo-EM (3.4 Å) Dendooven T, Zhang Z, Yang J, McLaughlin SH, Schwab J, Scheres SHW, Yatskevich S, Barford D (2023) "Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere." Sci Adv, 9, eadg7480. doi: 10.1126/sciadv.adg7480. cryo-EM structure of cbf1-ccan bound topologically to centromeric DNA. SNAP output
8ow0 cell cycle cryo-EM (3.4 Å) Dendooven T, Zhang Z, Yang J, McLaughlin SH, Schwab J, Scheres SHW, Yatskevich S, Barford D (2023) "Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere." Sci Adv, 9, eadg7480. doi: 10.1126/sciadv.adg7480. cryo-EM structure of cbf1-ccan bound topologically to a centromeric cenp-a nucleosome. SNAP output
8ow4 DNA binding protein X-ray (2.75 Å) Lopez-Sagaseta J, Erausquin E, Hernandez-Morales S, Urdiciain A, Lasarte JJ, Lozano T "2.75 angstrom crystal structure of human NFAT1 with bound DNA." Not published. 2.75 angstrom crystal structure of human nfat1 with bound DNA. SNAP output
8ox0 DNA binding protein cryo-EM (2.52 Å) Hu H, van Roon AM, Ghanim GE, Ahsan B, Oluwole AO, Peak-Chew SY, Robinson CV, Nguyen THD (2023) "Structural basis of telomeric nucleosome recognition by shelterin factor TRF1." Sci Adv, 9, eadi4148. doi: 10.1126/sciadv.adi4148. Structure of apo telomeric nucleosome. SNAP output
8ox1 DNA binding protein cryo-EM (2.7 Å) Hu H, van Roon AM, Ghanim GE, Ahsan B, Oluwole AO, Peak-Chew SY, Robinson CV, Nguyen THD (2023) "Structural basis of telomeric nucleosome recognition by shelterin factor TRF1." Sci Adv, 9, eadi4148. doi: 10.1126/sciadv.adi4148. Structure of trf1core in complex with telomeric nucleosome. SNAP output
8oy3 lyase X-ray (2.16 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (3 picosecond pump-probe delay). SNAP output
8oy4 lyase X-ray (2.35 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (300 ps pump-probe delay). SNAP output
8oy5 lyase X-ray (2.27 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (1 nanosecond pump-probe delay). SNAP output
8oy6 lyase X-ray (2.35 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (3 nanosecond pump-probe delay). SNAP output
8oy7 lyase X-ray (2.36 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (10 nanosecond pump-probe delay). SNAP output
8oy8 lyase X-ray (2.39 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (30 nanosecond timepoint). SNAP output
8oy9 lyase X-ray (2.24 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (1 microsecond pump-probe delay). SNAP output
8oya lyase X-ray (2.18 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (10 microsecond pump probe delay). SNAP output
8oyb lyase X-ray (2.25 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (30 microsecond pump-probe delay). SNAP output
8oyc lyase X-ray (2.5 Å) Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Gunther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ (2023) "Time-resolved crystallography captures light-driven DNA repair." Science, 382, 1015-1020. doi: 10.1126/science.adj4270. Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (100 microsecond timpeoint). SNAP output
8oz7 antiviral protein X-ray (2.75 Å) Gapinska M, Zajko W, Skowronek K, Figiel M, Krawczyk PS, Egorov AA, Dziembowski A, Johansson MJO, Nowotny M (2024) "Structure-functional characterization of Lactococcus AbiA phage defense system." Nucleic Acids Res., 52, 4723-4738. doi: 10.1093/nar/gkae230. Abortive infection DNA polymerase abia from lactococcus lactis. SNAP output
8ozd DNA binding protein cryo-EM (3.89 Å) Ni D, Lu X, Stahlberg H, Ekundayo B (2023) "Activation mechanism of a short argonaute-TIR prokaryotic immune system." Sci Adv, 9, eadh9002. doi: 10.1126/sciadv.adh9002. Cryoem structure of sparta complex dimer-3. SNAP output
8p4a transcription cryo-EM (3.6 Å) Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P (2023) "Structural insights into human co-transcriptional capping." Mol.Cell, 83, 2464-2477.e5. doi: 10.1016/j.molcel.2023.06.002. Structural insights into human co-transcriptional capping - structure 1. SNAP output
8p4b transcription cryo-EM (3.2 Å) Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P (2023) "Structural insights into human co-transcriptional capping." Mol.Cell, 83, 2464-2477.e5. doi: 10.1016/j.molcel.2023.06.002. Structural insights into human co-transcriptional capping - structure 2. SNAP output
8p4c transcription cryo-EM (3.8 Å) Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P (2023) "Structural insights into human co-transcriptional capping." Mol.Cell, 83, 2464-2477.e5. doi: 10.1016/j.molcel.2023.06.002. Structural insights into human co-transcriptional capping - structure 3. SNAP output
8p4d transcription cryo-EM (3.6 Å) Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P (2023) "Structural insights into human co-transcriptional capping." Mol.Cell, 83, 2464-2477.e5. doi: 10.1016/j.molcel.2023.06.002. Structural insights into human co-transcriptional capping - structure 4. SNAP output
8p4e transcription cryo-EM (3.9 Å) Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P (2023) "Structural insights into human co-transcriptional capping." Mol.Cell, 83, 2464. doi: 10.1016/j.molcel.2023.06.002. Structural insights into human co-transcriptional capping - structure 5. SNAP output
8p4f transcription cryo-EM (4.0 Å) Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P (2023) "Structural insights into human co-transcriptional capping." Mol.Cell, 83, 2464. doi: 10.1016/j.molcel.2023.06.002. Structural insights into human co-transcriptional capping - structure 6. SNAP output
8p5q DNA binding protein X-ray (2.14 Å) Rieu P, Beretta VM, Caselli F, Thevenon E, Lucas J, Rizk M, Franchini E, Caporali E, Paleni C, Nanao MH, Kater MM, Dumas R, Zubieta C, Parcy F, Gregis V (2024) "The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development." Proc.Natl.Acad.Sci.USA, 121, e2310464121. doi: 10.1073/pnas.2310464121. Structure of an alog domain from arabidopsis thaliana in complex with DNA. SNAP output
8p62 replication cryo-EM (3.9 Å) Henrikus SS, Gross MH, Willhoft O, Puhringer T, Lewis JS, McClure AW, Greiwe JF, Palm G, Nans A, Diffley JFX, Costa A (2024) "Unwinding of a eukaryotic origin of replication visualized by cryo-EM." Nat.Struct.Mol.Biol., 31, 1265-1276. doi: 10.1038/s41594-024-01280-z. S. cerevisiae ssDNA-scmge after DNA replication initiation. SNAP output
8pbc recombination cryo-EM (2.61 Å) Appleby R, Joudeh L, Cobbett K, Pellegrini L (2023) "Structural basis for stabilisation of the RAD51 nucleoprotein filament by BRCA2." Nat Commun, 14, 7003. doi: 10.1038/s41467-023-42830-1. Rad51 filament on ssDNA bound by the brca2 c-terminus. SNAP output
8pbd recombination cryo-EM (2.83 Å) Appleby R, Joudeh L, Cobbett K, Pellegrini L (2023) "Structural basis for stabilisation of the RAD51 nucleoprotein filament by BRCA2." Nat Commun, 14, 7003. doi: 10.1038/s41467-023-42830-1. Rad51 filament on dsDNA bound by the brca2 c-terminus. SNAP output
8pbl transcription cryo-EM (2.87 Å) Woodgate J, Mosaei H, Brazda P, Stevenson-Jones F, Zenkin N (2024) "Translation selectively destroys non-functional transcription complexes." Nature, 626, 891-896. doi: 10.1038/s41586-023-07014-3. E. coli RNA polymerase elongation complex stalled at thymine dimer lesion. SNAP output
8pc5 transcription cryo-EM (3.02 Å) Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V (2023) "Multivalency of nucleosome recognition by LEDGF." Nucleic Acids Res., 51, 10011-10025. doi: 10.1093/nar/gkad674. H3k36me3 nucleosome-ledgf-p75 pwwp domain complex. SNAP output
8pc6 transcription cryo-EM (3.04 Å) Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V (2023) "Multivalency of nucleosome recognition by LEDGF." Nucleic Acids Res., 51, 10011-10025. doi: 10.1093/nar/gkad674. H3k36me3 nucleosome-ledgf-p75 pwwp domain complex - pose 2. SNAP output
8pde DNA binding protein X-ray (2.4 Å) Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A (2024) "Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA." J.Mol.Biol., 436, 168541. doi: 10.1016/j.jmb.2024.168541. Crystal structure of the mads-box-mef2 domain of mef2d bound to dsDNA and hdac4 deacetylase binding motif. SNAP output
8pdy transcription cryo-EM (2.8 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. E. coli RNA polymerase paused at ops site. SNAP output
8pen transcription cryo-EM (3.1 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Fully recruited rfah bound to e. coli transcription complex paused at ops site (alternative state of rfah). SNAP output
8peo transcription cryo-EM (2.69 Å) Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V (2023) "Multivalency of nucleosome recognition by LEDGF." Nucleic Acids Res., 51, 10011-10025. doi: 10.1093/nar/gkad674. H3k36me2 nucleosome-ledgf-p75 pwwp domain complex. SNAP output
8pep transcription cryo-EM (3.33 Å) Koutna E, Lux V, Kouba T, Skerlova J, Novacek J, Srb P, Hexnerova R, Svachova H, Kukacka Z, Novak P, Fabry M, Poepsel S, Veverka V (2023) "Multivalency of nucleosome recognition by LEDGF." Nucleic Acids Res., 51, 10011-10025. doi: 10.1093/nar/gkad674. H3k36me2 nucleosome-ledgf-p75 pwwp domain complex - pose 2. SNAP output
8pfg transcription cryo-EM (3.1 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Autoinhibited rfah bound to e. coli transcription complex paused at ops site (encounter complex), not fully complementary scaffold. SNAP output
8pfj transcription cryo-EM (3.4 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Fully recruited rfah bound to e. coli transcription complex paused at ops site (not fully complementary scaffold; alternative state of rfah). SNAP output
8ph9 transcription cryo-EM (3.0 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. E. coli RNA polymerase paused at ops site (non-complementary scaffold). SNAP output
8phk transcription cryo-EM (3.1 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Fully recruited rfah bound to e. coli transcription complex paused at ops site. SNAP output
8pi7 DNA binding protein X-ray (3.2 Å) Kind L, Molnes J, Tjora E, Raasakka A, Myllykoski M, Colclough K, Saint-Martin C, Adelfalk C, Dusatkova P, Pruhova S, Valtonen-Andre C, Bellanne-Chantelot C, Arnesen T, Kursula P, Njolstad PR (2024) "Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes." JCI Insight, 9. doi: 10.1172/jci.insight.175278. DNA binding domain of hnf-1a bound to p2-hnf4a promoter DNA variant (p2 -169c>t). SNAP output
8pi8 DNA binding protein X-ray (2.3 Å) Kind L, Molnes J, Tjora E, Raasakka A, Myllykoski M, Colclough K, Saint-Martin C, Adelfalk C, Dusatkova P, Pruhova S, Valtonen-Andre C, Bellanne-Chantelot C, Arnesen T, Kursula P, Njolstad PR (2024) "Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes." JCI Insight, 9. doi: 10.1172/jci.insight.175278. DNA binding domain of hnf-1a bound to p2-hnf4a promoter DNA. SNAP output
8pi9 DNA binding protein X-ray (2.8 Å) Kind L, Molnes J, Tjora E, Raasakka A, Myllykoski M, Colclough K, Saint-Martin C, Adelfalk C, Dusatkova P, Pruhova S, Valtonen-Andre C, Bellanne-Chantelot C, Arnesen T, Kursula P, Njolstad PR (2024) "Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes." JCI Insight, 9. doi: 10.1172/jci.insight.175278. DNA binding domain of hnf-1a bound to p2-hnf4a promoter DNA variant (p2 -181g>a). SNAP output
8pia DNA binding protein X-ray (2.8 Å) Kind L, Molnes J, Tjora E, Raasakka A, Myllykoski M, Colclough K, Saint-Martin C, Adelfalk C, Dusatkova P, Pruhova S, Valtonen-Andre C, Bellanne-Chantelot C, Arnesen T, Kursula P, Njolstad PR (2024) "Molecular mechanism of HNF-1A-mediated HNF4A gene regulation and promoter-driven HNF4A-MODY diabetes." JCI Insight, 9. doi: 10.1172/jci.insight.175278. DNA binding domain of hnf-1a bound to p2-hnf4a promoter DNA variant (p2 -181g>t). SNAP output
8pib transcription cryo-EM (2.6 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Autoinhibited rfah bound to e. coli transcription complex paused at ops site (encounter complex). SNAP output
8pid transcription cryo-EM (3.0 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Backtracked e. coli transcription complex paused at ops site and bound to rfah. SNAP output
8pil transcription cryo-EM (3.2 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. E. coli transcription complex paused at ops site and bound to rfah and nusa. SNAP output
8pim transcription cryo-EM (3.4 Å) Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH (2024) "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein." Nat Commun, 15, 3040. doi: 10.1038/s41467-024-47368-4. Fully recruited rfah bound to e. coli transcription complex paused at ops site (not complementary scaffold). SNAP output
8pj9 RNA binding protein cryo-EM (3.24 Å) Sasnauskas G, Gaizauskaite U, Tamulaitiene G "Structural basis for spacer acquisition in a type II-A CRISPR-Cas system." Cas9 bound to cognate DNA, streptococcus thermophilus dgcc 7710 crispr3 system. SNAP output
8pk1 DNA binding protein cryo-EM (3.17 Å) Sasnauskas G, Gaizauskaite U, Tamulaitiene G "Structural basis for spacer acquisition in a type II-A CRISPR-Cas system." Cas1-cas2 crispr integrase bound to prespacer DNA, streptococcus thermophilus dgcc 7710 crispr3 system. SNAP output
8pki DNA binding protein cryo-EM (2.58 Å) Kobayashi W, Sappler AH, Bollschweiler D, Kummecke M, Basquin J, Arslantas EN, Ruangroengkulrith S, Hornberger R, Duderstadt K, Tachibana K (2024) "Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition." Nat.Struct.Mol.Biol., 31, 757-766. doi: 10.1038/s41594-024-01239-0. cryo-EM structure of nr5a2-nucleosome complex shl+5.5. SNAP output
8pkj DNA binding protein cryo-EM (2.5 Å) Kobayashi W, Sappler AH, Bollschweiler D, Kummecke M, Basquin J, Arslantas EN, Ruangroengkulrith S, Hornberger R, Duderstadt K, Tachibana K (2024) "Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition." Nat.Struct.Mol.Biol., 31, 757-766. doi: 10.1038/s41594-024-01239-0. cryo-EM structure of the nucleosome containing nr5a2 motif at shl+5.5. SNAP output
8pm4 RNA binding protein cryo-EM (2.93 Å) Bigelyte G, Duchovska B, Zedaveinyte R, Sasnauskas G, Sinkunas T, Dalgediene I, Tamulaitiene G, Silanskas A, Kazlauskas D, Valancauskas L, Madariaga-Marcos J, Seidel R, Siksnys V, Karvelis T (2024) "Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing." Nucleic Acids Res., 52, 3234-3248. doi: 10.1093/nar/gkae016. cryo-EM structure of the cas12m-crrna-target DNA complex. SNAP output
8pm5 transcription X-ray (2.4 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to taaat DNA sequence. SNAP output
8pm7 transcription X-ray (1.7 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to taatc DNA sequence. SNAP output
8pmc transcription X-ray (1.85 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to taatt DNA sequence. SNAP output
8pmf transcription X-ray (0.95 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to DNA sequences. SNAP output
8pmn transcription X-ray (1.3 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to DNA sequences. SNAP output
8pmv transcription X-ray (2.1 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to taagc DNA sequence. SNAP output
8pn4 transcription X-ray (2.6 Å) Morgunova E, Yin Y, Popov A, Taipale J "transcription factor BARHL2 bound to DNA sequences." Transcription factor barhl2 bound to DNA sequences. SNAP output
8pna transcription X-ray (1.45 Å) Morgunova E, Popov A, Yin Y, Taipale J "transcription factor BARHL2 bound to different DNA sequences." Transcription factor barhl2 bound to taatg DNA sequence. SNAP output
8pnc transcription X-ray (2.05 Å) Morgunova E, Popov A, Yin Y, Taipale J "Transcription factor BARHL2 bound to different DNA sequences." Transcription factor barhl2 bound to taagt DNA sequence. SNAP output
8po7 hydrolase X-ray (2.26 Å) Xin BG, Huang LY, Yuan LG, Liu NN, Li HH, Ai X, Lei DS, Hou XM, Rety S, Xi XG (2024) "Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition." Nucleic Acids Res., 52, 3406-3418. doi: 10.1093/nar/gkae138. Structure of escherichia coli hrpa in complex with adp and dinucleotide dcdc. SNAP output
8po8 hydrolase X-ray (2.52 Å) Xin BG, Huang LY, Yuan LG, Liu NN, Li HH, Ai X, Lei DS, Hou XM, Rety S, Xi XG (2024) "Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition." Nucleic Acids Res., 52, 3406-3418. doi: 10.1093/nar/gkae138. Structure of escherichia coli hrpa in complex with adp and oligonucleotide poly(dc)11 forming an i-motif. SNAP output
8pop DNA binding protein cryo-EM (3.0 Å) Chechik M, Greive SJ, Antson AA, Jenkins HT (2024) "Structural basis for DNA recognition by a viral genome-packaging machine." Proc.Natl.Acad.Sci.USA, 121, e2406138121. doi: 10.1073/pnas.2406138121. Hk97 small terminase in complex with DNA. SNAP output
8pp6 gene regulation cryo-EM (3.18 Å) Ciapponi M, Karlukova E, Schkolziger S, Benda C, Muller J (2024) "Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1." Nat.Struct.Mol.Biol., 31, 1023-1027. doi: 10.1038/s41594-024-01258-x. Human rybp-prc1 bound to h2ak118ub1 nucleosome. SNAP output
8pp7 gene regulation cryo-EM (2.91 Å) Ciapponi M, Karlukova E, Schkolziger S, Benda C, Muller J (2024) "Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1." Nat.Struct.Mol.Biol., 31, 1023-1027. doi: 10.1038/s41594-024-01258-x. Human rybp-prc1 bound to mononucleosome. SNAP output
8ppt DNA binding protein cryo-EM (2.9 Å) Betancurt-Anzola L, Martinez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L (2023) "Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases." Nat Commun, 14, 8306. doi: 10.1038/s41467-023-44125-x. Pyrococcus abyssi DNA polymerase d (pold) in its editing mode bound to a primer-template substrate containing a mismatch. SNAP output
8ppu DNA binding protein cryo-EM (3.02 Å) Betancurt-Anzola L, Martinez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L (2023) "Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases." Nat Commun, 14, 8306. doi: 10.1038/s41467-023-44125-x. Pyrococcus abyssi DNA polymerase d (pold) in its editing mode bound to a primer-template substrate containing three consecutive mismatches. SNAP output
8ppv DNA binding protein cryo-EM (3.02 Å) Betancurt-Anzola L, Martinez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L (2023) "Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases." Nat Commun, 14, 8306. doi: 10.1038/s41467-023-44125-x. Intermediate conformer of pyrococcus abyssi DNA polymerase d (pold) bound to a primer-template substrate containing three consecutive mismatches. SNAP output
8pvv DNA binding protein cryo-EM (2.81 Å) Manakova E, Golovinas E, Poceviciute R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaite E, Jurgelaitis E, Grybauskas A, Venclovas C, Zaremba M (2024) "The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein." Nucleic Acids Res., 52, 2530-2545. doi: 10.1093/nar/gkad1241. Archaeoglobus fulgidus afago complex with afago-n protein (fafago) bound with 30 nt RNA guide and 51 nt DNA target. SNAP output
8pw0 DNA binding protein X-ray (2.2 Å) Mota C, Webster M, Saidi M, Kapp U, Zubieta C, Giachin G, Manso JA, de Sanctis D (2024) "Metal ion activation and DNA recognition by the Deinococcus radiodurans manganese sensor DR2539." Febs J., 291, 3384-3402. doi: 10.1111/febs.17140. Manganese-dependent transcriptional repressor dr2539 complexed with manganese and bound to dr1709 promotor. SNAP output
8q2n DNA binding protein cryo-EM (2.98 Å) Sasnauskas G, Gaizauskaite U, Tamulaitiene G "Structural basis for spacer acquisition in a type II-A CRISPR-Cas system." Cas1-cas2 crispr integrase bound to prespacer and target DNA, streptococcus thermophilus dgcc 7710 crispr3 system. SNAP output
8q3w DNA binding protein cryo-EM (3.18 Å) de la Gandara A, Spinola-Amilibia M, Araujo-Bazan L, Nunez-Ramirez R, Berger JM, Arias-Palomo E (2024) "Molecular basis for transposase activation by a dedicated AAA+ ATPase." Nature, 630, 1003-1011. doi: 10.1038/s41586-024-07550-6. Atp-bound istb in complex to duplex DNA. SNAP output
8q40 DNA binding protein X-ray (2.21 Å) Jungfer K, Sigg A, Jinek M (2024) "Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2." Nucleic Acids Res., 52, 462-473. doi: 10.1093/nar/gkad1102. Crystal structure of ca4 activated can2 in complex with a cleaved DNA substrate. SNAP output
8q41 DNA binding protein X-ray (2.38 Å) Jungfer K, Sigg A, Jinek M (2024) "Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2." Nucleic Acids Res., 52, 462-473. doi: 10.1093/nar/gkad1102. Crystal structure of can2 (e341a) bound to ca4 and tttaaa ssDNA. SNAP output
8q42 DNA binding protein X-ray (1.97 Å) Jungfer K, Sigg A, Jinek M (2024) "Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2." Nucleic Acids Res., 52, 462-473. doi: 10.1093/nar/gkad1102. Crystal structure of ca4-bound can2 (e341a) in complex with oligo-a DNA. SNAP output
8q43 DNA binding protein X-ray (2.28 Å) Jungfer K, Sigg A, Jinek M (2024) "Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2." Nucleic Acids Res., 52, 462-473. doi: 10.1093/nar/gkad1102. Crystal structure of ca4-bound can2 (e341a) in complex with oligo-c DNA. SNAP output
8q44 DNA binding protein X-ray (2.3 Å) Jungfer K, Sigg A, Jinek M (2024) "Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2." Nucleic Acids Res., 52, 462-473. doi: 10.1093/nar/gkad1102. Crystal structure of ca4-bound can2 (e364r) in complex with oligo-t DNA. SNAP output
8q5o hydrolase X-ray (2.33 Å) Szafran K, Rafalski D, Skowronek K, Wojciechowski M, Kazrani AA, Gilski M, Xu SY, Bochtler M (2024) "Structural analysis of the BisI family of modification dependent restriction endonucleases." Nucleic Acids Res., 52, 9103-9118. doi: 10.1093/nar/gkae634. N-terminal domain of restriction endonuclease eco15i with tetra-methylated target DNA.. SNAP output
8q63 transcription cryo-EM (3.68 Å) Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K (2023) "Structures illustrate step-by-step mitochondrial transcription initiation." Nature, 622, 872-879. doi: 10.1038/s41586-023-06643-y. cryo-EM structure of ic8', a second state of yeast mitochondrial RNA polymerase transcription initiation complex with 8-mer RNA, pppgpgpupapapapupg. SNAP output
8q72 DNA binding protein cryo-EM (4.17 Å) Roisne-Hamelin F, Liu HW, Taschner M, Li Y, Gruber S (2024) "Structural basis for plasmid restriction by SMC JET nuclease." Mol.Cell, 84, 883. doi: 10.1016/j.molcel.2024.01.009. E. coli plasmid-borne jetabcd(e248a) core in a cleavage-competent state. SNAP output
8q7d virus cryo-EM (3.07 Å) Cienikova Z, Novacek J, Siborova M, Popelarova B, Fuzik T, Benesik M, Bardy P, Plevka P "Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812." Neck of phage 812 after tail contraction (c12). SNAP output
8q9n transcription X-ray (1.51 Å) Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A (2024) "Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA." J.Mol.Biol., 436, 168541. doi: 10.1016/j.jmb.2024.168541. Crystal structure of the mads-box-mef2 domain of mef2d bound to dsDNA and mitr deacetylase binding motif mutant l151v.. SNAP output
8q9p transcription X-ray (2.2 Å) Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A (2024) "Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA." J.Mol.Biol., 436, 168541. doi: 10.1016/j.jmb.2024.168541. Crystal structure of the mads-box-mef2 domain of mef2d bound to dsDNA and hdac5 deacetylase binding motif. SNAP output
8q9q transcription X-ray (2.11 Å) Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A (2024) "Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA." J.Mol.Biol., 436, 168541. doi: 10.1016/j.jmb.2024.168541. Crystal structure of the mads-box-mef2 domain of mef2d bound to dsDNA and hdac7 deacetylase binding motif. SNAP output
8q9r transcription X-ray (2.25 Å) Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A (2024) "Folding of Class IIa HDAC Derived Peptides into alpha-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA." J.Mol.Biol., 436, 168541. doi: 10.1016/j.jmb.2024.168541. Crystal structure of mads-box-mef2d n-terminal domain bound to dsDNA and hdac9 deacetylase binding motif. SNAP output
