| 1a1t |
viral protein-RNA |
NMR |
De Guzman RN, Wu ZR, Stalling CC, Pappalardo L, Borer PN, Summers MF |
(1998) "Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element." Science, 279, 384-388. doi: 10.1126/science.279.5349.384. |
Structure of the hiv-1 nucleocapsid protein bound to the sl3 psi-RNA recognition element, NMR, 25 structures. SNAP output |
| 1a34 |
virus-RNA |
X-ray (1.81 Å) |
Larson SB, Day J, Greenwood A, McPherson A |
(1998) "Refined structure of satellite tobacco mosaic virus at 1.8 A resolution." J.Mol.Biol., 277, 37-59. doi: 10.1006/jmbi.1997.1570. |
Satellite tobacco mosaic virus-RNA complex. SNAP output |
| 1a4t |
transcription-RNA |
NMR |
Cai Z, Gorin A, Frederick R, Ye X, Hu W, Majumdar A, Kettani A, Patel DJ |
(1998) "Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex." Nat.Struct.Biol., 5, 203-212. doi: 10.1038/nsb0398-203. |
Solution structure of phage p22 n peptide-box b RNA complex, NMR, 20 structures. SNAP output |
| 1a9n |
RNA binding protein-RNA |
X-ray (2.38 Å) |
Price SR, Evans PR, Nagai K |
(1998) "Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA." Nature, 394, 645-650. doi: 10.1038/29234. |
Crystal structure of the spliceosomal u2b''-u2a' protein complex bound to a fragment of u2 small nuclear RNA. SNAP output |
| 1aq3 |
virus-RNA |
X-ray (2.8 Å) |
van den Worm SH, Stonehouse NJ, Valegard K, Murray JB, Walton C, Fridborg K, Stockley PG, Liljas L |
(1998) "Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments." Nucleic Acids Res., 26, 1345-1351. doi: 10.1093/nar/26.5.1345. |
Bacteriophage ms2 capsid protein-RNA complex. SNAP output |
| 1aq4 |
virus-RNA |
X-ray (3.0 Å) |
van den Worm SH, Stonehouse NJ, Valegard K, Murray JB, Walton C, Fridborg K, Stockley PG, Liljas L |
(1998) "Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments." Nucleic Acids Res., 26, 1345-1351. doi: 10.1093/nar/26.5.1345. |
Structure of a ms2 coat protein mutant in complex with an RNA operator. SNAP output |
| 1asy |
complex (aminoacyl-trna synthase-trna) |
X-ray (2.9 Å) |
Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D |
(1991) "Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp)." Science, 252, 1682-1689. |
Class ii aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-trna synthetase complexed with trna asp. SNAP output |
| 1asz |
complex (aminoacyl-trna synthase-trna) |
X-ray (3.0 Å) |
Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D |
(1994) "The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction." EMBO J., 13, 327-337. |
The active site of yeast aspartyl-trna synthetase: structural and functional aspects of the aminoacylation reaction. SNAP output |
| 1aud |
RNA binding protein-RNA |
NMR |
Allain FH, Howe PW, Neuhaus D, Varani G |
(1997) "Structural basis of the RNA-binding specificity of human U1A protein." EMBO J., 16, 5764-5774. doi: 10.1093/emboj/16.18.5764. |
U1a-utrrna, NMR, 31 structures. SNAP output |
| 1av6 |
transferase-RNA |
X-ray (2.8 Å) |
Hodel AE, Gershon PD, Quiocho FA |
(1998) "Structural basis for sequence-nonspecific recognition of 5'-capped mRNA by a cap-modifying enzyme." Mol.Cell, 1, 443-447. doi: 10.1016/S1097-2765(00)80044-1. |
Vaccinia methyltransferase vp39 complexed with m7g capped RNA hexamer and s-adenosylhomocysteine. SNAP output |
| 1b23 |
gene regulation-RNA |
X-ray (2.6 Å) |
Nissen P, Thirup S, Kjeldgaard M, Nyborg J |
(1999) "The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA." Structure Fold.Des., 7, 143-156. doi: 10.1016/S0969-2126(99)80021-5. |
E. coli cysteinyl-trna and t. aquaticus elongation factor ef-tu:gtp ternary complex. SNAP output |
| 1b2m |
hydrolase-RNA |
X-ray (2.0 Å) |
Arni RK, Watanabe L, Ward RJ, Kreitman RJ, Kumar K, Walz Jr FG |
(1999) "Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis." Biochemistry, 38, 2452-2461. doi: 10.1021/bi982612q. |
Three-dimensional structure of ribonulcease t1 complexed with an isosteric phosphonate analogue of gpu: alternate substrate binding modes and catalysis.. SNAP output |
| 1b7f |
RNA-binding protein-RNA |
X-ray (2.6 Å) |
Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y, Muto Y, Yokoyama S |
(1999) "Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein." Nature, 398, 579-585. doi: 10.1038/19242. |
Sxl-lethal protein-RNA complex. SNAP output |
| 1biv |
viral protein-RNA |
NMR |
Ye X, Kumar RA, Patel DJ |
(1995) "Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex." Chem.Biol., 2, 827-840. doi: 10.1016/1074-5521(95)90089-6. |
Bovine immunodeficiency virus tat-tar complex, NMR, 5 structures. SNAP output |
| 1bmv |
virus-RNA |
X-ray (3.0 Å) |
Chen ZG, Stauffacher C, Li Y, Schmidt T, Bomu W, Kamer G, Shanks M, Lomonossoff G, Johnson JE |
(1989) "Protein-RNA interactions in an icosahedral virus at 3.0 A resolution." Science, 245, 154-159. |
Protein-RNA interactions in an icosahedral virus at 3.0 angstroms resolution. SNAP output |
| 1c04 |
ribosome |
X-ray (5.0 Å) |
Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA |
(1999) "Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit." Nature, 400, 841-847. doi: 10.1038/23641. |
Identification of known protein and RNA structures in a 5 a map of the large ribosomal subunit from haloarcula marismortui. SNAP output |
| 1c0a |
ligase-RNA |
X-ray (2.4 Å) |
Eiler S, Dock-Bregeon A, Moulinier L, Thierry JC, Moras D |
(1999) "Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step." EMBO J., 18, 6532-6541. doi: 10.1093/emboj/18.22.6532. |
Crystal structure of the e. coli aspartyl-trna synthetase : trnaasp : aspartyl-adenylate complex. SNAP output |
| 1c9s |
RNA binding protein-RNA |
X-ray (1.9 Å) |
Antson AA, Dodson EJ, Dodson G, Greaves RB, Chen X, Gollnick P |
(1999) "Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA." Nature, 401, 235-242. doi: 10.1038/45730. |
Crystal structure of a complex of trp RNA-binding attenuation protein with a 53-base single stranded RNA containing eleven gag triplets separated by au dinucleotides. SNAP output |
| 1cgm |
virus |
fiber diffraction |
Wang H, Stubbs G |
(1994) "Structure determination of cucumber green mottle mosaic virus by X-ray fiber diffraction. Significance for the evolution of tobamoviruses." J.Mol.Biol., 239, 371-384. doi: 10.1006/jmbi.1994.1379. |
Structure determination of cucumber green mottle mosaic virus by x-ray fiber diffraction. significance for the evolution of tobamoviruses. SNAP output |
| 1cvj |
gene regulation-RNA |
X-ray (2.6 Å) |
Deo RC, Bonanno JB, Sonenberg N, Burley SK |
(1999) "Recognition of polyadenylate RNA by the poly(A)-binding protein." Cell(Cambridge,Mass.), 98, 835-845. doi: 10.1016/S0092-8674(00)81517-2. |
X-ray crystal structure of the poly(a)-binding protein in complex with polyadenylate RNA. SNAP output |
| 1cwp |
virus-RNA |
X-ray (3.2 Å) |
Speir JA, Munshi S, Wang G, Baker TS, Johnson JE |
(1995) "Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy." Structure, 3, 63-77. doi: 10.1016/S0969-2126(01)00135-6. |
Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by x-ray crystallography and cryo-electron microscopy. SNAP output |
| 1d6k |
ribosome |
NMR |
Stoldt M, Wohnert J, Ohlenschlager O, Gorlach M, Brown LR |
(1999) "The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition." EMBO J., 18, 6508-6521. doi: 10.1093/emboj/18.22.6508. |
NMR solution structure of the 5s rrna e-loop-l25 complex. SNAP output |
| 1d9d |
transferase-DNA, RNA |
X-ray (2.18 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. |
Crystall structure of the complex of DNA polymerase i klenow fragment with short DNA fragment carrying 2'-0-aminopropyl-RNA modifications 5'-d(tcg)-ap(auc)-3'. SNAP output |
| 1d9f |
transferase-DNA, RNA |
X-ray (3.0 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 tetramer carrying 2'-o-(3-aminopropyl)-RNA modification 5'-d(tt)-ap(u)-d(t)-3'. SNAP output |
| 1ddl |
virus-RNA |
X-ray (2.7 Å) |
Larson SB, Day J, Canady MA, Greenwood A, McPherson A |
(2000) "Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution." J.Mol.Biol., 301, 625-642. doi: 10.1006/jmbi.2000.3983. |
Desmodium yellow mottle tymovirus. SNAP output |
| 1dfu |
ribosome |
X-ray (1.8 Å) |
Lu M, Steitz TA |
(2000) "Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution." Proc.Natl.Acad.Sci.USA, 97, 2023-2028. doi: 10.1073/pnas.97.5.2023. |
Crystal structure of e.coli ribosomal protein l25 complexed with a 5s rrna fragment at 1.8 Å resolution. SNAP output |
| 1di2 |
RNA binding protein-RNA |
X-ray (1.9 Å) |
Ryter JM, Schultz SC |
(1998) "Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA." EMBO J., 17, 7505-7513. doi: 10.1093/emboj/17.24.7505. |
Crystal structure of a dsrna-binding domain complexed with dsrna: molecular basis of double-stranded RNA-protein interactions. SNAP output |
| 1dk1 |
ribosome |
X-ray (2.8 Å) |
Nikulin A, Serganov A, Ennifar E, Tishchenko S, Nevskaya N, Shepard W, Portier C, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P |
(2000) "Crystal structure of the S15-rRNA complex." Nat.Struct.Biol., 7, 273-277. doi: 10.1038/74028. |
Detailed view of a key element of the ribosome assembly: crystal structure of the s15-rrna complex. SNAP output |
| 1drz |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Ferre-D'Amare AR, Zhou K, Doudna JA |
(1998) "Crystal structure of a hepatitis delta virus ribozyme." Nature, 395, 567-574. doi: 10.1038/26912. |
U1a spliceosomal protein-hepatitis delta virus genomic ribozyme complex. SNAP output |
| 1dul |
signaling protein-RNA |
X-ray (1.8 Å) |
Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA |
(2000) "Crystal structure of the ribonucleoprotein core of the signal recognition particle." Science, 287, 1232-1239. doi: 10.1126/science.287.5456.1232. |
Structure of the ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 1dz5 |
ribonucleoprotein-RNA |
NMR |
Varani L, Gunderson SI, Mattaj IW, Kay LE, Neuhaus D, Varani G |
(2000) "The NMR Structure of the 38kDa U1A Protein-Pie RNA Complex Reveals the Basis of Cooperativity in Regulation of Polyadenylation by Human U1A Protein." Nat.Struct.Biol., 7, 329. doi: 10.1038/74101. |
The NMR structure of the 38kda u1a protein-pie RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human u1a protein. SNAP output |
| 1e7k |
RNA binding protein |
X-ray (2.9 Å) |
Vidovic I, Nottrott S, Hartmuth K, Luhrmann R, Ficner R |
(2000) "Crystal Structure of the Spliceosomal 15.5Kd Protein Bound to a U4 Snrna Fragment." Mol.Cell, 6, 1331. doi: 10.1016/S1097-2765(00)00131-3. |
Crystal structure of the spliceosomal 15.5kd protein bound to a u4 snrna fragment. SNAP output |
| 1e8o |
alu ribonucleoprotein particle |
X-ray (3.2 Å) |
Weichenrieder O, Wild K, Strub K, Cusack S |
(2000) "Structure and Assembly of the Alu Domain of the Mammalian Signal Recognition Particle." Nature, 408, 167. doi: 10.1038/35041507. |
Core of the alu domain of the mammalian srp. SNAP output |
| 1ec6 |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Lewis HA, Musunuru K, Jensen KB, Edo C, Chen H, Darnell RB, Burley SK |
(2000) "Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome." Cell(Cambridge,Mass.), 100, 323-332. doi: 10.1016/S0092-8674(00)80668-6. |
Crystal structure of nova-2 kh3 k-homology RNA-binding domain bound to 20-mer RNA hairpin. SNAP output |
| 1efw |
ligase-RNA |
X-ray (3.0 Å) |
Briand C, Poterszman A, Eiler S, Webster G, Thierry J, Moras D |
(2000) "An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase." J.Mol.Biol., 299, 1051-1060. doi: 10.1006/jmbi.2000.3819. |
Crystal structure of aspartyl-trna synthetase from thermus thermophilus complexed to trnaasp from escherichia coli. SNAP output |
| 1eiy |
ligase-RNA |
X-ray (3.3 Å) |
Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M |
(1997) "The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe." Structure, 5, 59-68. doi: 10.1016/S0969-2126(97)00166-4. |
The crystal structure of phenylalanyl-trna synthetase from thermus thermophilus complexed with cognate trnaphe. SNAP output |
| 1ekz |
cell cycle-RNA |
NMR |
Ramos A, Grunert S, Adams J, Micklem DR, Proctor MR, Freund S, Bycroft M, St Johnston D, Varani G |
(2000) "RNA recognition by a Staufen double-stranded RNA-binding domain." EMBO J., 19, 997-1009. doi: 10.1093/emboj/19.5.997. |
NMR structure of the complex between the third dsrbd from drosophila staufen and a RNA hairpin. SNAP output |
| 1eqq |
replication-RNA |
X-ray (3.2 Å) |
Matsumoto T, Morimoto Y, Shibata N, Kinebuchi T, Shimamoto N, Tsukihara T, Yasuoka N |
(2000) "Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis." J.Biochem.(Tokyo), 127, 329-335. |
Single stranded DNA binding protein and ssDNA complex. SNAP output |
| 1etf |
viral protein-RNA |
NMR |
Battiste JL, Mao H, Rao NS, Tan R, Muhandiram DR, Kay LE, Frankel AD, Williamson JR |
(1996) "Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex." Science, 273, 1547-1551. |
Rev response element (rre) RNA complexed with rev peptide, NMR, minimized average structure. SNAP output |
| 1etg |
viral protein-RNA |
NMR |
Battiste JL, Mao H, Rao NS, Tan R, Muhandiram DR, Kay LE, Frankel AD, Williamson JR |
(1996) "Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex." Science, 273, 1547-1551. |
Rev response element (rre) RNA complexed with rev peptide, NMR, 19 structures. SNAP output |
| 1euq |
ligase-RNA |
X-ray (3.1 Å) |
Sherlin LD, Bullock TL, Newberry KJ, Lipman RS, Hou YM, Beijer B, Sproat BS, Perona JJ |
(2000) "Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases." J.Mol.Biol., 299, 431-446. doi: 10.1006/jmbi.2000.3749. |
Crystal structure of glutaminyl-trna synthetase complexed with a trna-gln mutant and an active-site inhibitor. SNAP output |
| 1euy |
ligase-RNA |
X-ray (2.6 Å) |
Sherlin LD, Bullock TL, Newberry KJ, Lipman RS, Hou YM, Beijer B, Sproat BS, Perona JJ |
(2000) "Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases." J.Mol.Biol., 299, 431-446. doi: 10.1006/jmbi.2000.3749. |
Glutaminyl-trna synthetase complexed with a trna mutant and an active site inhibitor. SNAP output |
| 1exd |
ligase-RNA |
X-ray (2.7 Å) |
Bullock TL, Sherlin LD, Perona JJ |
(2000) "Tertiary core rearrangements in a tight binding transfer RNA aptamer." Nat.Struct.Biol., 7, 497-504. doi: 10.1038/75910. |
Crystal structure of a tight-binding glutamine trna bound to glutamine aminoacyl trna synthetase. SNAP output |
| 1exy |
RNA binding protein-RNA |
NMR |
Jiang F, Gorin A, Hu W, Majumdar A, Baskerville S, Xu W, Ellington A, Patel DJ |
(1999) "Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples." Structure Fold.Des., 7, 1461-1472. doi: 10.1016/S0969-2126(00)88337-9. |
Solution structure of htlv-1 peptide bound to its RNA aptamer target. SNAP output |
| 1f6u |
structural protein-RNA |
NMR |
Amarasinghe GK, De Guzman RN, Turner RB, Chancellor KJ, Wu ZR, Summers MF |
(2000) "NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition." J.Mol.Biol., 301, 491-511. doi: 10.1006/jmbi.2000.3979. |
NMR structure of the hiv-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. implications for genome recognition. SNAP output |
| 1f7u |
ligase-RNA |
X-ray (2.2 Å) |
Delagoutte B, Moras D, Cavarelli J |
(2000) "tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding." EMBO J., 19, 5599-5610. doi: 10.1093/emboj/19.21.5599. |
Crystal structure of the arginyl-trna synthetase complexed with the trna(arg) and l-arg. SNAP output |
| 1f7v |
ligase-RNA |
X-ray (2.9 Å) |
Delagoutte B, Moras D, Cavarelli J |
(2000) "tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding." EMBO J., 19, 5599-5610. doi: 10.1093/emboj/19.21.5599. |
Crystal structure of yeast arginyl-trna synthetase complexed with the trnaarg. SNAP output |
| 1f7y |
ribosome |
X-ray (2.8 Å) |
Ennifar E, Nikulin A, Tishchenko S, Serganov A, Nevskaya N, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P |
(2000) "The crystal structure of UUCG tetraloop." J.Mol.Biol., 304, 35-42. doi: 10.1006/jmbi.2000.4204. |
The crystal structure of two uucg loops highlights the role played by 2'-hydroxyl groups in its unusual stability. SNAP output |
| 1f8v |
virus-RNA |
X-ray (3.0 Å) |
Tang L, Johnson KN, Ball LA, Lin T, Yeager M, Johnson JE |
(2001) "The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA." Nat.Struct.Biol., 8, 77-83. doi: 10.1038/83089. |
The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA. SNAP output |
| 1feu |
ribosome |
X-ray (2.3 Å) |
Fedorov R, Meshcheryakov V, Gongadze G, Fomenkova N, Nevskaya N, Selmer M, Laurberg M, Kristensen O, Al-Karadaghi S, Liljas A, Garber M, Nikonov S |
(2001) "Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins." Acta Crystallogr.,Sect.D, 57, 968-976. doi: 10.1107/S0907444901006291. |
Crystal structure of ribosomal protein tl5, one of the ctc family proteins, complexed with a fragment of 5s rrna.. SNAP output |
| 1ffy |
ligase-RNA |
X-ray (2.2 Å) |
Silvian LF, Wang J, Steitz TA |
(1999) "Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin." Science, 285, 1074-1077. doi: 10.1126/science.285.5430.1074. |
Insights into editing from an ile-trna synthetase structure with trna(ile) and mupirocin. SNAP output |
| 1fje |
structural protein-RNA |
NMR |
Allain FH, Bouvet P, Dieckmann T, Feigon J |
(2000) "Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin." EMBO J., 19, 6870-6881. doi: 10.1093/emboj/19.24.6870. |
Solution structure of nucleolin rbd12 in complex with snre RNA. SNAP output |
| 1fjg |
ribosome |
X-ray (3.0 Å) |
Carter AP, Clemons Jr WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V |
(2000) "Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics." Nature, 407, 340-348. doi: 10.1038/35030019. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotics streptomycin, spectinomycin, and paromomycin. SNAP output |
| 1fka |
ribosome |
X-ray (3.3 Å) |
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A |
(2000) "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution." Cell(Cambridge,Mass.), 102, 615-623. doi: 10.1016/S0092-8674(00)00084-2. |
Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. SNAP output |
| 1fnx |
immune system-RNA |
NMR |
Inoue M, Hirao M, Kasashima K, Kim I-S, Kawai G, Kigawa T, Sakamoto H, Muto Y, Yokoyama S |
(2000) "Solution structure of mouse HuC RNA-binding domains complexed with an AU-Rich element reveals determinants of neuronal differentiation." |
Solution structure of the huc rbd1-rbd2 complexed with the au-rich element. SNAP output |
| 1fxl |
transcription-RNA |
X-ray (1.8 Å) |
Wang X, Tanaka Hall TM |
(2001) "Structural basis for recognition of AU-rich element RNA by the HuD protein." Nat.Struct.Biol., 8, 141-145. doi: 10.1038/84131. |
Crystal structure of hud and au-rich element of the c-fos RNA. SNAP output |
| 1g1x |
ribosome |
X-ray (2.6 Å) |
Agalarov SC, Sridhar Prasad G, Funke PM, Stout CD, Williamson JR |
(2000) "Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain." Science, 288, 107-112. doi: 10.1126/science.288.5463.107. |
Structure of ribosomal proteins s15, s6, s18, and 16s ribosomal RNA. SNAP output |
| 1g2e |
transcription-RNA |
X-ray (2.3 Å) |
Wang X, Tanaka Hall TM |
(2001) "Structural basis for recognition of AU-rich element RNA by the HuD protein." Nat.Struct.Biol., 8, 141-145. doi: 10.1038/84131. |
Crystal structure of hud and au-rich element of the tumor necrosis factor alpha RNA. SNAP output |
| 1g59 |
ligase-RNA |
X-ray (2.4 Å) |
Sekine S, Nureki O, Shimada A, Vassylyev DG, Yokoyama S |
(2001) "Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase." Nat.Struct.Biol., 8, 203-206. doi: 10.1038/84927. |
Glutamyl-trna synthetase complexed with trna(glu).. SNAP output |
| 1g70 |
viral protein-RNA |
NMR |
Gosser Y, Hermann T, Majumdar A, Hu W, Frederick R, Jiang F, Xu W, Patel DJ |
(2001) "Peptide-triggered conformational switch in HIV-1 RRE RNA complexes." Nat.Struct.Biol., 8, 146-150. doi: 10.1038/84138. |
Complex of hiv-1 rre-iib RNA with rsg-1.2 peptide. SNAP output |
| 1gax |
ligase-RNA |
X-ray (2.9 Å) |
Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S |
(2000) "Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase." Cell(Cambridge,Mass.), 103, 793-803. doi: 10.1016/S0092-8674(00)00182-3. |
Crystal structure of thermus thermophilus valyl-trna synthetase complexed with trna(val) and valyl-adenylate analogue. SNAP output |
| 1gtf |
RNA binding protein-RNA |
X-ray (1.75 Å) |
Hopcroft NH, Wendt AL, Gollnick P, Antson AA |
(2002) "Specificity of Trap-RNA Interactions: Crystal Structures of Two Complexes with Different RNA Sequences." Acta Crystallogr.,Sect.D, 58, 615. doi: 10.1107/S0907444902003189. |
The structure of the trp RNA-binding attenuation protein (trap) bound to a 53-nucleotide RNA molecule containing gaguu repeats. SNAP output |
| 1gtn |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Hopcroft NH, Wendt AL, Gollnick P, Antson AA |
(2002) "Specificity of Trap-RNA Interactions: Crystal Structures of Two Complexes with Different RNA Sequences." Acta Crystallogr.,Sect.D, 58, 615. doi: 10.1107/S0907444902003189. |
Structure of the trp RNA-binding attenuation protein (trap) bound to an RNA molecule containing 11 gagcc repeats. SNAP output |
| 1gtr |
complex (ligase-trna) |
X-ray (2.5 Å) |
Rould MA, Perona JJ, Steitz TA |
(1991) "Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase." Nature, 352, 213-218. doi: 10.1038/352213a0. |
Structural basis of anticodon loop recognition by glutaminyl-trna synthetase. SNAP output |
| 1gts |
ligase-RNA |
X-ray (2.8 Å) |
Perona JJ, Rould MA, Steitz TA |
(1993) "Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase." Biochemistry, 32, 8758-8771. doi: 10.1021/bi00085a006. |
Structural basis for transfer RNA aminoaceylation by escherichia coli glutaminyl-trna synthetase. SNAP output |
| 1h2c |
virus-viral protein |
X-ray (1.6 Å) |
Gomis-Ruth FX, Dessen A, Timmins J, Bracher A, Kolesnikowa L, Becker S, Klenk HD, Weissenhorn W |
(2003) "The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties." Structure, 11, 423. doi: 10.1016/S0969-2126(03)00050-9. |
Ebola virus matrix protein vp40 n-terminal domain in complex with RNA (high-resolution vp40[55-194] variant).. SNAP output |
| 1h2d |
virus-viral protein |
X-ray (2.6 Å) |
Gomis-Ruth FX, Dessen A, Timmins J, Bracher A, Kolesnikowa L, Becker S, Klenk HD, Weissenhorn W |
(2003) "The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties." Structure, 11, 423. doi: 10.1016/S0969-2126(03)00050-9. |
Ebola virus matrix protein vp40 n-terminal domain in complex with RNA (low-resolution vp40[31-212] variant).. SNAP output |
| 1h3e |
ligase |
X-ray (2.9 Å) |
Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S |
(2002) "Class I Tyrosyl-tRNA Synthetase Has a Class II Mode or tRNA Recognition." Embo J., 21, 3829. doi: 10.1093/EMBOJ/CDF373. |
Tyrosyl-trna synthetase from thermus thermophilus complexed with wild-type trnatyr(gua) and with atp and tyrosinol. SNAP output |
| 1h4q |
aminoacyl-trna synthetase |
X-ray (3.0 Å) |
Yaremchuk A, Tukalo M, Grotli M, Cusack S |
(2001) "A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase." J.Mol.Biol., 309, 989. doi: 10.1006/JMBI.2001.4712. |
Prolyl-trna synthetase from thermus thermophilus complexed with trnapro(cgg), atp and prolinol. SNAP output |
| 1h4s |
aminoacyl-trna synthetase |
X-ray (2.85 Å) |
Yaremchuk A, Tukalo M, Grotli M, Cusack S |
(2001) "A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase." J.Mol.Biol., 309, 989. doi: 10.1006/JMBI.2001.4712. |
Prolyl-trna synthetase from thermus thermophilus complexed with trnapro(cgg) and a prolyl-adenylate analogue. SNAP output |
| 1hc8 |
ribosome |
X-ray (2.8 Å) |
Conn GL, Gittis AG, Lattman EE, Misra VK, Draper DE |
(2002) "A Compact RNA Tertiary Structure Contains a Buried Backbone-K+ Complex." J.Mol.Biol., 318, 963. doi: 10.1016/S0022-2836(02)00147-X. |
Crystal structure of a conserved ribosomal protein-RNA complex. SNAP output |
| 1hji |
bacteriophage hk022 |
NMR |
Faber C, Schaerpf M, Becker T, Sticht H, Roesch P |
(2001) "The Structure of the Coliphage Hk022 Nun Protein-Lambda-Phage Boxb RNA Complex. Implications for the Mechanism of Transcription Termination." J.Biol.Chem., 276, 32064. doi: 10.1074/JBC.M102975200. |
Bacteriophage hk022 nun-protein-nutboxb-RNA complex. SNAP output |
| 1hnw |
ribosome |
X-ray (3.4 Å) |
Brodersen DE, Clemons Jr WM, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V |
(2000) "The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit." Cell(Cambridge,Mass.), 103, 1143-1154. doi: 10.1016/S0092-8674(00)00216-6. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with tetracycline. SNAP output |
| 1hnx |
ribosome |
X-ray (3.4 Å) |
Brodersen DE, Clemons Jr WM, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V |
(2000) "The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit." Cell(Cambridge,Mass.), 103, 1143-1154. doi: 10.1016/S0092-8674(00)00216-6. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with pactamycin. SNAP output |
| 1hnz |
ribosome |
X-ray (3.3 Å) |
Brodersen DE, Clemons Jr WM, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V |
(2000) "The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit." Cell(Cambridge,Mass.), 103, 1143-1154. doi: 10.1016/S0092-8674(00)00216-6. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with hygromycin b. SNAP output |
| 1hq1 |
signaling protein-RNA |
X-ray (1.52 Å) |
Batey RT, Sagar MB, Doudna JA |
(2001) "Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle." J.Mol.Biol., 307, 229-246. doi: 10.1006/jmbi.2000.4454. |
Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. SNAP output |
| 1hr0 |
ribosome |
X-ray (3.2 Å) |
Carter AP, Clemons Jr WM, Brodersen DE, Morgan-Warren RJ, Hartsch T, Wimberly BT, Ramakrishnan V |
(2001) "Crystal structure of an initiation factor bound to the 30S ribosomal subunit." Science, 291, 498-501. doi: 10.1126/science.1057766. |
Crystal structure of initiation factor if1 bound to the 30s ribosomal subunit. SNAP output |
| 1hvu |
transferase-RNA |
X-ray (4.75 Å) |
Jaeger J, Restle T, Steitz TA |
(1998) "The structure of HIV-1 reverse transcriptase complexed with an RNA pseudoknot inhibitor." EMBO J., 17, 4535-4542. doi: 10.1093/emboj/17.15.4535. |
Human immunodeficiency virus type 1 reverse transcriptase complexed with a 33-base nucleotide RNA pseudoknot. SNAP output |
| 1i5l |
RNA binding protein-RNA |
X-ray (2.75 Å) |
Toro I, Thore S, Mayer C, Basquin J, Seraphin B, Suck D |
(2001) "RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex." EMBO J., 20, 2293-2303. doi: 10.1093/emboj/20.9.2293. |
Crystal structure of an sm-like protein (af-sm1) from archaeoglobus fulgidus complexed with short poly-u RNA. SNAP output |
| 1i6u |
ribosome |
X-ray (2.6 Å) |
Tishchenko S, Nikulin A, Fomenkova N, Nevskaya N, Nikonov O, Dumas P, Moine H, Ehresmann B, Ehresmann C, Piendl W, Lamzin V, Garber M, Nikonov S |
(2001) "Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii." J.Mol.Biol., 311, 311-324. doi: 10.1006/jmbi.2001.4877. |
RNA-protein interactions: the crystal structure of ribosomal protein s8-rrna complex from methanococcus jannaschii. SNAP output |
| 1i94 |
ribosome |
X-ray (3.2 Å) |
Pioletti M, Schlunzen F, Harms J, Zarivach R, Gluhmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F |
(2001) "Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3." EMBO J., 20, 1829-1839. doi: 10.1093/emboj/20.8.1829. |
Crystal structures of the small ribosomal subunit with tetracycline, edeine and if3. SNAP output |
| 1i9f |
de-novo protein-RNA |
NMR |
Zhang Q, Harada K, Cho HS, Frankel AD, Wemmer DE |
(2001) "Structural characterization of the complex of the Rev response element RNA with a selected peptide." Chem.Biol., 8, 511-520. doi: 10.1016/S1074-5521(01)00027-8. |
Structural characterization of the complex of the rev response element RNA with a selected peptide. SNAP output |
| 1ibk |
ribosome |
X-ray (3.31 Å) |
Ogle JM, Brodersen DE, Clemons Jr WM, Tarry MJ, Carter AP, Ramakrishnan V |
(2001) "Recognition of cognate transfer RNA by the 30S ribosomal subunit." Science, 292, 897-902. doi: 10.1126/science.1060612. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotic paromomycin. SNAP output |
| 1ibl |
ribosome |
X-ray (3.11 Å) |
Ogle JM, Brodersen DE, Clemons Jr WM, Tarry MJ, Carter AP, Ramakrishnan V |
(2001) "Recognition of cognate transfer RNA by the 30S ribosomal subunit." Science, 292, 897-902. doi: 10.1126/science.1060612. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with a messenger RNA fragment and cognate transfer RNA anticodon stem-loop bound at the a site and with the antibiotic paromomycin. SNAP output |
| 1ibm |
ribosome |
X-ray (3.31 Å) |
Ogle JM, Brodersen DE, Clemons Jr WM, Tarry MJ, Carter AP, Ramakrishnan V |
(2001) "Recognition of cognate transfer RNA by the 30S ribosomal subunit." Science, 292, 897-902. doi: 10.1126/science.1060612. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with a messenger RNA fragment and cognate transfer RNA anticodon stem-loop bound at the a site. SNAP output |
| 1il2 |
ligase-RNA |
X-ray (2.6 Å) |
Moulinier L, Eiler S, Eriani G, Gangloff J, Thierry JC, Gabriel K, McClain WH, Moras D |
(2001) "The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism." EMBO J., 20, 5290-5301. doi: 10.1093/emboj/20.18.5290. |
Crystal structure of the e. coli aspartyl-trna synthetase:yeast trnaasp:aspartyl-adenylate complex. SNAP output |
| 1ivs |
ligase-RNA |
X-ray (2.9 Å) |
Fukai S, Nureki O, Sekine S-I, Shimada A, Vassylyev DG, Yokoyama S |
(2003) "Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase." RNA, 9, 100-111. doi: 10.1261/rna.2760703. |
Crystal structure of thermus thermophilus valyl-trna synthetase complexed with trna(val) and valyl-adenylate analogue. SNAP output |
| 1j1u |
ligase-RNA |
X-ray (1.95 Å) |
Kobayashi T, Nureki O, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S |
(2003) "Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion." NAT.STRUCT.BIOL., 10, 425-432. doi: 10.1038/nsb934. |
Crystal structure of archaeal tyrosyl-trna synthetase complexed with trna(tyr) and l-tyrosine. SNAP output |
| 1j2b |
transferase-RNA |
X-ray (3.3 Å) |
Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S |
(2003) "Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme." Cell(Cambridge,Mass.), 113, 383-394. doi: 10.1016/S0092-8674(03)00280-0. |
Crystal structure of archaeosine trna-guanine transglycosylase complexed with lambda-form trna(val). SNAP output |
| 1j5e |
ribosome |
X-ray (3.05 Å) |
Wimberly BT, Brodersen DE, Clemons Jr WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V |
(2000) "Structure of the 30S ribosomal subunit." Nature, 407, 327-339. doi: 10.1038/35030006. |
Structure of the thermus thermophilus 30s ribosomal subunit. SNAP output |
| 1jbr |
hydrolase-RNA |
X-ray (2.15 Å) |
Yang X, Gerczei T, Glover LT, Correll CC |
(2001) "Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping." Nat.Struct.Biol., 8, 968-973. doi: 10.1038/nsb1101-968. |
Crystal structure of the ribotoxin restrictocin and a 31-mer srd RNA inhibitor. SNAP output |
| 1jbs |
hydrolase-RNA |
X-ray (1.97 Å) |
Yang X, Gerczei T, Glover LT, Correll CC |
(2001) "Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping." Nat.Struct.Biol., 8, 968-973. doi: 10.1038/nsb1101-968. |
Crystal structure of ribotoxin restrictocin and a 29-mer srd RNA analog. SNAP output |
| 1jbt |
hydrolase-RNA |
X-ray (2.7 Å) |
Yang X, Gerczei T, Glover LT, Correll CC |
(2001) "Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping." Nat.Struct.Biol., 8, 968-973. doi: 10.1038/nsb1101-968. |
Crystal structure of ribotoxin restrictocin complexed with a 29-mer sarcin-ricin domain RNA analog. SNAP output |
| 1jid |
signaling protein-RNA |
X-ray (1.8 Å) |
Wild K, Sinning I, Cusack S |
(2001) "Crystal structure of an early protein-RNA assembly complex of the signal recognition particle." Science, 294, 598-601. doi: 10.1126/science.1063839. |
Human srp19 in complex with helix 6 of human srp RNA. SNAP output |
| 1jj2 |
ribosome |
X-ray (2.4 Å) |
Klein DJ, Schmeing TM, Moore PB, Steitz TA |
(2001) "The kink-turn: a new RNA secondary structure motif." EMBO J., 20, 4214-4221. doi: 10.1093/emboj/20.15.4214. |
Fully refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution. SNAP output |
| 1k1g |
gene regulation-RNA |
NMR |
Liu Z, Luyten I, Bottomley MJ, Messias AC, Houngninou-Molango S, Sprangers R, Zanier K, Kramer A, Sattler M |
(2001) "Structural basis for recognition of the intron branch site RNA by splicing factor 1." Science, 294, 1098-1102. doi: 10.1126/science.1064719. |
Structural basis for recognition of the intron branch site RNA by splicing factor 1. SNAP output |
| 1k73 |
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 anisomycin bound to the 50s ribosomal subunit. SNAP output |
| 1k8a |
ribosome |
X-ray (3.0 Å) |
Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA |
(2002) "The structures of four macrolide antibiotics bound to the large ribosomal subunit." Mol.Cell, 10, 117-128. doi: 10.1016/S1097-2765(02)00570-1. |
Co-crystal structure of carbomycin a bound to the 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1k8w |
lyase-RNA |
X-ray (1.85 Å) |
Hoang C, Ferre-D'Amare AR |
(2001) "Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme." Cell(Cambridge,Mass.), 107, 929-939. doi: 10.1016/S0092-8674(01)00618-3. |
Crystal structure of the e. coli pseudouridine synthase trub bound to a t stem-loop RNA. SNAP output |
| 1k9m |
ribosome |
X-ray (3.0 Å) |
Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA |
(2002) "The structures of four macrolide antibiotics bound to the large ribosomal subunit." Mol.Cell, 10, 117-128. doi: 10.1016/S1097-2765(02)00570-1. |
Co-crystal structure of tylosin bound to the 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1kd1 |
ribosome |
X-ray (3.0 Å) |
Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA |
(2002) "The structures of four macrolide antibiotics bound to the large ribosomal subunit." Mol.Cell, 10, 117-128. doi: 10.1016/S1097-2765(02)00570-1. |
Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1knz |
viral protein-RNA |
X-ray (2.45 Å) |
Deo RC, Groft CM, Rajashankar KR, Burley SK |
(2002) "Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer." Cell(Cambridge,Mass.), 108, 71-81. doi: 10.1016/S0092-8674(01)00632-8. |
Recognition of the rotavirus mrna 3' consensus by an asymmetric nsp3 homodimer. SNAP output |
| 1kog |
ligase-RNA |
X-ray (3.5 Å) |
Torres-Larios A, Dock-Bregeon AC, Romby P, Rees B, Sankaranarayanan R, Caillet J, Springer M, Ehresmann C, Ehresmann B, Moras D |
(2002) "Structural basis of translational control by Escherichia coli threonyl tRNA synthetase." Nat.Struct.Biol., 9, 343-347. |
Crystal structure of e. coli threonyl-trna synthetase interacting with the essential domain of its mrna operator. SNAP output |
| 1kq2 |
translation-RNA |
X-ray (2.71 Å) |
Schumacher MA, Pearson RF, Moller T, Valentin-Hansen P, Brennan RG |
(2002) "Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein." EMBO J., 21, 3546-3556. doi: 10.1093/emboj/cdf322. |
Crystal structure of an hfq-RNA complex. SNAP output |
| 1kqs |
ribosome |
X-ray (3.1 Å) |
Schmeing TM, Seila AC, Hansen JL, Freeborn B, Soukup JK, Scaringe SA, Strobel SA, Moore PB, Steitz TA |
(2002) "A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits." Nat.Struct.Biol., 9, 225-230. |
The haloarcula marismortui 50s complexed with a pretranslocational intermediate in protein synthesis. SNAP output |
| 1kuq |
ribosome |
X-ray (2.84 Å) |
Revtovich SV, Nikulin AD, Nikonov SV |
(2004) "Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA." Biochemistry Mosc., 69, 1319-1323. doi: 10.1007/s10541-005-0076-5. |
Crystal structure of t3c mutant s15 ribosomal protein in complex with 16s rrna. SNAP output |
| 1l1c |
transcription-RNA |
NMR |
Yang Y, Declerck N, Manival X, Aymerich S, Kochoyan M |
(2002) "Solution structure of the LicT-RNA antitermination complex: CAT clamping RAT." EMBO J., 21, 1987-1997. doi: 10.1093/emboj/21.8.1987. |
Structure of the lict bacterial antiterminator protein in complex with its RNA target. SNAP output |
| 1l9a |
signaling protein-RNA |
X-ray (2.9 Å) |
Oubridge C, Kuglstatter A, Jovine L, Nagai K |
(2002) "Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle." Mol.Cell, 9, 1251-1261. doi: 10.1016/S1097-2765(02)00530-0. |
Crystal structure of srp19 in complex with the s domain of signal recognition particle RNA. SNAP output |
| 1laj |
virus-RNA |
X-ray (3.4 Å) |
Lucas RW, Larson SB, Canady MA, McPherson A |
(2002) "The Structure of Tomato Aspermy Virus by X-Ray Crystallography." J.STRUCT.BIOL., 139, 90-102. doi: 10.1016/S1047-8477(02)00561-0. |
The structure of tomato aspermy virus by x-ray crystallography. SNAP output |
| 1lng |
signaling protein-RNA |
X-ray (2.3 Å) |
Hainzl T, Huang S, Sauer-Eriksson AE |
(2002) "Structure of the SRP19 RNA complex and implications for signal recognition particle assembly." Nature, 417, 767-771. doi: 10.1038/nature00768. |
Crystal structure of the srp19-7s.s srp RNA complex of m. jannaschii. SNAP output |
| 1m1k |
ribosome |
X-ray (3.2 Å) |
Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA |
(2002) "The structures of four macrolide antibiotics bound to the large ribosomal subunit." Mol.Cell, 10, 117-128. doi: 10.1016/S1097-2765(02)00570-1. |
Co-crystal structure of azithromycin bound to the 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1m5k |
translation-RNA |
X-ray (2.4 Å) |
Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR |
(2002) "Transition state stabilization by a catalytic RNA." Science, 298, 1421-1424. doi: 10.1126/science.1076093. |
Crystal structure of a hairpin ribozyme in the catalytically-active conformation. SNAP output |
| 1m5o |
translation-RNA |
X-ray (2.2 Å) |
Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR |
(2002) "Transition state stabilization by a catalytic RNA." Science, 298, 1421-1424. doi: 10.1126/science.1076093. |
Transition state stabilization by a catalytic RNA. SNAP output |
| 1m5p |
translation-RNA |
X-ray (2.6 Å) |
Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR |
(2002) "Transition state stabilization by a catalytic RNA." Science, 298, 1421-1424. doi: 10.1126/science.1076093. |
Transition state stabilization by a catalytic RNA. SNAP output |
| 1m5v |
translation-RNA |
X-ray (2.4 Å) |
Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR |
(2002) "Transition state stabilization by a catalytic RNA." Science, 298, 1421-1424. doi: 10.1126/science.1076093. |
Transition state stabilization by a catalytic RNA. SNAP output |
| 1m8v |
RNA binding protein-RNA |
X-ray (2.6 Å) |
Thore S, Mayer C, Sauter C, Weeks S, Suck D |
(2003) "Crystal Structure of Pyrococcus abyssii Sm core and its Complex with RNA: Common Features of RNA-binding in Archaea and Eukarya." J.Biol.Chem., 278, 1239-1247. doi: 10.1074/jbc.M207685200. |
Structure of pyrococcus abyssii sm protein in complex with a uridine heptamer. SNAP output |
| 1m8w |
RNA binding protein-RNA |
X-ray (2.2 Å) |
Wang X, McLachlan J, Zamore PD, Hall TMT |
(2002) "MODULAR RECOGNITION OF RNA BY A HUMAN PUMILIO-HOMOLOGY DOMAIN." CELL(CAMBRIDGE,MASS.), 110, 501-512. doi: 10.1016/S0092-8674(02)00873-5. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with nre1-19 RNA. SNAP output |
| 1m8x |
RNA binding protein-RNA |
X-ray (2.2 Å) |
Wang X, McLachlan J, Zamore PD, Hall TMT |
(2002) "MODULAR RECOGNITION OF RNA BY A HUMAN PUMILIO-HOMOLOGY DOMAIN." CELL(CAMBRIDGE,MASS.), 110, 501-512. doi: 10.1016/S0092-8674(02)00873-5. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with nre1-14 RNA. SNAP output |
| 1m8y |
RNA binding protein-RNA |
X-ray (2.6 Å) |
Wang X, McLachlan J, Zamore PD, Hall TMT |
(2002) "MODULAR RECOGNITION OF RNA BY A HUMAN PUMILIO-HOMOLOGY DOMAIN." CELL(CAMBRIDGE,MASS.), 110, 501-512. doi: 10.1016/S0092-8674(02)00873-5. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with nre2-10 RNA. SNAP output |
| 1m90 |
ribosome |
X-ray (2.8 Å) |
Hansen JL, Schmeing TM, Moore PB, Steitz TA |
(2002) "Structural insights into peptide bond formation." Proc.Natl.Acad.Sci.USA, 99, 11670-11675. doi: 10.1073/pnas.172404099. |
Co-crystal structure of cca-phe-caproic acid-biotin and sparsomycin bound to the 50s ribosomal subunit. SNAP output |
| 1mfq |
signaling protein-RNA |
X-ray (3.1 Å) |
Kuglstatter A, Oubridge C, Nagai K |
(2002) "Induced structural changes of 7SL RNA during the assembly of human
signal recognition particle." Nat.Struct.Biol., 9, 740-744. doi: 10.1038/nsb843. |
Crystal structure analysis of a ternary s-domain complex of human signal recognition particle. SNAP output |
| 1mji |
ribosome |
X-ray (2.5 Å) |
Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M, Tanaka I, Garber M, Gongadze G, Nikonov S |
(2002) "Detailed analysis of RNA-protein interactions within the bacterial ribosomal
protein L5/5S rRNA complex." RNA, 8, 1548-1557. |
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein l5-5s rrna complex. SNAP output |
| 1mms |
ribosome |
X-ray (2.57 Å) |
Wimberly BT, Guymon R, McCutcheon JP, White SW, Ramakrishnan V |
(1999) "A detailed view of a ribosomal active site: the structure of the L11-RNA complex." Cell(Cambridge,Mass.), 97, 491-502. doi: 10.1016/S0092-8674(00)80759-X. |
Crystal structure of the ribosomal protein l11-RNA complex. SNAP output |
| 1mnb |
viral protein-RNA |
NMR |
Puglisi JD, Chen L, Blanchard S, Frankel AD |
(1995) "Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex." Science, 270, 1200-1203. |
Biv tat peptide (residues 68-81), NMR, minimized average structure. SNAP output |
| 1mzp |
ribosome |
X-ray (2.65 Å) |
Nikulin A, Eliseikina I, Tishchenko S, Nevskaya N, Davydova N, Platonova O, Piendl W, Selmer M, Liljas A, Drygin D, Zimmermann R, Garber M, Nikonov S |
(2003) "Structure of the L1 protuberance in the ribosome." Nat.Struct.Biol., 10, 104-108. doi: 10.1038/nsb886. |
Structure of the l1 protuberance in the ribosome. SNAP output |
| 1n1h |
transferase-RNA |
X-ray (2.8 Å) |
Tao Y, Farsetta DL, Nibert ML, Harrison SC |
(2002) "RNA Synthesis in a Cage--Structural Studies of Reovirus Polymerase [lambda] 3." Cell(Cambridge,Mass.), 111, 733-745. doi: 10.1016/S0092-8674(02)01110-8. |
Initiation complex of polymerase lambda3 from reovirus. SNAP output |
| 1n32 |
ribosome |
X-ray (3.0 Å) |
Ogle JM, Murphy IV FV, Tarry MJ, Ramakrishnan V |
(2002) "Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form." Cell(Cambridge,Mass.), 111, 721-732. doi: 10.1016/S0092-8674(02)01086-3. |
Structure of the thermus thermophilus 30s ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin. SNAP output |
| 1n33 |
ribosome |
X-ray (3.35 Å) |
Ogle JM, Murphy IV FV, Tarry MJ, Ramakrishnan V |
(2002) "Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form." Cell(Cambridge,Mass.), 111, 721-732. doi: 10.1016/S0092-8674(02)01086-3. |
Structure of the thermus thermophilus 30s ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position at the a site with paromomycin. SNAP output |
| 1n34 |
ribosome |
X-ray (3.8 Å) |
Ogle JM, Murphy IV FV, Tarry MJ, Ramakrishnan V |
(2002) "Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form." Cell(Cambridge,Mass.), 111, 721-732. doi: 10.1016/S0092-8674(02)01086-3. |
Structure of the thermus thermophilus 30s ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position. SNAP output |
| 1n35 |
transferase-RNA |
X-ray (2.5 Å) |
Tao Y, Farsetta DL, Nibert ML, Harrison SC |
(2002) "RNA Synthesis in a Cage--Structural Studies of Reovirus Polymerase [lambda] 3." Cell(Cambridge,Mass.), 111, 733-745. doi: 10.1016/S0092-8674(02)01110-8. |
Lambda3 elongation complex with four phosphodiester bond formed. SNAP output |
| 1n36 |
ribosome |
X-ray (3.65 Å) |
Ogle JM, Murphy IV FV, Tarry MJ, Ramakrishnan V |
(2002) "Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form." Cell(Cambridge,Mass.), 111, 721-732. doi: 10.1016/S0092-8674(02)01086-3. |
Structure of the thermus thermophilus 30s ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position. SNAP output |
| 1n38 |
transferase-RNA |
X-ray (2.8 Å) |
Tao Y, Farsetta DL, Nibert ML, Harrison SC |
(2002) "RNA Synthesis in a Cage--Structural Studies of Reovirus Polymerase [lambda] 3." Cell(Cambridge,Mass.), 111, 733-745. doi: 10.1016/S0092-8674(02)01110-8. |
Reovirus polymerase lambda3 elongation complex with one phosphodiester bond formed. SNAP output |
| 1n77 |
ligase-RNA |
X-ray (2.4 Å) |
Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S |
(2003) "ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding." EMBO J., 22, 676-688. doi: 10.1093/emboj/cdg053. |
Crystal structure of thermus thermophilus glutamyl-trna synthetase complexed with trna(glu) and atp.. SNAP output |
| 1n78 |
ligase-RNA |
X-ray (2.1 Å) |
Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S |
(2003) "ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding." EMBO J., 22, 676-688. doi: 10.1093/emboj/cdg053. |
Crystal structure of thermus thermophilus glutamyl-trna synthetase complexed with trna(glu) and glutamol-amp.. SNAP output |
| 1n8r |
ribosome-antibiotic |
X-ray (3.0 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. |
Structure of large ribosomal subunit in complex with virginiamycin m. SNAP output |
| 1nb7 |
transferase-RNA |
X-ray (2.9 Å) |
O'Farrell D, Trowbridge R, Rowlands D, Jager J |
(2003) "Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation." J.Mol.Biol., 326, 1025-1035. doi: 10.1016/S0022-2836(02)01439-0. |
Hc-j4 RNA polymerase complexed with short RNA template strand. SNAP output |
| 1nji |
ribosome |
X-ray (3.0 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. |
Structure of chloramphenicol bound to the 50s ribosomal subunit. SNAP output |
| 1njm |
ribosome |
X-ray (3.6 Å) |
Bashan A, Agmon I, Zarivatch R, Schluenzen F, Harms JM, Berisio R, Bartels H, Franceschi F, Auerbach T, Hansen HA, Kossoy E, Kessler M, Yonath A |
(2003) "Structural basis of the ribosomal machinery for Peptide bond formation,
translocation, and nascent chain progression." Mol.Cell, 11, 91-102. doi: 10.1016/S1097-2765(03)00009-1. |
The crystal structure of the 50s large ribosomal subunit from deinococcus radiodurans complexed with a trna acceptor stem mimic (asm) and the antibiotic sparsomycin. SNAP output |
| 1njp |
ribosome |
X-ray (3.5 Å) |
Bashan A, Agmon I, Zarivatch R, Schluenzen F, Harms JM, Berisio R, Bartels H, Franceschi F, Auerbach T, Hansen HA, Kossoy E, Kessler M, Yonath A |
(2003) "Structural basis of the ribosomal machinery for Peptide bond formation,
translocation, and nascent chain progression." Mol.Cell, 11, 91-102. doi: 10.1016/S1097-2765(03)00009-1. |
The crystal structure of the 50s large ribosomal subunit from deinococcus radiodurans complexed with a trna acceptor stem mimic (asm). SNAP output |
| 1nyb |
transcription-RNA |
NMR |
Cilley CD, Williamson JR |
(2003) "Structural mimicry in the phage phi21 N peptide-boxB RNA complex." RNA, 9, 663-676. doi: 10.1261/rna.2189203. |
Solution structure of the bacteriophage phi21 n peptide-boxb RNA complex. SNAP output |
| 1o0b |
ligase-RNA |
X-ray (2.7 Å) |
Bullock TL, Uter N, Nissan TA, Perona JJ |
(2003) "Amino Acid Discrimination by a class I aminoacyl-tRNA synthetase
specified by negative determinants." J.Mol.Biol., 328, 395-408. doi: 10.1016/S0022-2836(03)00305-X. |
Crystal structure of l-glutamine and ampcpp bound to glutamine aminoacyl trna synthetase. SNAP output |
| 1o0c |
ligase-RNA |
X-ray (2.7 Å) |
Bullock TL, Uter N, Nissan TA, Perona JJ |
(2003) "Amino Acid Discrimination by a class I aminoacyl-tRNA synthetase
specified by negative determinants." J.Mol.Biol., 328, 395-408. doi: 10.1016/S0022-2836(03)00305-X. |
Crystal structure of l-glutamate and ampcpp bound to glutamine aminoacyl trna synthetase. SNAP output |
| 1ob2 |
hydrolase-nuclear protein |
X-ray (3.35 Å) |
Nielsen RC, Kristensen O, Kjeldgaard M, Thirup S, Nissen P |
"Kirromycin Defines a Specific Domain Arrangement of Elongation Factor EF-TU." |
E. coli elongation factor ef-tu complexed with the antibiotic kirromycin, a gtp analog, and phe-trna. SNAP output |
| 1ob5 |
hydrolase |
X-ray (3.1 Å) |
Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P |
(2006) "Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics." J.Biol.Chem., 281, 2893. doi: 10.1074/JBC.M505951200. |
T. aquaticus elongation factor ef-tu complexed with the antibiotic enacyloxin iia, a gtp analog, and phe-trna. SNAP output |
| 1oln |
ribosome-antibiotic |
multiple methods: solution nmr, theoretical model |
Lentzen G, Klinck R, Matassova N, Aboul-Ela F, Murchie AIH |
(2003) "Structural Basis for Contrasting Activities of Ribosome Binding Thiazole Antibiotics." Chem.Biol., 10, 769. doi: 10.1016/S1074-5521(03)00173-X. |
Model for thiostrepton antibiotic binding to l11 substrate from 50s ribosomal RNA. SNAP output |
| 1ooa |
transcription-RNA |
X-ray (2.45 Å) |
Huang DB, Vu D, Cassiday LA, Zimmerman JM, Maher III LJ, Ghosh G |
(2003) "Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer." Proc.Natl.Acad.Sci.USA, 100, 9268-9273. doi: 10.1073/pnas.1632011100. |
Crystal structure of nf-kb(p50)2 complexed to a high-affinity RNA aptamer. SNAP output |
| 1p6v |
RNA binding protein-RNA |
X-ray (3.2 Å) |
Gutmann S, Haebel PW, Metzinger L, Sutter M, Felden B, Ban N |
(2003) "Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB." Nature, 424, 699-703. doi: 10.1038/nature01831. |
Crystal structure of the trna domain of transfer-messenger RNA in complex with smpb. SNAP output |
| 1pgl |
virus-RNA |
X-ray (2.8 Å) |
Lin T, Cavarelli J, Johnson JE |
(2003) "Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus." Virology, 314, 26-33. doi: 10.1016/S0042-6822(03)00457-4. |
Bean pod mottle virus (bpmv), middle component. SNAP output |
| 1pvo |
transcription-RNA |
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 rho transcription termination factor in complex with ssrna substrate and anppnp. SNAP output |
| 1q2r |
transferase-RNA |
X-ray (2.9 Å) |
Xie W, Liu X, Huang RH |
(2003) "Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate." Nat.Struct.Biol., 10, 781-788. doi: 10.1038/nsb976. |
Chemical trapping and crystal structure of a catalytic trna guanine transglycosylase covalent intermediate. SNAP output |
| 1q2s |
transferase-RNA |
X-ray (3.2 Å) |
Xie W, Liu X, Huang RH |
(2003) "Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate." Nat.Struct.Biol., 10, 781-788. doi: 10.1038/nsb976. |
Chemical trapping and crystal structure of a catalytic trna guanine transglycosylase covalent intermediate. SNAP output |
| 1q7y |
ribosome |
X-ray (3.2 Å) |
Hansen JL, Schmeing TM, Moore PB, Steitz TA |
(2002) "Structural Insights Into Peptide Bond Formation." Proc.Natl.Acad.Sci.USA, 99, 11670-11675. doi: 10.1073/pnas.172404099. |
Crystal structure of ccdap-puromycin bound at the peptidyl transferase center of the 50s ribosomal subunit. SNAP output |
| 1q81 |
ribosome |
X-ray (2.95 Å) |
Hansen JL, Schmeing TM, Moore PB, Steitz TA |
(2002) "Structural Insights into Peptide Bond Formation." Proc.Natl.Acad.Sci.USA, 99, 11670-11675. doi: 10.1073/pnas.172404099. |
Crystal structure of minihelix with 3' puromycin bound to a-site of the 50s ribosomal subunit.. SNAP output |
| 1q82 |
ribosome |
X-ray (2.98 Å) |
Hansen JL, Schmeing TM, Moore PB, Steitz TA |
(2002) "Structural Insights Into Peptide Bond Formation." Proc.Natl.Acad.Sci.USA, 99, 11670-11675. doi: 10.1073/pnas.172404099. |
Crystal structure of cc-puromycin bound to the a-site of the 50s ribosomal subunit. SNAP output |
| 1q86 |
ribosome |
X-ray (3.0 Å) |
Hansen JL, Schmeing TM, Moore PB, Steitz TA |
(2002) "Structural insights into peptide bond formation." Proc.Natl.Acad.Sci.USA, 99, 11670-11675. doi: 10.1073/pnas.172404099. |
Crystal structure of cca-phe-cap-biotin bound simultaneously at half occupancy to both the a-site and p-site of the the 50s ribosomal subunit.. SNAP output |
| 1qa6 |
ribosome |
X-ray (2.8 Å) |
Conn GL, Draper DE, Lattman EE, Gittis AG |
(1999) "Crystal structure of a conserved ribosomal protein-RNA complex." Science, 284, 1171-1174. doi: 10.1126/science.284.5417.1171. |
Crystal structure of a conserved ribosomal protein-RNA complex. SNAP output |
| 1qf6 |
ligase-RNA |
X-ray (2.9 Å) |
Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D |
(1999) "The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site." Cell(Cambridge,Mass.), 97, 371-381. doi: 10.1016/S0092-8674(00)80746-1. |
Structure of e. coli threonyl-trna synthetase complexed with its cognate trna. SNAP output |
| 1qfq |
transcription-RNA |
NMR |
Schaerpf M, Sticht H, Schweimer K, Boehm M, Hoffmann S, Roesch P |
(2000) "Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex." Eur.J.Biochem., 267, 2397-2408. doi: 10.1046/j.1432-1327.2000.01251.x. |
Bacteriophage lambda n-protein-nutboxb-RNA complex. SNAP output |
| 1qrs |
ligase-RNA |
X-ray (2.6 Å) |
Arnez JG, Steitz TA |
(1996) "Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP." Biochemistry, 35, 14725-14733. doi: 10.1021/bi961532o. |
Glutaminyl-trna synthetase mutant d235n complexed with glutamine transfer RNA. SNAP output |
| 1qrt |
ligase-RNA |
X-ray (2.7 Å) |
Arnez JG, Steitz TA |
(1996) "Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP." Biochemistry, 35, 14725-14733. doi: 10.1021/bi961532o. |
Glutaminyl-trna synthetase mutant d235g complexed with glutamine transfer RNA. SNAP output |
| 1qru |
ligase-RNA |
X-ray (3.0 Å) |
Arnez JG, Steitz TA |
(1996) "Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP." Biochemistry, 35, 14725-14733. doi: 10.1021/bi961532o. |
Glutaminyl-trna synthetase mutant i129t complexed with glutamine transfer RNA. SNAP output |
| 1qtq |
ligase-RNA |
X-ray (2.25 Å) |
Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA |
(1998) "How glutaminyl-tRNA synthetase selects glutamine." Structure, 6, 439-449. doi: 10.1016/S0969-2126(98)00046-X. |
Glutaminyl-trna synthetase complexed with trna and an amino acid analog. SNAP output |
| 1qu2 |
ligase-RNA |
X-ray (2.2 Å) |
Silvian LF, Wang J, Steitz TA |
(1999) "Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin." Science, 285, 1074-1077. doi: 10.1126/science.285.5430.1074. |
Insights into editing from an ile-trna synthetase structure with trna(ile) and mupirocin. SNAP output |
| 1qu3 |
ligase-RNA |
X-ray (2.9 Å) |
Silvian LF, Wang J, Steitz TA |
(1999) "Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin." Science, 285, 1074-1077. doi: 10.1126/science.285.5430.1074. |
Insights into editing from an ile-trna synthetase structure with trna(ile) and mupirocin. SNAP output |
| 1qvf |
ribosome |
X-ray (3.1 Å) |
Schmeing TM, Moore PB, Steitz TA |
(2003) "Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit." RNA, 9, 1345-1352. doi: 10.1261/rna.5120503. |
Structure of a deacylated trna minihelix bound to the e site of the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1qvg |
ribosome |
X-ray (2.9 Å) |
Schmeing TM, Moore PB, Steitz TA |
(2003) "Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit." RNA, 9, 1345-1352. doi: 10.1261/rna.5120503. |
Structure of cca oligonucleotide bound to the trna binding sites of the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1qzw |
signaling protein-RNA |
X-ray (4.1 Å) |
Rosendal KR, Wild K, Montoya G, Sinning I |
(2003) "Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication." Proc.Natl.Acad.Sci.USA, 100, 14701-14706. doi: 10.1073/pnas.2436132100. |
Crystal structure of the complete core of archaeal srp and implications for inter-domain communication. SNAP output |
| 1r3e |
lyase-RNA |
X-ray (2.1 Å) |
Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM |
(2003) "Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit." Proc.Natl.Acad.Sci.USA, 100, 12648-12653. doi: 10.1073/pnas.2135585100. |
Crystal structure of trna pseudouridine synthase trub and its RNA complex: RNA-protein recognition through a combination of rigid docking and induced fit. SNAP output |
| 1r9f |
viral protein-RNA |
X-ray (1.85 Å) |
Ye K, Malinina L, Patel DJ |
(2003) "Recognition of small interfering RNA by a viral suppressor of RNA." Nature, 426, 874-878. doi: 10.1038/nature02213. |
Crystal structure of p19 complexed with 19-bp small interfering RNA. SNAP output |
| 1rc7 |
hydrolase-RNA |
X-ray (2.15 Å) |
Blaszczyk J, Gan J, Tropea JE, Court DL, Waugh DS, Ji X |
(2004) "Noncatalytic Assembly of Ribonuclease III with Double-Stranded RNA." Structure, 12, 457-466. doi: 10.1016/j.str.2004.02.004. |
Crystal structure of rnase iii mutant e110k from aquifex aeolicus complexed with ds-RNA at 2.15 angstrom resolution. SNAP output |
| 1rgo |
RNA binding protein |
NMR |
Hudson BP, Martinez-Yamout MA, Dyson HJ, Wright PE |
(2004) "Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d." NAT.STRUCT.MOL.BIOL., 11, 257-264. doi: 10.1038/nsmb738. |
Structural basis for recognition of the mrna class ii au-rich element by the tandem zinc finger domain of tis11d. SNAP output |
| 1rkj |
transcription-RNA |
NMR |
Johansson C, Finger LD, Trantirek L, Mueller TD, Kim S, Laird-Offringa IA, Feigon J |
(2004) "Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target." J.Mol.Biol., 337, 799-816. doi: 10.1016/j.jmb.2004.01.056. |
Solution structure of the complex formed by the two n-terminal RNA-binding domains of nucleolin and a pre-rrna target. SNAP output |
| 1rlg |
structural protein-RNA |
X-ray (2.7 Å) |
Moore T, Zhang Y, Fenley MO, Li H |
(2004) "Molecular Basis of Box C/D RNA-Protein Interactions; Cocrystal Structure of Archaeal L7Ae and a Box C/D RNA." STRUCTURE, 12, 807-818. doi: 10.1016/j.str.2004.02.033. |
Molecular basis of box c-d RNA-protein interaction: co-crystal structure of the archaeal srnp intiation complex. SNAP output |
| 1rmv |
virus-RNA |
fiber diffraction |
Wang H, Stubbs G |
(1993) "Molecular dynamics in refinement against fiber diffraction data." Acta Crystallogr.,Sect.A, 49, 504-513. doi: 10.1107/S0108767392011255. |
Ribgrass mosaic virus, fiber diffraction. SNAP output |
| 1rpu |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Vargason JM, Szittya G, Burgyan J, Hall TMT |
(2003) "Size selective recognition of siRNA by an RNA silencing suppressor." Cell(Cambridge,Mass.), 115, 799-811. doi: 10.1016/S0092-8674(03)00984-X. |
Crystal structure of cirv p19 bound to sirna. SNAP output |
| 1ry1 |
translation |
cryo-EM (12.0 Å) |
Halic M, Becker T, Pool MR, Spahn CM, Grassucci RA, Frank J, Beckmann R |
(2004) "Structure of the signal recognition particle interacting with the elongation-arrested ribosome." Nature, 427, 808-814. doi: 10.1038/nature02342. |
Structure of the signal recognition particle interacting with the elongation-arrested ribosome. SNAP output |