8qa9 DNA binding protein X-ray (2.7 Å) McLean TC, Mundy JEA, Lawson DM, Le TBK "Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA." Crystal structure of the rk2 plasmid encoded co-complex of the c-terminally truncated transcriptional repressor protein korb complexed with the partner repressor protein kora bound to oa-DNA. SNAP output
8qbk immune system cryo-EM (2.99 Å) Carabias A, Camara-Wilpert S, Mestre MR, Lopez-Mendez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SH, Nielsen ML, Pinilla-Redondo R, Montoya G (2024) "Retron-Eco1 assembles NAD + -hydrolyzing filaments that provide immunity against bacteriophages." Mol.Cell, 84, 2185. doi: 10.1016/j.molcel.2024.05.001. Retron-eco1 filament with adp-ribosylated effector (local map with 1 segment). SNAP output
8qbl immune system cryo-EM (2.66 Å) Carabias A, Camara-Wilpert S, Mestre MR, Lopez-Mendez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SH, Nielsen ML, Pinilla-Redondo R, Montoya G (2024) "Retron-Eco1 assembles NAD + -hydrolyzing filaments that provide immunity against bacteriophages." Mol.Cell, 84, 2185. doi: 10.1016/j.molcel.2024.05.001. Retron-eco1 filament with inactive effector (e106a, 2 segments). SNAP output
8qbm immune system cryo-EM (3.09 Å) Carabias A, Camara-Wilpert S, Mestre MR, Lopez-Mendez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SH, Nielsen ML, Pinilla-Redondo R, Montoya G (2024) "Retron-Eco1 assembles NAD + -hydrolyzing filaments that provide immunity against bacteriophages." Mol.Cell, 84, 2185. doi: 10.1016/j.molcel.2024.05.001. Retron-eco1 filament with adp-ribosylated effector (full map with 2 segments). SNAP output
8qdx isomerase cryo-EM (3.0 Å) Vayssieres M, Marechal N, Yun L, Lopez Duran B, Murugasamy NK, Fogg JM, Zechiedrich L, Nadal M, Lamour V (2024) "Structural basis of DNA crossover capture by Escherichia coli DNA gyrase." Science, 384, 227-232. doi: 10.1126/science.adl5899. E. coli DNA gyrase bound to a DNA crossover. SNAP output
8qek virus cryo-EM (3.6 Å) Cienikova Z, Novacek J, Siborova M, Popelarova B, Fuzik T, Benesik M, Bardy P, Plevka P "Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812." Neck and tail of phage 812 after tail contraction (composite). SNAP output
8qem virus cryo-EM (3.96 Å) Cienikova Z, Novacek J, Siborova M, Popelarova B, Fuzik T, Benesik M, Bardy P, Plevka P "Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812." Neck channel of phage 812 after tail contraction (c1). SNAP output
8qg0 DNA binding protein cryo-EM (3.43 Å) Manakova E, Golovinas E, Poceviciute R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaite E, Jurgelaitis E, Grybauskas A, Venclovas C, Zaremba M (2024) "The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein." Nucleic Acids Res., 52, 2530-2545. doi: 10.1093/nar/gkad1241. Archaeoglobus fulgidus afago complex with afago-n protein (fafago) bound with 17 nt RNA guide and 17 nt DNA target. SNAP output
8qlp immune system cryo-EM (3.14 Å) Finocchio G, Koopal B, Potocnik A, Heijstek C, Westphal AH, Jinek M, Swarts DC (2024) "Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA." Nucleic Acids Res., 52, 2012-2029. doi: 10.1093/nar/gkad1248. Cryoem structure of the RNA-DNA bound sparta (babago-tir-apaz) tetrameric complex. SNAP output
8qmb isomerase X-ray (2.0 Å) Najmudin S, Pan XS, Wang B, Chayen NE, Fisher LM, Sanderson MR "The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin." Nucleant-assisted 2.0 Å resolution structure of the streptococcus pneumoniae topoisomerase iv-v18mer DNA complex with the novel fluoroquinolone delafloxacin. SNAP output
8qmc isomerase X-ray (2.402 Å) Najmudin S, Pan XS, Wang B, Chayen NE, Fisher LM, Sanderson MR "The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin." High resolution structure of the streptococcus pneumoniae topoisomerase iv-complex with the v-site 18mer dsDNA and novel fluoroquinolone delafloxacin. SNAP output
8qqi DNA binding protein cryo-EM (2.9 Å) Bakker AT, Kotsogianni I, Avalos M, Punt JM, Liu B, Piermarini D, Gagestein B, Slingerland CJ, Zhang L, Willemse JJ, Ghimire LB, van den Berg RJHBN, Janssen APA, Ottenhoff THM, van Boeckel CAA, van Wezel GP, Ghilarov D, Martin NI, van der Stelt M (2024) "Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria." Nat.Chem., 16, 1462-1472. doi: 10.1038/s41557-024-01516-x. E.coli DNA gyrase in complex with 217 bp substrate DNA and lei-800. SNAP output
8qqs isomerase cryo-EM (2.9 Å) Vayssieres M, Marechal N, Yun L, Lopez Duran B, Murugasamy NK, Fogg JM, Zechiedrich L, Nadal M, Lamour V (2024) "Structural basis of DNA crossover capture by Escherichia coli DNA gyrase." Science, 384, 227-232. doi: 10.1126/science.adl5899. E. coli DNA gyrase bound to a linear part of a DNA minicircle. SNAP output
8qqu isomerase cryo-EM (2.9 Å) Vayssieres M, Marechal N, Yun L, Lopez Duran B, Murugasamy NK, Fogg JM, Zechiedrich L, Nadal M, Lamour V (2024) "Structural basis of DNA crossover capture by Escherichia coli DNA gyrase." Science, 384, 227-232. doi: 10.1126/science.adl5899. Asymetric subunit of e. coli DNA gyrase bound to a linear part of a DNA minicircle. SNAP output
8qsz RNA binding protein cryo-EM (2.67 Å) Carrique L, Kus K, Vasiljeva L, Grimes JM "DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts." Structure of s. pombe RNA polymerase ii in complex with dsif and rat1-rai1. SNAP output
8qti transcription cryo-EM (3.09 Å) Koval T, Dohnalek L, Libor K, Kouba T "Molecular insights into RNA polymerase recycling by mycobacterial HelD." Mycobacterium smegnatis rnap open promoter complex with sigmaa and rbpa. SNAP output
8qu6 transcription cryo-EM (3.45 Å) Koval T, Dohnalek L, Libor K, Kouba T "Molecular insights into RNA polymerase recycling by mycobacterial HelD." Mycobacterium smegnatis RNA polymerase transcription initiation complex with sigmaa, rbpa, held and an upstream-fork promoter fragment. SNAP output
8que RNA binding protein cryo-EM (3.3 Å) de Martin Garrido N, Chen CS, Ramlaul K, Aylett CHS, Yakunina M (2024) "Structure of the Bacteriophage PhiKZ Non-virion RNA Polymerase Transcribing from its Promoter p119L." J.Mol.Biol., 436, 168713. doi: 10.1016/j.jmb.2024.168713. Structure of the bacteriophage phikz non-virion RNA polymerase bound to DNA and RNA. SNAP output
8qwe biosynthetic protein cryo-EM (3.14 Å) Jabalera Y, Tascon I, Samperio S, Lopez-Alonso JP, Gonzalez-Lopez M, Aransay AM, Abascal-Palacios G, Beisel CL, Ubarretxena-Belandia I, Perez-Jimenez R (2024) "A resurrected ancestor of Cas12a expands target access and substrate recognition for nucleic acid editing and detection." Nat.Biotechnol. doi: 10.1038/s41587-024-02461-3. Ternary complex of rechb - crrna - target dsDNA. SNAP output
8qwf biosynthetic protein cryo-EM (3.08 Å) Jabalera Y, Tascon I, Samperio S, Lopez-Alonso JP, Gonzalez-Lopez M, Aransay AM, Abascal-Palacios G, Beisel CL, Ubarretxena-Belandia I, Perez-Jimenez R (2024) "A resurrected ancestor of Cas12a expands target access and substrate recognition for nucleic acid editing and detection." Nat.Biotechnol. doi: 10.1038/s41587-024-02461-3. Rechb - crrna - target dsDNA complex in the presence of collateral dsDNA. SNAP output
8qzm DNA binding protein cryo-EM (3.1 Å) Wapenaar H, Clifford G, Rolls W, Burdett H, Zhang Y, Deak G, Zhou J, Taylor MRD, Mills J, Watson JA, Kumar D, Das A, Valsakumar D, Braham J, Voigt P, Wilson MD "The N-terminal region of DNMT3A combines multiple chromatin-reading motifs to guide recruitment." Structure of dnmt3a1 udr region bound to h2ak119ub nucleosome. SNAP output
8r0s viral protein X-ray (2.35 Å) Prabaharan C, Figiel M, Szczepanowski RH, Skowronek K, Zajko W, Thangaraj V, Chamera S, Nowak E, Nowotny M (2024) "Structural and biochemical characterization of cauliflower mosaic virus reverse transcriptase." J.Biol.Chem., 300, 107555. doi: 10.1016/j.jbc.2024.107555. Structure of reverse transcriptase from cauliflower mosaic virus in complex with RNA-DNA hybrid. SNAP output
8r1x DNA binding protein NMR Hill G, Yang JC, Easton L, Cerdan R, McLaughlin S, Stott K, Travers A, Neuhaus D (2024) "A Single Interfacial Point Mutation Rescues Solution Structure Determination of the Complex of HMG-D with a DNA Bulge." Chembiochem, e202400395. doi: 10.1002/cbic.202400395. Solution structure and chemical shift assignments for hmg-d y12f mutant complexed to a 14:12 da2 bulge DNA. SNAP output
8r2m transcription cryo-EM (3.44 Å) Koval T, Dohnalek L, Libor K, Kouba T "Molecular insights into RNA polymerase recycling by mycobacterial HelD." Mycobacterium smegnatis RNA polymerase transcription initiation complex with sigmaa, rbpa, held n-terminal domain and an upstream-fork promoter fragment; state iii conformation. SNAP output
8r3g DNA binding protein cryo-EM (4.4 Å) Soltysova M, Skerlova J, Pachl P, Skubnik K, Fabry M, Sieglova I, Farolfi M, Grishkovskaya I, Babiak M, Novacek J, Krasny L, Rezacova P (2024) "Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function." Nucleic Acids Res., 52, 7305-7320. doi: 10.1093/nar/gkae434. Central glycolytic genes regulator (cggr) bound to DNA operator. SNAP output
8r3m transcription cryo-EM (3.49 Å) Koval T, Dohnalek L, Libor K, Kouba T "Molecular insights into RNA polymerase recycling by mycobacterial HelD." Mycobacterium smegnatis RNA polymerase transcription initiation complex with sigmaa, rbpa, held n-terminal, co and pch loop domain, and an upstream-fork promoter fragment; state iii conformation. SNAP output
8r6p transcription cryo-EM (3.16 Å) Koval T, Dohnalek L, Libor K, Kouba T "Molecular insights into RNA polymerase recycling by mycobacterial HelD." Mycobacterium smegnatis RNA polymerase rp2-like transcription initiation complex with sigmaa, rbpa, held n-terminal domain and open promoter DNA. SNAP output
8r6r transcription cryo-EM (3.89 Å) Koval T, Dohnalek L, Libor K, Kouba T "Molecular insights into RNA polymerase recycling by mycobacterial HelD." Mycobacterium smegnatis RNA polymerase rp2-like transcription initiation complex with sigmaa, rbpa and open promoter DNA. SNAP output
8r7v DNA binding protein cryo-EM (3.12 Å) Haque T, Brace G "Identification of orthosteric inhibitors of MutSbeta ATPase function." Mutsbeta bound to compound chdi-00898647 in the canonical DNA-mismatch bound form. SNAP output
8r7y DNA binding protein X-ray (3.7 Å) Soltysova M, Skerlova J, Pachl P, Skubnik K, Fabry M, Sieglova I, Farolfi M, Grishkovskaya I, Babiak M, Novacek J, Krasny L, Rezacova P (2024) "Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function." Nucleic Acids Res., 52, 7305-7320. doi: 10.1093/nar/gkae434. Deoxyribonucleoside regulator deor in complex with the DNA operator. SNAP output
8ram gene regulation cryo-EM (2.8 Å) Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P (2024) "Mechanism of polyadenylation-independent RNA polymerase II termination." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01409-0. Structure of sen1 bound RNA polymerase ii pre-termination complex. SNAP output
8rap gene regulation cryo-EM (4.3 Å) Rengachari S, Hainthaler T, Oberthuer C, Lidschreiber M, Cramer P (2024) "Mechanism of polyadenylation-independent RNA polymerase II termination." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01409-0. Structure of sen1-adp.bef3 bound RNA polymerase ii pre-termination complex. SNAP output
8rc2 gene regulation cryo-EM (3.1 Å) Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P (2024) "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference." Nat Commun, 15, 9306. doi: 10.1038/s41467-024-53778-1. DNA bound type iv-a3 crispr effector complex from k. pneumoniae. SNAP output
8rc3 gene regulation cryo-EM (3.0 Å) Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P (2024) "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference." Nat Commun, 15, 9306. doi: 10.1038/s41467-024-53778-1. DNA bound type iv-a1 crispr effector complex from p. oleovorans. SNAP output
8rcd DNA binding protein cryo-EM (3.2 Å) Hanthi YW, Ramirez-Otero MA, Appleby R, De Antoni A, Joudeh L, Sannino V, Waked S, Ardizzoia A, Barra V, Fachinetti D, Pellegrini L, Costanzo V (2024) "RAD51 protects abasic sites to prevent replication fork breakage." Mol.Cell, 84, 3026-3043.e11. doi: 10.1016/j.molcel.2024.07.004. Rad51 nucleoprotein filament on abasic single-stranded DNA. SNAP output
8rcf DNA binding protein cryo-EM (3.4 Å) Hanthi YW, Ramirez-Otero MA, Appleby R, De Antoni A, Joudeh L, Sannino V, Waked S, Ardizzoia A, Barra V, Fachinetti D, Pellegrini L, Costanzo V (2024) "RAD51 protects abasic sites to prevent replication fork breakage." Mol.Cell, 84, 3026-3043.e11. doi: 10.1016/j.molcel.2024.07.004. Rad51 nucleoprotein filament on double-stranded abasic DNA. SNAP output
8rdu DNA binding protein cryo-EM (2.3 Å) Tenjo-Castano F, Sofos N, Stutzke LS, Temperini P, Fuglsang A, Pape T, Mesa P, Montoya G (2024) "Conformational landscape of the type V-K CRISPR-associated transposon integration assembly." Mol.Cell, 84, 2353. doi: 10.1016/j.molcel.2024.05.005. Conformational landscape of the type v-k crispr-associated transposonintegration assembly cast v-k composite map. SNAP output
8re4 transcription cryo-EM (2.8 Å) Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X (2024) "Structural basis of sigma 54 displacement and promoter escape in bacterial transcription." Proc.Natl.Acad.Sci.USA, 121, e2309670120. doi: 10.1073/pnas.2309670120. cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex. SNAP output
8rea transcription cryo-EM (3.4 Å) Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X (2024) "Structural basis of sigma 54 displacement and promoter escape in bacterial transcription." Proc.Natl.Acad.Sci.USA, 121, e2309670120. doi: 10.1073/pnas.2309670120. cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt post-translocated complex. SNAP output
8reb transcription cryo-EM (3.4 Å) Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X (2024) "Structural basis of sigma 54 displacement and promoter escape in bacterial transcription." Proc.Natl.Acad.Sci.USA, 121, e2309670120. doi: 10.1073/pnas.2309670120. cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex. SNAP output
8rec transcription cryo-EM (3.5 Å) Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X (2024) "Structural basis of sigma 54 displacement and promoter escape in bacterial transcription." Proc.Natl.Acad.Sci.USA, 121, e2309670120. doi: 10.1073/pnas.2309670120. cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex. SNAP output
8red transcription cryo-EM (3.9 Å) Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X (2024) "Structural basis of sigma 54 displacement and promoter escape in bacterial transcription." Proc.Natl.Acad.Sci.USA, 121, e2309670120. doi: 10.1073/pnas.2309670120. cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 8nt complex. SNAP output
8ree transcription cryo-EM (3.8 Å) Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X (2024) "Structural basis of sigma 54 displacement and promoter escape in bacterial transcription." Proc.Natl.Acad.Sci.USA, 121, e2309670120. doi: 10.1073/pnas.2309670120. cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex. SNAP output
8rev DNA binding protein cryo-EM (3.1 Å) Kuper J, Hove T, Maidl S, Neitz H, Sauer F, Kempf M, Schroeder T, Greiter E, Hobartner C, Kisker C (2024) "XPD stalled on cross-linked DNA provides insight into damage verification." Nat.Struct.Mol.Biol., 31, 1580-1588. doi: 10.1038/s41594-024-01323-5. Structure of xpd stalled at a y-fork DNA containing a interstrand crosslink. SNAP output
8rfj gene regulation cryo-EM (3.18 Å) Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P (2024) "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference." Nat Commun, 15, 9306. doi: 10.1038/s41467-024-53778-1. DNA bound type iv-a1 crispr effector complex with the ding helicase from p. oleovorans. SNAP output
8rjw DNA binding protein cryo-EM (2.3 Å) Liang CC, Greenhough LA, Masino L, Maslen S, Bajrami I, Tuppi M, Skehel M, Taylor IA, West SC (2024) "Mechanism of single-stranded DNA annealing by RAD52-RPA complex." Nature, 629, 697-703. doi: 10.1038/s41586-024-07347-7. Human rad52 open ring - ssDNA complex. SNAP output
8rkt DNA binding protein cryo-EM (2.35 Å) Tenjo-Castano F, Sofos N, Stutzke LS, Temperini P, Fuglsang A, Pape T, Mesa P, Montoya G (2024) "Conformational landscape of the type V-K CRISPR-associated transposon integration assembly." Mol.Cell, 84, 2353. doi: 10.1016/j.molcel.2024.05.005. Conformational landscape of the type v-k crispr-associated transposonintegration assembly cast v-k cas12k domain local-refinement map. SNAP output
8rku DNA binding protein cryo-EM (2.3 Å) Tenjo-Castano F, Sofos N, Stutzke LS, Temperini P, Fuglsang A, Pape T, Mesa P, Montoya G (2024) "Conformational landscape of the type V-K CRISPR-associated transposon integration assembly." Mol.Cell, 84, 2353. doi: 10.1016/j.molcel.2024.05.005. Conformational landscape of the type v-k crispr-associated transposonintegration assembly cast v-k tnsc domain local-refinement map. SNAP output
8rkv DNA binding protein cryo-EM (3.11 Å) Tenjo-Castano F, Sofos N, Stutzke LS, Temperini P, Fuglsang A, Pape T, Mesa P, Montoya G (2024) "Conformational landscape of the type V-K CRISPR-associated transposon integration assembly." Mol.Cell, 84, 2353. doi: 10.1016/j.molcel.2024.05.005. Conformational landscape of the type v-k crispr-associated transposonintegration assembly cast v-k tnsb domain local-refinement map. SNAP output
8rm6 DNA binding protein X-ray (2.05 Å) Lee XY, Van Eynde W, Helsen C, Willems H, Peperstraete K, De Block S, Voet A, Claessens F (2024) "Structural mechanism underlying variations in DNA binding by the androgen receptor." J.Steroid Biochem.Mol.Biol., 241, 106499. doi: 10.1016/j.jsbmb.2024.106499. Crystal structure of human androgen receptor DNA binding domain bound to its response element: c3(1)are. SNAP output
8rm7 structural protein X-ray (2.25 Å) Lee XY, Van Eynde W, Helsen C, Willems H, Peperstraete K, De Block S, Voet A, Claessens F (2024) "Structural mechanism underlying variations in DNA binding by the androgen receptor." J.Steroid Biochem.Mol.Biol., 241, 106499. doi: 10.1016/j.jsbmb.2024.106499. Crystal structure of human androgen receptor DNA binding domain bound to its response element: mmtv-177 gre-are. SNAP output
8rpx hydrolase X-ray (1.81 Å) Szafran K, Rafalski D, Skowronek K, Wojciechowski M, Kazrani AA, Gilski M, Xu SY, Bochtler M (2024) "Structural analysis of the BisI family of modification dependent restriction endonucleases." Nucleic Acids Res., 52, 9103-9118. doi: 10.1093/nar/gkae634. Nhoi restriction endonuclease in complex with quadruply methylated DNA target. SNAP output
8rxd DNA binding protein cryo-EM (3.13 Å) Rosa LT, Vernhes E, Soulet AL, Polard P, Fronzes R (2024) "Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria." Embo J. doi: 10.1038/s44318-024-00264-5. Comm helicase from legionella pneumophila, coordinating dsDNA and amp-pnp. SNAP output
8rxk DNA binding protein cryo-EM (3.23 Å) Rosa LT, Vernhes E, Soulet AL, Polard P, Fronzes R (2024) "Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria." Embo J. doi: 10.1038/s44318-024-00264-5. Comm helicase from legionella pneumophila, coordinating dsDNA and amp-pnp. SNAP output
8rz7 DNA binding protein cryo-EM (3.37 Å) Lee J-H, Thomsen M, Daub H, Steinbacher S, Sztyler A, Thieulin-Pardo G, Neudegger T, Plotnikov N, Iyer RR, Wilkinson H, Monteagudo E, Felsenfeld DP, Haque T, Finley M, Dominguez C, Vogt TF, Prasad BC "(CAG)2 DNA-bound MutSbeta in open form with kinked MSH2 clamp." (cag)2 DNA-bound mutsbeta in open form with kinked msh2 clamp. SNAP output
8rzv RNA binding protein X-ray (1.51 Å) Dunnett L, Prischi F "Structure of UP1 S4ES6E phosphomimetic mutant in complex with human telomeric repeat DNA." Structure of up1 s4es6e phosphomimetic mutant in complex with human telomeric repeat DNA. SNAP output
8s09 replication cryo-EM (3.1 Å) Weissmann F, Greiwe JF, Puehringer T, Eastwood EL, Couves EC, Miller TCR, Diffley JFX, Costa A (2024) "MCM Double Hexamer Loading Visualised with Human Proteins." Nature. H. sapiens mcm2-7 double hexamer bound to double stranded DNA. SNAP output
8s0c replication cryo-EM (4.0 Å) Weissmann F, Greiwe JF, Puehringer T, Eastwood EL, Couves EC, Miller TCR, Diffley JFX, Costa A (2024) "MCM Double Hexamer Loading Visualised with Human Proteins." Nature. H. sapiens orc1-5 bound to double stranded DNA as part of the mcm-orc complex. SNAP output
8s0e replication cryo-EM (3.8 Å) Weissmann F, Greiwe JF, Puehringer T, Eastwood EL, Couves EC, Miller TCR, Diffley JFX, Costa A (2024) "MCM Double Hexamer Loading Visualised with Human Proteins." Nature. H. sapiens occm bound to double stranded DNA. SNAP output
8s0f replication cryo-EM (4.1 Å) Weissmann F, Greiwe JF, Puehringer T, Eastwood EL, Couves EC, Miller TCR, Diffley JFX, Costa A (2024) "MCM Double Hexamer Loading Visualised with Human Proteins." Nature. H. sapiens oc1m bound to double stranded DNA. SNAP output
8s35 antiviral protein cryo-EM (2.9 Å) Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P (2024) "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference." Nat Commun, 15, 9306. doi: 10.1038/s41467-024-53778-1. DNA-bound type iv-a3 crispr effector in complex with ding helicase from k. pneumoniae (state i). SNAP output
8s36 antiviral protein cryo-EM (2.9 Å) Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P (2024) "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference." Nat Commun, 15, 9306. doi: 10.1038/s41467-024-53778-1. DNA-bound type iv-a3 crispr effector in complex with ding helicase from k. pneumoniae (state ii). SNAP output
8s37 antiviral protein cryo-EM (2.9 Å) Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P (2024) "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference." Nat Commun, 15, 9306. doi: 10.1038/s41467-024-53778-1. DNA-bound type iv-a3 crispr effector in complex with ding helicase from k. pneumoniae (state iii). SNAP output
8s4t DNA binding protein X-ray (2.67 Å) Breidenstein A, Lamy A, Bader CP, Sun WS, Wanrooij PH, Berntsson RP (2024) "PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs." Life Sci Alliance, 7. doi: 10.26508/lsa.202402693. DNA bound structure of prge from plasmid pcf10. SNAP output
8s52 transcription cryo-EM (2.9 Å) Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P (2024) "Three-step mechanism of promoter escape by RNA polymerase II." Mol.Cell, 84, 1699-1710.e6. doi: 10.1016/j.molcel.2024.03.016. RNA polymerase ii core initially transcribing complex with an ordered RNA of 10 nt. SNAP output
8s55 transcription cryo-EM (3.4 Å) Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P (2024) "Three-step mechanism of promoter escape by RNA polymerase II." Mol.Cell, 84, 1699-1710.e6. doi: 10.1016/j.molcel.2024.03.016. RNA polymerase ii early elongation complex bound to tfiie and tfiif - state a (composite structure). SNAP output
8s5n transcription cryo-EM (3.4 Å) Zhan Y, Grabbe F, Oberbeckmann E, Dienemann C, Cramer P (2024) "Three-step mechanism of promoter escape by RNA polymerase II." Mol.Cell, 84, 1699-1710.e6. doi: 10.1016/j.molcel.2024.03.016. RNA polymerase ii core initially transcribing complex with an ordered RNA of 12 nt. SNAP output
8s84 transferase X-ray (2.35 Å) Gutfreund C, Betz K (2024) "Structural Insights into a DNA Polymerase Reading the Xeno Nucleic Acid HNA." Nucleic Acids Res. Kod-h4 DNA polymerase mutant in a ternary complex with DNA-DNA and non-hydrolyzable triphosphate. SNAP output
8s8w viral protein X-ray (2.1 Å) Kremling V, Falke S, Fernandez-Garcia Y, Ehrt C, Kiene A, Klopprogge B, Scheer E, Barthels F, Middendorf P, Kuhn S, Gunther S, Rarey M, Chapman HN, Oberthur D, Sprenger J (2024) "SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery." Elife. doi: 10.7554/elife.98310.1. Sars-cov-2 nsp10-16 methyltransferase in complex with sangivamycin and m7gpppa-RNA (cap0-RNA). SNAP output