| 1s03 |
transcription-RNA |
X-ray (2.7 Å) |
Merianos HJ, Wang J, Moore PB |
(2004) "The structure of a ribosomal protein S8/spc operon mRNA complex." RNA, 10, 954-964. doi: 10.1261/rna.7030704. |
The structure of a ribosomal protein s8-spc operon mrna complex. SNAP output |
| 1s72 |
ribosome |
X-ray (2.4 Å) |
Klein DJ, Moore PB, Steitz TA |
(2004) "The Roles of Ribosomal Proteins in the Structure, Assembly and Evolution of the Large Ribosomal Subunit." J.Mol.Biol., 340, 141-177. doi: 10.1016/j.jmb.2004.03.076. |
Refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution. SNAP output |
| 1sds |
protein-RNA complex |
X-ray (1.8 Å) |
Hamma T, Ferre-D'Amare A |
(2004) "Structure of Protein L7Ae Bound to a K-Turn Derived from an Archaeal Box H/ACA sRNA at 1.8 A Resolution." STRUCTURE, 12, 893-903. doi: 10.1016/j.str.2004.03.015. |
Structure of protein l7ae bound to a k-turn derived from an archaeal box h-aca srna. SNAP output |
| 1ser |
ligase-RNA |
X-ray (2.9 Å) |
Biou V, Yaremchuk A, Tukalo M, Cusack S |
(1994) "The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)." Science, 263, 1404-1410. |
The 2.9 angstroms crystal structure of t. thermophilus seryl-trna synthetase complexed with trna ser. SNAP output |
| 1si3 |
gene regulation-RNA |
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. SNAP output |
| 1sj3 |
translation-RNA |
X-ray (2.2 Å) |
Ke A, Zhou K, Ding F, Cate JH, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme
catalysis." Nature, 429, 201-205. doi: 10.1038/nature02522. |
Hepatitis delta virus gemonic ribozyme precursor, with mg2+ bound. SNAP output |
| 1sj4 |
translation-RNA |
X-ray (2.7 Å) |
Ke A, Zhou K, Ding F, Cate JH, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme
catalysis." Nature, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of a c75u mutant hepatitis delta virus ribozyme precursor, in cu2+ solution. SNAP output |
| 1sjf |
translation-RNA |
X-ray (2.75 Å) |
Ke A, Zhou K, Ding F, Cate JH, Doudna JA |
(2004) "A conformational switch controls hepatitis delta virus ribozyme catalysis." Nature, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with c75u mutaion, in cobalt hexammine solution. SNAP output |
| 1sm1 |
ribosome-antibiotic |
X-ray (3.42 Å) |
Harms JM, Schlunzen F, Fucini P, Bartels H, Yonath A |
(2004) "Alterations at the Peptidyl Transferase Centre of the Ribosome Induced by the Synergistic Action of the Streptogramins Dalfopristin and Quinupristin." Bmc Biol., 2, 4. doi: 10.1186/1741-7007-2-4. |
Complex of the large ribosomal subunit from deinococcus radiodurans with quinupristin and dalfopristin. SNAP output |
| 1sz1 |
transferase-RNA |
X-ray (6.21 Å) |
Xiong Y, Steitz TA |
(2004) "Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template." Nature, 430, 640-645. doi: 10.1038/nature02711. |
Mechanism of cca-adding enzymes specificity revealed by crystal structures of ternary complexes. SNAP output |
| 1t0k |
ribosome |
X-ray (3.24 Å) |
Chao JA, Williamson JR |
(2004) "Joint X-Ray and NMR Refinement of the Yeast L30e-mRNA Complex." Structure, 12, 1165-1176. doi: 10.1016/j.str.2004.04.023. |
Joint x-ray and NMR refinement of yeast l30e-mrna complex. SNAP output |
| 1t2r |
nucleic acid binding protein-RNA |
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 |
| 1t4l |
RNA binding protein-RNA |
NMR |
Wu H, Henras A, Chanfreau G, Feigon J |
(2004) "Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III." Proc.Natl.Acad.Sci.USA, 101, 8307-8312. doi: 10.1073/pnas.0402627101. |
Solution structure of double-stranded RNA binding domain of s. cerevisiae rnase iii (rnt1p) in complex with the 5' terminal RNA hairpin of snr47 precursor. SNAP output |
| 1tfw |
transferase-RNA |
X-ray (2.2 Å) |
Xiong Y, Steitz TA |
(2004) "Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template." Nature, 430, 640-645. doi: 10.1038/nature02711. |
How cca is added to the 3' end of immature trna without the use of an oligonucleotide template. SNAP output |
| 1tfy |
transferase-RNA |
X-ray (3.2 Å) |
Xiong Y, Steitz TA |
(2004) "Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template." Nature, 430, 640-645. doi: 10.1038/nature02711. |
How cca is added to the 3' end of immature trna without the use of an oligonucleotide template. SNAP output |
| 1ttt |
complex (elongation factor-trna) |
X-ray (2.7 Å) |
Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J |
(1995) "Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog." Science, 270, 1464-1472. |
Phe-trna, elongation factor ef-tu:gdpnp ternary complex. SNAP output |
| 1u0b |
ligase-RNA |
X-ray (2.3 Å) |
Hauenstein S, Zhang CM, Hou YM, Perona JJ |
(2004) "Shape-selective RNA recognition by cysteinyl-tRNA synthetase." Nat.Struct.Mol.Biol., 11, 1134-1141. doi: 10.1038/nsmb849. |
Crystal structure of cysteinyl-trna synthetase binary complex with trnacys. SNAP output |
| 1u63 |
transcription-RNA |
X-ray (3.4 Å) |
Nevskaya N, Tishchenko S, Gabdoulkhakov A, Nikonova E, Nikonov O, Nikulin A, Platonova O, Garber M, Nikonov S, Piendl W |
(2005) "Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA." Nucleic Acids Res., 33, 478-485. doi: 10.1093/nar/gki194. |
The structure of a ribosomal protein l1-mrna complex. SNAP output |
| 1u6b |
structural protein-RNA |
X-ray (3.1 Å) |
Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA |
(2004) "Crystal Structure of a Self-Splicing Group I Intron with Both Exons." Nature, 430, 45-50. doi: 10.1038/nature02642. |
Crystal structure of a self-splicing group i intron with both exons. SNAP output |
| 1u6p |
viral protein-RNA |
NMR |
D'Souza V, Summers MF |
(2004) "Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus." Nature, 431, 586-590. doi: 10.1038/nature02944. |
NMR structure of the mlv encapsidation signal bound to the nucleocapsid protein. SNAP output |
| 1ull |
viral protein-RNA |
NMR |
Ye X, Gorin A, Ellington AD, Patel DJ |
(1996) "Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex." Nat.Struct.Biol., 3, 1026-1033. doi: 10.1038/nsb1296-1026. |
RNA aptamer complexed with hiv-1 rev peptide, NMR, 7 structures. SNAP output |
| 1un6 |
RNA-binding protein-RNA |
X-ray (3.1 Å) |
Lu D, Searles MA, Klug A |
(2003) "Crystal Structure of a Zinc-Finger-RNA Complex Reveals Two Modes of Molecular Recognition." Nature, 426, 96. doi: 10.1038/NATURE02088. |
The crystal structure of a zinc finger - RNA complex reveals two modes of molecular recognition. SNAP output |
| 1uon |
polymerase |
cryo-EM (7.6 Å) |
Zhang X, Walker SB, Chipman PR, Nibert ML, Baker TS |
(2003) "Reovirus Polymerase Lambda3 Localized by Cryo-Electron Microscopy of Virions at a Resolution of 7.6 A." Nat.Struct.Biol., 10, 1011. doi: 10.1038/NSB1009. |
Reovirus polymerase lambda-3 localized by electron cryomicroscopy of virions at 7.6-a resolution. 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 |
| 1utd |
RNA binding protein |
X-ray (2.1 Å) |
Hopcroft NH, Manfredo A, Wendt AL, Brzozowski AM, Gollnick P, Antson AA |
(2004) "The Interaction of RNA with Trap: The Role of Triplet Repeats and Separating Spacer Nucleotides." J.Mol.Biol., 338, 43. doi: 10.1016/J.JMB.2004.02.038. |
The structure of the trp RNA-binding attenuation protein (trap) bound to a 63-nucleotide RNA molecule containing gaguuu repeats. SNAP output |
| 1uvi |
polymerase |
X-ray (2.15 Å) |
Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI, Grimes JM |
(2004) "The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase." Structure, 12, 307-316. doi: 10.1016/j.str.2004.01.012. |
The structural basis for RNA specificity and ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 6nt RNA. SNAP output |
| 1uvj |
polymerase |
X-ray (1.9 Å) |
Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI, Grimes JM |
(2004) "The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase." Structure, 12, 307-316. doi: 10.1016/j.str.2004.01.012. |
The structural basis for RNA specificity and ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 7nt RNA. SNAP output |
| 1uvl |
transferase |
X-ray (2.0 Å) |
Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI, Grimes JM |
(2004) "The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase." Structure, 12, 307-316. doi: 10.1016/j.str.2004.01.012. |
The structural basis for RNA specificity and ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5nt RNA. conformation b. SNAP output |
| 1uvm |
transferase |
X-ray (2.0 Å) |
Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI, Grimes JM |
(2004) "The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase." Structure, 12, 307-316. doi: 10.1016/j.str.2004.01.012. |
The structural basis for RNA specificity and ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 with 5nt RNA conformation a. SNAP output |
| 1uvn |
polymerase |
X-ray (3.0 Å) |
Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI, Grimes JM |
(2004) "The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase." Structure, 12, 307-316. doi: 10.1016/j.str.2004.01.012. |
The structural basis for RNA specificity and ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 ca2+ inhibition complex. SNAP output |
| 1vbx |
translation-RNA |
X-ray (2.7 Å) |
Ke A, Zhou K, Ding F, Cate JHD, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme catalysis." NATURE, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with c75u mutaion, in edta solution. SNAP output |
| 1vby |
translation-RNA |
X-ray (2.9 Å) |
Ke A, Zhou K, Ding F, Cate JHD, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme catalysis." NATURE, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with c75u mutaion, and mn2+ bound. SNAP output |
| 1vbz |
translation-RNA |
X-ray (2.8 Å) |
Ke A, Zhou K, Ding F, Cate JHD, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme catalysis." NATURE, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with c75u mutaion, in ba2+ solution. SNAP output |
| 1vc0 |
translation-RNA |
X-ray (2.5 Å) |
Ke A, Zhou K, Ding F, Cate JHD, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme catalysis." NATURE, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with c75u mutaion, in imidazole and sr2+ solution. SNAP output |
| 1vc5 |
translation-RNA |
X-ray (3.4 Å) |
Ke A, Zhou K, Ding F, Cate JHD, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme catalysis." NATURE, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the wild type hepatitis delta virus gemonic ribozyme precursor, in edta solution. SNAP output |
| 1vc6 |
translation-RNA |
X-ray (2.8 Å) |
Ke A, Zhou K, Ding F, Cate JHD, Doudna JA |
(2004) "A Conformational Switch controls hepatitis delta virus ribozyme catalysis." NATURE, 429, 201-205. doi: 10.1038/nature02522. |
Crystal structure of the hepatitis delta virus gemonic ribozyme product with c75u mutaion, cleaved in imidazole and mg2+ solutions. SNAP output |
| 1vfg |
transferase-RNA |
X-ray (2.8 Å) |
Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev DG, Nureki O |
(2004) "Structural basis for template-independent RNA polymerization." Nature, 430, 700-704. doi: 10.1038/nature02712. |
Crystal structure of trna nucleotidyltransferase complexed with a primer trna and an incoming atp analog. SNAP output |
| 1vq4 |
ribosome |
X-ray (2.7 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 "daa" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vq6 |
ribosome |
X-ray (2.7 Å) |
Schmeing TM, Huang KS, Strobel SA, Steitz TA |
(2005) "An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA." Nature, 438, 520-524. doi: 10.1038/nature04152. |
The structure of c-hpmn and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vq7 |
ribosome |
X-ray (2.5 Å) |
Schmeing TM, Huang KS, Strobel SA, Steitz TA |
(2005) "An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA." Nature, 438, 520-524. doi: 10.1038/nature04152. |
The structure of the transition state analogue "dca" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vq8 |
ribosome |
X-ray (2.2 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 ccda-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vq9 |
ribosome |
X-ray (2.4 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 cca-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vqk |
ribosome |
X-ray (2.3 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 ccda-phe-cap-bio bound to the a site of the ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vql |
ribosome |
X-ray (2.3 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 "dcsn" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vqm |
ribosome |
X-ray (2.3 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 "dan" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vqn |
ribosome |
X-ray (2.4 Å) |
Schmeing TM, Huang KS, Strobel SA, Steitz TA |
(2005) "An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA." Nature, 438, 520-524. doi: 10.1038/nature04152. |
The structure of cc-hpmn and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 1vqo |
ribosome |
X-ray (2.2 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 ccpmn bound to the large ribosomal subunit haloarcula marismortui. SNAP output |
| 1vtm |
virus-RNA |
fiber diffraction |
Pattanayek R, Stubbs G |
(1992) "Structure of the U2 strain of tobacco mosaic virus refined at 3.5 A resolution using X-ray fiber diffraction." J.Mol.Biol., 228, 516-528. doi: 10.1016/0022-2836(92)90839-C. |
Structure of the u2 strain of tobacco mosaic virus refined at 3.5 angstroms resolution using x-ray fiber diffraction. SNAP output |
| 1w2b |
ribosome |
X-ray (3.5 Å) |
Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N |
(2004) "Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins." Nature, 431, 590. doi: 10.1038/NATURE02899. |
Trigger factor ribosome binding domain in complex with 50s. SNAP output |
| 1wmq |
transcription-RNA |
X-ray (1.6 Å) |
Kumarevel T, Mizuno H, Kumar PK |
(2005) "Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand." Nature, 434, 183-191. doi: 10.1038/nature03355. |
Structure of the hutp antitermination complex bound to a single stranded region of hut mrna. SNAP output |
| 1wne |
transferase-RNA |
X-ray (3.0 Å) |
Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2004) "Structure of Foot-and-Mouth Disease Virus RNA-dependent RNA Polymerase and Its Complex with a Template-Primer RNA." J.Biol.Chem., 279, 47212-47221. doi: 10.1074/jbc.M405465200. |
Foot and mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA. SNAP output |
| 1wpu |
transcription-RNA |
X-ray (1.48 Å) |
Kumarevel TS, Mizuno H, Kumar PKR |
"Structural basis for the HutP antitermination Complex:Role of divalent metal ions in allosteric activation." |
Crystal structure of the hutp antitermination complex bound to a single stranded region of hut mrna. SNAP output |
| 1wrq |
transcription-RNA |
X-ray (2.2 Å) |
Kumarevel T, Mizuno H, Kumar PKR |
"Crystal Structure of the HutP-antitermination complex." |
Crystal structure of hutp-antitermination complex. SNAP output |
| 1wsu |
translation-RNA |
X-ray (2.3 Å) |
Yoshizawa S, Rasubala L, Ose T, Kohda D, Fourmy D, Maenaka K |
(2005) "Structural basis for mRNA recognition by elongation factor SelB." Nat.Struct.Mol.Biol., 12, 198-203. doi: 10.1038/nsmb890. |
C-terminal domain of elongation factor selb complexed with secis RNA. SNAP output |
| 1wwd |
viral protein-RNA |
NMR |
Dey A, York D, Smalls-Mantey A, Summers MF |
(2005) "Composition and sequence-dependent binding of RNA to the nucleocapsid protein of Moloney murine leukemia virus(,)." Biochemistry, 44, 3735-3744. doi: 10.1021/bi047639q. |
NMR structure determined for mlv nc complex with RNA sequence aacagu. SNAP output |
| 1wwe |
viral protein-RNA |
NMR |
Dey A, York D, Smalls-Mantey A, Summers MF |
(2005) "Composition and sequence-dependent binding of RNA to the nucleocapsid protein of Moloney murine leukemia virus(,)." Biochemistry, 44, 3735-3744. doi: 10.1021/bi047639q. |
NMR structure determined for mlv nc complex with RNA sequence uuuugcu. SNAP output |
| 1wwf |
viral protein-RNA |
NMR |
Dey A, York D, Smalls-Mantey A, Summers MF |
(2005) "Composition and sequence-dependent binding of RNA to the nucleocapsid protein of Moloney murine leukemia virus(,)." Biochemistry, 44, 3735-3744. doi: 10.1021/bi047639q. |
NMR structure determined for mlv nc complex with RNA sequence ccuccgu. SNAP output |
| 1wwg |
viral protein-RNA |
NMR |
Dey A, York D, Smalls-Mantey A, Summers MF |
(2005) "Composition and sequence-dependent binding of RNA to the nucleocapsid protein of Moloney murine leukemia virus(,)." Biochemistry, 44, 3735-3744. doi: 10.1021/bi047639q. |
NMR structure determined for mlv nc complex with RNA sequence uaucug. SNAP output |
| 1wz2 |
ligase-RNA |
X-ray (3.21 Å) |
Fukunaga R, Yokoyama S |
"The crystal structure of Leucyl-tRNA synthetase and tRNA(leucine) complex." |
The crystal structure of leucyl-trna synthetase and trna(leucine) complex. SNAP output |
| 1xmo |
ribosome |
X-ray (3.25 Å) |
Murphy FV, Ramakrishnan V, Malkiewicz A, Agris PF |
(2004) "The role of modifications in codon discrimination by tRNA(Lys)(UUU)." Nat.Struct.Mol.Biol., 11, 1186-1191. doi: 10.1038/nsmb861. |
Crystal structure of mnm5u34t6a37-trnalysuuu complexed with aag-mrna in the decoding center. SNAP output |
| 1xmq |
ribosome |
X-ray (3.0 Å) |
Murphy FV, Ramakrishnan V, Malkiewicz A, Agris PF |
(2004) "The role of modifications in codon discrimination by tRNA(Lys)(UUU)." Nat.Struct.Mol.Biol., 11, 1186-1191. doi: 10.1038/nsmb861. |
Crystal structure of t6a37-asllysuuu aaa-mrna bound to the decoding center. SNAP output |
| 1xnq |
ribosome |
X-ray (3.05 Å) |
Murphy FV, Ramakrishnan V |
(2004) "Structure of a purine-purine wobble base pair in the decoding center of the ribosome." Nat.Struct.Mol.Biol., 11, 1251-1252. doi: 10.1038/nsmb866. |
Structure of an inosine-adenine wobble base pair complex in the context of the decoding center. SNAP output |
| 1xnr |
ribosome |
X-ray (3.1 Å) |
Murphy FV, Ramakrishnan V |
(2004) "Structure of a purine-purine wobble base pair in the decoding center of the ribosome." Nat.Struct.Mol.Biol., 11, 1251-1252. doi: 10.1038/nsmb866. |
Crystal structure of an inosine-cytosine wobble base pair in the context of the decoding center. SNAP output |
| 1xok |
viral protein-RNA |
X-ray (3.0 Å) |
Guogas LM, Filman DJ, Hogle JM, Gehrke L |
(2004) "Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication." Science, 306, 2108-2111. doi: 10.1126/science.1103399. |
Crystal structure of alfalfa mosaic virus RNA 3'utr in complex with coat protein n terminal peptide. SNAP output |
| 1xpo |
transcription-RNA |
X-ray (3.15 Å) |
Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM |
(2005) "Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic bicyclomycin." Structure, 13, 99-109. doi: 10.1016/j.str.2004.10.013. |
Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic bicyclomycin. SNAP output |
| 1xpr |
transcription-RNA |
X-ray (3.15 Å) |
Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM |
(2005) "Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic bicyclomycin." Structure, 13, 99-109. doi: 10.1016/j.str.2004.10.013. |
Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (fb). SNAP output |
| 1xpu |
transcription-RNA |
X-ray (3.05 Å) |
Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM |
(2005) "Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic bicyclomycin." Structure, 13, 99-109. doi: 10.1016/j.str.2004.10.013. |
Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (fpdb). SNAP output |
| 1y39 |
structural protein-RNA |
X-ray (2.8 Å) |
Dunstan MS, Guhathakurta D, Draper DE, Conn GL |
(2005) "Coevolution of Protein and RNA Structures within a Highly Conserved Ribosomal Domain." Chem.Biol., 12, 201-206. doi: 10.1016/j.chembiol.2004.11.019. |
Co-evolution of protein and RNA structures within a highly conserved ribosomal domain. SNAP output |
| 1y69 |
ribosome |
X-ray (3.33 Å) |
Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P |
(2005) "X-ray crystallography on ribosome recycling: mechanism of binding and action of RRF on the 50S ribosomal subunit." EMBO J., 24, 251-260. doi: 10.1038/sj.emboj.7600525. |
Rrf domain i in complex with the 50s ribosomal subunit from deinococcus radiodurans. SNAP output |
| 1yhq |
ribosome |
X-ray (2.4 Å) |
Tu D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance." Cell(Cambridge,Mass.), 121, 257-270. doi: 10.1016/j.cell.2005.02.005. |
Crystal structure of azithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1yi2 |
ribosome |
X-ray (2.65 Å) |
Tu D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance." Cell(Cambridge,Mass.), 121, 257-270. doi: 10.1016/j.cell.2005.02.005. |
Crystal structure of erythromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1yij |
ribosome |
X-ray (2.6 Å) |
Tu D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance." Cell(Cambridge,Mass.), 121, 257-270. doi: 10.1016/j.cell.2005.02.005. |
Crystal structure of telithromycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1yit |
ribosome-antibiotic |
X-ray (2.8 Å) |
TU D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance." Cell(Cambridge,Mass.), 121, 257. doi: 10.1016/J.CELL.2005.02.005. |
Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1yj9 |
ribosome |
X-ray (2.8 Å) |
Tu D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance." Cell(Cambridge,Mass.), 121, 257-270. doi: 10.1016/j.cell.2005.02.005. |
Crystal structure of the mutant 50s ribosomal subunit of haloarcula marismortui containing a three residue deletion in l22. SNAP output |
| 1yjn |
ribosome |
X-ray (3.0 Å) |
Tu D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance." Cell(Cambridge,Mass.), 121, 257-270. doi: 10.1016/j.cell.2005.02.005. |
Crystal structure of clindamycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1yjw |
ribosome-antibiotic |
X-ray (2.9 Å) |
Tu D, Blaha G, Moore PB, Steitz TA |
(2005) "Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance." Cell(Cambridge,Mass.), 121, 257. doi: 10.1016/J.CELL.2005.02.005. |
Crystal structure of quinupristin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui. SNAP output |
| 1ysh |
structural protein-RNA |
cryo-EM (9.5 Å) |
Halic M, Becker T, Frank J, Spahn CM, Beckmann R |
(2005) "Localization and dynamic behavior of ribosomal protein L30e." Nat.Struct.Mol.Biol., 12, 467-468. doi: 10.1038/nsmb933. |
Localization and dynamic behavior of ribosomal protein l30e. SNAP output |
| 1ytu |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Ma JB, Yuan YR, Meister G, Pei Y, Tuschl T, Patel DJ |
(2005) "Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein." Nature, 434, 666-670. doi: 10.1038/nature03514. |
Structural basis for 5'-end-specific recognition of the guide RNA strand by the a. fulgidus piwi protein. SNAP output |
| 1yty |
transcription-RNA |
X-ray (2.29 Å) |
Teplova M, Yuan YR, Phan AT, Malinina L, Ilin S, Teplov A, Patel DJ |
(2006) "Structural Basis for Recognition and Sequestration of UUU(OH) 3' Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen." Mol.Cell, 21, 75-85. doi: 10.1016/j.molcel.2005.10.027. |
Structural basis for recognition of uuuoh 3'-terminii of nascent RNA pol iii transcripts by la autoantigen. SNAP output |
| 1yvp |
RNA binding protein-RNA |
X-ray (2.2 Å) |
Stein AJ, Fuchs G, Fu C, Wolin SL, Reinisch KM |
(2005) "Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity." Cell(Cambridge,Mass.), 121, 529-539. doi: 10.1016/j.cell.2005.03.009. |
Ro autoantigen complexed with rnas. SNAP output |
| 1yyk |
hydrolase-RNA |
X-ray (2.5 Å) |
Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2005) "Intermediate states of ribonuclease III in complex with double-stranded RNA." Structure, 13, 1435-1442. doi: 10.1016/j.str.2005.06.014. |
Crystal structure of rnase iii from aquifex aeolicus complexed with double-stranded RNA at 2.5-angstrom resolution. SNAP output |
| 1yyo |
hydrolase-RNA |
X-ray (2.9 Å) |
Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2005) "Intermediate states of ribonuclease III in complex with double-stranded RNA." Structure, 13, 1435-1442. doi: 10.1016/j.str.2005.06.014. |
Crystal structure of rnase iii mutant e110k from aquifex aeolicus complexed with double-stranded RNA at 2.9-angstrom resolution. SNAP output |
| 1yyw |
hydrolase-RNA |
X-ray (2.8 Å) |
Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2005) "Intermediate states of ribonuclease III in complex with double-stranded RNA." Structure, 13, 1435-1442. doi: 10.1016/j.str.2005.06.014. |
Crystal structure of rnase iii from aquifex aeolicus complexed with double stranded RNA at 2.8-angstrom resolution. SNAP output |
| 1yz9 |
hydrolase-RNA |
X-ray (2.1 Å) |
Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2005) "Intermediate states of ribonuclease III in complex with double-stranded RNA." Structure, 13, 1435-1442. doi: 10.1016/j.str.2005.06.014. |
Crystal structure of rnase iii mutant e110q from aquifex aeolicus complexed with double stranded RNA at 2.1-angstrom resolution. SNAP output |
| 1zbh |
hydrolase-RNA |
X-ray (3.0 Å) |
Cheng Y, Patel DJ |
"Structural basis for 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease, a human nuclease that also targets siRNA." |
3'-end specific recognition of histone mrna stem-loop by 3'-exonuclease. SNAP output |
| 1zbn |
RNA binding protein-RNA |
NMR |
Calabro V, Daugherty MD, Frankel AD |
(2005) "A single intermolecular contact mediates intramolecular stabilization of both RNA and protein." Proc.Natl.Acad.Sci.Usa, 102, 6849-6854. doi: 10.1073/pnas.0409282102. |
Solution structure of biv tar hairpin complexed to jdv tat arginine-rich motif. SNAP output |
| 1zdh |
virus-RNA |
X-ray (2.7 Å) |
Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L |
(1997) "The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions." J.Mol.Biol., 270, 724-738. doi: 10.1006/jmbi.1997.1144. |
Ms2 coat protein-RNA complex. SNAP output |
| 1zdi |
virus-RNA |
X-ray (2.7 Å) |
Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L |
(1997) "The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions." J.Mol.Biol., 270, 724-738. doi: 10.1006/jmbi.1997.1144. |
RNA bacteriophage ms2 coat protein-RNA complex. SNAP output |
| 1zdj |
virus-RNA |
X-ray (2.9 Å) |
Grahn E, Stonehouse NJ, Murray JB, van den Worm S, Valegard K, Fridborg K, Stockley PG, Liljas L |
(1999) "Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements." RNA, 5, 131-138. doi: 10.1017/S1355838299981645. |
Structure of bacteriophage coat protein-loop RNA complex. SNAP output |
| 1zdk |
virus-RNA |
X-ray (2.86 Å) |
Grahn E, Stonehouse NJ, Murray JB, van den Worm S, Valegard K, Fridborg K, Stockley PG, Liljas L |
(1999) "Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements." RNA, 5, 131-138. doi: 10.1017/S1355838299981645. |
Structure of bacteriophage coat protein-loop RNA complex. SNAP output |
| 1ze2 |
lyase-RNA |
X-ray (3.0 Å) |
Phannachet K, Huang RH |
(2004) "Conformational change of pseudouridine 55
synthase upon its association with RNA substrate." Nucleic Acids Res., 32, 1422-1429. doi: 10.1093/nar/gkh287. |
Conformational change of pseudouridine 55 synthase upon its association with RNA substrate. SNAP output |
| 1zh5 |
transcription-RNA |
X-ray (1.85 Å) |
Teplova M, Yuan YR, Phan AT, Malinina L, Ilin S, Teplov A, Patel DJ |
(2006) "Structural Basis for Recognition and Sequestration of UUU(OH) 3' Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen." Mol.Cell, 21, 75-85. doi: 10.1016/j.molcel.2005.10.027. |
Structural basis for recognition of uuuoh 3'-terminii of nascent RNA pol iii transcripts by la autoantigen. SNAP output |
| 1zho |
structural protein-RNA |
X-ray (2.6 Å) |
Nevskaya N, Tishchenko S, Volchkov S, Kljashtorny V, Nikonova E, Nikonov O, Nikulin A, Kohrer C, Piendl W, Zimmermann R, Stockley P, Garber M, Nikonov S |
(2006) "New insights into the interaction of ribosomal protein L1 with RNA." J.Mol.Biol., 355, 747-759. doi: 10.1016/j.jmb.2005.10.084. |
The structure of a ribosomal protein l1 in complex with mrna. SNAP output |
| 1zjw |
ligase-RNA |
X-ray (2.5 Å) |
Gruic-Sovulj I, Uter N, Bullock T, Perona JJ |
(2005) "tRNA-dependent Aminoacyl-adenylate Hydrolysis by a Nonediting Class I Aminoacyl-tRNA Synthetase." J.Biol.Chem., 280, 23978-23986. doi: 10.1074/jbc.M414260200. |
Glutaminyl-trna synthetase complexed to glutamine and 2'deoxy a76 glutamine trna. SNAP output |
| 1zl3 |
lyase-RNA |
X-ray (2.8 Å) |
Hoang C, Hamilton CS, Mueller EG, Ferre-D'Amare AR |
(2005) "Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain." Protein Sci., 14, 2201-2206. doi: 10.1110/ps.051493605. |
Coupling of active site motions and RNA binding. SNAP output |
| 1zo1 |
translation-RNA |
cryo-EM (13.8 Å) |
Allen GS, Zavialov A, Gursky R, Ehrenberg M, Frank J |
(2005) "The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli." Cell(Cambridge,Mass.), 121, 703-712. doi: 10.1016/j.cell.2005.03.023. |
If2, if1, and trna fitted to cryo-EM data of e. coli 70s initiation complex. SNAP output |
| 1zse |
RNA-virus-viral protein |
X-ray (3.0 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2." Structure, 14, 487-495. doi: 10.1016/j.str.2005.12.006. |
RNA stemloop from bacteriophage qbeta complexed with an n87s mutant ms2 capsid. SNAP output |
| 1zzn |
structural protein-RNA |
X-ray (3.37 Å) |
Stahley MR, Strobel SA |
(2005) "Structural evidence for a two-metal-ion mechanism of group I intron splicing." Science, 309, 1587-1590. doi: 10.1126/science.1114994. |
Crystal structure of a group i intron-two exon complex that includes all catalytic metal ion ligands.. SNAP output |
| 2a1r |
hydrolase-RNA |
X-ray (2.6 Å) |
Wu M, Reuter M, Lilie H, Liu Y, Wahle E, Song H |
(2005) "Structural insight into poly(A) binding and catalytic mechanism of human PARN." Embo J., 24, 4082-4093. doi: 10.1038/sj.emboj.7600869. |
Crystal structure of parn nuclease domain. SNAP output |
| 2a8v |
protein-RNA |
X-ray (2.4 Å) |
Bogden CE, Fass D, Bergman N, Nichols MD, Berger JM |
(1999) "The structural basis for terminator recognition by the Rho transcription termination factor." Mol.Cell, 3, 487-493. doi: 10.1016/S1097-2765(00)80476-1. |
Rho transcription termination factor-RNA complex. SNAP output |
| 2a9x |
RNA binding protein-RNA |
NMR |
Leeper TC, Athanassiou Z, Dias RL, Robinson JA, Varani G |
(2005) "TAR RNA recognition by a cyclic peptidomimetic of Tat protein." Biochemistry, 44, 12362-12372. doi: 10.1021/bi0510532. |
Tar RNA recognition by a cyclic peptidomimetic of tat protein. SNAP output |
| 2ab4 |
isomerase-RNA |
X-ray (2.4 Å) |
Phannachet K, Elias Y, Huang RH |
(2005) "Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase." Biochemistry, 44, 15488-15494. doi: 10.1021/bi050961w. |
Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase. SNAP output |
| 2ad9 |
RNA binding protein-RNA |
NMR |
Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FHT |
(2005) "Structure of PTB bound to RNA: specific binding and implications for splicing regulation." Science, 309, 2054-2057. doi: 10.1126/science.1114066. |
Solution structure of polypyrimidine tract binding protein rbd1 complexed with cucucu RNA. SNAP output |
| 2adb |
RNA binding protein-RNA |
NMR |
Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FHT |
(2005) "Structure of PTB bound to RNA: specific binding and implications for splicing regulation." Science, 309, 2054-2057. doi: 10.1126/science.1114066. |
Solution structure of polypyrimidine tract binding protein rbd2 complexed with cucucu RNA. SNAP output |
| 2adc |
RNA binding protein-RNA |
NMR |
Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FHT |
(2005) "Structure of PTB bound to RNA: specific binding and implications for splicing regulation." Science, 309, 2054-2057. doi: 10.1126/science.1114066. |
Solution structure of polypyrimidine tract binding protein rbd34 complexed with cucucu RNA. SNAP output |
| 2ake |
ligase-RNA |
X-ray (3.1 Å) |
Shen N, Guo L, Yang B, Jin Y, Ding J |
(2006) "Structure of human tryptophanyl-tRNA synthetase in complex with tRNA(Trp) reveals the molecular basis of tRNA recognition and specificity." Nucleic Acids Res., 34, 3246-3258. doi: 10.1093/nar/gkl441. |
Structure of human tryptophanyl-trna synthetase in complex with trna(trp). SNAP output |
| 2ann |
RNA-binding protein-RNA |
X-ray (2.3 Å) |
Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley SK, Darnell RB, Patel DJ |
(2011) "Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1." Structure, 19, 930-944. doi: 10.1016/j.str.2011.05.002. |
Crystal structure (i) of nova-1 kh1-kh2 domain tandem with 25 nt RNA hairpin. SNAP output |
| 2anr |
RNA-binding protein-RNA |
X-ray (1.94 Å) |
Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley SK, Darnell RB, Patel DJ |
(2011) "Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1." Structure, 19, 930-944. doi: 10.1016/j.str.2011.05.002. |
Crystal structure (ii) of nova-1 kh1-kh2 domain tandem with 25nt RNA hairpin. SNAP output |
| 2asb |
transcription-RNA |
X-ray (1.5 Å) |
Beuth B, Pennell S, Arnvig KB, Martin SR, Taylor IA |
(2005) "Structure of a Mycobacterium tuberculosis NusA-RNA complex." Embo J., 24, 3576-3587. doi: 10.1038/sj.emboj.7600829. |
Structure of a mycobacterium tuberculosis nusa-RNA complex. SNAP output |
| 2atw |
transcription-RNA |
X-ray (2.25 Å) |
Beuth B, Pennell S, Arnvig KB, Martin SR, Taylor IA |
(2005) "Structure of a Mycobacterium tuberculosis NusA-RNA complex." Embo J., 24, 3576-3587. doi: 10.1038/sj.emboj.7600829. |
Structure of a mycobacterium tuberculosis nusa-RNA complex. SNAP output |
| 2az0 |
viral protein-RNA |
X-ray (2.6 Å) |
Chao JA, Lee JH, Chapados BR, Debler EW, Schneemann A, Williamson JR |
(2005) "Dual modes of RNA-silencing suppression by Flock House virus protein B2." Nat.Struct.Mol.Biol., 12, 952-957. doi: 10.1038/nsmb1005. |
Flock house virus b2-dsrna complex (p212121). SNAP output |
| 2az2 |
viral protein-RNA |
X-ray (2.6 Å) |
Chao JA, Lee JH, Chapados BR, Debler EW, Schneemann A, Williamson JR |
(2005) "Dual modes of RNA-silencing suppression by Flock House virus protein B2." Nat.Struct.Mol.Biol., 12, 952-957. doi: 10.1038/nsmb1005. |
Flock house virus b2-dsrna complex (p4122). SNAP output |
| 2azx |
ligase-RNA |
X-ray (2.8 Å) |
Yang XL, Otero FJ, Ewalt KL, Liu J, Swairjo MA, Kohrer C, RajBhandary UL, Skene RJ, McRee DE, Schimmel P |
(2006) "Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis." Embo J., 25, 2919-2929. doi: 10.1038/sj.emboj.7601154. |
Charged and uncharged trnas adopt distinct conformations when complexed with human tryptophanyl-trna synthetase. SNAP output |
| 2b2d |
virus-viral protein-RNA |
X-ray (2.9 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2." Structure, 14, 487-495. doi: 10.1016/j.str.2005.12.006. |
RNA stemloop operator from bacteriophage qbeta complexed with an n87s,e89k mutant ms2 capsid. SNAP output |
| 2b2e |
virus-viral protein-RNA |
X-ray (3.15 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2." Structure, 14, 487-495. doi: 10.1016/j.str.2005.12.006. |
RNA stemloop from bacteriophage ms2 complexed with an n87s,e89k mutant ms2 capsid. SNAP output |
| 2b2g |
virus-viral protein-RNA |
X-ray (3.02 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2." Structure, 14, 487-495. doi: 10.1016/j.str.2005.12.006. |
Ms2 wild-type RNA stemloop complexed with an n87s mutant ms2 capsid. SNAP output |
| 2b3j |
hydrolase-RNA |
X-ray (2.0 Å) |
Losey HC, Ruthenburg AJ, Verdine GL |
(2006) "Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA." Nat.Struct.Mol.Biol., 13, 153-159. doi: 10.1038/nsmb1047. |
Crystal structure of staphylococcus aureus trna adenosine deaminase, tada, in complex with RNA. SNAP output |
| 2b63 |
transferase-RNA |
X-ray (3.8 Å) |
Kettenberger H, Eisenfuehr A, Brueckner F, Theis M, Famulok M, Cramer P |
(2006) "Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs." Nat.Struct.Mol.Biol., 13, 44-48. doi: 10.1038/nsmb1032. |
Complete RNA polymerase ii-RNA inhibitor complex. SNAP output |
| 2b6g |
RNA binding protein |
NMR |
Johnson PE, Donaldson LW |
(2006) "RNA recognition by the Vts1p SAM domain." Nat.Struct.Mol.Biol., 13, 177-178. doi: 10.1038/nsmb1039. |
RNA recognition by the vts1 sam domain. SNAP output |
| 2bbv |
virus-RNA |
X-ray (2.8 Å) |
Wery JP, Reddy VS, Hosur MV, Johnson JE |
(1994) "The refined three-dimensional structure of an insect virus at 2.8 A resolution." J.Mol.Biol., 235, 565-586. doi: 10.1006/jmbi.1994.1014. |
The refined three-dimensional structure of an insect virus at 2.8 angstroms resolution. SNAP output |
| 2bgg |
RNA-binding protein-RNA |
X-ray (2.2 Å) |
Parker JS, Roe SM, Barford D |
(2005) "Structural Insights Into Mrna Recognition from a Piwi Domain-Sirna Guide Complex." Nature, 434, 663. doi: 10.1038/NATURE03462. |
The structure of a piwi protein from archaeoglobus fulgidus complexed with a 16nt sirna duplex.. SNAP output |
| 2bh2 |
transferase |
X-ray (2.15 Å) |
Lee TT, Agarwalla S, Stroud RM |
(2005) "A Unique RNA Fold in the Ruma-RNA-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function." Cell(Cambridge,Mass.), 120, 599. doi: 10.1016/J.CELL.2004.12.037. |
Crystal structure of e. coli 5-methyluridine methyltransferase ruma in complex with ribosomal RNA substrate and s-adenosylhomocysteine.. SNAP output |
| 2bny |
virus |
X-ray (3.0 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2." Structure, 14, 487. doi: 10.1016/J.STR.2005.12.006. |
Ms2 (n87a mutant) - RNA hairpin complex. SNAP output |
| 2bq5 |
virus-RNA |
X-ray (2.91 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2." Structure, 14, 487. doi: 10.1016/J.STR.2005.12.006. |
Ms2 (n87ae89k mutant) - RNA hairpin complex. SNAP output |
| 2bs0 |
virus-RNA |
X-ray (2.45 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2." Structure, 14, 487. doi: 10.1016/J.STR.2005.12.006. |
Ms2 (n87ae89k mutant) - variant qbeta RNA hairpin complex. SNAP output |
| 2bs1 |
virus-RNA |
X-ray (2.8 Å) |
Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SEV, Stonehouse NJ, Liljas L, Stockley PG |
(2006) "Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2." Structure, 14, 487. doi: 10.1016/J.STR.2005.12.006. |
Ms2 (n87ae89k mutant) - qbeta RNA hairpin complex. SNAP output |
| 2bte |
ligase |
X-ray (2.9 Å) |
Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S |
(2005) "The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer- Editing Conformation." Nat.Struct.Mol.Biol., 12, 923. doi: 10.1038/NSMB986. |
Thermus thermophilus leucyl-trna synthetase complexed with a trnaleu transcript in the post-editing conformation and a post- transfer editing substrate analogue. SNAP output |
| 2bu1 |
virus-RNA |
X-ray (2.2 Å) |
Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L |
(2001) "Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex." Rna, 7, 1616-1627. |
Ms2-RNA hairpin (5bru -5) complex. SNAP output |
| 2bx2 |
hydrolase |
X-ray (2.85 Å) |
Callaghan AJ, Marcaida MJ, Stead JA, Mcdowall KJ, Scott WG, Luisi BF |
(2005) "Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover." Nature, 437, 1187. doi: 10.1038/NATURE04084. |
Catalytic domain of e. coli rnase e. SNAP output |
| 2byt |
synthetase |
X-ray (3.3 Å) |
Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S |
(2005) "The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer-Editing Conformation." Nat.Struct.Mol.Biol., 12, 923. doi: 10.1038/NSMB986. |
Thermus thermophilus leucyl-trna synthetase complexed with a trnaleu transcript in the post-editing conformation. SNAP output |
| 2c06 |
toxin |
NMR |
Kamphuis MB, Bonvin AMJJ, Monti MC, Lemonnier M, Munoz-Gomez A, Van Den Heuvel RHH, Diaz-Orejas R, Boelens R |
(2006) "Model for RNA Binding and the Catalytic Site of the Rnase Kid of the Bacterial Pard Toxin-Antitoxin System." J.Mol.Biol., 357, 115. doi: 10.1016/J.JMB.2005.12.033. |
NMR-based model of the complex of the toxin kid and a 5-nucleotide substrate RNA fragment (auaca). SNAP output |
| 2c0b |
hydrolase |
X-ray (3.18 Å) |
Callaghan AJ, Marcaida MJ, Stead JA, Mcdowall KJ, Scott WG, Luisi BF |
(2005) "Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover." Nature, 437, 1187. doi: 10.1038/NATURE04084. |
Catalytic domain of e. coli rnase e in complex with 13-mer RNA. SNAP output |
| 2c4q |
virus-RNA |
X-ray (2.38 Å) |
Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L |
(2001) "Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex." Rna, 7, 1616-1627. |
Ms2-RNA hairpin (2one -5) complex. SNAP output |
| 2c4r |
hydrolase |
X-ray (3.6 Å) |
Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF |
(2005) "Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover." Nature, 437, 1187. doi: 10.1038/NATURE04084. |
Catalytic domain of e. coli rnase e. SNAP output |
| 2c4y |
virus-RNA |
X-ray (2.68 Å) |
Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L |
(2001) "Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex." Rna, 7, 1616-1627. |
Ms2-RNA hairpin (2thiouracil-5) complex. SNAP output |
| 2c4z |
virus-RNA |
X-ray (2.6 Å) |
Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L |
(2001) "Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex." Rna, 7, 1616-1627. |
Ms2-RNA hairpin (2su -5-6) complex. SNAP output |
| 2c50 |
virus-RNA |
X-ray (2.65 Å) |
Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L |
(2001) "Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex." Rna, 7, 1616-1627. |
Ms2-RNA hairpin (a -5) complex. SNAP output |
| 2c51 |
virus-RNA |
X-ray (2.8 Å) |
Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L |
(2001) "Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex." Rna, 7, 1616-1627. |
Ms2-RNA hairpin (g -5) complex. SNAP output |
| 2cjk |
RNA binding protein |
NMR |
Perez-Canadillas JM |
(2006) "Grabbing the message: structural basis of mRNA 3'UTR recognition by Hrp1." EMBO J., 25, 3167-3178. doi: 10.1038/sj.emboj.7601190. |
Structure of the RNA binding domain of hrp1 in complex with RNA. SNAP output |
| 2csx |
ligase-RNA |
X-ray (2.7 Å) |
Nakanishi K, Ogiso Y, Nakama T, Fukai S, Nureki O |
(2005) "Structural basis for anticodon recognition by methionyl-tRNA synthetase." Nat.Struct.Mol.Biol., 12, 931-932. doi: 10.1038/nsmb988. |
Crystal structure of aquifex aeolicus methionyl-trna synthetase complexed with trna(met). SNAP output |
| 2ct8 |
ligase-RNA |
X-ray (2.7 Å) |
Nakanishi K, Ogiso Y, Nakama T, Fukai S, Nureki O |
(2005) "Structural basis for anticodon recognition by methionyl-tRNA synthetase." Nat.Struct.Mol.Biol., 12, 931-932. doi: 10.1038/nsmb988. |
Crystal structure of aquifex aeolicus methionyl-trna synthetase complexed with trna(met) and methionyl-adenylate anologue. SNAP output |
| 2cv0 |
ligase-RNA |
X-ray (2.4 Å) |
Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S |
(2006) "Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase." Structure, 14, 1791-1799. doi: 10.1016/j.str.2006.10.005. |
Glutamyl-trna synthetase from thermus thermophilus in complex with trna(glu) and l-glutamate. SNAP output |
| 2cv1 |
ligase-RNA |
X-ray (2.41 Å) |
Sekine S, Yokoyama S |
"Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu), ATP, and an analog of L-glutamate: a quaternary complex." |
Glutamyl-trna synthetase from thermus thermophilus in complex with trna(glu), atp, and an analog of l-glutamate: a quaternary complex. SNAP output |
| 2cv2 |
ligase-RNA |
X-ray (2.69 Å) |
Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S |
(2006) "Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase." Structure, 14, 1791-1799. doi: 10.1016/j.str.2006.10.005. |
Glutamyl-trna synthetase from thermus thermophilus in complex with trna(glu) and an enzyme inhibitor, glu-ams. SNAP output |
| 2czj |
RNA binding protein-RNA |
X-ray (3.01 Å) |
Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S |
(2007) "Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA." Proc.Natl.Acad.Sci.Usa, 104, 8293-8298. doi: 10.1073/pnas.0700402104. |
Crystal structure of the trna domain of tmrna from thermus thermophilus hb8. SNAP output |
| 2d3o |
ribosome |
X-ray (3.35 Å) |
Schlunzen F, Wilson DN, Tian P, Harms JM, McInnes SJ, Hansen HA, Albrecht R, Buerger J, Wilbanks SM, Fucini P |
(2005) "The Binding Mode of the Trigger Factor on the Ribosome: Implications for Protein Folding and SRP Interaction." Structure, 13, 1685-1694. doi: 10.1016/j.str.2005.08.007. |
Structure of ribosome binding domain of the trigger factor on the 50s ribosomal subunit from d. radiodurans. SNAP output |
| 2d6f |
ligase-RNA |
X-ray (3.15 Å) |
Oshikane H, Sheppard K, Fukai S, Nakamura Y, Ishitani R, Numata T, Sherrer RL, Feng L, Schmitt E, Panvert M, Blanquet S, Mechulam Y, Soll D, Nureki O |
(2006) "Structural basis of RNA-dependent recruitment of glutamine to the genetic code." Science, 312, 1950-1954. doi: 10.1126/science.1128470. |
Crystal structure of glu-trna(gln) amidotransferase in the complex with trna(gln). 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 |
| 2der |
transferase-RNA |
X-ray (3.1 Å) |
Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O |
(2006) "Snapshots of tRNA sulphuration via an adenylated intermediate." Nature, 442, 419-424. doi: 10.1038/nature04896. |
Cocrystal structure of an RNA sulfuration enzyme mnma and trna-glu in the initial trna binding state. SNAP output |
| 2det |
transferase-RNA |
X-ray (3.4 Å) |
Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O |
(2006) "Snapshots of tRNA sulphuration via an adenylated intermediate." Nature, 442, 419-424. doi: 10.1038/nature04896. |
Cocrystal structure of an RNA sulfuration enzyme mnma and trna-glu in the pre-reaction state. SNAP output |
| 2deu |
transferase-RNA |
X-ray (3.4 Å) |
Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O |
(2006) "Snapshots of tRNA sulphuration via an adenylated intermediate." Nature, 442, 419-424. doi: 10.1038/nature04896. |
Cocrystal structure of an RNA sulfuration enzyme mnma and trna-glu in the adenylated intermediate state. SNAP output |
| 2dr2 |
ligase-RNA |
X-ray (3.0 Å) |
Shen N, Guo L, Yang B, Jin Y, Ding J |
(2006) "Structure of human tryptophanyl-tRNA synthetase in complex with tRNA(Trp) reveals the molecular basis of tRNA recognition and specificity." Nucleic Acids Res., 34, 3246-3258. doi: 10.1093/nar/gkl441. |
Structure of human tryptophanyl-trna synthetase in complex with trna(trp). SNAP output |
| 2dr5 |
transferase-RNA |
X-ray (2.8 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca adding enzyme with mini-helix lacking cca. SNAP output |
| 2dr7 |
transferase-RNA |
X-ray (2.8 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca-adding enzyme with trnaminidc. SNAP output |
| 2dr8 |
transferase-RNA |
X-ray (2.5 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca-adding enzyme with trnaminidc and ctp. SNAP output |
| 2dr9 |
transferase-RNA |
X-ray (2.8 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca-adding enzyme with trnaminidcc. SNAP output |
| 2dra |
transferase-RNA |
X-ray (2.5 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca-adding enzyme with trnaminidcc and atp. SNAP output |
| 2drb |
transferase-RNA |
X-ray (2.8 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca-adding enzyme with trnaminicca. SNAP output |
| 2du3 |
ligase-RNA |
X-ray (2.6 Å) |
Fukunaga R, Yokoyama S |
(2007) "Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea." Nat.Struct.Mol.Biol., 14, 272-279. doi: 10.1038/nsmb1219. |
Crystal structure of archaeoglobus fulgidus o-phosphoseryl-trna synthetase complexed with trnacys and o-phosphoserine. SNAP output |
| 2du4 |
ligase-RNA |
X-ray (2.8 Å) |
Fukunaga R, Yokoyama S |
(2007) "Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea." Nat.Struct.Mol.Biol., 14, 272-279. doi: 10.1038/nsmb1219. |
Crystal structure of archaeoglobus fulgidus o-phosphoseryl-trna synthetase complexed with trnacys. SNAP output |
| 2du5 |
ligase-RNA |
X-ray (3.2 Å) |
Fukunaga R, Yokoyama S |
(2007) "Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea." Nat.Struct.Mol.Biol., 14, 272-279. doi: 10.1038/nsmb1219. |
Crystal structure of archaeoglobus fulgidus o-phosphoseryl-trna synthetase e418n-e420n mutant complexed with trnaopal and o-phosphoserine ("opal complex"). SNAP output |
| 2du6 |
ligase-RNA |
X-ray (3.3 Å) |
Fukunaga R, Yokoyama S |
(2007) "Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea." Nat.Struct.Mol.Biol., 14, 272-279. doi: 10.1038/nsmb1219. |
Crystal structure of archaeoglobus fulgidus o-phosphoseryl-trna synthetase e418n-e420n mutant complexed with trnaamber and o-phosphoserine ("amber complex"). SNAP output |
| 2dvi |
transferase-RNA |
X-ray (2.61 Å) |
Tomita K, Ishitani R, Fukai S, Nureki O |
(2006) "Complete crystallographic analysis of the dynamics of CCA sequence addition." Nature, 443, 956-960. doi: 10.1038/nature05204. |
Complex structure of cca-adding enzyme, mini-dcc and ctp. SNAP output |
| 2dxi |
ligase-RNA |
X-ray (2.2 Å) |
Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S |
(2006) "Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase." Structure, 14, 1791-1799. doi: 10.1016/j.str.2006.10.005. |
2.2 a crystal structure of glutamyl-trna synthetase from thermus thermophilus complexed with trna(glu), atp, and l-glutamol. SNAP output |
| 2e5l |
ribosome |
X-ray (3.3 Å) |
Kaminishi T, Wilson DN, Takemoto C, Harms JM, Kawazoe M, Schluenzen F, Hanawa-Suetsugu K, Shirouzu M, Fucini P, Yokoyama S |
(2007) "A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction." Structure, 15, 289-297. doi: 10.1016/j.str.2006.12.008. |
A snapshot of the 30s ribosomal subunit capturing mrna via the shine- dalgarno interaction. SNAP output |
| 2e9r |
transferase-RNA |
X-ray (2.81 Å) |
Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2007) "Sequential structures provide insights into the fidelity of RNA replication." Proc.Natl.Acad.Sci.Usa, 104, 9463-9468. doi: 10.1073/pnas.0700518104. |
Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with ribavirin. SNAP output |
| 2e9t |
transferase-RNA |
X-ray (2.6 Å) |
Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2007) "Sequential structures provide insights into the fidelity of RNA replication." Proc.Natl.Acad.Sci.Usa, 104, 9463-9468. doi: 10.1073/pnas.0700518104. |
Foot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a template-primer RNA and 5f-utp. SNAP output |
| 2e9z |
transferase-RNA |
X-ray (3.0 Å) |
Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2007) "Sequential structures provide insights into the fidelity of RNA replication." Proc.Natl.Acad.Sci.Usa, 104, 9463-9468. doi: 10.1073/pnas.0700518104. |
Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, atp and utp. SNAP output |
| 2ec0 |
transferase-RNA |
X-ray (2.75 Å) |
Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2007) "Sequential structures provide insights into the fidelity of RNA replication." Proc.Natl.Acad.Sci.Usa, 104, 9463-9468. doi: 10.1073/pnas.0700518104. |
RNA-dependent RNA polymerase of foot-and-mouth disease virus in complex with a template-primer RNA and atp. SNAP output |
| 2err |
RNA binding protein |
NMR |
Auweter SD, Fasan R, Reymond L, Underwood JG, Black DL, Pitsch S, Allain FH |
(2006) "Molecular basis of RNA recognition by the human alternative splicing factor Fox-1." Embo J., 25, 163-173. doi: 10.1038/sj.emboj.7600918. |
NMR structure of the RNA binding domain of human fox-1 in complex with ugcaugu. SNAP output |
| 2ese |
protein-RNA complex |
NMR |
Oberstrass FC, Lee A, Stefl R, Janis M, Chanfreau G, Allain FH |
(2006) "Shape-specific recognition in the structure of the Vts1p SAM domain with RNA." Nat.Struct.Mol.Biol., 13, 160-167. doi: 10.1038/nsmb1038. |
Structure of the sam domain of vts1p in complex with RNA. SNAP output |
| 2ez6 |
hydrolase-RNA |
X-ray (2.05 Å) |
Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2006) "Structural Insight into the Mechanism of Double-Stranded RNA Processing by Ribonuclease III." Cell(Cambridge,Mass.), 124, 355-366. doi: 10.1016/j.cell.2005.11.034. |
Crystal structure of aquifex aeolicus rnase iii (d44n) complexed with product of double-stranded RNA processing. SNAP output |
| 2f4v |
ribosome |
X-ray (3.8 Å) |
Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S |
(2006) "Interactions of designer antibiotics and the bacterial ribosome aminoacyl-tRNA site." Chem.Biol., 13, 129-138. doi: 10.1016/j.chembiol.2005.11.004. |
30s ribosome + designer antibiotic. SNAP output |
| 2f8k |
RNA binding protein- RNA |
X-ray (2.0 Å) |
Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F |
(2006) "Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p." Nat.Struct.Mol.Biol., 13, 168-176. doi: 10.1038/nsmb1053. |
Sequence specific recognition of RNA hairpins by the sam domain of vts1. SNAP output |
| 2f8s |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Yuan YR, Pei Y, Chen HY, Tuschl T, Patel DJ |
(2006) "A Potential Protein-RNA Recognition Event along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA." Structure, 14, 1557-1565. doi: 10.1016/j.str.2006.08.009. |
Crystal structure of aa-ago with externally-bound sirna. SNAP output |
| 2f8t |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Yuan YR, Pei Y, Chen HY, Tuschl T, Patel DJ |
(2006) "A Potential Protein-RNA Recognition Event along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA." Structure, 14, 1557-1565. doi: 10.1016/j.str.2006.08.009. |
Crystal structure of aa-ago with externally-bound sirna. SNAP output |
| 2fk6 |
hydrolase-RNA |
X-ray (2.9 Å) |
Li de la Sierra-Gallay I, Mathy N, Pellegrini O, Condon C |
(2006) "Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA." Nat.Struct.Mol.Biol., 13, 376-377. doi: 10.1038/nsmb1066. |
Crystal structure of rnase z-trna(thr) complex. SNAP output |
| 2fmt |
complex (methyltransferase-trna) |
X-ray (2.8 Å) |
Schmitt E, Panvert M, Blanquet S, Mechulam Y |
(1998) "Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet." EMBO J., 17, 6819-6826. doi: 10.1093/emboj/17.23.6819. |
Methionyl-trnafmet formyltransferase complexed with formyl-methionyl-trnafmet. SNAP output |
| 2fy1 |
structural protein-RNA |
NMR |
Skrisovska L, Bourgeois CF, Stefl R, Grellscheid SN, Kister L, Wenter P, Elliott DJ, Stevenin J, Allain FH |
(2007) "The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction." EMBO Rep., 8, 372-379. doi: 10.1038/sj.embor.7400910. |
A dual mode of RNA recognition by the rbmy protein. SNAP output |
| 2fz2 |
virus-RNA |
X-ray (2.9 Å) |
Larson SB, Lucas RW, Greenwood A, McPherson A |
(2005) "The RNA of turnip yellow mosaic virus exhibits icosahedral order." Virology, 334, 245-254. doi: 10.1016/j.virol.2005.01.036. |
Structure of turnip yellow mosaic virus at 100 k. SNAP output |
| 2g4b |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Sickmier EA, Frato KE, Paranawithana S, Shen H, Green MR, Kielkopf CL |
(2006) "Structural basis of polypyrimidine tract recognition
by the essential splicing factor U2AF65." Mol.Cell, 23, 49-59. doi: 10.1016/j.molcel.2006.05.025. |
Structure of u2af65 variant with polyuridine tract. SNAP output |
| 2gic |
virus-viral protein-RNA |
X-ray (2.92 Å) |
Green TJ, Zhang X, Wertz GW, Luo M |
(2006) "Structure of the vesicular stomatitis virus nucleoprotein-RNA complex unveils how the RNA is sequestered." Science, 313, 357-360. doi: 10.1126/science.1126953. |
Crystal structure of a vesicular stomatitis virus nucleocapsid-RNA complex. SNAP output |
| 2gje |
translation-RNA |
X-ray (3.37 Å) |
Schumacher MA, Karamooz E, Zikova A, Trantirek L, Lukes J |
(2006) "Crystal Structures of T. brucei MRP1/MRP2 Guide-RNA Binding Complex Reveal RNA Matchmaking Mechanism." Cell(Cambridge,Mass.), 126, 701-711. doi: 10.1016/j.cell.2006.06.047. |
Structure of a guiderna-binding protein complex bound to a grna. SNAP output |
| 2gjw |
hydrolase-RNA |
X-ray (2.85 Å) |
Xue S, Calvin K, Li H |
(2006) "RNA Recognition and Cleavage by an Splicing Endonuclease." Science, 312, 902-910. doi: 10.1126/science.1126629. |
RNA recognition and cleavage by an splicing endonuclease. SNAP output |
| 2go5 |
translation-RNA |
cryo-EM (7.4 Å) |
Halic M, Gartmann M, Schlenker O, Mielke T, Pool MR, Sinning I, Beckmann R |
(2006) "Signal Recognition Particle Receptor Exposes the Ribosomal Translocon Binding Site." Science, 312, 745-747. doi: 10.1126/science.1124864. |
Structure of signal recognition particle receptor (sr) in complex with signal recognition particle (srp) and ribosome nascent chain complex. SNAP output |
| 2gtt |
viral protein, RNA binding protein |
X-ray (3.49 Å) |
Albertini AAV, Wernimont AK, Muziol T, Ravelli RBG, Clapier CR, Schoehn G, Weissenhorn W, Ruigrok RWH |
(2006) "Crystal Structure of the Rabies Virus Nucleoprotein-RNA Complex." Science, 313, 360-363. doi: 10.1126/science.1125280. |
Crystal structure of the rabies virus nucleoprotein-RNA complex. SNAP output |
| 2gxb |
hydrolase-RNA |
X-ray (2.25 Å) |
Placido D, Brown BA, Lowenhaupt K, Rich A, Athanasiadis A |
(2007) "A Left-Handed RNA Double Helix Bound by the Zalpha Domain of the RNA-Editing Enzyme ADAR1." Structure, 15, 395-404. doi: 10.1016/j.str.2007.03.001. |
Crystal structure of the za domain bound to z-RNA. SNAP output |
| 2hgh |
transcription-RNA |
NMR |
Lee BM, Xu J, Clarkson BK, Martinez-Yamout MA, Dyson JH, Case DA, Gottesfeld JM, Wright PE |
(2006) "Induced Fit and 'Lock and Key' Recognition of 5 S RNA by Zinc Fingers of Transcription Factor IIIA." J.Mol.Biol., 357, 275-291. doi: 10.1016/j.jmb.2005.12.010. |
Transcription factor iiia zinc fingers 4-6 bound to 5s rrna 55mer (NMR structure). SNAP output |
| 2hhh |
ribosome |
X-ray (3.35 Å) |
Schluenzen F, Takemoto C, Wilson DN, Kaminishi T, Harms JM, Hanawa-Suetsugu K, Szaflarski W, Kawazoe M, Shirouzo M, Nierhaus KH, Yokoyama S, Fucini P |
(2006) "The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation." Nat.Struct.Mol.Biol., 13, 871-878. doi: 10.1038/nsmb1145. |
Crystal structure of kasugamycin bound to the 30s ribosomal subunit. SNAP output |
| 2ht1 |
hydrolase-RNA |
X-ray (3.51 Å) |
Skordalakes E, Berger JM |
(2006) "Structural Insights into RNA-Dependent Ring Closure and ATPase Activation by the Rho Termination Factor." Cell(Cambridge,Mass.), 127, 553-564. doi: 10.1016/j.cell.2006.08.051. |
The closed ring structure of the rho transcription termination factor in complex with nucleic acid in the motor domains. 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 |
| 2hw8 |
structural protein-RNA |
X-ray (2.1 Å) |
Tishchenko S, Nikonova E, Nikulin A, Nevskaya N, Volchkov S, Piendl W, Garber M, Nikonov S |
(2006) "Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes." ACTA CRYSTALLOGR.,SECT.D, 62, 1545-1554. doi: 10.1107/S0907444906041655. |
Structure of ribosomal protein l1-mrna complex at 2.1 resolution.. SNAP output |
| 2hyi |
hydrolase-RNA binding protein-RNA |
X-ray (2.3 Å) |
Andersen CBF, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, Pedersen JS, Seraphin B, Le Hir H, Andersen GR |
(2006) "Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA." Science, 313, 1968-1972. doi: 10.1126/science.1131981. |
Structure of the human exon junction complex with a trapped dead-box helicase bound to RNA. SNAP output |
| 2i2y |
RNA binding protein-chimera-RNA |
NMR |
Hargous Y, Hautbergue GM, Tintaru AM, Skrisovska L, Golovanov AP, Stevenin J, Lian LY, Wilson SA, Allain FH |
(2006) "Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8." Embo J., 25, 5126-5137. doi: 10.1038/sj.emboj.7601385. |
Solution structure of the rrm of srp20 bound to the RNA cauc. SNAP output |
| 2i82 |
lyase-RNA |
X-ray (2.05 Å) |
Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferre-D'Amare AR |
(2006) "Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure." Mol.Cell, 24, 535-545. doi: 10.1016/j.molcel.2006.09.017. |
Crystal structure of pseudouridine synthase rlua: indirect sequence readout through protein-induced RNA structure. SNAP output |
| 2i91 |
RNA binding protein-RNA |
X-ray (2.65 Å) |
Fuchs G, Stein AJ, Fu C, Reinisch KM, Wolin SL |
(2006) "Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen." Nat.Struct.Mol.Biol., 13, 1002-1009. doi: 10.1038/nsmb1156. |
60kda ro autoantigen in complex with a fragment of misfolded RNA. SNAP output |
| 2ihx |
viral protein-RNA |
NMR |
Zhou J, Bean RL, Vogt VM, Summers M |
(2007) "Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein: muPsi RNA Packaging Signal Complex." J.Mol.Biol., 365, 453-467. doi: 10.1016/j.jmb.2006.10.013. |
Solution structure of the rous sarcoma virus nucleocapsid protein:upsi RNA packaging signal complex. SNAP output |
| 2ix1 |
hydrolase |
X-ray (2.74 Å) |
Frazao C, Mcvey CE, Amblar M, Barbas A, Vonrhein C, Arraiano CM, Carrondo MA |
(2006) "Unravelling the Dynamics of RNA Degradation by Ribonuclease II and its RNA-Bound Complex." Nature, 443, 110. doi: 10.1038/NATURE05080. |
Rnase ii d209n mutant. SNAP output |
| 2iy5 |
ligase |
X-ray (3.1 Å) |
Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M |
(2006) "The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end." Biochemistry, 45, 10572-10583. doi: 10.1021/bi060491l. |
Phenylalanyl-trna synthetase from thermus thermophilus complexed with trna and a phenylalanyl-adenylate analog. SNAP output |
| 2iz8 |
virus-RNA |
X-ray (3.3 Å) |
Helgstrand C, Grahn E, Moss T, Stonehouse NJ, Tars K, Stockley PG, Liljas L |
(2002) "Investigating the Structural Basis of Purine Specificity in the Structures of MS2 Coat Protein RNA Translational Operator Hairpins." Nucleic Acids Res., 30, 2678. doi: 10.1093/NAR/GKF371. |
Ms2-RNA hairpin (c-7) complex. SNAP output |
| 2iz9 |
virus-RNA |
X-ray (2.85 Å) |
Grahn E, Stonehouse NJ, Adams CJ, Fridborg K, Beigelman L, Matulic-Adamic J, Warriner SL, Stockley PG, Liljas L |
(2000) "Deletion of a Single Hydrogen Bonding Atom from the MS2 RNA Operator Leads to Dramatic Rearrangements at the RNA-Coat Protein Interface." Nucleic Acids Res., 28, 4611. doi: 10.1093/NAR/28.23.4611. |
Ms2-RNA hairpin (4one -5) complex. SNAP output |
| 2izm |
virus-RNA |
X-ray (2.7 Å) |
Helgstrand C, Grahn E, Moss T, Stonehouse NJ, Tars K, Stockley PG, Liljas L |
(2002) "Investigating the Structural Basis of Purine Specificity in the Structures of MS2 Coat Protein RNA Translational Operator Complexes." Nucleic Acids Res., 30, 2678. doi: 10.1093/NAR/GKF371. |
Ms2-RNA hairpin (c-10) complex. SNAP output |
| 2izn |
virus-RNA |
X-ray (2.56 Å) |
Helgstrand C, Grahn E, Moss T, Stonehouse NJ, Tars K, Stockley PG, Liljas L |
(2002) "Investigating the Structural Basis of Purine Specificity in the Structures of MS2 Coat Protein RNA Translational Operator Complexes." Nucleic Acids Res., 30, 2678. doi: 10.1093/NAR/GKF371. |
Ms2-RNA hairpin (g-10) complex. SNAP output |
| 2j0q |
hydrolase |
X-ray (3.2 Å) |
Bono F, Ebert J, Lorentzen E, Conti E |
(2006) "The Crystal Structure of the Exon Junction Complex Reveals How It Maintains a Stable Grip on Mrna." Cell(Cambridge,Mass.), 126, 713. doi: 10.1016/J.CELL.2006.08.006. |
The crystal structure of the exon junction complex at 3.2 Å resolution. SNAP output |
| 2j0s |
hydrolase |
X-ray (2.21 Å) |
Bono F, Ebert J, Lorentzen E, Conti E |
(2006) "The Crystal Structure of the Exon Junction Complex Reveals How It Mantains a Stable Grip on Mrna." Cell(Cambridge,Mass.), 126, 713. doi: 10.1016/J.CELL.2006.08.006. |
The crystal structure of the exon junction complex at 2.2 Å resolution. SNAP output |
| 2j28 |
ribosome |
cryo-EM (8.0 Å) |
Halic M, Blau M, Becker T, Mielke T, Pool MR, Wild K, Sinning I, Beckmann R |
(2006) "Following the Signal Sequence from Ribosomal Tunnel Exit to Signal Recognition Particle." Nature, 444, 508-511. doi: 10.1038/nature05326. |
Model of e. coli srp bound to 70s rncs. SNAP output |
| 2j37 |
ribosome |
cryo-EM (8.0 Å) |
Halic M, Blau M, Becker T, Mielke T, Pool MR, Wild K, Sinning I, Beckmann R |
(2006) "Following the signal sequence from ribosomal tunnel exit to signal recognition particle." Nature, 444, 507-511. doi: 10.1038/nature05326. |
Model of mammalian srp bound to 80s rncs. 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 |
| 2jlu |
hydrolase-RNA |
X-ray (2.04 Å) |
Luo D, Xu T, Watson RP, Scherer-Becker D, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, Vasudevan SG, Lescar J |
(2008) "Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein." Embo J., 27, 3209. doi: 10.1038/EMBOJ.2008.232. |
Dengue virus 4 ns3 helicase in complex with ssrna. SNAP output |
| 2jlv |
hydrolase-RNA |
X-ray (1.9 Å) |
Luo DH, Xu T, Watson RP, Becker DS, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, Vasudevan SG, Lescar J |
(2008) "Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein." Embo J., 27, 3209. doi: 10.1038/EMBOJ.2008.232. |
Dengue virus 4 ns3 helicase in complex with ssrna and amppnp. SNAP output |
| 2jlw |
hydrolase-RNA |
X-ray (2.6 Å) |
Luo DH, Xu T, Watson RP, Becker DS, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, Vasudevan SG, Lescar J |
(2008) "Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein." Embo J., 27, 3209. doi: 10.1038/EMBOJ.2008.232. |
Dengue virus 4 ns3 helicase in complex with ssrna2. SNAP output |
| 2jlx |
hydrolase-RNA |
X-ray (2.2 Å) |
Luo DH, Xu T, Watson RP, Scherer-Becker D, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, Vasudevan SG, Lescar J |
(2008) "Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein." Embo J., 27, 3209. doi: 10.1038/EMBOJ.2008.232. |
Dengue virus 4 ns3 helicase in complex with ssrna and adp-vanadate. SNAP output |
| 2jly |
hydrolase-RNA |
X-ray (2.4 Å) |
Luo D, Xu T, Watson RP, Scherer-Becker D, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, Vasudevan SG, Lescar J |
(2008) "Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein." Embo J., 27, 3209. doi: 10.1038/EMBOJ.2008.232. |
Dengue virus 4 ns3 helicase in complex with ssrna and adp-phosphate. SNAP output |
| 2jlz |
hydrolase-RNA |
X-ray (2.2 Å) |
Luo D, Xu T, Watson RP, Scherer-Becker D, Sampath A, Jahnke W, Yeong SS, Wang CH, Lim SP, Strongin A, Vasudevan SG, Lescar J |
(2008) "Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein." Embo J., 27, 3209. doi: 10.1038/EMBOJ.2008.232. |
Dengue virus 4 ns3 helicase in complex with ssrna and adp. SNAP output |
| 2jpp |
translation-RNA |
NMR |
Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH-T |
(2007) "Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA." Nat.Struct.Mol.Biol., 14, 807-813. doi: 10.1038/nsmb1285. |
Structural basis of rsma-csra RNA recognition: structure of rsme bound to the shine-dalgarno sequence of hcna mrna. SNAP output |
| 2jq7 |
ribosome-antibiotic |
NMR |
Jonker HRA, Ilin S, Grimm SK, Woehnert J, Schwalbe H |
(2007) "L11 Domain Rearrangement Upon Binding to RNA and Thiostrepton Studied by NMR Spectroscopy." Nucleic Acids Res., 35, 441. doi: 10.1093/NAR/GKL1066. |
Model for thiostrepton binding to the ribosomal l11-RNA. SNAP output |
| 2kdq |
RNA binding protein-RNA |
NMR |
Davidson A, Leeper TC, Athanassiou Z, Patora-Komisarska K, Karn J, Robinson JA, Varani G |
(2009) "Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein." Proc.Natl.Acad.Sci.USA, 106, 11931-11936. doi: 10.1073/pnas.0900629106. |
Simultaneous recognition of hiv-1 tar RNA bulge and loop sequences by cyclic peptide mimic of tat protein. SNAP output |
| 2kfy |
RNA binding protein-RNA |
NMR |
Dominguez C, Fisette JF, Chabot B, Allain FH |
(2010) "Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs." Nat.Struct.Mol.Biol., 17, 853-861. doi: 10.1038/nsmb.1814. |
NMR structure of the first qrrm of hnrnp f in complex with agggau g-tract RNA. SNAP output |
| 2kg0 |
RNA binding protein-RNA |
NMR |
Dominguez C, Fisette JF, Chabot B, Allain FH |
(2010) "Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs." Nat.Struct.Mol.Biol., 17, 853-861. doi: 10.1038/nsmb.1814. |
Structure of the second qrrm domain of hnrnp f in complex with a agggau g-tract RNA. SNAP output |
| 2kg1 |
RNA binding protein-RNA |
NMR |
Dominguez C, Fisette JF, Chabot B, Allain FH |
(2010) "Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs." Nat.Struct.Mol.Biol., 17, 853-861. doi: 10.1038/nsmb.1814. |
Structure of the third qrrm domain of hnrnp f in complex with a agggau g-tract RNA. SNAP output |
| 2kh9 |
splicing-RNA |
NMR |
Martin-Tumasz S, Reiter NJ, Brow DA, Butcher SE |
(2010) "Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24." Rna, 16, 792-804. doi: 10.1261/rna.1913310. |
Solution structure of yeast prp24-rrm2 bound to a fragment of u6 RNA. SNAP output |
| 2km8 |
RNA binding protein-RNA |
NMR |
Leeper TC, Qu X, Lu C, Moore C, Varani G |
(2010) "Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1." J.Mol.Biol., 401, 334-349. doi: 10.1016/j.jmb.2010.06.032. |
Interdomain rrm packing contributes to RNA recognition in the rna15, hrp1, anchor RNA 3' processing ternary complex. SNAP output |
| 2kmj |
RNA-peptide |
NMR |
Ferner J, Suhartono M, Breitung S, Jonker HRA, Hennig M, Wohnert J, Gobel M, Schwalbe H |
(2009) "Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries." Chembiochem, 10, 1490-1494. doi: 10.1002/cbic.200900220. |
High resolution NMR solution structure of a complex of hiv-2 tar RNA and a synthetic tripeptide in a 1:2 stoichiometry. SNAP output |
| 2kx5 |
RNA binding protein-RNA |
NMR |
Davidson A, Patora-Komisarska K, Robinson JA, Varani G |
(2011) "Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein." Nucleic Acids Res., 39, 248-256. doi: 10.1093/nar/gkq713. |
Recognition of hiv tar RNA by peptide mimetic of tat protein. SNAP output |
| 2kxn |
RNA binding protein-RNA |
NMR |
Clery A, Jayne S, Benderska N, Dominguez C, Stamm S, Allain FH |
(2011) "Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-beta1." Nat.Struct.Mol.Biol., 18, 443-450. doi: 10.1038/nsmb.2001. |
NMR structure of human tra2beta1 rrm in complex with aagaac RNA. SNAP output |
| 2l2k |
hydrolase-RNA |
NMR |
Stefl R, Oberstrass FC, Hood JL, Jourdan M, Zimmermann M, Skrisovska L, Maris C, Peng L, Hofr C, Emeson RB, Allain FH |
(2010) "The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove." Cell(Cambridge,Mass.), 143, 225-237. doi: 10.1016/j.cell.2010.09.026. |
Solution NMR structure of the r-g stem loop RNA-adar2 dsrbm2 complex. SNAP output |
| 2l3c |
hydrolase-RNA |
NMR |
Stefl R, Oberstrass FC, Hood JL, Jourdan M, Zimmermann M, Skrisovska L, Maris C, Peng L, Hofr C, Emeson RB, Allain FH |
(2010) "The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove." Cell(Cambridge,Mass.), 143, 225-237. doi: 10.1016/j.cell.2010.09.026. |
Solution structure of adar2 dsrbm1 bound to lsl RNA. SNAP output |
| 2l3j |
hydrolase-RNA |
NMR |
Stefl R, Oberstrass FC, Hood JL, Jourdan M, Zimmermann M, Skrisovska L, Maris C, Peng L, Hofr C, Emeson RB, Allain FH |
(2010) "The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove." Cell(Cambridge,Mass.), 143, 225-237. doi: 10.1016/j.cell.2010.09.026. |
The solution structure of the adar2 dsrbm-RNA complex reveals a sequence-specific read out of the minor groove. SNAP output |
| 2l41 |
RNA binding protein-RNA |
NMR |
Hobor F, Pergoli R, Kubicek K, Hrossova D, Bacikova V, Zimmermann M, Pasulka J, Hofr C, Vanacova S, Stefl R |
(2011) "Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (NAB) 3 protein." J.Biol.Chem., 286, 3645-3657. doi: 10.1074/jbc.M110.158774. |
Nab3 rrm - ucuu complex. SNAP output |
| 2l5d |
RNA binding protein-RNA |
NMR |
Zeng L, Zhang Q, Yan K, Zhou MM |
(2011) "Structural insights into piRNA recognition by the human PIWI-like 1 PAZ domain." Proteins, 79, 2004-2009. doi: 10.1002/prot.23003. |
Solution structures of human piwi-like 1 paz domain with ssrna (5'-pugaca). SNAP output |
| 2la5 |
RNA binding protein-RNA |
NMR |
Phan AT, Kuryavyi V, Darnell JC, Serganov A, Majumdar A, Ilin S, Raslin T, Polonskaia A, Chen C, Clain D, Darnell RB, Patel DJ |
(2011) "Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction." Nat.Struct.Mol.Biol., 18, 796-804. doi: 10.1038/nsmb.2064. |
RNA duplex-quadruplex junction complex with fmrp rgg peptide. SNAP output |
| 2lbs |
hydrolase-RNA |
NMR |
Wang Z, Hartman E, Roy K, Chanfreau G, Feigon J |
(2011) "Structure of a Yeast RNase III dsRBD Complex with a Noncanonical RNA Substrate Provides New Insights into Binding Specificity of dsRBDs." Structure, 19, 999-1010. doi: 10.1016/j.str.2011.03.022. |
Solution structure of double-stranded RNA binding domain of s. cerevisiae rnase iii (rnt1p) in complex with aagu tetraloop hairpin. SNAP output |
| 2leb |
RNA binding protein-RNA |
NMR |
Daubner GM, Clery A, Jayne S, Stevenin J, Allain FH |
(2012) "A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well." Embo J., 31, 162-174. doi: 10.1038/emboj.2011.367. |
Solution structure of human srsf2 (sc35) rrm in complex with 5'-uccagu-3'. SNAP output |
| 2lec |
RNA binding protein-RNA |
NMR |
Daubner GM, Clery A, Jayne S, Stevenin J, Allain FH |
(2012) "A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well." Embo J., 31, 162-174. doi: 10.1038/emboj.2011.367. |
Solution structure of human srsf2 (sc35) rrm in complex with 5'-uggagu-3'. SNAP output |
| 2li8 |
transcription-RNA |
NMR |
Loughlin FE, Gebert LF, Towbin H, Brunschweiger A, Hall J, Allain FH |
(2011) "Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28." Nat.Struct.Mol.Biol., 19, 84-89. doi: 10.1038/nsmb.2202. |
The solution structure of the lin28-znf domains bound to aggagau of pre-let-7 mirna. SNAP output |
| 2lup |
RNA binding protein-RNA |
NMR |
Wang Z, Hartman E, Roy K, Chanfreau G, Feigon J |
(2011) "Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs." Structure, 19, 999-1010. doi: 10.1016/j.str.2011.03.022. |
Rdc refined solution structure of double-stranded RNA binding domain of s. cerevisiae rnase iii (rnt1p) in complex with the terminal RNA hairpin of snr47 precursor. SNAP output |
| 2m8d |
RNA binding protein-RNA |
NMR |
Clery A, Sinha R, Anczukow O, Corrionero A, Moursy A, Daubner GM, Valcarcel J, Krainer AR, Allain FH |
(2013) "Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition." Proc.Natl.Acad.Sci.USA, 110, E2802-E2811. doi: 10.1073/pnas.1303445110. |
Structure of srsf1 rrm2 in complex with the RNA 5'-ugaaggac-3'. SNAP output |
| 2mb0 |
splicing-RNA |
NMR |
Moursy A, Allain FH, Clery A |
(2014) "Characterization of the RNA recognition mode of hnRNP G extends its role in SMN2 splicing regulation." Nucleic Acids Res., 42, 6659-6672. doi: 10.1093/nar/gku244. |
Solution structure of hnrnp g rrm in complex with the RNA 5'-aucaaa-3'. SNAP output |
| 2mf0 |
RNA binding protein-RNA |
NMR |
Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH |
(2014) "Structural basis of the non-coding RNA RsmZ acting as a protein sponge." Nature, 509, 588-592. doi: 10.1038/nature13271. |
Structural basis of the non-coding RNA rsmz acting as protein sponge: conformer l of rsmz(1-72)-rsme(dimer) 1to3 complex. SNAP output |
| 2mf1 |
RNA binding protein-RNA |
NMR |
Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FH |
(2014) "Structural basis of the non-coding RNA RsmZ acting as a protein sponge." Nature, 509, 588-592. doi: 10.1038/nature13271. |
Structural basis of the non-coding RNA rsmz acting as protein sponge: conformer r of rsmz(1-72)-rsme(dimer) 1to3 complex. SNAP output |
| 2mfc |
translation-RNA |
NMR |
Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH |
(2014) "Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition." Nucleic Acids Res., 42, 5332-5346. doi: 10.1093/nar/gku141. |
Csr-rsm protein-RNA recognition - a molecular affinity ruler: rsmz(sl1)-rsme(dimer) 2:1 complex. SNAP output |
| 2mfe |
translation-RNA |
NMR |
Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH |
(2014) "Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition." Nucleic Acids Res., 42, 5332-5346. doi: 10.1093/nar/gku141. |
Csr-rsm protein-RNA recognition - a molecular affinity ruler: rsmz(sl2)-rsme(dimer) 2:1 complex. SNAP output |
| 2mff |
translation-RNA |
NMR |
Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH |
(2014) "Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition." Nucleic Acids Res., 42, 5332-5346. doi: 10.1093/nar/gku141. |
Csr-rsm protein-RNA recognition - a molecular affinity ruler: rsmz(sl3)-rsme(dimer) 2:1 complex. SNAP output |
| 2mfg |
translation-RNA |
NMR |
Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH |
(2014) "Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition." Nucleic Acids Res., 42, 5332-5346. doi: 10.1093/nar/gku141. |
Csr-rsm protein-RNA recognition - a molecular affinity ruler: rsmz(sl4)-rsme(dimer) 2:1 complex. SNAP output |
| 2mfh |
translation-RNA |
NMR |
Duss O, Michel E, Diarra Dit Konte N, Schubert M, Allain FH |
(2014) "Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition." Nucleic Acids Res., 42, 5332-5346. doi: 10.1093/nar/gku141. |
Csr-rsm protein-RNA recognition - a molecular affinity ruler: rsmz(36-44)-rsme(dimer) 2:1 complex. SNAP output |
| 2mgz |
RNA binding protein-RNA |
NMR |
Kuwasako K, Takahashi M, Unzai S, Tsuda K, Yoshikawa S, He F, Kobayashi N, Guntert P, Shirouzu M, Ito T, Tanaka A, Yokoyama S, Hagiwara M, Kuroyanagi H, Muto Y |
(2014) "RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing." Nat.Struct.Mol.Biol., 21, 778-786. doi: 10.1038/nsmb.2870. |
Solution structure of rbfox family asd-1 rrm and sup-12 rrm in ternary complex with RNA. SNAP output |
| 2mjh |
RNA binding protein |
NMR |
Daubner GM, Brummer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FH |
(2014) "Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1." Nucleic Acids Res., 42, 8092-8105. doi: 10.1093/nar/gku445. |
Solution structure of the gld-1 RNA-binding domain in complex with RNA. SNAP output |
| 2mki |
translation regulator-RNA |
NMR |
Afroz T, Skrisovska L, Belloc E, Guillen-Boixet J, Mendez R, Allain FH-T |
(2014) "A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins." Genes Dev., 28, 1498-1514. doi: 10.1101/gad.241133.114. |
Solution structure of tandem rrm domains of cytoplasmic polyadenylation element binding protein 4 (cpeb4) in complex with RNA. SNAP output |
| 2mkk |
translation regulator-RNA |
NMR |
Afroz T, Skrisovska L, Belloc E, Guillen-Boixet J, Mendez R, Allain FH-T |
(2014) "A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins." Genes Dev., 28, 1498-1514. doi: 10.1101/gad.241133.114. |
Structural model of tandem rrm domains of cytoplasmic polyadenylation element binding protein 1 (cpeb1) in complex with RNA. SNAP output |
| 2mkn |
RNA binding protein-RNA |
NMR |
Burge RG, Martinez-Yamout MA, Dyson HJ, Wright PE |
(2014) "Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids." Biochemistry, 53, 1495-1510. doi: 10.1021/bi401675h. |
Structural characterization of interactions between the double-stranded RNA-binding zinc finger protein jaz and dsrna. SNAP output |
| 2mqo |
RNA binding protein-RNA |
NMR |
Blatter M, Allain F |
"Structural Investigation of hnRNP L bound to RNA." |
Structural investigation of hnrnp l bound to RNA. SNAP output |
| 2mqp |
RNA binding protein-RNA |
NMR |
Blatter M, Allain F |
"Structural Investigation of hnRNP L bound to RNA." |
Structural investigation of hnrnp l bound to RNA. SNAP output |
| 2mqq |
RNA binding protein-RNA |
NMR |
Blatter M, Allain F |
"Structural Investigation of hnRNP L bound to RNA." |
Structural investigation of hnrnp l bound to RNA. SNAP output |
| 2mqv |
viral protein-RNA |
NMR |
Miller SB, Yildiz FZ, Lo JA, Wang B, D'Souza VM |
(2014) "A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing." Nature, 515, 591-595. doi: 10.1038/nature13709. |
Solution NMR structure of the u5-primer binding site (u5-pbs) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein. SNAP output |
| 2ms0 |
viral protein-RNA |
NMR |
Miller SB, Yildiz FZ, Lo JA, Wang B, D'Souza VM |
(2014) "A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing." Nature, 515, 591-595. doi: 10.1038/nature13709. |
Solution NMR structure pf trnapro:mlv-nucleocapsid (1:2) complex. SNAP output |
| 2ms1 |
viral protein-RNA |
NMR |
Miller SB, Yildiz FZ, Lo JA, Wang B, D'Souza VM |
(2014) "A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing." Nature, 515, 591-595. doi: 10.1038/nature13709. |
Solution NMR structure of trnapro:mlv nucleocapsid protein (1:1) complex. SNAP output |
| 2mtv |
RNA binding protein-RNA |
NMR |
Theler D, Dominguez C, Blatter M, Boudet J, Allain FH |
(2014) "Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA." Nucleic Acids Res., 42, 13911-13919. doi: 10.1093/nar/gku1116. |
Solution structure of the yth domain of yt521-b in complex with n6-methyladenosine containing RNA. SNAP output |
| 2mxy |
RNA binding protein-RNA |
NMR |
Cienikova Z, Damberger FF, Hall J, Allain FH, Maris C |
(2014) "Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif." J.Am.Chem.Soc., 136, 14536-14544. doi: 10.1021/ja507690d. |
Solution structure of hnrnp c rrm in complex with 5'-auuuuuc-3' RNA. SNAP output |
| 2mz1 |
RNA binding protein-RNA |
NMR |
Cienikova Z, Damberger FF, Hall J, Allain FH, Maris C |
(2014) "Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif." J.Am.Chem.Soc., 136, 14536-14544. doi: 10.1021/ja507690d. |
Solution structure of hnrnp c rrm in complex with 5'-uuuuc-3' RNA. SNAP output |
| 2n3o |
RNA binding protein-RNA |
NMR |
Maris C, Jayne SF, Damberger FF, Ravindranathan S, Allain FH-T |
"C-terminal helix folding upon pyrimidine-rich hairpin binding to PTB RRM1. Implications for PTB function in Encephalomyocarditis virus IRES activity." |
Structure of ptb rrm1(41-163) bound to an RNA stemloop containing a structured loop derived from viral internal ribosomal entry site RNA. SNAP output |
| 2n7c |
RNA binding protein-RNA |
NMR |
Ganguly AK, Verma G, Bhavesh NS |
(2019) "The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition." J. Mol. Biol., 431, 498-510. doi: 10.1016/j.jmb.2018.11.020. |
Solution structure of plasmodium falciparum sr1-rrm1 in complex with acauca RNA. SNAP output |
| 2n82 |
RNA binding protein-RNA |
NMR |
Chen Y, Zubovic L, Yang F, Godin K, Pavelitz T, Castellanos J, Macchi P, Varani G |
(2016) "Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer." Nucleic Acids Res., 44, 4381-4395. doi: 10.1093/nar/gkw177. |
Solution structure of the complex of microrna 20b pre-element with rbfox rrm. SNAP output |
| 2n8l |
RNA binding protein-RNA |
NMR |
Nicastro G, Candel AM, Ramos A, Hollingworth D |
"Zipcode-binding-protein-1 KH3KH4(DD) domains in complex with the RNA target GCACACCC." |
Zipcode-binding-protein-1 kh3kh4(dd) domains in complex with the kh3 RNA target. SNAP output |
| 2n8m |
RNA binding protein-RNA |
NMR |
Nicastro G, Ramos A, Candel A, Hollingworth D |
"Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the RNA target UCGGACU." |
Zipcode-binding-protein-1 kh3(dd)kh4 domains in complex with the kh4 RNA target. SNAP output |
| 2noq |
ribosome |
cryo-EM (7.3 Å) |
Schuler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM |
(2006) "Structure of the ribosome-bound cricket paralysis virus IRES RNA." Nat.Struct.Mol.Biol., 13, 1092-1096. doi: 10.1038/nsmb1177. |
Structure of ribosome-bound cricket paralysis virus ires RNA. 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 |
| 2nre |
isomerase-RNA |
X-ray (4.0 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 |
| 2nue |
hydrolase-RNA |
X-ray (2.9 Å) |
Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X |
(2007) "A stepwise model for double-stranded RNA processing by ribonuclease III." Mol.Microbiol., 67, 143-154. doi: 10.1111/j.1365-2958.2007.06032.x. |
Crystal structure of rnase iii from aquifex aeolicus complexed with ds-RNA at 2.9-angstrom resolution. SNAP output |
| 2nuf |
hydrolase-RNA |
X-ray (2.5 Å) |
Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X |
(2007) "A stepwise model for double-stranded RNA processing by ribonuclease III." Mol.Microbiol., 67, 143-154. doi: 10.1111/j.1365-2958.2007.06032.x. |
Crystal structure of rnase iii from aquifex aeolicus complexed with ds-RNA at 2.5-angstrom resolution. SNAP output |
| 2nug |
hydrolase-RNA |
X-ray (1.7 Å) |
Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X |
(2007) "A stepwise model for double-stranded RNA processing by ribonuclease III." Mol.Microbiol., 67, 143-154. doi: 10.1111/j.1365-2958.2007.06032.x. |
Crystal structure of rnase iii from aquifex aeolicus complexed with ds-RNA at 1.7-angstrom resolution. SNAP output |
| 2nz4 |
structural protein-RNA |
X-ray (2.498 Å) |
Cochrane JC, Lipchock SV, Strobel SA |
(2007) "Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor." Chem.Biol., 14, 97-105. doi: 10.1016/j.chembiol.2006.12.005. |
Structural investigation of the glms ribozyme bound to its catalytic cofactor. SNAP output |
| 2ogm |
ribosome |
X-ray (3.5 Å) |
Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A |
(2007) "Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity." Proc.Natl.Acad.Sci.Usa, 104, 4291-4296. doi: 10.1073/pnas.0700041104. |
The crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with the pleuromutilin derivative sb-571519. SNAP output |
| 2oih |
structural protein-RNA |
X-ray (2.4 Å) |
Ke A, Ding F, Batchelor JD, Doudna JA |
(2007) "Structural roles of monovalent cations in the HDV ribozyme." Structure, 15, 281-287. doi: 10.1016/j.str.2007.01.017. |
Hepatitis delta virus gemonic ribozyme precursor with c75u mutation and bound to monovalent cation tl+. SNAP output |
| 2oj3 |
structural protein-RNA |
X-ray (2.9 Å) |
Ke A, Ding F, Batchelor JD, Doudna JA |
(2007) "Structural roles of monovalent cations in the HDV ribozyme." Structure, 15, 281-287. doi: 10.1016/j.str.2007.01.017. |
Hepatitis delta virus ribozyme precursor structure, with c75u mutation, bound to tl+ and cobalt hexammine (co(nh3)63+). SNAP output |
| 2om3 |
virus |
cryo-EM (4.4 Å) |
Sachse C, Chen JZ, Coureux PD, Stroupe ME, Fandrich M, Grigorieff N |
(2007) "High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus." J.Mol.Biol., 371, 812-835. doi: 10.1016/j.jmb.2007.05.088. |
High-resolution cryo-EM structure of tobacco mosaic virus. SNAP output |
| 2om7 |
ribosome |
cryo-EM (7.3 Å) |
Connell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schuler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM |
(2007) "Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors." Mol.Cell, 25, 751-764. doi: 10.1016/j.molcel.2007.01.027. |
Structural basis for interaction of the ribosome with the switch regions of gtp-bound elongation factors. SNAP output |
| 2otj |
ribosome |
X-ray (2.9 Å) |
Schroeder SJ, Blaha G, Tirado-Rives J, Steitz TA, Moore PB |
(2007) "The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole." J.Mol.Biol., 367, 1471-1479. doi: 10.1016/j.jmb.2007.01.081. |
13-deoxytedanolide bound to the large subunit of haloarcula marismortui. SNAP output |
| 2otl |
ribosome |
X-ray (2.7 Å) |
Schroeder SJ, Blaha G, Tirado-Rives J, Steitz TA, Moore PB |
(2007) "The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole." J.Mol.Biol., 367, 1471-1479. doi: 10.1016/j.jmb.2007.01.081. |
Girodazole bound to the large subunit of haloarcula marismortui. SNAP output |
| 2ozb |
RNA binding protein-RNA |
X-ray (2.6 Å) |
Liu S, Li P, Dybkov O, Nottrott S, Hartmuth K, Luhrmann R, Carlomagno T, Wahl MC |
(2007) "Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP." Science, 316, 115-120. doi: 10.1126/science.1137924. |
Structure of a human prp31-15.5k-u4 snrna complex. SNAP output |
| 2pjp |
translation-RNA |
X-ray (2.3 Å) |
Soler N, Fourmy D, Yoshizawa S |
(2007) "Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB." J.Mol.Biol., 370, 728-741. doi: 10.1016/j.jmb.2007.05.001. |
Structure of the mrna-binding domain of elongation factor selb from e.coli in complex with secis RNA. SNAP output |
| 2ply |
translation-RNA |
X-ray (2.6 Å) |
Soler N, Fourmy D, Yoshizawa S |
(2007) "Structural insight into a molecular switch in tandem winged-helix motifs from elongation factor SelB." J.Mol.Biol., 370, 728-741. doi: 10.1016/j.jmb.2007.05.001. |
Structure of the mrna binding fragment of elongation factor selb in complex with secis RNA.. SNAP output |
| 2po1 |
hydrolase-hydrolase-RNA |
X-ray (1.94 Å) |
Navarro MVAS, Oliveira CC, Zanchin NI, Guimaraes BG |
(2008) "Insights into the mechanism of progressive RNA degradation by the archaeal exosome." J.Biol.Chem., 283, 14120-14131. doi: 10.1074/jbc.M801005200. |
Crystal structure of the p. abyssi exosome rnase ph ring complexed with a single stranded 10-mer poly(a) RNA. SNAP output |
| 2pxb |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 2 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxd |
signaling protein-RNA |
X-ray (2.0 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 1 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxe |
signaling protein-RNA |
X-ray (2.0 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 4 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxf |
signaling protein-RNA |
X-ray (2.0 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 5 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxk |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 8 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxl |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 9 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxp |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 13 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxq |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 14 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxt |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 15 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxu |
signaling protein-RNA |
X-ray (2.5 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 16 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2pxv |
signaling protein-RNA |
X-ray (2.0 Å) |
Keel AY, Rambo RP, Batey RT, Kieft JS |
(2007) "A General Strategy to Solve the Phase Problem in RNA Crystallography." Structure, 15, 761-772. doi: 10.1016/j.str.2007.06.003. |
Variant 6 of ribonucleoprotein core of the e. coli signal recognition particle. SNAP output |
| 2py9 |
RNA and DNA binding protein-RNA |
X-ray (2.56 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. |
Protein-RNA interaction involving kh1 domain from human poly(c)-binding protein-2. SNAP output |
| 2q66 |
transferase-RNA |
X-ray (1.8 Å) |
Balbo PB, Bohm A |
(2007) "Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis." Structure, 15, 1117-1131. doi: 10.1016/j.str.2007.07.010. |
Structure of yeast poly(a) polymerase with atp and oligo(a). SNAP output |
| 2qa4 |
ribosome |
X-ray (3.0 Å) |
Kavran JM, Steitz TA |
(2007) "Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: Analysis of L11 movements." J.Mol.Biol., 371, 1047-1059. doi: 10.1016/j.jmb.2007.05.091. |
A more complete structure of the the l7-l12 stalk of the haloarcula marismortui 50s large ribosomal subunit. SNAP output |
| 2qex |
ribosome |
X-ray (2.9 Å) |
Schroeder SJ, Blaha G, Moore PB |
(2007) "Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit." Antimicrob.Agents Chemother., 51, 4462-4465. doi: 10.1128/AAC.00455-07. |
Negamycin binds to the wall of the nascent chain exit tunnel of the 50s ribosomal subunit. SNAP output |
| 2qqp |
virus |
X-ray (3.8 Å) |
Speir JA, Taylor DJ, Natarajan P, Pringle FM, Ball LA, Johnson JE |
(2010) "Evolution in action: N and C termini of subunits in related T = 4 viruses exchange roles as molecular switches." Structure, 18, 700-709. doi: 10.1016/j.str.2010.03.010. |
Crystal structure of authentic providence virus. SNAP output |
| 2qux |
structural protein-RNA |
X-ray (2.44 Å) |
Chao JA, Patskovsky Y, Almo SC, Singer RH |
(2008) "Structural basis for the coevolution of a viral RNA-protein complex." Nat.Struct.Mol.Biol., 15, 103-105. doi: 10.1038/nsmb1327. |
Pp7 coat protein dimer in complex with RNA hairpin. SNAP output |
| 2r7r |
transferase-RNA |
X-ray (2.6 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1-RNA (ugugacc) complex. SNAP output |
| 2r7s |
transferase-RNA |
X-ray (3.24 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1 - RNA (ugugcc) complex. SNAP output |
| 2r7t |
transferase-RNA |
X-ray (3.0 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1-RNA (ugugaacc) complex. SNAP output |
| 2r7u |
transferase-RNA |
X-ray (3.1 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1-RNA (aaaagcc) complex. SNAP output |
| 2r7v |
transferase-RNA |
X-ray (2.8 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1-RNA (ggcuuu) complex. SNAP output |
| 2r7w |
transferase-RNA |
X-ray (2.6 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1-RNA (ugugacc)-mrna 5'-cap (m7gpppg) complex. SNAP output |
| 2r7x |
transferase-RNA |
X-ray (2.8 Å) |
Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC |
(2008) "Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1." Structure, 16, 1678-1688. doi: 10.1016/j.str.2008.09.006. |
Crystal structure of rotavirus sa11 vp1-RNA (ugugacc)-gtp complex. SNAP output |
| 2r8s |
immune system-RNA |
X-ray (1.95 Å) |
Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA |
(2008) "Synthetic antibodies for specific recognition and crystallization of structured RNA." Proc.Natl.Acad.Sci.Usa, 105, 82-87. doi: 10.1073/pnas.0709082105. |
High resolution structure of a specific synthetic fab bound to p4-p6 RNA ribozyme domain. SNAP output |
| 2r92 |
transferase-RNA |
X-ray (3.8 Å) |
Lehmann E, Brueckner F, Cramer P |
(2007) "Molecular basis of RNA-dependent RNA polymerase II activity." Nature, 450, 445-449. doi: 10.1038/nature06290. |
Elongation complex of RNA polymerase ii with artificial rdrp scaffold. SNAP output |
| 2r93 |
transferase-RNA |
X-ray (4.0 Å) |
Lehmann E, Brueckner F, Cramer P |
(2007) "Molecular basis of RNA-dependent RNA polymerase II activity." Nature, 450, 445-449. doi: 10.1038/nature06290. |
Elongation complex of RNA polymerase ii with a hepatitis delta virus-derived RNA stem loop. SNAP output |
| 2rd2 |
ligase-RNA |
X-ray (2.6 Å) |
Bullock TL, Rodriguez-Hernandez A, Corigliano EM, Perona JJ |
(2008) "A rationally engineered misacylating aminoacyl-tRNA synthetase." Proc.Natl.Acad.Sci.Usa, 105, 7428-7433. doi: 10.1073/pnas.0711812105. |
Glutaminyl-trna synthetase mutant c229r with bound analog 5'-o-[n-(l-glutaminyl)-sulfamoyl]adenosine. SNAP output |
| 2re8 |
ligase-RNA |
X-ray (2.6 Å) |
Bullock TL, Rodriguez-Hernandez A, Corigliano EM, Perona JJ |
(2008) "A rationally engineered misacylating aminoacyl-tRNA synthetase." Proc.Natl.Acad.Sci.Usa, 105, 7428-7433. doi: 10.1073/pnas.0711812105. |
Glutaminyl-trna synthetase mutant c229r with bound analog 5'-o-[n-(l-glutamyl)-sulfamoyl]adenosine. SNAP output |
| 2rfk |
isomerase-RNA |
X-ray (2.87 Å) |
Liang B, Xue S, Terns RM, Terns MP, Li H |
(2007) "Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex." Nat.Struct.Mol.Biol., 14, 1189-1195. doi: 10.1038/nsmb1336. |
Substrate RNA positioning in the archaeal h-aca ribonucleoprotein complex. SNAP output |
| 2rkj |
ligase-RNA |
X-ray (4.5 Å) |
Paukstelis PJ, Chen JH, Chase E, Lambowitz AM, Golden BL |
(2008) "Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA." Nature, 451, 94-97. doi: 10.1038/nature06413. |
Cocrystal structure of a tyrosyl-trna synthetase splicing factor with a group i intron RNA. SNAP output |
| 2rqc |
transcription-RNA |
NMR |
Tsuda K, Kuwasako K, Takahashi M, Someya T, Inoue M, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Guntert P, Muto Y, Yokoyama S |
(2009) "Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3." Nucleic Acids Res., 37, 5151-5166. doi: 10.1093/nar/gkp546. |
Solution structure of RNA-binding domain 3 of cugbp1 in complex with RNA (ug)3. SNAP output |
| 2rra |
RNA binding protein-RNA |
NMR |
Tsuda K, Someya T, Kuwasako K, Takahashi M, He F, Unzai S, Inoue M, Harada T, Watanabe S, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Guntert P, Yokoyama S, Muto Y |
(2011) "Structural basis for the dual RNA-recognition modes of human Tra2-beta RRM." Nucleic Acids Res., 39, 1538-1553. doi: 10.1093/nar/gkq854. |
Solution structure of RNA binding domain in human tra2 beta protein in complex with RNA (gaagaa). SNAP output |
| 2rs2 |
RNA binding protein-RNA |
NMR |
Ohyama T, Nagata T, Tsuda K, Kobayashi N, Imai T, Okano H, Yamazaki T, Katahira M |
(2011) "Structure of Musashi1 in a complex with target RNA: the role of aromatic stacking interactions." Nucleic Acids Res. doi: 10.1093/nar/gkr1139. |
1h, 13c, and 15n chemical shift assignments for musashi1 rbd1:r(guagu) complex. SNAP output |
| 2rsk |
membrane protein-RNA |
NMR |
Mashima T, Nishikawa F, Kamatari YO, Fujiwara H, Saimura M, Nagata T, Kodaki T, Nishikawa S, Kuwata K, Katahira M |
(2013) "Anti-prion activity of an RNA aptamer and its structural basis." Nucleic Acids Res., 41, 1355-1362. doi: 10.1093/nar/gks1132. |
RNA aptamer against prion protein in complex with the partial binding peptide. SNAP output |
| 2ru3 |
RNA binding protein-RNA |
NMR |
Kuwasako K, Takahashi M, Unzai S, Tsuda K, Yoshikawa S, He F, Kobayashi N, Guntert P, Shirouzu M, Ito T, Tanaka A, Yokoyama S, Hagiwara M, Kuroyanagi H, Muto Y |
(2014) "RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing." Nat.Struct.Mol.Biol., 21, 778-786. doi: 10.1038/nsmb.2870. |
Solution structure of c.elegans sup-12 rrm in complex with RNA. SNAP output |
| 2ru7 |
membrane protein-RNA |
NMR |
Hayashi T, Oshima H, Mashima T, Nagata T, Katahira M, Kinoshita M |
(2014) "Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition." Nucleic Acids Res. doi: 10.1093/nar/gku382. |
Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein. SNAP output |
| 2tmv |
virus-RNA |
fiber diffraction |
Namba K, Pattanayek R, Stubbs G |
(1989) "Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction." J.Mol.Biol., 208, 307-325. doi: 10.1016/0022-2836(89)90391-4. |
Visualization of protein-nucleic acid interactions in a virus. refined structure of intact tobacco mosaic virus at 2.9 angstroms resolution by x-ray fiber diffraction. SNAP output |
| 2uu9 |
ribosome |
X-ray (3.1 Å) |
Weixlbaumer A, Murphy 4th FV, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V |
(2007) "Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines." Nat. Struct. Mol. Biol., 14, 498-502. doi: 10.1038/nsmb1242. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a valine-asl with cmo5u in position 34 bound to an mrna with a gug-codon in the a-site and paromomycin.. SNAP output |
| 2uua |
ribosome |
X-ray (2.9 Å) |
Weixlbaumer A, Murphy 4th FV, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V |
(2007) "Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines." Nat. Struct. Mol. Biol., 14, 498-502. doi: 10.1038/nsmb1242. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a valine-asl with cmo5u in position 34 bound to an mrna with a guc-codon in the a-site and paromomycin.. SNAP output |
| 2uub |
ribosome |
X-ray (2.8 Å) |
Weixlbaumer A, Murphy FV, Dziergowska A, Malkiewicz A, Vendeix FAP, Agris PF, Ramakrishnan V |
(2007) "Mechanism for Expanding the Decoding Capacity of Transfer Rnas by Modification of Uridines." Nat.Struct.Mol.Biol., 14, 498. doi: 10.1038/NSMB1242. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a valine-asl with cmo5u in position 34 bound to an mrna with a guu-codon in the a-site and paromomycin.. SNAP output |
| 2uuc |
ribosome |
X-ray (3.1 Å) |
Weixlbaumer A, Murphy FV, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V |
(2007) "Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines." Nat. Struct. Mol. Biol., 14, 498-502. doi: 10.1038/nsmb1242. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a valine-asl with cmo5u in position 34 bound to an mrna with a gua-codon in the a-site and paromomycin.. SNAP output |
| 2uwm |
translation |
X-ray (2.31 Å) |
Ose T, Soler N, Rasubala L, Kuroki K, Kohda D, Fourmy D, Yoshizawa S, Maenaka K |
(2007) "Structural Basis for Dynamic Interdomain Movement and RNA Recognition of the Selenocysteine-Specific Elongation Factor Selb." Structure, 15, 577. doi: 10.1016/J.STR.2007.03.007. |
C-terminal domain(wh2-wh4) of elongation factor selb in complex with secis RNA. SNAP output |
| 2uxb |
ribosome |
X-ray (3.1 Å) |
Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V |
(2007) "Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit." RNA, 13, 817-823. doi: 10.1261/rna.367307. |
Crystal structure of an extended trna anticodon stem loop in complex with its cognate mrna gggu in the context of the thermus thermophilus 30s subunit.. SNAP output |
| 2uxc |
ribosome |
X-ray (2.9 Å) |
Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V |
(2007) "Structures of Trnas with an Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit." RNA, 13, 817. doi: 10.1261/RNA.367307. |
Crystal structure of an extended trna anticodon stem loop in complex with its cognate mrna ucgu in the context of the thermus thermophilus 30s subunit.. SNAP output |
| 2uxd |
ribosome |
X-ray (3.2 Å) |
Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V |
(2007) "Structures of Trnas with an Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit." RNA, 13, 817. doi: 10.1261/RNA.367307. |
Crystal structure of an extended trna anticodon stem loop in complex with its cognate mrna cggg in the context of the thermus thermophilus 30s subunit.. SNAP output |
| 2v0g |
ligase |
X-ray (3.5 Å) |
Rock F, Mao W, Yaremchuk A, Tukalo M, Crepin T, Zhou H, Zhang Y, Hernandez V, Akama T, Baker S, Plattner J, Shapiro L, Martinis SA, Benkovic SJ, Cusack S, Alley MRK |
(2007) "An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site." Science, 316, 1759. doi: 10.1126/SCIENCE.1142189. |
Leucyl-trna synthetase from thermus thermophilus complexed with a trna(leu) transcript with 5-fluoro-1,3-dihydro-1-hydroxy-2,1- benzoxaborole (an2690) forming an adduct to the ribose of adenosine- 76 in the enzyme editing site.. SNAP output |
| 2v3c |
signaling protein |
X-ray (2.5 Å) |
Hainzl T, Huang S, Sauer-Eriksson AE |
(2007) "Interaction of Signal-Recognition Particle 54 Gtpase Domain and Signal-Recognition Particle RNA in the Free Signal-Recognition Particle." Proc.Natl.Acad.Sci.USA, 104, 14911. doi: 10.1073/PNAS.0702467104. |
Crystal structure of the srp54-srp19-7s.s srp RNA complex of m. jannaschii. SNAP output |
| 2vnu |
hydrolase-RNA |
X-ray (2.3 Å) |
Lorentzen E, Basquin J, Tomecki R, Dziembowski A, Conti E |
(2008) "Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the Rnase II Nuclease Family." Mol.Cell, 29, 717. doi: 10.1016/J.MOLCEL.2008.02.018. |
Crystal structure of sc rrp44. SNAP output |
| 2vod |
RNA binding protein |
X-ray (2.1 Å) |
Kotik-Kogan O, Valentine ER, Sanfelice D, Conte MR, Curry S |
(2008) "Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3' Ends by the Human La Protein." Structure, 16, 852. doi: 10.1016/J.STR.2008.02.021. |
Crystal structure of n-terminal domains of human la protein complexed with RNA oligomer auauuuu. SNAP output |
| 2von |
RNA binding protein |
X-ray (2.1 Å) |
Kotik-Kogan O, Valentine ER, Sanfelice D, Conte MR, Curry S |
(2008) "Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3' Ends by the Human La Protein." Structure, 16, 852. doi: 10.1016/J.STR.2008.02.021. |
Crystal structure of n-terminal domains of human la protein complexed with RNA oligomer auaauuu. SNAP output |
| 2voo |
RNA binding protein |
X-ray (1.8 Å) |
Kotik-Kogan O, Valentine ER, Sanfelice D, Conte MR, Curry S |
(2008) "Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3' Ends by the Human La Protein." Structure, 16, 852. doi: 10.1016/J.STR.2008.02.021. |
Crystal structure of n-terminal domains of human la protein complexed with RNA oligomer uuuuuuuu. SNAP output |
| 2vop |
RNA binding protein |
X-ray (2.8 Å) |
Kotik-Kogan O, Valentine ER, Sanfelice D, Conte MR, Curry S |
(2008) "Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3' Ends by the Human La Protein." Structure, 16, 852. doi: 10.1016/J.STR.2008.02.021. |
Crystal structure of n-terminal domains of human la protein complexed with RNA oligomer auuuu. SNAP output |
| 2vpl |
translation |
X-ray (2.3 Å) |
Tishchenko S, Kljashtorny V, Kostareva O, Nevskaya N, Nikulin A, Gulak P, Piendl W, Garber M, Nikonov S |
(2008) "Domain II of Thermus thermophilus ribosomal protein L1 hinders recognition of its mRNA." J. Mol. Biol., 383, 301-305. doi: 10.1016/j.jmb.2008.08.058. |
The structure of the complex between the first domain of l1 protein from thermus thermophilus and mrna from methanococcus jannaschii. SNAP output |
| 2vqe |
ribosome |
X-ray (2.5 Å) |
Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, Takai K, Watanabe K, Ramakrishnan V, Suzuki T |
(2008) "Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding." J.Biol.Chem., 283, 18801. doi: 10.1074/JBC.M800233200. |
Modified uridines with c5-methylene substituents at the first position of the trna anticodon stabilize u-g wobble pairing during decoding. SNAP output |
| 2vqf |
ribosome |
X-ray (2.9 Å) |
Kurata S, Weixlbaumer A, Ohtsuki T, Shimazaki T, Wada T, Kirino Y, Takai K, Watanabe K, Ramakrishnan V, Suzuki T |
(2008) "Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding." J.Biol.Chem., 283, 18801. doi: 10.1074/JBC.M800233200. |
Modified uridines with c5-methylene substituents at the first position of the trna anticodon stabilize u-g wobble pairing during decoding. SNAP output |
| 2vrt |
hydrolase |
X-ray (3.5 Å) |
Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, Luisi BF |
(2008) "The Crystal Structure of the Escherichia Coli Rnase E Apoprotein and a Mechanism for RNA Degradation." Structure, 16, 1238. doi: 10.1016/J.STR.2008.04.017. |
Crystal structure of e. coli rnase e possessing m1 RNA fragments - catalytic domain. SNAP output |
| 2w2h |
RNA binding protein |
X-ray (3.25 Å) |
Anand K, Schulte A, Vogel-Bachmayr K, Scheffzek K, Geyer M |
(2008) "Structural Insights Into the Cyclin T1-Tat-Tar RNA Transcription Activation Complex from Eiav." Nat.Struct.Mol.Biol., 15, 1287. doi: 10.1038/NSMB.1513. |
Structural basis of transcription activation by the cyclin t1-tat-tar RNA complex from eiav. SNAP output |
| 2wj8 |
RNA binding protein-RNA |
X-ray (3.29 Å) |
Tawar RG, Duquerroy S, Vonrhein C, Varela PF, Damier-Piolle L, Castagne N, Maclellan K, Bedouelle H, Bricogne G, Bhella D, Eleouet J, Rey FA |
(2009) "Crystal Structure of a Nucleocapsid-Like Nucleoprotein-RNA Complex of Respiratory Syncytial Virus." Science, 326, 1279. doi: 10.1126/SCIENCE.1177634. |
Respiratory syncitial virus ribonucleoprotein. SNAP output |
| 2ww9 |
ribosome |
cryo-EM (8.6 Å) |
Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon E, Beckmann R |
(2009) "Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome." Science, 326, 1369. doi: 10.1126/SCIENCE.1178535. |
cryo-EM structure of the active yeast ssh1 complex bound to the yeast 80s ribosome. SNAP output |
| 2wwa |
ribosome |
cryo-EM (8.9 Å) |
Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon E, Beckmann R |
(2009) "Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome." Science, 326, 1369. doi: 10.1126/SCIENCE.1178535. |
cryo-EM structure of idle yeast ssh1 complex bound to the yeast 80s ribosome. SNAP output |
| 2wwb |
ribosome |
cryo-EM (6.48 Å) |
Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon E, Beckmann R |
(2009) "Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome." Science, 326, 1369. doi: 10.1126/SCIENCE.1178535. |
cryo-EM structure of the mammalian sec61 complex bound to the actively translating wheat germ 80s ribosome. SNAP output |
| 2wyy |
virus |
cryo-EM (10.0 Å) |
Ge P, Tsao J, Schein S, Green TJ, Luo M, Zhou ZH |
(2010) "Cryo-Em Model of the Bullet-Shaped Vesicular Stomatitis Virus." Science, 327, 689. doi: 10.1126/SCIENCE.1181766. |
Cryoem model of the vesicular stomatitis virus. 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 |
| 2x1f |
transcription-RNA |
X-ray (1.6 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 bound RNA (gu). SNAP output |
| 2x7n |
ribosomal protein-RNA |
cryo-EM (11.8 Å) |
Gartmann M, Blau M, Armache J-P, Mielke T, Topf M, Beckmann R |
(2010) "Mechanism of Eif6-Mediated Inhibition of Ribosomal Subunit Joining." J.Biol.Chem., 285, 14848. doi: 10.1074/JBC.C109.096057. |
Mechanism of eif6s anti-association activity. SNAP output |
| 2xb2 |
hydrolase |
X-ray (3.4 Å) |
Buchwald G, Ebert J, Basquin C, Sauliere J, Jayachandran U, Bono F, Le Hir H, Conti E |
(2010) "Insights Into the Recruitment of the Nmd Machinery from the Crystal Structure of a Core Ejc-Upf3B Complex." Proc.Natl.Acad.Sci.USA, 107, 10050. doi: 10.1073/PNAS.1000993107. |
Crystal structure of the core mago-y14-eif4aiii-barentsz-upf3b assembly shows how the ejc is bridged to the nmd machinery. SNAP output |
| 2xbm |
RNA binding protein |
X-ray (2.9 Å) |
Yap LJ, Luo DH, Chung KY, Lim SP, Bodenreider C, Noble C, Shi PY, Lescar J |
(2010) "Crystal Structure of the Dengue Virus Methyltransferase Bound to a 5'-Capped Octameric RNA." Plos One, 5, 12836. doi: 10.1371/JOURNAL.PONE.0012836. |
Crystal structure of the dengue virus methyltransferase bound to a 5'- capped octameric RNA. SNAP output |
| 2xc7 |
RNA binding protein |
NMR |
Mourao A, Varrot A, Mackereth CD, Cusack S, Sattler M |
(2010) "Structure and RNA Recognition by the Snrna and Snorna Transport Factor Phax." RNA, 16, 1205. doi: 10.1261/RNA.2009910. |
Solution structure of phax-rbd in complex with ssrna. SNAP output |
| 2xd0 |
toxin-RNA |
X-ray (3.0 Å) |
Blower TR, Pei XY, Short FL, Fineran PC, Humphreys DP, Luisi BF, Salmond GP |
(2011) "A processed noncoding RNA regulates an altruistic bacterial antiviral system." Nat. Struct. Mol. Biol., 18, 185-190. doi: 10.1038/nsmb.1981. |
A processed non-coding RNA regulates a bacterial antiviral system. SNAP output |
| 2xdb |
toxin-RNA |
X-ray (2.55 Å) |
Blower TR, Pei XY, Short FL, Fineran PC, Humphreys DP, Luisi BF, Salmond GPC |
(2011) "A Processed Noncoding RNA Regulates an Altruistic Bacterial Antiviral System." Nat.Struct.Mol.Biol., 18, 185. doi: 10.1038/NSMB.1981. |
A processed non-coding RNA regulates a bacterial antiviral system. SNAP output |
| 2xdd |
toxin-RNA |
X-ray (3.2 Å) |
Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GPC |
(2009) "The Phage Abortive Infection System, Toxin, Functions as a Protein-RNA Toxin-Antitoxin Pair." Proc.Natl.Acad.Sci.USA, 106, 894. doi: 10.1073/PNAS.0808832106. |
A processed non-coding RNA regulates a bacterial antiviral system. SNAP output |
| 2xea |
virus |
cryo-EM (4.6 Å) |
Clare DK, Orlova EV |
(2010) "4.6 A Cryo-Em Reconstruction of Tobacco Mosaic Virus from Images Recorded at 300 Kev on a 4Kx4K Ccd Camera." J.Struct.Biol., 171, 303. doi: 10.1016/J.JSB.2010.06.011. |
4.6 angstrom cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 kev on a 4kx4k ccd camera. SNAP output |
| 2xfm |
RNA-protein |
NMR |
Simon B, Kirkpatrick JP, Eckhardt S, Reuter M, Rocha EA, Andrade-Navarro MA, Sehr P, Pillai RS, Carlomagno T |
(2011) "Recognition of 2'-O-Methylated 3'-End of Pirna by the Paz Domain of a Piwi Protein." Structure, 19, 172. doi: 10.1016/J.STR.2010.11.015. |
Complex structure of the miwi paz domain bound to methylated single stranded RNA. SNAP output |
| 2xgj |
hydrolase-RNA |
X-ray (2.9 Å) |
Weir JR, Bonneau F, Hentschel J, Conti E |
(2010) "Structural Analysis Reveals the Characteristic Features of Mtr4, a Dexh Helicase Involved in Nuclear RNA Processing and Surveillance." Proc.Natl.Acad.Sci.USA, 107, 12139. doi: 10.1073/PNAS.1004953107. |
Structure of mtr4, a dexh helicase involved in nuclear RNA processing and surveillance. SNAP output |
| 2xkv |
protein transport |
cryo-EM (13.5 Å) |
Estrozi LF, Boehringer D, Shan S-O, Ban N, Schaffitzel C |
(2011) "Cryo-Em Structure of the E. Coli Translating Ribosome in Complex with Srp and its Receptor." Nat.Struct.Mol.Biol., 18, 88. doi: 10.1038/NSMB.1952. |
Atomic model of the srp-ftsy early conformation. 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 |
| 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 |
| 2xpj |
virus |
X-ray (3.4 Å) |
Sagurthi SR, Rajaram V, Savithri HS, Murthy MRN |
"Crystal Structure of Natural Bottom Component of Phmv." |
Crystal structure of physalis mottle virus with intact ordered RNA. SNAP output |
| 2xs2 |
RNA binding protein-RNA |
X-ray (1.35 Å) |
Jenkins HT, Malkova B, Edwards TA |
(2011) "Kinked beta-strands mediate high-affinity recognition of mRNA targets by the germ-cell regulator DAZL." Proc. Natl. Acad. Sci. U.S.A., 108, 18266-18271. doi: 10.1073/pnas.1105211108. |
Crystal structure of the rrm domain of mouse deleted in azoospermia-like in complex with RNA, uuguucuu. SNAP output |
| 2xs5 |
RNA binding protein-RNA |
X-ray (1.6 Å) |
Jenkins HT, Edwards TA |
(2011) "Kinked Beta-Strands Mediate High-Affinity Recognition of Mrna Targets by the Germ-Cell Regulator Dazl." Proc.Natl.Acad.Sci.USA, 108, 18266. doi: 10.1073/PNAS.1105211108. |
Crystal structure of the rrm domain of mouse deleted in azoospermia- like in complex with mvh RNA, uguuc. SNAP output |
| 2xs7 |
RNA binding protein-RNA |
X-ray (1.45 Å) |
Jenkins HT, Edwards TA |
(2011) "Kinked Beta-Strands Mediate High-Affinity Recognition of Mrna Targets by the Germ-Cell Regulator Dazl." Proc.Natl.Acad.Sci.USA, 108, 18266. doi: 10.1073/PNAS.1105211108. |
Crystal structure of the rrm domain of mouse deleted in azoospermia- like in complex with sycp3 RNA, uuguuu. SNAP output |
| 2xxa |
protein transport |
X-ray (3.94 Å) |
Ataide SF, Schmitz N, Shen K, Ke A, Shan S, Doudna JA, Ban N |
(2011) "The Crystal Structure of the Signal Recognition Particle in Complex with its Receptor." Science, 331, 881. doi: 10.1126/SCIENCE.1196473. |
The crystal structure of the signal recognition particle (srp) in complex with its receptor(sr). SNAP output |
| 2xzl |
hydrolase-RNA |
X-ray (2.4 Å) |
Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E |
(2011) "Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2." Mol.Cell, 41, 693. doi: 10.1016/J.MOLCEL.2011.02.010. |
Upf1-RNA complex. SNAP output |
| 2xzo |
hydrolase-RNA |
X-ray (2.395 Å) |
Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E |
(2011) "Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2." Mol.Cell, 41, 693. doi: 10.1016/J.MOLCEL.2011.02.010. |
Upf1 helicase - RNA complex. SNAP output |
| 2y8w |
hydrolase-RNA |
X-ray (1.8 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 of crispr endoribonuclease cse3 bound to 20 nt RNA. SNAP output |
| 2y8y |
hydrolase-RNA |
X-ray (1.44 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 b of crispr endoribonuclease cse3 bound to 19 nt RNA. 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 |
| 2yh1 |
transcription |
NMR |
Mackereth CD, Madl T, Bonnal S, Simon B, Zanier K, Gasch A, Rybin V, Valcarcel J, Sattler M |
(2011) "Multi-Domain Conformational Selection Underlies Pre-Mrna Splicing Regulation by U2Af." Nature, 475, 408. doi: 10.1038/NATURE10171. |
Model of human u2af65 tandem rrm1 and rrm2 domains with eight-site uridine binding. SNAP output |
| 2yhm |
viral protein-RNA |
X-ray (3.6 Å) |
El Omari K, Dhaliwal B, Ren J, Abrescia NGA, Lockyer M, Powell KL, Hawkins AR, Stammers DK |
(2011) "Structures of Respiratory Syncytial Virus Nucleocapsid Protein from Two Crystal Forms: Details of Potential Packing Interactions in the Native Helical Form." Acta Crystallogr.,Sect.F, 67, 1179. doi: 10.1107/S1744309111029228. |
Structure of respiratory syncytial virus nucleocapsid protein, p212121 crystal form. SNAP output |
| 2yjy |
RNA binding protein-RNA |
X-ray (2.598 Å) |
Dong S, Wang Y, Cassidy-Amstutz C, Lu G, Bigler R, Jezyk MR, Li C, Hall TM, Wang Z |
(2011) "Specific and Modular Binding Code for Cytosine Recognition in Pumilio/Fbf (Puf) RNA-Binding Domains." J.Biol.Chem., 286, 26732. doi: 10.1074/JBC.M111.244889. |
A specific and modular binding code for cytosine recognition in puf domains. SNAP output |
| 2ykg |
hydrolase |
X-ray (2.5 Å) |
Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM |
(2011) "Structural Insights Into RNA Recognition by Rig-I." Cell(Cambridge,Mass.), 147, 409. doi: 10.1016/J.CELL.2011.09.023. |
Structural insights into RNA recognition by rig-i. SNAP output |
| 2ykr |
ribosome-hydrolase |
cryo-EM (9.8 Å) |
Guo Q, Yuan Y, Xu Y, Feng B, Liu L, Chen K, Sun M, Yang Z, Lei J, Gao N |
(2011) "Structural Basis for the Function of a Small Gtpase Rsga on the 30S Ribosomal Subunit Maturation Revealed by Cryoelectron Microscopy." Proc.Natl.Acad.Sci.USA, 108, 13100. doi: 10.1073/PNAS.1104645108. |
30s ribosomal subunit with rsga bound in the presence of gmppnp. SNAP output |
| 2zh1 |
transferase-RNA |
X-ray (2.8 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminida. SNAP output |
| 2zh2 |
transferase-RNA |
X-ray (2.66 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidac. SNAP output |
| 2zh3 |
transferase-RNA |
X-ray (2.5 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidca. SNAP output |
| 2zh4 |
transferase-RNA |
X-ray (2.65 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidcg. SNAP output |
| 2zh5 |
transferase-RNA |
X-ray (2.6 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidcu. SNAP output |
| 2zh6 |
transferase-RNA |
X-ray (2.5 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidcu and atp. SNAP output |
| 2zh7 |
transferase-RNA |
X-ray (3.0 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidg. SNAP output |
| 2zh8 |
transferase-RNA |
X-ray (2.65 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidgc. SNAP output |