8s8x viral protein X-ray (1.99 Å) Kremling V, Falke S, Fernandez-Garcia Y, Ehrt C, Kiene A, Klopprogge B, Scheer E, Barthels F, Middendorf P, Kuhn S, Gunther S, Rarey M, Chapman HN, Oberthur D, Sprenger J (2024) "SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery." Elife. doi: 10.7554/elife.98310.1. Sars-cov-2 nsp10-16 methyltransferase in complex with toyocamycin and m7gpppa-RNA (cap0-RNA). SNAP output
8s9i DNA binding protein X-ray (3.53 Å) He X, Yun MK, White SW "Crystal structure of the gp32 C-terminal peptide/Dda/dT8." Crystal structure of the gp32 c-terminal peptide-dda-dt8. SNAP output
8scg replication-DNA X-ray (2.0 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 0h (ground state). SNAP output
8sci replication-DNA X-ray (2.67 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 1h. SNAP output
8scj replication-DNA X-ray (2.68 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 2h. SNAP output
8sck replication-DNA X-ray (2.3 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 4h. SNAP output
8scl replication-DNA X-ray (2.44 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 6h. SNAP output
8scm replication-DNA X-ray (2.3 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 8h. SNAP output
8scn replication-DNA X-ray (2.3 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment mutant f710y-d598a with 3'-amino primer, dgtp, and calcium time-resolved 24h (product state). SNAP output
8sco replication-DNA X-ray (1.92 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 0h (ground state). SNAP output
8scp replication-DNA X-ray (2.08 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 1h. SNAP output
8scq replication-DNA X-ray (2.18 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 2h. SNAP output
8scr replication-DNA X-ray (2.0 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 4h. SNAP output
8scs replication-DNA X-ray (2.1 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 8h. SNAP output
8sct replication-DNA X-ray (2.34 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 24h. SNAP output
8scu replication-DNA X-ray (2.38 Å) Lelyveld VS, Fang Z, Szostak JW (2023) "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity." Science, 382, 423-429. doi: 10.1126/science.adh5339. Bst DNA polymerase i large fragment wildtype d598a with 3'-amino primer, dgtp, and calcium time-resolved 48h (product state). SNAP output
8sfh DNA binding protein-DNA-RNA cryo-EM (3.4 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with a 5bp R-loop." Wt crispr-cas12a with a 5bp r-loop. SNAP output
8sfi DNA binding protein-DNA-RNA cryo-EM (3.5 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with a 8bp R-loop." Wt crispr-cas12a with a 8bp r-loop. SNAP output
8sfj DNA binding protein-DNA-RNA cryo-EM (3.6 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with a 10bp R-loop." Wt crispr-cas12a with a 10bp r-loop. SNAP output
8sfl DNA binding protein-DNA-RNA cryo-EM (3.3 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with a 15bp R-loop." Wt crispr-cas12a with a 15bp r-loop. SNAP output
8sfn DNA binding protein-DNA-RNA cryo-EM (3.3 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with a 16bp R-loop and nontarget strand in the RuvC active site." Wt crispr-cas12a with a 16bp r-loop and nontarget strand in the ruvc active site.. SNAP output
8sfo DNA binding protein-DNA-RNA cryo-EM (3.3 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site." Wt crispr-cas12a with a 20bp r-loop and nontarget strand in the ruvc active site.. SNAP output
8sfp DNA binding protein-DNA-RNA cryo-EM (3.8 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a with the target strand in the RuvC active site." Wt crispr-cas12a with the target strand in the ruvc active site.. SNAP output
8sfq DNA binding protein-DNA-RNA cryo-EM (3.5 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a post nontarget strand-cleavage with the the RuvC active site exposed." Wt crispr-cas12a post nontarget strand-cleavage with the the ruvc active site exposed.. SNAP output
8sfr DNA binding protein-DNA-RNA cryo-EM (3.5 Å) Strohkendl I, Taylor DW "WT CRISPR-Cas12a post nontarget strand cleavage." Wt crispr-cas12a post nontarget strand cleavage.. SNAP output
8sh0 DNA binding protein-DNA X-ray (2.16 Å) Tesmer VM, Brenner KA, Nandakumar J (2023) "Human POT1 protects the telomeric ds-ss DNA junction by capping the 5' end of the chromosome." Science, 381, 771-778. doi: 10.1126/science.adi2436. Structure of human pot1 DNA binding domain bound to a 5'-phosphorylated junction of a telomeric DNA hairpin with a 3'-overhang. SNAP output
8sh1 DNA binding protein-DNA X-ray (2.6 Å) Tesmer VM, Brenner KA, Nandakumar J (2023) "Human POT1 protects the telomeric ds-ss DNA junction by capping the 5' end of the chromosome." Science, 381, 771-778. doi: 10.1126/science.adi2436. Structure of human pot1 DNA binding domain bound to a 5'-phosphorylated junction of a telomeric double-stranded DNA duplex with a 3'-overhang. SNAP output
8siy replication cryo-EM (2.9 Å) Sahu S, Ekundayo BE, Kumar A, Bleichert F (2023) "A dual role for the chromatin reader ORCA/LRWD1 in targeting the origin recognition complex to chromatin." Embo J., 42, e114654. doi: 10.15252/embj.2023114654. Origin recognition complex associated (orca) protein bound to h4k20me3-nucleosome. SNAP output
8sj0 transferase-DNA X-ray (2.55 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound 2'-datp. SNAP output
8sj1 transferase-DNA X-ray (2.81 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound 3'-datp. SNAP output
8sj2 transferase-DNA X-ray (2.23 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of cgas with dsDNA and bound atp and 2'-dgtp. SNAP output
8sjd recombination-DNA cryo-EM (5.1 Å) Lannes L, Furman CM, Hickman AB, Dyda F (2023) "Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding." Nat Commun, 14, 4470. doi: 10.1038/s41467-023-40210-3. cryo-EM structure of the hermes transposase bound to two right-ends of its DNA transposon.. SNAP output
8ski transferase-DNA X-ray (2.163 Å) Jung H "Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA." Crystal structure of human DNA polymerase eta incorporating 5f-dutp across hx. SNAP output
8skt transferase-DNA X-ray (2.69 Å) Wu S, Gabelli SB, Sohn J (2024) "The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS." Nat Commun, 15, 4012. doi: 10.1038/s41467-024-48365-3. Structure of ternary complex of mouse cgas with dsDNA and bound atp with 5 mm mn2+. SNAP output
8sln hydrolase-DNA X-ray (2.2 Å) Lu H, Chen Z, Xie T, Zhong S, Suo S, Song S, Wang L, Xu H, Tian B, Zhao Y, Zhou R, Hua Y (2024) "The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA." Nat Commun, 15, 1892. doi: 10.1038/s41467-024-46208-9. Crystal structure of deinococcus geothermalis ppri complexed with ssDNA. SNAP output
8smh transcription X-ray (1.37 Å) Vernon TN, Terrell JR, Albrecht AV, Germann MW, Wilson WD, Poon GMK (2024) "Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors." Structure, 32, 83-96.e4. doi: 10.1016/j.str.2023.11.003. Chimeric ets-domain of murine pu.1 harboring the corresponding beta-strand 3 (s3) residues from murine ets-1 in complex with d(aataagcggaagtggg). SNAP output
8smj transcription-DNA X-ray (1.39 Å) Vernon TN, Terrell JR, Albrecht AV, Germann MW, Wilson WD, Poon GMK (2024) "Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors." Structure, 32, 83-96.e4. doi: 10.1016/j.str.2023.11.003. Chimeric ets-domain of murine pu.1 harboring the corresponding beta-strand 3 (s3) residues from murine ets-1 in complex with d(aataagcggaatgggg). SNAP output
8smw structural protein-DNA-transferase cryo-EM (3.3 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a. no density for ub.) (class 1). SNAP output
8smx structural protein-DNA-transferase cryo-EM (3.2 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a. no density for ub.) (class 2). SNAP output
8smy structural protein-DNA-transferase cryo-EM (3.2 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a. no density for ub.) (class 3). SNAP output
8smz structural protein-DNA-transferase cryo-EM (3.2 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a. no density for ub.) (class 4). SNAP output
8sn0 structural protein-DNA-transferase cryo-EM (3.2 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a. no density for ub.) (class 5). SNAP output
8sn1 structural protein-DNA-transferase cryo-EM (3.3 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a. no density for ub.) (class 6). SNAP output
8sn2 transferase-DNA cryo-EM (3.6 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c (ubch5c chemically conjugated to histone h2a). SNAP output
8sn3 transferase-DNA cryo-EM (3.8 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a) (class 1). SNAP output
8sn4 transferase-DNA cryo-EM (3.7 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a) (class 2). SNAP output
8sn5 transferase-DNA cryo-EM (3.9 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a) (class 3). SNAP output
8sn6 transferase-DNA cryo-EM (3.7 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a) (class 4). SNAP output
8sn7 transferase-DNA cryo-EM (3.7 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a) (class 5). SNAP output
8sn8 transferase-DNA cryo-EM (3.7 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c~ub (ubch5c chemically conjugated to histone h2a) (class 6). SNAP output
8sn9 transferase-DNA cryo-EM (3.9 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c with backside ubiquitin (ubch5c chemically conjugated to histone h2a) (class 1). SNAP output
8sna transferase-DNA cryo-EM (4.0 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168 and ubch5c with backside ubiquitin (ubch5c chemically conjugated to histone h2a) (class 2). SNAP output
8sok DNA binding protein cryo-EM (4.1 Å) Cai SW, Takai H, Zaug AJ, Dilgen TC, Cech TR, Walz T, de Lange T (2024) "POT1 recruits and regulates CST-Pol alpha /primase at human telomeres." Cell, 187, 3638-3651.e18. doi: 10.1016/j.cell.2024.05.002. cryo-EM structure of human cst bound to pot1(esdl)-tpp1 in the presence of telomeric ssDNA. SNAP output
8sp0 immune system cryo-EM (3.33 Å) Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM (2023) "Oligomerization-mediated activation of a short prokaryotic Argonaute." Nature, 621, 154-161. doi: 10.1038/s41586-023-06456-z. Symmetric dimer of mapsparta bound with grna-tDNA hybrid. SNAP output
8sp1 transcription-DNA X-ray (1.62 Å) Vernon TN, Terrell JR, Albrecht AV, Germann MW, Wilson WD, Poon GMK (2024) "Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors." Structure, 32, 83-96.e4. doi: 10.1016/j.str.2023.11.003. Chimeric ets-domain of murine pu.1 harboring the corresponding beta-strand 3 (s3) residues from murine ets-1 in complex with d(aataagcgiaagtggg). SNAP output
8sp3 immune system cryo-EM (3.52 Å) Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM (2023) "Oligomerization-mediated activation of a short prokaryotic Argonaute." Nature, 621, 154-161. doi: 10.1038/s41586-023-06456-z. Asymmetric dimer of mapsparta bound with grna-tDNA hybrid. SNAP output
8spo immune system cryo-EM (2.98 Å) Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM (2023) "Oligomerization-mediated activation of a short prokaryotic Argonaute." Nature, 621, 154-161. doi: 10.1038/s41586-023-06456-z. Tetramerized activation of mapsparta bound with nad+. SNAP output
8spq immune system cryo-EM (3.26 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tgg pam DNA. SNAP output
8sps transcription-DNA cryo-EM (3.0 Å) Guan R, Lian T, Zhou BR, Wheeler D, Bai Y (2023) "Structural mechanism of LIN28B nucleosome targeting by OCT4." Mol.Cell, 83, 1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. High resolution structure of esrrb nucleosome bound oct4 at site a and site b. SNAP output
8spu transcription-DNA cryo-EM (2.8 Å) Guan R, Lian T, Zhou BR, Wheeler D, Bai Y (2023) "Structural mechanism of LIN28B nucleosome targeting by OCT4." Mol.Cell, 83, 1970-1982.e6. doi: 10.1016/j.molcel.2023.05.030. Structure of esrrb nucleosome bound oct4 at site c. SNAP output
8sqh immune system-hydrolase cryo-EM (3.69 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting ttc pam DNA. SNAP output
8squ immune system cryo-EM (3.28 Å) Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM (2023) "Oligomerization-mediated activation of a short prokaryotic Argonaute." Nature, 621, 154-161. doi: 10.1038/s41586-023-06456-z. Monomeric mapsparta bound with guide RNA and target DNA hybrid. SNAP output
8sro transcription-DNA cryo-EM (3.3 Å) Zhang W, Leng F, Wang X, Ramirez RN, Park J, Benoist C, Hur S (2023) "FOXP3 recognizes microsatellites and bridges DNA through multimerization." Nature, 624, 433-441. doi: 10.1038/s41586-023-06793-z. Foxp3 tetramer on tttg repeats. SNAP output
8srp transcription-DNA cryo-EM (3.7 Å) Zhang W, Leng F, Wang X, Ramirez RN, Park J, Benoist C, Hur S (2023) "FOXP3 recognizes microsatellites and bridges DNA through multimerization." Nature, 624, 433-441. doi: 10.1038/s41586-023-06793-z. Foxp3 forms ladder-like multimer to bridge tttg repeats. SNAP output
8srs immune system cryo-EM (2.79 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tac pam DNA. SNAP output
8ssq transcription-DNA X-ray (3.12 Å) Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X (2023) "Structures of CTCF-DNA complexes including all 11 zinc fingers." Nucleic Acids Res., 51, 8447-8462. doi: 10.1093/nar/gkad594. Znfs 3-11 of ccctc-binding factor (ctcf) complexed with 35mer DNA 35-4. SNAP output
8ssr transcription-DNA X-ray (3.14 Å) Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X (2023) "Structures of CTCF-DNA complexes including all 11 zinc fingers." Nucleic Acids Res., 51, 8447-8462. doi: 10.1093/nar/gkad594. Znfs 3-11 of ccctc-binding factor (ctcf) complexed with 35mer DNA 35-20. SNAP output
8sss transcription-DNA X-ray (2.3 Å) Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X (2023) "Structures of CTCF-DNA complexes including all 11 zinc fingers." Nucleic Acids Res., 51, 8447-8462. doi: 10.1093/nar/gkad594. Znfs 1-7 of ccctc-binding factor (ctcf) complexed with 23mer. SNAP output
8sst transcription-DNA X-ray (2.19 Å) Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X (2023) "Structures of CTCF-DNA complexes including all 11 zinc fingers." Nucleic Acids Res., 51, 8447-8462. doi: 10.1093/nar/gkad594. Znfs 1-7 of ccctc-binding factor (ctcf) k365t mutant complexed with 23mer. SNAP output
8ssu transcription-DNA X-ray (2.89 Å) Yang J, Horton JR, Liu B, Corces VG, Blumenthal RM, Zhang X, Cheng X (2023) "Structures of CTCF-DNA complexes including all 11 zinc fingers." Nucleic Acids Res., 51, 8447-8462. doi: 10.1093/nar/gkad594. Znfs 3-11 of ccctc-binding factor (ctcf) complexed with 19mer DNA. SNAP output
8suk transcription X-ray (2.45 Å) Schumacher MA, Lent N, Chen VB, Salinas R (2023) "Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding." Nat Commun, 14, 7239. doi: 10.1038/s41467-023-42823-0. Structure of rhodococcus sp. usk13 darr-c-di-amp complex. SNAP output
8sv3 DNA binding protein-DNA X-ray (1.51 Å) Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M (2023) "Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry." Biochemistry, 62, 2854-2867. doi: 10.1021/acs.biochem.3c00327. 7-deazapurines and 5-halogenpyrimidine DNA duplex. SNAP output
8sv4 DNA binding protein-DNA X-ray (2.3 Å) Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M (2023) "Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry." Biochemistry, 62, 2854-2867. doi: 10.1021/acs.biochem.3c00327. 7-deazapurines and 5-halogenpyrimidine DNA duplex. SNAP output
8sva transcription-DNA X-ray (2.96 Å) Schumacher MA, Lent N, Chen VB, Salinas R (2023) "Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding." Nat Commun, 14, 7239. doi: 10.1038/s41467-023-42823-0. Structure of the rhodococcus sp. usk13 darr-20 bp DNA complex. SNAP output
8svd transcription-DNA X-ray (3.49 Å) Schumacher MA, Lent N, Chen VB, Salinas R (2023) "Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding." Nat Commun, 14, 7239. doi: 10.1038/s41467-023-42823-0. Structure of m. baixiangningiae darr-DNA complex reveals novel dimer-of-dimers DNA binding. SNAP output
8svf nuclear protein-DNA-RNA cryo-EM (3.2 Å) Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ (2023) "Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1." Sci Adv, 9, eadg9832. doi: 10.1126/sciadv.adg9832. Bap1-asxl1 bound to the h2ak119ub nucleosome. SNAP output
8swb hydrolase-RNA X-ray (2.0 Å) Iwamoto N, Cho Y-J "Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level." Rnase h complex with streopure aso and RNA. SNAP output
8swc hydrolase-RNA X-ray (2.68 Å) Iwamoto N, Cho Y-J "Crystal structure of RNase H/RNA/PO-ASO complex at an atomic level." Rnase h complex with aso (ooo) and RNA. SNAP output
8sxt RNA binding protein-RNA-DNA cryo-EM (3.3 Å) Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sanchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Isik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Gotte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS (2024) "Structures, functions and adaptations of the human LINE-1 ORF2 protein." Nature, 626, 194-206. doi: 10.1038/s41586-023-06947-z. Structure of line-1 orf2p with template:primer hybrid. SNAP output
8sy5 transcription-DNA-RNA cryo-EM (2.7 Å) Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D (2023) "A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase." Nat Commun, 14, 8219. doi: 10.1038/s41467-023-43735-9. E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural ds-btp base pair in the active site. SNAP output
8sy6 transcription-DNA-RNA cryo-EM (3.28 Å) Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D (2023) "A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase." Nat Commun, 14, 8219. doi: 10.1038/s41467-023-43735-9. E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural db-utp base pair in the active site. SNAP output
8sy7 transcription-DNA-RNA cryo-EM (2.65 Å) Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D (2023) "A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase." Nat Commun, 14, 8219. doi: 10.1038/s41467-023-43735-9. E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural db-stp base pair in the active site. SNAP output
8syi transcription cryo-EM (2.94 Å) Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS (2024) "Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase." Proc.Natl.Acad.Sci.USA, 121, e2311480121. doi: 10.1073/pnas.2311480121. Cyanobacterial rnap-ec. SNAP output
8syp transcription-DNA cryo-EM (2.6 Å) Lian T, Guan R, Zhou BR, Bai Y (2024) "Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP alpha." Nat.Struct.Mol.Biol., 31, 633-643. doi: 10.1038/s41594-023-01189-z. Genomic cx3cr1 nucleosome. SNAP output
8t0f transcription-DNA X-ray (2.61 Å) Chatterjee A, Katiki M, Murali R "Crystal structure of the PEG10 promoter-bound ONECUT2 DNA-binding domain." Crystal structure of the peg10 promoter-bound onecut2 DNA-binding domain. SNAP output
8t11 transcription-DNA X-ray (2.91 Å) Chatterjee A, Katiki M, Murali R "Crystal structure of the PEG10 promoter-bound ONECUT2 R479A/R480A mutant DNA-binding domain." Crystal structure of the peg10 promoter-bound onecut2 r479a-r480a mutant DNA-binding domain. SNAP output
8t1u transferase-DNA X-ray (2.91 Å) Chen J, Lu J, Liu J, Fang J, Zhong X, Song J (2023) "DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2." J.Biol.Chem., 299, 105433. doi: 10.1016/j.jbc.2023.105433. Crystal structure of the drm2-cta DNA complex. SNAP output
8t3t DNA binding protein-transferase-DNA cryo-EM (3.21 Å) Zhao F, Hicks CW, Wolberger C (2023) "Mechanism of histone H2B monoubiquitination by Bre1." Nat.Struct.Mol.Biol., 30, 1623-1627. doi: 10.1038/s41594-023-01137-x. Structure of bre1-nucleosome complex - state3. SNAP output
8t3w DNA binding protein-transferase-DNA cryo-EM (3.25 Å) Zhao F, Hicks CW, Wolberger C (2023) "Mechanism of histone H2B monoubiquitination by Bre1." Nat.Struct.Mol.Biol., 30, 1623-1627. doi: 10.1038/s41594-023-01137-x. Structure of bre1-nucleosome complex - state2. SNAP output
8t3x transferase-DNA X-ray (2.73 Å) Maola VA, Yik EJ, Hajjar M, Lee JJ, Holguin MJ, Quijano RN, Nguyen KK, Ho KL, Medina JV, Chim N, Chaput JC (2024) "Directed evolution of a highly efficient TNA polymerase achieved by homologous recombination." Nat Catal. doi: 10.1038/s41929-024-01233-1. Tna polymerase, closed ternary. SNAP output
8t3y DNA binding protein-transferase-DNA cryo-EM (3.47 Å) Zhao F, Hicks CW, Wolberger C (2023) "Mechanism of histone H2B monoubiquitination by Bre1." Nat.Struct.Mol.Biol., 30, 1623-1627. doi: 10.1038/s41594-023-01137-x. Structure of bre1-nucleosome complex - state1. SNAP output
8t6o immune system cryo-EM (3.1 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tac pam DNA with 0 bp r-loop. SNAP output
8t6s immune system cryo-EM (3.28 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tac pam DNA with 10 bp r-loop. SNAP output
8t6t immune system cryo-EM (3.04 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tac pam DNA with 13 bp r-loop. SNAP output
8t6x immune system cryo-EM (3.08 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tac pam DNA with 18 bp r-loop. SNAP output
8t6y immune system cryo-EM (2.88 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex bound to non-target DNA with 1 bp r-loop. SNAP output
8t76 immune system cryo-EM (3.42 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex targeting tac pam DNA with 3 bp r-loop. SNAP output
8t77 immune system cryo-EM (3.25 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex bound to non-target DNA with 6 bp r-loop. SNAP output
8t78 immune system cryo-EM (3.02 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex bound to non-target DNA with 8 bp r-loop. SNAP output
8t79 immune system cryo-EM (3.04 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spry-cas9:grna complex bound to non-target DNA with 10 bp r-loop. SNAP output
8t7e transferase-DNA cryo-EM (3.08 Å) Buchel G, Nayak AR, Herbine K, Sarfallah A, Sokolova VO, Zamudio-Ochoa A, Temiakov D (2023) "Structural basis for DNA proofreading." Nat Commun, 14, 8501. doi: 10.1038/s41467-023-44198-8. cryo-EM structure of the backtracking initiation complex (vii) of human mitochondrial DNA polymerase gamma. SNAP output
8t9c virus-DNA cryo-EM (2.7 Å) Penzes JJ, Holm M, Firlar E, Kaelber JT "Sequencing-free discovery by cryo-EM of a pathogenic parvovirus causing mass mortality of farmed beetles." Zophobas morio black wasting virus strain ut-morio virion structure. SNAP output
8t9f gene regulation cryo-EM (2.6 Å) Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ (2023) "Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1." Mol.Cell, 83, 2872-2883.e7. doi: 10.1016/j.molcel.2023.07.020. Catalytic and non-catalytic mechanisms of histone h4 lysine 20 methyltransferase suv420h1. SNAP output
8t9h gene regulation cryo-EM (3.37 Å) Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ (2023) "Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1." Mol.Cell, 83, 2872-2883.e7. doi: 10.1016/j.molcel.2023.07.020. Catalytic and non-catalytic mechanisms of histone h4 lysine 20 methyltransferase suv420h1. SNAP output
8t9u transcription X-ray (1.47 Å) Vernon TN, Terrell JR, Albrecht AV, Germann MW, Wilson WD, Poon GMK (2024) "Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors." Structure, 32, 83-96.e4. doi: 10.1016/j.str.2023.11.003. Human pu.1 ets-domain (165-270) in complex with d(aataagcgiaagtggg). SNAP output
8t9x virus-DNA cryo-EM (2.0 Å) Penzes JJ, Holm M, Firlar E, Kaelber JT "Sequencing-free discovery by cryo-EM of a pathogenic parvovirus causing mass mortality of farmed beetles." Zophobas morio black wasting virus strain nj2-molitor virion structure. SNAP output
8tac de novo protein-DNA X-ray (2.34 Å) Doyle L, Stoddard BL "Designed DNA binding protein." Designed DNA binding protein. SNAP output