| 2zh9 |
transferase-RNA |
X-ray (2.9 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidu. SNAP output |
| 2zha |
transferase-RNA |
X-ray (2.95 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminidu and ctp. SNAP output |
| 2zhb |
transferase-RNA |
X-ray (3.05 Å) |
Toh Y, Numata T, Watanabe K, Takeshita D, Nureki O, Tomita K |
(2008) "Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme." Embo J., 27, 1944-1952. doi: 10.1038/emboj.2008.124. |
Complex structure of afcca with trnaminiduc. SNAP output |
| 2zi0 |
gene regulation-RNA |
X-ray (2.82 Å) |
Chen H-Y, Yang J, Lin C, Yuan YA |
(2008) "Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b." Embo Rep., 9, 754-760. doi: 10.1038/embor.2008.118. |
Crystal structure of tav2b-sirna complex. SNAP output |
| 2zjp |
ribosome-antibiotic |
X-ray (3.7 Å) |
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P |
(2008) "Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin." Mol.Cell, 30, 26. doi: 10.1016/J.MOLCEL.2008.01.009. |
Thiopeptide antibiotic nosiheptide bound to the large ribosomal subunit of deinococcus radiodurans. SNAP output |
| 2zjq |
ribosome |
X-ray (3.3 Å) |
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P |
(2008) "Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin." Mol.Cell, 30, 26-38. doi: 10.1016/j.molcel.2008.01.009. |
Interaction of l7 with l11 induced by microccocin binding to the deinococcus radiodurans 50s subunit. SNAP output |
| 2zjr |
ribosome |
X-ray (2.91 Å) |
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P |
(2008) "Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin." Mol.Cell, 30, 26-38. doi: 10.1016/j.molcel.2008.01.009. |
Refined native structure of the large ribosomal subunit (50s) from deinococcus radiodurans. SNAP output |
| 2zko |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Cheng A, Wong SM, Yuan YA |
(2009) "Structural basis for dsRNA recognition by NS1 protein of influenza A virus." Cell Res., 19, 187-195. doi: 10.1038/cr.2008.288. |
Structural basis for dsrna recognition by ns1 protein of human influenza virus a. SNAP output |
| 2zm5 |
transferase-RNA |
X-ray (2.55 Å) |
Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I |
(2009) "Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon." Biochemistry, 48, 5057-5065. doi: 10.1021/bi900337d. |
Crystal structure of trna modification enzyme miaa in the complex with trna(phe). SNAP output |
| 2zm6 |
ribosome |
X-ray (3.3 Å) |
Kaminishi T, Wang H, Kawazoe M, Ishii R, Hanawa-Suetsugu K, Nomura M, Takemoto C, Shirouzu M, Paola F, Yokoyama S |
"Crystal structure of the Thermus thermophilus 30S ribosomal subunit." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit. SNAP output |
| 2zni |
ligase-RNA |
X-ray (3.1 Å) |
Nozawa K, O'Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Soll D, Nureki O |
(2009) "Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality." Nature, 457, 1163-1167. doi: 10.1038/nature07611. |
Crystal structure of pyrrolysyl-trna synthetase-trna(pyl) complex from desulfitobacterium hafniense. SNAP output |
| 2zue |
ligase-RNA |
X-ray (2.0 Å) |
Konno M, Sumida T, Uchikawa E, Mori Y, Yanagisawa T, Sekine S, Yokoyama S |
(2009) "Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)." Febs J., 276, 4763-4779. doi: 10.1111/j.1742-4658.2009.07178.x. |
Crystal structure of pyrococcus horikoshii arginyl-trna synthetase complexed with trna(arg) and an atp analog (anp). SNAP output |
| 2zuf |
ligase-RNA |
X-ray (2.3 Å) |
Konno M, Sumida T, Uchikawa E, Mori Y, Yanagisawa T, Sekine S, Yokoyama S |
(2009) "Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)." Febs J., 276, 4763-4779. doi: 10.1111/j.1742-4658.2009.07178.x. |
Crystal structure of pyrococcus horikoshii arginyl-trna synthetase complexed with trna(arg). SNAP output |
| 2zxu |
transferase-RNA |
X-ray (2.75 Å) |
Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I |
(2009) "Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon." Biochemistry, 48, 5057-5065. doi: 10.1021/bi900337d. |
Crystal structure of trna modification enzyme miaa in the complex with trna(phe) and dmaspp. SNAP output |
| 2zzm |
transferase-RNA |
X-ray (2.65 Å) |
Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S |
(2009) "Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation." Nat.Struct.Mol.Biol., 16, 1109-1115. doi: 10.1038/nsmb.1653. |
The complex structure of atrm5 and trnaleu. SNAP output |
| 2zzn |
transferase-RNA |
X-ray (2.95 Å) |
Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S |
(2009) "Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation." Nat.Struct.Mol.Biol., 16, 1109-1115. doi: 10.1038/nsmb.1653. |
The complex structure of atrm5 and trnacys. SNAP output |
| 3a2k |
ligase-RNA |
X-ray (3.65 Å) |
Nakanishi K, Bonnefond L, Kimura S, Suzuki T, Ishitani R, Nureki O |
(2009) "Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase." Nature, 461, 1144-1148. doi: 10.1038/nature08474. |
Crystal structure of tils complexed with trna. SNAP output |
| 3a6p |
protein transport-nuclear protein-RNA |
X-ray (2.92 Å) |
Okada C, Yamashita E, Lee SJ, Shibata S, Katahira J, Nakagawa A, Yoneda Y, Tsukihara T |
(2009) "A high-resolution structure of the pre-microRNA nuclear export machinery." Science, 326, 1275-1279. doi: 10.1126/science.1178705. |
Crystal structure of exportin-5:rangtp:pre-mirna complex. SNAP output |
| 3adb |
transferase-RNA |
X-ray (2.8 Å) |
Chiba S, Itoh Y, Sekine S, Yokoyama S |
(2010) "Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine." Mol.Cell, 39, 410-420. doi: 10.1016/j.molcel.2010.07.018. |
Crystal structure of o-phosphoseryl-trna kinase complexed with selenocysteine trna and amppnp (crystal type 1). SNAP output |
| 3adc |
transferase-RNA |
X-ray (2.9 Å) |
Chiba S, Itoh Y, Sekine S, Yokoyama S |
(2010) "Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine." Mol.Cell, 39, 410-420. doi: 10.1016/j.molcel.2010.07.018. |
Crystal structure of o-phosphoseryl-trna kinase complexed with selenocysteine trna and amppnp (crystal type 2). SNAP output |
| 3add |
transferase-RNA |
X-ray (2.4 Å) |
Chiba S, Itoh Y, Sekine S, Yokoyama S |
(2010) "Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine." Mol.Cell, 39, 410-420. doi: 10.1016/j.molcel.2010.07.018. |
Crystal structure of o-phosphoseryl-trna kinase complexed with selenocysteine trna and amppnp (crystal type 3). SNAP output |
| 3adi |
gene regulation-RNA |
X-ray (3.2 Å) |
Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA |
(2010) "Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing." Structure, 18, 594-605. doi: 10.1016/j.str.2010.02.006. |
Structure of arabidopsis hyl1 and its molecular implications for mirna processing. SNAP output |
| 3adl |
gene regulation-RNA |
X-ray (2.2 Å) |
Yang SW, Chen HY, Yang J, Machida S, Chua NH, Yuan YA |
(2010) "Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing." Structure, 18, 594-605. doi: 10.1016/j.str.2010.02.006. |
Structure of trbp2 and its molecule implications for mirna processing. SNAP output |
| 3aev |
translation-RNA binding protein-RNA |
X-ray (2.8 Å) |
Jia MZ, Horita S, Nagata K, Tanokura M |
(2010) "An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA." J.Mol.Biol., 398, 774-785. doi: 10.1016/j.jmb.2010.03.055. |
Crystal structure of a-eif2alpha-adim2p-rrna complex from pyrococcus horikoshii ot3. SNAP output |
| 3af6 |
hydrolase-RNA |
X-ray (2.6 Å) |
Nishida Y, Ishikawa H, Baba S, Nakagawa N, Kuramitsu S, Masui R |
(2010) "Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii." Proteins, 78, 2395-2398. doi: 10.1002/prot.22748. |
The crystal structure of an archaeal cpsf subunit, ph1404 from pyrococcus horikoshii complexed with RNA-analog. SNAP output |
| 3agv |
immune system-RNA |
X-ray (2.15 Å) |
Nomura Y, Sugiyama S, Sakamoto T, Miyakawa S, Adachi H, Takano K, Murakami S, Inoue T, Mori Y, Nakamura Y, Matsumura H |
(2010) "Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex." Nucleic Acids Res., 38, 7822-7829. doi: 10.1093/nar/gkq615. |
Crystal structure of a human igg-aptamer complex. SNAP output |
| 3ahu |
translation-RNA |
X-ray (2.2 Å) |
Someya T, Baba S, Fujimoto M, Kumasaka T, Kawai G, Nakamura K |
"Crystal structure of YmaH (Hfq) from Bacillus subtilis in complex with an RNA aptamer." |
Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer.. SNAP output |
| 3akz |
ligase-RNA |
X-ray (2.9 Å) |
Ito T, Yokoyama S |
(2010) "Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions." Nature, 467, 612-616. doi: 10.1038/nature09411. |
Crystal structure of thermotoga maritima nondiscriminating glutamyl-trna synthetase in complex with trnagln and a glutamyl-amp analog. SNAP output |
| 3al0 |
ligase-RNA |
X-ray (3.368 Å) |
Ito T, Yokoyama S |
(2010) "Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions." Nature, 467, 612-616. doi: 10.1038/nature09411. |
Crystal structure of the glutamine transamidosome from thermotoga maritima in the glutamylation state.. SNAP output |
| 3am1 |
transferase-RNA |
X-ray (2.4 Å) |
Sherrer RL, Araiso Y, Aldag C, Ishitani R, Ho JML, Soll D, Nureki O |
(2011) "C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec)." Nucleic Acids Res., 39, 1034-1041. doi: 10.1093/nar/gkq845. |
Crystal structure of o-phosphoseryl-trna kinase complexed with anticodon-stem-loop truncated trna(sec). SNAP output |
| 3amt |
RNA binding protein-RNA |
X-ray (2.9 Å) |
Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T |
(2011) "Structural basis of tRNA agmatinylation essential for AUA codon decoding." Nat.Struct.Mol.Biol., 18, 1275-1280. doi: 10.1038/nsmb.2144. |
Crystal structure of the tias-trna(ile2)-atp complex. SNAP output |
| 3amu |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T |
(2011) "Structural basis of tRNA agmatinylation essential for AUA codon decoding." Nat.Struct.Mol.Biol., 18, 1275-1280. doi: 10.1038/nsmb.2144. |
Crystal structure of the tias-trna(ile2)-ampcpp-agmatine complex. SNAP output |
| 3avt |
translation, transferase-RNA |
X-ray (2.607 Å) |
Takeshita D, Tomita K |
(2012) "Molecular basis for RNA polymerization by Q beta replicase." Nat.Struct.Mol.Biol., 19, 229-237. doi: 10.1038/nsmb.2204. |
Structure of viral RNA polymerase complex 1. SNAP output |
| 3avu |
translation, transferase-RNA |
X-ray (2.907 Å) |
Takeshita D, Tomita K |
(2012) "Molecular basis for RNA polymerization by Q beta replicase." Nat.Struct.Mol.Biol., 19, 229-237. doi: 10.1038/nsmb.2204. |
Structure of viral RNA polymerase complex 2. SNAP output |
| 3avv |
translation, transferase-RNA |
X-ray (3.119 Å) |
Takeshita D, Tomita K |
(2012) "Molecular basis for RNA polymerization by Q beta replicase." Nat.Struct.Mol.Biol., 19, 229-237. doi: 10.1038/nsmb.2204. |
Structure of viral RNA polymerase complex 3. SNAP output |
| 3avw |
translation, transferase-RNA |
X-ray (2.602 Å) |
Takeshita D, Tomita K |
(2012) "Molecular basis for RNA polymerization by Q beta replicase." Nat.Struct.Mol.Biol., 19, 229-237. doi: 10.1038/nsmb.2204. |
Structure of viral RNA polymerase complex 4. SNAP output |
| 3avx |
translation, transferase-RNA |
X-ray (2.406 Å) |
Takeshita D, Tomita K |
(2012) "Molecular basis for RNA polymerization by Q beta replicase." Nat.Struct.Mol.Biol., 19, 229-237. doi: 10.1038/nsmb.2204. |
Structure of viral RNA polymerase complex 5. SNAP output |
| 3avy |
translation, transferase-RNA |
X-ray (2.616 Å) |
Takeshita D, Tomita K |
(2012) "Molecular basis for RNA polymerization by Q beta replicase." Nat.Struct.Mol.Biol., 19, 229-237. doi: 10.1038/nsmb.2204. |
Structure of viral RNA polymerase complex 6. SNAP output |
| 3b0u |
oxidoreductase-RNA |
X-ray (1.948 Å) |
Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I |
(2011) "Molecular basis of dihydrouridine formation on tRNA." Proc.Natl.Acad.Sci.USA, 108, 19593-19598. doi: 10.1073/pnas.1112352108. |
Trna-dihydrouridine synthase from thermus thermophilus in complex with trna fragment. SNAP output |
| 3b0v |
oxidoreductase-RNA |
X-ray (3.51 Å) |
Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I |
(2011) "Molecular basis of dihydrouridine formation on tRNA." Proc.Natl.Acad.Sci.USA, 108, 19593-19598. doi: 10.1073/pnas.1112352108. |
Trna-dihydrouridine synthase from thermus thermophilus in complex with trna. SNAP output |
| 3bo0 |
ribosome |
cryo-EM (9.6 Å) |
Menetret JF, Schaletzky J, Clemons WM, Osborne AR, Skanland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW |
(2007) "Ribosome binding of a single copy of the SecY complex: implications for protein translocation." Mol.Cell, 28, 1083-1092. doi: 10.1016/j.molcel.2007.10.034. |
Ribosome-secy complex. SNAP output |
| 3bo1 |
ribosome |
cryo-EM (9.6 Å) |
Menetret JF, Schaletzky J, Clemons WM, Osborne AR, Skanland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW |
(2007) "Ribosome binding of a single copy of the SecY complex: implications for protein translocation." Mol.Cell, 28, 1083-1092. doi: 10.1016/j.molcel.2007.10.034. |
Ribosome-secy complex. SNAP output |
| 3bo2 |
nuclear protein-RNA |
X-ray (3.31 Å) |
Lipchock SV, Strobel SA |
(2008) "A relaxed active site after exon ligation by the group I intron." Proc.Natl.Acad.Sci.Usa, 105, 5699-5704. doi: 10.1073/pnas.0712016105. |
A relaxed active site following exon ligation by a group i intron. SNAP output |
| 3bo3 |
nuclear protein-RNA |
X-ray (3.4 Å) |
Lipchock SV, Strobel SA |
(2008) "A relaxed active site after exon ligation by the group I intron." Proc.Natl.Acad.Sci.Usa, 105, 5699-5704. doi: 10.1073/pnas.0712016105. |
A relaxed active site following exon ligation by a group i intron. SNAP output |
| 3bo4 |
nuclear protein-RNA |
X-ray (3.33 Å) |
Lipchock SV, Strobel SA |
(2008) "A relaxed active site after exon ligation by the group I intron." Proc.Natl.Acad.Sci.Usa, 105, 5699-5704. doi: 10.1073/pnas.0712016105. |
A relaxed active site following exon ligation by a group i intron. SNAP output |
| 3boy |
transcription-RNA |
X-ray (1.7 Å) |
Kumarevel T, Balasundaresan D, Jeyakanthan J, Shinkai A, Yokoyama S, Kumar PKR |
"Crystal Structure of HutP complexed with the 55-mer RNA." |
Crystal structure of the hutp antitermination complex bound to the hut mrna. SNAP output |
| 3bsb |
RNA binding protein-RNA |
X-ray (2.8 Å) |
Gupta YK, Nair DT, Wharton RP, Aggarwal AK |
(2008) "Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity." Structure, 16, 549-557. doi: 10.1016/j.str.2008.01.006. |
Crystal structure of human pumilio1 in complex with cyclinb reverse RNA. SNAP output |
| 3bsn |
transferase-RNA |
X-ray (1.8 Å) |
Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK |
(2008) "Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase." J.Biol.Chem., 283, 7705-7712. doi: 10.1074/jbc.M709563200. |
Norwalk virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA. SNAP output |
| 3bso |
transferase-RNA |
X-ray (1.74 Å) |
Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK |
(2008) "Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase." J.Biol.Chem., 283, 7705-7712. doi: 10.1074/jbc.M709563200. |
Norwalk virus polymerase bound to cytidine 5'-triphosphate and primer-template RNA. SNAP output |
| 3bsx |
RNA binding protein-RNA |
X-ray (2.32 Å) |
Gupta YK, Nair DT, Wharton RP, Aggarwal AK |
(2008) "Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity." Structure, 16, 549-557. doi: 10.1016/j.str.2008.01.006. |
Crystal structure of human pumilio 1 in complex with puf5 RNA. SNAP output |
| 3bt7 |
transferase-RNA |
X-ray (2.43 Å) |
Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J |
(2008) "Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases." Proc.Natl.Acad.Sci.Usa, 105, 6876-6881. doi: 10.1073/pnas.0802247105. |
Structure of e. coli 5-methyluridine methyltransferase trma in complex with 19 nucleotide t-arm analogue. SNAP output |
| 3bx2 |
transcription, RNA binding protein-RNA |
X-ray (2.84 Å) |
Miller MT, Higgin JJ, Hall TMT |
(2008) "Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p." Nat.Struct.Mol.Biol., 15, 397-402. doi: 10.1038/nsmb.1390. |
Puf4 RNA binding domain bound to ho endonuclease RNA 3' utr recognition sequence. SNAP output |
| 3bx3 |
transcription, RNA binding protein-RNA |
X-ray (3.0 Å) |
Miller MT, Higgin JJ, Hall TMT |
(2008) "Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p." Nat.Struct.Mol.Biol., 15, 397-402. doi: 10.1038/nsmb.1390. |
Puf4 t650c-c724r mutant bound to cox17 RNA 3' utr recognition sequence. SNAP output |
| 3cc2 |
ribosome |
X-ray (2.4 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
The refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution with rrna sequence for the 23s rrna and genome-derived sequences for r-proteins. SNAP output |
| 3cc4 |
ribosome |
X-ray (2.7 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Co-crystal structure of anisomycin bound to the 50s ribosomal subunit. SNAP output |
| 3cc7 |
ribosome |
X-ray (2.7 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation c2487u. SNAP output |
| 3cce |
ribosome |
X-ray (2.75 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation u2535a. SNAP output |
| 3ccj |
ribosome |
X-ray (3.3 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation c2534u. SNAP output |
| 3ccl |
ribosome |
X-ray (2.9 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation u2535c. density for anisomycin is visible but not included in model.. SNAP output |
| 3ccm |
ribosome |
X-ray (2.55 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation g2611u. SNAP output |
| 3ccq |
ribosome |
X-ray (2.9 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation a2488u. SNAP output |
| 3ccr |
ribosome |
X-ray (3.0 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation a2488c. density for anisomycin is visible but not included in the model.. SNAP output |
| 3ccs |
ribosome |
X-ray (2.95 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation g2482a. SNAP output |
| 3ccu |
ribosome |
X-ray (2.8 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation g2482c. SNAP output |
| 3ccv |
ribosome |
X-ray (2.9 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation g2616a. SNAP output |
| 3cd6 |
ribosome |
X-ray (2.75 Å) |
Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA |
(2008) "Mutations outside the anisomycin-binding site can make ribosomes drug-resistant." J.Mol.Biol., 379, 505-519. doi: 10.1016/j.jmb.2008.03.075. |
Co-cystal of large ribosomal subunit mutant g2616a with cc-puromycin. SNAP output |
| 3cf5 |
ribosome-antibiotic |
X-ray (3.3 Å) |
Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P |
(2008) "Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off by Thiostrepton and Micrococcin." Mol.Cell, 30, 26. doi: 10.1016/J.MOLCEL.2008.01.009. |
Thiopeptide antibiotic thiostrepton bound to the large ribosomal subunit of deinococcus radiodurans. SNAP output |
| 3ciy |
immune system-RNA |
X-ray (3.41 Å) |
Liu L, Botos I, Wang Y, Leonard JN, Shiloach J, Segal DM, Davies DR |
(2008) "Structural basis of toll-like receptor 3 signaling with double-stranded RNA." Science, 320, 379-381. doi: 10.1126/science.1155406. |
Mouse toll-like receptor 3 ectodomain complexed with double-stranded RNA. SNAP output |
| 3cma |
ribosome |
X-ray (2.8 Å) |
Simonovic M, Steitz TA |
(2008) "Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA." Rna, 14, 2372-2378. doi: 10.1261/rna.1118908. |
The structure of cca and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 3cme |
ribosome |
X-ray (2.95 Å) |
Simonovic M, Steitz TA |
(2008) "Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA." Rna, 14, 2372-2378. doi: 10.1261/rna.1118908. |
The structure of ca and cca-phe-cap-bio bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 3cpw |
ribosome |
X-ray (2.7 Å) |
Ippolito JA, Kanyo ZK, Wang D, Franceschi FJ, Moore PB, Steitz TA, Duffy EM |
(2008) "Crystal Structure of the Oxazolidinone Antibiotic
Linezolid Bound to the 50S Ribosomal Subunit." J.Med.Chem., 51, 3353-3356. doi: 10.1021/jm800379d. |
The structure of the antibiotic linezolid bound to the large ribosomal subunit of haloarcula marismortui. SNAP output |
| 3cul |
RNA-RNA binding |
X-ray (2.8 Å) |
Xiao H, Murakami H, Suga H, Ferre-D'Amare AR |
(2008) "Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme." Nature, 454, 358-361. doi: 10.1038/nature07033. |
Aminoacyl-trna synthetase ribozyme. SNAP output |
| 3cun |
RNA-RNA binding |
X-ray (3.0 Å) |
Xiao H, Murakami H, Suga H, Ferre-D'Amare AR |
(2008) "Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme." Nature, 454, 358-361. doi: 10.1038/nature07033. |
Aminoacyl-trna synthetase ribozyme. SNAP output |
| 3cxc |
ribosome |
X-ray (3.0 Å) |
Zhou J, Bhattacharjee A, Chen S, Chen Y, Duffy E, Farmer J, Goldberg J, Hanselmann R, Ippolito JA, Lou R, Orbin A, Oyelere A, Salvino J, Springer D, Tran J, Wang D, Wu Y, Johnson G |
(2008) "Design at the atomic level: design of biaryloxazolidinones as potent orally active antibiotics." Bioorg.Med.Chem.Lett., 18, 6175-6178. doi: 10.1016/j.bmcl.2008.10.011. |
The structure of an enhanced oxazolidinone inhibitor bound to the 50s ribosomal subunit of h. marismortui. SNAP output |
| 3cz3 |
viral protein-RNA |
X-ray (3.23 Å) |
Ma JB, Li F, Ding SW, Patel DJ |
"Structural Basis for siRNA Recognition by 2b, a Viral Suppressor of Non-Cell Autonomous RNA Silencing." |
Crystal structure of tomato aspermy virus 2b in complex with sirna. 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 |
| 3dd2 |
hydrolase-hydrolase inhibitor-RNA |
X-ray (1.9 Å) |
Long SB, Long MB, White RR, Sullenger BA |
(2008) "Crystal structure of an RNA aptamer bound to thrombin." Rna, 14, 2504-2512. doi: 10.1261/rna.1239308. |
Crystal structure of an RNA aptamer bound to human thrombin. SNAP output |
| 3deg |
ribosome |
cryo-EM (10.9 Å) |
Connell SR, Topf M, Qin Y, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CMT |
(2008) "A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation." Nat.Struct.Mol.Biol., 15, 910-915. doi: 10.1038/nsmb.1469. |
Complex of elongating escherichia coli 70s ribosome and ef4(lepa)-gmppnp. SNAP output |
| 3dh3 |
isomerase-RNA |
X-ray (3.0 Å) |
Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM |
(2009) "Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome." J.Mol.Biol., 388, 785-800. doi: 10.1016/j.jmb.2009.03.029. |
Crystal structure of rluf in complex with a 22 nucleotide RNA substrate. SNAP output |
| 3dkn |
protein transport-RNA |
cryo-EM (8.7 Å) |
Menetret JF, Hegde RS, Aguiar M, Gygi SP, Park E, Rapoport TA, Akey CW |
(2008) "Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome." Structure, 16, 1126-1137. doi: 10.1016/j.str.2008.05.003. |
Sec61 in the canine ribosome-channel complex from the endoplasmic reticulum. SNAP output |
| 3dll |
ribosome |
X-ray (3.5 Å) |
Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P |
(2008) "The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning." Proc.Natl.Acad.Sci.Usa, 105, 13339-13344. doi: 10.1073/pnas.0804276105. |
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect trna positioning. SNAP output |
| 3egz |
RNA |
X-ray (2.2 Å) |
Xiao H, Edwards TE, Ferre-D'Amare AR |
(2008) "Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch." Chem.Biol., 15, 1125-1137. doi: 10.1016/j.chembiol.2008.09.004. |
Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch. SNAP output |
| 3eph |
transferase-RNA |
X-ray (2.95 Å) |
Zhou C, Huang RH |
(2008) "Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism." Proc.Natl.Acad.Sci.Usa, 105, 16142-16147. doi: 10.1073/pnas.0805680105. |
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on trna: insight into trna recognition and reaction mechanism. SNAP output |
| 3epj |
transferase-RNA |
X-ray (3.1 Å) |
Zhou C, Huang RH |
(2008) "Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism." Proc.Natl.Acad.Sci.Usa, 105, 16142-16147. doi: 10.1073/pnas.0805680105. |
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on trna: insight into trna recognition and reaction mechanism. SNAP output |
| 3epk |
transferase-RNA |
X-ray (3.2 Å) |
Zhou C, Huang RH |
(2008) "Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism." Proc.Natl.Acad.Sci.Usa, 105, 16142-16147. doi: 10.1073/pnas.0805680105. |
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on trna: insight into trna recognition and reaction mechanism. SNAP output |
| 3epl |
transferase-RNA |
X-ray (3.6 Å) |
Zhou C, Huang RH |
(2008) "Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism." Proc.Natl.Acad.Sci.Usa, 105, 16142-16147. doi: 10.1073/pnas.0805680105. |
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on trna: insight into trna recognition and reaction mechanism. SNAP output |
| 3eqt |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Li X, Ranjith-Kumar CT, Brooks MT, Dharmaiah S, Herr AB, Kao C, Li P |
(2009) "The RIG-I-like Receptor LGP2 Recognizes the Termini of Double-stranded RNA." J.Biol.Chem., 284, 13881-13891. doi: 10.1074/jbc.M900818200. |
Crystal structure of human lgp2 c-terminal domain in complex with dsrna. SNAP output |
| 3er9 |
transcription, transferase-RNA |
X-ray (2.06 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 uu and 3'-deoxy atp. SNAP output |
| 3ex7 |
hydrolase-RNA binding protein-RNA |
X-ray (2.301 Å) |
Nielsen KH, Chamieh H, Andersen CB, Fredslund F, Hamborg K, Le Hir H, Andersen GR |
(2009) "Mechanism of ATP turnover inhibition in the EJC." Rna, 15, 67-75. doi: 10.1261/rna.1283109. |
The crystal structure of ejc in its transition state. SNAP output |
| 3fht |
hydrolase-RNA |
X-ray (2.2 Å) |
von Moeller H, Basquin C, Conti E |
(2009) "The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner." Nat.Struct.Mol.Biol., 16, 247-254. doi: 10.1038/nsmb.1561. |
Crystal structure of human dbp5 in complex with amppnp and RNA. SNAP output |
| 3foz |
transferase-RNA |
X-ray (2.5 Å) |
Seif E, Hallberg BM |
(2009) "RNA-Protein Mutually Induced Fit: STRUCTURE OF ESCHERICHIA COLI ISOPENTENYL-tRNA TRANSFERASE IN COMPLEX WITH tRNA(Phe)." J.Biol.Chem., 284, 6600-6604. doi: 10.1074/jbc.C800235200. |
Structure of e. coli isopentenyl-trna transferase in complex with e. coli trna(phe). SNAP output |
| 3fte |
transferase-RNA |
X-ray (3.0 Å) |
Tu C, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2009) "Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase." Structure, 17, 374-385. doi: 10.1016/j.str.2009.01.010. |
Crystal structure of a. aeolicus ksga in complex with RNA. SNAP output |
| 3ftf |
transferase-RNA |
X-ray (2.8 Å) |
Tu C, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X |
(2009) "Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase." Structure, 17, 374-385. doi: 10.1016/j.str.2009.01.010. |
Crystal structure of a. aeolicus ksga in complex with RNA and sah. SNAP output |
| 3g0h |
hydrolase-RNA |
X-ray (2.7 Å) |
Collins R, Karlberg T, Lehtio L, Schutz P, van den Berg S, Dahlgren LG, Hammarstrom M, Weigelt J, Schuler H |
(2009) "The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch." J.Biol.Chem., 284, 10296-10300. doi: 10.1074/jbc.C900018200. |
Human dead-box RNA helicase ddx19, in complex with an atp-analogue and RNA. SNAP output |
| 3g4s |
ribosome |
X-ray (3.2 Å) |
Gurel G, Blaha G, Moore PB, Steitz TA |
(2009) "U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome." J.Mol.Biol., 389, 146-156. doi: 10.1016/j.jmb.2009.04.005. |
Co-crystal structure of tiamulin bound to the large ribosomal subunit. SNAP output |
| 3g6e |
ribosome |
X-ray (2.7 Å) |
Gurel G, Blaha G, Moore PB, Steitz TA |
(2009) "U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome." J.Mol.Biol., 389, 146-156. doi: 10.1016/j.jmb.2009.04.005. |
Co-crystal structure of homoharringtonine bound to the large ribosomal subunit. SNAP output |
| 3g71 |
ribosome |
X-ray (2.85 Å) |
Gurel G, Blaha G, Moore PB, Steitz TA |
(2009) "U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome." J.Mol.Biol., 389, 146-156. doi: 10.1016/j.jmb.2009.04.005. |
Co-crystal structure of bruceantin bound to the large ribosomal subunit. SNAP output |
| 3g8s |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Cochrane JC, Lipchock SV, Smith KD, Strobel SA |
(2009) "Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme." Biochemistry, 48, 3239-3246. doi: 10.1021/bi802069p. |
Crystal structure of the pre-cleaved bacillus anthracis glms ribozyme. SNAP output |
| 3g8t |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Cochrane JC, Lipchock SV, Smith KD, Strobel SA |
(2009) "Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme." Biochemistry, 48, 3239-3246. doi: 10.1021/bi802069p. |
Crystal structure of the g33a mutant bacillus anthracis glms ribozyme bound to glcn6p. SNAP output |
| 3g96 |
RNA binding protein-RNA |
X-ray (3.01 Å) |
Cochrane JC, Lipchock SV, Smith KD, Strobel SA |
(2009) "Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme." Biochemistry, 48, 3239-3246. doi: 10.1021/bi802069p. |
Crystal structure of the bacillus anthracis glms ribozyme bound to man6p. SNAP output |
| 3g9c |
RNA binding protein-RNA |
X-ray (2.9 Å) |
Cochrane JC, Lipchock SV, Smith KD, Strobel SA |
(2009) "Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme." Biochemistry, 48, 3239-3246. doi: 10.1021/bi802069p. |
Crystal structure of the product bacillus anthracis glms ribozyme. SNAP output |
| 3g9y |
transcription-RNA |
X-ray (1.4 Å) |
Loughlin FE, Mansfield RE, Vaz PM, McGrath AP, Setiyaputra S, Gamsjaeger R, Chen ES, Morris BJ, Guss JM, Mackay JP |
(2009) "The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences." Proc.Natl.Acad.Sci.USA, 106, 5581-5586. doi: 10.1073/pnas.0802466106. |
Crystal structure of the second zinc finger from zranb2-znf265 bound to 6 nt ssrna sequence agguaa. SNAP output |
| 3gib |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Link TM, Valentin-Hansen P, Brennan RG |
(2009) "Structure of Escherichia coli Hfq bound to polyriboadenylate RNA." Proc.Natl.Acad.Sci.USA, 106, 19292-19297. doi: 10.1073/pnas.0908744106. |
Crystal structure of the complex of the e. coli hfq with poly(a). SNAP output |
| 3gpq |
viral protein-RNA |
X-ray (2.0 Å) |
Malet H, Coutard B, Jamal S, Dutartre H, Papageorgiou N, Neuvonen M, Ahola T, Forrester N, Gould EA, Lafitte D, Ferron F, Lescar J, Gorbalenya AE, de Lamballerie X, Canard B |
(2009) "The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket." J.Virol., 83, 6534-6545. doi: 10.1128/JVI.00189-09. |
Crystal structure of macro domain of chikungunya virus in complex with RNA. SNAP output |
| 3h5x |
transferase-RNA |
X-ray (1.77 Å) |
Zamyatkin DF, Parra F, Machin A, Grochulski P, Ng KK |
(2009) "Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site." J.Mol.Biol., 390, 10-16. doi: 10.1016/j.jmb.2009.04.069. |
Crystal structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to norovirus gii RNA polymerase. SNAP output |
| 3h5y |
transferase-RNA |
X-ray (1.77 Å) |
Zamyatkin DF, Parra F, Machin A, Grochulski P, Ng KK |
(2009) "Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site." J.Mol.Biol., 390, 10-16. doi: 10.1016/j.jmb.2009.04.069. |
Norovirus polymerase+primer-template+ctp complex at 6 mm mncl2. 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 |
| 3hay |
isomerase-biosynthetic protein-RNA |
X-ray (4.99 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 full h-aca rnp from pyrococcus furiosus. SNAP output |
| 3hhn |
ligase-RNA |
X-ray (2.987 Å) |
Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP |
(2009) "Crystal structure of the catalytic core of an RNA-polymerase ribozyme." Science, 326, 1271-1275. doi: 10.1126/science.1174676. |
Crystal structure of class i ligase ribozyme self-ligation product, in complex with u1a rbd. SNAP output |
| 3hhz |
viral protein-RNA |
X-ray (3.5 Å) |
Green TJ, Luo M |
(2009) "Structure of the vesicular stomatitis virus nucleocapsid in complex with the nucleocapsid-binding domain of the small polymerase cofactor, P." Proc.Natl.Acad.Sci.USA, 106, 11713-11718. doi: 10.1073/pnas.0903228106. |
Complex of the vesicular stomatitis virus nucleocapsid and the nucleocapsid-binding domain of the phosphoprotein. SNAP output |
| 3hjw |
isomerase-RNA |
X-ray (2.35 Å) |
Liang B, Zhou J, Kahen E, Terns RM, Terns MP, Li H |
(2009) "Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA." Nat.Struct.Mol.Biol., 16, 740-746. doi: 10.1038/nsmb.1624. |
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. SNAP output |
| 3hjy |
isomerase-RNA |
X-ray (3.65 Å) |
Liang B, Zhou J, Kahen E, Terns RM, Terns MP, Li H |
(2009) "Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA." Nat.Struct.Mol.Biol., 16, 740-746. doi: 10.1038/nsmb.1624. |
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. SNAP output |
| 3hl2 |
transferase |
X-ray (2.81 Å) |
Palioura S, Sherrer RL, Steitz TA, Soll D, Simonovic M |
(2009) "The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation." Science, 325, 321-325. doi: 10.1126/science.1173755. |
The crystal structure of the human sepsecs-trnasec complex. SNAP output |
| 3hsb |
RNA binding protein-RNA |
X-ray (2.2 Å) |
Someya T, Baba S, Fujimoto M, Kawai G, Kumasaka T, Nakamura K |
(2012) "Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq." Nucleic Acids Res., 40, 1856-1867. doi: 10.1093/nar/gkr892. |
Crystal structure of ymah (hfq) from bacillus subtilis in complex with an RNA aptamer. SNAP output |
| 3htx |
transferase-RNA |
X-ray (3.1 Å) |
Huang Y, Ji L, Huang Q, Vassylyev DG, Chen X, Ma JB |
(2009) "Structural insights into mechanisms of the small RNA methyltransferase HEN1." Nature, 461, 823-827. doi: 10.1038/nature08433. |
Crystal structure of small RNA methyltransferase hen1. SNAP output |
| 3i55 |
ribosome-antibiotic |
X-ray (3.11 Å) |
Gurel G, Blaha G, Steitz TA, Moore PB |
(2009) "Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui." Antimicrob.Agents Chemother., 53, 5010-5014. doi: 10.1128/AAC.00817-09. |
Co-crystal structure of mycalamide a bound to the large ribosomal subunit. SNAP output |
| 3i56 |
ribosome-antibiotic |
X-ray (2.9 Å) |
Gurel G, Blaha G, Steitz TA, Moore PB |
(2009) "Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui." Antimicrob.Agents Chemother., 53, 5010-5014. doi: 10.1128/AAC.00817-09. |
Co-crystal structure of triacetyloleandomcyin bound to the large ribosomal subunit. SNAP output |
| 3i5x |
hydrolase-RNA |
X-ray (1.9 Å) |
Del Campo M, Lambowitz AM |
(2009) "Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA." Mol.Cell, 35, 598-609. doi: 10.1016/j.molcel.2009.07.032. |
Structure of mss116p bound to ssrna and amp-pnp. SNAP output |
| 3i5y |
hydrolase-RNA |
X-ray (2.49 Å) |
Del Campo M, Lambowitz AM |
(2009) "Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA." Mol.Cell, 35, 598-609. doi: 10.1016/j.molcel.2009.07.032. |
Structure of mss116p bound to ssrna containing a single 5-bru and amp-pnp. SNAP output |
| 3i61 |
hydrolase-RNA |
X-ray (2.1 Å) |
Del Campo M, Lambowitz AM |
(2009) "Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA." Mol.Cell, 35, 598-609. doi: 10.1016/j.molcel.2009.07.032. |
Structure of mss116p bound to ssrna and adp-beryllium fluoride. SNAP output |
| 3i62 |
hydrolase-RNA |
X-ray (1.95 Å) |
Del Campo M, Lambowitz AM |
(2009) "Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA." Mol.Cell, 35, 598-609. doi: 10.1016/j.molcel.2009.07.032. |
Structure of mss116p bound to ssrna and adp-aluminum fluoride. SNAP output |
| 3iab |
hydrolase-RNA |
X-ray (2.7 Å) |
Perederina A, Esakova O, Quan C, Khanova E, Krasilnikov AS |
(2010) "Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain." Embo J., 29, 761-769. doi: 10.1038/emboj.2009.396. |
Crystal structure of rnase p -rnase mrp proteins pop6, pop7 in a complex with the p3 domain of rnase mrp RNA. SNAP output |
| 3ice |
transcription regulator-RNA |
X-ray (2.8 Å) |
Thomsen ND, Berger JM |
(2009) "Running in reverse: the structural basis for translocation polarity in hexameric helicases." Cell(Cambridge,Mass.), 139, 523-534. doi: 10.1016/j.cell.2009.08.043. |
Rho transcription termination factor bound to RNA and adp-bef3. SNAP output |
| 3icq |
RNA binding protein |
X-ray (3.2 Å) |
Cook AG, Fukuhara N, Jinek M, Conti E |
(2009) "Structures of the tRNA export factor in the nuclear and cytosolic states." Nature, 461, 60-65. doi: 10.1038/nature08394. |
Karyopherin nuclear state. SNAP output |
| 3id5 |
transferase-ribosomal protein-RNA |
X-ray (4.01 Å) |
Ye K, Jia R, Lin J, Ju M, Peng J, Xu A, Zhang L |
(2009) "Structural organization of box C/D RNA-guided RNA methyltransferase." Proc.Natl.Acad.Sci.USA, 106, 13808-13813. doi: 10.1073/pnas.0905128106. |
Crystal structure of sulfolobus solfataricus c-d rnp assembled with nop5, fibrillarin, l7ae and a split half c-d RNA. SNAP output |
| 3ie1 |
hydrolase-RNA |
X-ray (2.85 Å) |
Ishikawa H, Nakagawa N, Kuramitsu S, Masui R |
"Crystal structure of H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with RNA." |
Crystal structure of h380a mutant ttha0252 from thermus thermophilus hb8 complexed with RNA. SNAP output |
| 3iem |
hydrolase-RNA |
X-ray (2.5 Å) |
Ishikawa H, Nakagawa N, Kuramitsu S, Masui R |
"Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog." |
Crystal structure of ttha0252 from thermus thermophilus hb8 complexed with RNA analog. SNAP output |
| 3iev |
nucleotide binding protein-RNA |
X-ray (1.9 Å) |
Tu C, Zhou X, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X |
(2009) "Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis." Proc.Natl.Acad.Sci.USA, 106, 14843-14848. doi: 10.1073/pnas.0904032106. |
Crystal structure of era in complex with mggnp and the 3' end of 16s rrna. SNAP output |
| 3irw |
RNA binding protein-RNA |
X-ray (2.7 Å) |
Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA |
(2009) "Structural basis of ligand binding by a c-di-GMP riboswitch." Nat.Struct.Mol.Biol., 16, 1218-1223. doi: 10.1038/nsmb.1702. |
Structure of a c-di-gmp riboswitch from v. cholerae. SNAP output |
| 3ivk |
immune system - RNA |
X-ray (3.1 Å) |
Shechner DM, Grant RA, Bagby SC, Koldobskaya Y, Piccirilli JA, Bartel DP |
(2009) "Crystal structure of the catalytic core of an RNA-polymerase ribozyme." Science, 326, 1271-1275. doi: 10.1126/science.1174676. |
Crystal structure of the catalytic core of an RNA polymerase ribozyme complexed with an antigen binding antibody fragment. SNAP output |
| 3iwn |
RNA-RNA binding protein |
X-ray (3.2 Å) |
Kulshina N, Baird NJ, Ferre-D'Amare AR |
(2009) "Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch." Nat.Struct.Mol.Biol., 16, 1212-1217. doi: 10.1038/nsmb.1701. |
Co-crystal structure of a bacterial c-di-gmp riboswitch. SNAP output |
| 3iyq |
ribosomal protein-RNA |
cryo-EM (13.0 Å) |
Weis F, Bron P, Giudice E, Rolland JP, Thomas D, Felden B, Gillet R |
(2010) "tmRNA-SmpB: a journey to the centre of the bacterial ribosome." Embo J., 29, 3810-3818. doi: 10.1038/emboj.2010.252. |
Tmrna-smpb: a journey to the center of the bacterial ribosome. SNAP output |
| 3iyr |
ribosomal protein-RNA |
cryo-EM (13.0 Å) |
Weis F, Bron P, Giudice E, Rolland JP, Thomas D, Felden B, Gillet R |
(2010) "tmRNA-SmpB: a journey to the centre of the bacterial ribosome." Embo J., 29, 3810-3818. doi: 10.1038/emboj.2010.252. |
Tmrna-smpb: a journey to the center of the bacterial ribosome. SNAP output |
| 3iz4 |
RNA binding protein-RNA |
cryo-EM (13.6 Å) |
Fu J, Hashem Y, Wower I, Lei J, Liao HY, Zwieb C, Wower J, Frank J |
(2010) "Visualizing the transfer-messenger RNA as the ribosome resumes translation." Embo J., 29, 3819-3825. doi: 10.1038/emboj.2010.255. |
Modified e. coli tmrna in the resume state with the trna-like domain in the ribosomal p site interacting with the smpb. SNAP output |
| 3izy |
RNA, ribosomal protein |
cryo-EM (10.8 Å) |
Yassin AS, Haque ME, Datta PP, Elmore K, Banavali NK, Spremulli LL, Agrawal RK |
(2011) "Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1." Proc.Natl.Acad.Sci.USA, 108, 3918-3923. doi: 10.1073/pnas.1017425108. |
Mammalian mitochondrial translation initiation factor 2. SNAP output |
| 3izz |
RNA, ribosomal protein |
cryo-EM (10.8 Å) |
Yassin AS, Haque ME, Datta PP, Elmore K, Banavali NK, Spremulli LL, Agrawal RK |
(2011) "Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1." Proc.Natl.Acad.Sci.USA, 108, 3918-3923. doi: 10.1073/pnas.1017425108. |
Models for ribosome components that are nearest neighbors to the bovine mitochondrial initiation factor2 bound to the e. coli ribosome. SNAP output |
| 3j06 |
virus |
cryo-EM (3.3 Å) |
Ge P, Zhou ZH |
(2011) "Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches." Proc.Natl.Acad.Sci.USA, 108, 9637-9642. doi: 10.1073/pnas.1018104108. |
Cryoem helical reconstruction of tmv. SNAP output |
| 3j0d |
translation |
cryo-EM (11.1 Å) |
Yokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK |
(2012) "Structural insights into initial and intermediate steps of the ribosome-recycling process." Embo J., 31, 1836-1846. doi: 10.1038/emboj.2012.22. |
Models for the t. thermophilus ribosome recycling factor bound to the e. coli post-termination complex. SNAP output |
| 3j0e |
translation |
cryo-EM (9.9 Å) |
Yokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK |
(2012) "Structural insights into initial and intermediate steps of the ribosome-recycling process." Embo J., 31, 1836-1846. doi: 10.1038/emboj.2012.22. |
Models for the t. thermophilus ribosome recycling factor and the e. coli elongation factor g bound to the e. coli post-termination complex. SNAP output |
| 3j0l |
ribosome |
cryo-EM (9.8 Å) |
Budkevich T, Giesebrecht J, Altman RB, Munro JB, Mielke T, Nierhaus KH, Blanchard SC, Spahn CM |
(2011) "Structure and dynamics of the Mammalian ribosomal pretranslocation complex." Mol.Cell, 44, 214-224. doi: 10.1016/j.molcel.2011.07.040. |
Core of mammalian 80s pre-ribosome in complex with trnas fitted to a 9.8a cryo-EM map: classic pre state 1. SNAP output |
| 3j0o |
ribosome |
cryo-EM (9.0 Å) |
Budkevich T, Giesebrecht J, Altman RB, Munro JB, Mielke T, Nierhaus KH, Blanchard SC, Spahn CM |
(2011) "Structure and dynamics of the Mammalian ribosomal pretranslocation complex." Mol.Cell, 44, 214-224. doi: 10.1016/j.molcel.2011.07.040. |
Core of mammalian 80s pre-ribosome in complex with trnas fitted to a 9a cryo-EM map: classic pre state 2. SNAP output |
| 3j0p |
ribosome |
cryo-EM (10.6 Å) |
Budkevich T, Giesebrecht J, Altman RB, Munro JB, Mielke T, Nierhaus KH, Blanchard SC, Spahn CM |
(2011) "Structure and dynamics of the Mammalian ribosomal pretranslocation complex." Mol.Cell, 44, 214-224. doi: 10.1016/j.molcel.2011.07.040. |
Core of mammalian 80s pre-ribosome in complex with trnas fitted to a 10.6a cryo-EM map: rotated pre state 1. SNAP output |
| 3j0q |
ribosome |
cryo-EM (10.6 Å) |
Budkevich T, Giesebrecht J, Altman RB, Munro JB, Mielke T, Nierhaus KH, Blanchard SC, Spahn CM |
(2011) "Structure and dynamics of the Mammalian ribosomal pretranslocation complex." Mol.Cell, 44, 214-224. doi: 10.1016/j.molcel.2011.07.040. |
Core of mammalian 80s pre-ribosome in complex with trnas fitted to a 10.6a cryo-EM map: rotated pre state 2. SNAP output |
| 3j16 |
ribosome |
cryo-EM (7.2 Å) |
Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache J-P, Sieber H, Ungewickell C, Berninghausen O, Daberkow I, Karcher A, Thomm M, Hopfner KP, Green R, Beckmann R |
(2012) "Structural basis of highly conserved ribosome recycling in eukaryotes and archaea." Nature, 482, 501-506. doi: 10.1038/nature10829. |
Models of ribosome-bound dom34p and rli1p and their ribosomal binding partners. SNAP output |
| 3j3v |
ribosome |
cryo-EM (13.3 Å) |
Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N |
(2013) "Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit." Nucleic Acids Res., 41, 7073-7083. doi: 10.1093/nar/gkt423. |
Atomic model of the immature 50s subunit from bacillus subtilis (state i-a). SNAP output |
| 3j3w |
ribosome |
cryo-EM (10.7 Å) |
Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N |
(2013) "Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit." Nucleic Acids Res., 41, 7073-7083. doi: 10.1093/nar/gkt423. |
Atomic model of the immature 50s subunit from bacillus subtilis (state ii-a). SNAP output |
| 3j45 |
ribosome-protein transport |
cryo-EM (9.5 Å) |
Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW |
(2013) "Structure of the SecY channel during initiation of protein translocation." Nature, 506, 102-106. doi: 10.1038/nature12720. |
Structure of a non-translocating secy protein channel with the 70s ribosome. SNAP output |
| 3j46 |
ribosome-protein transport |
cryo-EM (10.1 Å) |
Park E, Menetret JF, Gumbart JC, Ludtke SJ, Li W, Whynot A, Rapoport TA, Akey CW |
(2013) "Structure of the SecY channel during initiation of protein translocation." Nature, 506, 102-106. doi: 10.1038/nature12720. |
Structure of the secy protein translocation channel in action. SNAP output |
| 3j5l |
ribosome-antibiotic |
cryo-EM (6.6 Å) |
Arenz S, Ramu H, Gupta P, Berninghausen O, Beckmann R, Vazquez-Laslop N, Mankin AS, Wilson DN |
(2014) "Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide." Nat Commun, 5, 3501. doi: 10.1038/ncomms4501. |
Structure of the e. coli 50s subunit with ermbl nascent chain. SNAP output |
| 3j5s |
ribosome-translation |
cryo-EM (7.5 Å) |
Chen B, Boel G, Hashem Y, Ning W, Fei J, Wang C, Gonzalez RL, Hunt JF, Frank J |
(2014) "EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics." Nat.Struct.Mol.Biol., 21, 152-159. doi: 10.1038/nsmb.2741. |
Etta binds to ribosome exit site and regulates translation by restricting ribosome and trna dynamics. SNAP output |
| 3j5y |
translation-RNA |
cryo-EM (9.7 Å) |
des Georges A, Hashem Y, Unbehaun A, Grassucci RA, Taylor D, Hellen CU, Pestova TV, Frank J |
(2014) "Structure of the mammalian ribosomal pre-termination complex associated with eRF1*eRF3*GDPNP." Nucleic Acids Res., 42, 3409-3418. doi: 10.1093/nar/gkt1279. |
Structure of the mammalian ribosomal pre-termination complex associated with erf1-erf3-gdpnp. SNAP output |
| 3j7a |
ribosome-inhibitor |
cryo-EM (3.2 Å) |
Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SH |
(2014) "Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine." Elife, 3, e03080. doi: 10.7554/eLife.03080. |
cryo-EM structure of the plasmodium falciparum 80s ribosome bound to the anti-protozoan drug emetine, small subunit. SNAP output |
| 3j7y |
ribosome |
cryo-EM (3.4 Å) |
Brown A, Amunts A, Bai XC, Sugimoto Y, Edwards PC, Murshudov G, Scheres SH, Ramakrishnan V |
(2014) "Structure of the large ribosomal subunit from human mitochondria." Science, 346, 718-722. doi: 10.1126/science.1258026. |
Structure of the large ribosomal subunit from human mitochondria. SNAP output |
| 3j7z |
ribosome-antibiotic |
cryo-EM (3.9 Å) |
Arenz S, Meydan S, Starosta AL, Berninghausen O, Beckmann R, Vazquez-Laslop N, Wilson DN |
(2014) "Drug Sensing by the Ribosome Induces Translational Arrest via Active Site Perturbation." Mol.Cell, 56, 446-452. doi: 10.1016/j.molcel.2014.09.014. |
Structure of the e. coli 50s subunit with ermcl nascent chain. SNAP output |
| 3j80 |
ribosome |
cryo-EM (3.75 Å) |
Hussain T, Llacer JL, Fernandez IS, Munoz A, Martin-Marcos P, Savva CG, Lorsch JR, Hinnebusch AG, Ramakrishnan V |
(2014) "Structural changes enable start codon recognition by the eukaryotic translation initiation complex." Cell(Cambridge,Mass.), 159, 597-607. doi: 10.1016/j.cell.2014.10.001. |
Cryoem structure of 40s-eif1-eif1a preinitiation complex. SNAP output |
| 3j81 |
ribosome |
cryo-EM (4.0 Å) |
Hussain T, Llacer JL, Fernandez IS, Munoz A, Martin-Marcos P, Savva CG, Lorsch JR, Hinnebusch AG, Ramakrishnan V |
(2014) "Structural changes enable start codon recognition by the eukaryotic translation initiation complex." Cell(Cambridge,Mass.), 159, 597-607. doi: 10.1016/j.cell.2014.10.001. |
Cryoem structure of a partial yeast 48s preinitiation complex. SNAP output |
| 3j8g |
ribosome |
cryo-EM (5.0 Å) |
Zhang X, Yan K, Zhang Y, Li N, Ma C, Li Z, Zhang Y, Feng B, Liu J, Sun Y, Xu Y, Lei J, Gao N |
(2014) "Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly." Nucleic Acids Res. doi: 10.1093/nar/gku1135. |
Electron cryo-microscopy structure of enga bound with the 50s ribosomal subunit. SNAP output |
| 3j9b |
RNA binding protein-transferase-RNA |
cryo-EM (4.3 Å) |
Chang S, Sun D, Liang H, Wang J, Li J, Guo L, Wang X, Guan C, Boruah BM, Yuan L, Feng F, Yang M, Wang L, Wang Y, Wojdyla J, Li L, Wang J, Wang M, Cheng G, Wang HW, Liu Y |
(2015) "Cryo-EM Structure of Influenza Virus RNA Polymerase Complex at 4.3 angstrom Resolution." Mol.Cell. doi: 10.1016/j.molcel.2014.12.031. |
Electron cryo-microscopy of an RNA polymerase. SNAP output |
| 3jam |
translation |
cryo-EM (3.46 Å) |
Llacer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V |
(2015) "Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex." Mol.Cell, 59, 399-412. doi: 10.1016/j.molcel.2015.06.033. |
Cryoem structure of 40s-eif1a-eif1 complex from yeast. SNAP output |
| 3jap |
translation |
cryo-EM (4.9 Å) |
Llacer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V |
(2015) "Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex." Mol.Cell, 59, 399-412. doi: 10.1016/j.molcel.2015.06.033. |
Structure of a partial yeast 48s preinitiation complex in closed conformation. SNAP output |
| 3jaq |
translation |
cryo-EM (6.0 Å) |
Llacer JL, Hussain T, Marler L, Aitken CE, Thakur A, Lorsch JR, Hinnebusch AG, Ramakrishnan V |
(2015) "Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex." Mol.Cell, 59, 399-412. doi: 10.1016/j.molcel.2015.06.033. |
Structure of a partial yeast 48s preinitiation complex in open conformation. SNAP output |
| 3jb7 |
transferase-viral protein-RNA |
cryo-EM (4.001 Å) |
Zhang X, Ding K, Yu X, Chang W, Sun J, Hong Zhou Z |
(2015) "In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus." Nature, 527, 531-534. doi: 10.1038/nature15767. |
In situ structures of the segmented genome and RNA polymerase complex inside a dsrna virus. SNAP output |
| 3jb9 |
RNA binding protein-RNA |
cryo-EM (3.6 Å) |
Yan C, Hang J, Wan R, Huang M, Wong C, Shi Y |
(2015) "Structure of a yeast spliceosome at 3.6-angstrom resolution." Science, 349, 1182-1191. doi: 10.1126/science.aac7629. |
cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution. SNAP output |
| 3jcm |
transcription |
cryo-EM (3.8 Å) |
Wan R, Yan C, Bai R, Wang L, Huang M, Wong CC, Shi Y |
(2016) "The 3.8 angstrom structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis." Science, 351, 466-475. doi: 10.1126/science.aad6466. |
cryo-EM structure of the spliceosomal u4-u6.u5 tri-snrnp. SNAP output |
| 3jd5 |
ribosome |
cryo-EM (7.0 Å) |
Kaushal PS, Sharma MR, Booth TM, Haque EM, Tung CS, Sanbonmatsu KY, Spremulli LL, Agrawal RK |
(2014) "Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome." Proc.Natl.Acad.Sci.USA, 111, 7284-7289. doi: 10.1073/pnas.1401657111. |
cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. SNAP output |
| 3k0j |
RNA-RNA binding protein |
X-ray (3.1 Å) |
Kulshina N, Edwards TE, Ferre-D'Amare AR |
(2010) "Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch." Rna, 16, 186-196. doi: 10.1261/rna.1847310. |
Crystal structure of the e. coli thim riboswitch in complex with thiamine pyrophosphate and the u1a crystallization module. SNAP output |
| 3k49 |
RNA binding protein - RNA |
X-ray (2.5 Å) |
Zhu D, Stumpf CR, Krahn JM, Wickens M, Hall TM |
(2009) "A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs." Proc.Natl.Acad.Sci.USA, 106, 20192-20197. doi: 10.1073/pnas.0812079106. |
Puf3 RNA binding domain bound to cox17 RNA 3' utr recognition sequence site b. SNAP output |
| 3k4e |
RNA binding protein - RNA |
X-ray (3.2 Å) |
Zhu D, Stumpf CR, Krahn JM, Wickens M, Hall TM |
(2009) "A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs." Proc.Natl.Acad.Sci.USA, 106, 20192-20197. doi: 10.1073/pnas.0812079106. |
Puf3 RNA binding domain bound to cox17 RNA 3' utr recognition sequence site a. SNAP output |
| 3k5q |
RNA-RNA binding protein |
X-ray (2.2 Å) |
Wang Y, Opperman L, Wickens M, Hall TM |
(2009) "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106. |
Crystal structure of fbf-2-fbe complex. SNAP output |
| 3k5y |
RNA-RNA binding protein |
X-ray (2.3 Å) |
Wang Y, Opperman L, Wickens M, Hall TM |
(2009) "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106. |
Crystal structure of fbf-2-gld-1 fbea complex. SNAP output |
| 3k5z |
RNA-RNA binding protein |
X-ray (2.4 Å) |
Wang Y, Opperman L, Wickens M, Hall TM |
(2009) "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106. |
Crystal structure of fbf-2-gld-1 fbea g4a mutant complex. SNAP output |
| 3k61 |
RNA-RNA binding protein |
X-ray (2.21 Å) |
Wang Y, Opperman L, Wickens M, Hall TM |
(2009) "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106. |
Crystal structure of fbf-2-fog-1 fbea complex. SNAP output |
| 3k62 |
RNA-RNA binding protein |
X-ray (1.9 Å) |
Wang Y, Opperman L, Wickens M, Hall TM |
(2009) "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106. |
Crystal structure of fbf-2-gld-1 fbeb complex. SNAP output |
| 3k64 |
RNA-RNA binding protein |
X-ray (2.0 Å) |
Wang Y, Opperman L, Wickens M, Hall TM |
(2009) "Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein." Proc.Natl.Acad.Sci.USA, 106, 20186-20191. doi: 10.1073/pnas.0812076106. |
Crystal structure of fbf-2-fem-3 pme complex. SNAP output |
| 3kfu |
ligase-RNA |
X-ray (3.0 Å) |
Blaise M, Bailly M, Frechin M, Behrens MA, Fischer F, Oliveira CL, Becker HD, Pedersen JS, Thirup S, Kern D |
(2010) "Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation." Embo J., 29, 3118-3129. doi: 10.1038/emboj.2010.192. |
Crystal structure of the transamidosome. SNAP output |
| 3klv |
transferase-RNA |
X-ray (2.6 Å) |
Ferrer-Orta C, Sierra M, Agudo R, de la Higuera I, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2010) "Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin." J.Virol., 84, 6188-6199. doi: 10.1128/JVI.02420-09. |
M296i g62s mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA. SNAP output |
| 3kmq |
transferase-RNA |
X-ray (2.11 Å) |
Ferrer-Orta C, Sierra M, Agudo R, de la Higuera I, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2010) "Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin." J.Virol., 84, 6188-6199. doi: 10.1128/JVI.02420-09. |
G62s mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, tetragonal structure. SNAP output |
| 3kms |
transferase-RNA |
X-ray (2.2 Å) |
Ferrer-Orta C, Sierra M, Agudo R, de la Higuera I, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2010) "Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin." J.Virol., 84, 6188-6199. doi: 10.1128/JVI.02420-09. |
G62s mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA trigonal structure. SNAP output |
| 3kna |
transferase-RNA |
X-ray (2.8 Å) |
Ferrer-Orta C, Sierra M, Agudo R, de la Higuera I, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2010) "Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin." J.Virol., 84, 6188-6199. doi: 10.1128/JVI.02420-09. |
M296i mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA. SNAP output |
| 3koa |
transferase-RNA |
X-ray (2.4 Å) |
Ferrer-Orta C, Sierra M, Agudo R, de la Higuera I, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N |
(2010) "Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin." J.Virol., 84, 6188-6199. doi: 10.1128/JVI.02420-09. |
M296i mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA and gtp. SNAP output |
| 3ks8 |
viral protein-RNA |
X-ray (2.401 Å) |
Kimberlin CR, Bornholdt ZA, Li S, Woods VL, Macrae IJ, Saphire EO |
(2009) "Ebolavirus VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression." Proc.Natl.Acad.Sci.USA, 107, 314-319. doi: 10.1073/pnas.0910547107. |
Crystal structure of reston ebolavirus vp35 RNA binding domain in complex with 18bp dsrna. SNAP output |
| 3ktv |
RNA-RNA binding protein |
X-ray (3.8 Å) |
Wild K, Bange G, Bozkurt G, Segnitz B, Hendricks A, Sinning I |
(2010) "Structural insights into the assembly of the human and archaeal signal recognition particles." Acta Crystallogr.,Sect.D, 66, 295-303. doi: 10.1107/S0907444910000879. |
Crystal structure of the human srp19-s-domain srp RNA complex. SNAP output |
| 3ktw |
RNA-RNA binding protein |
X-ray (3.2 Å) |
Wild K, Bange G, Bozkurt G, Segnitz B, Hendricks A, Sinning I |
(2010) "Structural insights into the assembly of the human and archaeal signal recognition particles." Acta Crystallogr.,Sect.D, 66, 295-303. doi: 10.1107/S0907444910000879. |
Crystal structure of the srp19-s-domain srp RNA complex of sulfolobus solfataricus. SNAP output |
| 3l25 |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Leung DW, Prins KC, Borek DM, Farahbakhsh M, Tufariello JM, Ramanan P, Nix JC, Helgeson LA, Otwinowski Z, Honzatko RB, Basler CF, Amarasinghe GK |
(2010) "Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35." Nat.Struct.Mol.Biol., 17, 165-172. doi: 10.1038/nsmb.1765. |
Crystal structure of zaire ebola vp35 interferon inhibitory domain bound to 8 bp dsrna. SNAP output |
| 3l26 |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Leung DW, Prins KC, Borek DM, Farahbakhsh M, Tufariello JM, Ramanan P, Nix JC, Helgeson LA, Otwinowski Z, Honzatko RB, Basler CF, Amarasinghe GK |
(2010) "Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35." Nat.Struct.Mol.Biol., 17, 165-172. doi: 10.1038/nsmb.1765. |
Crystal structure of zaire ebola vp35 interferon inhibitory domain bound to 8 bp dsrna. SNAP output |
| 3l3c |
RNA binding protein-RNA |
X-ray (2.85 Å) |
Cochrane JC, Lipchock SV, Smith KD, Strobel SA |
(2009) "Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme." Biochemistry, 48, 3239-3246. doi: 10.1021/bi802069p. |
Crystal structure of the bacillus anthracis glms ribozyme bound to glc6p. SNAP output |
| 3lob |
virus |
X-ray (3.6 Å) |
Banerjee M, Speir JA, Kwan MH, Huang R, Aryanpur PP, Bothner B, Johnson JE |
(2010) "Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate." J.Virol., 84, 4737-4746. doi: 10.1128/JVI.02670-09. |
Crystal structure of flock house virus calcium mutant. SNAP output |
| 3lqx |
RNA-RNA binding protein |
X-ray (1.93 Å) |
Batey RT, Doudna JA |
(2002) "Structural and Energetic Analysis of Metal Ions Essential to SRP Signal Recognition Domain Assembly." Biochemistry, 41, 11703-11710. |
Srp ribonucleoprotein core complexed with cobalt hexammine. SNAP output |
| 3lrn |
hydrolase-RNA |
X-ray (2.6 Å) |
Lu C, Xu H, Ranjith-Kumar CT, Brooks MT, Hou TY, Hu F, Herr AB, Strong RK, Kao CC, Li P |
(2010) "The Structural Basis of 5' Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain." Structure, 18, 1032-1043. doi: 10.1016/j.str.2010.05.007. |
Crystal structure of human rig-i ctd bound to a 14 bp gc 5' ppp dsrna. SNAP output |
| 3lrr |
hydrolase-RNA |
X-ray (2.15 Å) |
Lu C, Xu H, Ranjith-Kumar CT, Brooks MT, Hou TY, Hu F, Herr AB, Strong RK, Kao CC, Li P |
(2010) "The Structural Basis of 5' Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain." Structure, 18, 1032-1043. doi: 10.1016/j.str.2010.05.007. |
Crystal structure of human rig-i ctd bound to a 12 bp au rich 5' ppp dsrna. SNAP output |
| 3lwo |
isomerase-RNA binding protein-RNA |
X-ray (2.855 Å) |
Zhou J, Lv C, Liang B, Chen M, Yang W, Li H |
(2010) "Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study." J.Mol.Biol., 401, 690-695. doi: 10.1016/j.jmb.2010.06.061. |
Structure of h-aca rnp bound to a substrate RNA containing 5bru. SNAP output |
| 3lwp |
isomerase-RNA binding protein-RNA |
X-ray (2.5 Å) |
Zhou J, Lv C, Liang B, Chen M, Yang W, Li H |
(2010) "Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study." J.Mol.Biol., 401, 690-695. doi: 10.1016/j.jmb.2010.06.061. |
Structure of h-aca rnp bound to a substrate RNA containing 5brdu. SNAP output |
| 3lwq |
isomerase-RNA binding protein-RNA |
X-ray (2.678 Å) |
Zhou J, Liang B, Li H |
(2010) "Functional and Structural Impact of Target Uridine Substitutions on the H/ACA Ribonucleoprotein Particle Pseudouridine Synthase ." Biochemistry, 49, 6276-6281. doi: 10.1021/bi1006699. |
Structure of h-aca rnp bound to a substrate RNA containing 3mu. SNAP output |
| 3lwr |
isomerase-RNA binding protein-RNA |
X-ray (2.203 Å) |
Zhou J, Liang B, Li H |
(2010) "Functional and Structural Impact of Target Uridine Substitutions on the H/ACA Ribonucleoprotein Particle Pseudouridine Synthase ." Biochemistry, 49, 6276-6281. doi: 10.1021/bi1006699. |
Structure of h-aca rnp bound to a substrate RNA containing 4su. SNAP output |
| 3lwv |
isomerase-RNA binding protein-RNA |
X-ray (2.499 Å) |
Zhou J, Liang B, Li H |
(2010) "Functional and Structural Impact of Target Uridine Substitutions on the H/ACA Ribonucleoprotein Particle Pseudouridine Synthase ." Biochemistry, 49, 6276-6281. doi: 10.1021/bi1006699. |
Structure of h-aca rnp bound to a substrate RNA containing 2'-deoxyuridine. SNAP output |
| 3m7n |
hydrolase-RNA |
X-ray (2.4 Å) |
Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner K-P |
(2010) "Quantitative analysis of processive RNA degradation by the archaeal RNA exosome." Nucleic Acids Res., 38, 5166-5176. doi: 10.1093/nar/gkq238. |
Archaeoglobus fulgidus exosome with RNA bound to the active site. SNAP output |
| 3m85 |
hydrolase-RNA |
X-ray (3.0 Å) |
Hartung S, Niederberger T, Hartung M, Tresch A, Hopfner K-P |
(2010) "Quantitative analysis of processive RNA degradation by the archaeal RNA exosome." Nucleic Acids Res., 38, 5166-5176. doi: 10.1093/nar/gkq238. |
Archaeoglobus fulgidus exosome y70a with RNA bound to the active site. SNAP output |
| 3mdg |
RNA binding-RNA |
X-ray (2.22 Å) |
Yang Q, Gilmartin GM, Doublie S |
(2010) "Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing." Proc.Natl.Acad.Sci.USA, 107, 10062-10067. doi: 10.1073/pnas.1000848107. |
Crystal structure of the 25kda subunit of human cleavage factor im in complex with RNA uuguau. SNAP output |
| 3mdi |
RNA binding-RNA |
X-ray (2.07 Å) |
Yang Q, Gilmartin GM, Doublie S |
(2010) "Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing." Proc.Natl.Acad.Sci.USA, 107, 10062-10067. doi: 10.1073/pnas.1000848107. |
Crystal structure of the 25kda subunit of human cleavage factor im in complex with RNA uguaaa. SNAP output |
| 3mj0 |
RNA-RNA binding protein |
X-ray (2.306 Å) |
Huang Y, Ding L, Ma J |
"Crystal Structure of drosophila Ago2 PAZ domain in complex with 3'-end 2'-O-methylated RNA." |
Crystal structure of drosophia ago-paz domain in complex with 3'-end 2'-o-methylated RNA. SNAP output |
| 3moj |
RNA binding protein-RNA |
X-ray (2.902 Å) |
Hardin JW, Hu YX, McKay DB |
(2010) "Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif." J.Mol.Biol., 402, 412-427. doi: 10.1016/j.jmb.2010.07.040. |
Structure of the RNA binding domain of the bacillus subtilis yxin protein complexed with a fragment of 23s ribosomal RNA. SNAP output |
| 3mqk |
isomerase-RNA binding protein-RNA |
X-ray (2.8 Å) |
Zhou J, Liang B, Li H |
(2011) "Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide." Rna, 17, 244-250. doi: 10.1261/rna.2415811. |
Cbf5-nop10-gar1 complex binding with 17mer RNA containing aca trinucleotide. SNAP output |
| 3mum |
RNA binding protein-RNA |
X-ray (2.9 Å) |
Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA |
(2010) "Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch ." Biochemistry, 49, 7351-7359. doi: 10.1021/bi100671e. |
Crystal structure of the g20a mutant c-di-gmp riboswith bound to c-di-gmp. SNAP output |
| 3mur |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA |
(2010) "Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch ." Biochemistry, 49, 7351-7359. doi: 10.1021/bi100671e. |
Crystal structure of the c92u mutant c-di-gmp riboswith bound to c-di-gmp. SNAP output |
| 3mut |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA |
(2010) "Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch ." Biochemistry, 49, 7351-7359. doi: 10.1021/bi100671e. |
Crystal structure of the g20a-c92u mutant c-di-gmp riboswith bound to c-di-gmp. SNAP output |
| 3muv |
RNA binding protein-RNA |
X-ray (3.2 Å) |
Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA |
(2010) "Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch ." Biochemistry, 49, 7351-7359. doi: 10.1021/bi100671e. |
Crystal structure of the g20a-c92u mutant c-di-gmp riboswith bound to c-di-amp. SNAP output |
| 3mxh |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA |
(2010) "Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch ." Biochemistry, 49, 7351-7359. doi: 10.1021/bi100671e. |
Native structure of a c-di-gmp riboswitch from v. cholerae. SNAP output |
| 3ncu |
RNA binding protein-RNA |
X-ray (2.55 Å) |
Wang Y, Ludwig J, Schuberth C, Goldeck M, Schlee M, Li H, Juranek S, Sheng G, Micura R, Tuschl T, Hartmann G, Patel DJ |
(2010) "Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I." Nat.Struct.Mol.Biol., 17, 781-787. doi: 10.1038/nsmb.1863. |
Structural and functional insights into pattern recognition by the innate immune receptor rig-i. SNAP output |
| 3ndb |
signaling protein-RNA |
X-ray (3.0 Å) |
Hainzl T, Huang S, Merilainen G, Brannstrom K, Sauer-Eriksson AE |
(2011) "Structural basis of signal-sequence recognition by the signal recognition particle." Nat.Struct.Mol.Biol., 18, 389-391. doi: 10.1038/nsmb.1994. |
Crystal structure of a signal sequence bound to the signal recognition particle. SNAP output |
| 3nl0 |
transferase-RNA |
X-ray (2.6 Å) |
Agudo R, Ferrer-Orta C, Arias A, de la Higuera I, Perales C, Perez-Luque R, Verdaguer N, Domingo E |
(2010) "A multi-step process of viral adaptation to a mutagenic nucleoside analogue by modulation of transition types leads to extinction-escape." Plos Pathog., 6, e1001072. doi: 10.1371/journal.ppat.1001072. |
Mutant p44s m296i of foot-and-mouth disease virus RNA-dependent RNA polymerase. SNAP output |
| 3nma |
transferase-RNA |
X-ray (2.6 Å) |
Agudo R, Ferrer-Orta C, Arias A, de la Higuera I, Perales C, Perez-Luque R, Verdaguer N, Domingo E |
(2010) "A multi-step process of viral adaptation to a mutagenic nucleoside analogue by modulation of transition types leads to extinction-escape." Plos Pathog., 6, e1001072. doi: 10.1371/journal.ppat.1001072. |
Mutant p169s of foot-and-mouth disease virus RNA dependent RNA-polymerase. SNAP output |
| 3nmr |
RNA binding protein-RNA |
X-ray (1.85 Å) |
Teplova M, Song J, Gaw HY, Teplov A, Patel DJ |
(2010) "Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1." Structure, 18, 1364-1377. doi: 10.1016/j.str.2010.06.018. |
Crystal structure of cugbp1 rrm1-2-RNA complex. SNAP output |
| 3nmu |
transferase-RNA |
X-ray (2.729 Å) |
Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H |
(2010) "Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle." Mol.Cell, 39, 939-949. doi: 10.1016/j.molcel.2010.08.022. |
Crystal structure of substrate-bound halfmer box c-d rnp. SNAP output |
| 3nna |
RNA binding protein-RNA |
X-ray (1.899 Å) |
Teplova M, Song J, Gaw HY, Teplov A, Patel DJ |
(2010) "Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1." Structure, 18, 1364-1377. doi: 10.1016/j.str.2010.06.018. |
Crystal structure of cugbp1 rrm1-2-RNA complex. SNAP output |
| 3nnc |
RNA binding protein-RNA |
X-ray (2.2 Å) |
Teplova M, Song J, Gaw HY, Teplov A, Patel DJ |
(2010) "Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1." Structure, 18, 1364-1377. doi: 10.1016/j.str.2010.06.018. |
Crystal structure of cugbp1 rrm1-2-RNA complex. SNAP output |
| 3nnh |
RNA binding protein-RNA |
X-ray (2.75 Å) |
Teplova M, Song J, Gaw HY, Teplov A, Patel DJ |
(2010) "Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1." Structure, 18, 1364-1377. doi: 10.1016/j.str.2010.06.018. |
Crystal structure of the cugbp1 rrm1 with guuguuuuguuu RNA. SNAP output |
| 3nvi |
transferase-RNA |
X-ray (2.709 Å) |
Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H |
(2010) "Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle." Mol.Cell, 39, 939-949. doi: 10.1016/j.molcel.2010.08.022. |
Structure of n-terminal truncated nop56-58 bound with l7ae and box c-d RNA. SNAP output |
| 3nvk |
transferase-RNA |
X-ray (3.209 Å) |
Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H |
(2010) "Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle." Mol.Cell, 39, 939-949. doi: 10.1016/j.molcel.2010.08.022. |
Structural basis for substrate placement by an archaeal box c-d ribonucleoprotein particle. SNAP output |
| 3o3i |
RNA binding protein |
X-ray (2.801 Å) |
Tian Y, Simanshu DK, Ma JB, Patel DJ |
(2011) "Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains." Proc.Natl.Acad.Sci.USA, 108, 903-910. doi: 10.1073/pnas.1017762108. |
Crystal structure of human hiwi1 paz domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-oh at its 3'-end. SNAP output |
| 3o6e |
RNA binding protein-RNA |
X-ray (2.904 Å) |
Tian Y, Simanshu DK, Ma JB, Patel DJ |
(2011) "Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains." Proc.Natl.Acad.Sci.USA, 108, 903-910. doi: 10.1073/pnas.1017762108. |
Crystal structure of human hiwi1 paz domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-och3 at its 3'-end. SNAP output |
| 3o7v |
RNA binding protein-RNA |
X-ray (2.1 Å) |
Tian Y, Simanshu DK, Ma JB, Patel DJ |
(2011) "Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains." Proc.Natl.Acad.Sci.USA, 108, 903-910. doi: 10.1073/pnas.1017762108. |
Crystal structure of human hiwi1 (v361m) paz domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-och3 at its 3'-end. SNAP output |
| 3o8c |
hydrolase-RNA |
X-ray (2.0 Å) |
Appleby TC, Anderson R, Fedorova O, Pyle AM, Wang R, Liu X, Brendza KM, Somoza JR |
(2011) "Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV." J.Mol.Biol., 405, 1139-1153. doi: 10.1016/j.jmb.2010.11.034. |
Visualizing atp-dependent RNA translocation by the ns3 helicase from hcv. SNAP output |
| 3o8r |
hydrolase-RNA |
X-ray (2.304 Å) |
Appleby TC, Anderson R, Fedorova O, Pyle AM, Wang R, Liu X, Brendza KM, Somoza JR |
(2011) "Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV." J.Mol.Biol., 405, 1139-1153. doi: 10.1016/j.jmb.2010.11.034. |
Visualizing atp-dependent RNA translocation by the ns3 helicase from hcv. SNAP output |
| 3og8 |
hydrolase-RNA |
X-ray (2.4 Å) |
Lu C, Ranjith-Kumar CT, Hao L, Kao CC, Li P |
(2011) "Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5' triphosphate." Nucleic Acids Res., 39, 1565-1575. doi: 10.1093/nar/gkq974. |
Crystal structure of human rig-i ctd bound to a 14-bp blunt-ended dsrna. SNAP output |
| 3oij |
ribosomal protein |
X-ray (3.0 Å) |
Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA |
(2011) "Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis." Nucleic Acids Res., 39, 2445-2457. doi: 10.1093/nar/gkq1131. |
Crystal structure of saccharomyces cerevisiae nep1-emg1 bound to s-adenosylhomocysteine and 2 molecules of cognate RNA. SNAP output |
| 3oin |
ribosomal protein |
X-ray (1.9 Å) |
Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA |
(2011) "Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis." Nucleic Acids Res., 39, 2445-2457. doi: 10.1093/nar/gkq1131. |
Crystal structure of saccharomyces cerevisiae nep1-emg1 bound to s-adenosylhomocysteine and 1 molecule of cognate RNA. SNAP output |
| 3ol6 |
transferase-RNA |
X-ray (2.5 Å) |
Gong P, Peersen OB |
(2010) "Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 22505-22510. doi: 10.1073/pnas.1007626107. |
Poliovirus polymerase elongation complex. SNAP output |
| 3ol7 |
transferase-RNA |
X-ray (2.7 Å) |
Gong P, Peersen OB |
(2010) "Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 22505-22510. doi: 10.1073/pnas.1007626107. |
Poliovirus polymerase elongation complex with ctp. SNAP output |
| 3ol8 |
transferase-RNA |
X-ray (2.75 Å) |
Gong P, Peersen OB |
(2010) "Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 22505-22510. doi: 10.1073/pnas.1007626107. |
Poliovirus polymerase elongation complex with ctp-mn. SNAP output |
| 3ol9 |
transferase-RNA |
X-ray (2.25 Å) |
Gong P, Peersen OB |
(2010) "Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 22505-22510. doi: 10.1073/pnas.1007626107. |
Poliovirus polymerase elongation complex with 3'-deoxy-ctp. SNAP output |
| 3ola |
transferase-RNA |
X-ray (2.55 Å) |
Gong P, Peersen OB |
(2010) "Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 22505-22510. doi: 10.1073/pnas.1007626107. |
Poliovirus polymerase elongation complex with 2'-deoxy-ctp. SNAP output |
| 3olb |
transferase-RNA |
X-ray (2.41 Å) |
Gong P, Peersen OB |
(2010) "Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase." Proc.Natl.Acad.Sci.USA, 107, 22505-22510. doi: 10.1073/pnas.1007626107. |
Poliovirus polymerase elongation complex with 2',3'-dideoxy-ctp. SNAP output |
| 3oto |
ribosome |
X-ray (3.69 Å) |
Demirci H, Murphy F, Belardinelli R, Kelley AC, Ramakrishnan V, Gregory ST, Dahlberg AE, Jogl G |
(2010) "Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function." Rna, 16, 2319-2324. doi: 10.1261/rna.2357210. |
Crystal structure of the 30s ribosomal subunit from a ksga mutant of thermus thermophilus (hb8). SNAP output |
| 3ouy |
transferase-RNA |
X-ray (2.69 Å) |
Pan B, Xiong Y, Steitz TA |
(2010) "How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA." Science, 330, 937-940. doi: 10.1126/science.1194985. |
How the cca-adding enzyme selects adenine over cytosine at position 76 of trna. SNAP output |
| 3ov7 |
transferase-RNA |
X-ray (3.0 Å) |
Pan B, Xiong Y, Steitz TA |
(2010) "How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA." Science, 330, 937-940. doi: 10.1126/science.1194985. |
How the cca-adding enzyme selects adenine over cytosine in position 76 of trna. SNAP output |
| 3ova |
transferase-RNA |
X-ray (1.98 Å) |
Pan B, Xiong Y, Steitz TA |
(2010) "How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA." Science, 330, 937-940. doi: 10.1126/science.1194985. |
How the cca-adding enzyme selects adenine over cytosine in position 76 of trna. SNAP output |
| 3ovb |
transferase-RNA |
X-ray (1.95 Å) |
Pan B, Xiong Y, Steitz TA |
(2010) "How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA." Science, 330, 937-940. doi: 10.1126/science.1194985. |
How the cca-adding enzyme selects adenine over cytosine in position 76 of trna. SNAP output |
| 3ovs |
transferase-RNA |
X-ray (2.8 Å) |
Pan B, Xiong Y, Steitz TA |
(2010) "How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA." Science, 330, 937-940. doi: 10.1126/science.1194985. |
How the cca-adding enzyme selects adenine over cytosine in position 76 of trna. SNAP output |
| 3ow2 |
ribosome |
X-ray (2.7 Å) |
|
|
Crystal structure of enhanced macrolide bound to 50s ribosomal subunit. SNAP output |
| 3p49 |
RNA binding protein-RNA |
X-ray (3.55 Å) |
Butler EB, Xiong Y, Wang J, Strobel SA |
(2011) "Structural basis of cooperative ligand binding by the glycine riboswitch." Chem.Biol., 18, 293-298. doi: 10.1016/j.chembiol.2011.01.013. |
Crystal structure of a glycine riboswitch from fusobacterium nucleatum. SNAP output |
| 3pdm |
virus |
fiber diffraction |
Tewary SK, Oda T, Kendall A, Bian W, Stubbs G, Wong SM, Swaminathan K |
(2010) "Structure of Hibiscus latent Singapore virus by fiber diffraction: A non-conserved His122 contributes to coat protein stability." J.Mol.Biol. doi: 10.1016/j.jmb.2010.12.032. |
Hibiscus latent singapore virus. SNAP output |
| 3pew |
hydrolase-RNA |
X-ray (1.501 Å) |
Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K |
(2011) "A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP(6) in mRNA export." Nature, 472, 238-242. doi: 10.1038/nature09862. |
S. cerevisiae dbp5 l327v bound to RNA and adp bef3. SNAP output |
| 3pey |
hydrolase-RNA |
X-ray (1.401 Å) |
Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K |
(2011) "A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP(6) in mRNA export." Nature, 472, 238-242. doi: 10.1038/nature09862. |
S. cerevisiae dbp5 bound to RNA and adp bef3. SNAP output |
| 3pf4 |
gene regulation-RNA |
X-ray (1.38 Å) |
Sachs R, Max KE, Heinemann U, Balbach J |
(2012) "RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution." Rna, 18, 65-76. doi: 10.1261/rna.02809212. |
Crystal structure of bs-cspb in complex with r(gucuuua). SNAP output |
| 3pf5 |
gene regulation-RNA |
X-ray (1.68 Å) |
Sachs R, Max KE, Heinemann U, Balbach J |
(2012) "RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution." Rna, 18, 65-76. doi: 10.1261/rna.02809212. |
Crystal structure of bs-cspb in complex with ru6. SNAP output |
| 3pio |
ribosome-antibiotic |
X-ray (3.25 Å) |
Belousoff MJ, Shapira T, Bashan A, Zimmerman E, Rozenberg H, Arakawa K, Kinashi H, Yonath A |
(2011) "Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit." Proc.Natl.Acad.Sci.USA, 108, 2717-2722. doi: 10.1073/pnas.1019406108. |
Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit. SNAP output |
| 3pip |
ribosome-antibiotic |
X-ray (3.45 Å) |
Belousoff MJ, Shapira T, Bashan A, Zimmerman E, Rozenberg H, Arakawa K, Kinashi H, Yonath A |
(2011) "Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit." Proc.Natl.Acad.Sci.USA, 108, 2717-2722. doi: 10.1073/pnas.1019406108. |
Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit. SNAP output |
| 3pkm |
hydrolase-RNA |
X-ray (3.103 Å) |
Wang R, Preamplume G, Terns MP, Terns RM, Li H |
(2011) "Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage." Structure, 19, 257-264. doi: 10.1016/j.str.2010.11.014. |
Crystal structure of cas6 with its substrate RNA. SNAP output |
| 3pla |
transferase-RNA |
X-ray (3.15 Å) |
Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K |
(2011) "Structural basis for site-specific ribose methylation by box C/D RNA protein complexes." Nature, 469, 559-563. doi: 10.1038/nature09688. |
Crystal structure of a catalytically active substrate-bound box c-d rnp from sulfolobus solfataricus. SNAP output |
| 3ptx |
viral protein-RNA |
X-ray (3.0 Å) |
Green TJ, Rowse M, Tsao J, Kang J, Ge P, Zhou ZH, Luo M |
(2011) "Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus." J.Virol., 85, 2714-2722. doi: 10.1128/JVI.01927-10. |
Crystal structure of a vesicular stomatitis virus nucleocapsid-polya complex. SNAP output |
| 3pu0 |
viral protein-RNA |
X-ray (3.09 Å) |
Green TJ, Rowse M, Tsao J, Kang J, Ge P, Zhou ZH, Luo M |
(2011) "Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus." J.Virol., 85, 2714-2722. doi: 10.1128/JVI.01927-10. |
Crystal structure of a vesicular stomatitis virus nucleocapsid-polyc complex. SNAP output |
| 3pu1 |
viral protein-RNA |
X-ray (3.14 Å) |
Green TJ, Rowse M, Tsao J, Kang J, Ge P, Zhou ZH, Luo M |
(2011) "Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus." J.Virol., 85, 2714-2722. doi: 10.1128/JVI.01927-10. |
Crystal structure of a vesicular stomatitis virus nucleocapsid-polyg complex. SNAP output |
| 3pu4 |
viral protein-RNA |
X-ray (3.0 Å) |
Green TJ, Rowse M, Tsao J, Kang J, Ge P, Zhou ZH, Luo M |
(2011) "Access to RNA Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus." J.Virol., 85, 2714-2722. doi: 10.1128/JVI.01927-10. |
Crystal structure of a vesicular stomatitis virus nucleocapsid-polyu complex. SNAP output |
| 3q0l |
RNA binding protein-RNA |
X-ray (2.503 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with p38alpha nrea. SNAP output |
| 3q0m |
RNA binding protein-RNA |
X-ray (2.705 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with p38alpha nreb. SNAP output |
| 3q0n |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with erk2 nre. SNAP output |
| 3q0o |
RNA binding protein-RNA |
X-ray (2.804 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with erk2 nre. SNAP output |
| 3q0p |
RNA binding protein-RNA |
X-ray (2.6 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio1 in complex with hunchback nre. SNAP output |
| 3q0q |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio2 in complex with p38alpha nrea. SNAP output |
| 3q0r |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio2 in complex with p38alpha nreb. SNAP output |
| 3q0s |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Lu G, Hall TM |
(2011) "Alternate modes of cognate RNA recognition by human PUMILIO proteins." Structure, 19, 361-367. doi: 10.1016/j.str.2010.12.019. |
Crystal structure of the pumilio-homology domain from human pumilio2 in complex with erk2 nre. SNAP output |
| 3q2t |
RNA binding protein-RNA |
X-ray (3.061 Å) |
Yang Q, Coseno M, Gilmartin GM, Doublie S |
(2011) "Crystal Structure of a Human Cleavage Factor CFI(m)25/CFI(m)68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping." Structure, 19, 368-377. doi: 10.1016/j.str.2010.12.021. |
Crystal structure of cfim68 rrm-cfim25-RNA complex. SNAP output |
| 3qg9 |
RNA binding protein-RNA |
X-ray (2.25 Å) |
Koh YY, Wang Y, Qiu C, Opperman L, Gross L, Tanaka Hall TM, Wickens M |
(2011) "Stacking interactions in PUF-RNA complexes." Rna, 17, 718-727. doi: 10.1261/rna.2540311. |
Crystal structure of fbf-2-gld-1 fbea a7u mutant complex. SNAP output |
| 3qgb |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Koh YY, Wang Y, Qiu C, Opperman L, Gross L, Tanaka Hall TM, Wickens M |
(2011) "Stacking interactions in PUF-RNA complexes." Rna, 17, 718-727. doi: 10.1261/rna.2540311. |
Crystal structure of fbf-2 r288y mutant in complex with gld-1 fbea. SNAP output |
| 3qgc |
RNA binding protein-RNA |
X-ray (1.9 Å) |
Koh YY, Wang Y, Qiu C, Opperman L, Gross L, Tanaka Hall TM, Wickens M |
(2011) "Stacking interactions in PUF-RNA complexes." Rna, 17, 718-727. doi: 10.1261/rna.2540311. |
Crystal structure of fbf-2 r288y mutant in complex with gld-1 fbea a7u mutant. SNAP output |
| 3qjj |
immune system-RNA |
X-ray (2.8 Å) |
Wang R, Zheng H, Preamplume G, Li H |
"Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA." |
One ramp protein binding different RNA substrates. SNAP output |
| 3qjl |
immune system-RNA |
X-ray (2.7 Å) |
Wang R, Zheng H, Preamplume G, Li H |
"Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA." |
One ramp protein binding different RNA substrates. SNAP output |
| 3qjp |
immune system-RNA |
X-ray (3.3 Å) |
Wang R, Zheng H, Preamplume G, Li H |
"Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA." |
An ramp protein binding different RNA substrates. SNAP output |
| 3qrp |
RNA binding protein-RNA |
X-ray (2.352 Å) |
Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM |
(2011) "Recognition and maturation of effector RNAs in a CRISPR interference pathway." Nat.Struct.Mol.Biol., 18, 688-692. doi: 10.1038/nsmb.2042. |
Structure of thermus thermophilus cse3 bound to an RNA representing a product mimic complex. SNAP output |
| 3qrq |
RNA binding protein-RNA |
X-ray (3.194 Å) |
Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM |
(2011) "Recognition and maturation of effector RNAs in a CRISPR interference pathway." Nat.Struct.Mol.Biol., 18, 688-692. doi: 10.1038/nsmb.2042. |
Structure of thermus thermophilus cse3 bound to an RNA representing a pre-cleavage complex. SNAP output |
| 3qrr |
RNA binding protein-RNA |
X-ray (3.099 Å) |
Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM |
(2011) "Recognition and maturation of effector RNAs in a CRISPR interference pathway." Nat.Struct.Mol.Biol., 18, 688-692. doi: 10.1038/nsmb.2042. |
Structure of thermus thermophilus cse3 bound to an RNA representing a product complex. SNAP output |
| 3qsu |
chaperone-RNA |
X-ray (2.2 Å) |
Horstmann N, Orans J, Valentin-Hansen P, Shelburne SA, Brennan RG |
(2012) "Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract." Nucleic Acids Res., 40, 11023-11035. doi: 10.1093/nar/gks809. |
Structure of staphylococcus aureus hfq in complex with a7 RNA. SNAP output |
| 3qsy |
translation-RNA |
X-ray (3.2 Å) |
Stolboushkina E, Nikonov S, Zelinskaya N, Arkhipova V, Nikulin A, Garber M, Nikonov O |
(2013) "Crystal structure of the archaeal translation initiation factor 2 in complex with a GTP analogue and Met-tRNAf(Met.)." J.Mol.Biol., 425, 989-998. doi: 10.1016/j.jmb.2012.12.023. |
Recognition of the methionylated initiator trna by the translation initiation factor 2 in archaea. SNAP output |
| 3r1h |
RNA binding protein-RNA |
X-ray (3.15 Å) |
Shechner DM, Bartel DP |
(2011) "The structural basis of RNA-catalyzed RNA polymerization." Nat.Struct.Mol.Biol., 18, 1036-1042. doi: 10.1038/nsmb.2107. |
Crystal structure of the class i ligase ribozyme-substrate preligation complex, c47u mutant, ca2+ bound. SNAP output |
| 3r1l |
RNA binding protein-RNA |
X-ray (3.125 Å) |
Shechner DM, Bartel DP |
(2011) "The structural basis of RNA-catalyzed RNA polymerization." Nat.Struct.Mol.Biol., 18, 1036-1042. doi: 10.1038/nsmb.2107. |
Crystal structure of the class i ligase ribozyme-substrate preligation complex, c47u mutant, mg2+ bound. SNAP output |
| 3r2c |
transcription-RNA |
X-ray (1.902 Å) |
Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X |
(2011) "Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination." Nucleic Acids Res., 39, 7803-7815. doi: 10.1093/nar/gkr418. |
Crystal structure of antitermination factors nusb and nuse in complex with boxa RNA. SNAP output |
| 3r2d |
transcription-RNA |
X-ray (2.199 Å) |
Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X |
(2011) "Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination." Nucleic Acids Res., 39, 7803-7815. doi: 10.1093/nar/gkr418. |
Crystal structure of antitermination factors nusb and nuse in complex with dsrna. SNAP output |
| 3r9w |
hydrolase-RNA |
X-ray (2.05 Å) |
Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X |
(2011) "The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA." Proc.Natl.Acad.Sci.USA, 108, 10156-10161. doi: 10.1073/pnas.1017679108. |
Crystal structure of era in complex with mggdpnp and nucleotides 1506-1542 of 16s ribosomal RNA. SNAP output |
| 3r9x |
hydrolase-transferase-RNA |
X-ray (2.8 Å) |
Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, Waugh DS, Court DL, Ji X |
(2011) "The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA." Proc.Natl.Acad.Sci.USA, 108, 10156-10161. doi: 10.1073/pnas.1017679108. |
Crystal structure of era in complex with mggdpnp, nucleotides 1506-1542 of 16s ribosomal RNA, and ksga. SNAP output |
| 3rc8 |
hydrolase-RNA |
X-ray (2.9 Å) |
Jedrzejczak R, Wang J, Dauter M, Szczesny RJ, Stepien PP, Dauter Z |
(2011) "Human Suv3 protein reveals unique features among SF2 helicases." Acta Crystallogr.,Sect.D, 67, 988-996. doi: 10.1107/S0907444911040248. |
Human mitochondrial helicase suv3 in complex with short RNA fragment. SNAP output |
| 3rer |
chaperone-RNA |
X-ray (1.7 Å) |
Wang W, Wang L, Zou Y, Zhang J, Gong Q, Wu J, Shi Y |
(2011) "Cooperation of Escherichia coli Hfq hexamers in DsrA binding." Genes Dev., 25, 2106-2117. doi: 10.1101/gad.16746011. |
Crystal structure of e. coli hfq in complex with au6a RNA and adp. SNAP output |
| 3rtj |
hydrolase-RNA |
X-ray (3.0 Å) |
Monzingo AF, Robertus JD |
(1992) "X-ray analysis of substrate analogs in the ricin A-chain active site." J.Mol.Biol., 227, 1136-1145. |
Crystal structure of ricin bound with dinucleotide apg. SNAP output |
| 3rw6 |
transport protein-RNA |
X-ray (2.3 Å) |
Teplova M, Wohlbold L, Khin NW, Izaurralde E, Patel DJ |
(2011) "Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP." Nat.Struct.Mol.Biol., 18, 990-998. doi: 10.1038/nsmb.2094. |
Structure of nuclear RNA export factor tap bound to cte RNA. SNAP output |
| 3s4g |
virus |
X-ray (6.0 Å) |
Lane SW, Dennis CA, Lane CL, Trinh CH, Rizkallah PJ, Stockley PG, Phillips SE |
(2011) "Construction and crystal structure of recombinant STNV capsids." J.Mol.Biol., 413, 41-50. doi: 10.1016/j.jmb.2011.07.062. |
Low resolution structure of stnv complexed with RNA. SNAP output |
| 3siu |
splicing-RNA |
X-ray (2.626 Å) |
Liu S, Ghalei H, Luhrmann R, Wahl MC |
(2011) "Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31." Rna, 17, 1655-1663. doi: 10.1261/rna.2690611. |
Structure of a hprp31-15.5k-u4atac 5' stem loop complex, monomeric form. SNAP output |
| 3siv |
splicing-RNA |
X-ray (3.304 Å) |
Liu S, Ghalei H, Luhrmann R, Wahl MC |
(2011) "Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31." Rna, 17, 1655-1663. doi: 10.1261/rna.2690611. |
Structure of a hprp31-15.5k-u4atac 5' stem loop complex, dimeric form. SNAP output |
| 3sn2 |
lyase-RNA |
X-ray (2.99 Å) |
Walden WE, Selezneva A, Volz K |
(2012) "Accommodating variety in iron-responsive elements: Crystal structure of transferrin receptor 1 B IRE bound to iron regulatory protein 1." Febs Lett., 586, 32-35. doi: 10.1016/j.febslet.2011.11.018. |
Crystal structure analysis of iron regulatory protein 1 in complex with transferrin receptor ire b RNA. SNAP output |
| 3snp |
lyase-RNA |
X-ray (2.8 Å) |
Walden WE, Selezneva AI, Dupuy J, Volbeda A, Fontecilla-Camps JC, Theil EC, Volz K |
(2006) "Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA." Science, 314, 1903-1908. doi: 10.1126/science.1133116. |
Crystal structure analysis of iron regulatory protein 1 in complex with ferritin h ire RNA. SNAP output |
| 3sqw |
hydrolase-RNA |
X-ray (1.909 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 deletion) bound to ssrna and amp-pnp. 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 |
| 3t1h |
ribosome-antibiotic |
X-ray (3.11 Å) |
Vendeix FA, Murphy FV, Cantara WA, Leszczynska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF |
(2012) "Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism." J.Mol.Biol., 416, 467-485. doi: 10.1016/j.jmb.2011.12.048. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human anti-codon stem loop (hasl) of transfer RNA lysine 3 (trnalys3) bound to an mrna with an aaa-codon in the a-site and paromomycin. SNAP output |
| 3t1y |
ribosome-antibiotic |
X-ray (2.8 Å) |
Vendeix FA, Murphy FV, Cantara WA, Leszczynska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF |
(2012) "Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism." J.Mol.Biol., 416, 467-485. doi: 10.1016/j.jmb.2011.12.048. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human anti-codon stem loop (hasl) of transfer RNA lysine 3 (trnalys3) bound to an mrna with an aag-codon in the a-site and paromomycin. SNAP output |
| 3t3n |
hydrolase-RNA |
X-ray (3.09 Å) |
Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C |
(2011) "Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J." Structure, 19, 1252-1261. doi: 10.1016/j.str.2011.06.018. |
Molecular basis for the recognition and cleavage of RNA (uuccgu) by the bifunctional 5'-3' exo-endoribonuclease rnase j. SNAP output |
| 3t3o |
hydrolase-RNA |
X-ray (2.5 Å) |
Dorleans A, Li de la Sierra-Gallay I, Piton J, Zig L, Gilet L, Putzer H, Condon C |
(2011) "Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J." Structure, 19, 1252-1261. doi: 10.1016/j.str.2011.06.018. |
Molecular basis for the recognition and cleavage of RNA (cugg) by the bifunctional 5'-3' exo-endoribonuclease rnase j. SNAP output |
| 3t5n |
viral protein-RNA |
X-ray (1.787 Å) |
Hastie KM, Liu T, Li S, King LB, Ngo N, Zandonatti MA, Woods VL, de la Torre JC, Saphire EO |
(2011) "Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding." Proc.Natl.Acad.Sci.USA, 108, 19365-19370. doi: 10.1073/pnas.1108515108. |
1.8a crystal structure of lassa virus nucleoprotein in complex with ssrna. SNAP output |
| 3t5q |
viral protein-RNA |
X-ray (3.0 Å) |
Hastie KM, Liu T, Li S, King LB, Ngo N, Zandonatti MA, Woods VL, de la Torre JC, Saphire EO |
(2011) "Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding." Proc.Natl.Acad.Sci.USA, 108, 19365-19370. doi: 10.1073/pnas.1108515108. |
3a structure of lassa virus nucleoprotein in complex with ssrna. SNAP output |
| 3trz |
RNA binding protein-RNA |
X-ray (2.9 Å) |
Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P |
(2011) "Molecular Basis for Interaction of let-7 MicroRNAs with Lin28." Cell(Cambridge,Mass.), 147, 1080-1091. doi: 10.1016/j.cell.2011.10.020. |
Mouse lin28a in complex with let-7d microrna pre-element. SNAP output |
| 3ts0 |
RNA binding protein-RNA |
X-ray (2.763 Å) |
Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P |
(2011) "Molecular Basis for Interaction of let-7 MicroRNAs with Lin28." Cell(Cambridge,Mass.), 147, 1080-1091. doi: 10.1016/j.cell.2011.10.020. |
Mouse lin28a in complex with let-7f-1 microrna pre-element. SNAP output |
| 3ts2 |
RNA binding protein-RNA |
X-ray (2.01 Å) |
Nam Y, Chen C, Gregory RI, Chou JJ, Sliz P |
(2011) "Molecular Basis for Interaction of let-7 MicroRNAs with Lin28." Cell(Cambridge,Mass.), 147, 1080-1091. doi: 10.1016/j.cell.2011.10.020. |
Mouse lin28a in complex with let-7g microrna pre-element. SNAP output |
| 3tup |
ligase-RNA |
X-ray (3.05 Å) |
Klipcan L, Moor N, Finarov I, Kessler N, Sukhanova M, Safro MG |
(2012) "Crystal Structure of Human Mitochondrial PheRS Complexed with tRNA(Phe) in the Active "Open" State." J.Mol.Biol., 415, 527-537. doi: 10.1016/j.jmb.2011.11.029. |
Crystal structure of human mitochondrial phers complexed with trnaphe in the active open state. SNAP output |
| 3u2e |
lyase-RNA |
X-ray (2.32 Å) |
Filippova EV, Minasov G, Shuvalova L, Kiryukhina O, Massa C, Schirmer T, Joachimiak A, Anderson WF, Midwest Center for Structural Genomics (MCSG) |
"EAL domain from Caulobacter crescentus in complex with 5'-pGpG and Mg++." |
Eal domain of phosphodiesterase pdea in complex with 5'-pgpg and mg++. SNAP output |
| 3u4m |
RNA-RNA binding protein |
X-ray (2.0 Å) |
Tishchenko S, Gabdulkhakov A, Nevskaya N, Sarskikh A, Kostareva O, Nikonova E, Sycheva A, Moshkovskii S, Garber M, Nikonov S |
(2012) "High-resolution crystal structure of the isolated ribosomal L1 stalk." Acta Crystallogr.,Sect.D, 68, 1051-1057. doi: 10.1107/S0907444912020136. |
Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s RNA from thermus thermophilus. SNAP output |
| 3u56 |
RNA-RNA binding protein |
X-ray (2.1 Å) |
Tishchenko SV, Nikonova EY, Kostareva OS, Gabdulkhakov AG, Sarskikh AV, Piendl W, Nikonov SV, Garber MB, Nevskaya NA |
"Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus." |
Crystal structure of mutant ribosomal protein t217v tthl1 in complex with 80nt 23s RNA from thermus thermophilus. SNAP output |
| 3ucu |
signaling protein-RNA |
X-ray (2.8 Å) |
Smith KD, Lipchock SV, Strobel SA |
(2012) "Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer." Biochemistry, 51, 425-432. doi: 10.1021/bi2016662. |
The c-di-gmp-i riboswitch bound to pgpg. SNAP output |
| 3ucz |
signaling protein-RNA |
X-ray (2.8 Å) |
Smith KD, Lipchock SV, Strobel SA |
(2012) "Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer." Biochemistry, 51, 425-432. doi: 10.1021/bi2016662. |
The c-di-gmp-i riboswitch bound to gpg. SNAP output |
| 3ud3 |
signaling protein-RNA |
X-ray (3.1 Å) |
Smith KD, Lipchock SV, Strobel SA |
(2012) "Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer." Biochemistry, 51, 425-432. doi: 10.1021/bi2016662. |
The c92u mutant c-di-gmp-i riboswitch bound to pgpa. SNAP output |
| 3ud4 |
signaling protein-RNA |
X-ray (2.7 Å) |
Smith KD, Lipchock SV, Strobel SA |
(2012) "Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer." Biochemistry, 51, 425-432. doi: 10.1021/bi2016662. |
The c92u mutant c-di-gmp-i riboswitch bound to gpa. SNAP output |
| 3umy |
rrna binding protein-RNA |
X-ray (1.9 Å) |
Tishchenko SV, Nikonova EY, Kostareva OS, Gabdulkhakov AG, Sarskikh AV, Piendl W, Nikonov SV, Garber MB, Nevskaya NA |
"Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt 23S RNA from Thermus thermophilus." |
Crystal structure of mutant ribosomal protein t217a tthl1 in complex with 80nt 23s RNA from thermus thermophilus. SNAP output |
| 3uzs |
transferase-RNA |
X-ray (4.52 Å) |
Tesmer VM, Lennarz S, Mayer G, Tesmer JJ |
(2012) "Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer." Structure, 20, 1300-1309. doi: 10.1016/j.str.2012.05.002. |
Structure of the c13.28 RNA aptamer bound to the g protein-coupled receptor kinase 2-heterotrimeric g protein beta 1 and gamma 2 subunit complex. SNAP output |
| 3uzt |
transferase-RNA |
X-ray (3.51 Å) |
Tesmer VM, Lennarz S, Mayer G, Tesmer JJ |
(2012) "Molecular mechanism for inhibition of g protein-coupled receptor kinase 2 by a selective RNA aptamer." Structure, 20, 1300-1309. doi: 10.1016/j.str.2012.05.002. |
Structure of the c13.18 RNA aptamer in complex with g protein-coupled receptor kinase 2. SNAP output |
| 3v11 |
translation-RNA |
X-ray (5.0 Å) |
Schmitt E, Panvert M, Lazennec-Schurdevin C, Coureux PD, Perez J, Thompson A, Mechulam Y |
(2012) "Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA." Nat.Struct.Mol.Biol., 19, 450-454. doi: 10.1038/nsmb.2259. |
Structure of the ternary initiation complex aif2:gdpnp:methionylated initiator trna. SNAP output |
| 3v6y |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Qiu C, Kershner A, Wang Y, Holley CH, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT |
(2012) "Divergence of PUF protein specificity through variations in an RNA-binding pocket." J.Biol.Chem. |
Crystal structure of fbf-2 in complex with a mutant gld-1 fbea13 RNA. SNAP output |
| 3v71 |
RNA binding protein-RNA |
X-ray (2.902 Å) |
Qiu C, Kershner A, Wang Y, Holley CH, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT |
(2012) "Divergence of PUF protein specificity through variations in an RNA-binding pocket." J.Biol.Chem. |
Crystal structure of puf-6 in complex with 5be13 RNA. SNAP output |
| 3v74 |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Wang Y, Qiu C, Kershner A, Holley CP, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT |
(2012) "Divergence of PUF protein specificity through variations in an RNA-binding pocket." J.Biol.Chem. |
Crystal structure of fbf-2 in complex with gld-1 fbea13 RNA. SNAP output |
| 3v7e |
ribosomal protein-RNA |
X-ray (2.8 Å) |
Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR |
(2012) "YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops." Rna, 18, 759-770. doi: 10.1261/rna.031518.111. |
Crystal structure of ybxf bound to the sam-i riboswitch aptamer. SNAP output |
| 3vjr |
hydrolase-RNA |
X-ray (2.4 Å) |
Ito K, Murakami R, Mochizuki M, Qi H, Shimizu Y, Miura K, Ueda T, Uchiumi T |
(2012) "Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase." Nucleic Acids Res., 40, 10521-10531. doi: 10.1093/nar/gks790. |
Crystal structure of peptidyl-trna hydrolase from escherichia coli in complex with the cca-acceptor-t[psi]c domain of trna. SNAP output |
| 3vnu |
translation, transferase-RNA |
X-ray (3.2 Å) |
Takeshita D, Yamashita S, Tomita K |
(2012) "Mechanism for template-independent terminal adenylation activity of Q beta replicase." Structure, 20, 1661-1669. doi: 10.1016/j.str.2012.07.004. |
Complex structure of viral RNA polymerase i. SNAP output |
| 3vnv |
translation, transferase-RNA |
X-ray (2.604 Å) |
Takeshita D, Yamashita S, Tomita K |
(2012) "Mechanism for template-independent terminal adenylation activity of Q beta replicase." Structure, 20, 1661-1669. doi: 10.1016/j.str.2012.07.004. |
Complex structure of viral RNA polymerase ii. SNAP output |
| 3vyx |
hydrolase-RNA |
X-ray (2.29 Å) |
Fu Q, Yuan YA |
(2013) "Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)." Nucleic Acids Res. doi: 10.1093/nar/gkt042. |
Structural insights into risc assembly facilitated by dsrna binding domains of human RNA helicase (dhx9). SNAP output |
| 3vyy |
hydrolase-RNA |
X-ray (2.9 Å) |
Fu Q, Yuan YA |
(2013) "Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)." Nucleic Acids Res. doi: 10.1093/nar/gkt042. |
Structural insights into risc assembly facilitated by dsrna binding domains of human RNA helicase a (dhx9). SNAP output |
| 3w1k |
transferase-RNA |
X-ray (7.5 Å) |
Itoh Y, Brocker MJ, Sekine S, Hammond G, Suetsugu S, Soll D, Yokoyama S |
(2013) "Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation." Science, 340, 75-78. doi: 10.1126/science.1229521. |
Crystal structure of the selenocysteine synthase sela and trnasec complex. SNAP output |
| 3w3s |
ligase-RNA |
X-ray (3.095 Å) |
Itoh Y, Sekine S, Suetsugu S, Yokoyama S |
(2013) "Tertiary structure of bacterial selenocysteine tRNA." Nucleic Acids Res., 41, 6729-6738. doi: 10.1093/nar/gkt321. |
Crystal structure of a. aeolicus trnasec in complex with m. kandleri serrs. SNAP output |
| 3wbm |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Guo L, Ding J, Guo R, Hou Y, Wang DC, Huang L |
(2014) "Biochemical and structural insights into RNA binding by Ssh10b, a member of the highly conserved Sac10b protein family in Archaea." J.Biol.Chem., 289, 1478-1490. doi: 10.1074/jbc.M113.521351. |
Crystal structure of protein-RNA complex. SNAP output |
| 3wc1 |
transferase-RNA |
X-ray (4.18 Å) |
Nakamura A, Nemoto T, Heinemann IU, Yamashita K, Sonoda T, Komoda K, Tanaka I, Soll D, Yao M |
(2013) "Structural basis of reverse nucleotide polymerization." Proc.Natl.Acad.Sci.USA, 110, 20970-20975. doi: 10.1073/pnas.1321312111. |
Crystal structure of c. albicans trna(his) guanylyltransferase (thg1) with a g-1 deleted trna(his). SNAP output |
| 3wc2 |
transferase-RNA |
X-ray (3.641 Å) |
Nakamura A, Nemoto T, Heinemann IU, Yamashita K, Sonoda T, Komoda K, Tanaka I, Soll D, Yao M |
(2013) "Structural basis of reverse nucleotide polymerization." Proc.Natl.Acad.Sci.USA, 110, 20970-20975. doi: 10.1073/pnas.1321312111. |
Crystal structure of c. albicans trna(his) guanylyltransferase (thg1) with a trna(phe)(gug). SNAP output |
| 3wfq |
transferase-RNA |
X-ray (3.619 Å) |
Yamashita S, Takeshita D, Tomita K |
(2014) "Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase." Structure, 22, 315-325. doi: 10.1016/j.str.2013.12.002. |
Trna processing enzyme complex 1. SNAP output |
| 3wfr |
transferase-RNA |
X-ray (3.501 Å) |
Yamashita S, Takeshita D, Tomita K |
(2014) "Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase." Structure, 22, 315-325. doi: 10.1016/j.str.2013.12.002. |
Trna processing enzyme complex 2. SNAP output |
| 3wfs |
transferase-RNA |
X-ray (3.311 Å) |
Yamashita S, Takeshita D, Tomita K |
(2014) "Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase." Structure, 22, 315-325. doi: 10.1016/j.str.2013.12.002. |
Trna processing enzyme complex 3. SNAP output |
| 3wqy |
ligase-RNA |
X-ray (3.3 Å) |
Naganuma M, Sekine S, Chong YE, Guo M, Yang XL, Gamper H, Hou YM, Schimmel P, Yokoyama S |
(2014) "The selective tRNA aminoacylation mechanism based on a single G.U pair." Nature, 510, 507-511. doi: 10.1038/nature13440. |
Crystal structure of archaeoglobus fulgidus alanyl-trna synthetase in complex with wild-type trna(ala) having g3.u70. SNAP output |
| 3wqz |
ligase-RNA |
X-ray (3.489 Å) |
Naganuma M, Sekine S, Chong YE, Guo M, Yang XL, Gamper H, Hou YM, Schimmel P, Yokoyama S |
(2014) "The selective tRNA aminoacylation mechanism based on a single G.U pair." Nature, 510, 507-511. doi: 10.1038/nature13440. |
Crystal structure of archaeoglobus fulgidus alanyl-trna synthetase in complex with a trna(ala) variant having a3.u70. SNAP output |
| 3wzi |
transcription-RNA |
X-ray (2.9 Å) |
Yan X, Guo W, Yuan YA |
(2015) "Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease." Rna Biol. doi: 10.1080/15476286.2015.1051300. |
Crystal structure of afcsx3 in complex with ssrna. SNAP output |
| 3zc0 |
hydrolase-RNA |
X-ray (2.982 Å) |
Parizotto EA, Lowe ED, Parker JS |
(2013) "Structural Basis for Duplex RNA Recognition and Cleavage by Archaeoglobus Fulgidus C3Po." Nat.Struct.Mol.Biol., 20, 380. doi: 10.1038/NSMB.2487. |
Structure of afc3po - duplex RNA complex. SNAP output |
| 3zd6 |
hydrolase-RNA |
X-ray (2.8 Å) |
Kohlway A, Luo D, Rawling DC, Ding SC, Pyle AM |
(2013) "Defining the Functional Determinants for RNA Surveillance by Rig-I." Embo Rep., 14, 772. doi: 10.1038/EMBOR.2013.108. |
Snapshot 1 of rig-i scanning on RNA duplex. SNAP output |
| 3zd7 |
hydrolase-RNA |
X-ray (2.5 Å) |
Kohlway A, Luo D, Rawling DC, Ding SC, Pyle AM |
(2013) "Defining the Functional Determinants for RNA Surveillance by Rig-I." Embo Rep., 14, 772. doi: 10.1038/EMBOR.2013.108. |
Snapshot 3 of rig-i scanning on RNA duplex. 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 |
| 3zjt |
ligase-RNA |
X-ray (2.2 Å) |
Hernandez V, Crepin T, Palencia A, Cusack S, Akama T, Baker SJ, Bu W, Feng L, Freund YR, Liu L, Meewan M, Mohan M, Mao W, Rock FL, Sexton H, Sheoran A, Zhang Y, Zhang Y, Zhou Y, Nieman JA, Anugula MR, Keramane EM, Savariraj K, Reddy DS, Sharma R, Subedi R, Singh R, O'Leary A, Simon NL, De Marsh PL, Mushtaq S, Warner M, Livermore DM, Alley MRK, Plattner JJ |
(2013) "Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria." Antimicrob.Agents Chemother., 57, 1394. doi: 10.1128/AAC.02058-12. |
Ternary complex of e.coli leucyl-trna synthetase, trna(leu)574 and the benzoxaborole an3017 in the editing conformation. SNAP output |
| 3zju |
ligase-RNA |
X-ray (2.4 Å) |
Hernandez V, Crepin T, Palencia A, Cusack S, Akama T, Baker SJ, Bu W, Feng L, Freund YR, Liu L, Meewan M, Mohan M, Mao W, Rock FL, Sexton H, Sheoran A, Zhang Y, Zhang Y, Zhou Y, Nieman JA, Anugula MR, Keramane EM, Savariraj K, Reddy DS, Sharma R, Subedi R, Singh R, O'Leary A, Simon NL, De Marsh PL, Mushtaq S, Warner M, Livermore DM, Alley MRK, Plattner JJ |
(2013) "Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria." Antimicrob.Agents Chemother., 57, 1394. doi: 10.1128/AAC.02058-12. |
Ternary complex of e .coli leucyl-trna synthetase, trna(leu) and the benzoxaborole an3016 in the editing conformation. SNAP output |
| 3zjv |
ligase-RNA |
X-ray (2.31 Å) |
Hernandez V, Crepin T, Palencia A, Cusack S, Akama T, Baker SJ, Bu W, Feng L, Freund YR, Liu L, Meewan M, Mohan M, Mao W, Rock FL, Sexton H, Sheoran A, Zhang Y, Zhang Y, Zhou Y, Nieman JA, Anugula MR, Keramane EM, Savariraj K, Reddy DS, Sharma R, Subedi R, Singh R, O'Leary A, Simon NL, De Marsh PL, Mushtaq S, Warner M, Livermore DM, Alley MRK, Plattner JJ |
(2013) "Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria." Antimicrob.Agents Chemother., 57, 1394. doi: 10.1128/AAC.02058-12. |
Ternary complex of e .coli leucyl-trna synthetase, trna(leu) and the benzoxaborole an3213 in the editing conformation. SNAP output |
| 3zla |
viral protein-RNA |
X-ray (3.2 Å) |
Ariza A, Tanner SJ, Walter CT, Dent KC, Shepherd DA, Wu W, Matthews SV, Hiscox JA, Green TJ, Luo M, Elliott RM, Fooks AR, Ashcroft AE, Stonehouse NJ, Ranson NA, Barr JN, Edwards TA |
(2013) "Nucleocapsid Protein Structures from Orthobunyaviruses Reveal Insight Into Ribonucleoprotein Architecture and RNA Polymerization." Nucleic Acids Res., 41, 5912. doi: 10.1093/NAR/GKT268. |
Crystal structure of the nucleocapsid protein from bunyamwera virus bound to RNA. SNAP output |
| 3zn8 |
protein transport |
cryo-EM (12.0 Å) |
Von Loeffelholz O, Knoops K, Ariosa A, Zhang X, Karuppasamy M, Huard K, Schoehn G, Berger I, Shan SO, Schaffitzel C |
(2013) "Structural Basis of Signal Sequence Surveillance and Selection by the Srp-Sr Complex." Nat.Struct.Mol.Biol., 20, 604. doi: 10.1038/NSMB.2546. |
Structural basis of signal sequence surveillance and selection by the srp-sr complex. SNAP output |
| 484d |
RNA binding protein-RNA |
NMR |
Ye X, Gorin A, Frederick R, Hu W, Majumdar A, Xu W, McLendon G, Ellington A, Patel DJ |
(1999) "RNA architecture dictates the conformations of a bound peptide." Chem.Biol., 6, 657-669. doi: 10.1016/S1074-5521(99)80117-3. |
Solution structure of hiv-1 rev peptide-RNA aptamer complex. SNAP output |
| 4a2i |
ribosome-hydrolase |
cryo-EM (16.5 Å) |
Jomaa A, Stewart G, Mears JA, Kireeva I, Brown ED, Ortega J |
(2011) "Cryo-Electron Microscopy Structure of the 30S Subunit in Complex with the Yjeq Biogenesis Factor." RNA, 17, 2026. doi: 10.1261/RNA.2922311. |
Cryo-electron microscopy structure of the 30s subunit in complex with the yjeq biogenesis factor. SNAP output |
| 4a2x |
RNA binding protein-RNA |
X-ray (4.0 Å) |
Kowalinski E, Lunardi T, McCarthy AA, Louber J, Brunel J, Grigorov B, Gerlier D, Cusack S |
(2011) "Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA." Cell, 147, 423-435. doi: 10.1016/j.cell.2011.09.039. |
Structure of duck rig-i c-terminal domain (ctd) with 14-mer dsrna. SNAP output |
| 4a36 |
RNA binding protein-RNA |
X-ray (3.7 Å) |
Kowalinski E, Lunardi T, Mccarthy AA, Louber J, Brunel J, Grigorov B, Gerlier D, Cusack S |
(2011) "Structural Basis for the Activation of Innate Immune Pattern Recognition Receptor Rig-I by Viral RNA." Cell(Cambridge,Mass.), 147, 423. doi: 10.1016/J.CELL.2011.09.039. |
Structure of duck rig-i helicase domain bound to 19-mer dsrna and atp transition state analogue. SNAP output |
| 4adv |
translation |
cryo-EM (13.5 Å) |
Boehringer D, O'Farrell HC, Rife JP, Ban N |
(2012) "Structural Insights Into Methyltransferase Ksga Function in 30S Ribosomal Subunit Biogenesis." J.Biol.Chem., 287, 10453-10459. doi: 10.1074/JBC.M111.318121. |
Structure of the e. coli methyltransferase ksga bound to the e. coli 30s ribosomal subunit. SNAP output |
| 4afy |
hydrolase |
X-ray (2.01 Å) |
Robert-Paganin J, Nonin-Lecomte S, Rety S |
(2012) "Crystal Structure of an Eal Domain in Complex with Reaction Product 5'-Pgpg." Plos One, 7, 52424. doi: 10.1371/JOURNAL.PONE.0052424. |
Crystal structure of the fimx eal domain in complex with reaction product pgpg. 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 |
| 4al6 |
hydrolase-RNA |
X-ray (2.63 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 s148acsy4-crrna complex. SNAP output |
| 4al7 |
hydrolase-RNA |
X-ray (2.32 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.2012.10. |
Crystal structure of the csy4-minimal crrna complex. SNAP output |
| 4alp |
chaperone-RNA |
X-ray (1.48 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 hexauridine. SNAP output |
| 4ang |
virus |
X-ray (3.5 Å) |
Persson M, Tars K, Liljas L |
(2013) "Prr1 Coat Protein Binding to its RNA Translational Operator." Acta Crystallogr.,Sect.D, 69, 367. doi: 10.1107/S0907444912047464. |
Small RNA phage prr1 in complex with an RNA operator fragment. SNAP output |
| 4aq7 |
ligase-RNA |
X-ray (2.5 Å) |
Palencia A, Crepin T, Vu MT, Lincecum Jr TL, Martinis SA, Cusack S |
(2012) "Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase." Nat.Struct.Mol.Biol., 19, 677. doi: 10.1038/NSMB.2317. |
Ternary complex of e. coli leucyl-trna synthetase, trna(leu) and leucyl-adenylate analogue in the aminoacylation conformation. SNAP output |
| 4aqy |
ribosome |
X-ray (3.5 Å) |
Matt T, Ng CL, Lang K, Sha SH, Akbergenov R, Shcherbakov D, Meyer M, Duscha S, Xie J, Dubbaka SR, Perez-Fernandez D, Vasella A, Ramakrishnan V, Schacht J, Bottger EC |
(2012) "Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin." Proc.Natl.Acad.Sci.USA, 109, 10984. doi: 10.1073/PNAS.1204073109. |
Structure of ribosome-apramycin complexes. SNAP output |
| 4arc |
ligase-RNA |
X-ray (2.0 Å) |
Palencia A, Crepin T, Vu MT, Lincecum Jr TL, Martinis SA, Cusack S |
(2012) "Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase." Nat.Struct.Mol.Biol., 19, 677. doi: 10.1038/NSMB.2317. |
Ternary complex of e. coli leucyl-trna synthetase, trna(leu) and leucine in the editing conformation. SNAP output |
| 4ari |
ligase-RNA |
X-ray (2.08 Å) |
Palencia A, Crepin T, Vu MT, Lincecum Jr TL, Martinis SA, Cusack S |
(2012) "Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase." Nat.Struct.Mol.Biol., 19, 677. doi: 10.1038/NSMB.2317. |
Ternary complex of e. coli leucyl-trna synthetase, trna(leu) and the benzoxaborole an2679 in the editing conformation. SNAP output |
| 4as1 |
ligase-RNA |
X-ray (2.02 Å) |
Palencia A, Crepin T, Vu MT, Lincecum Jr TL, Martinis SA, Cusack S |
(2012) "Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase." Nat.Struct.Mol.Biol., 19, 677. doi: 10.1038/NSMB.2317. |
Ternary complex of e. coli leucyl-trna synthetase, trna(leu) and the benzoxaborole an2679 in the editing conformation. SNAP output |
| 4ato |
toxin-antitoxin |
X-ray (2.2 Å) |
Short FL, Pei XY, Blower TR, Ong SL, Fineran PC, Luisi BF, Salmond GPC |
(2013) "Selectivity and Self-Assembly in the Control of a Bacterial Toxin by an Antitoxic Noncoding RNA Pseudoknot." Proc.Natl.Acad.Sci.USA, 110, E241. doi: 10.1073/PNAS.1216039110. |
New insights into the mechanism of bacterial type iii toxin-antitoxin systems: selective toxin inhibition by a non-coding RNA pseudoknot. SNAP output |
| 4ay2 |
hydrolase-RNA |
X-ray (2.8 Å) |
Luo D, Kohlway A, Vela A, Pyle AM |
(2012) "Visualizing the Determinants of Viral RNA Recognition by Innate Immune Sensor Rig-I." Structure, 20, 1983. doi: 10.1016/J.STR.2012.08.029. |
Capturing 5' tri-phosphorylated RNA duplex by rig-i. SNAP output |
| 4b3g |
hydrolase-RNA |
X-ray (2.85 Å) |
Lim SC, Bowler MW, Lai TF, Song H |
(2012) "The Ighmbp2 Helicase Structure Reveals the Molecular Basis for Disease-Causing Mutations in Dmsa1." Nucleic Acids Res., 40, 11009. doi: 10.1093/NAR/GKS792. |
Crystal structure of ighmbp2 helicase in complex with RNA. SNAP output |
| 4b3m |
ribosome |
X-ray (2.9 Å) |
Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubakka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC |
(2014) "4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics." Nat.Commun., 5, 3112. doi: 10.1038/NCOMMS4112. |
Crystal structure of the 30s ribosome in complex with compound 1. SNAP output |
| 4b3r |
ribosome |
X-ray (3.0 Å) |
Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubakka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC |
(2014) "4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics." Nat.Commun., 5, 3112. doi: 10.1038/NCOMMS4112. |
Crystal structure of the 30s ribosome in complex with compound 30. SNAP output |
| 4b3s |
ribosome |
X-ray (3.15 Å) |
Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubakka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC |
(2014) "4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics." Nat.Commun., 5, 3112. doi: 10.1038/NCOMMS4112. |
Crystal structure of the 30s ribosome in complex with compound 37. SNAP output |
| 4b3t |
ribosome |
X-ray (3.0 Å) |
Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubakka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC |
(2014) "4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics." Nat.Commun., 5, 3112. doi: 10.1038/NCOMMS4112. |
Crystal structure of the 30s ribosome in complex with compound 39. SNAP output |
| 4b8t |
transcription-RNA |
NMR |
Nicastro G, Garcia-Mayoral MF, Hollingworth D, Kelly G, Martin SR, Briata P, Gherzi R, Ramos A |
(2012) "Noncanonical G Recognition Mediates Ksrp Regulation of Let-7 Biogenesis." Nat.Struct.Mol.Biol., 19, 1282. doi: 10.1038/NSMB.2427. |
RNA binding protein solution structure of the third kh domain of ksrp in complex with the g-rich target sequence.. SNAP output |
| 4ba2 |
hydrolase-RNA |
X-ray (2.501 Å) |
Lorentzen E, Conti E |
(2012) "Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction." Archaea, 2012, 21869. doi: 10.1155/2012/721869. |
Archaeal exosome (rrp4-rrp41(d182a)-rrp42) bound to inorganic phosphate. SNAP output |
| 4bhh |
viral protein-RNA |
X-ray (3.4 Å) |
Reguera J, Malet H, Weber F, Cusack S |
(2013) "Structural Basis for Encapsidation of Genomic RNA by La Crosse Orthobunyavirus Nucleoprotein." Proc.Natl.Acad.Sci.USA, 110, 7246. doi: 10.1073/PNAS.1302298110. |
Crystal structure of tetramer of la crosse virus nucleoprotein in complex with ssrna. SNAP output |
| 4bkk |
viral protein-RNA |
cryo-EM |
Bakker SE, Duquerroy S, Galloux M, Loney C, Conner E, Eleouet JF, Rey FA, Bhella D |
(2013) "The Respiratory Syncytial Virus Nucleoprotein-RNA Complex Forms a Left-Handed Helical Nucleocapsid." J.Gen.Virol., 94, 1734. doi: 10.1099/VIR.0.053025-0. |
The respiratory syncytial virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.. SNAP output |
| 4bpb |
hydrolase-RNA |
X-ray (2.584 Å) |
Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM |
(2011) "Structural Insights Into RNA Recognition by Rig-I." Cell(Cambridge,Mass.), 147, 409. doi: 10.1016/J.CELL.2011.09.023. |
Structural insights into RNA recognition by rig-i. SNAP output |
| 4bs2 |
transcription |
NMR |
Lukavsky PJ, Daujotyte D, Tollervey JR, Ule J, Stuani C, Buratti E, Baralle FE, Damberger FF, Allain FHT |
(2013) "Molecular Basis of Ug-Rich RNA Recognition by the Human Splicing Factor Tdp-43." Nat.Struct.Mol.Biol., 20, 1443. doi: 10.1038/NSMB.2698. |
NMR structure of human tdp-43 tandem rrms in complex with ug-rich RNA. SNAP output |
| 4bw0 |
RNA-RNA binding protein |
X-ray (2.33 Å) |
Huang L, Lilley DMJ |
(2013) "The Molecular Recognition of Kink-Turn Structure by the L7Ae Class of Proteins." RNA, 19, 1703. doi: 10.1261/RNA.041517.113. |
The molecular recognition of kink turn structure by the l7ae class of proteins. SNAP output |
| 4by9 |
transferase-RNA |
NMR |
Lapinaite A, Simon B, Skjaerven L, Rakwalska-Bange M, Gabel F, Carlomagno T |
(2013) "The Structure of the Box C/D Enzyme Reveals Regulation of RNA Methylation." Nature, 502, 519. doi: 10.1038/NATURE12581. |
The structure of the box cd enzyme reveals regulation of rrna methylation. SNAP output |
| 4c4w |
RNA binding protein-RNA |
X-ray (2.95 Å) |
Huang L, Lilley DMJ |
(2014) "Structure of a Rare, Non-Standard Sequence K-Turn Bound by L7Ae Protein." Nucleic Acids Res., 42, 4734. doi: 10.1093/NAR/GKU087. |
Structure of a rare, non-standard sequence k-turn bound by l7ae protein. SNAP output |
| 4c7o |
nuclear protein-RNA |
X-ray (2.6 Å) |
Voigts-Hoffmann F, Schmitz N, Shen K, Shan SO, Ataide SF, Ban N |
(2013) "The Structural Basis of Ftsy Recruitment and Gtpase Activation by Srp RNA." Mol.Cell, 52, 643. doi: 10.1016/J.MOLCEL.2013.10.005. |