8tas gene regulation cryo-EM (4.1 Å) Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hansel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S (2024) "Activation of automethylated PRC2 by dimerization on chromatin." Mol.Cell, 84, 3885-3898.e8. doi: 10.1016/j.molcel.2024.08.025. Prc2 monomer bound to nucleosome. SNAP output
8tci transferase X-ray (3.19 Å) Khudaverdyan N, Lu J, Chen X, Herle G, Song J (2024) "The structure of DNA methyltransferase DNMT3C reveals an activity-tuning mechanism for DNA methylation." J.Biol.Chem., 300, 107633. doi: 10.1016/j.jbc.2024.107633. Crystal structure of dnmt3c-dnmt3l in complex with cgg DNA. SNAP output
8tfd viral protein X-ray (1.55 Å) Esler MA, Belica CA, Rollie JA, Brown WL, Moghadasi SA, Shi K, Harki DA, Harris RS, Aihara H (2024) "A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain." Nucleic Acids Res. doi: 10.1093/nar/gkae874. Crystal structure of a stem-loop DNA aptamer complexed with sars-cov-2 nucleocapsid protein RNA-binding domain. SNAP output
8tg4 transferase X-ray (1.37 Å) Jacewicz A, Dantuluri S, Shuman S (2023) "Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD." Proc.Natl.Acad.Sci.USA, 120, e2312999120. doi: 10.1073/pnas.2312999120. Trna 2'-phosphotransferase (tpt1) from aeropyrum pernix in complex with adp-ribose-2"-phosphate and 2'-oh RNA. SNAP output
8th9 lyase X-ray (2.08 Å) Eckenroth BE, Bumgarner JD, Matsumoto-Elliott O, David SS, Doublie S (2023) "Structural and biochemical insights into NEIL2's preference for abasic sites." Nucleic Acids Res., 51, 12508-12521. doi: 10.1093/nar/gkad1075. Structure of mammalian neil2 from monodelphis domestica in complex with thf-containing DNA. SNAP output
8thu gene regulation-DNA cryo-EM (3.1 Å) Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ (2023) "Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1." Mol.Cell, 83, 2872-2883.e7. doi: 10.1016/j.molcel.2023.07.020. Catalytic and non-catalytic mechanisms of histone h4 lysine 20 methyltransferase suv420h1. SNAP output
8tip DNA binding protein-DNA X-ray (2.79 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with blunt ends and 5' terminal phosphates.. SNAP output
8tiq DNA binding protein-DNA X-ray (2.45 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with blunt ends and 3' terminal phosphates.. SNAP output
8tir DNA binding protein-DNA X-ray (3.11 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 1 sticky bases and 5' terminal phosphates.. SNAP output
8tis DNA binding protein-DNA X-ray (2.54 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 1 sticky bases and 3' terminal phosphates.. SNAP output
8tit DNA binding protein-DNA X-ray (2.84 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 2 sticky base overhangs and no terminal phosphates.. SNAP output
8tiu DNA binding protein-DNA X-ray (3.9 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 2 sticky base overhangs and 3' terminal phosphates.. SNAP output
8tiv DNA binding protein-DNA X-ray (3.35 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with blunt ends and 5' terminal phosphates and crosslinked with edc.. SNAP output
8tiw DNA binding protein-DNA X-ray (3.11 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with blunt ends and 3' terminal phosphates and crosslinked with edc.. SNAP output
8tix DNA binding protein-DNA X-ray (2.91 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 1 sticky bases and 5' terminal phosphates and crosslinked with edc.. SNAP output
8tiy DNA binding protein-DNA X-ray (3.11 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 1 sticky bases and 3' terminal phosphates and crosslinked with edc.. SNAP output
8tiz DNA binding protein-DNA X-ray (3.11 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 2 sticky base overhangs and no terminal phosphates and crosslinked with edc.. SNAP output
8tj0 DNA binding protein-DNA X-ray (3.24 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 2 sticky base overhangs and 5' terminal phosphates and crosslinked with edc.. SNAP output
8tj1 DNA binding protein-DNA X-ray (3.15 Å) Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) "Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals." Acs Nanosci Au, 4, 338-348. doi: 10.1021/acsnanoscienceau.4c00013. Isoreticular, interpenetrating co-crystal of replication initiator protein repe54 and symmetrical expanded duplex (31mer) containing the cognate repe54 sequence and an additional g-c rich sequence with 2 sticky base overhangs and 3' terminal phosphates and crosslinked with edc.. SNAP output
8tje virus-DNA cryo-EM (3.4 Å) Penzes JJ, Holm M, Firlar E, Kaelber JT "Sequencing-free discovery by cryo-EM of a pathogenic parvovirus causing mass mortality of farmed beetles." Zophobas morio black wasting virus strain or-molitor virion structure. SNAP output
8tkl transcription-DNA X-ray (3.0 Å) Zhu N, Mealka M, Mitchel S, Milani C, Acuna LM, Rogers E, Lahana AN, Huxford T (2023) "X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA." Biomolecules, 13. doi: 10.3390/biom13091310. Murine nf-kappab p50 rel homology region homodimer in complex with a test 16-mer kappab-like DNA. SNAP output
8tkm transcription-DNA X-ray (2.8 Å) Zhu N, Mealka M, Mitchel S, Milani C, Acuna LM, Rogers E, Lahana AN, Huxford T (2023) "X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA." Biomolecules, 13. doi: 10.3390/biom13091310. Murine nf-kappab p50 rel homology region homodimer in complex with 17-mer kappab DNA from human interleukin-6 (il-6) promoter. SNAP output
8tkn DNA binding protein-DNA X-ray (2.8 Å) Zhu N, Mealka M, Mitchel S, Milani C, Acuna LM, Rogers E, Lahana AN, Huxford T (2023) "X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA." Biomolecules, 13. doi: 10.3390/biom13091310. Murine nf-kappab p50 rel homology region homodimer in complex with 10-mer kappab DNA from human neutrophil gelatinase-associated lipocalin (ngal) promoter. SNAP output
8tle DNA binding protein-DNA X-ray (2.08 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (mouse) binds non-b-form 36-mer DNA oligo (sg c2-form 1). SNAP output
8tlf DNA binding protein-DNA X-ray (1.64 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (mouse) binds non-b-form DNA oligo 36-mer (sg c2-form 2). SNAP output
8tlg DNA binding protein-DNA X-ray (2.09 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (mouse) binds non-b-form 34-mer DNA oligo. SNAP output
8tlh DNA binding protein-DNA X-ray (1.94 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (mouse) binds non-b-form 32-mer DNA oligo. SNAP output
8tlj DNA binding protein-DNA X-ray (2.3 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (mouse) binds non-b-form 32-mer DNA oligo containing a 5mc. SNAP output
8tlk DNA binding protein-DNA X-ray (2.99 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (human) binds non-b-form 32-mer DNA oligo containing a 5mc. SNAP output
8tll DNA binding protein-DNA X-ray (2.58 Å) Hardikar S, Ren R, Ying Z, Zhou J, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Coletta LD, Shen J, Dan J, Zhang X, Cheng X, Chen T (2024) "The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA." Sci Adv, 10, eadr0036. doi: 10.1126/sciadv.adr0036. Cdca7 (mouse) binds non-b-form 26-mer DNA oligo. SNAP output
8tlo transcription X-ray (2.76 Å) Viennet T, Yin M, Jayaraj A, Kim W, Sun ZJ, Fujiwara Y, Zhang K, Seruggia D, Seo HS, Dhe-Paganon S, Orkin SH, Arthanari H (2024) "Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6." Structure. doi: 10.1016/j.str.2024.09.022. Crystal structure analysis of bcl11a in complex with DNA. SNAP output
8tlq DNA binding protein-DNA cryo-EM (3.53 Å) Malik R, Johnson RE, Ubarretxena-Belandia I, Prakash L, Prakash S, Aggarwal AK (2024) "Cryo-EM structure of the Rev1-Pol zeta holocomplex reveals the mechanism of their cooperativity in translesion DNA synthesis." Nat.Struct.Mol.Biol., 31, 1394-1403. doi: 10.1038/s41594-024-01302-w. cryo-EM structure of the rev1-polzeta-DNA-dctp complex. SNAP output
8tlt DNA binding protein-DNA cryo-EM (2.85 Å) Malik R, Johnson RE, Ubarretxena-Belandia I, Prakash L, Prakash S, Aggarwal AK (2024) "Cryo-EM structure of the Rev1-Pol zeta holocomplex reveals the mechanism of their cooperativity in translesion DNA synthesis." Nat.Struct.Mol.Biol., 31, 1394-1403. doi: 10.1038/s41594-024-01302-w. cryo-EM structure of rev1(deltan)-polzeta-DNA-dctp complex. SNAP output
8to1 transcription-DNA cryo-EM (2.8 Å) Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA (2024) "Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01349-9. Escherichia coli RNA polymerase unwinding intermediate (i1a) at the lambda pr promoter. SNAP output
8to6 transcription-DNA cryo-EM (2.9 Å) Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA (2024) "Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01349-9. Escherichia coli RNA polymerase unwinding intermediate (i1d) at the lambda pr promoter. SNAP output
8to8 transcription-DNA cryo-EM (2.9 Å) Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA (2024) "Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01349-9. Escherichia coli RNA polymerase unwinding intermediate (i1b) at the lambda pr promoter. SNAP output
8toe transcription-DNA cryo-EM (2.9 Å) Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA (2024) "Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01349-9. Escherichia coli RNA polymerase unwinding intermediate (i1c) at the lambda pr promoter. SNAP output
8tof transcription-DNA cryo-EM (2.8 Å) Markert JW, Vos SM, Farnung L (2023) "Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex." Nat Commun, 14, 8128. doi: 10.1038/s41467-023-43968-8. Rpd3s bound to an h3k36cme3 modified nucleosome. SNAP output
8tom transcription-DNA cryo-EM (3.1 Å) Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA (2024) "Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01349-9. Escherichia coli RNA polymerase closed complex intermediate at the lambda pr promoter. SNAP output
8tp8 transcription-DNA X-ray (2.74 Å) Schumacher MA, Cannistraci E, Salinas R, Lloyd D, Messner E, Gozzi K (2024) "Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site." Nucleic Acids Res., 52, 1435-1449. doi: 10.1093/nar/gkad1198. Structure of the c. crescentus wyl-activator, drid, bound to ssDNA and cognate DNA. SNAP output
8tpk transcription-DNA X-ray (3.46 Å) Schumacher MA, Cannistraci E, Salinas R, Lloyd D, Messner E, Gozzi K (2024) "Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site." Nucleic Acids Res., 52, 1435-1449. doi: 10.1093/nar/gkad1198. P6522 crystal form of c. crescentus drid-ssDNA-DNA complex. SNAP output
8tqs blood clotting X-ray (2.207 Å) Yu H, Kumar S, Frederiksen JW, Kolyadko VN, Pitoc G, Layzer J, Yan A, Rempel R, Francis S, Krishnaswamy S, Sullenger BA (2024) "Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors." Nat Commun, 15, 3977. doi: 10.1038/s41467-024-48211-6. Complex of human thrombin (s195a) bound to a bivalent inhibitor comprised of DNA aptamer hd22 conjugated to dabigatran with a linker.. SNAP output
8tug transcription-DNA-RNA cryo-EM (3.5 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of cpd-stalled pol ii in complex with rad26 (engaged state). SNAP output
8tvc hydrolase-DNA X-ray (1.93 Å) Yang H, Pacheco J, Kim K, Bokani A, Ito F, Ebrahimi D, Chen XS (2024) "Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain." Nat Commun, 15, 8773. doi: 10.1038/s41467-024-52671-1. Crystal structure of ra3g-ssDNA-aa. SNAP output
8tvp transcription-DNA-RNA cryo-EM (3.7 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of cpd-stalled pol ii in complex with rad26 (open state). SNAP output
8tvq transcription-DNA-RNA cryo-EM (4.6 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of cpd stalled 10-subunit pol ii in complex with rad26. SNAP output
8tvs transcription-DNA-RNA cryo-EM (4.4 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of backtracked pol ii in complex with rad26. SNAP output
8tvv transcription-DNA-RNA cryo-EM (3.7 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of backtracked pol ii. SNAP output
8tvw transcription-DNA-RNA cryo-EM (3.6 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of cpd-stalled pol ii (conformation 1). SNAP output
8tvx transcription-DNA-RNA cryo-EM (3.7 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of cpd-stalled pol ii (conformation 2). SNAP output
8tvy transcription-DNA-RNA cryo-EM (3.1 Å) Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE (2024) "Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair." Proc.Natl.Acad.Sci.USA, 121, e2314245121. doi: 10.1073/pnas.2314245121. cryo-EM structure of cpd lesion containing RNA polymerase ii elongation complex with rad26 and elf1 (closed state). SNAP output
8twb DNA binding protein-DNA cryo-EM (3.2 Å) Yuan Z, Georgescu R, Yao NY, Yurieva O, O'Donnell ME, Li H (2024) "Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis." Science, 385, eadk5901. doi: 10.1126/science.adk5901. cryo-EM structure of s. cerevisiae ctf18-rfc-pcna-DNA complex. SNAP output
8tx4 hydrolase-DNA X-ray (1.9 Å) Yang H, Pacheco J, Kim K, Bokani A, Ito F, Ebrahimi D, Chen XS (2024) "Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain." Nat Commun, 15, 8773. doi: 10.1038/s41467-024-52671-1. Crystal structure of ra3g-ssDNA-ga. SNAP output
8txo transcription cryo-EM (3.1 Å) Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Dordevic-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D (2024) "Overcoming resolution attenuation during tilted cryo-EM data collection." Nat Commun, 15, 389. doi: 10.1038/s41467-023-44555-7. E. coli DNA-directed RNA polymerase transcription elongation complex bound to the unnatural dz-ptp base pair in the active site. SNAP output
8txv transferase cryo-EM (3.8 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle ubiquitylated at histone h2a k15 in complex with rnf168 (class 1). SNAP output
8txw transferase cryo-EM (3.6 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle ubiquitylated at histone h2a k15 in complex with rnf168 (class 2). SNAP output
8txx transferase cryo-EM (3.7 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle ubiquitylated at histone h2a k15 in complex with rnf168 (class 3). SNAP output
8tzz immune system-RNA-DNA cryo-EM (3.56 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spg cas9 with ngc pam DNA target. SNAP output
8u0j immune system-DNA cryo-EM (3.1 Å) Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW (2024) "Plasmid targeting and destruction by the DdmDE bacterial defence system." Nature, 630, 961-967. doi: 10.1038/s41586-024-07515-9. Ddme in complex with guide and target DNA. SNAP output
8u0o transferase-DNA X-ray (2.05 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2024) "DNA polymerase lambda Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining." DNA Repair (Amst), 136, 103645. doi: 10.1016/j.dnarep.2024.103645. Synaptic complex of human DNA polymerase lambda dl variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus. SNAP output
8u0p transferase-DNA X-ray (1.9 Å) Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC (2024) "DNA polymerase lambda Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining." DNA Repair (Amst), 136, 103645. doi: 10.1016/j.dnarep.2024.103645. Synaptic complex of human DNA polymerase lambda dl variant engaged on a noncomplementary DNA double-strand break. SNAP output
8u0u immune system-DNA cryo-EM (3.04 Å) Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW (2024) "Plasmid targeting and destruction by the DdmDE bacterial defence system." Nature, 630, 961-967. doi: 10.1038/s41586-024-07515-9. Ddmd dimer in complex with ssDNA. SNAP output
8u0w immune system-DNA cryo-EM (2.99 Å) Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW (2024) "Plasmid targeting and destruction by the DdmDE bacterial defence system." Nature, 630, 961-967. doi: 10.1038/s41586-024-07515-9. Ddmd monomer in complex with ssDNA. SNAP output
8u13 structural protein-DNA-transferase cryo-EM (3.8 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle ubiquitylated at histone h2a lysine 15 in complex with rnf168-ubch5c (class 1). SNAP output
8u14 structural protein-DNA-transferase cryo-EM (3.9 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle ubiquitylated at histone h2a lysine 15 in complex with rnf168-ubch5c (class 2). SNAP output
8u3b transcription-DNA cryo-EM (3.23 Å) Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B (2024) "Structural basis for transcription activation by the nitrate-responsive regulator NarL." Nucleic Acids Res., 52, 1471-1482. doi: 10.1093/nar/gkad1231. cryo-EM structure of e. coli narl-transcription activation complex at 3.2a. SNAP output
8u3k immune system-DNA cryo-EM (2.5 Å) Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW (2024) "Plasmid targeting and destruction by the DdmDE bacterial defence system." Nature, 630, 961-967. doi: 10.1038/s41586-024-07515-9. Ddmde handover complex. SNAP output
8u3y immune system-DNA-RNA cryo-EM (3.1 Å) Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW (2024) "Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9." Nat Commun, 15, 3663. doi: 10.1038/s41467-024-47830-3. Spg cas9 with ngg pam DNA target. SNAP output
8u5h structural protein-transferase-DNA cryo-EM (3.23 Å) Chen X, Song J "Cryo-EM structure of human DNMT3A N-terminal domain bound to H2AK119Ub nucleosome." cryo-EM structure of human dnmt3a udr bound to h2ak119ub1-modified nucleosome. SNAP output
8u6x ligase-DNA X-ray (2.44 Å) Pan J, Singh A, Hanning K, Hicks J, Williamson A (2024) "A role for the ATP-dependent DNA ligase lig E of Neisseria gonorrhoeae in biofilm formation." Bmc Microbiol., 24, 29. doi: 10.1186/s12866-024-03193-9. Atp-dependent DNA ligase lig e from neisseria gonorrhoeae. SNAP output
8u72 RNA binding protein-RNA-DNA cryo-EM (3.15 Å) Kottur J, Malik R, Aggarwal AK (2024) "Nucleic acid mediated activation of a short prokaryotic Argonaute immune system." Nat Commun, 15, 4852. doi: 10.1038/s41467-024-49271-4. cryo-EM structure of the sparta oligomer with guide RNA and target DNA. SNAP output
8u8l DNA binding protein-DNA X-ray (2.2 Å) Padmanaban S, Lambacher NJ, Tesmer VM, Zhang J, Shibuya H, Nandakumar J (2024) "Caenorhabditis elegans telomere-binding proteins TEBP-1 and TEBP-2 adapt the Myb module to dimerize and bind telomeric DNA." Proc.Natl.Acad.Sci.USA, 121, e2316651121. doi: 10.1073/pnas.2316651121. X-ray crystal structure of tebp-2 mcd3 with ds DNA. SNAP output
8u8u transcription-DNA-RNA cryo-EM (2.9 Å) Herbine K, Nayak AR, Temiakov D (2024) "Structural basis for substrate binding and selection by human mitochondrial RNA polymerase." Nat Commun, 15, 7134. doi: 10.1038/s41467-024-50817-9. cryo-EM structure of cognate substrate atp bound in the entry site (es) of human mitochondrial transcription elongation complex. SNAP output
8u8v transcription-DNA-RNA cryo-EM (2.74 Å) Herbine K, Nayak AR, Temiakov D (2024) "Structural basis for substrate binding and selection by human mitochondrial RNA polymerase." Nat Commun, 15, 7134. doi: 10.1038/s41467-024-50817-9. cryo-EM structure of substrate atp bound in the insertion site (is) of human mitochondrial transcription elongation complex. SNAP output
8u9l DNA binding protein-DNA X-ray (3.091 Å) Chang A, Wu Y, Li SX, Smale S, Chen L "Crystal Structure of RelA-cRel chimera complex with DNA." Crystal structure of rela-crel chimera complex with DNA. SNAP output
8u9r transcription X-ray (3.34 Å) Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G (2024) "Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser." Proc.Natl.Acad.Sci.USA, 121, e2318527121. doi: 10.1073/pnas.2318527121. Structural basis of transcription: RNA polymerase ii substrate binding and metal coordination using a free-electron laser. SNAP output
8u9x transcription X-ray (3.05 Å) Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G (2024) "Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser." Proc.Natl.Acad.Sci.USA, 121, e2318527121. doi: 10.1073/pnas.2318527121. Structural basis of transcription: RNA polymerase ii substrate binding and metal coordination at 3.0 a of t834p mutant using a free-electron laser. SNAP output
8ua7 DNA binding protein-DNA cryo-EM (3.3 Å) Toner CM, Hoitsma NM, Weerawarana S, Luger K (2024) "Characterization of Medusavirus encoded histones reveals nucleosome-like structures and a unique linker histone." Nat Commun, 15, 9138. doi: 10.1038/s41467-024-53364-5. Medusavirus nucleosome core particle. SNAP output
8ucu replication, transferase-DNA-RNA cryo-EM (2.85 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. Partial DNA termination subcomplex of xenopus laevis DNA polymerase alpha-primase. SNAP output
8ucv replication, transferase-DNA-RNA cryo-EM (3.81 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. Complete DNA termination subcomplex 1 of xenopus laevis DNA polymerase alpha-primase. SNAP output
8ucw replication, transferase-DNA-RNA cryo-EM (3.64 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. Complete DNA termination subcomplex 2 of xenopus laevis DNA polymerase alpha-primase. SNAP output
8udk transferase-DNA X-ray (3.43 Å) Park J, Herrmann GK, Roy A, Shumate CK, Cisneros GA, Yin YW (2024) "An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol gamma." Sci Adv, 10, eadl3214. doi: 10.1126/sciadv.adl3214. Human mitochondrial DNA polymerase gamma r853a ternary complex. SNAP output
8udl transferase-DNA cryo-EM (2.37 Å) Park J, Herrmann GK, Roy A, Shumate CK, Cisneros GA, Yin YW (2024) "An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol gamma." Sci Adv, 10, eadl3214. doi: 10.1126/sciadv.adl3214. Human mitochondrial DNA polymerase gamma binary complex. SNAP output
8uff transcription X-ray (1.66 Å) Terrell JR, Paul A, Ogbonna EN, Farahat AA, Poon GMK, Wilson WD "Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders." Human pu.1 ets-domain (165-270) bound to d(aataaaaggaagtggg) in ternary complex with db1976. SNAP output
8ufk transcription X-ray (2.41 Å) Terrell JR, Paul A, Ogbonna EN, Farahat AA, Poon GMK, Wilson WD "Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders." Human pu.1 ets-domain (165-270) bound to d(aataaaagcggaagtg). SNAP output
8ufz transcription X-ray (3.06 Å) Terrell JR, Paul A, Ogbonna EN, Farahat AA, Poon GMK, Wilson WD "Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders." Human pu.1 ets-domain (165-270) bound to d(aataaaagcggaagtg) in ternary complex with db1976. SNAP output
8ugq viral protein cryo-EM (3.17 Å) McKenna R, Bennett AB, Mietzsch M, Hull JA "The two states of Maize Streak Virus (MSV) Geminivirus Architecture." Cryoem structure of maize streak virus (msv) - geminivirus. SNAP output
8uh7 replication-DNA X-ray (2.628 Å) Marcus K, Huang Y, Subramanian S, Gee CL, Gorday K, Ghaffari-Kashani S, Luo XR, Zheng L, O'Donnell M, Subramaniam S, Kuriyan J (2024) "Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM." Nat.Struct.Mol.Biol., 31, 424-435. doi: 10.1038/s41594-023-01177-3. Structure of t4 bacteriophage clamp loader bound to the t4 clamp, primer-template DNA, and atp analog. SNAP output
8uha transcription-DNA-RNA cryo-EM (3.5 Å) Su BG, Vos SM (2024) "Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing." Mol.Cell, 84, 1243. doi: 10.1016/j.molcel.2024.01.023. Structure of paused transcription complex pol ii-dsif-nelf - tilted. SNAP output
8uhg transcription-DNA-RNA cryo-EM (2.7 Å) Su BG, Vos SM (2024) "Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing." Mol.Cell, 84, 1243. doi: 10.1016/j.molcel.2024.01.023. Structure of paused transcription complex pol ii-dsif-nelf - poised post-translocated. SNAP output
8uhk transcription X-ray (3.08 Å) Terrell JR, Paul A, Ogbonna EN, Farahat AA, Poon GMK, Wilson WD "Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders." Human pu.1 ets-domain (165-270) bound to d(aaaataaaaggaagtg). SNAP output