The structural basis of ftsy recruitment and gtpase activation by srp RNA. 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 |
| 4c8z |
hydrolase-RNA |
X-ray (2.503 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) product complex. SNAP output |
| 4c9d |
hydrolase-RNA |
X-ray (3.0 Å) |
Niewoehner O, Jinek M, Doudna JA |
(2014) "Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases." Nucleic Acids Res., 42, 1341-1353. doi: 10.1093/nar/gkt922. |
Cas6 (tthb231) product complex. SNAP output |
| 4ce4 |
ribosome |
cryo-EM (4.9 Å) |
Greber BJ, Boehringer D, Leitner A, Bieri P, Voigts-Hoffmann F, Erzberger JP, Leibundgut M, Aebersold R, Ban N |
(2014) "Architecture of the Large Subunit of the Mammalian Mitochondrial Ribosome." Nature, 505, 515. doi: 10.1038/NATURE12890. |
39s large subunit of the porcine mitochondrial ribosome. SNAP output |
| 4cio |
RNA binding protein-RNA |
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 ggugugc RNA. SNAP output |
| 4cqn |
ligase-RNA |
X-ray (2.5 Å) |
Cvetesic N, Palencia A, Halasz I, Cusack S, Gruic-Sovulj I |
(2014) "The Physiological Target for Leurs Translational Quality Control is Norvaline." Embo J., 33, 1639. doi: 10.15252/EMBJ.201488199. |
Crystal structure of the e.coli leurs-trna complex with the non- cognate isoleucyl adenylate analogue. SNAP output |
| 4csf |
viral protein-RNA |
X-ray (2.598 Å) |
Olal D, Dick A, Woods VL, Liu T, Li S, Devignot S, Weber F, Saphire EO, Daumke O |
(2014) "Structural Insights Into RNA Encapsidation and Helical Assembly of the Toscana Virus Nucleoprotein." Nucleic Acids Res., 42, 6025. doi: 10.1093/NAR/GKU229. |
Structural insights into toscana virus RNA encapsidation. SNAP output |
| 4csu |
ribosome |
cryo-EM (5.5 Å) |
Feng B, Mandava CS, Guo Q, Wang J, Cao W, Li N, Zhang Y, Zhang Y, Wang Z, Wu J, Sanyal S, Lei J, Gao N |
(2014) "Structural and Functional Insights Into the Mode of Action of a Universally Conserved Obg Gtpase." Plos Biol., 12, 1866. doi: 10.1371/JOURNAL.PBIO.1001866. |
cryo-EM structures of the 50s ribosome subunit bound with obge. SNAP output |
| 4cxg |
translation |
cryo-EM (8.7 Å) |
Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM |
(2014) "Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement." Cell(Cambridge,Mass.), 158, 121. doi: 10.1016/J.CELL.2014.04.044. |
Regulation of the mammalian elongation cycle by 40s subunit rolling: a eukaryotic-specific ribosome rearrangement. SNAP output |
| 4cxh |
translation |
cryo-EM (8.9 Å) |
Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM |
(2014) "Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement." Cell(Cambridge,Mass.), 158, 121. doi: 10.1016/J.CELL.2014.04.044. |
Regulation of the mammalian elongation cycle by 40s subunit rolling: a eukaryotic-specific ribosome rearrangement. SNAP output |
| 4d25 |
hydrolase |
X-ray (1.9 Å) |
Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Coute Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS |
(2014) "RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts." Cell(Cambridge,Mass.), 157, 1698. doi: 10.1016/J.CELL.2014.05.018. |
Crystal structure of the bombyx mori vasa helicase (e339q) in complex with RNA and amppnp. SNAP output |
| 4d26 |
hydrolase |
X-ray (2.1 Å) |
Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Coute Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS |
(2014) "RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts." Cell(Cambridge,Mass.), 157, 1698. doi: 10.1016/J.CELL.2014.05.018. |
Crystal structure of the bombyx mori vasa helicase (e339q) in complex with RNA,adp and pi. SNAP output |
| 4d5l |
ribosome |
cryo-EM (9.0 Å) |
Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CMT |
(2015) "Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires." Mol.Cell, 57, 422. doi: 10.1016/J.MOLCEL.2014.12.016. |
cryo-EM structures of ribosomal 80s complexes with termination factors and cricket paralysis virus ires reveal the ires in the translocated state. SNAP output |
| 4d5n |
ribosome-RNA |
cryo-EM (9.0 Å) |
Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CMT |
(2015) "Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires." Mol.Cell, 57, 422. doi: 10.1016/J.MOLCEL.2014.12.016. |
cryo-EM structures of ribosomal 80s complexes with termination factors and cricket paralysis virus ires reveal the ires in the translocated state. SNAP output |
| 4d61 |
ribosome |
cryo-EM (9.0 Å) |
Muhs M, Hilal T, Mielke T, Skabkin MA, Sanbonmatsu KY, Pestova TV, Spahn CMT |
(2015) "Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires." Mol.Cell, 57, 422. doi: 10.1016/J.MOLCEL.2014.12.016. |
cryo-EM structures of ribosomal 80s complexes with termination factors and cricket paralysis virus ires reveal the ires in the translocated state. SNAP output |
| 4db2 |
RNA binding protein-RNA |
X-ray (3.157 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 an RNA duplex. SNAP output |
| 4dr1 |
ribosome |
X-ray (3.6 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the apo 30s ribosomal subunit from thermus thermophilus (hb8). SNAP output |
| 4dr2 |
ribosome-antibiotic |
X-ray (3.249 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with multiple copies of paromomycin molecules bound. SNAP output |
| 4dr3 |
ribosome-antibiotic |
X-ray (3.348 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with streptomycin bound. SNAP output |
| 4dr4 |
ribosome-antibiotic |
X-ray (3.969 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, cognate transfer RNA anticodon stem-loop and multiple copies of paromomycin molecules bound. SNAP output |
| 4dr5 |
ribosome-antibiotic |
X-ray (3.45 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, crystallographically disordered cognate transfer RNA anticodon stem-loop and streptomycin bound. SNAP output |
| 4dr6 |
ribosome-antibiotic |
X-ray (3.3 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound. SNAP output |
| 4dr7 |
ribosome-antibiotic |
X-ray (3.75 Å) |
Demirci H, Murphy F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
(2013) "A structural basis for streptomycin-induced misreading of the genetic code." Nat Commun, 4, 1355. doi: 10.1038/ncomms2346. |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position, and streptomycin bound. SNAP output |
| 4duy |
ribosome |
X-ray (3.386 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u13c. SNAP output |
| 4duz |
ribosome-antibiotic |
X-ray (3.651 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u13c, bound with streptomycin. SNAP output |
| 4dv0 |
ribosome |
X-ray (3.853 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u20g. SNAP output |
| 4dv1 |
ribosome-antibiotic |
X-ray (3.849 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, u20g, bound with streptomycin. SNAP output |
| 4dv2 |
ribosome |
X-ray (3.646 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, c912a. SNAP output |
| 4dv3 |
ribosome-antibiotic |
X-ray (3.547 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, c912a, bound with streptomycin. SNAP output |
| 4dv4 |
ribosome |
X-ray (3.651 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a914g. SNAP output |
| 4dv5 |
ribosome-antibiotic |
X-ray (3.683 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a914g, bound with streptomycin. SNAP output |
| 4dv6 |
ribosome |
X-ray (3.297 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a915g. SNAP output |
| 4dv7 |
ribosome-antibiotic |
X-ray (3.294 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the thermus thermophilus 30s ribosomal subunit with a 16s rrna mutation, a915g, bound with streptomycin. SNAP output |
| 4dwa |
viral protein-RNA |
X-ray (3.01 Å) |
Krey T, Bontems F, Vonrhein C, Vaney MC, Bricogne G, Rumenapf T, Rey FA |
(2012) "Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity." Structure, 20, 862-873. doi: 10.1016/j.str.2012.03.018. |
Crystal structure of an active-site mutant of the glycoprotein erns from the pestivirus bvdv-1 in complex with a cpupc trinucleotide. SNAP output |
| 4dzs |
RNA binding protein-RNA |
X-ray (3.14 Å) |
Valley CT, Porter DF, Qiu C, Campbell ZT, Hall TM, Wickens M |
(2012) "Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site." Proc.Natl.Acad.Sci.USA, 109, 6054-6059. doi: 10.1073/pnas.1200521109. |
Crystal structure of yeast puf4p RNA binding domain in complex with ho-4be mutant RNA. SNAP output |
| 4e78 |
viral protein, transferase-RNA |
X-ray (2.9 Å) |
Mosley RT, Edwards TE, Murakami E, Lam AM, Grice RL, Du J, Sofia MJ, Furman PA, Otto MJ |
(2012) "Structure of hepatitis C virus polymerase in complex with primer-template RNA." J.Virol., 86, 6503-6511. doi: 10.1128/JVI.00386-12. |
Crystal structure of a product state assembly of hcv ns5b genotype 2a jfh-1 isolate with beta hairpin loop deletion bound to primer-template RNA with 3'-dg. SNAP output |
| 4e7a |
viral protein, transferase-RNA |
X-ray (3.0 Å) |
Mosley RT, Edwards TE, Murakami E, Lam AM, Grice RL, Du J, Sofia MJ, Furman PA, Otto MJ |
(2012) "Structure of hepatitis C virus polymerase in complex with primer-template RNA." J.Virol., 86, 6503-6511. doi: 10.1128/JVI.00386-12. |
Crystal structure of a product state assembly of hcv ns5b genotype 2a jfh-1 isolate with beta hairpin deletion bound to primer-template RNA with a 2',3'-ddc. 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 |
| 4ejt |
transcription regulator-RNA |
X-ray (3.0 Å) |
Chang YM, Chen CK-M, Chang YC, Jeng WY, Hou MH, Wang AH-J |
(2012) "Functional studies of ssDNA binding ability of MarR family protein TcaR from Staphylococcus epidermidis." Plos One, 7, e45665. doi: 10.1371/journal.pone.0045665. |
Staphylococcus epidermidis tcar in complex with RNA. SNAP output |
| 4erd |
RNA binding protein-RNA |
X-ray (2.589 Å) |
Singh M, Wang Z, Koo BK, Patel A, Cascio D, Collins K, Feigon J |
(2012) "Structural Basis for Telomerase RNA Recognition and RNP Assembly by the Holoenzyme La Family Protein p65." Mol.Cell, 47, 16-26. doi: 10.1016/j.molcel.2012.05.018. |
Crystal structure of the c-terminal domain of tetrahymena telomerase protein p65 in complex with stem iv of telomerase RNA. SNAP output |
| 4eya |
transcription-RNA |
X-ray (3.2 Å) |
Stagno JR, Ma B, Li J, Altieri AS, Byrd RA, Ji X |
(2012) "Crystal structure of a plectonemic RNA supercoil." Nat Commun, 3, 901. doi: 10.1038/ncomms1903. |
Crystal structure of a plectonemic RNA supercoil. SNAP output |
| 4f02 |
translation-RNA |
X-ray (2.0 Å) |
Safaee N, Kozlov G, Noronha AM, Xie J, Wilds CJ, Gehring K |
(2012) "Interdomain Allostery Promotes Assembly of the Poly(A) mRNA Complex with PABP and eIF4G." Mol.Cell, 48, 375-386. doi: 10.1016/j.molcel.2012.09.001. |
Crystal structure of the pabp-binding site of eif4g in complex with rrm1-2 of pabp and poly(a). SNAP output |
| 4f1n |
RNA binding protein-RNA |
X-ray (3.187 Å) |
Nakanishi K, Weinberg DE, Bartel DP, Patel DJ |
(2012) "Structure of yeast Argonaute with guide RNA." Nature, 486, 368-374. doi: 10.1038/nature11211. |
Crystal structure of kluyveromyces polysporus argonaute with a guide RNA. SNAP output |
| 4f3t |
hydrolase-RNA |
X-ray (2.25 Å) |
Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ, Joshua-Tor L |
(2012) "The Structure of Human Argonaute-2 in Complex with miR-20a." Cell(Cambridge,Mass.), 150, 100-110. doi: 10.1016/j.cell.2012.05.017. |
Human argonaute-2 - mir-20a complex. SNAP output |
| 4fsj |
virus |
X-ray (3.5 Å) |
Speir JA, Chen Z, Reddy VS, Johnson JE |
(2012) "Structural study of virus assembly intermediates reveals maturation event sequence and a staging position for externalized lytic peptides." |
Crystal structure of the virus like particle of flock house virus. SNAP output |
| 4ftb |
virus |
X-ray (2.7 Å) |
Speir JA, Chen Z, Reddy VS, Johnson JE |
(2012) "Structural study of virus assembly intermediates reveals maturation event sequence and a staging position for externalized lytic peptides." |
Crystal structure of the authentic flock house virus particle. SNAP output |
| 4fte |
virus |
X-ray (3.5 Å) |
Speir JA, Chen Z, Reddy VS, Johnson JE |
(2012) "Structural study of virus assembly intermediates reveals maturation event sequence and a staging position for externalized lytic peptides." |
Crystal structure of the d75n mutant capsid of flock house virus. SNAP output |
| 4fts |
virus |
X-ray (3.2 Å) |
Speir JA, Chen Z, Reddy VS, Johnson JE |
(2012) "Structural study of virus assembly intermediates reveals maturation event sequence and a staging position for externalized lytic peptides." |
Crystal structure of the n363t mutant of the flock house virus capsid. SNAP output |
| 4fvu |
hydrolase-RNA |
X-ray (2.91 Å) |
Hastie KM, King LB, Zandonatti MA, Saphire EO |
(2012) "Structural Basis for the dsRNA Specificity of the Lassa Virus NP Exonuclease." Plos One, 7, e44211. doi: 10.1371/journal.pone.0044211. |
Structural basis for the dsrna specificity of the lassa virus np exonuclease. SNAP output |
| 4fwt |
translation, transferase-RNA |
X-ray (3.2 Å) |
Takeshita D, Yamashita S, Tomita K |
(2012) "Mechanism for template-independent terminal adenylation activity of Q beta replicase." Structure, 20, 1661-1669. doi: 10.1016/j.str.2012.07.004. |
Complex structure of viral RNA polymerase form iii. SNAP output |
| 4g0a |
hydrolase-RNA |
X-ray (2.1 Å) |
Hu L, Chow DC, Patton JT, Palzkill T, Estes MK, Prasad BV |
(2012) "Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5' GG Sequence for RTPase Activity." J.Virol., 86, 10547-10557. doi: 10.1128/JVI.01201-12. |
Crystallographic analysis of rotavirus nsp2-RNA complex reveals specific recognition of 5'-gg sequence for rtpase activity. SNAP output |
| 4g9z |
viral protein-RNA |
X-ray (2.03 Å) |
Jiang X, Huang Q, Wang W, Dong H, Ly H, Liang Y, Dong C |
(2013) "Structures of Arenaviral Nucleoproteins with Triphosphate dsRNA Reveal a Unique Mechanism of Immune Suppression." J.Biol.Chem., 288, 16949-16959. doi: 10.1074/jbc.M112.420521. |
Lassa nucleoprotein with dsrna reveals novel mechanism for immune suppression. SNAP output |
| 4gcw |
hydrolase-RNA |
X-ray (3.0 Å) |
Pellegrini O, Li de la Sierra-Gallay I, Piton J, Gilet L, Condon C |
(2012) "Activation of tRNA Maturation by Downstream Uracil Residues in B. subtilis." Structure, 20, 1769-1777. doi: 10.1016/j.str.2012.08.002. |
Crystal structure of rnase z in complex with precursor trna(thr). SNAP output |
| 4gha |
viral protein,RNA binding protein-RNA |
X-ray (2.5 Å) |
Bale S, Julien JP, Bornholdt ZA, Kimberlin CR, Halfmann P, Zandonatti MA, Kunert J, Kroon GJ, Kawaoka Y, Macrae IJ, Wilson IA, Saphire EO |
(2012) "Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism." Plos Pathog., 8, e1002916. doi: 10.1371/journal.ppat.1002916. |
Crystal structure of marburg virus vp35 RNA binding domain bound to 12-bp dsrna. SNAP output |
| 4ghl |
transcription, viral protein-RNA |
X-ray (2.02 Å) |
Ramanan P, Edwards MR, Shabman RS, Leung DW, Endlich-Frazier AC, Borek DM, Otwinowski Z, Liu G, Huh J, Basler CF, Amarasinghe GK |
(2012) "Structural basis for Marburg virus VP35-mediated immune evasion mechanisms." Proc.Natl.Acad.Sci.USA, 109, 20661-20666. doi: 10.1073/pnas.1213559109. |
Structural basis for marburg virus vp35 mediate immune evasion mechanisms. SNAP output |
| 4gkj |
ribosome-antibiotic |
X-ray (3.298 Å) |
Cantara WA, Murphy FV, Demirci H, Agris PF |
(2013) "Expanded use of sense codons is regulated by modified cytidines in tRNA." Proc.Natl.Acad.Sci.USA, 110, 10964-10969. doi: 10.1073/pnas.1222641110. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human mitochondrial anticodon stem loop (asl) of transfer RNA methionine (trnamet) bound to an mrna with an aug-codon in the a-site and paromomycin.. SNAP output |
| 4gkk |
ribosome-antibiotic |
X-ray (3.2 Å) |
Cantara WA, Murphy FV, Demirci H, Agris PF |
(2013) "Expanded use of sense codons is regulated by modified cytidines in tRNA." Proc.Natl.Acad.Sci.USA, 110, 10964-10969. doi: 10.1073/pnas.1222641110. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human mitochondrial anticodon stem loop (asl) of transfer RNA methionine (trnamet) bound to an mrna with an aua-codon in the a-site and paromomycin. SNAP output |
| 4gl2 |
RNA binding protein-RNA |
X-ray (3.557 Å) |
Wu B, Peisley A, Richards C, Yao H, Zeng X, Lin C, Chu F, Walz T, Hur S |
(2013) "Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5." Cell(Cambridge,Mass.), 152, 276-289. doi: 10.1016/j.cell.2012.11.048. |
Structural basis for dsrna duplex backbone recognition by mda5. SNAP output |
| 4gv3 |
RNA binding protein-RNA |
X-ray (1.68 Å) |
Jiang X, Huang Q, Wang W, Dong H, Ly H, Liang Y, Dong C |
(2013) "Structures of Arenaviral Nucleoproteins with Triphosphate dsRNA Reveal a Unique Mechanism of Immune Suppression." J.Biol.Chem., 288, 16949-16959. doi: 10.1074/jbc.M112.420521. |
Structures of lassa and tacaribe viral nucleoproteins with or without 5 triphosphate dsrna substrate reveal a unique 3 -5 exoribonuclease mechanism to suppress type i interferon production. SNAP output |
| 4gv6 |
RNA binding protein-RNA |
X-ray (1.98 Å) |
Jiang X, Huang Q, Wang W, Dong H, Ly H, Liang Y, Dong C |
(2013) "Structures of Arenaviral Nucleoproteins with Triphosphate dsRNA Reveal a Unique Mechanism of Immune Suppression." J.Biol.Chem., 288, 16949-16959. doi: 10.1074/jbc.M112.420521. |
Structures of lassa and tacaribe viral nucleoproteins with or without 5 triphosphate dsrna substrate reveal a unique 3 -5 exoribonuclease mechanism to suppress type i interferon production. SNAP output |
| 4gv9 |
RNA binding protein-RNA |
X-ray (2.46 Å) |
Jiang X, Huang Q, Wang W, Dong H, Ly H, Liang Y, Dong C |
(2013) "Structures of Arenaviral Nucleoproteins with Triphosphate dsRNA Reveal a Unique Mechanism of Immune Suppression." J.Biol.Chem., 288, 16949-16959. doi: 10.1074/jbc.M112.420521. |
Lassa nucleoprotein c-terminal domain in complex with triphosphated dsrna soaking for 5 min. SNAP output |
| 4h5o |
viral protein-RNA |
X-ray (3.9 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 pentamer bound to single-stranded RNA. SNAP output |
| 4h5p |
viral protein-RNA |
X-ray (2.15 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 tetramer bound to single-stranded RNA. SNAP output |
| 4hor |
RNA binding protein-RNA |
X-ray (1.861 Å) |
Abbas YM, Pichlmair A, Gorna MW, Superti-Furga G, Nagar B |
(2013) "Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins." Nature, 494, 60-64. doi: 10.1038/nature11783. |
Crystal structure of full-length human ifit5 with 5`-triphosphate oligocytidine. SNAP output |
| 4hos |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Abbas YM, Pichlmair A, Gorna MW, Superti-Furga G, Nagar B |
(2013) "Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins." Nature, 494, 60-64. doi: 10.1038/nature11783. |
Crystal structure of full-length human ifit5 with 5`-triphosphate oligouridine. SNAP output |
| 4hot |
RNA binding protein-RNA |
X-ray (2.501 Å) |
Abbas YM, Pichlmair A, Gorna MW, Superti-Furga G, Nagar B |
(2013) "Structural basis for viral 5'-PPP-RNA recognition by human IFIT proteins." Nature, 494, 60-64. doi: 10.1038/nature11783. |
Crystal structure of full-length human ifit5 with 5`-triphosphate oligoadenine. SNAP output |
| 4ht8 |
RNA binding protein-RNA |
X-ray (1.9 Å) |
Wang W, Wang L, Wu J, Gong Q, Shi Y |
(2013) "Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA." Nucleic Acids Res., 41, 5938-5948. doi: 10.1093/nar/gkt276. |
Crystal structure of e coli hfq bound to poly(a) a7. SNAP output |
| 4ht9 |
RNA binding protein-RNA |
X-ray (1.8 Å) |
Wang W, Wang L, Wu J, Gong Q, Shi Y |
(2013) "Hfq-bridged ternary complex is important for translation activation of rpoS by DsrA." Nucleic Acids Res., 41, 5938-5948. doi: 10.1093/nar/gkt276. |
Crystal structure of e coli hfq bound to two rnas. SNAP output |
| 4i67 |
hydrolase-RNA |
X-ray (2.33 Å) |
Steimer L, Wurm JP, Linden MH, Rudolph MG, Wohnert J, Klostermeier D |
(2013) "Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera." Nucleic Acids Res., 41, 6259-6272. doi: 10.1093/nar/gkt323. |
Crystal structure of the rrm domain of RNA helicase hera from t. thermophilus in complex with gggc RNA. SNAP output |
| 4ifd |
hydrolase-RNA |
X-ray (2.805 Å) |
Makino DL, Baumgartner M, Conti E |
(2013) "Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex." Nature, 495, 70-75. doi: 10.1038/nature11870. |
Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA. SNAP output |
| 4ig8 |
transferase-RNA |
X-ray (2.7 Å) |
Donovan J, Dufner M, Korennykh A |
(2013) "Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1." Proc.Natl.Acad.Sci.USA, 110, 1652-1657. doi: 10.1073/pnas.1218528110. |
Structural basis for cytosolic double-stranded RNA surveillance by human oas1. SNAP output |
| 4ii9 |
transferase-peptide-RNA |
X-ray (1.66 Å) |
Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Etheve-Quelquejeu M, Arthur M |
(2013) "The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors." Angew.Chem.Int.Ed.Engl., 52, 7278-7281. doi: 10.1002/anie.201301411. |
Crystal structure of weissella viridescens femxvv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate. SNAP output |
| 4ijs |
RNA binding protein-RNA |
X-ray (3.2 Å) |
Li BB, Wang Q, Pan X, Fernandez de Castro I, Sun Y, Guo Y, Tao X, Risco C, Sui SF, Lou ZY |
(2013) "Bunyamwera virus possesses a distinct nucleocapsid protein to facilitate genome encapsidation." Proc.Natl.Acad.Sci.USA, 110, 9048-9053. doi: 10.1073/pnas.1222552110. |
Crystal structure of nucleocapsid protein encoded by the prototypic member of orthobunyavirus. SNAP output |
| 4ill |
hydrolase-RNA |
X-ray (2.484 Å) |
Shao Y, Li H |
(2013) "Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6." Structure, 21, 385-393. doi: 10.1016/j.str.2013.01.010. |
Recognition and cleavage of a non-structured crispr RNA by its processing endoribonuclease cas6. SNAP output |
| 4ilm |
hydrolase-RNA |
X-ray (3.068 Å) |
Shao Y, Li H |
(2013) "Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6." Structure, 21, 385-393. doi: 10.1016/j.str.2013.01.010. |
Crispr RNA processing endoribonuclease. SNAP output |
| 4io9 |
ribosome-ribosome inhibitor |
X-ray (3.2 Å) |
Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V |
(2013) "Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates." Bioorg.Med.Chem.Lett., 23, 1727-1731. doi: 10.1016/j.bmcl.2013.01.067. |
Crystal structure of compound 4d bound to large ribosomal subunit (50s) from deinococcus radiodurans. SNAP output |
| 4ioa |
ribosome-ribosome inhibitor |
X-ray (3.2 Å) |
Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V |
(2013) "Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates." Bioorg.Med.Chem.Lett., 23, 1727-1731. doi: 10.1016/j.bmcl.2013.01.067. |
Crystal structure of compound 4e bound to large ribosomal subunit (50s) from deinococcus radiodurans. SNAP output |
| 4ioc |
ribosome-ribosome inhibitor |
X-ray (3.6 Å) |
Magee TV, Han S, McCurdy SP, Nguyen TT, Granskog K, Marr ES, Maguire BA, Huband MD, Chen JM, Subashi TA, Shanmugasundaram V |
(2013) "Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates." Bioorg.Med.Chem.Lett., 23, 1727-1731. doi: 10.1016/j.bmcl.2013.01.067. |
Crystal structure of compound 4f bound to large ribosomal subunit (50s) from deinococcus radiodurans. SNAP output |
| 4iqx |
transferase-DNA |
X-ray (2.5 Å) |
Agudo R, Ferrer-Orta C, Arias A, de la Higuera I, Perales C, Perez-Luque R, Verdaguer N, Domingo E |
(2010) "A multi-step process of viral adaptation to a mutagenic nucleoside analogue by modulation of transition types leads to extinction-escape." Plos Pathog., 6, e1001072. doi: 10.1371/journal.ppat.1001072. |
Mutant p44s p169s m296i of foot-and-mouth disease virus RNA-dependent RNA polymerase. SNAP output |
| 4j1g |
viral protein-RNA |
X-ray (2.789 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-ssrna complex. SNAP output |
| 4j39 |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Katorcha E, Tamjar J, Popov AN, Malinina L |
"Procrustean bed of RNA silencing suppression." |
Crystal structure of p19 in complex with double-helical 19mer RNA p(cag)3c(cug)3. SNAP output |
| 4j5v |
RNA binding protein-RNA |
X-ray (2.15 Å) |
Tamjar J, Katorcha E, Cabo A, Delgado S, Popov AN, Malinina L |
"Structural insights into CNG-repetitive RNAs associated with human Trinucleotide Repeat Expansion Diseases (TREDs)." |
Crystal structure of p19 in complex with double-helical RNA 19mer p(cag)3c(ccg)3. SNAP output |
| 4j7l |
hydrolase-RNA |
X-ray (1.8 Å) |
Jiao X, Chang JH, Kilic T, Tong L, Kiledjian M |
(2013) "A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing." Mol.Cell, 50, 104-115. doi: 10.1016/j.molcel.2013.02.017. |
Crystal structure of mouse dxo in complex with product RNA and two magnesium ions. SNAP output |
| 4j7m |
hydrolase-RNA |
X-ray (1.7 Å) |
Jiao X, Chang JH, Kilic T, Tong L, Kiledjian M |
(2013) "A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing." Mol.Cell, 50, 104-115. doi: 10.1016/j.molcel.2013.02.017. |
Crystal structure of mouse dxo in complex with substrate mimic RNA and calcium ion. SNAP output |
| 4jgn |
RNA binding protein-RNA |
X-ray (1.86 Å) |
Katorcha E, Tamjar J, Popov AN, Malinina L |
"Procrustean bed of RNA silencing suppression." |
Crystal structure of RNA silencing suppressor p19 with 1nt-5'-overhanging double-helical RNA 20mer puug(cug)5cu. SNAP output |
| 4ji0 |
ribosome |
X-ray (3.492 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji1 |
ribosome-antibiotic |
X-ray (3.144 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji2 |
ribosome |
X-ray (3.64 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji3 |
ribosome |
X-ray (3.35 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji4 |
ribosome-antibiotic |
X-ray (3.692 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji5 |
ribosome-antibiotic |
X-ray (3.85 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji6 |
ribosome |
X-ray (3.55 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji7 |
ribosome |
X-ray (3.5 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4ji8 |
ribosome-antibiotic |
X-ray (3.742 Å) |
Demirci H, Wang L, Murphy FV, Murphy EL, Carr JF, Blanchard SC, Jogl G, Dahlberg AE, Gregory ST |
(2013) "The central role of protein S12 in organizing the structure of the decoding site of the ribosome." Rna, 19, 1791-1801. doi: 10.1261/rna.040030.113. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4jk0 |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Katorcha E, Tamjar J, Popov AN, Malinina L |
"Procrustean bed of RNA silencing suppression." |
Crystal structure of t89q-mutant of RNA silencing suppressor p19 with 2nt-5'-overhanging double-helical RNA 21mer puuug(cug)5cu. SNAP output |
| 4jng |
viral protein-RNA |
X-ray (2.12 Å) |
Dong HH, Li P, Bottcher B, Elliott RM, Dong CJ |
(2013) "Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism." Rna, 19, 1129-1136. doi: 10.1261/rna.039057.113. |
Schmallenberg virus nucleoprotein-RNA complex. SNAP output |
| 4jnx |
RNA binding protein-RNA |
X-ray (1.95 Å) |
Katorcha E, Tamjar J, Popov AN, Malinina L |
"Procrustean bed of RNA silencing suppression." |
Crystal structure of RNA silencing suppressor p19 complexed with double-helical RNA 20mer pg(cug)6c. SNAP output |
| 4jv5 |
ribosome |
X-ray (3.162 Å) |
Fernandez IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V |
(2013) "Unusual base pairing during the decoding of a stop codon by the ribosome." Nature, 500, 107-110. doi: 10.1038/nature12302. |
Crystal structures of pseudouridinilated stop codons with asls. SNAP output |
| 4jvh |
RNA binding protein |
X-ray (3.501 Å) |
Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel DJ |
(2013) "Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites." Genes Dev., 27, 928-940. doi: 10.1101/gad.216531.113. |
Structure of the star domain of quaking protein in complex with RNA. SNAP output |
| 4jvy |
RNA binding protein |
X-ray (2.853 Å) |
Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel DJ |
(2013) "Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites." Genes Dev., 27, 928-940. doi: 10.1101/gad.216531.113. |
Structure of the star (signal transduction and activation of RNA) domain of gld-1 bound to RNA. SNAP output |
| 4jxx |
ligase-RNA |
X-ray (2.3 Å) |
Rodriguez-Hernandez A, Spears JL, Gaston KW, Limbach PA, Gamper H, Hou YM, Kaiser R, Agris PF, Perona JJ |
(2013) "Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position." J.Mol.Biol., 425, 3888-3906. doi: 10.1016/j.jmb.2013.05.018. |
Crystal structure of e coli e. coli glutaminyl-trna synthetase bound to trna(gln)(cug) and atp from novel cryostabilization conditions. SNAP output |
| 4jxz |
ligase-RNA |
X-ray (2.4 Å) |
Rodriguez-Hernandez A, Spears JL, Gaston KW, Limbach PA, Gamper H, Hou YM, Kaiser R, Agris PF, Perona JJ |
(2013) "Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position." J.Mol.Biol., 425, 3888-3906. doi: 10.1016/j.jmb.2013.05.018. |
Structure of e. coli glutaminyl-trna synthetase bound to atp and a trna(gln) acceptor containing a uug anticodon. SNAP output |
| 4jya |
ribosome |
X-ray (3.098 Å) |
Fernandez IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V |
(2013) "Unusual base pairing during the decoding of a stop codon by the ribosome." Nature, 500, 107-110. doi: 10.1038/nature12302. |
Crystal structures of pseudouridinilated stop codons with asls. SNAP output |
| 4jyz |
ligase-RNA |
X-ray (2.5 Å) |
Rodriguez-Hernandez A, Spears JL, Gaston KW, Limbach PA, Gamper H, Hou YM, Kaiser R, Agris PF, Perona JJ |
(2013) "Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position." J.Mol.Biol., 425, 3888-3906. doi: 10.1016/j.jmb.2013.05.018. |
Crystal structure of e. coli glutaminyl-trna synthetase bound to atp and native trna(gln) containing the cmnm5s2u34 anticodon wobble base. 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 |
| 4jzv |
hydrolase-RNA |
X-ray (2.2 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) - second guanosine residue in guanosine binding pocket. SNAP output |
| 4k0k |
ribosome |
X-ray (3.4 Å) |
Fernandez IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V |
(2013) "Unusual base pairing during the decoding of a stop codon by the ribosome." Nature, 500, 107-110. doi: 10.1038/nature12302. |
Crystal structure of the thermus thermophilus 30s ribosomal subunit complexed with a serine-asl and mrna containing a stop codon. SNAP output |
| 4k4s |
transferase-RNA |
X-ray (2.4 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Poliovirus polymerase elongation complex (r3_form). SNAP output |
| 4k4t |
transferase-RNA |
X-ray (2.75 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Poliovirus polymerase elongation complex (r4_form). SNAP output |
| 4k4u |
transferase-RNA |
X-ray (2.85 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Poliovirus polymerase elongation complex (r5_form). SNAP output |
| 4k4v |
transferase-RNA |
X-ray (2.63 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Poliovirus polymerase elongation complex (r5+1_form). SNAP output |
| 4k4w |
transferase-RNA |
X-ray (2.69 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Poliovirus polymerase elongation complex (r5+2_form). SNAP output |
| 4k4x |
transferase-RNA |
X-ray (2.37 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Coxsackievirus b3 polymerase elongation complex (r2_form), RNA. SNAP output |
| 4k4y |
transferase-RNA |
X-ray (2.72 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Coxsackievirus b3 polymerase elongation complex (r2+1_form). SNAP output |
| 4k4z |
transferase-RNA |
X-ray (2.17 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Coxsackievirus b3 polymerase elongation complex (r2_mg_form). SNAP output |
| 4k50 |
transferase-RNA |
X-ray (2.93 Å) |
Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB |
(2013) "Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts." Plos One, 8, e60272. doi: 10.1371/journal.pone.0060272. |
Rhinovirus 16 polymerase elongation complex (r1_form). SNAP output |
| 4khp |
ribosome-antibiotic |
X-ray (3.1 Å) |
Tourigny DS, Fernandez IS, Kelley AC, Vakiti RR, Chattopadhyay AK, Dorich S, Hanessian S, Ramakrishnan V |
(2013) "Crystal Structure of a Bioactive Pactamycin Analog Bound to the 30S Ribosomal Subunit." J.Mol.Biol., 425, 3907-3910. doi: 10.1016/j.jmb.2013.05.004. |
Structure of the thermus thermophilus 30s ribosomal subunit in complex with de-6-msa-pactamycin. SNAP output |
| 4kji |
RNA binding protein-RNA |
X-ray (3.2 Å) |
Morris ER, Hall G, Li C, Heeb S, Kulkarni RV, Lovelock L, Silistre H, Messina M, Camara M, Emsley J, Williams P, Searle MS |
(2013) "Structural Rearrangement in an RsmA/CsrA Ortholog of Pseudomonas aeruginosa Creates a Dimeric RNA-Binding Protein, RsmN." Structure, 21, 1659-1671. doi: 10.1016/j.str.2013.07.007. |
Novel re-arrangement of an rsma-csra family protein to create a structurally distinct new RNA-binding family member. SNAP output |
| 4knq |
RNA binding protein-RNA |
X-ray (1.82 Å) |
Tamjar J, Katorcha E, Cabo A, Delgado S, Popov AN, Malinina L |
"Structural insights into CNG-repetitive RNAs associated with human Trinucleotide Repeat Expansion Diseases (TREDs)." |
Crystal structure of 1nt-5'-overhanging double-helical ccg-repetitive RNA 20mer complexed with rss p19. SNAP output |
| 4kq0 |
RNA binding protein-RNA |
X-ray (2.1 Å) |
Tamjar J, Katorcha E, Cabo A, Delgado S, Popov AN, Malinina L |
"Structural insights into CNG-repetitive RNAs associated with human Trinucleotide Repeat Expansion Diseases (TREDs)." |
Crystal structure of double-helical cgg-repetitive RNA 19mer complexed with rss p19. SNAP output |
| 4kr2 |
ligase-RNA |
X-ray (3.292 Å) |
Qin X, Hao Z, Tian Q, Zhang Z, Zhou C, Xie W |
(2014) "Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation." J.Biol.Chem., 289, 20359-20369. doi: 10.1074/jbc.M114.557249. |
Glycyl-trna synthetase in complex with trna-gly. SNAP output |
| 4kr3 |
ligase-RNA |
X-ray (3.235 Å) |
Qin X, Hao Z, Tian Q, Zhang Z, Zhou C, Xie W |
(2014) "Cocrystal Structures of Glycyl-tRNA Synthetase in Complex with tRNA Suggest Multiple Conformational States in Glycylation." J.Biol.Chem., 289, 20359-20369. doi: 10.1074/jbc.M114.557249. |
Glycyl-trna synthetase mutant e71g in complex with trna-gly. SNAP output |
| 4kr6 |
transferase-RNA |
X-ray (2.85 Å) |
Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R |
(2014) "Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification." Nucleic Acids Res., 42, 6673-6685. doi: 10.1093/nar/gku249. |
Crystal structure of a 4-thiouridine synthetase - RNA complex. SNAP output |
| 4kr7 |
transferase-RNA |
X-ray (3.421 Å) |
Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R |
(2014) "Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification." Nucleic Acids Res., 42, 6673-6685. doi: 10.1093/nar/gku249. |
Crystal structure of a 4-thiouridine synthetase - RNA complex with bound atp. SNAP output |
| 4kr9 |
transferase-RNA |
X-ray (3.5 Å) |
Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R |
(2014) "Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification." Nucleic Acids Res., 42, 6673-6685. doi: 10.1093/nar/gku249. |
Crystal structure of a 4-thiouridine synthetase - RNA complex at 3.5 angstrom resolution. SNAP output |
| 4kre |
transcription-RNA |
X-ray (1.754 Å) |
Faehnle CR, Elkayam E, Haase AD, Hannon GJ, Joshua-Tor L |
(2013) "The making of a slicer: activation of human argonaute-1." Cell Rep, 3, 1901-1909. doi: 10.1016/j.celrep.2013.05.033. |
Structure of human argonaute-1 bound to endogenous sf9 RNA. SNAP output |
| 4krf |
transcription-RNA |
X-ray (2.101 Å) |
Faehnle CR, Elkayam E, Haase AD, Hannon GJ, Joshua-Tor L |
(2013) "The making of a slicer: activation of human argonaute-1." Cell Rep, 3, 1901-1909. doi: 10.1016/j.celrep.2013.05.033. |
Structure of human argonaute-1 let-7 complex. SNAP output |
| 4ktg |
RNA binding protein-RNA |
X-ray (1.92 Å) |
Tamjar J, Katorcha E, Cabo A, Delgado S, Popov AN, Malinina L |
"Structural insights into CNG-repetitive RNAs associated with human Trinucleotide Repeat Expansion Diseases (TREDs)." |
Crystal structure of double-helical ggc-repetitive RNA 19mer complexed with rss p19. SNAP output |
| 4kvb |
ribosome |
X-ray (4.198 Å) |
Connetti JL, Murphy EL, Dahlberg AE, Gregory ST, Jogl G |
"Structural robustness of the ribosome inferred from the X-ray crystal structure of a 30S ribosomal subunit lacking ribosomal protein S17." |
Thermus thermophilus hb27 30s ribosomal subunit lacking ribosomal protein s17. 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 |
| 4kzd |
immune system-RNA |
X-ray (2.186 Å) |
Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA |
(2014) "A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore." Nat.Chem.Biol., 10, 686-691. doi: 10.1038/nchembio.1561. |
Crystal structure of an RNA aptamer in complex with fluorophore and fab. SNAP output |
| 4kze |
immune system-RNA |
X-ray (2.404 Å) |
Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA |
(2014) "A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore." Nat.Chem.Biol., 10, 686-691. doi: 10.1038/nchembio.1561. |
Crystal structure of an RNA aptamer in complex with fab. SNAP output |
| 4l8h |
structural protein |
X-ray (2.4 Å) |
Rumnieks J, Tars K |
(2014) "Crystal structure of the bacteriophage q beta coat protein in complex with the RNA operator of the replicase gene." J.Mol.Biol., 426, 1039-1049. doi: 10.1016/j.jmb.2013.08.025. |
Bacteriophage qbeta coat protein in complex with RNA operator hairpin. SNAP output |
| 4l8r |
RNA-RNA binding protein-hydrolase |
X-ray (2.6 Å) |
Tan D, Marzluff WF, Dominski Z, Tong L |
(2013) "Structure of Histone Mrna Stem-Loop, Human Stem-Loop Binding Protein, and 3'Hexo Ternary Complex." Science, 339, 318. doi: 10.1126/SCIENCE.1228705. |
Structure of mrna stem-loop, human stem-loop binding protein and 3'hexo ternary complex. SNAP output |
| 4lck |
ribosomal protein-RNA |
X-ray (3.2 Å) |
Zhang J, Ferre-D'Amare AR |
(2013) "Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA." Nature, 500, 363-366. doi: 10.1038/nature12440. |
Co-crystal structure of a t-box riboswitch stem i domain in complex with its cognate trna. SNAP output |
| 4lf4 |
ribosome |
X-ray (3.34 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lf5 |
ribosome |
X-ray (3.753 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lf6 |
ribosome |
X-ray (3.31 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lf7 |
ribosome |
X-ray (3.15 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lf8 |
ribosome |
X-ray (3.15 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lf9 |
ribosome |
X-ray (3.28 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lfa |
ribosome |
X-ray (3.65 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lfb |
ribosome |
X-ray (3.009 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) "Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lfc |
ribosome |
X-ray (3.602 Å) |
Demirci H, Belardinelli R, Carr J, Murphy IV F, Jogl G, Dahlberg AE, Gregory ST |
(2013) |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4lg2 |
RNA binding protein-RNA |
X-ray (2.7 Å) |
Bale S, Julien JP, Bornholdt ZA, Krois AS, Wilson IA, Saphire EO |
(2013) "Ebolavirus VP35 coats the backbone of double-stranded RNA for interferon antagonism." J.Virol., 87, 10385-10388. doi: 10.1128/JVI.01452-13. |
Crystal structure of reston ebola virus vp35 RNA binding domain bound to 12-bp dsrna. SNAP output |
| 4lgt |
isomerase-RNA |
X-ray (1.3 Å) |
Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM |
(2014) "The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs." Nucleic Acids Res., 42, 2037-2048. doi: 10.1093/nar/gkt1050. |
Crystal structure of the catalytic domain of rlub in complex with a 21-nucleotide RNA substrate. SNAP output |
| 4lj0 |
RNA binding protein |
X-ray (2.15 Å) |
Kuhlmann SI, Valkov E, Stewart M |
(2014) "Structural basis for the molecular recognition of polyadenosine RNA by Nab2 Zn fingers." Nucleic Acids Res., 42, 672-680. doi: 10.1093/nar/gkt876. |
Nab2 zn fingers complexed with polyadenosine. SNAP output |
| 4lmz |
RNA binding protein |
X-ray (2.78 Å) |
Bhatt H, Manickam Y, Bhavesh NS |
"sequence specific RNA recognition of ETR3 RRM 1-2 domains." |
Structural insight into RNA recognition by rrm1+2 domain of human etr-3 protein. SNAP output |
| 4lq3 |
viral protein-replication inhibitor-RNA |
X-ray (2.6 Å) |
Tarantino D, Pezzullo M, Mastrangelo E, Croci R, Rohayem J, Robel I, Bolognesi M, Milani M |
(2014) "Naphthalene-sulfonate inhibitors of human norovirus RNA-dependent RNA-polymerase." Antiviral Res., 102, 23-28. doi: 10.1016/j.antiviral.2013.11.016. |
Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor ppnds. SNAP output |
| 4m2z |
hydrolase-RNA |
X-ray (2.85 Å) |
Court DL, Gan J, Liang YH, Shaw GX, Tropea JE, Costantino N, Waugh DS, Ji X |
(2013) "RNase III: Genetics and Function; Structure and Mechanism." Annu. Rev. Genet., 47, 405-431. doi: 10.1146/annurev-genet-110711-155618. |
Crystal structure of rnase iii complexed with double-stranded RNA and cmp (type ii cleavage). SNAP output |
| 4m30 |
hydrolase-RNA |
X-ray (2.501 Å) |
Court DL, Gan J, Liang YH, Shaw GX, Tropea JE, Costantino N, Waugh DS, Ji X |
(2013) "RNase III: Genetics and Function; Structure and Mechanism." Annu. Rev. Genet., 47, 405-431. doi: 10.1146/annurev-genet-110711-155618. |
Crystal structure of rnase iii complexed with double-stranded RNA and amp (type ii cleavage). SNAP output |
| 4m4o |
hydrolase-RNA |
X-ray (2.0 Å) |
Malashkevich VN, Padlan FC, Toro R, Girvin M, Almo SC |
"Crystal structure of the aptamer minE-lysozyme complex." |
Crystal structure of the aptamer mine-lysozyme complex. SNAP output |
| 4m59 |
RNA binding protein-RNA |
X-ray (2.46 Å) |
Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang HW, Wang J, Zhu JK, Shi Y, Yan N |
(2013) "Structural basis for the modular recognition of single-stranded RNA by PPR proteins." Nature, 504, 168-171. doi: 10.1038/nature12651. |
Crystal structure of the pentatricopeptide repeat protein ppr10 in complex with an 18-nt psaj RNA element. SNAP output |
| 4m6d |
hydrolase-RNA |
X-ray (2.68 Å) |
Malashkevich VN, Padlan FC, Toro R, Girvin M, Almo SC |
"Crystal structure of the aptamer minF-lysozyme complex." |
Crystal structure of the aptamer minf-lysozyme complex.. SNAP output |
| 4m7a |
RNA binding protein |
X-ray (2.781 Å) |
Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y |
(2014) "Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA." Nature, 506, 116-120. doi: 10.1038/nature12803. |
Crystal structure of lsm2-8 complex bound to the 3' end sequence of u6 snrna. SNAP output |
| 4m7d |
RNA binding protein |
X-ray (2.595 Å) |
Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y |
(2014) "Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA." Nature, 506, 116-120. doi: 10.1038/nature12803. |
Crystal structure of lsm2-8 complex bound to the RNA fragment cguuu. SNAP output |
| 4mdx |
hydrolase-RNA |
X-ray (1.5 Å) |
Simanshu DK, Yamaguchi Y, Park JH, Inouye M, Patel DJ |
(2013) "Structural Basis of mRNA Recognition and Cleavage by Toxin MazF and Its Regulation by Antitoxin MazE in Bacillus subtilis." Mol.Cell, 52, 447-458. doi: 10.1016/j.molcel.2013.09.006. |
Crystal structure of bacillus subtilis mazf in complex with RNA. SNAP output |
| 4n0t |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Montemayor EJ, Curran EC, Liao HH, Andrews KL, Treba CN, Butcher SE, Brow DA |
(2014) "Core structure of the U6 small nuclear ribonucleoprotein at 1.7- angstrom resolution." Nat.Struct.Mol.Biol., 21, 544-551. doi: 10.1038/nsmb.2832. |
Core structure of the u6 small nuclear ribonucleoprotein at 1.7 angstrom resolution. SNAP output |
| 4n2q |
splicing-RNA |
X-ray (2.8 Å) |
Ke J, Chen RZ, Ban T, Zhou XE, Gu X, Tan MH, Chen C, Kang Y, Brunzelle JS, Zhu JK, Melcher K, Xu HE |
(2013) "Structural basis for RNA recognition by a dimeric PPR-protein complex." Nat.Struct.Mol.Biol., 20, 1377-1382. doi: 10.1038/nsmb.2710. |
Crystal structure of tha8 in complex with zm4 RNA. SNAP output |
| 4n2s |
splicing-RNA |
X-ray (3.0 Å) |
Ke J, Chen RZ, Ban T, Zhou XE, Gu X, Tan MH, Chen C, Kang Y, Brunzelle JS, Zhu JK, Melcher K, Xu HE |
(2013) "Structural basis for RNA recognition by a dimeric PPR-protein complex." Nat.Struct.Mol.Biol., 20, 1377-1382. doi: 10.1038/nsmb.2710. |
Crystal structure of tha8 in complex with zm1a-6 RNA. SNAP output |
| 4n48 |
transferase-RNA |
X-ray (2.704 Å) |
Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM |
(2014) "Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation." Nat Commun, 5, 3004. doi: 10.1038/ncomms4004. |
Cap-specific mrna (nucleoside-2'-o-)-methyltransferase 1 protein in complex with capped RNA fragment. SNAP output |
| 4ngb |
hydrolase-RNA |
X-ray (2.25 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 12-mer sirna having uu-3' ends (2.25 angstrom resolution). SNAP output |
| 4ngc |
hydrolase-RNA |
X-ray (2.104 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 12-mer sirna having ua-3' ends (2.1 angstrom resolution). SNAP output |
| 4ngd |
hydrolase-RNA |
X-ray (1.958 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 12-mer sirna having 5'-p and uu-3' ends (1.95 angstrom resolution). SNAP output |
| 4ngf |
hydrolase-RNA |
X-ray (3.101 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 17-mer sirna having 5'-p and uu-3' ends (3.1 angstrom resolution). SNAP output |
| 4ngg |
hydrolase-RNA |
X-ray (2.6 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 13-mer sirna having 5'-a and uu-3' ends (2.6 angstrom resolution). SNAP output |
| 4nh3 |
hydrolase-RNA |
X-ray (2.616 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 13-mer sirna having 5'-pu and uu-3' ends (2.6 angstrom resolution). SNAP output |
| 4nh5 |
hydrolase-RNA |
X-ray (2.55 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 14-mer sirna having 5'-puu and uu-3' ends (2.55 angstrom resolution). SNAP output |
| 4nh6 |
hydrolase-RNA |
X-ray (2.551 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 15-mer sirna having 5'-puuu and uu-3' ends (2.55 angstrom resolution). SNAP output |
| 4nha |
hydrolase-RNA |
X-ray (3.401 Å) |
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ |
(2014) "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003. |
Structure of human dicer platform-paz-connector helix cassette in complex with 16-mer sirna having 5'-p and uu-3' ends (3.4 angstrom resolution). 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 |
| 4nku |
transferase-RNA |
X-ray (1.94 Å) |
Munoz-Tello P, Gabus C, Thore S |
(2014) "A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure." Nucleic Acids Res., 42, 3372-3380. doi: 10.1093/nar/gkt1278. |
Structure of cid1 in complex with its short product apu. SNAP output |
| 4nl3 |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Kovach AR, Hoff KE, Canty JT, Orans J, Brennan RG |
(2014) "Recognition of U-rich RNA by Hfq from the Gram-positive pathogen Listeria monocytogenes." Rna, 20, 1548-1559. doi: 10.1261/rna.044032.113. |
Crystal structure of listeria monocytogenes hfq in complex with u6 RNA. SNAP output |
| 4nxm |
ribosome |
X-ray (3.65 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the 30s ribosomal subunit from a gidb (rsmg) mutant of thermus thermophilus (hb8). SNAP output |
| 4nxn |
ribosome-antibiotic |
X-ray (3.544 Å) |
Demirci H, Murphy IV F, Murphy E, Gregory ST, Dahlberg AE, Jogl G |
"A structural basis for streptomycin resistance." |
Crystal structure of the 30s ribosomal subunit from a gidb (rsmg) mutant of thermus thermophilus (hb8), bound with streptomycin. SNAP output |
| 4o26 |
RNA binding protein-RNA |
X-ray (3.001 Å) |
Huang J, Brown AF, Wu J, Xue J, Bley CJ, Rand DP, Wu L, Zhang R, Chen JJ, Lei M |
(2014) "Structural basis for protein-RNA recognition in telomerase." Nat.Struct.Mol.Biol., 21, 507-512. doi: 10.1038/nsmb.2819. |
Crystal structure of the trbd domain of tert and the cr4-5 of tr. SNAP output |
| 4o8j |
ligase-RNA |
X-ray (2.04 Å) |
Desai KK, Bingman CA, Cheng CL, Phillips Jr GN, Raines RT |
(2014) "Structure of RNA 3'-phosphate cyclase bound to substrate RNA." Rna, 20, 1560-1566. doi: 10.1261/rna.045823.114. |
Crystal structure of rtca, the RNA 3'-terminal phosphate cyclase from pyrococcus horikoshii, in complex with racaaa3'phosphate and adenine.. SNAP output |
| 4oau |
hydrolase-RNA |
X-ray (2.6 Å) |
Han Y, Donovan J, Rath S, Whitney G, Chitrakar A, Korennykh A |
(2014) "Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response." Science, 343, 1244-1248. doi: 10.1126/science.1249845. |
Complete human rnase l in complex with biological activators.. SNAP output |
| 4oav |
hydrolase-RNA |
X-ray (2.1 Å) |
Han Y, Donovan J, Rath S, Whitney G, Chitrakar A, Korennykh A |
(2014) "Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response." Science, 343, 1244-1248. doi: 10.1126/science.1249845. |
Complete human rnase l in complex with 2-5a (5'-ppp heptamer), amppcp and RNA substrate.. SNAP output |
| 4oe1 |
RNA binding protein-RNA |
X-ray (2.8 Å) |
Li Q, Yan C, Xu H, Wang Z, Long J, Li W, Wu J, Yin P, Yan N |
(2014) "Examination of the dimerization states of the single-stranded RNA recognition protein pentatricopeptide repeat 10 (PPR10)." J.Biol.Chem., 289, 31503-31512. doi: 10.1074/jbc.M114.575472. |
Crystal structure of the pentatricopeptide repeat protein ppr10 (c256s-c430s-c449s) in complex with an 18-nt psaj RNA element. SNAP output |
| 4ohy |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A |
(2014) "RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1." Mol.Cell, 54, 975-986. doi: 10.1016/j.molcel.2014.04.005. |
C. elegans clp1 bound to ssrna dinucleotide gc, amp-pnp, and mg2+(inhibited substrate bound state). SNAP output |
| 4ohz |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A |
(2014) "RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1." Mol.Cell, 54, 975-986. doi: 10.1016/j.molcel.2014.04.005. |
Bound to ssrna tetranucleotide gaaa, adp, and mg2+. SNAP output |
| 4oi0 |
RNA binding protein-RNA |
X-ray (2.2 Å) |
Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A |
(2014) "RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1." Mol.Cell, 54, 975-986. doi: 10.1016/j.molcel.2014.04.005. |
Bound to ssrna dinucleotide gc, adp, alf4-, and mg2+(transition state, data set i). SNAP output |
| 4oi1 |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A |
(2014) "RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1." Mol.Cell, 54, 975-986. doi: 10.1016/j.molcel.2014.04.005. |
Clp1 bound to ssrna dinucleotide gc, adp, alf4-, and mg2+(transition state, data set ii). SNAP output |
| 4ola |
hydrolase-RNA |
X-ray (2.3 Å) |
Schirle NT, MacRae IJ |
(2012) "The crystal structure of human Argonaute2." Science, 336, 1037-1040. doi: 10.1126/science.1221551. |
Crystal structure of human argonaute2. SNAP output |
| 4olb |
hydrolase-RNA |
X-ray (2.899 Å) |
Schirle NT, MacRae IJ |
(2012) "The crystal structure of human Argonaute2." Science, 336, 1037-1040. doi: 10.1126/science.1221551. |
Crystal structure of human argonaute2 bound to tryptophan. SNAP output |
| 4oo1 |
hydrolase-RNA |
X-ray (3.3 Å) |
Wasmuth EV, Januszyk K, Lima CD |
(2014) "Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA." Nature, 511, 435-439. doi: 10.1038/nature13406. |
Structure of an rrp6-RNA exosome complex bound to poly(a) RNA. SNAP output |
| 4oog |
hydrolase-RNA |
X-ray (2.5 Å) |
Liang YH, Lavoie M, Comeau MA, Abou Elela S, Ji X |
(2014) "Structure of a Eukaryotic RNase III Postcleavage Complex Reveals a Double-Ruler Mechanism for Substrate Selection." Mol.Cell, 54, 431-444. doi: 10.1016/j.molcel.2014.03.006. |
Crystal structure of yeast rnase iii (rnt1p) complexed with the product of dsrna processing. SNAP output |
| 4oq8 |
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 icosahedral constraints. 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 |
| 4ox9 |
ribosome-antibiotic |
X-ray (3.8 Å) |
Dunkle JA, Vinal K, Desai PM, Zelinskaya N, Savic M, West DM, Conn GL, Dunham CM |
(2014) "Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA." Proc.Natl.Acad.Sci.USA, 111, 6275-6280. doi: 10.1073/pnas.1402789111. |
Crystal structure of the aminoglycoside resistance methyltransferase npma bound to the 30s ribosomal subunit. SNAP output |
| 4p3e |
RNA binding protein-RNA |
X-ray (3.5 Å) |
Grotwinkel JT, Wild K, Segnitz B, Sinning I |
(2014) "SRP RNA remodeling by SRP68 explains its role in protein translocation." Science, 344, 101-104. doi: 10.1126/science.1249094. |
Structure of the human srp s domain. SNAP output |
| 4pdb |
ribosomal protein-RNA |
X-ray (2.6 Å) |
Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP |
(2014) "Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis." Nucleic Acids Res., 42, 10795-10808. doi: 10.1093/nar/gku743. |
Crystal structure of bacillus anthracis ribosomal protein s8 in complex with an RNA aptamer. 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 |
| 4pjo |
splicing |
X-ray (3.3 Å) |
Kondo Y, Oubridge C, van Roon AM, Nagai K |
(2015) "Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition." Elife, 4. doi: 10.7554/eLife.04986. |
Minimal u1 snrnp. SNAP output |
| 4pkd |
gene regulation |
X-ray (2.5 Å) |
Kondo Y, Oubridge C, van Roon AM, Nagai K |
(2015) "Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition." Elife, 4. doi: 10.7554/eLife.04986. |
U1-70k in complex with u1 snrna stem-loops 1 and u1-a rrm in complex with stem-loop 2. SNAP output |
| 4pmi |
RNA binding protein-RNA |
X-ray (3.2 Å) |
Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD |
(2014) "RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex." Elife, 4, e04120. doi: 10.7554/eLife.04120. |
Crystal structure of rev and rev-response-element RNA complex. SNAP output |
| 4pmw |
hydrolase-RNA |
X-ray (2.95 Å) |
Faehnle CR, Walleshauser J, Joshua-Tor L |
(2014) "Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway." Nature, 514, 252-256. doi: 10.1038/nature13553. |
Structure of mouse dis3l2 in complex with oligou RNA substrate. SNAP output |
| 4pr6 |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS |
(2014) "New tools provide a second look at HDV ribozyme structure, dynamics and cleavage." Nucleic Acids Res., 42, 12833-12846. doi: 10.1093/nar/gku992. |
A second look at the hdv ribozyme structure and dynamics.. SNAP output |
| 4prf |
RNA binding protein-RNA |
X-ray (2.395 Å) |
Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS |
(2014) "New tools provide a second look at HDV ribozyme structure, dynamics and cleavage." Nucleic Acids Res., 42, 12833-12846. doi: 10.1093/nar/gku992. |
A second look at the hdv ribozyme structure and dynamics.. SNAP output |
| 4q9q |
RNA |
X-ray (2.45 Å) |
Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA |
(2014) "A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore." Nat.Chem.Biol., 10, 686-691. doi: 10.1038/nchembio.1561. |
Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with fab. SNAP output |
| 4q9r |
RNA-immune system |
X-ray (3.12 Å) |
Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA |
(2014) "A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore." Nat.Chem.Biol., 10, 686-691. doi: 10.1038/nchembio.1561. |
Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with fab. SNAP output |
| 4qei |
ligase-RNA |
X-ray (2.875 Å) |
Deng X, Qin X, Chen L, Jia Q, Zhang Y, Zhang Z, Lei D, Ren G, Zhou Z, Wang Z, Li Q, Xie W |
(2016) "Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis." J.Biol.Chem., 291, 5740-5752. doi: 10.1074/jbc.M115.679126. |
Two distinct conformational states of glyrs captured in crystal lattice. SNAP output |
| 4qg3 |
ribosomal protein-RNA |
X-ray (2.0 Å) |
Tishchenko S, Kostareva O, Gabdulkhakov A, Mikhaylina A, Nikonova E, Nevskaya N, Sarskikh A, Piendl W, Garber M, Nikonov S |
(2015) "Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions." Acta Crystallogr.,Sect.D, 71, 376-386. doi: 10.1107/S1399004714026248. |
Crystal structure of mutant ribosomal protein g219v tthl1 in complex with 80nt 23s RNA from thermus thermophilus. SNAP output |
| 4qi2 |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Schlundt A, Heinz GA, Janowski R, Geerlof A, Stehle R, Heissmeyer V, Niessing D, Sattler M |
(2014) "Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation." Nat.Struct.Mol.Biol., 21, 671-678. doi: 10.1038/nsmb.2855. |
X-ray structure of the roq domain from murine roquin-1 in complex with a 23-mer tnf-cde RNA. SNAP output |
| 4qik |
RNA binding protein-RNA |
X-ray (1.9 Å) |
Tan D, Zhou M, Kiledjian M, Tong L |
(2014) "The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA." Nat.Struct.Mol.Biol., 21, 679-685. doi: 10.1038/nsmb.2857. |
Crystal structure of the roq domain of human roquin in complex with the tnf23 RNA duplex. SNAP output |
| 4qil |
RNA binding protein-RNA |
X-ray (2.9 Å) |
Tan D, Zhou M, Kiledjian M, Tong L |
(2014) "The ROQ domain of Roquin recognizes mRNA constitutive-decay element and double-stranded RNA." Nat.Struct.Mol.Biol., 21, 679-685. doi: 10.1038/nsmb.2857. |
Crystal structure of the roq domain of human roquin in complex with the hmg19 stem-loop RNA. SNAP output |
| 4qm6 |
transferase-RNA |
X-ray (1.5 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 RNA. SNAP output |
| 4qoz |
RNA-hydrolase-RNA binding protein |
X-ray (2.304 Å) |
Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM |
(2014) "Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation." Proc.Natl.Acad.Sci.USA, 111, E2937-E2946. doi: 10.1073/pnas.1406381111. |
Crystal structure of the histone mrna stem-loop, stem-loop binding protein (phosphorylated), and 3'hexo ternary complex. SNAP output |
| 4qpx |
hydrolase-RNA |
X-ray (1.86 Å) |
Zamyatkin D, Rao C, Hoffarth E, Jurca G, Rho H, Parra F, Grochulski P, Ng KK |
(2014) "Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase." Acta Crystallogr.,Sect.D, 70, 3099-3109. doi: 10.1107/S1399004714021518. |
Nv polymerase post-incorporation-like complex. SNAP output |
| 4qqb |
tranlation-RNA |
X-ray (2.8 Å) |
Hennig J, Militti C, Popowicz GM, Wang I, Sonntag M, Geerlof A, Gabel F, Gebauer F, Sattler M |
(2014) "Structural basis for the assembly of the Sxl-Unr translation regulatory complex." Nature, 515, 287-290. doi: 10.1038/nature13693. |
Structural basis for the assembly of the sxl-unr translation regulatory complex. SNAP output |
| 4qu6 |
RNA binding protein-RNA |
X-ray (1.75 Å) |
Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL) |
"Crystal structure of a G-rich RNA sequence binding factor 1 (GRSF1) from Homo sapiens at 1.75 A resolution." |