8ui0 transcription-DNA-RNA cryo-EM (2.7 Å) Su BG, Vos SM (2024) "Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing." Mol.Cell, 84, 1243. doi: 10.1016/j.molcel.2024.01.023. Structure of poised transcription complex pol ii-dsif-nelf - pre-translocated. SNAP output
8uis transcription-RNA-DNA cryo-EM (3.23 Å) Su BG, Vos SM (2024) "Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing." Mol.Cell, 84, 1243. doi: 10.1016/j.molcel.2024.01.023. Structure of transcription complex pol ii-dsif-nelf-tfiis. SNAP output
8ujt transferase-DNA X-ray (2.31 Å) Tomar R, Li S, Egli M, Stone MP (2024) "Replication Bypass of the N -(2-Deoxy-d-erythro-pentofuranosyl)-urea DNA Lesion by Human DNA Polymerase eta." Biochemistry, 63, 754-766. doi: 10.1021/acs.biochem.3c00569. Crystal structure of human polymerase eta with incoming dampnpp nucleotide opposite urea lesion. SNAP output
8ujv transferase-DNA X-ray (2.23 Å) Tomar R, Li S, Egli M, Stone MP (2024) "Replication Bypass of the N -(2-Deoxy-d-erythro-pentofuranosyl)-urea DNA Lesion by Human DNA Polymerase eta." Biochemistry, 63, 754-766. doi: 10.1021/acs.biochem.3c00569. Crystal structure of human polymerase eta with incoming dcmpnpp nucleotide opposite urea lesion. SNAP output
8ujx transferase-DNA X-ray (2.17 Å) Tomar R, Li S, Egli M, Stone MP (2024) "Replication Bypass of the N -(2-Deoxy-d-erythro-pentofuranosyl)-urea DNA Lesion by Human DNA Polymerase eta." Biochemistry, 63, 754-766. doi: 10.1021/acs.biochem.3c00569. Crystal structure of human polymerase eta with incoming dgmpnpp nucleotide opposite urea lesion. SNAP output
8uk4 transferase-DNA X-ray (3.02 Å) Tomar R, Li S, Egli M, Stone MP (2024) "Replication Bypass of the N -(2-Deoxy-d-erythro-pentofuranosyl)-urea DNA Lesion by Human DNA Polymerase eta." Biochemistry, 63, 754-766. doi: 10.1021/acs.biochem.3c00569. Crystal structure of human polymerase eta with incoming dtmpnpp nucleotide opposite urea lesion. SNAP output
8uk9 DNA binding protein-DNA X-ray (3.1 Å) Marcus K, Huang Y, Subramanian S, Gee CL, Gorday K, Ghaffari-Kashani S, Luo XR, Zheng L, O'Donnell M, Subramaniam S, Kuriyan J (2024) "Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM." Nat.Struct.Mol.Biol., 31, 424-435. doi: 10.1038/s41594-023-01177-3. Structure of t4 bacteriophage clamp loader mutant d110c bound to the t4 clamp, primer-template DNA, and atp analog. SNAP output
8ukq transcription X-ray (3.5 Å) Gao S, Hou P, Oh J, Wang D, Greenberg MM (2024) "Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG." J.Am.Chem.Soc., 146, 6274-6282. doi: 10.1021/jacs.3c14476. RNA polymerase ii elongation complex with fapy-dg lesion in apo state. SNAP output
8ukr transcription-DNA-RNA X-ray (3.78 Å) Gao S, Hou P, Oh J, Wang D, Greenberg MM (2024) "Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG." J.Am.Chem.Soc., 146, 6274-6282. doi: 10.1021/jacs.3c14476. RNA polymerase ii elongation complex with fapy-dg lesion soaking with atp before chemistry. SNAP output
8uks transcription-DNA-RNA X-ray (3.4 Å) Gao S, Hou P, Oh J, Wang D, Greenberg MM (2024) "Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG." J.Am.Chem.Soc., 146, 6274-6282. doi: 10.1021/jacs.3c14476. RNA polymerase ii elongation complex with fapy-dg lesion soaking with ctp before chemistry. SNAP output
8ukt transcription-DNA-RNA X-ray (3.6 Å) Gao S, Hou P, Oh J, Wang D, Greenberg MM (2024) "Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG." J.Am.Chem.Soc., 146, 6274-6282. doi: 10.1021/jacs.3c14476. RNA polymerase ii elongation complex with fapy-dg lesion with amp added. SNAP output
8uku transcription-DNA-RNA X-ray (3.6 Å) Gao S, Hou P, Oh J, Wang D, Greenberg MM (2024) "Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG." J.Am.Chem.Soc., 146, 6274-6282. doi: 10.1021/jacs.3c14476. RNA polymerase ii elongation complex with fapy-dg lesion with cmp added. SNAP output
8umf immune system cryo-EM (2.9 Å) Bravo JPK, Taylor DW "Structure-guided engineering of PsCas9 yields a high fidelity and activity enzyme for in vivo gene editing." Structure of pscas9 in complex with grna and DNA in product state. SNAP output
8umh transcription cryo-EM (4.1 Å) Yang C, Murakami K "consensus map of PICdeltaTFIIK form2." Consensus map of picdeltatfiik form2. SNAP output
8umi transcription cryo-EM (3.7 Å) Yang C, Murakami K "consensus map of PICdeltaTFIIK form1." Consensus map of picdeltatfiik form1. SNAP output
8umy replication-DNA cryo-EM (2.83 Å) He Q, Wang F, O'Donnell ME, Li H (2024) "Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC." Proc.Natl.Acad.Sci.USA, 121, e2319727121. doi: 10.1073/pnas.2319727121. Atomic model of the human ctf18-rfc-pcna-DNA ternary complex with narrow pcna opening state ii (state 6). SNAP output
8un0 replication-DNA cryo-EM (3.0 Å) He Q, Wang F, O'Donnell ME, Li H (2024) "Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC." Proc.Natl.Acad.Sci.USA, 121, e2319727121. doi: 10.1073/pnas.2319727121. Atomic model of the human ctf18-rfc-pcna-DNA ternary complex with cracked and closed pcna (state 7). SNAP output
8unf replication cryo-EM (3.15 Å) Marcus K, Huang Y, Subramanian S, Gee CL, Gorday K, Ghaffari-Kashani S, Luo XR, Zheng L, O'Donnell M, Subramaniam S, Kuriyan J (2024) "Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM." Nat.Struct.Mol.Biol., 31, 424-435. doi: 10.1038/s41594-023-01177-3. cryo-EM structure of t4 bacteriophage clamp loader with sliding clamp and DNA. SNAP output
8uoq transcription cryo-EM (3.8 Å) Yang C, Basnet P, Sharmin S, Shen H, Kaplan CD, Murakami K (2024) "Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3." Nucleic Acids Res., 52, 11602-11611. doi: 10.1093/nar/gkae805. Composite map of pic_delta_tfiik form2. SNAP output
8uot transcription cryo-EM (3.7 Å) Yang C, Basnet P, Sharmin S, Shen H, Kaplan CD, Murakami K (2024) "Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3." Nucleic Acids Res., 52, 11602-11611. doi: 10.1093/nar/gkae805. Composite map of picdeltatfiik form1. SNAP output
8upf transferase-DNA cryo-EM (3.2 Å) Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G (2024) "Mechanisms of RNF168 nucleosome recognition and ubiquitylation." Mol.Cell, 84, 839-853.e12. doi: 10.1016/j.molcel.2023.12.036. cryo-EM structure of the human nucleosome core particle in complex with rnf168-ubch5c. SNAP output
8urk DNA binding protein X-ray (2.11 Å) Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Ahlsen G, Rechkoblit O, Shapiro L, Filizola M, Fang G, Aggarwal AK (2024) "Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation." Nat Commun, 15, 7839. doi: 10.1038/s41467-024-52130-x. Crystal structure of DNA n6-adenine methyltransferase m.bcejiv from burkholderia cenocepacia in complex with duplex DNA substrates. SNAP output
8urq DNA binding protein cryo-EM (3.3 Å) Yu Y, Wang J, Liu K, Zheng Z, Arter M, Claeys Bouuaert C, Pu S, Patel DJ, Keeney S (2024) "Cryo-EM structures of the Spo11 core complex bound to DNA." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01382-8. Spo11 core complex with gapped DNA. SNAP output
8uru DNA binding protein cryo-EM (3.7 Å) Yu Y, Wang J, Liu K, Zheng Z, Arter M, Claeys Bouuaert C, Pu S, Patel DJ, Keeney S (2024) "Cryo-EM structures of the Spo11 core complex bound to DNA." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01382-8. Spo11 core complex with hairpin DNA. SNAP output
8urw transcription cryo-EM (2.79 Å) Qayyum MZ, Imashimizu M, Leanca M, Vishwakarma RK, Riaz-Bradley A, Yuzenkova Y, Murakami KS (2024) "Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase." Proc.Natl.Acad.Sci.USA, 121, e2311480121. doi: 10.1073/pnas.2311480121. Cyanobacterial RNA polymerase elongation complex with nusg and ctp. SNAP output
8uvk DNA binding protein-DNA X-ray (2.21 Å) Zhang Z, Yan Y, Pang J, Dai L, Zhang Q, Yu EW (2024) "Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator." Mbio, 15, e0343023. doi: 10.1128/mbio.03430-23. Cosr DNA bound form ii. SNAP output
8uvx DNA binding protein-DNA X-ray (2.9 Å) Zhang Z, Yan Y, Pang J, Dai L, Zhang Q, Yu EW (2024) "Structural basis of DNA recognition of the Campylobacter jejuni CosR regulator." Mbio, 15, e0343023. doi: 10.1128/mbio.03430-23. Cosr DNA bound form i. SNAP output
8uw1 gene regulation cryo-EM (2.88 Å) Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C (2024) "Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch." Sci Adv, 10, eadp0975. doi: 10.1126/sciadv.adp0975. cryo-EM structure of dnmt3a1 udr in complex with h2ak119ub-nucleosome. SNAP output
8uw3 RNA binding protein-RNA-DNA cryo-EM (3.2 Å) Thawani A, Ariza AJF, Nogales E, Collins K (2024) "Template and target-site recognition by human LINE-1 in retrotransposition." Nature, 626, 186-193. doi: 10.1038/s41586-023-06933-5. Human line-1 retrotransposon orf2 protein engaged with template RNA in elongation state. SNAP output
8ux1 nuclear protein cryo-EM (2.5 Å) Huang SK, Rubinstein JL, Kay LE "Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle." cryo-EM structure of ran bound to rcc1 and the nucleosome core particle. SNAP output
8uxq structural protein cryo-EM (6.3 Å) Tan D, Sokolova V "Structure of human HP1 in complex with H2A.Z nucleosome." Structure of heterochromatin protein 1 (hp1) alpha in complex with an h2a.z nucleosome. SNAP output
8uza hydrolase-RNA-DNA cryo-EM (3.17 Å) Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA (2024) "Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9." Cell, 187, 3249. doi: 10.1016/j.cell.2024.04.031. cryo-EM structure of geocas9 in complex with sgrna and target DNA. SNAP output
8uzb hydrolase-RNA-DNA cryo-EM (2.63 Å) Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA (2024) "Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9." Cell, 187, 3249. doi: 10.1016/j.cell.2024.04.031. cryo-EM structure of igeocas9 in complex with sgrna and target DNA. SNAP output
8v08 hydrolase-DNA X-ray (3.0 Å) Yuan M, Peng L, Huang D, Gavin A, Luan F, Tran J, Feng Z, Zhu X, Matteson J, Wilson IA, Nemazee D (2024) "Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4." Structure, 32, 766-779.e7. doi: 10.1016/j.str.2024.02.019. Crystal structure of human pld4 co-crystallized with 5'pi-ssDNA. SNAP output
8v1q transferase-DNA cryo-EM (2.7 Å) Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J (2024) "Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance." Cell, 187, 5572-5586.e15. doi: 10.1016/j.cell.2024.07.048. Herpes simplex virus 1 polymerase holoenzyme bound to DNA in both open-closed conformations. SNAP output
8v1r transferase-DNA cryo-EM (2.9 Å) Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J (2024) "Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance." Cell, 187, 5572-5586.e15. doi: 10.1016/j.cell.2024.07.048. Herpes simplex virus 1 polymerase holoenzyme bound to DNA and dttp in closed conformation. SNAP output
8v1s transferase-DNA cryo-EM (3.26 Å) Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J (2024) "Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance." Cell, 187, 5572-5586.e15. doi: 10.1016/j.cell.2024.07.048. Herpes simplex virus 1 polymerase holoenzyme bound to mismatched DNA in editing conformation. SNAP output
8v1t transferase-DNA cryo-EM (2.8 Å) Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J (2024) "Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance." Cell, 187, 5572-5586.e15. doi: 10.1016/j.cell.2024.07.048. Herpes simplex virus 1 polymerase holoenzyme bound to DNA and acyclovir triphosphate in closed conformation. SNAP output
8v25 DNA binding protein-DNA cryo-EM (3.32 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2bk120ub-modified nucleosome ubiquitin position 1. SNAP output
8v26 DNA binding protein-DNA cryo-EM (3.33 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2bk120ub-modified nucleosome ubiquitin position 2. SNAP output
8v27 DNA binding protein-DNA cryo-EM (3.34 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2bk120ub-modified nucleosome ubiquitin position 3. SNAP output
8v28 DNA binding protein-DNA cryo-EM (3.36 Å) Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C (2024) "Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch." Nucleic Acids Res., 52, 9978-9995. doi: 10.1093/nar/gkae698. H2bk120ub-modified nucleosome ubiquitin position 4. SNAP output
8v32 DNA binding protein-DNA cryo-EM (3.01 Å) Wang S, Siddique R, Hall MC, Rice PA, Chang L (2024) "Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition." Cell. doi: 10.1016/j.cell.2024.09.023. Tnsd-tnsc-DNA complex. SNAP output
8v4y DNA binding protein-DNA cryo-EM (2.8 Å) Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y (2024) "Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking." Nat Commun, 15, 2225. doi: 10.1038/s41467-024-46178-y. cryo-EM structure of singly-bound snf2h-nucleosome complex with snf2h at inactive shl2 (conformation 1). SNAP output
8v54 DNA binding protein-DNA cryo-EM (4.1 Å) Riccio AA, Brannon AJ, Krahn JM, Bouvette J, Williams JG, Borgnia MJ, Copeland WC (2024) "Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis." Nucleic Acids Res., 52, 7863-7875. doi: 10.1093/nar/gkae539. Engaged conformation of the human mitochondrial DNA polymerase gamma bound to DNA. SNAP output
8v55 DNA binding protein-DNA cryo-EM (4.2 Å) Riccio AA, Brannon AJ, Krahn JM, Bouvette J, Williams JG, Borgnia MJ, Copeland WC (2024) "Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis." Nucleic Acids Res., 52, 7863-7875. doi: 10.1093/nar/gkae539. Human mitochondrial DNA polymerase gamma bound to a replication fork in an open conformation. SNAP output
8v5r DNA binding protein-DNA cryo-EM (3.0 Å) Riccio AA, Brannon AJ, Krahn JM, Bouvette J, Williams JG, Borgnia MJ, Copeland WC (2024) "Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis." Nucleic Acids Res., 52, 7863-7875. doi: 10.1093/nar/gkae539. Active conformation of DNA polymerase gamma bound to DNA. SNAP output
8v6g replication, transferase cryo-EM (11.16 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. DNA initiation complex (configuration 1) of xenopus laevis DNA polymerase alpha-primase. SNAP output
8v6h replication, transferase-DNA-RNA cryo-EM (11.11 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. DNA initiation complex (configuration 2) of xenopus laevis DNA polymerase alpha-primase. SNAP output
8v6i replication, transferase-DNA-RNA cryo-EM (14.06 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. DNA elongation complex (configuration 1) of xenopus laevis DNA polymerase alpha-primase. SNAP output
8v6j replication, transferase-DNA-RNA cryo-EM (11.11 Å) Mullins EA, Salay LE, Durie CL, Bradley NP, Jackman JE, Ohi MD, Chazin WJ, Eichman BF (2024) "A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase." Nat.Struct.Mol.Biol., 31, 777-790. doi: 10.1038/s41594-024-01227-4. DNA elongation complex (configuration 2) of xenopus laevis DNA polymerase alpha-primase. SNAP output
8v6v DNA binding protein-DNA cryo-EM (2.8 Å) Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y (2024) "Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking." Nat Commun, 15, 2225. doi: 10.1038/s41467-024-46178-y. cryo-EM structure of doubly-bound snf2h-nucleosome complex. SNAP output
8v7a transferase-DNA X-ray (1.95 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-dT primer dCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion." Human DNA polymerase eta-DNA-dt primer dctp insertion ternary complex at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
8v7b transferase-DNA X-ray (1.9 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion." Human DNA polymerase eta-DNA-dt primer aractp insertion ternary complex at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
8v7c transferase-DNA X-ray (1.79 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-dT primer gemCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion." Human DNA polymerase eta-DNA-dt primer gemctp insertion ternary complex at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
8v7d transferase-DNA X-ray (1.95 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-dT primer rCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion." Human DNA polymerase eta-DNA-dt primer rctp insertion ternary complex at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
8v7e transferase-DNA X-ray (1.82 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer-dAMPNPP ternary complex with Mg2+." Human DNA polymerase eta-DNA-arac-ended primer-dampnpp ternary complex with mg2+. SNAP output
8v7f transferase-DNA X-ray (2.2 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer-dAMPNPP ternary complex with Mn2+." Human DNA polymerase eta-DNA-arac-ended primer-dampnpp ternary complex with mn2+. SNAP output
8v7g transferase-DNA X-ray (1.52 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer-dAMPNPP ternary complex with Mn2+." Human DNA polymerase eta-DNA-gemc-ended primer-dampnpp ternary complex with mg2+. SNAP output
8v7h transferase-DNA X-ray (1.68 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer ternary complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion." Human DNA polymerase eta-DNA-arac-ended primer ternary complex:ground state at ph7.0 (k+ mes) with 1 ca2+ ion. SNAP output
8v7i transferase-DNA X-ray (1.72 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 1 mM Mg2+ for 1800s." Human DNA polymerase eta-DNA-arac-ended primer ternary complex:reaction with 1 mm mg2+ for 1800s. SNAP output
8v7j transferase-DNA X-ray (1.66 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 20 mM Mg2+ for 600s." Human DNA polymerase eta-DNA-arac-ended primer ternary complex:reaction with 20 mm mg2+ for 600s. SNAP output
8v7k transferase-DNA X-ray (1.65 Å) Chang C, Gao Y "Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 10 mM Mn2+ for 1800s." Human DNA polymerase eta-DNA-arac-ended primer ternary complex:reaction with 10 mm mn2+ for 1800s. SNAP output
8v7l DNA binding protein-DNA cryo-EM (2.9 Å) Chio US, Palovcak E, Smith AAA, Autzen H, Munoz EN, Yu Z, Wang F, Agard DA, Armache JP, Narlikar GJ, Cheng Y (2024) "Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking." Nat Commun, 15, 2225. doi: 10.1038/s41467-024-46178-y. cryo-EM structure of singly-bound snf2h-nucleosome complex with snf2h at inactive shl2 (conformation 2). SNAP output
8v9n transcription X-ray (1.78 Å) Ogbonna EN, Terrell JR, Paul A, Farahat AA, Poon GMK, Boykin DW, Wilson WD (2024) "Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics." Rsc Adv, 14, 29675-29682. doi: 10.1039/d4ra05957c. Human pu.1 ets-domain (165-270) bound to d(aatagaaggaagtggg). SNAP output
8val replication, transferase-DNA cryo-EM (3.7 Å) Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA (2024) "Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication." J.Biol.Chem., 300, 107166. doi: 10.1016/j.jbc.2024.107166. Structure of the e. coli clamp loader bound to the beta clamp in a open-dnap-t conformation. SNAP output
8vaq replication-DNA cryo-EM (3.8 Å) Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA (2024) "Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication." J.Biol.Chem., 300, 107166. doi: 10.1016/j.jbc.2024.107166. Structure of the e. coli clamp loader bound to the beta clamp in a closed-dna1 conformation. SNAP output
8var replication-DNA cryo-EM (3.9 Å) Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA (2024) "Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication." J.Biol.Chem., 300, 107166. doi: 10.1016/j.jbc.2024.107166. Structure of the e. coli clamp loader bound to the beta clamp in a closed-dna2 conformation. SNAP output
8vas replication-DNA cryo-EM (3.8 Å) Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA (2024) "Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication." J.Biol.Chem., 300, 107166. doi: 10.1016/j.jbc.2024.107166. Structure of the e. coli clamp loader bound to the beta clamp in an altered-collar conformation. SNAP output
8vcj DNA binding protein-DNA cryo-EM (3.32 Å) Shen Y, Krishnan SS, Petassi MT, Hancock MA, Peters JE, Guarne A (2024) "Assembly of the Tn7 targeting complex by a regulated stepwise process." Mol.Cell, 84, 2368-2381.e6. doi: 10.1016/j.molcel.2024.05.012. Cryoem structure of the tnsc(1-503)-tnsd(1-318)-DNA complex in a 7:2:1 stoichiometry from e. coli tn7 bound to atpgs and adp. SNAP output
8vct DNA binding protein-DNA cryo-EM (3.83 Å) Shen Y, Krishnan SS, Petassi MT, Hancock MA, Peters JE, Guarne A (2024) "Assembly of the Tn7 targeting complex by a regulated stepwise process." Mol.Cell, 84, 2368-2381.e6. doi: 10.1016/j.molcel.2024.05.012. Cyoem structure of the tnsc(1-503)-tnsd(1-318)-DNA complex in a 6:2:1 stoichiometry from e. coli tn7 bound to atpgs and adp. SNAP output
8vdn ligase-DNA X-ray (2.39 Å) Balu KE, Gulkis M, Almohdar D, Caglayan M (2024) "Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA." J.Biol.Chem., 300, 107216. doi: 10.1016/j.jbc.2024.107216. DNA ligase 1 with nick dg:c. SNAP output
8vds ligase-DNA X-ray (2.79 Å) Balu KE, Gulkis M, Almohdar D, Caglayan M (2024) "Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA." J.Biol.Chem., 300, 107216. doi: 10.1016/j.jbc.2024.107216. DNA ligase 1 with nick DNA 3'rg:c. SNAP output
8vdt ligase-DNA X-ray (2.78 Å) Balu KE, Gulkis M, Almohdar D, Caglayan M (2024) "Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA." J.Biol.Chem., 300, 107216. doi: 10.1016/j.jbc.2024.107216. DNA ligase 1 with nick DNA 3'ra:t. SNAP output
8vf8 DNA binding protein-DNA X-ray (1.98 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Binary DNA polymerase beta bound to DNA containing primer terminal dc base-paired with fapydg. SNAP output
8vf9 DNA binding protein-DNA X-ray (1.9 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Binary DNA polymerase beta bound to DNA containing primer terminal da base-paired with fapydg. SNAP output
8vfa DNA binding protein-DNA X-ray (2.05 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Ternary DNA polymerase beta bound to DNA containing primer terminal dc base-paired with fapydg. SNAP output
8vfb DNA binding protein-DNA X-ray (2.64 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Ternary DNA polymerase beta bound to DNA containing primer terminal da base-paired with fapydg. SNAP output
8vfc DNA binding protein-DNA X-ray (2.48 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Binary DNA polymerase beta bound to DNA containing primer terminal t base-paired with fapydg. SNAP output
8vfe DNA binding protein-DNA X-ray (2.09 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Binary DNA polymerase beta bound to DNA containing primer terminal fapydg base-paired with a t. SNAP output
8vff DNA binding protein-DNA X-ray (1.69 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Binary DNA polymerase beta bound to DNA containing primer terminal fapydg base-paired with a da. SNAP output
8vfg DNA binding protein-DNA X-ray (1.54 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Binary DNA polymerase beta bound to DNA containing primer terminal fapydg base-paired with a dc. SNAP output
8vfh DNA binding protein-DNA X-ray (2.01 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Ternary DNA polymerase beta bound to DNA containing primer terminal fapydg base-paired with a dc. SNAP output
8vfi DNA binding protein-DNA X-ray (1.77 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Ternary DNA polymerase beta bound to DNA containing primer terminal fapydg base-paired with a da. SNAP output
8vfj DNA binding protein-DNA X-ray (2.14 Å) Gao S, Oden PN, Ryan BJ, Yang H, Freudenthal BD, Greenberg MM (2024) "Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta." Nucleic Acids Res., 52, 5392-5405. doi: 10.1093/nar/gkae277. Polymerase beta host guest complex containing fapydg base paired with tmp. SNAP output
8vfx nuclear protein-DNA cryo-EM (2.65 Å) Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y (2024) "Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4." Mol.Cell, 84, 3061. doi: 10.1016/j.molcel.2024.07.016. cryo-EM structure of 186bp albn1 nucleosome aided by scfv. SNAP output
8vfy nuclear protein-DNA cryo-EM (2.89 Å) Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y (2024) "Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4." Mol.Cell, 84, 3061. doi: 10.1016/j.molcel.2024.07.016. cryo-EM structure of foxa1 in complex with albn1 nucleosome (class 1). SNAP output
8vfz nuclear protein-DNA cryo-EM (4.1 Å) Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y (2024) "Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4." Mol.Cell, 84, 3061. doi: 10.1016/j.molcel.2024.07.016. cryo-EM structure of foxa1 in complex with albn1 nucleosome (class 2). SNAP output
8vg0 nuclear protein-DNA cryo-EM (3.07 Å) Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y (2024) "Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4." Mol.Cell, 84, 3061. doi: 10.1016/j.molcel.2024.07.016. cryo-EM structure of gata4 in complex with albn1 nucleosome. SNAP output
8vg1 nuclear protein-DNA cryo-EM (2.48 Å) Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y (2024) "Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4." Mol.Cell, 84, 3061. doi: 10.1016/j.molcel.2024.07.016. cryo-EM structure of foxa1 and gata4 in complex with albn1 nucleosome. SNAP output
8vg2 nuclear protein-DNA cryo-EM (3.04 Å) Zhou BR, Bai Y (2024) "Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome." Mol.Cell. cryo-EM structure of foxa1 and gata4 in complex with h14 chromatosome. SNAP output
8vmo hydrolase X-ray (1.68 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:ground state at ph7.0 (k+ mes) with na+. SNAP output
8vmp hydrolase X-ray (1.45 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 10s. SNAP output
8vmq hydrolase X-ray (1.48 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 20s. SNAP output
8vmr hydrolase-DNA X-ray (1.5 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 40s. SNAP output
8vms hydrolase X-ray (1.42 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 80s. SNAP output
8vmt hydrolase X-ray (1.48 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 160s. SNAP output
8vmu hydrolase X-ray (1.52 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 320s. SNAP output
8vmv hydrolase-DNA X-ray (1.59 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph7.0 (k+ mes) with 500 um mg2+ for 600s. SNAP output
8vmw hydrolase X-ray (1.6 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:ground state at ph6.0 (k+ mes) with na+. SNAP output
8vmx hydrolase X-ray (1.45 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 10s. SNAP output
8vmy hydrolase X-ray (1.53 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 20s. SNAP output
8vmz hydrolase X-ray (1.57 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 40s. SNAP output
8vn0 hydrolase X-ray (1.6 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 80s. SNAP output
8vn1 hydrolase X-ray (1.79 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 160s. SNAP output
8vn2 hydrolase X-ray (1.63 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 320s. SNAP output
8vn3 hydrolase-DNA X-ray (1.63 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 600s. SNAP output
8vn4 hydrolase-DNA X-ray (1.75 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 1200s. SNAP output
8vn5 hydrolase X-ray (1.65 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:ground state at ph8.0 (tris) with na+. SNAP output
8vn6 hydrolase X-ray (1.54 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 10s. SNAP output
8vn7 hydrolase-DNA X-ray (1.67 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 20s. SNAP output
8vn8 hydrolase X-ray (1.6 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 40s. SNAP output
8vn9 hydrolase X-ray (1.69 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 80s. SNAP output
8vna hydrolase X-ray (1.54 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 160s. SNAP output
8vnb hydrolase-DNA X-ray (1.72 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 240s. SNAP output
8vnc hydrolase-DNA X-ray (1.62 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 320s. SNAP output
8vnd hydrolase-DNA X-ray (1.6 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph8.0 (tris) with 500 um mg2+ for 600s. SNAP output
8vne hydrolase X-ray (1.57 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 10s. SNAP output
8vnf hydrolase X-ray (1.5 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 20s. SNAP output
8vng hydrolase X-ray (1.6 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 40s. SNAP output
8vnh hydrolase X-ray (1.76 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 80s. SNAP output
8vnj hydrolase X-ray (1.61 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 120s. SNAP output
8vnk hydrolase X-ray (1.61 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 160s. SNAP output
8vnl hydrolase-DNA X-ray (1.64 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 240s. SNAP output
8vnm hydrolase X-ray (1.59 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 320s. SNAP output
8vnn hydrolase-DNA X-ray (1.79 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 480s. SNAP output
8vno hydrolase-DNA X-ray (1.7 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mn2+ for 600s. SNAP output
8vnp hydrolase X-ray (1.79 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex at ph6.0 (k+ mes) with 0.2 m sodium malonate. SNAP output
8vnq hydrolase X-ray (1.93 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease h98a i-ppoi-DNA complex at ph6.0 (k+ mes) with 1 mm mn2+ for 1800s. SNAP output
8vnr hydrolase X-ray (1.98 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease h98a i-ppoi-DNA complex at ph6.0 (k+ mes) with 1 mm mn2+ for 600s and then 100 mm imidazole for 15 hrs. SNAP output
8vns hydrolase-DNA X-ray (2.11 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 200 mm mn2+ for 600s. SNAP output
8vnt hydrolase-DNA X-ray (1.62 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease i-ppoi-DNA complex:reaction at ph6.0 (k+ mes) with 500 um mg2+ for 1800s. SNAP output
8vnu hydrolase X-ray (2.2 Å) Chang C, Gao Y "Homing endonuclease I-PpoI-DNA complex:reaction with 500 uM Mg2+ for 160s." Homing endonuclease h98a i-ppoi-DNA complex at ph6.0 (k+ mes) with 70 mm tl+ for 1800s. SNAP output
8vws DNA binding protein-DNA cryo-EM (3.1 Å) Weaver TM, Ling JA, Freudenthal BD "Nucleosome containing 8oxoG at SHL-6." Nucleosome containing 8oxog at shl-6. SNAP output
8vwt DNA binding protein-DNA cryo-EM (3.3 Å) Weaver TM, Ling JA, Freudenthal BD "OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map)." Ogg1 bound to a nucleosome containing 8oxog at shl-6 (composite map). SNAP output
8vwu DNA binding protein-DNA cryo-EM (3.0 Å) Weaver TM, Ling JA, Freudenthal BD "Nucleosome containing 8oxoG at SHL4." Nucleosome containing 8oxog at shl4. SNAP output
8vwv DNA binding protein-DNA cryo-EM (3.6 Å) Weaver TM, Ling JA, Freudenthal BD "OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map)." Ogg1 bound to a nucleosome containing 8oxog at shl4 (composite map). SNAP output
8vx4 hydrolase, lyase-DNA cryo-EM (3.7 Å) You Q, Feng X, Cai Y, Baylin SB, Li H (2024) "Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations." Commun Biol, 7, 1202. doi: 10.1038/s42003-024-06919-7. Human ogg1 bound to a 35-bp DNA with an 8-oxog in the middle. SNAP output
8vx5 structural protein-DNA cryo-EM (3.3 Å) You Q, Feng X, Cai Y, Baylin SB, Li H (2024) "Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations." Commun Biol, 7, 1202. doi: 10.1038/s42003-024-06919-7. Nucleosome core particle containing an 8-oxog damage site. SNAP output
8vx6 hydrolase, lyase-structural protein-DNA cryo-EM (3.2 Å) You Q, Feng X, Cai Y, Baylin SB, Li H (2024) "Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations." Commun Biol, 7, 1202. doi: 10.1038/s42003-024-06919-7. Human ogg1 bound at the nucleosomal DNA entry site. SNAP output
8vxa immune system-DNA cryo-EM (2.79 Å) Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA (2024) "Hachiman is a genome integrity sensor." Biorxiv. doi: 10.1101/2024.02.29.582594. Structure of hamb-DNA complex, conformation 1, from the escherichia coli hachiman defense system. SNAP output
8vxc immune system-DNA cryo-EM (2.93 Å) Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA (2024) "Hachiman is a genome integrity sensor." Biorxiv. doi: 10.1101/2024.02.29.582594. Structure of hamb-DNA complex, conformation 2, from the escherichia coli hachiman defense system. SNAP output
8vxy immune system cryo-EM (3.19 Å) Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA (2024) "Hachiman is a genome integrity sensor." Biorxiv. doi: 10.1101/2024.02.29.582594. Structure of hama(e138a,k140a)b-plasmid DNA complex from the escherichia coli hachiman defense system. SNAP output
8vzl ligase-DNA X-ray (2.41 Å) Balu KE, Gulkis M, Almohdar D, Caglayan M (2024) "Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA." J.Biol.Chem., 300, 107216. doi: 10.1016/j.jbc.2024.107216. DNA ligase 1 captured with pre-step 3 ligation at the rg:c nicksite. SNAP output
8vzm ligase-DNA X-ray (2.51 Å) Balu KE, Gulkis M, Almohdar D, Caglayan M (2024) "Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA." J.Biol.Chem., 300, 107216. doi: 10.1016/j.jbc.2024.107216. DNA ligase 1 captured with pre-step 3 ligation at the ra:t nicksite. SNAP output
8w09 viral protein cryo-EM (3.2 Å) Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R (2024) "HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro." J.Mol.Biol., 436, 168557. doi: 10.1016/j.jmb.2024.168557. Hiv-1 wild-type intasome core. SNAP output
8w0a transferase-DNA cryo-EM (3.2 Å) Ito F, Li Z, Minakhin L, Khant HA, Pomerantz RT, Chen XS (2024) "Structural Basis for Pol theta-Helicase DNA Binding and Microhomology-Mediated End-Joining." Biorxiv. doi: 10.1101/2024.06.07.597860. Human DNA polymerase theta helicase domain in complex with ssDNA, dimer form. SNAP output
8w2p DNA binding protein-DNA cryo-EM (3.14 Å) Shen BW, Heiter D, Xu S, Stoddard BL "Structural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI." Bsaxi-DNA complex i. SNAP output
8w2q DNA binding protein-DNA cryo-EM (3.06 Å) Shen BW, Heiter D, Xu S, Stoddard BL "Structural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI." Bsaxi-DNA complex ii. SNAP output
8w2r viral protein cryo-EM (3.23 Å) Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R (2024) "HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro." J.Mol.Biol., 436, 168557. doi: 10.1016/j.jmb.2024.168557. Hiv-1 p5-in intasome core. SNAP output
8w34 viral protein cryo-EM (2.83 Å) Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R (2024) "HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro." J.Mol.Biol., 436, 168557. doi: 10.1016/j.jmb.2024.168557. Hiv-1 intasome core assembled with wild-type integrase, 1f. SNAP output
8w7m replication cryo-EM (4.12 Å) Xu Z, Feng J, Yu D, Huo Y, Ma X, Lam WH, Liu Z, Li XD, Ishibashi T, Dang S, Zhai Y (2023) "Synergism between CMG helicase and leading strand DNA polymerase at replication fork." Nat Commun, 14, 5849. doi: 10.1038/s41467-023-41506-0. Yeast replisome in state v. SNAP output
8w8e transcription cryo-EM (3.9 Å) Li Y, Wang Q, Xu Y, Li Z (2024) "Structures of co-transcriptional RNA capping enzymes on paused transcription complex." Nat Commun, 15, 4622. doi: 10.1038/s41467-024-48963-1. Human co-transcriptional RNA capping enzyme rngtt. SNAP output
8w8f transcription cryo-EM (4.0 Å) Li Y, Wang Q, Xu Y, Li Z (2024) "Structures of co-transcriptional RNA capping enzymes on paused transcription complex." Nat Commun, 15, 4622. doi: 10.1038/s41467-024-48963-1. Human co-transcriptional RNA capping enzyme rngtt-cmtr1. SNAP output
8w8n transcription-DNA-RNA X-ray (2.693 Å) Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH (2024) "Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase." Proc.Natl.Acad.Sci.USA, 121, e2321017121. doi: 10.1073/pnas.2321017121. Thermus thermophilus initiation transcription complex in the pre-translocated state. SNAP output
8w8o transcription-DNA-RNA X-ray (2.512 Å) Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH (2024) "Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase." Proc.Natl.Acad.Sci.USA, 121, e2321017121. doi: 10.1073/pnas.2321017121. Thermus thermophilus initiation complex in the half-translocated state. SNAP output
8w8p transcription-DNA-RNA X-ray (3.165 Å) Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH (2024) "Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase." Proc.Natl.Acad.Sci.USA, 121, e2321017121. doi: 10.1073/pnas.2321017121. Thermus thermophilus initiation transcription complex containing cmpcpp in the post-translocated state. SNAP output
8w9d DNA binding protein-DNA cryo-EM (3.9 Å) Wang C, Chu C, Guo Z, Zhan X (2024) "Structures and dynamics of Rpd3S complex bound to nucleosome." Sci Adv, 10, eadk7678. doi: 10.1126/sciadv.adk7678. cryo-EM structure of the rpd3s-nucleosome complex from budding yeast in state 1. SNAP output
8w9e DNA binding protein-DNA cryo-EM (3.6 Å) Wang C, Chu C, Guo Z, Zhan X (2024) "Structures and dynamics of Rpd3S complex bound to nucleosome." Sci Adv, 10, eadk7678. doi: 10.1126/sciadv.adk7678. cryo-EM structure of the rpd3s-nucleosome complex from budding yeast in state 2. SNAP output
8w9f DNA binding protein-DNA cryo-EM (4.4 Å) Wang C, Chu C, Guo Z, Zhan X (2024) "Structures and dynamics of Rpd3S complex bound to nucleosome." Sci Adv, 10, eadk7678. doi: 10.1126/sciadv.adk7678. cryo-EM structure of the rpd3s-nucleosome complex from budding yeast in state 3. SNAP output
8wat transcription cryo-EM (2.82 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 10 (tc10), the early elongation complex with pol ii positioned 10nt downstream of tss. SNAP output
8wau transcription cryo-EM (2.78 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 11 (tc11), the early elongation complex with pol ii positioned 11nt downstream of tss. SNAP output
8wav transcription cryo-EM (2.72 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 12 (tc12), the early elongation complex with pol ii positioned 12nt downstream of tss. SNAP output
8waw transcription cryo-EM (3.02 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 13 (tc13), the early elongation complex with pol ii positioned 13nt downstream of tss. SNAP output
8wax transcription cryo-EM (2.75 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 14 (tc14), the early elongation complex with pol ii positioned 14nt downstream of tss. SNAP output
8way transcription cryo-EM (2.85 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 15 (tc15), the early elongation complex with pol ii positioned 15nt downstream of tss. SNAP output
8waz transcription cryo-EM (2.76 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 16 (tc16), the early elongation complex with pol ii positioned 16nt downstream of tss. SNAP output
8wb0 transcription cryo-EM (2.94 Å) Chen X, Liu W, Wang Q, Wang X, Ren Y, Qu X, Li W, Xu Y (2023) "Structural visualization of transcription initiation in action." Science, 382, eadi5120. doi: 10.1126/science.adi5120. De novo transcribing complex 17 (tc17), the early elongation complex with pol ii positioned 17nt downstream of tss. SNAP output
8wd8 DNA binding protein-DNA cryo-EM (2.9 Å) Wang L, Chen W, Zhang C, Xie X, Huang F, Chen M, Mao W, Yu N, Wei Q, Ma L, Li Z (2024) "Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute." Mol.Cell, 84, 675-686.e4. doi: 10.1016/j.molcel.2024.01.004. cryo-EM structure of ttdago-guide DNA-target DNA complex. SNAP output
8wg5 nuclear protein cryo-EM (3.05 Å) Ai H, He Z, Deng Z, Chu GC, Shi Q, Tong Z, Li JB, Pan M, Liu L (2024) "Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01342-2. cryo-EM structure of usp16 bound to h2ak119ub nucleosome. SNAP output
8wgy DNA binding protein-DNA cryo-EM (2.91 Å) Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C (2024) "Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer." Sci Adv, 10, eadl1150. doi: 10.1126/sciadv.adl1150. Mpox e5 hexamer amp-pnp and ssDNA bound form with clear primase domain. SNAP output
8wgz DNA binding protein-DNA cryo-EM (3.22 Å) Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C (2024) "Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer." Sci Adv, 10, eadl1150. doi: 10.1126/sciadv.adl1150. Mpox e5 double hexamer ssDNA bound conformation. SNAP output
8wh0 DNA binding protein-DNA cryo-EM (2.51 Å) Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C (2024) "Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer." Sci Adv, 10, eadl1150. doi: 10.1126/sciadv.adl1150. Mpox e5 hexamer ssDNA and amp-pnp bound conformation. SNAP output
8wh4 DNA binding protein-DNA cryo-EM (3.03 Å) Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C (2024) "Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer." Sci Adv, 10, eadl1150. doi: 10.1126/sciadv.adl1150. Mpox e5 hexamer ssDNA bound apo conformation. SNAP output
8wh5 gene regulation cryo-EM (3.58 Å) Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J (2024) "Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation." Nat.Plants, 10, 374-380. doi: 10.1038/s41477-024-01640-z. Structure of ddm1-nucleosome complex in the apo state. SNAP output
8wh6 DNA binding protein-DNA cryo-EM (3.27 Å) Xu Y, Wu Y, Zhang Y, Gao K, Wu X, Yang Y, Li D, Yang B, Zhang Z, Dong C (2024) "Essential and multifunctional mpox virus E5 helicase-primase in double and single hexamer." Sci Adv, 10, eadl1150. doi: 10.1126/sciadv.adl1150. Mpox e5 hexamer adp and ssDNA bound and clear primase domain conformation. SNAP output
8wh8 gene regulation cryo-EM (3.6 Å) Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J (2024) "Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation." Nat.Plants, 10, 374-380. doi: 10.1038/s41477-024-01640-z. Structure of ddm1-nucleosome complex in adp state. SNAP output
8wh9 gene regulation cryo-EM (3.31 Å) Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J (2024) "Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation." Nat.Plants, 10, 374-380. doi: 10.1038/s41477-024-01640-z. Structure of ddm1-nucleosome complex in adp-befx state. SNAP output
8wha gene regulation cryo-EM (4.05 Å) Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J (2024) "Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation." Nat.Plants, 10, 374-380. doi: 10.1038/s41477-024-01640-z. Structure of ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2. SNAP output
8whb gene regulation cryo-EM (3.17 Å) Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J (2024) "Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation." Nat.Plants, 10, 374-380. doi: 10.1038/s41477-024-01640-z. Structure of nucleosome core particle of arabidopsis thaliana. SNAP output
8wmh DNA binding protein-DNA-RNA cryo-EM (2.6 Å) Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG (2024) "Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity." Nature, 630, 484-492. doi: 10.1038/s41586-024-07486-x. Structure of cbcas9 bound to 6-nucleotide complementary DNA substrate. SNAP output
8wmm DNA binding protein-DNA-RNA cryo-EM (2.98 Å) Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG (2024) "Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity." Nature, 630, 484-492. doi: 10.1038/s41586-024-07486-x. Structure of cbcas9-pcriic1 complex bound to 28-bp DNA substrate (20-nt complementary). SNAP output
8wmn DNA binding protein-DNA-RNA cryo-EM (2.82 Å) Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG (2024) "Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity." Nature, 630, 484-492. doi: 10.1038/s41586-024-07486-x. Structure of cbcas9-pcriic1 complex bound to 62-bp DNA substrate (symmetric 20-nt complementary). SNAP output
8woh DNA binding protein X-ray (3.2 Å) Wen Y, Wu BX "human dsDNA sensor CCDC25 complexed with 18bp DNA." Human dsDNA sensor ccdc25 complexed with 18bp DNA. SNAP output
8wpe viral protein cryo-EM (2.7 Å) Wang X, Ma L, Li N, Gao N (2023) "Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5." Mol.Cell, 83, 4398. doi: 10.1016/j.molcel.2023.10.038. Structure of monkeypox virus polymerase complex f8-a22-e4-h5 (tag-free a22) with exogenous DNA. SNAP output
8wpf viral protein cryo-EM (3.0 Å) Wang X, Ma L, Li N, Gao N (2023) "Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5." Mol.Cell, 83, 4398. doi: 10.1016/j.molcel.2023.10.038. Structure of monkeypox virus polymerase complex f8-a22-e4-h5 with exogenous DNA bearing one abasic site. SNAP output
8wpk viral protein cryo-EM (2.7 Å) Wang X, Ma L, Li N, Gao N (2023) "Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5." Mol.Cell, 83, 4398. doi: 10.1016/j.molcel.2023.10.038. Structure of monkeypox virus polymerase complex f8-a22-e4-h5 with exgenous DNA. SNAP output
8wpp viral protein cryo-EM (3.1 Å) Wang X, Ma L, Li N, Gao N (2023) "Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5." Mol.Cell, 83, 4398. doi: 10.1016/j.molcel.2023.10.038. Structure of monkeypox virus polymerase complex f8-a22-e4-h5 with endogenous DNA. SNAP output
8wq5 RNA binding protein-DNA X-ray (1.65 Å) Chen X, Wei Q, Yang Z, Chen X, Guo S, Jiang M, Wang M (2024) "Structural basis for RNA recognition by the C-terminal RRM domain of human RBM45." J.Biol.Chem., 300, 107640. doi: 10.1016/j.jbc.2024.107640. Crystal structure of the c-terminal rrm domain of an rbp in complex with ssDNA. SNAP output
8wr4 DNA binding protein-DNA-RNA cryo-EM (3.07 Å) Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG (2024) "Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity." Nature, 630, 484-492. doi: 10.1038/s41586-024-07486-x. Structure of cbcas9-pcriic1 complex bound to 62-bp DNA substrate (non-targeting complex). SNAP output
8wt6 recombination-DNA-RNA cryo-EM (2.5 Å) Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H (2024) "Structural mechanism of bridge RNA-guided recombination." Nature, 630, 994-1002. doi: 10.1038/s41586-024-07570-2. cryo-EM structure of the is621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange state. SNAP output
8wt7 recombination-RNA-DNA cryo-EM (2.7 Å) Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H (2024) "Structural mechanism of bridge RNA-guided recombination." Nature, 630, 994-1002. doi: 10.1038/s41586-024-07570-2. cryo-EM structure of the is621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange locked state. SNAP output
8wt8 recombination-RNA-DNA cryo-EM (2.9 Å) Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H (2024) "Structural mechanism of bridge RNA-guided recombination." Nature, 630, 994-1002. doi: 10.1038/s41586-024-07570-2. cryo-EM structure of the is621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (holliday junction intermediate). SNAP output
8wt9 recombination-RNA-DNA cryo-EM (2.7 Å) Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H (2024) "Structural mechanism of bridge RNA-guided recombination." Nature, 630, 994-1002. doi: 10.1038/s41586-024-07570-2. cryo-EM structure of the is621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (holliday junction resolution). SNAP output
8wus RNA binding protein-RNA-DNA cryo-EM (2.9 Å) Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O (2024) "Structural basis for pegRNA-guided reverse transcription by a prime editor." Nature, 631, 224-231. doi: 10.1038/s41586-024-07497-8. Spcas9-mmlv rt-pegrna-target DNA complex (termination). SNAP output
8wuv RNA binding protein-RNA-DNA cryo-EM (3.0 Å) Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O (2024) "Structural basis for pegRNA-guided reverse transcription by a prime editor." Nature, 631, 224-231. doi: 10.1038/s41586-024-07497-8. Spcas9-mmlv rt-pegrna-target DNA complex (elongation 16-nt). SNAP output
8wvz DNA binding protein-DNA cryo-EM (3.15 Å) Shi TH, Guo YY, Yan RH "Structure of ADP-Form AsfvPrimPol Hexamer." Structure of adp-form asfvprimpol hexamer. SNAP output
8wy5 DNA binding protein-DNA cryo-EM (3.12 Å) Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L (2024) "Structures and activation mechanism of the Gabija anti-phage system." Nature, 629, 467-473. doi: 10.1038/s41586-024-07270-x. Structure of gabija gaja in complex with DNA. SNAP output