Crystal structure of a g-rich RNA sequence binding factor 1 (grsf1) from homo sapiens at 1.75 Å resolution. SNAP output |
| 4qu7 |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL) |
"Crystal structure of a G-rich RNA sequence binding factor 1 (GRSF1) from Homo sapiens at 2.50 A resolution." |
Crystal structure of a g-rich RNA sequence binding factor 1 (grsf1) from homo sapiens at 2.50 Å resolution. SNAP output |
| 4qvc |
RNA binding protein-RNA |
X-ray (1.99 Å) |
Wang LJ, Wang WW, Li FD, Zhang J, Wu JH, Gong QG, Shi YY |
(2015) "Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq." Nucleic Acids Res., 43, 2400-2411. doi: 10.1093/nar/gkv072. |
E.coli hfq in complex with RNA aus. SNAP output |
| 4qvd |
RNA binding protein-RNA |
X-ray (1.972 Å) |
Wang LJ, Wang WW, Li FD, Zhang J, Wu JH, Gong QG, Shi YY |
(2015) "Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq." Nucleic Acids Res., 43, 2400-2411. doi: 10.1093/nar/gkv072. |
E.coli hfq in complex with RNA ads. SNAP output |
| 4qvi |
ribosomal protein-RNA |
X-ray (1.9 Å) |
Tishchenko S, Kostareva O, Gabdulkhakov A, Mikhaylina A, Nikonova E, Nevskaya N, Sarskikh A, Piendl W, Garber M, Nikonov S |
(2015) "Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions." Acta Crystallogr.,Sect.D, 71, 376-386. doi: 10.1107/S1399004714026248. |
Crystal structure of mutant ribosomal protein m218l tthl1 in complex with 80nt 23s RNA from thermus thermophilus. SNAP output |
| 4r3i |
RNA binding protein-RNA |
X-ray (1.8 Å) |
Xu C, Wang X, Liu K, Roundtree IA, Tempel W, Li Y, Lu Z, He C, Min J |
(2014) "Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain." Nat.Chem.Biol., 10, 927-929. doi: 10.1038/nchembio.1654. |
The crystal structure of an RNA complex. SNAP output |
| 4r8i |
cytokine-RNA |
X-ray (2.05 Å) |
Oberthur D, Achenbach J, Gabdulkhakov A, Buchner K, Maasch C, Falke S, Rehders D, Klussmann S, Betzel C |
(2015) "Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2." Nat Commun, 6, 6923. doi: 10.1038/ncomms7923. |
High resolution structure of a mirror-image RNA oligonucleotide aptamer in complex with the chemokine ccl2. SNAP output |
| 4rcj |
RNA binding protein-RNA |
X-ray (1.6 Å) |
Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J |
(2015) "Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins." J.Biol.Chem., 290, 24902-24913. doi: 10.1074/jbc.M115.680389. |
Crystal structure of ythdf1 yth domain in complex with 5mer m6a RNA. SNAP output |
| 4rcm |
RNA binding protein-RNA |
X-ray (1.8 Å) |
Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J |
(2015) "Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins." J.Biol.Chem., 290, 24902-24913. doi: 10.1074/jbc.M115.680389. |
Crystal structure of the pho92 yth domain in complex with m6a. SNAP output |
| 4rdx |
ligase-RNA |
X-ray (2.55 Å) |
Tian Q, Wang C, Liu Y, Xie W |
(2015) "Structural basis for recognition of G-1-containing tRNA by histidyl-tRNA synthetase." Nucleic Acids Res., 43, 2980-2990. doi: 10.1093/nar/gkv129. |
Structure of histidinyl-trna synthetase in complex with trna(his). SNAP output |
| 4rmo |
toxin-RNA |
X-ray (2.2 Å) |
Rao F, Short FL, Voss JE, Blower TR, Orme AL, Whittaker TE, Luisi BF, Salmond GP |
(2015) "Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system." Nucleic Acids Res., 43, 9529-9540. doi: 10.1093/nar/gkv868. |
Crystal structure of the cptin type iii toxin-antitoxin system from eubacterium rectale. SNAP output |
| 4rqe |
ligase-RNA |
X-ray (4.0 Å) |
Wang C, Guo Y, Tian Q, Jia Q, Gao Y, Zhang Q, Zhou C, Xie W |
(2015) "SerRS-tRNA
Sec
complex structures reveal mechanism
of the first step in selenocysteine biosynthesis." Nucleic Acids Res. doi: 10.1093/nar/gkv996. |
Human seryl-trna synthetase dimer complexed with two molecules of trnasec. SNAP output |
| 4rqf |
ligase-RNA |
X-ray (3.503 Å) |
Wang C, Guo Y, Tian Q, Jia Q, Gao Y, Zhang Q, Zhou C, Xie W |
(2015) "SerRS-tRNA Sec complex structures reveal mechanism
of the first step in selenocysteine biosynthesis." Nucleic Acids Res. doi: 10.1093/nar/gkv996. |
Human seryl-trna synthetase dimer complexed with one molecule of trnasec. SNAP output |
| 4rwn |
transferase-RNA |
X-ray (2.0 Å) |
Lohofener J, Steinke N, Kay-Fedorov P, Baruch P, Nikulin A, Tishchenko S, Manstein DJ, Fedorov R |
(2015) "The Activation Mechanism of 2'-5'-Oligoadenylate Synthetase Gives New Insights Into OAS/cGAS Triggers of Innate Immunity." Structure, 23, 851-862. doi: 10.1016/j.str.2015.03.012. |
Crystal structure of the pre-reactive state of porcine oas1. SNAP output |
| 4rwo |
transferase-RNA |
X-ray (2.2 Å) |
Lohofener J, Steinke N, Kay-Fedorov P, Baruch P, Nikulin A, Tishchenko S, Manstein DJ, Fedorov R |
(2015) "The Activation Mechanism of 2'-5'-Oligoadenylate Synthetase Gives New Insights Into OAS/cGAS Triggers of Innate Immunity." Structure, 23, 851-862. doi: 10.1016/j.str.2015.03.012. |
Crystal structure of the porcine oas1 l149r mutant in complex with dsrna and apcpp in the amp donor position. SNAP output |
| 4rwp |
transferase-RNA |
X-ray (2.25 Å) |
Lohofener J, Steinke N, Kay-Fedorov P, Baruch P, Nikulin A, Tishchenko S, Manstein DJ, Fedorov R |
(2015) "The Activation Mechanism of 2'-5'-Oligoadenylate Synthetase Gives New Insights Into OAS/cGAS Triggers of Innate Immunity." Structure, 23, 851-862. doi: 10.1016/j.str.2015.03.012. |
Crystal structure of porcine oas1 in complex with dsrna. SNAP output |
| 4s2x |
hydrolase-RNA |
X-ray (1.5 Å) |
Vasilyev N, Serganov A |
(2015) "Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay." J.Biol.Chem., 290, 9487-9499. doi: 10.1074/jbc.M114.634824. |
Structure of e. coli rpph bound to RNA and two magnesium ions. SNAP output |
| 4s2y |
hydrolase-RNA |
X-ray (1.6 Å) |
Vasilyev N, Serganov A |
(2015) "Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay." J.Biol.Chem., 290, 9487-9499. doi: 10.1074/jbc.M114.634824. |
Structure of e. coli rpph bound to RNA and three magnesium ions. SNAP output |
| 4s3n |
transferase-RNA |
X-ray (2.0 Å) |
Donovan J, Whitney G, Rath S, Korennykh A |
(2015) "Structural mechanism of sensing long dsRNA via a noncatalytic domain in human oligoadenylate synthetase 3." Proc.Natl.Acad.Sci.USA, 112, 3949-3954. doi: 10.1073/pnas.1419409112. |
Crystal structure of human oas3 domain i in complex with dsrna. SNAP output |
| 4tu0 |
viral protein |
X-ray (2.3 Å) |
Morin B, Ferron FP, Malet H, Coutard B, Canard B |
"CRYSTAL STRUCTURE OF CHIKUNGUNYA VIRUS NSP3 MACRO DOMAIN IN COMPLEX WITH A 2'-5' OLIGOADENYLATE TRIMER." |
Crystal structure of chikungunya virus nsp3 macro domain in complex with a 2'-5' oligoadenylate trimer. SNAP output |
| 4tuw |
RNA binding protein-RNA |
X-ray (2.902 Å) |
Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM |
(2014) "Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation." Proc.Natl.Acad.Sci.USA, 111, E2937-E2946. doi: 10.1073/pnas.1406381111. |
Drosophila stem-loop binding protein complexed with histone mrna stem-loop, phospho mimic of tpnk and c-terminal region. SNAP output |
| 4tux |
RNA binding protein-RNA |
X-ray (3.08 Å) |
Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM |
(2014) "Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation." Proc.Natl.Acad.Sci.USA, 111, E2937-E2946. doi: 10.1073/pnas.1406381111. |
Drosophila stem-loop binding protein complexed with histone mrna stem-loop. SNAP output |
| 4tv0 |
RNA binding protein-RNA |
X-ray (2.601 Å) |
Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM |
(2014) "Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation." Proc.Natl.Acad.Sci.USA, 111, E2937-E2946. doi: 10.1073/pnas.1406381111. |
Drosophila stem-loop binding protein complexed with histone mrna stem-loop, selenomethionine derivative. SNAP output |
| 4tyw |
RNA binding protein-RNA |
X-ray (2.197 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 ssrna and adp-bef. SNAP output |
| 4tyy |
RNA binding protein-RNA |
X-ray (2.74 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 ssrna and cdp-bef. SNAP output |
| 4tz0 |
RNA binding protein-RNA |
X-ray (2.35 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 ssrna and gdp-bef. SNAP output |
| 4tz6 |
RNA binding protein-RNA |
X-ray (3.209 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 ssrna and udp-bef. SNAP output |
| 4tzp |
ribosomal protein-RNA |
X-ray (8.503 Å) |
Zhang J, Ferre-D'Amare AR |
(2014) "Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration." Structure, 22, 1363-1371. doi: 10.1016/j.str.2014.07.011. |
As grown, untreated co-crystals of the ternary complex containing a t-box stem i RNA, its cognate trnagly, and b. subtilis ybxf protein. SNAP output |
| 4tzv |
ribosomal protein-RNA |
X-ray (5.03 Å) |
Zhang J, Ferre-D'Amare AR |
(2014) "Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration." Structure, 22, 1363-1371. doi: 10.1016/j.str.2014.07.011. |
Co-crystals of the ternary complex containing a t-box stem i RNA, its cognate trnagly, and b. subtilis ybxf protein, treated by removing lithium sulfate post crystallization. SNAP output |
| 4tzw |
ribosomal protein-RNA |
X-ray (4.671 Å) |
Zhang J, Ferre-D'Amare AR |
(2014) "Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration." Structure, 22, 1363-1371. doi: 10.1016/j.str.2014.07.011. |
Co-crystals of the ternary complex containing a t-box stem i RNA, its cognate trnagly, and b. subtilis ybxf protein, treated by removing lithium sulfate and replacing mg2+ with sr2+ post crystallization. SNAP output |
| 4tzz |
ribosomal protein-RNA |
X-ray (3.64 Å) |
Zhang J, Ferre-D'Amare AR |
(2014) "Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration." Structure, 22, 1363-1371. doi: 10.1016/j.str.2014.07.011. |
Co-crystals of the ternary complex containing a t-box stem i RNA, its cognate trnagly, and b. subtilis ybxf protein, treated by removing lithium sulfate and increasing peg3350 concentration from 20% to 45% post crystallization. SNAP output |
| 4u67 |
ribosome |
X-ray (3.65 Å) |
Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A |
(2017) "The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel." Structure, 25, 1233-1241.e3. doi: 10.1016/j.str.2017.06.004. |
Crystal structure of the large ribosomal subunit (50s) of deinococcus radiodurans containing a three residue insertion in l22. SNAP output |
| 4u7u |
RNA binding protein-RNA |
X-ray (3.003 Å) |
Zhao H, Sheng G, Wang J, Wang M, Bunkoczi G, Gong W, Wei Z, Wang Y |
(2014) "Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli." Nature, 515, 147-150. doi: 10.1038/nature13733. |
Crystal structure of RNA-guided immune cascade complex from e.coli. SNAP output |
| 4u8t |
RNA binding protein-RNA |
X-ray (2.7 Å) |
Luo S, Tong L |
(2014) "Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain." Proc.Natl.Acad.Sci.USA, 111, 13834-13839. doi: 10.1073/pnas.1412742111. |
Crystal structure of yth domain of zygosaccharomyces rouxii mrb1 protein in complex with n6-methyladenosine RNA. SNAP output |
| 4udv |
viral protein |
cryo-EM (3.35 Å) |
Fromm SA, Bharat TAM, Jakobi AJ, Hagen WJH, Sachse C |
(2015) "Seeing Tobacco Mosaic Virus Through Direct Electron Detectors." J.Struct.Biol., 189, 87. doi: 10.1016/J.JSB.2014.12.002. |
cryo-EM structure of tmv at 3.35 Å resolution. SNAP output |
| 4ue4 |
translation |
cryo-EM (7.0 Å) |
Beckert B, Kedrov A, Sohmen D, Kempf G, Wild K, Sinning I, Stahlberg H, Wilson DN, Beckmann R |
(2015) "Translational Arrest by a Prokaryotic Signal Recognition Particle is Mediated by RNA Interactions." Nat.Struct.Mol.Biol., 22, 767. doi: 10.1038/NSMB.3086. |
Structural basis for targeting and elongation arrest of bacillus signal recognition particle. SNAP output |
| 4ue5 |
translation |
cryo-EM (9.0 Å) |
Beckert B, Kedrov A, Sohmen D, Kempf G, Wild K, Sinning I, Stahlberg H, Wilson DN, Beckmann R |
(2015) "Translational Arrest by a Prokaryotic Signal Recognition Particle is Mediated by RNA Interactions." Nat.Struct.Mol.Biol., 22, 767. doi: 10.1038/NSMB.3086. |
Structural basis for targeting and elongation arrest of bacillus signal recognition particle. SNAP output |
| 4uer |
translation |
cryo-EM (6.47 Å) |
Aylett CHS, Boehringer D, Erzberger JP, Schaefer T, Ban N |
(2015) "Structure of a Yeast 40S-Eif1-Eif1A-Eif3-Eif3J Initiation Complex." Nat.Struct.Mol.Biol., 22, 269. doi: 10.1038/NSMB.2963. |
40s-eif1-eif1a-eif3-eif3j translation initiation complex from lachancea kluyveri. SNAP output |
| 4uft |
RNA binding protein |
cryo-EM (4.3 Å) |
Gutsche I, Desfosses A, Effantin G, Ling WL, Haupt M, Ruigrok RWH, Sachse C, Schoehn G |
(2015) "Near-Atomic Cryo-Em Structure of the Helical Measles Virus Nucleocapsid." Science, 348, 704. doi: 10.1126/SCIENCE.AAA5137. |
Structure of the helical measles virus nucleocapsid. SNAP output |
| 4uy8 |
ribosome |
cryo-EM (3.8 Å) |
Bischoff L, Berninghausen O, Beckmann R |
(2014) "Molecular Basis for the Ribosome Functioning as an L-Tryptophan Sensor." Cell Rep., 9, 469. doi: 10.1016/J.CELREP.2014.09.011. |
Molecular basis for the ribosome functioning as a l-tryptophan sensor - cryo-EM structure of a tnac stalled e.coli ribosome. SNAP output |
| 4uyj |
signaling protein |
X-ray (3.35 Å) |
Bousset L, Mary C, Brooks MA, Scherrer A, Strub K, Cusack S |
(2014) "Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation." RNA, 20, 1955. doi: 10.1261/RNA.047209.114. |
Crystal structure of a signal recognition particle alu domain in the elongation arrest conformation. SNAP output |
| 4uyk |
signaling protein |
X-ray (3.22 Å) |
Bousset L, Mary C, Brooks MA, Scherrer A, Strub K, Cusack S |
(2014) "Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation." RNA, 20, 1955. doi: 10.1261/RNA.047209.114. |
Crystal structure of a signal recognition particle alu domain in the elongation arrest conformation. SNAP output |
| 4v19 |
ribosome |
cryo-EM (3.4 Å) |
Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N |
(2014) "The Complete Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome." Nature, 515, 283. doi: 10.1038/NATURE13895. |
Structure of the large subunit of the mammalian mitoribosome, part 1 of 2. SNAP output |
| 4v2s |
RNA binding protein-RNA |
X-ray (3.48 Å) |
Dimastrogiovanni D, Frohlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF |
(2014) "Recognition of the small regulatory RNA RydC by the bacterial Hfq protein." Elife, 3. doi: 10.7554/eLife.05375. |
Crystal structure of hfq in complex with the srna rydc. SNAP output |
| 4w5n |
hydrolase-RNA |
X-ray (2.9 Å) |
Schirle NT, Sheu-Gruttadauria J, MacRae IJ |
(2014) "Gene regulation. Structural basis for microRNA targeting." Science, 346, 608-613. doi: 10.1126/science.1258040. |
The crystal structure of human argonaute2 bound to a defined guide RNA. SNAP output |
| 4w5o |
hydrolase-RNA |
X-ray (1.802 Å) |
Schirle NT, Sheu-Gruttadauria J, MacRae IJ |
(2014) "Gene regulation. Structural basis for microRNA targeting." Science, 346, 608-613. doi: 10.1126/science.1258040. |
The crystal structure of human argonaute2 bound to a guide and target RNA containing seed pairing from 2-9. SNAP output |
| 4w5q |
hydrolase-RNA |
X-ray (3.101 Å) |
Schirle NT, Sheu-Gruttadauria J, MacRae IJ |
(2014) "Gene regulation. Structural basis for microRNA targeting." Science, 346, 608-613. doi: 10.1126/science.1258040. |
The crystal structure of human argonaute2 bound to a guide and target RNA containing seed pairing from 2-8. SNAP output |
| 4w5r |
hydrolase-RNA |
X-ray (2.5 Å) |
Schirle NT, Sheu-Gruttadauria J, MacRae IJ |
(2014) "Gene regulation. Structural basis for microRNA targeting." Science, 346, 608-613. doi: 10.1126/science.1258040. |
The crystal structure of human argonaute2 bound to a guide and target RNA containing seed pairing from 2-8 (long target). SNAP output |
| 4w5t |
hydrolase-RNA |
X-ray (2.5 Å) |
Schirle NT, Sheu-Gruttadauria J, MacRae IJ |
(2014) "Gene regulation. Structural basis for microRNA targeting." Science, 346, 608-613. doi: 10.1126/science.1258040. |
The crystal structure of human argonaute2 bound to a guide and target RNA containing seed pairing from 2-7. SNAP output |
| 4w90 |
RNA binding protein-RNA |
X-ray (3.118 Å) |
Jones CP, Ferre-D'Amare AR |
(2014) "Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA." Embo J., 33, 2692-2703. doi: 10.15252/embj.201489209. |
Crystal structure of bacillus subtilis cyclic-di-amp riboswitch ydao. SNAP output |
| 4w92 |
RNA binding protein-RNA |
X-ray (3.209 Å) |
Jones CP, Ferre-D'Amare AR |
(2014) "Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA." Embo J., 33, 2692-2703. doi: 10.15252/embj.201489209. |
Crystal structure of bacillus subtilis cyclic-di-amp riboswitch ydao. 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 |
| 4wc2 |
transferase-RNA |
X-ray (2.8 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Crystal structure of trna nucleotidyltransferase complexed with a primer trna and an incoming atp analog. SNAP output |
| 4wc3 |
transferase-RNA |
X-ray (3.1 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Structure of trna-processing enzyme complex 1. SNAP output |
| 4wc4 |
transferase-RNA |
X-ray (3.501 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Trna-processing enzyme complex 2. SNAP output |
| 4wc5 |
transferase-RNA |
X-ray (3.41 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Structure of trna-processing enzyme complex 3. SNAP output |
| 4wc6 |
transferase-RNA |
X-ray (3.41 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Structure of trna-processing enzyme complex 4. SNAP output |
| 4wc7 |
transferase-RNA |
X-ray (3.102 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Structure of trna-processing enzyme complex 5. SNAP output |
| 4wce |
ribosome |
X-ray (3.526 Å) |
Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A |
(2015) "Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus." Proc.Natl.Acad.Sci.USA, 112, E5805-E5814. doi: 10.1073/pnas.1517952112. |
The crystal structure of the large ribosomal subunit of staphylococcus aureus. SNAP output |
| 4wf9 |
ribosome |
X-ray (3.427 Å) |
Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A |
(2015) "Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus." Proc.Natl.Acad.Sci.USA, 112, E5805-E5814. doi: 10.1073/pnas.1517952112. |
The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with telithromycin. SNAP output |
| 4wfn |
ribosome |
X-ray (3.54 Å) |
Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A |
(2017) "The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel." Structure, 25, 1233-1241.e3. doi: 10.1016/j.str.2017.06.004. |
Crystal structure of the large ribosomal subunit (50s) of deinococcus radiodurans containing a three residue insertion in l22 in complex with erythromycin. SNAP output |
| 4wj3 |
ligase-RNA |
X-ray (3.705 Å) |
Suzuki T, Nakamura A, Kato K, Soll D, Tanaka I, Sheppard K, Yao M |
(2015) "Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis." Proc.Natl.Acad.Sci.USA, 112, 382-387. doi: 10.1073/pnas.1423314112. |
Crystal structure of the asparagine transamidosome from pseudomonas aeruginosa. SNAP output |
| 4wj4 |
ligase-RNA |
X-ray (3.294 Å) |
Suzuki T, Nakamura A, Kato K, Soll D, Tanaka I, Sheppard K, Yao M |
(2015) "Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis." Proc.Natl.Acad.Sci.USA, 112, 382-387. doi: 10.1073/pnas.1423314112. |
Crystal structure of non-discriminating aspartyl-trna synthetase from pseudomonas aeruginosa complexed with trna(asn) and aspartic acid. 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 |
| 4wrt |
transferase-RNA |
X-ray (2.7 Å) |
Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crepin T, Hart D, Lunardi T, Nanao M, Ruigrok RW, Cusack S |
(2014) "Structural insight into cap-snatching and RNA synthesis by influenza polymerase." Nature, 516, 361-366. doi: 10.1038/nature14009. |
Crystal structure of influenza b polymerase with bound vrna promoter (form flub2). SNAP output |
| 4wsa |
transferase-RNA |
X-ray (3.4 Å) |
Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crepin T, Hart D, Lunardi T, Nanao M, Ruigrok RW, Cusack S |
(2014) "Structural insight into cap-snatching and RNA synthesis by influenza polymerase." Nature, 516, 361-366. doi: 10.1038/nature14009. |
Crystal structure of influenza b polymerase bound to the vrna promoter (flub1 form). SNAP output |
| 4wsb |
transferase-RNA |
X-ray (2.65 Å) |
Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crepin T, Hart D, Lunardi T, Nanao M, Ruigrok RW, Cusack S |
(2014) "Structural insight into cap-snatching and RNA synthesis by influenza polymerase." Nature, 516, 361-366. doi: 10.1038/nature14009. |
Bat influenza a polymerase with bound vrna promoter. SNAP output |
| 4wta |
transferase-RNA |
X-ray (2.8 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 udp, mn2+ and symmetrical primer template 5'-caaaauuu. SNAP output |
| 4wtc |
transferase-RNA |
X-ray (2.75 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 cdp, mn2+ and symmetrical primer template 5'-agaaauuu. SNAP output |
| 4wtd |
transferase-RNA |
X-ray (2.7 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 adp, mn2+ and symmetrical primer template 5'-auaaauuu. SNAP output |
| 4wte |
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 gdp, mn2+ and symmetrical primer template 5'-acaaauuu. SNAP output |
| 4wtf |
transferase-RNA |
X-ray (2.65 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 gs-639475, mn2+ and symmetrical primer template 5'-caaaauuu. 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 |
| 4wti |
transferase-RNA |
X-ray (2.8 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 in complex with RNA template 5'-acgg, RNA primer 5'-pcc, mn2+, and gdp. SNAP output |
| 4wtj |
transferase-RNA |
X-ray (2.2 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 in complex with RNA template 5'-aucc, RNA primer 5'-pgg, mn2+, and adp. SNAP output |
| 4wtk |
transferase-RNA |
X-ray (2.5 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 in complex with RNA template 5'-agcc, RNA primer 5'-pgg, mn2+, and cdp. SNAP output |
| 4wtl |
transferase-RNA |
X-ray (2.0 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 in complex with RNA template 5'-uacc, RNA primer 5'-pgg, mn2+, and udp. SNAP output |
| 4wtm |
transferase-RNA |
X-ray (2.15 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 in complex with RNA template 5'-uagg, RNA primer 5'-pcc, mn2+, and udp. SNAP output |
| 4wzm |
transferase |
X-ray (2.52 Å) |
Ferrer-Orta C, de la Higuera I, Caridi F, Sanchez-Aparicio MT, Moreno E, Perales C, Singh K, Sarafianos SG, Sobrino F, Domingo E, Verdaguer N |
(2015) "Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition." J.Virol., 89, 6848-6859. doi: 10.1128/JVI.03283-14. |
Mutant k18e of RNA dependent RNA polymerase from foot-and-mouth disease virus complexed with RNA. SNAP output |
| 4wzq |
transferase |
X-ray (2.8 Å) |
Ferrer-Orta C, de la Higuera I, Caridi F, Sanchez-Aparicio MT, Moreno E, Perales C, Singh K, Sarafianos SG, Sobrino F, Domingo E, Verdaguer N |
(2015) "Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition." J.Virol., 89, 6848-6859. doi: 10.1128/JVI.03283-14. |
Mutant k20e of RNA dependent RNA polymerase 3d from foot-and-mouth disease virus complexed with RNA. SNAP output |
| 4x0a |
transferase-RNA |
X-ray (3.505 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Structure of trna-processing enzyme complex 6. SNAP output |
| 4x0b |
transferase-RNA |
X-ray (3.2 Å) |
Yamashita S, Martinez A, Tomita K |
(2015) "Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme." Structure, 23, 830-842. doi: 10.1016/j.str.2015.03.013. |
Structure of trna-processing enzyme complex 7. SNAP output |
| 4x2b |
transferase |
X-ray (2.94 Å) |
Ferrer-Orta C, de la Higuera I, Caridi F, Sanchez-Aparicio MT, Moreno E, Perales C, Singh K, Sarafianos SG, Sobrino F, Domingo E, Verdaguer N |
(2015) "Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition." J.Virol., 89, 6848-6859. doi: 10.1128/JVI.03283-14. |
K20a RNA dependent RNA polymerase mutant from foot-and-mouth disease virus complexed with an RNA. SNAP output |
| 4x4n |
transferase-RNA |
X-ray (2.953 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix. SNAP output |
| 4x4o |
RNA binding protein |
X-ray (3.201 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix and ctp. SNAP output |
| 4x4p |
RNA binding protein |
X-ray (3.0 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix ending in ccac. SNAP output |
| 4x4q |
RNA binding protein |
X-ray (3.15 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix ending in ccac and ctp. SNAP output |
| 4x4r |
RNA binding protein |
X-ray (3.202 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix ending in ccacc and ampcpp. SNAP output |
| 4x4s |
RNA binding protein |
X-ray (3.25 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix ending in ccacc and ctp. SNAP output |
| 4x4t |
transferase-RNA |
X-ray (2.5 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a g70a arginyl-trna minihelix ending in ccacca. SNAP output |
| 4x4u |
RNA binding protein |
X-ray (2.7 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a human menbeta minihelix ending in ccacc. SNAP output |
| 4x4v |
RNA binding protein |
X-ray (2.6 Å) |
Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L |
(2015) "On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme." Cell, 160, 644-658. doi: 10.1016/j.cell.2015.01.005. |
Crystal structure of the a.fulgidus cca-adding enzyme in complex with a human menbeta minihelix ending in ccacc and ampcpp. SNAP output |
| 4x62 |
ribosome-antibiotic |
X-ray (3.45 Å) |
Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD |
(2016) "N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics." Nat.Struct.Mol.Biol., 23, 110-115. doi: 10.1038/nsmb.3148. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4x64 |
ribosome-antibiotic |
X-ray (3.35 Å) |
Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD |
(2016) "N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics." Nat.Struct.Mol.Biol., 23, 110-115. doi: 10.1038/nsmb.3148. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4x65 |
ribosome-antibiotic |
X-ray (3.345 Å) |
Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD |
(2016) "N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics." Nat.Struct.Mol.Biol., 23, 110-115. doi: 10.1038/nsmb.3148. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4x66 |
ribosome-antibiotic |
X-ray (3.446 Å) |
Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD |
(2016) "N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics." Nat.Struct.Mol.Biol., 23, 110-115. doi: 10.1038/nsmb.3148. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 4xbf |
oxidoreductase-transcription-RNA |
X-ray (2.803 Å) |
Hirschi A, Martin WJ, Luka Z, Loukachevitch LV, Reiter NJ |
(2016) "G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme." RNA, 22, 1250-1260. doi: 10.1261/rna.057265.116. |
Structure of lsd1:corest in complex with ssrna. SNAP output |
| 4xco |
RNA binding protein |
X-ray (2.9 Å) |
Hainzl T, Sauer-Eriksson AE |
(2015) "Signal-sequence induced conformational changes in the signal recognition particle." Nat Commun, 6, 7163. doi: 10.1038/ncomms8163. |
Signal-sequence induced conformational changes in the signal recognition particle. SNAP output |
| 4xjn |
viral protein-RNA |
X-ray (3.11 Å) |
Alayyoubi M, Leser GP, Kors CA, Lamb RA |
(2015) "Structure of the paramyxovirus parainfluenza virus 5 nucleoprotein-RNA complex." Proc.Natl.Acad.Sci.USA, 112, E1792-E1799. doi: 10.1073/pnas.1503941112. |
Structure of the parainfluenza virus 5 nucleocapsid-RNA complex: an insight into paramyxovirus polymerase activity. SNAP output |
| 4xww |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Zhao Y, Lu M, Zhang H, Hu J, Zhou C, Xu Q, Shah AMUH, Xu H, Wang L, Hua Y |
(2015) "Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J." Nucleic Acids Res., 43, 5550-5559. doi: 10.1093/nar/gkv444. |
Crystal structure of rnase j complexed with RNA. SNAP output |
| 4y91 |
RNA binding protein-RNA |
X-ray (2.656 Å) |
Patterson J, Randolph PS, Mura C |
"Crystal Structure of a Thermotoga maritima Hfq homolog." |
Crystal structure of a thermotoga maritima hfq homolog. SNAP output |
| 4yb1 |
RNA-RNA binding protein |
X-ray (2.081 Å) |
Ren A, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ |
(2015) "Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch." Cell Rep, 11, 1-12. doi: 10.1016/j.celrep.2015.03.004. |
20a mutant c-di-gmp vc2 riboswitch bound with 3',3'-cgamp. SNAP output |
| 4yco |
oxidoreductase |
X-ray (2.1 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 trnaphe. 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 |
| 4yhh |
ribosome |
X-ray (3.417 Å) |
Schedlbauer A, Kaminishi T, Ochoa-Lizarralde B, Dhimole N, Zhou S, Lopez-Alonso JP, Connell SR, Fucini P |
(2015) "Structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome." Antimicrob.Agents Chemother., 59, 2849-2854. doi: 10.1128/AAC.04895-14. |
Crystal structure of the 30s ribosomal subunit from thermus thermophilus in complex with tigecycline. SNAP output |
| 4yhw |
splicing |
X-ray (3.25 Å) |
Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Luhrmann R, Wahl MC |
(2015) "A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing." Elife, 4, e07320. doi: 10.7554/eLife.07320. |
Yeast prp3 (296-469) in complex with fragment of u4-u6 di-snrna. SNAP output |
| 4yoe |
RNA binding protein-RNA |
X-ray (1.92 Å) |
Morgan CE, Meagher JL, Levengood JD, Delproposto J, Rollins C, Stuckey JA, Tolbert BS |
(2015) "The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein." J.Mol.Biol., 427, 3241-3257. doi: 10.1016/j.jmb.2015.05.009. |
Structure of up1 bound to RNA 5'-agu-3'. SNAP output |
| 4yvi |
transferase-RNA |
X-ray (3.01 Å) |
Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S |
(2015) "Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD." Proc.Natl.Acad.Sci.USA, 112, E4197-E4205. doi: 10.1073/pnas.1422981112. |
Crystal structure of h. influenzae trmd in complex with sinefungin and trna. SNAP output |
| 4yvj |
transferase-RNA |
X-ray (2.9 Å) |
Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S |
(2015) "Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD." Proc.Natl.Acad.Sci.USA, 112, E4197-E4205. doi: 10.1073/pnas.1422981112. |
Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36u). SNAP output |
| 4yvk |
transferase-RNA |
X-ray (3.002 Å) |
Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S |
(2015) "Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD." Proc.Natl.Acad.Sci.USA, 112, E4197-E4205. doi: 10.1073/pnas.1422981112. |
Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36c). SNAP output |
| 4yy3 |
ribosome |
X-ray (3.6 Å) |
Schureck MA, Maehigashi T, Miles SJ, Marquez J, Dunham CM |
(2016) "mRNA bound to the 30S subunit is a HigB toxin substrate." Rna, 22, 1261-1270. doi: 10.1261/rna.056218.116. |
30s ribosomal subunit- higb complex. SNAP output |
| 4yye |
ligase-RNA |
X-ray (2.301 Å) |
Holman KM, Wu J, Ling J, Simonovic M |
(2016) "The crystal structure of yeast mitochondrial ThrRS in complex with the canonical threonine tRNA." Nucleic Acids Res., 44, 1428-1439. doi: 10.1093/nar/gkv1501. |
Crystal structure of the yeast mitochondrial threonyl-trna synthetase (mst1) in complex with the canonical trnathr and threonyl sulfamoyl adenylate. SNAP output |
| 4z0c |
immune system |
X-ray (2.3 Å) |
Song W, Wang J, Han Z, Zhang Y, Zhang H, Wang W, Chang J, Xia B, Fan S, Zhang D, Wang J, Wang HW, Chai J |
(2015) "Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13." Nat.Struct.Mol.Biol., 22, 782-787. doi: 10.1038/nsmb.3080. |
Crystal structure of tlr13-ssrna13 complex. SNAP output |
| 4z31 |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Zhang Q, Fan L, Hou F, Dong A, Wang YX, Tong Y |
(2015) "New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins." Sci Rep, 5, 15660. doi: 10.1038/srep15660. |
Crystal structure of the rc3h2 roq domain in complex with stem-loop and double-stranded forms of RNA. SNAP output |
| 4z4c |
hydrolase-RNA |
X-ray (2.303 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 bound to t1-c target RNA. SNAP output |
| 4z4d |
gene regulation-RNA |
X-ray (1.6 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 bound to t1-g target RNA. SNAP output |
| 4z4e |
gene regulation-RNA |
X-ray (1.8 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 bound to t1-u target RNA. SNAP output |
| 4z4f |
gene regulation-RNA |
X-ray (2.8 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 bound to t1-dap target RNA. SNAP output |
| 4z4g |
gene regulation-RNA |
X-ray (2.7 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 bound to t1-inosine target RNA. SNAP output |
| 4z4h |
gene regulation-RNA |
X-ray (2.504 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 a481t mutant bound to t1-a target RNA. SNAP output |
| 4z4i |
gene regulation-RNA |
X-ray (2.801 Å) |
Schirle NT, Sheu-Gruttadauria J, Chandradoss SD, Joo C, MacRae IJ |
(2015) "Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets." Elife, 4. doi: 10.7554/eLife.07646. |
Human argonaute2 a481t mutant bound to t1-g target RNA. SNAP output |
| 4z7k |
hydrolase-RNA-DNA |
X-ray (3.0 Å) |
Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H |
(2016) "A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6." Structure, 24, 547-554. doi: 10.1016/j.str.2016.02.009. |
Crystal structure of crispr RNA processing endoribonuclease cas6b. SNAP output |
| 4z7l |
hydrolase-RNA |
X-ray (3.503 Å) |
Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H |
(2016) "A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6." Structure, 24, 547-554. doi: 10.1016/j.str.2016.02.009. |
Crystal structure of cas6b. SNAP output |
| 4z92 |
virus |
X-ray (3.1 Å) |
Kalynych S, Palkova L, Plevka P |
(2015) "The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid." J.Virol., 90, 1377-1386. doi: 10.1128/JVI.02346-15. |
Crystal structure of parechovirus-1 virion. SNAP output |
| 4zdo |
transferase-RNA |
X-ray (2.65 Å) |
Puppala AK, French RL, Matthies D, Baxa U, Subramaniam S, Simonovic M |
(2016) "Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase." Sci Rep, 6, 32563. doi: 10.1038/srep32563. |
The crystal structure of t325s mutant of human sepsecs in complex with selenocysteine trna (trnasec). SNAP output |
| 4zdp |
transferase-RNA |
X-ray (2.703 Å) |
Puppala AK, French RL, Matthies D, Baxa U, Subramaniam S, Simonovic M |
(2016) "Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase." Sci Rep, 6, 32563. doi: 10.1038/srep32563. |
The crystal structure of y334c mutant of human sepsecs in complex with selenocysteine trna (trnasec). SNAP output |
| 4zld |
RNA binding protein-RNA |
X-ray (1.6 Å) |
Sakurai S, Ohto U, Shimizu T |
(2015) "Structure of human Roquin-2 and its complex with constitutive-decay element RNA." Acta Crystallogr.,Sect.F, 71, 1048-1054. doi: 10.1107/S2053230X15011887. |
Crystal structure of human roquin-2 roq domain in complex with roquin cde RNA. SNAP output |
| 4zlr |
translation |
X-ray (2.3 Å) |
Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G |
(2015) "The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation." Cell Rep, 13, 1206-1220. doi: 10.1016/j.celrep.2015.09.068. |
Structure of the brat-nhl domain bound to consensus RNA motif. SNAP output |
| 4zt0 |
hydrolase-RNA |
X-ray (2.9 Å) |
Jiang F, Zhou K, Ma L, Gressel S, Doudna JA |
(2015) "A Cas9-guide RNA complex preorganized for target DNA recognition." Science, 348, 1477-1481. doi: 10.1126/science.aab1452. |
Crystal structure of catalytically-active streptococcus pyogenes cas9 in complex with single-guide RNA at 2.9 angstrom resolution. SNAP output |
| 4zt9 |
hydrolase-RNA |
X-ray (3.1 Å) |
Jiang F, Zhou K, Ma L, Gressel S, Doudna JA |
(2015) "A Cas9-guide RNA complex preorganized for target DNA recognition." Science, 348, 1477-1481. doi: 10.1126/science.aab1452. |
Nuclease-inactive streptococcus pyogenes cas9 (d10a-h840a, dcas9) in complex with single-guide RNA at 3.1 angstrom resolution. SNAP output |
| 5a0t |
hydrolase-RNA |
X-ray (2.283 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 |
| 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 |
| 5a2q |
ribosome |
cryo-EM (3.9 Å) |
Quade N, Boehringer D, Leibundgut M, Van Den Heuvel J, Ban N |
(2015) "Cryo-Em Structure of Hepatitis C Virus Ires Bound to the Human Ribosome at 3.9 Angstrom Resolution." Nat.Commun., 6, 7646. doi: 10.1038/NCOMMS8646. |
Structure of the hcv ires bound to the human ribosome. SNAP output |
| 5a2t |
viral protein |
cryo-EM (5.6 Å) |
Dimaio F, Chen C, Yu X, Frenz B, Hsu Y, Lin N, Egelman EH |
(2015) "The Molecular Basis for Flexibility in the Flexible Filamentous Plant Viruses." Nat.Struct.Mol.Biol., 22, 642. doi: 10.1038/NSMB.3054. |
The molecular basis for flexibility in the flexible filamentous plant viruses. SNAP output |
| 5a79 |
virus |
cryo-EM (4.1 Å) |
Clare DK, Pechnikova EV, Skurat EV, Makarov VV, Sokolova OS, Solovyev AG, Orlova EV |
(2015) "Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy." Structure, 23, 1815. doi: 10.1016/J.STR.2015.06.028. |
Novel inter-subunit contacts in barley stripe mosaic virus revealed by cryo-EM. SNAP output |
| 5a7a |
virus |
cryo-EM (4.1 Å) |
Clare DK, Pechnikova EV, Skurat EV, Makarov VV, Sokolova OS, Solovyev AG, Orlova EV |
(2015) "Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy." Structure, 23, 1815. doi: 10.1016/J.STR.2015.06.028. |
Novel inter-subunit contacts in barley stripe mosaic virus revealed by cryo-EM. SNAP output |
| 5a8l |
translation |
cryo-EM (3.8 Å) |
Matheisl S, Berninghausen O, Becker T, Beckmann R |
(2015) "Structure of a Human Translation Termination Complex." Nucleic Acids Res., 43, 8615. doi: 10.1093/NAR/GKV909. |
Human erf1 and the hcmv nascent peptide in the translation termination complex. SNAP output |
| 5ady |
ribosome |
cryo-EM (4.5 Å) |
Zhang Y, Mandava CS, Cao W, Li X, Zhang D, Li N, Zhang Y, Zhang X, Qin Y, Mi K, Lei J, Sanyal S, Gao N |
(2015) "Hflx is a Ribosome Splitting Factor Rescuing Stalled Ribosomes Under Stress Conditions." Nat.Struct.Mol.Biol., 22, 906. doi: 10.1038/NSMB.3103. |
cryo-EM structures of the 50s ribosome subunit bound with hflx. SNAP output |
| 5ah5 |
ligase-RNA |
X-ray (2.1 Å) |
Chopra S, Palencia A, Virus C, Schulwitz S, Temple BR, Cusack S, Reader J |
(2016) "Structural Characterization of Antibiotic Self-Immunity tRNA Synthetase in Plant Tumour Biocontrol Agent." Nat.Commun., 7, 12928. doi: 10.1038/NCOMMS12928. |
Crystal structure of the ternary complex of agrobacterium radiobacter k84 agnb2 leurs-trna-leuams. SNAP output |
| 5aj3 |
ribosome |
cryo-EM (3.6 Å) |
Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N |
(2015) "Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome." Science, 348, 303-308. doi: 10.1126/science.aaa3872. |
Structure of the small subunit of the mammalian mitoribosome. SNAP output |
| 5aka |
ribosome |
cryo-EM (5.7 Å) |
von Loeffelholz O, Jiang Q, Ariosa A, Karuppasamy M, Huard K, Berger I, Shan S, Schaffitzel C |
(2015) "Ribosome-Srp-Ftsy Cotranslational Targeting Complex in the Closed State." Proc.Natl.Acad.Sci.USA, 112, 3943-3948. doi: 10.1073/PNAS.1424453112. |
Em structure of ribosome-srp-ftsy complex in closed state. SNAP output |
| 5amq |
hydrolase |
X-ray (3.0 Å) |
Gerlach P, Malet H, Cusack S, Reguera J |
(2015) "Structural Insights Into Bunyavirus Replication and its Regulation by the Vrna Promoter." Cell, 161, 1267-1279. doi: 10.1016/J.CELL.2015.05.006. |
Structure of the la crosse bunyavirus polymerase in complex with the 3' and 5' viral RNA. SNAP output |
| 5amr |
hydrolase |
X-ray (2.57 Å) |
Gerlach P, Malet H, Cusack S, Reguera J |
(2015) "Structural Insights Into Bunyavirus Replication and its Regulation by the Vrna Promoter." Cell(Cambridge,Mass.), 161, 1267. doi: 10.1016/J.CELL.2015.05.006. |
Structure of the la crosse bunyavirus polymerase in complex with the 3' viral RNA. SNAP output |
| 5an9 |
translation |
cryo-EM (3.3 Å) |
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ |
(2015) "Mechanism of Eif6 Release from the Nascent 60S Ribosomal Subunit." Nat.Struct.Mol.Biol., 22, 914. doi: 10.1038/NSMB.3112. |
Mechanism of eif6 release from the nascent 60s ribosomal subunit. SNAP output |
| 5anb |
translation |
cryo-EM (4.1 Å) |
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ |
(2015) "Mechanism of Eif6 Release from the Nascent 60S Ribosomal Subunit." Nat.Struct.Mol.Biol., 22, 914. doi: 10.1038/NSMB.3112. |
Mechanism of eif6 release from the nascent 60s ribosomal subunit. SNAP output |
| 5anc |
translation |
cryo-EM (4.2 Å) |
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ |
(2015) "Mechanism of Eif6 Release from the Nascent 60S Ribosomal Subunit." Nat.Struct.Mol.Biol., 22, 914. doi: 10.1038/NSMB.3112. |
Mechanism of eif6 release from the nascent 60s ribosomal subunit. SNAP output |
| 5aor |
hydrolase-RNA |
X-ray (2.08 Å) |
Prabu JR, Muller M, Thomae AW, Schussler S, Bonneau F, Becker PB, Conti E |
(2015) "Structure of the RNA Helicase Mle Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling." Mol.Cell, 60, 487. doi: 10.1016/J.MOLCEL.2015.10.011. |
Structure of mle RNA adp alf4 complex. 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 |
| 5axm |
transferase-RNA |
X-ray (2.21 Å) |
Kimura S, Suzuki T, Chen M, Kato K, Yu J, Nakamura A, Tanaka I, Yao M |
(2016) "Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein." Sci Adv, 2, e1501397. doi: 10.1126/sciadv.1501397. |
Crystal structure of thg1 like protein (tlp) with trna(phe). SNAP output |
| 5axn |
transferase-RNA |
X-ray (2.703 Å) |
Kimura S, Suzuki T, Chen M, Kato K, Yu J, Nakamura A, Tanaka I, Yao M |
(2016) "Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein." Sci Adv, 2, e1501397. doi: 10.1126/sciadv.1501397. |
Crystal structure of thg1 like protein (tlp) with trna(phe) and gdpnp. SNAP output |
| 5b63 |
ligase |
X-ray (3.0 Å) |
Zhou M, Ye S, Stephen P, Zhang R, Wang ED, Giege R, Lin SX |
"Crystal structures of E.coli arginyl-tRNA synthetase (ArgRS) in complex with substrate tRNA(Arg)." |
Crystal structures of e.coli arginyl-trna synthetase (argrs) in complex with substrate trna(arg). SNAP output |
| 5br8 |
ribosome |
X-ray (3.4 Å) |
Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster A, Young ID, Michels-Clark T, Aquila A, Mengning L, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H |
"Ambient-temperature crystal structure of 30S ribosomal subunit from Thermus thermophilus in complex with paromomycin." |
Ambient-temperature crystal structure of 30s ribosomal subunit from thermus thermophilus in complex with paromomycin. SNAP output |
| 5bte |
hydrolase-RNA |
X-ray (2.4 Å) |
Wang VY, Jiao X, Kiledjian M, Tong L |
(2015) "Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes." Nucleic Acids Res., 43, 6596-6606. doi: 10.1093/nar/gkv620. |
Crystal structure of ashbya gossypii rai1 in complex with pu(s)6-mn2+. SNAP output |
| 5bud |
hydrolase-RNA |
X-ray (1.99 Å) |
Wang VY, Jiao X, Kiledjian M, Tong L |
(2015) "Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes." Nucleic Acids Res., 43, 6596-6606. doi: 10.1093/nar/gkv620. |
Crystal structure of candida albicans rai1 in complex with pu5-mn2+. SNAP output |
| 5bym |
RNA binding protein-RNA |
X-ray (2.708 Å) |
Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Tanaka Hall TM, Wickens M |
(2015) "RNA regulatory networks diversified through curvature of the PUF protein scaffold." Nat Commun, 6, 8213. doi: 10.1038/ncomms9213. |
Crystal structure of the RNA-binding domain of yeast puf5p bound to smx2 RNA. SNAP output |
| 5bz1 |
RNA binding protein-RNA |
X-ray (2.15 Å) |
Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Tanaka Hall TM, Wickens M |
(2015) "RNA regulatory networks diversified through curvature of the PUF protein scaffold." Nat Commun, 6, 8213. doi: 10.1038/ncomms9213. |
Crystal structure of the RNA-binding domain of yeast puf5p bound to mfa2 RNA. SNAP output |
| 5bz5 |
RNA binding protein-RNA |
X-ray (2.8 Å) |
Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Tanaka Hall TM, Wickens M |
(2015) "RNA regulatory networks diversified through curvature of the PUF protein scaffold." Nat Commun, 6, 8213. doi: 10.1038/ncomms9213. |
Crystal structure of the RNA-binding domain of yeast puf5p bound to amn1 RNA. SNAP output |
| 5bzu |
RNA binding protein-RNA |
X-ray (2.501 Å) |
Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Tanaka Hall TM, Wickens M |
(2015) "RNA regulatory networks diversified through curvature of the PUF protein scaffold." Nat Commun, 6, 8213. doi: 10.1038/ncomms9213. |
Crystal structure of the RNA-binding domain of yeast puf5p bound to aat2 RNA. SNAP output |
| 5bzv |
RNA binding protein-RNA |
X-ray (2.354 Å) |
Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Tanaka Hall TM, Wickens M |
(2015) "RNA regulatory networks diversified through curvature of the PUF protein scaffold." Nat Commun, 6, 8213. doi: 10.1038/ncomms9213. |
Crystal structure of the RNA-binding domain of yeast puf5p bound to smx2 RNA. SNAP output |
| 5c0w |
hydrolase-RNA |
X-ray (4.6 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. |
Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates. SNAP output |
| 5c0x |
hydrolase-RNA |
X-ray (3.812 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. |
Structure of a 12-subunit nuclear exosome complex bound to structured RNA. 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 |
| 5c9h |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Jansson LI, Akiyama BM, Ooms A, Lu C, Rubin SM, Stone MD |
(2015) "Structural basis of template-boundary definition in Tetrahymena telomerase." Nat.Struct.Mol.Biol., 22, 883-888. doi: 10.1038/nsmb.3101. |
Structural basis of template boundary definition in tetrahymena telomerase. SNAP output |
| 5ccb |
transferase-RNA |
X-ray (2.0 Å) |
Finer-Moore J, Czudnochowski N, O'Connell JD, Wang AL, Stroud RM |
(2015) "Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target." J.Mol.Biol., 427, 3862-3876. doi: 10.1016/j.jmb.2015.10.005. |
Crystal structure of human m1a58 methyltransferase in a complex with trna3lys and sah. SNAP output |
| 5ccx |
transferase-RNA |
X-ray (2.1 Å) |
Finer-Moore J, Czudnochowski N, O'Connell JD, Wang AL, Stroud RM |
(2015) "Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target." J.Mol.Biol., 427, 3862-3876. doi: 10.1016/j.jmb.2015.10.005. |
Structure of the product complex of trna m1a58 methyltransferase with trna3lys as substrate. SNAP output |
| 5cd1 |
transferase-RNA |
X-ray (3.6 Å) |
Finer-Moore J, Czudnochowski N, O'Connell JD, Wang AL, Stroud RM |
(2015) "Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target." J.Mol.Biol., 427, 3862-3876. doi: 10.1016/j.jmb.2015.10.005. |
Structure of an asymmetric tetramer of human trna m1a58 methyltransferase in a complex with sah and trna3lys. SNAP output |
| 5cd4 |
hydrolase-RNA |
X-ray (3.2 Å) |
van Erp PB, Jackson RN, Carter J, Golden SM, Bailey S, Wiedenheft B |
(2015) "Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli." Nucleic Acids Res., 43, 8381-8391. doi: 10.1093/nar/gkv793. |
The type ie crispr cascade complex from e. coli, with two assemblies in the asymmetric unit arranged back-to-back. SNAP output |
| 5d0a |
oxidoreductase-RNA |
X-ray (2.1 Å) |
Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL |
(2016) "Molecular basis of cobalamin-dependent RNA modification." Nucleic Acids Res., 44, 9965-9976. doi: 10.1093/nar/gkw806. |
Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop. SNAP output |
| 5d0b |
oxidoreductase-RNA |
X-ray (2.645 Å) |
Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL |
(2016) "Molecular basis of cobalamin-dependent RNA modification." Nucleic Acids Res., 44, 9965-9976. doi: 10.1093/nar/gkw806. |
Crystal structure of epoxyqueuosine reductase with a trna-tyr epoxyqueuosine-modified trna stem loop. SNAP output |
| 5d6g |
translation |
X-ray (3.3 Å) |
Gabdulkhakov AG, Mitroshin IV, Garber MB |
"CRYSTAL STRUCTURE OF FRAGMENT OF RIBOSOMAL PROTEIN P0 IN COMPLEX WITH 74NT 23S RNA FROM METHANOCOCCUS JANNASCHII." |
Crystal structure of fragment of ribosomal protein p0 in complex with 74nt 23s RNA from methanococcus jannaschii. SNAP output |
| 5d8h |
ribosomal protein |
X-ray (2.8 Å) |
Gabdulkhakov AG, Mitroshin IV, Garber MB |
"CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON." |
Crystal structure of the base of the ribosomal p stalk from methanococcus jannaschii with antibiotic thiostrepton. SNAP output |
| 5dar |
ribosomal protein |
X-ray (2.9 Å) |
Gabdulkhakov AG, Mitroshin IV, Garber MB |
"CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII." |
Crystal structure of the base of the ribosomal p stalk from methanococcus jannaschii. SNAP output |
| 5dcv |
RNA binding protein-RNA |
X-ray (3.401 Å) |
Oshima K, Kakiuchi Y, Tanaka Y, Ueda T, Nakashima T, Kimura M, Yao M |
(2016) "Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38." Biochem.Biophys.Res.Commun., 474, 541-546. doi: 10.1016/j.bbrc.2016.04.118. |
Crystal structure of phorpp38-sl12m complex. SNAP output |
| 5ddo |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ |
(2015) "Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch." Cell Rep, 13, 1800-1813. doi: 10.1016/j.celrep.2015.10.062. |
Structural and dynamic basis for low affinity-high selectivity binding of l-glutamine by the gln-riboswitch. SNAP output |
| 5ddp |
RNA binding protein-RNA |
X-ray (2.302 Å) |
Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ |
(2015) "Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch." Cell Rep, 13, 1800-1813. doi: 10.1016/j.celrep.2015.10.062. |
L-glutamine riboswitch bound with l-glutamine. SNAP output |
| 5ddq |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ |
(2015) "Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch." Cell Rep, 13, 1800-1813. doi: 10.1016/j.celrep.2015.10.062. |
L-glutamine riboswitch bound with l-glutamine soaked with mn2+. SNAP output |
| 5ddr |
RNA binding protein-RNA |
X-ray (2.605 Å) |
Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ |
(2015) "Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch." Cell Rep, 13, 1800-1813. doi: 10.1016/j.celrep.2015.10.062. |
L-glutamine riboswitch bound with l-glutamine soaked with cs+. SNAP output |
| 5de5 |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A |
(2015) "Crystal structure reveals specific recognition of a G-quadruplex RNA by a beta-turn in the RGG motif of FMRP." Proc.Natl.Acad.Sci.USA, 112, E5391-E5400. doi: 10.1073/pnas.1515737112. |
Crystal structure of the complex between human fmrp rgg motif and g-quadruplex RNA.. SNAP output |
| 5de8 |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A |
(2015) "Crystal structure reveals specific recognition of a G-quadruplex RNA by a beta-turn in the RGG motif of FMRP." Proc.Natl.Acad.Sci.USA, 112, E5391-E5400. doi: 10.1073/pnas.1515737112. |
Crystal structure of the complex between human fmrp rgg motif and g-quadruplex RNA, iridium hexammine bound form.. SNAP output |
| 5dea |
RNA binding protein-RNA |
X-ray (2.8 Å) |
Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A |
(2015) "Crystal structure reveals specific recognition of a G-quadruplex RNA by a beta-turn in the RGG motif of FMRP." Proc.Natl.Acad.Sci.USA, 112, E5391-E5400. doi: 10.1073/pnas.1515737112. |
Crystal structure of the complex between human fmrp rgg motif and g-quadruplex RNA, cesium bound form.. SNAP output |
| 5det |
RNA binding protein-RNA |
X-ray (1.95 Å) |
Teplova M, Farazi TA, Tuschl T, Patel DJ |
(2016) "Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS." Q. Rev. Biophys., 49, e1. doi: 10.1017/S0033583515000207. |
X-ray structure of human rbpms in complex with the RNA. SNAP output |
| 5dm6 |
ribosome |
X-ray (2.9 Å) |
Kaminishi T, Schedlbauer A, Fabbretti A, Brandi L, Ochoa-Lizarralde B, He CG, Milon P, Connell SR, Gualerzi CO, Fucini P |
(2015) "Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A." Nucleic Acids Res., 43, 10015-10025. doi: 10.1093/nar/gkv975. |
Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans. SNAP output |
| 5dm7 |
ribosome |
X-ray (3.0 Å) |
Kaminishi T, Schedlbauer A, Fabbretti A, Brandi L, Ochoa-Lizarralde B, He CG, Milon P, Connell SR, Gualerzi CO, Fucini P |
(2015) "Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A." Nucleic Acids Res., 43, 10015-10025. doi: 10.1093/nar/gkv975. |
Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a. SNAP output |
| 5dno |
RNA binding protein-RNA |
X-ray (1.8 Å) |
Wang CY, Zhu YW, Bao HY, Jiang YY, Xu C, Wu JH, Shi YY |
(2016) "A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1." Nucleic Acids Res., 44, 969-982. doi: 10.1093/nar/gkv1382. |
Crystal structure of mmi1 yth domain complex with RNA. SNAP output |
| 5do4 |
hydrolase-RNA |
X-ray (1.859 Å) |
Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, Lybrand TP, Frydman C, Monteiro RQ, Gomer RH, Nawrot B, Yang X |
(2016) "Evoking picomolar binding in RNA by a single phosphorodithioate linkage." Nucleic Acids Res., 44, 8052-8064. doi: 10.1093/nar/gkw725. |
Thrombin-RNA aptamer complex. SNAP output |
| 5dto |
viral protein-RNA |
X-ray (2.603 Å) |
Zhao Y, Soh TS, Lim SP, Chung KY, Swaminathan K, Vasudevan SG, Shi P-Y, Lescar J, Luo D |
(2015) "Molecular basis for specific viral RNA recognition and 2'-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5)." Proc.Natl.Acad.Sci.USA, 112, 14834-14839. doi: 10.1073/pnas.1514978112. |
Dengue virus full length ns5 complexed with viral cap 0-RNA and sah. SNAP output |
| 5dv7 |
RNA binding protein |
X-ray (3.5 Å) |
Jayachandran U, Grey H, Cook AG |
(2016) "Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA." Nucleic Acids Res., 44, 1924-1936. doi: 10.1093/nar/gkv1508. |
Crystal structure of nf90 tandem dsrbds with dsrna. SNAP output |
| 5e02 |
hydrolase, RNA binding protein-RNA |
X-ray (3.8 Å) |
Conrad KS, Hurley JM, Widom J, Ringelberg CS, Loros JJ, Dunlap JC, Crane BR |
(2016) "Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock." Embo J., 35, 1707-1719. doi: 10.15252/embj.201694327. |
Structure of RNA helicase frh a critical component of the neurospora crassa circadian clock. SNAP output |
| 5e08 |
immune system-RNA |
X-ray (2.38 Å) |
Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA |
(2016) "Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment." J.Mol.Biol., 428, 4100-4114. doi: 10.1016/j.jmb.2016.08.029. |
Specific recognition of a single-stranded RNA sequence by an engineered synthetic antibody fragment. SNAP output |
| 5e3h |
hydrolase-RNA |
X-ray (2.7 Å) |
Jiang F, Ramanathan A, Miller MT, Tang GQ, Gale M, Patel SS, Marcotrigiano J |
(2011) "Structural basis of RNA recognition and activation by innate immune receptor RIG-I." Nature, 479, 423-427. doi: 10.1038/nature10537. |
Structural basis for RNA recognition and activation of rig-i. SNAP output |
| 5e6m |
ligase-RNA |
X-ray (2.927 Å) |
Qin X, Deng X, Chen L, Xie W |
(2016) "Crystal Structure of the Wild-Type Human GlyRS Bound with tRNA(Gly) in a Productive Conformation." J.Mol.Biol., 428, 3603-3614. doi: 10.1016/j.jmb.2016.05.018. |
Crystal structure of human wild type glyrs bound with trnagly. SNAP output |
| 5ed1 |
hydrolase-RNA |
X-ray (2.77 Å) |
Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA |
(2016) "Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity." Nat.Struct.Mol.Biol., 23, 426-433. doi: 10.1038/nsmb.3203. |
Human adenosine deaminase acting on dsrna (adar2) mutant e488q bound to dsrna sequence derived from s. cerevisiae bdf2 gene. SNAP output |
| 5ed2 |
hydrolase-RNA |
X-ray (2.95 Å) |
Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA |
(2016) "Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity." Nat.Struct.Mol.Biol., 23, 426-433. doi: 10.1038/nsmb.3203. |
Human adenosine deaminase acting on dsrna (adar2) mutant e488q bound to dsrna sequence derived from human gli1 gene. SNAP output |
| 5eeu |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 1.31 mgy. SNAP output |
| 5eev |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 3.88 mgy. SNAP output |
| 5eew |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 6.45 mgy. SNAP output |
| 5eex |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 9.02 mgy. SNAP output |
| 5eey |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 11.6 mgy. SNAP output |
| 5eez |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 14.2 mgy. SNAP output |
| 5ef0 |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 16.7 mgy. SNAP output |
| 5ef1 |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 19.3 mgy. SNAP output |
| 5ef2 |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 21.9 mgy. SNAP output |
| 5ef3 |
RNA binding protein |
X-ray (1.98 Å) |
Bury CS, McGeehan JE, Antson AA, Carmichael I, Gerstel M, Shevtsov MB, Garman EF |
(2016) "RNA protects a nucleoprotein complex against radiation damage." Acta Crystallogr D Struct Biol, 72, 648-657. doi: 10.1107/S2059798316003351. |
Radiation damage to the trap-RNA complex: dose (dwd) 25.0 mgy. SNAP output |
| 5eim |
RNA binding protein-RNA |
X-ray (1.54 Å) |
Wu BX, Xu JH, Su SC, Liu H, Gan J, Ma JB |
(2017) "Structural insights into the specific recognition of DSR by the YTH domain containing protein Mmi1." Biochem. Biophys. Res. Commun., 491, 310-316. doi: 10.1016/j.bbrc.2017.07.104. |
Yth domain-containing protein mmi1 and RNA complex. SNAP output |
| 5elh |
RNA binding protein-RNA |
X-ray (1.8 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 1-3 (znf1-3), bound to RNA. 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 |
| 5elr |
RNA binding protein |
X-ray (2.3 Å) |
Feracci M, Foot JN, Grellscheid SN, Danilenko M, Stehle R, Gonchar O, Kang HS, Dalgliesh C, Meyer NH, Liu Y, Lahat A, Sattler M, Eperon IC, Elliott DJ, Dominguez C |
(2016) "Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68." Nat Commun, 7, 10355. doi: 10.1038/ncomms10355. |
Structure of the kh-qua2 domain of t-star in complex with aauaau RNA. SNAP output |
| 5els |
RNA binding protein |
X-ray (2.873 Å) |
Feracci M, Foot JN, Grellscheid SN, Danilenko M, Stehle R, Gonchar O, Kang HS, Dalgliesh C, Meyer NH, Liu Y, Lahat A, Sattler M, Eperon IC, Elliott DJ, Dominguez C |
(2016) "Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68." Nat Commun, 7, 10355. doi: 10.1038/ncomms10355. |
Structure of the kh domain of t-star in complex with aaauaa RNA. SNAP output |
| 5elt |
RNA binding protein |
X-ray (2.13 Å) |
Feracci M, Foot JN, Grellscheid SN, Danilenko M, Stehle R, Gonchar O, Kang HS, Dalgliesh C, Meyer NH, Liu Y, Lahat A, Sattler M, Eperon IC, Elliott DJ, Dominguez C |