8x1z transferase X-ray (2.62 Å) Yasutake Y, Hattori SI, Kumamoto H, Tamura N, Maeda K, Mitsuya H (2024) "Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations." Sci Rep, 14, 15742. doi: 10.1038/s41598-024-66505-z. Hiv-1 reverse transcriptase mutant q151m-y115f-f116y:DNA:e-cfcp-tp ternary complex. SNAP output
8x20 transferase X-ray (2.7 Å) Yasutake Y, Hattori SI, Kumamoto H, Tamura N, Maeda K, Mitsuya H (2024) "Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations." Sci Rep, 14, 15742. doi: 10.1038/s41598-024-66505-z. Hiv-1 reverse transcriptase mutant q151m-y115f-f116y-l74v:DNA:e-cfcp-tp ternary complex. SNAP output
8x21 transferase X-ray (2.33 Å) Yasutake Y, Hattori SI, Kumamoto H, Tamura N, Maeda K, Mitsuya H (2024) "Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations." Sci Rep, 14, 15742. doi: 10.1038/s41598-024-66505-z. Hiv-1 reverse transcriptase mutant q151m-y115f-f116y-l74v:DNA:etv-tp ternary complex. SNAP output
8x22 transferase X-ray (2.31 Å) Yasutake Y, Hattori SI, Kumamoto H, Tamura N, Maeda K, Mitsuya H (2024) "Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations." Sci Rep, 14, 15742. doi: 10.1038/s41598-024-66505-z. Hiv-1 reverse transcriptase mutant q151m-y115f-f116y-l74v:DNA:dgtp ternary complex. SNAP output
8x51 DNA binding protein-DNA cryo-EM (2.92 Å) Li J, Cheng R, Wang Z, Yuan W, Xiao J, Zhao X, Du X, Xia S, Wang L, Zhu B, Wang L (2024) "Structures and activation mechanism of the Gabija anti-phage system." Nature, 629, 467-473. doi: 10.1038/s41586-024-07270-x. Structure of DNA-bound gaja dimer (focused refinement). SNAP output
8x5v RNA binding protein-RNA-DNA X-ray (2.0 Å) Nakane T, Nakagawa R, Ishiguro S, Okazaki S, Mori H, Shuto Y, Yamashita K, Yachie N, Nishimasu H, Nureki O (2024) "Structure and engineering of Brevibacillus laterosporus Cas9." Commun Biol, 7, 803. doi: 10.1038/s42003-024-06422-z. Blcas9-sgrna-target DNA complex. SNAP output
8x6f transcription-DNA cryo-EM (3.7 Å) Yuan L, Liu Q, Xu L, Wu B, Feng Y (2024) "Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase." Nat Commun, 15, 4850. doi: 10.1038/s41467-024-49229-6. cryo-EM structure of staphylococcus aureus siga-dependent rnap-promoter open complex. SNAP output
8x6g transcription cryo-EM (3.3 Å) Yuan L, Liu Q, Xu L, Wu B, Feng Y (2024) "Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase." Nat Commun, 15, 4850. doi: 10.1038/s41467-024-49229-6. cryo-EM structure of staphylococcus aureus sigb-dependent rnap-promoter open complex. SNAP output
8x7i nuclear protein-DNA cryo-EM (3.27 Å) Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M (2024) "Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168." Biorxiv. doi: 10.1101/2024.01.02.573964. cryo-EM structures of rnf168-ubch5c-ub in complex with h2ak13ub nucleosomes determined by intein-based e2-ub-ncp conjugation strategy. SNAP output
8x7j nuclear protein-DNA cryo-EM (3.39 Å) Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M (2024) "Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168." Biorxiv. doi: 10.1101/2024.01.02.573964. cryo-EM structures of rnf168-ubch5c-ub-nucleosomes complex determined by activity-based chemical trapping strategy. SNAP output
8x7k nuclear protein-DNA cryo-EM (3.27 Å) Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M (2024) "Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168." Biorxiv. doi: 10.1101/2024.01.02.573964. cryo-EM structures of rnf168-ubch5c-ub in complex with h2ak13ub nucleosomes determined by activity-based chemical trapping strategy (adjacent h2ak13-15 dual-monoubiquitination). SNAP output
8xa9 hydrolase-DNA X-ray (2.32 Å) Mao EYC, Yen HY, Wu CC (2024) "Structural basis of how MGME1 processes DNA 5' ends to maintain mitochondrial genome integrity." Nucleic Acids Res., 52, 4067-4078. doi: 10.1093/nar/gkae186. Human mgme1 in complex with 5'-overhang DNA. SNAP output
8xak hydrolase-DNA X-ray (3.5 Å) Hong Z, Byrd AK, Gao J, Das P, Tan VQ, Malone EG, Osei B, Marecki JC, Protacio RU, Wahls WP, Raney KD, Song H (2024) "Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge." Nat Commun, 15, 6104. doi: 10.1038/s41467-024-50575-8. Structure of pif1-g4 complex. SNAP output
8xas DNA binding protein X-ray (2.346 Å) Zhou CM, Li JX, Zhang TQ, Xu ZG, Ma ML, Zhang P, Wang JW (2024) "The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin." Proc.Natl.Acad.Sci.USA, 121, e2319335121. doi: 10.1073/pnas.2319335121. Crystal structure of atarr1-dbd in complex with a DNA fragment. SNAP output
8xbt DNA binding protein-DNA cryo-EM (4.12 Å) Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H (2024) "Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site." Nature, 628, 212-220. doi: 10.1038/s41586-024-07196-4. The cryo-EM structure of the octameric rad51 ring bound to the nucleosome with the linker DNA binding. SNAP output
8xbw DNA binding protein-DNA cryo-EM (2.89 Å) Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H (2024) "Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site." Nature, 628, 212-220. doi: 10.1038/s41586-024-07196-4. The cryo-EM structure of the rad51 n-terminal lobe domain bound to the histone h4 tail of the nucleosome. SNAP output
8xj7 replication cryo-EM (2.74 Å) Zhang W, Liu Y, Yang M, Yang J, Shao Z, Gao Y, Jiang X, Cui R, Zhang Y, Zhao X, Shao Q, Cao C, Li H, Li L, Liu H, Gao H, Gan J (2024) "Structural and functional insights into the helicase protein E5 of Mpox virus." Cell Discov, 10, 67. doi: 10.1038/s41421-024-00680-1. The cryo-EM structure of mpxv e5 in complex with DNA. SNAP output
8xj8 replication cryo-EM (2.67 Å) Zhang W, Liu Y, Yang M, Yang J, Shao Z, Gao Y, Jiang X, Cui R, Zhang Y, Zhao X, Shao Q, Cao C, Li H, Li L, Liu H, Gao H, Gan J (2024) "Structural and functional insights into the helicase protein E5 of Mpox virus." Cell Discov, 10, 67. doi: 10.1038/s41421-024-00680-1. The cryo-EM structure of mpxv e5 c-terminal in complex with DNA. SNAP output
8xmd transcription-DNA-RNA cryo-EM (3.4 Å) Huang K, Fang CL, Zhang Y "Transcription of the Plant RNA polymerase IV is prone to backtracking." Pre-translocated pol iv transcription elongation complex. SNAP output
8xp8 DNA-antibiotic X-ray (1.64 Å) Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH (2024) "Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation." Nucleic Acids Res., 52, 8566-8579. doi: 10.1093/nar/gkae594. Crystal structure of d(acgmccgt-acggcgt) in complex with echinomycin. SNAP output
8xpb DNA-antibiotic X-ray (2.0 Å) Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH (2024) "Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation." Nucleic Acids Res., 52, 8566-8579. doi: 10.1093/nar/gkae594. Crystal structure of d(acgccgt-acggcgt) in complex with echinomycin. SNAP output
8xrf replication X-ray (2.94 Å) Yang J, Gan JH (2024) "The crystal structure of AsfvTopII in complex with G-DNA." Nat Commun. The crystal structure of asfvtopii in complex with g-DNA. SNAP output
8xri replication X-ray (2.92 Å) Yang J, Gan JH (2024) "The crystal structure of AsfvTopII in complex with both G-DNA and T-DNA." Nat Commun. The crystal structure of asfvtopii in complex with both g-DNA and t-DNA. SNAP output
8xvb viral protein-DNA cryo-EM (3.4 Å) Zhao X, Gao Y, Gong Q, Zhang K, Li S (2024) "Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition." Nat Commun, 15, 6445. doi: 10.1038/s41467-024-50722-1. cryo-EM structure of atp-DNA-mub filaments. SNAP output
8xyc DNA binding protein-DNA-RNA cryo-EM (2.51 Å) Zhang S, Lin S, Liu JJG "Ternary structure of dVemCas12e-sgRNA-dsDNA." Ternary structure of dvemcas12e-sgrna-dsDNA. SNAP output
8y2i DNA binding protein-DNA-RNA cryo-EM (2.92 Å) Zhang S, Lin S, Liu JJG "Ternary structure of dVemCas12e-sgRNA-dsDNA." Ternary structure of dlescas12e-sgrna-dsDNA. SNAP output
8y7z structural protein-RNA-DNA cryo-EM (2.57 Å) Cui N, Zhang JT, Li Z, Wei XY, Wang J, Jia N (2024) "Tetramerization-dependent activation of the Sir2-associated short prokaryotic Argonaute immune system." Nat Commun, 15, 8610. doi: 10.1038/s41467-024-52910-5. cryo-EM structure of the monomeric sparsa grna-ssDNA complex. SNAP output
8y80 structural protein-RNA-DNA cryo-EM (3.38 Å) Cui N, Zhang JT, Li Z, Wei XY, Wang J, Jia N (2024) "Tetramerization-dependent activation of the Sir2-associated short prokaryotic Argonaute immune system." Nat Commun, 15, 8610. doi: 10.1038/s41467-024-52910-5. cryo-EM structure of the tetrameric sparsa grna-ssDNA complex. SNAP output
8y82 structural protein-RNA-DNA cryo-EM (3.4 Å) Cui N, Zhang JT, Li Z, Wei XY, Wang J, Jia N (2024) "Tetramerization-dependent activation of the Sir2-associated short prokaryotic Argonaute immune system." Nat Commun, 15, 8610. doi: 10.1038/s41467-024-52910-5. cryo-EM structure of the tetrameric sparsa grna-ssDNA-nad+ complex. SNAP output
8ybj DNA binding protein-DNA cryo-EM (2.38 Å) Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H (2024) "Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K." Genes Cells, 29, 769-781. doi: 10.1111/gtc.13143. cryo-EM structure of human nucleosome core particle composed of the widom 601 DNA sequence. SNAP output
8ybk DNA binding protein-DNA cryo-EM (2.69 Å) Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H (2024) "Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K." Genes Cells, 29, 769-781. doi: 10.1111/gtc.13143. cryo-EM structure of the human nucleosome containing the h3.1 e97k mutant. SNAP output
8ydb RNA binding protein-DNA-RNA cryo-EM (3.4 Å) Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z (2024) "Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems." Mol.Cell, 84, 3141. doi: 10.1016/j.molcel.2024.06.033. Type i-fhnh cascade-dsDNA intermediate complex. SNAP output
8yeo RNA binding protein-DNA-RNA cryo-EM (3.44 Å) Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z (2024) "Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems." Mol.Cell, 84, 3141. doi: 10.1016/j.molcel.2024.06.033. Type i-fhnh cascade-dsDNA r-loop complex. SNAP output
8yey DNA binding protein X-ray (2.0 Å) Hu C, Chen Z, Wang G, Yang H, Ding J (2024) "Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role." Structure, 32, 1208. doi: 10.1016/j.str.2024.05.012. Trip4 asch domain in complex with ssDNA-1. SNAP output
8yfi DNA binding protein X-ray (2.02 Å) Hu C, Chen Z, Wang G, Yang H, Ding J (2024) "Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role." Structure, 32, 1208. doi: 10.1016/j.str.2024.05.012. Trip4 asch domain in complex with a 12bp dsDNA (5'-tgaggtacctca-3'). SNAP output
8yfj DNA binding protein X-ray (1.84 Å) Hu C, Chen Z, Wang G, Yang H, Ding J (2024) "Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role." Structure, 32, 1208. doi: 10.1016/j.str.2024.05.012. Trip4 asch domain in complex with a 12bp dsDNA (5'-attggatccaat-3'). SNAP output
8yfq transcription cryo-EM (3.3 Å) Yanagisawa T, Murayama Y, Ehara H, Goto M, Aoki M, Sekine SI (2024) "Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex." Nat Commun, 15, 7854. doi: 10.1038/s41467-024-52157-0. Cryo em structure of komagataella phaffii rnapii-rat1-rai1 pre-termination complex. SNAP output
8yge isomerase-DNA cryo-EM (2.76 Å) Liu R, Sun J, Li LF, Cheng Y, Li M, Fu L, Li S, Peng G, Wang Y, Liu S, Qu X, Ran J, Li X, Pang E, Qiu HJ, Wang Y, Qi J, Wang H, Gao GF (2024) "Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R." Nucleic Acids Res., 52, 11301-11316. doi: 10.1093/nar/gkae703. Pp1192r-DNA-m-amsa complex DNA binding-cleavage domain. SNAP output
8ygj RNA binding protein-DNA-RNA cryo-EM (3.2 Å) Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O (2024) "Structural basis for pegRNA-guided reverse transcription by a prime editor." Nature, 631, 224-231. doi: 10.1038/s41586-024-07497-8. Spcas9-mmlv rt-pegrna-target DNA complex (elongation 28-nt). SNAP output
8yha RNA binding protein-DNA-RNA cryo-EM (3.4 Å) Zhang C, Chen F, Wang F, Xu H, Xue J, Li Z (2024) "Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems." Mol.Cell, 84, 3141. doi: 10.1016/j.molcel.2024.06.033. Type i-ehnh cascade-ssDNA complex. SNAP output
8ylg transcription X-ray (1.8 Å) Song WS, Ki DU, Cho HY, Kwon OH, Cho H, Yoon SI (2024) "Structural basis of transcriptional regulation by UrtR in response to uric acid." Nucleic Acids Res. doi: 10.1093/nar/gkae922. Crystal structure of burkholderia thailandensis mftr in complex with operator DNA. SNAP output
8yli transcription X-ray (2.9 Å) Song WS, Ki DU, Cho HY, Kwon OH, Cho H, Yoon SI (2024) "Structural basis of transcriptional regulation by UrtR in response to uric acid." Nucleic Acids Res. doi: 10.1093/nar/gkae922. Crystal structure of pectobacterium atrosepticum pecs in complex with operator DNA. SNAP output
8ylu isomerase cryo-EM (2.8 Å) Chen YT, Xin YH "structure of phage T6 topoisomerase II central domain bound with DNA." Structure of phage t6 topoisomerase ii central domain bound with DNA. SNAP output
8ymz DNA-DNA binding protein X-ray (2.95 Å) Yang Y, Zhang S, Xu L, Pan Y, Xuan Y, Kai Y, Chen X (2024) "Structural insights into the recognition of purine-pyrimidine dinucleotide repeats by zinc finger protein ZBTB43." Febs J. doi: 10.1111/febs.17286. Structure of zbtb43 in complex with caca containing b-form DNA. SNAP output
8yo4 isomerase cryo-EM (3.2 Å) Chen YT, Xin YH, Xian RQ "structure of phage T4 topoisomerase II central domain bound with DNA." Structure of phage t4 topoisomerase ii central domain bound with DNA. SNAP output
8yo7 isomerase cryo-EM (3.16 Å) Chen YT, Xin YH, Xian RQ "structure of phage T6 topoisomerase II central domain bound with DNA and m-AMSA." Structure of phage t6 topoisomerase ii central domain bound with DNA and m-amsa. SNAP output
8yqz viral protein cryo-EM (2.78 Å) Feng XY "Regulation of early transcription and late transcript processing enzymes packaging for African swine fever virus from endogenous vRNAP-M1249L supercomplex structures." African swine fever virus RNA polymerase--DNA complex. SNAP output
8yrs DNA binding protein X-ray (2.43 Å) Das T, Das AK, Ganguly A "Crystal structure of human RECQ1 helicase containing a flexible linker in complex with tailed duplex DNA." Crystal structure of human recq1 helicase containing a flexible linker in complex with tailed duplex DNA. SNAP output
8yti DNA binding protein-DNA X-ray (2.7 Å) Adhireksan Z, Sharma D, Qiuye B, Lee PL, Padavattan S, Davey CA "Linker Histones Associate Heterogeneously with Nucleosomes in the Condensed State." Crystal structure of nucleosome-h1x linker histone assembly (sticky-169a DNA fragment). SNAP output
8yv8 DNA binding protein cryo-EM (3.0 Å) Wassing I, Nishiyama A, Arita K, Funabiki H "CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS." cryo-EM structure of cdca7 bound to nucleosome including hemimethylated cpg site in widom601 positioning sequence.. SNAP output
8yxw DNA binding protein X-ray (2.1 Å) Hu C, Chen Z, Wang G, Yang H, Ding J (2024) "Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role." Structure, 32, 1208. doi: 10.1016/j.str.2024.05.012. Trip4 asch domain in complex with a 12bp dsDNA (5'-tgaggtacctcc-3'). SNAP output
8yxx DNA binding protein X-ray (2.65 Å) Hu C, Chen Z, Wang G, Yang H, Ding J (2024) "Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role." Structure, 32, 1208. doi: 10.1016/j.str.2024.05.012. Trip4 asch domain in complex with a 12bp dsDNA (5'-tgaggtacctcg-3'). SNAP output
8yzs DNA binding protein X-ray (2.31 Å) Ren J, Wang J, Ren Y, Zhang Y, Wei P, Wang M, Zhang Y, Li M, Yuan C, Gong H, Jiang J, Wang Z (2024) "Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP." Nucleic Acids Res., 52, 11349-11361. doi: 10.1093/nar/gkae762. Structure of the nacc1 ben domain in complex with its target DNA. SNAP output
8yzt DNA binding protein X-ray (2.58 Å) Ren J, Wang J, Ren Y, Zhang Y, Wei P, Wang M, Zhang Y, Li M, Yuan C, Gong H, Jiang J, Wang Z (2024) "Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP." Nucleic Acids Res., 52, 11349-11361. doi: 10.1093/nar/gkae762. Crystal structure of the banp ben domain in complex with its target DNA. SNAP output
8z0l antiviral protein-DNA-RNA cryo-EM (2.57 Å) Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H (2024) "Structural basis for the type I-F Cas8-HNH system." Embo J., 43, 4656-4667. doi: 10.1038/s44318-024-00229-8. cryo-EM structure of cas8-hnh system at partial r-loop state. SNAP output
8z79 oxidoreductase-DNA X-ray (2.65 Å) Wen Y, Guo W, Meng C, Yang J, Xu S, Chen H, Gan J, Wu B (2024) "Structural insights into the biosynthetic mechanism of N alpha-GlyT and 5-NmdU hypermodifications of DNA." Nucleic Acids Res., 52, 11083-11097. doi: 10.1093/nar/gkae784. Crystal structure of 5-n-alpha-glycinylthymidine (n-alpha-glyt) fad-dependent lyase gp47-ngto from pseudomonas phage pamx11 in complex with dsDNA. SNAP output
9ant transcription-DNA X-ray (2.4 Å) Fraenkel E, Pabo CO (1998) "Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex." Nat.Struct.Biol., 5, 692-697. Antennapedia homeodomain-DNA complex. SNAP output
9b0l DNA binding protein-DNA-RNA cryo-EM (2.99 Å) Schargel RD, Qayyum MZ, Tanwar AS, Kalathur RC, Kellogg EH (2024) "Structure of Fanzor2 reveals insights into the evolution of the TnpB superfamily." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01394-4. cryo-EM structure of acanthamoeba polyphaga mimivirus fanzor2 ternary complex. SNAP output
9b3p structural protein-DNA cryo-EM (3.0 Å) Jung H, Sokolova V, Lee G, Stevens VR, Tan D (2024) "Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z." Epigenomes, 8. doi: 10.3390/epigenomes8020021. The cryo-EM structure of the h2a.z-h3.3 double-variant nucleosome. SNAP output
9b7y DNA binding protein-DNA cryo-EM (2.51 Å) Panagoda N, Sampson N "Elucidation of the structure and the DNA binding motif of the Mycobacterium tuberculosis Mce3R repressor." cryo-EM structure of tetr regulator mce3r from mycobacterium tuberculosis bound to a DNA oligonucleotide. SNAP output
9b8r DNA binding protein-DNA cryo-EM (3.5 Å) Yuan Z, Georgescu R, Yao NY, Yurieva O, O'Donnell ME, Li H (2024) "Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis." Science, 385, eadk5901. doi: 10.1126/science.adk5901. cryo-EM structure of s. cerevisiae pole-core-DNA. SNAP output
9b8s DNA binding protein-DNA cryo-EM (5.01 Å) He Q, Wang F, Yao NY, O'Donnell ME, Li H (2024) "Structures of the human leading strand Pol epsilon-PCNA holoenzyme." Nat Commun, 15, 7847. doi: 10.1038/s41467-024-52257-x. Human polymerase epsilon bound to pcna and DNA in the nucleotide exchange state. SNAP output
9b8t DNA binding protein-DNA cryo-EM (2.95 Å) He Q, Wang F, Yao NY, O'Donnell ME, Li H (2024) "Structures of the human leading strand Pol epsilon-PCNA holoenzyme." Nat Commun, 15, 7847. doi: 10.1038/s41467-024-52257-x. Human polymerase epsilon bound to pcna and DNA in the nucleotide bound state. SNAP output
9b8u transcription-DNA X-ray (2.9 Å) Srivastava D, Gowribidanur-Chinnaswamy P, Gaur P, Spies M, Swaroop A, Artemyev NO (2024) "Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element." Structure, 32, 1751-1759.e4. doi: 10.1016/j.str.2024.07.004. Crystal structure of crx-ret4 oligonucleotide complex. SNAP output
9baq transferase-DNA binding protein-DNA cryo-EM (2.79 Å) Song J, Shao Z "CryoEM structure of DIM2-HP1-H3K9me3-DNA complex." Cryoem structure of dim2-hp1-h3k9me3-DNA complex. SNAP output
9bct transcription cryo-EM (2.5 Å) You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH (2024) "Structural basis of archaeal FttA-dependent transcription termination." Nature, 635, 229-236. doi: 10.1038/s41586-024-07979-9. cryo-EM structure of thermococcus kodakarensis ftta-dependent transcription pre-termination complex containing 44 nt RNA. SNAP output
9bcu transcription cryo-EM (2.2 Å) You L, Wang C, Molodtsov V, Kuznedelov K, Miao X, Wenck BR, Ulisse P, Sanders TJ, Marshall CJ, Firlar E, Kaelber JT, Santangelo TJ, Ebright RH (2024) "Structural basis of archaeal FttA-dependent transcription termination." Nature, 635, 229-236. doi: 10.1038/s41586-024-07979-9. cryo-EM structure of thermococcus kodakarensis ftta-dependent transcription pre-termination complex containing 52 nt RNA. SNAP output
9bdc transcription-DNA-RNA cryo-EM (2.54 Å) Herbine K, Nayak AR, Temiakov D (2024) "Structural basis for substrate binding and selection by human mitochondrial RNA polymerase." Nat Commun, 15, 7134. doi: 10.1038/s41467-024-50817-9. cryo-EM structure of the tefm bound human mitochondrial transcription elongation complex in a closed fingers domain conformation. SNAP output
9bdd transcription-DNA-RNA cryo-EM (2.86 Å) Herbine K, Nayak AR, Temiakov D (2024) "Structural basis for substrate binding and selection by human mitochondrial RNA polymerase." Nat Commun, 15, 7134. doi: 10.1038/s41467-024-50817-9. cryo-EM structure of non-cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex. SNAP output
9bdu DNA binding protein-DNA X-ray (2.03 Å) Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VY, Wang Y, Ghosh G (2024) "Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA." Proc.Natl.Acad.Sci.USA, 121, e2405555121. doi: 10.1073/pnas.2405555121. Nf-kappab rela homo-dimer bound to at-centric kappab DNA. SNAP output
9bdv DNA binding protein-DNA X-ray (1.9 Å) Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VY, Wang Y, Ghosh G (2024) "Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA." Proc.Natl.Acad.Sci.USA, 121, e2405555121. doi: 10.1073/pnas.2405555121. Nf-kappab rela homo-dimer bound to ta-centric kappab DNA. SNAP output
9bdw DNA binding protein-DNA X-ray (1.87 Å) Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VY, Wang Y, Ghosh G (2024) "Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA." Proc.Natl.Acad.Sci.USA, 121, e2405555121. doi: 10.1073/pnas.2405555121. Nf-kappab rela homo-dimer bound to gc-centric kappab DNA. SNAP output
9bdx DNA binding protein-DNA X-ray (3.6 Å) Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VY, Wang Y, Ghosh G (2024) "Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA." Proc.Natl.Acad.Sci.USA, 121, e2405555121. doi: 10.1073/pnas.2405555121. Nf-kappab rela homo-dimer bound to cg-centric kappab DNA. SNAP output
9bf5 immune system-DNA cryo-EM (3.07 Å) Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM (2024) "DdmDE eliminates plasmid invasion by DNA-guided DNA targeting." Cell, 187, 5253-5266.e16. doi: 10.1016/j.cell.2024.07.028. Structure of v. cholerae ddmd in complex with ssDNA. SNAP output
9bgk immune system-DNA cryo-EM (3.28 Å) Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM (2024) "DdmDE eliminates plasmid invasion by DNA-guided DNA targeting." Cell, 187, 5253-5266.e16. doi: 10.1016/j.cell.2024.07.028. Structure of v.cholera ddmde (2d:1e) in complex with DNA. SNAP output
9bh8 DNA binding protein cryo-EM (3.6 Å) Zerio CJ, Bai Y, Sosa-Alvarado BA, Guzi T, Lander GC "Human polymerase theta helicase positions DNA microhomologies for double-strand break repair." Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology searching conformation. SNAP output
9bh9 DNA binding protein cryo-EM (3.5 Å) Zerio CJ, Bai Y, Sosa-Alvarado BA, Guzi T, Lander GC "Human polymerase theta helicase positions DNA microhomologies for double-strand break repair." Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology aligning conformation. SNAP output
9bha DNA binding protein cryo-EM (3.5 Å) Zerio CJ, Bai Y, Sosa-Alvarado BA, Guzi T, Lander GC "Human polymerase theta helicase positions DNA microhomologies for double-strand break repair." Human DNA polymerase theta helicase domain dimer bound to DNA in the microhomology annealed conformation. SNAP output
9bs2 hydrolase-DNA X-ray (1.51 Å) Trasvina-Arenas CH, Dissanayake UC, Tamayo N, Hashemian SM, Lin WJ, Demir M, Hoyos-Gonzalez N, Fisher AJ, Cisneros GA, Horvath MP, David SS "Structural and functional profiling of MUTYH cancer-associated variants reveal an allosteric role for its [4Fe-4S] cluster cofactor." Glycosylase muty variant r149q in complex with DNA containing d(8-oxo-g) paired with a product analog (thf) to 1.51 Å resolution. SNAP output
9bs3 ligase-DNA X-ray (2.69 Å) Balu KE, Tang Q, Almohdar D, Ratcliffe J, Kalaycioglu M, Caglayan M (2024) "Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair." J.Biol.Chem., 300, 107688. doi: 10.1016/j.jbc.2024.107688. Wild type DNA ligase 1 with 5'-rg:c. SNAP output
9bs4 ligase-DNA X-ray (2.4 Å) Balu KE, Tang Q, Almohdar D, Ratcliffe J, Kalaycioglu M, Caglayan M (2024) "Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair." J.Biol.Chem., 300, 107688. doi: 10.1016/j.jbc.2024.107688. DNA ligase 1 e346a-e592a double mutant with 5'-rg:c. SNAP output
9bvd DNA binding protein-DNA X-ray (2.48 Å) Racca JD, Chen YS, Brabender AR, Battistin U, Weiss MA, Georgiadis MM (2024) "Role of nucleobase-specific interactions in the binding and bending of DNA by human male sex determination factor SRY." J.Biol.Chem., 300, 107683. doi: 10.1016/j.jbc.2024.107683. Crystal structure of sry hmg box bound to DNA. SNAP output
9bvt transcription X-ray (3.4 Å) Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G (2024) "Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser." Proc.Natl.Acad.Sci.USA, 121, e2318527121. doi: 10.1073/pnas.2318527121. RNA pol ii - high mn(+2) concentration. SNAP output
9bw0 transcription X-ray (3.51 Å) Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G (2024) "Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser." Proc.Natl.Acad.Sci.USA, 121, e2318527121. doi: 10.1073/pnas.2318527121. RNA polymerase ii - no atp. SNAP output
9bw1 DNA binding protein-DNA cryo-EM (3.65 Å) Wang S, Siddique R, Hall MC, Rice PA, Chang L (2024) "Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition." Cell. doi: 10.1016/j.cell.2024.09.023. Tnsabcd-DNA transpososome. SNAP output
9c0i transferase-DNA-RNA cryo-EM (2.91 Å) Wilkinson ME, Li D, Gao A, Macrae RK, Zhang F (2024) "Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA." Science, 386, eadq3977. doi: 10.1126/science.adq3977. Structure of the drt2 reverse transcriptase in complex with its non-coding RNA. SNAP output
9c0j transferase-DNA-RNA cryo-EM (3.17 Å) Wilkinson ME, Li D, Gao A, Macrae RK, Zhang F (2024) "Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA." Science, 386, eadq3977. doi: 10.1126/science.adq3977. Structure of the elongating drt2 reverse transcriptase in complex with its non-coding RNA and dntps. SNAP output
9c3s DNA binding protein X-ray (2.16 Å) Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Ahlsen G, Rechkoblit O, Shapiro L, Filizola M, Fang G, Aggarwal AK (2024) "Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation." Nat Commun, 15, 7839. doi: 10.1038/s41467-024-52130-x. Crystal structure of DNA n6-adenine methyltransferase m.bcejiv from burkholderia cenocepacia in complex with duplex DNA substrate containing gtatac as recognition sequence. SNAP output
9c3t DNA binding protein X-ray (2.37 Å) Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Ahlsen G, Rechkoblit O, Shapiro L, Filizola M, Fang G, Aggarwal AK (2024) "Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation." Nat Commun, 15, 7839. doi: 10.1038/s41467-024-52130-x. Crystal structure of DNA n6-adenine methyltransferase m.bcejiv from burkholderia cenocepacia in complex with duplex DNA substrate containing gtaaac as recognition sequence. SNAP output
9c3u DNA binding protein X-ray (2.77 Å) Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Ahlsen G, Rechkoblit O, Shapiro L, Filizola M, Fang G, Aggarwal AK (2024) "Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation." Nat Commun, 15, 7839. doi: 10.1038/s41467-024-52130-x. Crystal structure of DNA n6-adenine methyltransferase m.bcejiv from burkholderia cenocepacia in complex with duplex DNA substrate containing gtttac as recognition sequence. SNAP output
9c4c gene regulation cryo-EM (3.09 Å) Shi H, Fu Y, Glasfeld A, Ahuja S "The structure of two MntR dimers bound to the native mnep promoter sequence." The structure of two mntr dimers bound to the native mnep promoter sequence. SNAP output
9c4d gene regulation cryo-EM (4.17 Å) Shi H, Fu Y, Glasfeld A, Ahuja S "The structure of 4 MntR homodimers bound to the promoter sequence of mnep." The structure of 4 mntr homodimers bound to the promoter sequence of mnep. SNAP output
9c5g DNA binding protein-DNA X-ray (2.77 Å) Blankenchip CL, Corbett KD "Bacterial WYL domain transcriptional repressors sense single-stranded DNA to control gene expression." Structure of r. leguminosarum capw bound to single-stranded DNA. SNAP output
9c5q transferase-DNA cryo-EM (3.1 Å) Ito F, Li Z, Minakhin L, Khant HA, Pomerantz RT, Chen XS (2024) "Structural Basis for Pol theta-Helicase DNA Binding and Microhomology-Mediated End-Joining." Biorxiv. doi: 10.1101/2024.06.07.597860. Human DNA polymerase theta helicase domain in microhomology annealed state 2, dimer form. SNAP output
9c6q immune system-DNA cryo-EM (3.18 Å) Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM (2024) "DdmDE eliminates plasmid invasion by DNA-guided DNA targeting." Cell, 187, 5253-5266.e16. doi: 10.1016/j.cell.2024.07.028. Structure of v. cholerae monomeric ddmd bound with ssDNA. SNAP output
9c7a RNA binding protein-RNA-DNA X-ray (1.4 Å) Maji D, Jenkins JL, Boutz PL, Kielkopf CL (2024) "Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions." Biochemistry. doi: 10.1021/acs.biochem.4c00344. Crystal structure of r149w neurodevelopmental disease-associated u2af2 variant. SNAP output
9c7b RNA binding protein-RNA-DNA X-ray (1.4 Å) Maji D, Jenkins JL, Boutz PL, Kielkopf CL (2024) "Recurrent Neurodevelopmentally Associated Variants of the Pre-mRNA Splicing Factor U2AF2 Alter RNA Binding Affinities and Interactions." Biochemistry. doi: 10.1021/acs.biochem.4c00344. Crystal structure of r150h neurodevelopmental disease-associated u2af2 variant. SNAP output
9c9m viral protein cryo-EM (2.01 Å) Li M, Li Z, Chen X, Cui Y, Engelman AN, Craigie R (2024) "HIV-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies by Cryo-EM and Reveal the Role of the Integrase C-Terminal Tail in HIV-1 Integration." Viruses, 16. doi: 10.3390/v16071166. Hiv-1 intasome core bound with dtg. SNAP output
9c9y isomerase-DNA cryo-EM (3.35 Å) Yang X, Chen X, Yang W, Pommier Y "Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics." Human top3b-tdrd3 core complex in DNA pre-cleavage state. SNAP output
9ca0 isomerase-DNA cryo-EM (3.48 Å) Yang X, Chen X, Yang W, Pommier Y "Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics." Human top3b-tdrd3 core complex in DNA pre-cleavage state. SNAP output
9ca1 isomerase-DNA cryo-EM (3.26 Å) Yang X, Chen X, Yang W, Pommier Y "Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics." Human top3b-tdrd3 core complex in DNA religation state. SNAP output
9cay DNA binding protein-DNA cryo-EM (3.17 Å) Lo CY, Ung AR, Koley T, Nelson SW, Gao Y (2024) "Cryo-EM structures of the Plasmodium falciparum apicoplast DNA polymerase." J.Mol.Biol., 168842. doi: 10.1016/j.jmb.2024.168842. Ternary structure of plasmodium falciparum apicoplast DNA polymerase (exo-minus). SNAP output
9ces RNA binding protein-RNA-DNA cryo-EM (3.28 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Guillardia theta fanzor (gtfz) state 2. SNAP output
9cet RNA binding protein-RNA-DNA cryo-EM (3.0 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Guillardia theta fanzor (gtfz) state 3. SNAP output
9ceu RNA binding protein-RNA-DNA cryo-EM (3.29 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Spizellomyces punctatus fanzor (spufz) state 1. SNAP output
9cev RNA binding protein-RNA-DNA cryo-EM (3.26 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Spizellomyces punctatus fanzor (spufz) state 2. SNAP output
9cew RNA binding protein-RNA-DNA cryo-EM (2.88 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Spizellomyces punctatus fanzor (spufz) state 3. SNAP output
9cex RNA binding protein-RNA-DNA cryo-EM (3.27 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Spizellomyces punctatus fanzor (spufz) state 4. SNAP output
9cey RNA binding protein-RNA-DNA cryo-EM (3.22 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Spizellomyces punctatus fanzor (spufz) state 5. SNAP output
9cez RNA binding protein-RNA-DNA cryo-EM (3.41 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Spizellomyces punctatus fanzor (spufz) state 6. SNAP output
9cf0 RNA binding protein-isomerase-DNA cryo-EM (3.47 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Parasitella parasitica fanzor (ppfz) state 1. SNAP output
9cf1 RNA binding protein-isomerase-RNA-DNA cryo-EM (3.52 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Parasitella parasitica fanzor (ppfz) state 2. SNAP output
9cf2 RNA binding protein-isomerase-RNA-DNA cryo-EM (3.15 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Parasitella parasitica fanzor (ppfz) state 3. SNAP output
9cf3 RNA binding protein-isomerase-RNA-DNA cryo-EM (3.2 Å) Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F (2024) "Structural insights into the diversity and DNA cleavage mechanism of Fanzor." Cell, 187, 5238-5252.e20. doi: 10.1016/j.cell.2024.07.050. Parasitella parasitica fanzor (ppfz) state 4. SNAP output
9chw transferase-DNA X-ray (2.16 Å) Tomar R, Ghodke PP, Patra A, Smyth E, Pontarelli A, Copp W, Guengerich FP, Chaput JC, Wilds CJ, Stone MP, Egli M (2024) "DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta." Biochemistry, 63, 2425-2439. doi: 10.1021/acs.biochem.4c00387. Crystal structure of human polymerase eta with incoming dampnpp nucleotide opposite threofuranosyl thymidine in DNA template. SNAP output
9ci9 transferase-DNA X-ray (2.09 Å) Tomar R, Ghodke PP, Patra A, Smyth E, Pontarelli A, Copp W, Guengerich FP, Chaput JC, Wilds CJ, Stone MP, Egli M (2024) "DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta." Biochemistry, 63, 2425-2439. doi: 10.1021/acs.biochem.4c00387. Crystal structure of human polymerase eta with incoming dcmpnpp nucleotide across threofuranosyl thymidine in DNA template at extension stage. SNAP output
9d2x transcription-DNA X-ray (2.29 Å) Terrell JR, Vernon TN, Poon GMK "The Structure of the DNA-binding Domain of the Class III ETS-Family Member SpiD from Raja eglanteria." Spid ets-domain (168-273) in complex with the DNA sequence d(aataaaaggaagtggg). SNAP output
9dp1 hydrolase-DNA X-ray (2.29 Å) DeHart KD, Hoitsma NM, Thompson SH, Freudenthal BD "N174 Physically and Chemically Stabilizes the Endonuclease Reaction of APE1." Ape1 n174a substrate complex with abasic DNA. SNAP output
9dp2 hydrolase-DNA X-ray (1.99 Å) DeHart KD, Freudnethal BD, Hoitsma NM, Thompson SH "N174 Physically and Chemically Stabilizes Abasic DNA During the APE1 Endonuclease Reaction." Ape1 n174a product complex with abasic DNA. SNAP output
9dp3 hydrolase-DNA X-ray (2.1 Å) DeHart KD, Hoitsma NM, Thompson SH, Freudenthal BD "N174 Physically and Chemically Stabilizes Abasic DNA During the APE1 Endonuclease Reaction." Ape1 n174d product complex with abasic DNA. SNAP output
9dp4 hydrolase-DNA X-ray (2.25 Å) DeHart KD, Hoitsma NM, Thompson SH, Freudenthal BD "N174 Physically and Chemically Stabilizes the APE1 Endonuclease Reaction." Ape1 n174q product complex with abasic DNA. SNAP output
9dr1 transferase-DNA-RNA cryo-EM (3.7 Å) Porta JC, Ellinger E, Liu Y, Chauvier A, Walter NG "Structural basis of RNA-mediated regulation of transcriptional pausing." E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state. SNAP output
9dzm transcription-DNA X-ray (2.54 Å) Terrell JR, Poon GMK "Coupled heterogeneity to dimeric site-specific binding by the POU-Family Transcription Factor OCT2." Dimeric human oct2 (pou2f2) pou domain bound to palindromic more DNA. SNAP output
9emi transferase X-ray (2.27 Å) Gutfreund C, Betz K (2024) "Structural Insights into a DNA Polymerase Reading the Xeno Nucleic Acid HNA." Nucleic Acids Res. Kod-h4 DNA polymerase mutant in a ternary complex containing six hna nucleotides and a non-hydrolyzable triphosphate. SNAP output
9enp transferase cryo-EM (2.12 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase-processivity factor complex in exonuclease state with 1-bp DNA mismatch. SNAP output
9enq transferase cryo-EM (2.12 Å) Gustavsson E, Grunewald K, Elias P, Hallberg BM (2024) "Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM." Nucleic Acids Res., 52, 7292-7304. doi: 10.1093/nar/gkae374. Hsv-1 DNA polymerase-processivity factor complex in exonuclease state active site with 1-bp DNA mismatch. SNAP output
9eoz DNA binding protein cryo-EM (3.1 Å) Ren M, Gut F, Fan Y, Ma J, Shan X, Yikilmazsoy A, Likhodeeva M, Hopfner KP, Zhou C (2024) "Structural basis for human OGG1 processing 8-oxodGuo within nucleosome core particles." Nat Commun, 15, 9407. doi: 10.1038/s41467-024-53811-3. Human ogg1 bound to a nucleosome core particle with 8-oxodguo lesion at shl6.0. SNAP output
9ezy immune system cryo-EM (2.56 Å) Loeff L, Adams DW, Chanez C, Stutzmann S, Righi L, Blokesch M, Jinek M (2024) "Molecular mechanism of plasmid elimination by the DdmDE defense system." Science, 385, 188-194. doi: 10.1126/science.adq0534. Vibrio cholerae ddmd-ddme holo complex. SNAP output
9ezz DNA binding protein X-ray (1.95 Å) Hu Y, Schwab S, Deiss S, Escudeiro P, van Heesch T, Joiner JD, Vreede J, Hartmann MD, Lupas AN, Alvarez BH, Alva V, Dame RT (2024) "Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending." Nucleic Acids Res., 52, 8193-8204. doi: 10.1093/nar/gkae485. Bacterial histone protein hbb from bdellovibrio bacteriovorus bound to DNA. SNAP output
9f0e DNA binding protein X-ray (1.85 Å) Hu Y, Schwab S, Deiss S, Escudeiro P, van Heesch T, Joiner JD, Vreede J, Hartmann MD, Lupas AN, Alvarez BH, Alva V, Dame RT (2024) "Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending." Nucleic Acids Res., 52, 8193-8204. doi: 10.1093/nar/gkae485. Bacterial histone protein hbb from bdellovibrio bacteriovorus bound to DNA. SNAP output
9f6d replication cryo-EM (3.6 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to DNA and pcna (open conformation). SNAP output
9f6e replication cryo-EM (3.74 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to DNA and pcna (ajar conformation). SNAP output
9f6f replication cryo-EM (3.75 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to DNA and pcna (closed conformation). SNAP output
9f6i replication cryo-EM (3.3 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to t-c mismatched DNA (post-insertion state). SNAP output
9f6j replication cryo-EM (3.9 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to t-c mismatched DNA (polymerase arrest state). SNAP output
9f6k replication cryo-EM (4.2 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to t-c mismatched DNA (frayed substrate state). SNAP output
9f6l replication cryo-EM (3.9 Å) Roske JJ, Yeeles JTP (2024) "Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol epsilon." Nat.Struct.Mol.Biol. doi: 10.1038/s41594-024-01370-y. Human DNA polymerase epsilon bound to t-c mismatched DNA (mismatch excision state). SNAP output
9fd2 transcription cryo-EM (3.4 Å) Lee S-H, Sixma TK (2024) "Structure of Pol II-TC-NER-STK19 complex." Mol.Cell. doi: 10.1016/j.molcel.2024.10.030. Structure of pol ii-tc-ner-stk19 complex. SNAP output
9ffb DNA binding protein cryo-EM (3.59 Å) Alcon P, Kaczmarczyk AP, Ray KK, Liolios T, Guilbaud G, Sijacki T, Shen Y, McLaughlin SH, Sale JE, Knipscheer P, Rueda DS, Passmore LA (2024) "FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions." Nature, 632, 1165-1173. doi: 10.1038/s41586-024-07770-w. Ss-dsDNA-fancd2-fanci complex. SNAP output
9fff DNA binding protein cryo-EM (3.68 Å) Alcon P, Kaczmarczyk AP, Ray KK, Liolios T, Guilbaud G, Sijacki T, Shen Y, McLaughlin SH, Sale JE, Knipscheer P, Rueda DS, Passmore LA (2024) "FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions." Nature, 632, 1165-1173. doi: 10.1038/s41586-024-07770-w. DsDNA-fancd2-fanci complex. SNAP output
9fgq cell cycle cryo-EM (2.5 Å) Cirillo L, Young R, Veerapathiran S, Roberti A, Martin M, Abubacar A, Perosa C, Coates C, Muhammad R, Roumeliotis TI, Choudhary JS, Alfieri C, Pines J (2024) "Spatial control of the APC/C ensures the rapid degradation of cyclin B1." Embo J., 43, 4324-4355. doi: 10.1038/s44318-024-00194-2. Structure of human apc3loop 375-381 bound to the ncp. SNAP output
9fh9 cell cycle cryo-EM (2.5 Å) Cirillo L, Young R, Veerapathiran S, Roberti A, Martin M, Abubacar A, Perosa C, Coates C, Muhammad R, Roumeliotis TI, Choudhary JS, Alfieri C, Pines J (2024) "Spatial control of the APC/C ensures the rapid degradation of cyclin B1." Embo J., 43, 4324-4355. doi: 10.1038/s44318-024-00194-2. Structure of cyclinb1 n-terminus bound to the ncp. SNAP output
9fz6 isomerase X-ray (2.58 Å) Morgan H, Nicholls R, Warren AJ, Ward S, Evans G, Long F, Murshudov G, Duman R, Bax BD "How do gepotidacin and zolifodacin stabilize DNA-cleavage complexes with bacterial type IIA topoisomerases? 1. Experimental definition of metal binding sites." A 2.58a crystal structure of s. aureus DNA gyrase and DNA with metals identified through anomalous scattering. SNAP output
9gbv isomerase cryo-EM (2.32 Å) Michalczyk E, Pakosz-Stepien Z, Liston J, Gittins O, Pabis M, Heddle JG, Ghilarov D (2024) "Structure of Escherichia coli DNA gyrase with chirally wrapped DNA supports ratchet-and-pawl mechanism for an ATP-powered supercoiling motor." Proceedings of the National Academy of Sciences USA. E.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment. SNAP output
9gd0 DNA binding protein cryo-EM (2.8 Å) Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L (2024) "Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT." Mol.Cell, 84, 3423. doi: 10.1016/j.molcel.2024.08.022. Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.. SNAP output
9gd3 DNA binding protein cryo-EM (3.0 Å) Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L (2024) "Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT." Mol.Cell, 84, 3423. doi: 10.1016/j.molcel.2024.08.022. Structure of a mononucleosome bound by one copy of chd1 with the dbd on the exit-side DNA.. SNAP output
9gef DNA binding protein X-ray (2.62 Å) Wang B, Najmudin S, Pan XS, Mykhaylyk V, Orr C, Wagner A, Govada L, Chayen NE, Fisher LM, Sanderson MR (2024) "Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases." Proc.Natl.Acad.Sci.USA, 121, e2413357121. doi: 10.1073/pnas.2413357121. Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized streptococcus pneumoniae topoisomerase iv DNA cleavage complex. SNAP output
9ggq isomerase cryo-EM (2.6 Å) Michalczyk E, Pakosz-Stepien Z, Liston JD, Gittins O, Pabis M, Heddle JG, Ghilarov D (2024) "Structural basis of chiral wrap and T-segment capture by Escherichia coli DNA gyrase." Proceedings of the National Academy of Sciences USA. E.coli gyrase holocomplex with cleaved chirally wrapped 217 bp DNA fragment and moxifloxacin. SNAP output
9gpj RNA binding protein X-ray (1.53 Å) Dunnett L, Prischi F "Structure of UP1 S4DS6D phosphomimetic mutant in complex with human telomeric repeat DNA." Structure of up1 s4ds6d phosphomimetic mutant in complex with human telomeric repeat DNA. SNAP output
9ica transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxyadenosine-5'-o-(1-thiotriphosphate), soaked in the presence of datp(alpha)s and mncl2. SNAP output
9icb transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxyadenosine-5'-triphosphate, soaked in the presence of datp and cocl2. SNAP output
9icc transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxyadenosine-5'-triphosphate, soaked in the presence of datp and crcl3. SNAP output
9ice transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (1 millimolar) and cucl2 (0.1 millimolar). SNAP output
9icf transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxyadenosine-5'-triphosphate, soaked in the presence of datp and zncl2. SNAP output
9icg transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dctp (1 millimolar) and zncl2 (1 millimolar). SNAP output
9ich transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dgtp (1 millimolar) and zncl2 (1 millimolar). SNAP output
9ici transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of dttp (1 millimolar) and zncl2 (1 millimolar). SNAP output
9icj transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA. SNAP output
9ick transferase-DNA X-ray (2.7 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of artificial mother liquor. SNAP output
9icl transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of pyrophosphate and mncl2. SNAP output
9icm transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity." Biochemistry, 35, 12742-12761. doi: 10.1021/bi952955d. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of double stranded DNA (no 5'-phosphate). SNAP output
9icn transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2',3'-dideoxycytidine-5'-triphosphate, soaked in the presence of ddctp and mgcl2. SNAP output
9ico transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of dttp and mgcl2. SNAP output
9icp transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of pyrophosphate (1 millimolar) and mgcl2 (5 millimolar). SNAP output
9icq transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of datp (1 millimolar) and mncl2 (5 millimolar). SNAP output
9icr transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxycytidine-5'-triphosphate, soaked in the presence of dctp and mncl2. SNAP output
9ics transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2',3'-dideoxycytidine-5'-triphosphate, soaked in the presence of ddctp and mncl2. SNAP output
9ict transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxyguanosine-5'-triphosphate, soaked in the presence of dgtp and mncl2. SNAP output
9icu transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; soaked in the presence of dttp (1 millimolar) and mncl2 (5 millimolar). SNAP output
9icv transferase-DNA X-ray (2.7 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (e.c.2.7.7.7)-DNA complex + 2'-deoxyadenosine-5'-triphosphate, soaked in the presence of datp and zncl2. SNAP output
9icw transferase-DNA X-ray (2.6 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity." Biochemistry, 35, 12742-12761. doi: 10.1021/bi952955d. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA; native structure. SNAP output
9icx transferase-DNA X-ray (2.6 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity." Biochemistry, 35, 12742-12761. doi: 10.1021/bi952955d. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with six base pairs of DNA (non gapped DNA only). SNAP output
9icy transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity." Biochemistry, 35, 12742-12761. doi: 10.1021/bi952955d. DNA polymerase beta (e.c.2.7.7.7) complexed with seven base pairs of DNA (non gapped DNA only). SNAP output
9ipu nuclear protein cryo-EM (4.3 Å) Shi Q, Deng ZH, Zhang LY, Tong ZB, Chu G-C, Ai HS, Liu L "Chemically and Site-specifically Ubiquitylated Linker Histone H1 Facilitates RNF168-Mediated Nucleosomal H2A Ubiquitylation." cryo-EM structure of the rnf168(1-193)-ubch5c-ub ubiquitylation module bound to h1.0-k63-ub3 modified chromatosome. SNAP output
9ja1 biosynthetic protein cryo-EM (2.98 Å) Ma J, Yi G, Zhang P "The RNA polymerase II elongation complex from Saccharomyces cerevisiae." The RNA polymerase ii elongation complex from saccharomyces cerevisiae. SNAP output
9jpj transcription X-ray (3.72 Å) Sun P, Wang B "Crystal structure of DhdR inducer binding domain." Crystal structure of dhdr in complex with DNA. SNAP output
9mht transferase-DNA X-ray (2.39 Å) O'Gara M, Horton JR, Roberts RJ, Cheng X (1998) "Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base." Nat.Struct.Biol., 5, 872-877. doi: 10.1038/2312. Cytosine-specific methyltransferase hhai-DNA complex. SNAP output
pdb id class method authors reference annotation