(2016) "Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68." Nat Commun, 7, 10355. doi: 10.1038/ncomms10355. |
Structure of the qua1-kh domain of t-star in complex with uaau RNA. SNAP output |
| 5elx |
hydrolase |
X-ray (1.81 Å) |
Wong EV, Cao W, Voros J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM |
(2016) "Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5)." J.Mol.Biol., 428, 492-508. doi: 10.1016/j.jmb.2015.12.018. |
S. cerevisiae dbp5 bound to RNA and mant-adp bef3. SNAP output |
| 5emo |
RNA binding protein |
X-ray (3.03 Å) |
Feracci M, Foot JN, Grellscheid SN, Danilenko M, Stehle R, Gonchar O, Kang HS, Dalgliesh C, Meyer NH, Liu Y, Lahat A, Sattler M, Eperon IC, Elliott DJ, Dominguez C |
(2016) "Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68." Nat Commun, 7, 10355. doi: 10.1038/ncomms10355. |
Structure of the star domain of t-star in complex with auuaaa RNA. SNAP output |
| 5en1 |
RNA binding protein-RNA |
X-ray (2.58 Å) |
Wu BX, Su SC, Patil DP, Liu HH, Gan JH, Jaffrey SR, Ma JB |
(2018) "Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1." Nat Commun. doi: 10.1038/s41467-017-02770-z. |
Crystal structure of hnrnpa2b1 in complex with RNA. SNAP output |
| 5ex7 |
translation-RNA |
X-ray (2.6 Å) |
Wang Y, Yu Z, Wang M, Liu CP, Yang N, Xu RM |
"Crystal structure of Brat NHL domain in complex with an 8-nt hunchback mRNA." |
Crystal structure of brat nhl domain in complex with an 8-nt hunchback mrna. SNAP output |
| 5f5f |
RNA binding protein |
X-ray (3.0 Å) |
Janowski R, Heinz GA, Schlundt A, Wommelsdorf N, Brenner S, Gruber AR, Blank M, Buch T, Buhmann R, Zavolan M, Niessing D, Heissmeyer V, Sattler M |
(2016) "Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40." Nat Commun, 7, 11032. doi: 10.1038/ncomms11032. |
X-ray structure of roquin roq domain in complex with a selex-derived hexa-loop RNA motif. SNAP output |
| 5f5h |
RNA binding protein |
X-ray (2.23 Å) |
Janowski R, Heinz GA, Schlundt A, Wommelsdorf N, Brenner S, Gruber AR, Blank M, Buch T, Buhmann R, Zavolan M, Niessing D, Heissmeyer V, Sattler M |
(2016) "Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40." Nat Commun, 7, 11032. doi: 10.1038/ncomms11032. |
X-ray structure of roquin roq domain in complex with ox40 hexa-loop RNA motif. SNAP output |
| 5f6c |
hydrolase |
X-ray (3.002 Å) |
Bandyra KJ, Wandzik JM, Luisi BF |
(2018) "Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E." Mol. Cell, 72, 275-285.e4. doi: 10.1016/j.molcel.2018.08.039. |
The structure of e. coli rnase e catalytically inactive mutant with RNA bound. SNAP output |
| 5f8g |
transferase-RNA |
X-ray (2.78 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c1s1 form). SNAP output |
| 5f8h |
transferase-RNA |
X-ray (2.45 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c1s1-2 form). SNAP output |
| 5f8i |
transferase-RNA |
X-ray (2.503 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c1s2-3 form). SNAP output |
| 5f8j |
transferase-RNA |
X-ray (2.675 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c1s4 form). SNAP output |
| 5f8l |
transferase-RNA |
X-ray (2.812 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c3s1 form). SNAP output |
| 5f8m |
transferase-RNA |
X-ray (2.83 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c3s4-5 form). SNAP output |
| 5f8n |
transferase-RNA |
X-ray (2.484 Å) |
Shu B, Gong P |
(2016) "Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation." Proc.Natl.Acad.Sci.USA, 113, E4005-E4014. doi: 10.1073/pnas.1602591113. |
Enterovirus 71 polymerase elongation complex (c3s6 form). SNAP output |
| 5f98 |
hydrolase-RNA |
X-ray (3.28 Å) |
Devarkar SC, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel SS, Marcotrigiano J |
(2016) "Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I." Proc.Natl.Acad.Sci.USA, 113, 596-601. doi: 10.1073/pnas.1515152113. |
Crystal structure of rig-i in complex with cap-0 RNA. SNAP output |
| 5f9f |
hydrolase-RNA |
X-ray (2.601 Å) |
Devarkar SC, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel SS, Marcotrigiano J |
(2016) "Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I." Proc.Natl.Acad.Sci.USA, 113, 596-601. doi: 10.1073/pnas.1515152113. |
Crystal structure of rig-i helicase-rd in complex with 24-mer blunt-end hairpin RNA. SNAP output |
| 5f9h |
hydrolase-RNA |
X-ray (3.1 Å) |
Devarkar SC, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel SS, Marcotrigiano J |
(2016) "Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I." Proc.Natl.Acad.Sci.USA, 113, 596-601. doi: 10.1073/pnas.1515152113. |
Crystal structure of rig-i helicase-rd in complex with 24-mer 5' triphosphate hairpin RNA. SNAP output |
| 5fj4 |
transcription |
X-ray (2.95 Å) |
Huang L, Wang J, Lilley DMJ |
(2016) "A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function." Nucleic Acids Res., 44, 5390. doi: 10.1093/NAR/GKW201. |
Structure of the standard kink turn hmkt-7 as stem loop bound with u1a and l7ae proteins. SNAP output |
| 5flx |
ribosome |
cryo-EM (3.9 Å) |
Yamamoto H, Collier M, Loerke J, Ismer J, Schmidt A, Hilal T, Sprink T, Yamamoto K, Mielke T, Burger J, Shaikh TR, Dabrowski M, Hildebrand PW, Scheerer P, Spahn CM |
(2015) "Molecular Architecture of the Ribosome-Bound Hepatitis C Virus Internal Ribosomal Entry Site RNA." Embo J., 34, 3042. doi: 10.15252/EMBJ.201592469. |
Mammalian 40s hcv-ires complex. SNAP output |
| 5fmz |
transcription |
X-ray (3.4 Å) |
Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S |
(2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains." Mol.Cell, 61, 125. doi: 10.1016/J.MOLCEL.2015.11.016. |
Crystal structure of influenza b polymerase with bound 5' vrna. SNAP output |
| 5fn1 |
virus |
cryo-EM (3.9 Å) |
Agirrezabala X, Mendez-Lopez E, Lasso G, Sanchez-Pina MA, Aranda M, Valle M |
(2015) "The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses." Elife, 4, e11795. doi: 10.7554/eLife.11795. |
Electron cryo-microscopy of filamentous flexible virus pepmv (pepino mosaic virus). SNAP output |
| 5fvc |
viral protein |
X-ray (4.17 Å) |
Renner M, Bertinelli M, Leyrat C, Paesen GC, Saraiva de Oliveira LF, Huiskonen JT, Grimes JM |
(2016) "Nucleocapsid assembly in pneumoviruses is regulated by conformational switching of the N protein." Elife, 5, e12627. doi: 10.7554/eLife.12627. |
Structure of RNA-bound decameric hmpv nucleoprotein. SNAP output |
| 5g2x |
transferase |
cryo-EM (3.8 Å) |
Qu G, Kaushal PS, Wang J, Shigematsu H, Piazza CL, Agrawal RK, Belfort M, Wang H |
(2016) "Structure of a Group II Intron in Complex with its Reverse Transcriptase." Nat.Struct.Mol.Biol., 23, 549. doi: 10.1038/NSMB.3220. |
Structure a of group ii intron complexed with its reverse transcriptase. SNAP output |
| 5g4u |
RNA-protein |
X-ray (2.65 Å) |
Huang L, Lilley DMJ |
(2016) "A Quasi-Cyclic RNA Nano-Scale Molecular Object Constructed Using Kink Turns." Nanoscale, 8, 15189. doi: 10.1039/C6NR05186C. |
Association of three two-k-turn units based on kt-7 3bu,3nu, forming a triangular-shaped structure. SNAP output |
| 5g4v |
DNA binding |
X-ray (2.87 Å) |
Huang L, Lilley DMJ |
(2016) "A Quasi-Cyclic RNA Nano-Scale Molecular Object Constructed Using Kink Turns." Nanoscale, 8, 15189. doi: 10.1039/C6NR05186C. |
Association of four two-k-turn units based on kt-7 3bg,3nc, forming a square-shaped structure. SNAP output |
| 5gad |
ribosome |
cryo-EM (3.7 Å) |
Jomaa A, Boehringer D, Leibundgut M, Ban N |
(2016) "Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon." Nat Commun, 7, 10471. doi: 10.1038/ncomms10471. |
Rnc-srp-sr complex early state. SNAP output |
| 5gae |
ribosome |
cryo-EM (3.33 Å) |
Jomaa A, Boehringer D, Leibundgut M, Ban N |
(2016) "Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon." Nat Commun, 7, 10471. doi: 10.1038/ncomms10471. |
Rnc in complex with a translocating secyeg. SNAP output |
| 5gaf |
ribosome |
cryo-EM (4.3 Å) |
Jomaa A, Boehringer D, Leibundgut M, Ban N |
(2016) "Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon." Nat Commun, 7, 10471. doi: 10.1038/ncomms10471. |
Rnc in complex with srp. SNAP output |
| 5gag |
ribosome |
cryo-EM (3.8 Å) |
Jomaa A, Boehringer D, Leibundgut M, Ban N |
(2016) "Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon." Nat Commun, 7, 10471. doi: 10.1038/ncomms10471. |
Rnc in complex with srp-sr in the closed state. SNAP output |
| 5gah |
ribosome |
cryo-EM (3.8 Å) |
Jomaa A, Boehringer D, Leibundgut M, Ban N |
(2016) "Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon." Nat Commun, 7, 10471. doi: 10.1038/ncomms10471. |
Rnc in complex with srp with detached ng domain. SNAP output |
| 5gam |
transcription |
cryo-EM (3.7 Å) |
Nguyen THD, Galej WP, Bai XC, Oubridge C, Scheres SHW, Newman AJ, Nagai K |
(2016) "Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Angstrom resolution." Nature, 530, 298-302. doi: 10.1038/nature16940. |
Foot region of the yeast spliceosomal u4-u6.u5 tri-snrnp. SNAP output |
| 5gan |
transcription |
cryo-EM (3.6 Å) |
Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K |
(2016) "Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution." Nature, 530, 298-302. doi: 10.1038/nature16940. |
The overall structure of the yeast spliceosomal u4-u6.u5 tri-snrnp at 3.7 angstrom. SNAP output |
| 5gao |
transcription |
cryo-EM (3.6 Å) |
Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K |
(2016) "Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution." Nature, 530, 298-302. doi: 10.1038/nature16940. |
Head region of the yeast spliceosomal u4-u6.u5 tri-snrnp. SNAP output |
| 5gap |
transcription |
cryo-EM (3.6 Å) |
Nguyen TH, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SH, Nagai K |
(2016) "Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution." Nature, 530, 298-302. doi: 10.1038/nature16940. |
Body region of the u4-u6.u5 tri-snrnp. SNAP output |
| 5gin |
transferase-RNA |
X-ray (3.308 Å) |
Yang Z, Lin J, Ye K |
(2016) "Box C/D guide RNAs recognize a maximum of 10 nt of substrates." Proc.Natl.Acad.Sci.USA, 113, 10878-10883. doi: 10.1073/pnas.1604872113. |
Crystal structure of box c-d rnp with 12 nt guide regions and 9 nt substrates. SNAP output |
| 5gio |
transferase-RNA |
X-ray (3.604 Å) |
Yang Z, Lin J, Ye K |
(2016) "Box C/D guide RNAs recognize a maximum of 10 nt of substrates." Proc.Natl.Acad.Sci.USA, 113, 10878-10883. doi: 10.1073/pnas.1604872113. |
Crystal structure of box c-d rnp with 12 nt guide regions and 13 nt substrates. SNAP output |
| 5gip |
transferase-RNA |
X-ray (3.129 Å) |
Yang Z, Lin J, Ye K |
(2016) "Box C/D guide RNAs recognize a maximum of 10 nt of substrates." Proc.Natl.Acad.Sci.USA, 113, 10878-10883. doi: 10.1073/pnas.1604872113. |
Crystal structure of box c-d rnp with 13 nt guide regions and 11 nt substrates. SNAP output |
| 5gjb |
hydrolase-RNA |
X-ray (1.702 Å) |
Tian HL, Ji XY, Yang XY, Zhang ZX, Lu ZK, Yang KL, Chen C, Zhao Q, Chi H, Mu ZY, Xie W, Wang ZF, Lou HQ, Yang HT, Rao ZH |
(2016) "Structural basis of Zika virus helicase in recognizing its substrates." Protein Cell, 7, 562-570. doi: 10.1007/s13238-016-0293-2. |
Zika virus ns3 helicase in complex with ssrna. SNAP output |
| 5gmf |
immune system-RNA |
X-ray (2.5 Å) |
Zhang Z, Ohto U, Shibata T, Krayukhina E, Taoka M, Yamauchi Y, Tanji H, Isobe T, Uchiyama S, Miyake K, Shimizu T |
(2016) "Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA." Immunity, 45, 737-748. doi: 10.1016/j.immuni.2016.09.011. |
Crystal structure of monkey tlr7 in complex with guanosine and polyu. SNAP output |
| 5gmg |
immune system-RNA |
X-ray (2.6 Å) |
Zhang Z, Ohto U, Shibata T, Krayukhina E, Taoka M, Yamauchi Y, Tanji H, Isobe T, Uchiyama S, Miyake K, Shimizu T |
(2016) "Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA." Immunity, 45, 737-748. doi: 10.1016/j.immuni.2016.09.011. |
Crystal structure of monkey tlr7 in complex with loxoribine and polyu. SNAP output |
| 5gmk |
RNA binding protein-RNA |
cryo-EM (3.4 Å) |
Wan R, Yan C, Bai R, Huang G, Shi Y |
(2016) "Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution." Science, 353, 895-904. doi: 10.1126/science.aag2235. |
cryo-EM structure of the catalytic step i spliceosome (c complex) at 3.4 angstrom resolution. SNAP output |
| 5guh |
hydrolase-RNA |
X-ray (2.4 Å) |
Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O |
(2016) "Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA." Cell, 167, 484-497.e9. doi: 10.1016/j.cell.2016.09.002. |
Crystal structure of silkworm piwi-clade argonaute siwi bound to pirna. SNAP output |
| 5gxh |
RNA binding protein-RNA |
X-ray (1.8 Å) |
Xu C, Ishikawa H, Izumikawa K, Li L, He H, Nobe Y, Yamauchi Y, Shahjee HM, Wu X-H, Yu Y-T, Isobe T, Takahashi N, Min J |
(2016) "Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly." Genes Dev., 30, 2376-2390. doi: 10.1101/gad.288340.116. |
The structure of the gemin5 wd40 domain with aauuuuug. SNAP output |
| 5gxi |
RNA binding protein-RNA |
X-ray (1.85 Å) |
Xu C, Ishikawa H, Izumikawa K, Li L, He H, Nobe Y, Yamauchi Y, Shahjee HM, Wu X-H, Yu Y-T, Isobe T, Takahashi N, Min J |
(2016) "Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly." Genes Dev., 30, 2376-2390. doi: 10.1101/gad.288340.116. |
Structure of the gemin5 wd40 domain in complex with aauuuuugag. SNAP output |
| 5h0r |
transferase-RNA |
cryo-EM (3.9 Å) |
Li X, Zhou N, Chen W, Zhu B, Wang X, Xu B, Wang J, Liu H, Cheng L |
(2017) "Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV." J. Mol. Biol., 429, 79-87. doi: 10.1016/j.jmb.2016.11.025. |
RNA dependent RNA polymerase ,vp4,dsrna. SNAP output |
| 5h1k |
splicing-RNA |
X-ray (1.9 Å) |
Jin W, Wang Y, Liu CP, Yang N, Jin M, Cong Y, Wang M, Xu RM |
(2016) "Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5." Genes Dev., 30, 2391-2403. doi: 10.1101/gad.291377.116. |
Crystal structure of wd40 repeat domains of gemin5 in complex with 13-nt u4 snrna fragment. SNAP output |
| 5h1l |
splicing-RNA |
X-ray (2.1 Å) |
Jin W, Wang Y, Liu CP, Yang N, Jin M, Cong Y, Wang M, Xu RM |
(2016) "Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5." Genes Dev., 30, 2391-2403. doi: 10.1101/gad.291377.116. |
Crystal structure of wd40 repeat domains of gemin5 in complex with 7-nt u4 snrna fragment. SNAP output |
| 5h1s |
ribosome |
cryo-EM (3.5 Å) |
Ahmed T, Yin Z, Bhushan S |
(2016) "Cryo-EM structure of the large subunit of the spinach chloroplast ribosome." Sci Rep, 6, 35793. doi: 10.1038/srep35793. |
Structure of the large subunit of the chloro-ribosome. SNAP output |
| 5h3u |
RNA binding protein-RNA |
X-ray (2.499 Å) |
Tang X, Bharath SR, Piao S, Tan VQ, Bowler MW, Song H |
(2016) "Structural basis for specific recognition of pre-snRNA by Gemin5." Cell Res., 26, 1353-1356. doi: 10.1038/cr.2016.133. |
Sm RNA bound to gemin5-wd. SNAP output |
| 5hab |
hydrolase |
X-ray (2.3 Å) |
Zheng X, Feng N, Li DF, Li J, Dong XZ |
"Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1." |
Crystal structure of mpy-rnase j (mutant h84a), an archaeal rnase j from methanolobus psychrophilus r15, complex with RNA. SNAP output |
| 5hc9 |
transferase |
X-ray (2.9 Å) |
Yamashita S, Tomita K |
(2016) "Mechanism of 3'-Matured tRNA Discrimination from 3'-Immature tRNA by Class-II CCA-Adding Enzyme." Structure, 24, 918-925. doi: 10.1016/j.str.2016.03.022. |
Thermotoga maritima cca-adding enzyme complexed with trna_cca. SNAP output |
| 5hjz |
hydrolase-RNA |
X-ray (1.976 Å) |
Yen TJ, Brennan RG |
"Structure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA." |
Structure of m. tuberculosis mazf-mt1 (rv2801c) in complex with RNA. SNAP output |
| 5hkv |
ribosome |
X-ray (3.66 Å) |
Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A |
(2017) "Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus." Nucleic Acids Res., 45, 10284-10292. doi: 10.1093/nar/gkx658. |
The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with lincomycin. SNAP output |
| 5hl7 |
ribosome |
X-ray (3.55 Å) |
Eyal Z, Matzov D, Krupkin M, Paukner S, Riedl R, Rozenberg H, Zimmerman E, Bashan A, Yonath A |
(2016) "A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism." Sci Rep, 6, 39004. doi: 10.1038/srep39004. |
The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with lefamulin. SNAP output |
| 5ho4 |
RNA binding protein-RNA |
X-ray (1.85 Å) |
Wu BX, Su SC, Patil DP, Liu H, Gan JH, Jaffrey SR, Ma JB |
(2018) "Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1." Nat Commun, 9, 420. doi: 10.1038/s41467-017-02770-z. |
Crystal structure of hnrnpa2b1 in complex with 10-mer RNA. SNAP output |
| 5hp2 |
hydrolase-RNA |
X-ray (2.983 Å) |
Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA |
(2016) "Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity." Nat.Struct.Mol.Biol., 23, 426-433. doi: 10.1038/nsmb.3203. |
Human adenosine deaminase acting on dsrna (adar2) bound to dsrna sequence derived from s. cerevisiae bdf2 gene with au basepair at reaction site. SNAP output |
| 5hp3 |
hydrolase-RNA |
X-ray (3.091 Å) |
Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA |
(2016) "Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity." Nat.Struct.Mol.Biol., 23, 426-433. doi: 10.1038/nsmb.3203. |
Human adenosine deaminase acting on dsrna (adar2) bound to dsrna sequence derived from s. cerevisiae bdf2 gene with ac mismatch at reaction site. SNAP output |
| 5hr6 |
transferase-RNA |
X-ray (2.88 Å) |
Schwalm EL, Grove TL, Booker SJ, Boal AK |
(2016) "Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA." Science, 352, 309-312. doi: 10.1126/science.aad5367. |
X-ray crystal structure of c118a rlmn with cross-linked trna purified from escherichia coli. SNAP output |
| 5hr7 |
oxidoreductase-RNA |
X-ray (2.4 Å) |
Schwalm EL, Grove TL, Booker SJ, Boal AK |
(2016) "Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA." Science, 352, 309-312. doi: 10.1126/science.aad5367. |
X-ray crystal structure of c118a rlmn from escherichia coli with cross-linked in vitro transcribed trna. SNAP output |
| 5hsw |
hydrolase |
X-ray (3.3 Å) |
Lee H, Patschull AOM, Bagneris C, Ryan H, Sanderson CM, Ebrahimi B, Nobeli I, Barrett TE |
(2017) "KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing." Nucleic Acids Res., 45, 4756-4767. doi: 10.1093/nar/gkw1340. |
Kshv sox RNA complex. 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 |
| 5i8q |
hydrolase |
X-ray (4.2 Å) |
He Y, Staley JP, Andersen GR, Nielsen KH |
(2017) "Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA." RNA, 23, 1110-1124. doi: 10.1261/rna.060954.117. |
S. cerevisiae prp43 in complex with RNA and adpnp. SNAP output |
| 5i9d |
RNA binding protein-RNA |
X-ray (2.596 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-u8a2 in complex with its target RNA u8a2. SNAP output |
| 5i9f |
RNA binding protein-RNA |
X-ray (2.194 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-u10 in complex with its target RNA u10. 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 |
| 5i9h |
RNA binding protein-RNA |
X-ray (2.504 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-u8g2 in complex with its target RNA u8g2. SNAP output |
| 5id6 |
hydrolase |
X-ray (2.382 Å) |
Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, Liu H, Li N, Zhang B, Yang D, Ma C, Wang S, Wu D, Ma Y, Fan S, Wang J, Gao N, Huang Z |
(2016) "The crystal structure of Cpf1 in complex with CRISPR RNA." Nature, 532, 522-526. doi: 10.1038/nature17944. |
Structure of cpf1-RNA complex. SNAP output |
| 5ip2 |
viral protein-RNA |
X-ray (3.3 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-ssrna complex. SNAP output |
| 5iwa |
translation |
X-ray (3.5 Å) |
Fabbretti A, Schedlbauer A, Brandi L, Kaminishi T, Giuliodori AM, Garofalo R, Ochoa-Lizarralde B, Takemoto C, Yokoyama S, Connell SR, Gualerzi CO, Fucini P |
(2016) "Inhibition of translation initiation complex formation by GE81112 unravels a 16S rRNA structural switch involved in P-site decoding." Proc.Natl.Acad.Sci.USA, 113, E2286-E2295. doi: 10.1073/pnas.1521156113. |
Crystal structure of the 30s ribosomal subunit from thermus thermophilus in complex with the ge81112 peptide antibiotic. SNAP output |
| 5j0m |
viral protein |
NMR |
Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M |
(2016) "Structure of a low-population binding intermediate in protein-RNA recognition." Proc.Natl.Acad.Sci.USA, 113, 7171-7176. doi: 10.1073/pnas.1521349113. |
Ground state sampled during rdc restrained replica-averaged metadynamics (ram) simulations of the hiv-1 tar complexed with cyclic peptide mimetic of tat. SNAP output |
| 5j1o |
viral protein |
NMR |
Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M |
(2016) "Structure of a low-population binding intermediate in protein-RNA recognition." Proc.Natl.Acad.Sci.USA, 113, 7171-7176. doi: 10.1073/pnas.1521349113. |
Excited state (bound-like) sampled during rdc restrained replica-averaged metadynamics (ram) simulations of the hiv-1 tar complexed with cyclic peptide mimetic of tat. SNAP output |
| 5j2w |
viral protein |
NMR |
Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M |
(2016) "Structure of a low-population binding intermediate in protein-RNA recognition." Proc.Natl.Acad.Sci.USA, 113, 7171-7176. doi: 10.1073/pnas.1521349113. |
Intermediate state lying on the pathway of release of tat from hiv-1 tar.. SNAP output |
| 5jaj |
RNA binding protein |
X-ray (1.5 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Structure of chicken lgp2 witha 5'p 10-mer dsrna and adp-alf4-mg.. SNAP output |
| 5jb2 |
immune system |
X-ray (2.2 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken lgp2 with 5'ppp 10-mer dsrna and adp-alf4-mg2+ at 2.2 Å resolution.. SNAP output |
| 5jb3 |
translation |
cryo-EM (5.34 Å) |
Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladiere L, Klaholz BP, Schmitt E, Mechulam Y |
(2016) "Cryo-EM study of start codon selection during archaeal translation initiation." Nat Commun, 7, 13366. doi: 10.1038/ncomms13366. |
cryo-EM structure of a full archaeal ribosomal translation initiation complex in the p-remote conformation. SNAP output |
| 5jbg |
immune system |
X-ray (2.0 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken lgp2 with 5'ppp 26-mer hairpin RNA with 3' gg overhang and adp-alf4-mg2+ at 2.0 Å resolution.. SNAP output |
| 5jbh |
transcription |
cryo-EM (5.34 Å) |
Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladiere L, Klaholz BP, Schmitt E, Mechulam Y |
(2016) "Cryo-EM study of start codon selection during archaeal translation initiation." Nat Commun, 7, 13366. doi: 10.1038/ncomms13366. |
cryo-EM structure of a full archaeal ribosomal translation initiation complex in the p-in conformation. SNAP output |
| 5jbj |
immune system |
X-ray (3.58 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken lgp2 with 5'p 12-mer dsrna at 3.6 Å resolution. SNAP output |
| 5jc3 |
immune system |
X-ray (2.6 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken mda5 with 5'p 10-mer dsrna and adp-mg2+ at 2.6 Å resolution (monoclinic form, twinned).. SNAP output |
| 5jc7 |
immune system |
X-ray (2.75 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken mda5 with 5'p 24-mer dsrna and adp-mg2+ at 2.75 Å resolution.. SNAP output |
| 5jcf |
immune system |
X-ray (2.6 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken mda5 with 5'p 10-mer dsrna and adp-mg2+ at 2.6 Å resolution (orthorhombic form).. SNAP output |
| 5jch |
immune system |
X-ray (2.95 Å) |
Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S |
(2016) "Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5." Mol.Cell, 62, 586-602. doi: 10.1016/j.molcel.2016.04.021. |
Crystal structure of chicken mda5 with 5'p 10-mer dsrna and adp-mg2+ at 2.95 Å resolution (untwinned).. SNAP output |
| 5jea |
hydrolase-RNA |
X-ray (2.65 Å) |
Kowalinski E, Kogel A, Ebert J, Reichelt P, Stegmann E, Habermann B, Conti E |
(2016) "Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex." Mol.Cell, 63, 125-134. doi: 10.1016/j.molcel.2016.05.028. |
Structure of a cytoplasmic 11-subunit RNA exosome complex including ski7, bound to RNA. SNAP output |
| 5jji |
transcription-RNA |
X-ray (2.601 Å) |
Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM |
(2016) "Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor." Proc. Natl. Acad. Sci. U.S.A., 113, E7691-E7700. doi: 10.1073/pnas.1616745113. |
Rho transcription termination factor bound to ru7 and 6 adp-bef3 molecules. SNAP output |
| 5jjk |
transcription-RNA |
X-ray (3.15 Å) |
Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM |
(2016) "Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor." Proc. Natl. Acad. Sci. U.S.A., 113, E7691-E7700. doi: 10.1073/pnas.1616745113. |
Rho transcription termination factor bound to ra7 and 6 adp-bef3 molecules. SNAP output |
| 5jjl |
transcription-RNA |
X-ray (3.2 Å) |
Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM |
(2016) "Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor." Proc. Natl. Acad. Sci. U.S.A., 113, E7691-E7700. doi: 10.1073/pnas.1616745113. |
Rho transcription termination factor bound to ru8 and 5 adp-bef3 molecules. SNAP output |
| 5jju |
hydrolase-RNA |
X-ray (2.312 Å) |
He Q, Wang F, Liu S, Zhu D, Cong H, Gao F, Li B, Wang H, Lin Z, Liao J, Gu L |
(2016) "Structural and biochemical insight into the mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP phosphodiesterase." J.Biol.Chem., 291, 14386-14387. doi: 10.1074/jbc.A115.699801. |
Crystal structure of rv2837c complexed with 5'-papa and 5'-amp. SNAP output |
| 5jpq |
ribosome |
cryo-EM (7.3 Å) |
Kornprobst M, Turk M, Kellner N, Cheng J, Flemming D, Kos-Braun I, Kos M, Thoms M, Berninghausen O, Beckmann R, Hurt E |
(2016) "Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome." Cell, 166, 380-393. doi: 10.1016/j.cell.2016.06.014. |
cryo-EM structure of the 90s pre-ribosome. SNAP output |
| 5jrc |
DNA binding protein |
X-ray (1.9 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 ssrna.. SNAP output |
| 5js1 |
hydrolase-RNA |
X-ray (2.499 Å) |
Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ |
(2016) "Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide." J.Am.Chem.Soc., 138, 8694-8697. doi: 10.1021/jacs.6b04454. |
Human argonaute2 bound to an sirna. SNAP output |
| 5js2 |
hydrolase-RNA |
X-ray (2.954 Å) |
Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ |
(2016) "Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide." J.Am.Chem.Soc., 138, 8694-8697. doi: 10.1021/jacs.6b04454. |
Human argonaute-2 bound to a modified sirna. SNAP output |
| 5jvg |
ribosome |
X-ray (3.428 Å) |
Krupkin M, Wekselman I, Matzov D, Eyal Z, Diskin Posner Y, Rozenberg H, Zimmerman E, Bashan A, Yonath A |
(2016) "Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding." Proc.Natl.Acad.Sci.USA, 113, E6796-E6805. doi: 10.1073/pnas.1614297113. |
The large ribosomal subunit from deinococcus radiodurans in complex with avilamycin. SNAP output |
| 5jvh |
ribosome |
X-ray (3.58 Å) |
Krupkin M, Wekselman I, Matzov D, Eyal Z, Diskin Posner Y, Rozenberg H, Zimmerman E, Bashan A, Yonath A |
(2016) "Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding." Proc.Natl.Acad.Sci.USA, 113, E6796-E6805. doi: 10.1073/pnas.1614297113. |
The crystal structure large ribosomal subunit (50s) of deinococcus radiodurans in complex with evernimicin. SNAP output |
| 5jxs |
transferase |
X-ray (2.8 Å) |
Herod MR, Ferrer-Orta C, Loundras EA, Ward JC, Verdaguer N, Rowlands DJ, Stonehouse NJ |
(2016) "Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication." J.Virol., 90, 6864-6883. doi: 10.1128/JVI.00469-16. |
Mutant gc216-7aa of 3d polymerase from foot-and-mouth disease virus. SNAP output |
| 5k0y |
translation |
cryo-EM (5.8 Å) |
Simonetti A, Brito Querido J, Myasnikov AG, Mancera-Martinez E, Renaud A, Kuhn L, Hashem Y |
(2016) "eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition." Mol.Cell, 63, 206-217. doi: 10.1016/j.molcel.2016.05.033. |
M48s late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eif2 ternary complex and eif3 i and g subunits relocated to the intersubunit face. SNAP output |
| 5k36 |
hydrolase-RNA |
X-ray (3.1 Å) |
Zinder JC, Wasmuth EV, Lima CD |
(2016) "Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3." Mol.Cell, 64, 734-745. doi: 10.1016/j.molcel.2016.09.038. |
Structure of an eleven component nuclear RNA exosome complex bound to RNA. 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 |
| 5kal |
transferase-RNA |
X-ray (2.75 Å) |
Rajappa-Titu L, Suematsu T, Munoz-Tello P, Long M, Demir O, Cheng KJ, Stagno JR, Luecke H, Amaro RE, Aphasizheva I, Aphasizhev R, Thore S |
(2016) "RNA Editing TUTase 1: structural foundation of substrate recognition, complex interactions and drug targeting." Nucleic Acids Res., 44, 10862-10878. doi: 10.1093/nar/gkw917. |
Terminal uridylyl transferase 4 from trypanosoma brucei with bound utp and upu. SNAP output |
| 5ki6 |
hydrolase-RNA |
X-ray (2.153 Å) |
Suter SR, Sheu-Gruttadauria J, Schirle NT, Valenzuela R, Ball-Jones AA, Onizuka K, MacRae IJ, Beal PA |
(2016) "Structure-Guided Control of siRNA Off-Target Effects." J.Am.Chem.Soc., 138, 8667-8669. doi: 10.1021/jacs.6b06137. |
Human argonaute-2 bound to a guide RNA with a nucleobase modification at position 1. SNAP output |
| 5kl1 |
RNA binding protein-RNA |
X-ray (3.701 Å) |
Weidmann CA, Qiu C, Arvola RM, Lou TF, Killingsworth J, Campbell ZT, Tanaka Hall TM, Goldstrohm AC |
(2016) "Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio." Elife, 5. doi: 10.7554/eLife.17096. |
Crystal structure of the pumilio-nos-hunchback RNA complex. SNAP output |
| 5kl8 |
RNA-binding protein-RNA |
X-ray (4.0 Å) |
Weidmann CA, Qiu C, Arvola RM, Lou TF, Killingsworth J, Campbell ZT, Tanaka Hall TM, Goldstrohm AC |
(2016) "Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio." Elife, 5. doi: 10.7554/eLife.17096. |
Crystal structure of the pumilio-nos-cyclinb RNA complex. SNAP output |
| 5kla |
RNA-binding protein-RNA |
X-ray (1.14 Å) |
Weidmann CA, Qiu C, Arvola RM, Lou TF, Killingsworth J, Campbell ZT, Tanaka Hall TM, Goldstrohm AC |
(2016) "Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio." Elife, 5. doi: 10.7554/eLife.17096. |
Crystal structure of the drosophila pumilio RNA-binding domain in complex with hunchback RNA. SNAP output |
| 5l1z |
transcription-RNA |
X-ray (5.9 Å) |
Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH |
(2016) "Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex." Elife, 5. doi: 10.7554/eLife.15910. |
Tar complex with hiv-1 tat-aff4-p-tefb. SNAP output |
| 5l2l |
RNA binding protein |
X-ray (1.55 Å) |
Aibara S, Gordon JM, Riesterer AS, McLaughlin SH, Stewart M |
(2017) "Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae." Nucleic Acids Res., 45, 1529-1538. doi: 10.1093/nar/gkw1224. |
Nab2 zn fingers 5-7 bound to a11g RNA. SNAP output |
| 5lj3 |
splicing |
cryo-EM (3.8 Å) |
Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K |
(2016) "Cryo-EM structure of the spliceosome immediately after branching." Nature, 537, 197-201. doi: 10.1038/nature19316. |
Structure of the core of the yeast spliceosome immediately after branching. SNAP output |
| 5lj5 |
splicing |
cryo-EM (3.8 Å) |
Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K |
(2016) "Cryo-EM structure of the spliceosome immediately after branching." Nature, 537, 197-201. doi: 10.1038/nature19316. |
Overall structure of the yeast spliceosome immediately after branching.. SNAP output |
| 5ll6 |
ribosome |
cryo-EM (3.9 Å) |
Heuer A, Gerovac M, Schmidt C, Trowitzsch S, Preis A, Kotter P, Berninghausen O, Becker T, Beckmann R, Tampe R |
(2017) "Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation." Nat. Struct. Mol. Biol., 24, 453-460. doi: 10.1038/nsmb.3396. |
Structure of the 40s abce1 post-splitting complex in ribosome recycling and translation initiation. SNAP output |
| 5lm7 |
transcription |
X-ray (3.35 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. |
Crystal structure of the lambda n-nus factor complex. SNAP output |
| 5lmn |
ribosome |
cryo-EM (3.55 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna translation pre-initiation complex (state-1a). SNAP output |
| 5lmo |
ribosome |
cryo-EM (4.3 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna translation pre-initiation complex (state-1b). SNAP output |
| 5lmp |
ribosome |
cryo-EM (5.35 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna translation pre-initiation complex (state-1c). SNAP output |
| 5lmq |
ribosome |
cryo-EM (4.2 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna-trna translation pre-initiation complex, open form (state-2a). SNAP output |
| 5lmr |
ribosome |
cryo-EM (4.45 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna-trna translation pre-initiation complex(state-2b). SNAP output |
| 5lms |
ribosome |
cryo-EM (5.1 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna-trna translation pre-initiation complex(state-2c). SNAP output |
| 5lmt |
ribosome |
cryo-EM (4.15 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if3-mrna-trna translation pre-initiation complex(state-3). SNAP output |
| 5lmu |
ribosome |
cryo-EM (4.0 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if3-mrna-trna translation pre-initiation complex, closed form (state-4). SNAP output |
| 5lmv |
ribosome |
cryo-EM (4.9 Å) |
Hussain T, Llacer JL, Wimberly BT, Kieft JS, Ramakrishnan V |
(2016) "Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation." Cell, 167, 133-144.e13. doi: 10.1016/j.cell.2016.08.074. |
Structure of bacterial 30s-if1-if2-if3-mrna-trna translation pre-initiation complex(state-iii). SNAP output |
| 5lta |
protein-RNA |
X-ray (2.621 Å) |
Tauchert MJ, Fourmann JB, Luhrmann R, Ficner R |
(2017) "Structural insights into the mechanism of the DEAH-box RNA helicase Prp43." Elife, 6. doi: 10.7554/eLife.21510. |
Crystal structure of the prp43-adp-bef3-u7-RNA complex. SNAP output |
| 5m0i |
transport protein |
X-ray (2.41 Å) |
Edelmann FT, Schlundt A, Heym RG, Jenner A, Niedner-Boblenz A, Syed MI, Paillart JC, Stehle R, Janowski R, Sattler M, Jansen RP, Niessing D |
(2017) "Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex." Nat. Struct. Mol. Biol., 24, 152-161. doi: 10.1038/nsmb.3351. |
Crystal structure of the nuclear complex with she2p and the ash1 mrna e3-localization element. SNAP output |
| 5m0j |
RNA binding protein |
X-ray (2.8 Å) |
Edelmann FT, Schlundt A, Heym RG, Jenner A, Niedner-Boblenz A, Syed MI, Paillart JC, Stehle R, Janowski R, Sattler M, Jansen RP, Niessing D |
(2017) "Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex." Nat. Struct. Mol. Biol., 24, 152-161. doi: 10.1038/nsmb.3351. |
Crystal structure of the cytoplasmic complex with she2p, she3p, and the ash1 mrna e3-localization element. SNAP output |
| 5m3h |
transferase |
X-ray (2.5 Å) |
Lukarska M, Fournier G, Pflug A, Resa-Infante P, Reich S, Naffakh N, Cusack S |
(2017) "Structural basis of an essential interaction between influenza polymerase and Pol II CTD." Nature, 541, 117-121. doi: 10.1038/nature20594. |
Bat influenza a-h17n10 polymerase bound to four heptad repeats of serine 5 phosphorylated pol ii ctd. SNAP output |
| 5m3j |
viral protein |
X-ray (3.5 Å) |
Lukarska M, Fournier G, Pflug A, Resa-Infante P, Reich S, Naffakh N, Cusack S |
(2017) "Structural basis of an essential interaction between influenza polymerase and Pol II CTD." Nature, 541, 117-121. doi: 10.1038/nature20594. |
Influenza b polymerase bound to four heptad repeats of serine 5 phosphorylated pol ii ctd. SNAP output |
| 5m73 |
RNA binding protein |
X-ray (3.4 Å) |
Becker MM, Lapouge K, Segnitz B, Wild K, Sinning I |
(2017) "Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction." Nucleic Acids Res., 45, 470-481. doi: 10.1093/nar/gkw1124. |
Structure of the human srp s domain with srp72 RNA-binding domain. SNAP output |
| 5m8i |
RNA binding protein |
NMR |
Diarra Dit Konte N, Krepl M, Damberger FF, Ripin N, Duss O, Sponer J, Allain FH |
(2017) "Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination." Nat Commun, 8, 654. doi: 10.1038/s41467-017-00631-3. |
Solution structure of cug-bp2 rrm3 in complex with 5'-uuuaa-3' RNA. SNAP output |
| 5me0 |
ribosome |
cryo-EM (13.5 Å) |
Lopez-Alonso JP, Fabbretti A, Kaminishi T, Iturrioz I, Brandi L, Gil-Carton D, Gualerzi CO, Fucini P, Connell SR |
(2017) "Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways." Nucleic Acids Res., 45, 2179-2187. doi: 10.1093/nar/gkw1251. |
Structure of the 30s pre-initiation complex 1 (30s ic-1) stalled by ge81112. SNAP output |
| 5me1 |
ribosome |
cryo-EM (13.5 Å) |
Lopez-Alonso JP, Fabbretti A, Kaminishi T, Iturrioz I, Brandi L, Gil-Carton D, Gualerzi CO, Fucini P, Connell SR |
(2017) "Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways." Nucleic Acids Res., 45, 2179-2187. doi: 10.1093/nar/gkw1251. |
Structure of the 30s pre-initiation complex 2 (30s ic-2) stalled by ge81112. SNAP output |
| 5mfx |
hydrolase |
X-ray (1.598 Å) |
Jenkins HT, Ge M, Chechik M, Greive SJ, Antson AA |
"How Zika virus NS3 helicase grips the first
nucleotide of the leading RNA strand." |
Zika ns3 helicase:RNA complex. SNAP output |
| 5mjv |
virus |
X-ray (3.09 Å) |
Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJ, Butcher SJ, Stockley PG, Twarock R |
(2017) "Genomic RNA folding mediates assembly of human parechovirus." Nat Commun, 8, 5. doi: 10.1038/s41467-016-0011-z. |
Rebuild and re-refined model for human parechovirus 1. SNAP output |
| 5mlc |
ribosome |
cryo-EM (3.9 Å) |
Graf M, Arenz S, Huter P, Donhofer A, Novacek J, Wilson DN |
(2017) "Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions." Nucleic Acids Res., 45, 2887-2896. doi: 10.1093/nar/gkw1272. |
cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. SNAP output |
| 5mmi |
ribosome |
cryo-EM (3.25 Å) |
Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N |
(2017) "The complete structure of the chloroplast 70S ribosome in complex with translation factor pY." EMBO J., 36, 475-486. doi: 10.15252/embj.201695959. |
Structure of the large subunit of the chloroplast ribosome. SNAP output |
| 5mmj |
ribosome |
cryo-EM (3.646 Å) |
Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N |
(2017) "The complete structure of the chloroplast 70S ribosome in complex with translation factor pY." EMBO J., 36, 475-486. doi: 10.15252/embj.201695959. |
Structure of the small subunit of the chloroplast ribosome. SNAP output |
| 5mpg |
splicing |
NMR |
Beusch I, Barraud P, Moursy A, Clery A, Allain FH |
(2017) "Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7." Elife, 6. doi: 10.7554/eLife.25736. |
Solution NMR structure of hnrnp a1 rrm1 in complex with 5'-uuagguc-3' RNA. SNAP output |
| 5mpl |
splicing |
NMR |
Beusch I, Barraud P, Moursy A, Clery A, Allain FH |
(2017) "Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7." Elife, 6. doi: 10.7554/eLife.25736. |
Hnrnp a1 rrm2 in complex with 5'-ucaguu-3' RNA. SNAP output |
| 5mps |
splicing |
cryo-EM (3.85 Å) |
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K |
(2017) "Structure of a spliceosome remodelled for exon ligation." Nature, 542, 377-380. doi: 10.1038/nature21078. |
Structure of a spliceosome remodeled for exon ligation. SNAP output |
| 5mq0 |
splicing |
cryo-EM (4.17 Å) |
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K |
(2017) "Structure of a spliceosome remodelled for exon ligation." Nature, 542, 377-380. doi: 10.1038/nature21078. |
Structure of a spliceosome remodeled for exon ligation. SNAP output |
| 5mqf |
splicing |
cryo-EM (5.9 Å) |
Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lu Hrmann R |
(2017) "Cryo-EM structure of a human spliceosome activated for step 2 of splicing." Nature, 542, 318-323. doi: 10.1038/nature21079. |
cryo-EM structure of a human spliceosome activated for step 2 of splicing (c* complex). SNAP output |
| 5msf |
virus-RNA |
X-ray (2.8 Å) |
Rowsell S, Stonehouse NJ, Convery MA, Adams CJ, Ellington AD, Hirao I, Peabody DS, Stockley PG, Phillips SE |
(1998) "Crystal structures of a series of RNA aptamers complexed to the same protein target." Nat.Struct.Biol., 5, 970-975. doi: 10.1038/2946. |
Ms2 protein capsid-RNA complex. SNAP output |
| 5msg |
viral protein |
X-ray (3.8 Å) |
Reich S, Guilligay D, Cusack S |
(2017) "An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase." Nucleic Acids Res., 45, 3353-3368. doi: 10.1093/nar/gkx043. |
Influenza b polymerase bound to vrna promoter and capped RNA primer. SNAP output |
| 5my1 |
ribosome |
cryo-EM (7.6 Å) |
Kohler R, Mooney RA, Mills DJ, Landick R, Cramer P |
(2017) "Architecture of a transcribing-translating expressome." Science, 356, 194-197. doi: 10.1126/science.aal3059. |
E. coli expressome. SNAP output |
| 5n8l |
RNA binding protein |
NMR |
Masliah G, Maris C, Konig SL, Yulikov M, Aeschimann F, Malinowska AL, Mabille J, Weiler J, Holla A, Hunziker J, Meisner-Kober N, Schuler B, Jeschke G, Allain FH |
(2018) "Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains." EMBO J., 37. doi: 10.15252/embj.201797089. |
Structure of trbp dsrbd 1 and 2 in complex with a 19 bp sirna (complex b). SNAP output |
| 5n8m |
RNA binding protein |
NMR |
Masliah G, Maris C, Konig SL, Yulikov M, Aeschimann F, Malinowska AL, Mabille J, Weiler J, Holla A, Hunziker J, Meisner-Kober N, Schuler B, Jeschke G, Allain FH |
(2018) "Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains." EMBO J., 37. doi: 10.15252/embj.201797089. |
Structure of trbp dsrbd 1 and 2 in complex with a 19 bp sirna (complex a). SNAP output |
| 5n94 |
hydrolase |
X-ray (2.428 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 polyu. SNAP output |
| 5new |
RNA |
X-ray (2.511 Å) |
Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mucke N, Wilmanns M, Gibson TJ, Barabas O |
(2017) "Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq." Sci Rep, 7, 9903. doi: 10.1038/s41598-017-10085-8. |
RNA-RNA base stacking in the crystal structure of an hfq6:RNA dimer. SNAP output |
| 5ng6 |
hydrolase |
X-ray (3.342 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 fncas12a bound to a crrna. SNAP output |
| 5no2 |
ribosome |
cryo-EM (5.16 Å) |
Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR |
(2017) "RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket." Nucleic Acids Res., 45, 6945-6959. doi: 10.1093/nar/gkx324. |
Rsga-gdpnp bound to the 30s ribosomal subunit (rsga assembly intermediate). SNAP output |
| 5no3 |
ribosome |
cryo-EM (5.16 Å) |
Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR |
(2017) "RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket." Nucleic Acids Res., 45, 6945-6959. doi: 10.1093/nar/gkx324. |
Rsga-gdpnp bound to the 30s ribosomal subunit (rsga assembly intermediate without us3). SNAP output |
| 5no4 |
ribosome |
cryo-EM (5.16 Å) |
Lopez-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR |
(2017) "RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket." Nucleic Acids Res., 45, 6945-6959. doi: 10.1093/nar/gkx324. |
Rsga-gdpnp bound to the 30s ribosomal subunit (rsga assembly intermediate with us3). SNAP output |
| 5npm |
RNA |
X-ray (2.7 Å) |
Kostareva OS, Nevskaya NA, Tishchenko SV, Gabdulkhakov AG, Garber MB, Nikonov SV |
(2018) "[Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA]." Mol.Biol.(Moscow), 52, 106-111. doi: 10.7868/S0026898418010147. |
Crystal structure of mutant ribosomal protein tthl1 lacking 8 n-terminal residues in complex with 80nt 23s RNA from thermus thermophilus. SNAP output |
| 5nrg |
ribosome |
X-ray (3.442 Å) |
Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A |
(2017) "Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus." Nucleic Acids Res., 45, 10284-10292. doi: 10.1093/nar/gkx658. |
The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02. SNAP output |
| 5ns3 |
RNA |
X-ray (2.4 Å) |
Liu Y, Lilley DMJ |
(2017) "Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA." Biophys. J., 113, 2336-2343. doi: 10.1016/j.bpj.2017.10.002. |
Crystal structures of cy5 cyanine fluorophores stacked onto the end of double-stranded RNA. SNAP output |
| 5ns4 |
RNA binding protein |
X-ray (2.4 Å) |
Liu Y, Lilley DMJ |
(2017) "Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA." Biophys. J., 113, 2336-2343. doi: 10.1016/j.bpj.2017.10.002. |
Crystal structures of cy3 cyanine fluorophores stacked onto the end of double-stranded RNA. SNAP output |
| 5o1y |
transcription |
X-ray (2.45 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 (guaa). SNAP output |
| 5o1z |
transcription |
X-ray (3.4 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 (cguaaa). 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 |
| 5o3j |
RNA binding protein |
X-ray (2.97 Å) |
Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M |
(2017) "Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins." Angew. Chem. Int. Ed. Engl., 56, 9322-9325. doi: 10.1002/anie.201702904. |
Crystal structure of tia-1 rrm2 in complex with RNA. SNAP output |
| 5o58 |
hydrolase |
X-ray (1.55 Å) |
Drexler DJ, Muller M, Rojas-Cordova CA, Bandera AM, Witte G |
(2017) "Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima." Structure, 25, 1887-1897.e4. doi: 10.1016/j.str.2017.10.001. |
Structure of the inactive t.maritima pde (tm1595) d80n d154n mutant with substrate 5'-papg. SNAP output |
| 5o5j |
ribosome |
cryo-EM (3.451 Å) |
Hentschel J, Burnside C, Mignot I, Leibundgut M, Boehringer D, Ban N |
(2017) "The Complete Structure of the Mycobacterium smegmatis 70S Ribosome." Cell Rep, 20, 149-160. doi: 10.1016/j.celrep.2017.06.029. |
Structure of the 30s small ribosomal subunit from mycobacterium smegmatis. SNAP output |
| 5o60 |
ribosome |
cryo-EM (3.203 Å) |
Hentschel J, Burnside C, Mignot I, Leibundgut M, Boehringer D, Ban N |
(2017) "The Complete Structure of the Mycobacterium smegmatis 70S Ribosome." Cell Rep, 20, 149-160. doi: 10.1016/j.celrep.2017.06.029. |
Structure of the 50s large ribosomal subunit from mycobacterium smegmatis. SNAP output |
| 5o7h |
antiviral protein |
X-ray (3.0 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 complex from shewanella putrefaciens. SNAP output |
| 5o9z |
splicing |
cryo-EM (4.5 Å) |
Bertram K, Agafonov DE, Dybkov O, Haselbach D, Leelaram MN, Will CL, Urlaub H, Kastner B, Luhrmann R, Stark H |
(2017) "Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation." Cell, 170, 701-713.e11. doi: 10.1016/j.cell.2017.07.011. |
cryo-EM structure of a pre-catalytic human spliceosome primed for activation (b complex). SNAP output |
| 5oa3 |
translation |
cryo-EM (4.3 Å) |
Weisser M, Schafer T, Leibundgut M, Bohringer D, Aylett CHS, Ban N |
(2017) "Structural and Functional Insights into Human Re-initiation Complexes." Mol. Cell, 67, 447-456.e7. doi: 10.1016/j.molcel.2017.06.032. |
Human 40s-eif2d-re-initiation complex. SNAP output |
| 5oc6 |
RNA binding protein |
X-ray (3.2 Å) |
Bou-Nader C, Barraud P, Pecqueur L, Perez J, Velours C, Shepard W, Fontecave M, Tisne C, Hamdane D |
(2019) "Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2." Nucleic Acids Res., 47, 3117-3126. doi: 10.1093/nar/gky1302. |
Crystal structure of human trna-dihydrouridine(20) synthase dsrbd in complex with a 22 nucleotide dsrna. SNAP output |
| 5odv |
virus |
cryo-EM (4.0 Å) |
Zamora M, Mendez-Lopez E, Agirrezabala X, Cuesta R, Lavin JL, Sanchez-Pina MA, Aranda MA, Valle M |
(2017) "Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses." Sci Adv, 3, eaao2182. doi: 10.1126/sciadv.aao2182. |
Structure of watermelon mosaic virus potyvirus.. SNAP output |
| 5omw |
translation |
X-ray (2.6 Å) |
Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I |
(2018) "Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase." J. Mol. Biol., 430, 1-16. doi: 10.1016/j.jmb.2017.10.024. |
Mutant t252a of e. coli leucyl-trna synthetase, trna(leu) and leucyl-adenylate analogue in the aminoacylation conformation. SNAP output |
| 5on2 |
translation |
X-ray (3.1 Å) |
Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I |
(2018) "Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase." J. Mol. Biol., 430, 1-16. doi: 10.1016/j.jmb.2017.10.024. |
Quaternary complex of mutant t252a of e. coli leucyl-trna synthetase with trna(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline in the aminoacylation conformation. SNAP output |
| 5on3 |
ligase |
X-ray (3.1 Å) |
Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I |
(2018) "Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase." J. Mol. Biol., 430, 1-16. doi: 10.1016/j.jmb.2017.10.024. |
Quaternary complex of mutant t252a of e. coli leucyl-trna synthetase with trna(leu), leucyl-adenylate analogue, and post-transfer editing analogue of leucine in the aminoacylation conformation. SNAP output |
| 5onh |
ligase |
X-ray (3.1 Å) |
Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I |
(2018) "Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase." J. Mol. Biol., 430, 1-16. doi: 10.1016/j.jmb.2017.10.024. |
Quaternary complex of wild type e. coli leucyl-trna synthetase with trna(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline in the aminoacylation conformation. SNAP output |
| 5ool |
ribosome |
cryo-EM (3.06 Å) |
Brown A, Rathore S, Kimanius D, Aibara S, Bai XC, Rorbach J, Amunts A, Ramakrishnan V |
(2017) "Structures of the human mitochondrial ribosome in native states of assembly." Nat. Struct. Mol. Biol., 24, 866-869. doi: 10.1038/nsmb.3464. |
Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rrna. SNAP output |
| 5oom |
ribosome |
cryo-EM (3.03 Å) |
Brown A, Rathore S, Kimanius D, Aibara S, Bai XC, Rorbach J, Amunts A, Ramakrishnan V |
(2017) "Structures of the human mitochondrial ribosome in native states of assembly." Nat. Struct. Mol. Biol., 24, 866-869. doi: 10.1038/nsmb.3464. |
Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rrna. SNAP output |
| 5opt |
ribosome |
cryo-EM (4.0 Å) |
Brito Querido J, Mancera-Martinez E, Vicens Q, Bochler A, Chicher J, Simonetti A, Hashem Y |
(2017) "The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein." Structure, 25, 1785-1794.e3. doi: 10.1016/j.str.2017.09.014. |
Structure of ksrp in context of trypanosoma cruzi 40s. SNAP output |
| 5osg |
ribosome |
cryo-EM (2.9 Å) |
Brito Querido J, Mancera-Martinez E, Vicens Q, Bochler A, Chicher J, Simonetti A, Hashem Y |
(2017) "The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein." Structure, 25, 1785-1794.e3. doi: 10.1016/j.str.2017.09.014. |
Structure of ksrp in context of leishmania donovani 80s. SNAP output |
| 5sup |
hydrolase-RNA |
X-ray (2.6 Å) |
Ren Y, Schmiege P, Blobel G |
(2017) "Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1." Elife, 6. doi: 10.7554/eLife.20070. |
Structure of mrna export factors. SNAP output |
| 5sze |
RNA-binding protein-RNA |
X-ray (1.5 Å) |
Stanek KA, Patterson-West J, Randolph PS, Mura C |
(2017) "Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode." Acta Crystallogr D Struct Biol, 73, 294-315. doi: 10.1107/S2059798317000031. |
Crystal structure of aquifex aeolicus hfq-RNA complex at 1.5a. SNAP output |
| 5t16 |
hydrolase-RNA |
X-ray (2.783 Å) |
Song H, Fang X, Jin L, Shaw GX, Wang YX, Ji X |
(2017) "The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III." Structure, 25, 353-363. doi: 10.1016/j.str.2016.12.013. |
Crystal structure of yeast rnase iii (rnt1p) complexed with a non-hydrolyzable RNA substrate analog. SNAP output |
| 5t7b |
hydrolase-RNA |
X-ray (2.529 Å) |
Elkayam E, Joshua-Tor L |
"Protein structure." |
Argonaute-2 - 5'-(e)-vinylphosphonate 2'-o-methyl-uridine modified mrttr guide RNA complex. SNAP output |
| 5t8y |
oxidoreductase-RNA |
X-ray (2.653 Å) |
Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL |
(2016) "Molecular basis of cobalamin-dependent RNA modification." Nucleic Acids Res., 44, 9965-9976. doi: 10.1093/nar/gkw806. |
Structure of epoxyqueuosine reductase from bacillus subtilis with the asp134 catalytic loop swung out of the active site.. SNAP output |
| 5tc1 |
viral protein-RNA |
cryo-EM (3.6 Å) |
Dai X, Li Z, Lai M, Shu S, Du Y, Zhou ZH, Sun R |
(2017) "In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus." Nature, 541, 112-116. doi: 10.1038/nature20589. |
In situ structures of the genome and genome-delivery apparatus in ssrna bacteriophage ms2. SNAP output |
| 5tf6 |
RNA binding protein-RNA |
X-ray (2.3 Å) |
Montemayor EJ, Didychuk AL, Liao H, Hu P, Brow DA, Butcher SE |
(2017) "Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core." Acta Crystallogr D Struct Biol, 73, 1-8. doi: 10.1107/S2059798316018222. |
Structure and conformational plasticity of the u6 small nuclear ribonucleoprotein core. SNAP output |
| 5the |
RNA binding protein-RNA |
X-ray (2.097 Å) |
Dayeh DM, Kruithoff BC, Nakanishi K |
(2018) "Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage." J. Biol. Chem., 293, 6308-6325. doi: 10.1074/jbc.RA117.001051. |
Crystal structure of the c-terminal lobe of a budding yeast argonaute. SNAP output |
| 5tsn |
transferase-RNA |
X-ray (2.1 Å) |
Shaik MM, Bhattacharjee N, Feliks M, Ng KK, Field MJ |
(2017) "Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences." Proteins, 85, 1435-1445. doi: 10.1002/prot.25304. |
Crystal structures of norwalk virus polymerase bound to an RNA primer-template duplex. SNAP output |
| 5tzs |
translation |
cryo-EM (5.1 Å) |
Chaker-Margot M, Barandun J, Hunziker M, Klinge S |
(2017) "Architecture of the yeast small subunit processome." Science, 355. doi: 10.1126/science.aal1880. |
Architecture of the yeast small subunit processome. SNAP output |
| 5u34 |
hydrolase-RNA |
X-ray (3.255 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 binary complex. SNAP output |
| 5u4j |
ribosome |
cryo-EM (3.7 Å) |
Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H |
(2017) "Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome." Nature, 541, 554-557. doi: 10.1038/nature21053. |
Structural basis of co-translational quality control by arfa and rf2 bound to ribosome. SNAP output |
| 5u9b |
RNA binding protein-RNA |
NMR |
Park S, Phukan PD, Zeeb M, Martinez-Yamout MA, Dyson HJ, Wright PE |
(2017) "Structural Basis for Interaction of the Tandem Zinc Finger Domains of Human Muscleblind with Cognate RNA from Human Cardiac Troponin T." Biochemistry, 56, 4154-4168. doi: 10.1021/acs.biochem.7b00484. |
Solution structure of the zinc fingers 1 and 2 of mbnl1 in complex with human cardiac troponin t pre-mrna. SNAP output |
| 5ud5 |
ligase-RNA |
X-ray (2.347 Å) |
Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Soll D |
(2017) "Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase." Nat. Chem. Biol., 13, 1261-1266. doi: 10.1038/nchembio.2497. |
Crystal structure of the trna binding domain of pyrrolysyl-trna synthetase bound to trna(pyl). SNAP output |
| 5udi |
RNA binding protein |
X-ray (1.58 Å) |
Abbas YM, Laudenbach BT, Martinez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B |
(2017) "Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations." Proc. Natl. Acad. Sci. U.S.A., 114, E2106-E2115. doi: 10.1073/pnas.1612444114. |
Ifit1 monomeric mutant (l457e-l464e) with m7gppp-aaaa (syn and anti conformations of cap). SNAP output |
| 5udj |
RNA binding protein |
X-ray (1.69 Å) |
Abbas YM, Laudenbach BT, Martinez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B |
(2017) "Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations." Proc. Natl. Acad. Sci. U.S.A., 114, E2106-E2115. doi: 10.1073/pnas.1612444114. |
Ifit1 monomeric mutant (l457e-l464e) with gppp-aaaa. SNAP output |
| 5udk |
RNA binding protein |
X-ray (1.65 Å) |
Abbas YM, Laudenbach BT, Martinez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B |
(2017) "Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations." Proc. Natl. Acad. Sci. U.S.A., 114, E2106-E2115. doi: 10.1073/pnas.1612444114. |
Ifit1 monomeric mutant (l457e-l464e) with ppp-aaaa. SNAP output |
| 5udl |
RNA binding protein |
X-ray (1.65 Å) |
Abbas YM, Laudenbach BT, Martinez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B |
(2017) "Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations." Proc. Natl. Acad. Sci. U.S.A., 114, E2106-E2115. doi: 10.1073/pnas.1612444114. |
Ifit1 n216a monomeric mutant (l457e-l464e) with m7gppp-aaaa (anti conformation of cap). SNAP output |
| 5udz |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Wang L, Nam Y, Lee AK, Yu C, Roth K, Chen C, Ransey EM, Sliz P |
(2017) "LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation." Cell Rep, 18, 2664-2675. doi: 10.1016/j.celrep.2017.02.044. |
Human lin28a in complex with let-7f-1 microrna pre-element. 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 |
| 5uk4 |
viral protein-RNA-immune system |
X-ray (3.204 Å) |
Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL |
(2017) "Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication." EMBO Rep., 18, 1027-1037. doi: 10.15252/embr.201643764. |
Vesicular stomatits virus n protein in complex with inhibitory nanobody 1307. SNAP output |
| 5ukb |
viral protein-RNA-immune system |
X-ray (5.473 Å) |
Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL |
(2017) "Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication." EMBO Rep., 18, 1027-1037. doi: 10.15252/embr.201643764. |
Vsv n protein in complex with inhibitory nanobody 1004. SNAP output |
| 5uz4 |
ribosome-hydrolase |
cryo-EM (5.8 Å) |
Razi A, Guarne A, Ortega J |
(2017) "The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly." Proc. Natl. Acad. Sci. U.S.A., 114, E3396-E3403. doi: 10.1073/pnas.1618016114. |
The cryo-EM structure of yjeq bound to the 30s subunit suggests a fidelity checkpoint function for this protein in ribosome assembly. SNAP output |
| 5uz9 |
immune system-RNA |
cryo-EM (3.4 Å) |
Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B |
(2017) "Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex." Cell, 169, 47-57.e11. doi: 10.1016/j.cell.2017.03.012. |
Cryo em structure of anti-crisprs, acrf1 and acrf2, bound to type i-f crrna-guided crispr surveillance complex. SNAP output |
| 5uzz |
transport protein-RNA |
NMR |
Shortridge MD, Walker MJ, Pavelitz T, Chen Y, Yang W, Varani G |
(2017) "A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing." ACS Chem. Biol., 12, 1611-1620. doi: 10.1021/acschembio.7b00180. |
Structure of wild type pre-mir21 apical loop. SNAP output |
| 5v6x |
ligase-RNA |
X-ray (2.76 Å) |
Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Soll D |
(2017) "Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase." Nat. Chem. Biol., 13, 1261-1266. doi: 10.1038/nchembio.2497. |
Crystal structure of the trna binding domain of pyrrolysyl-trna synthetase mutant (32a ntd) bound to trna(pyl). SNAP output |
| 5v7c |
RNA binding protein |
X-ray (2.59 Å) |
Lahr RM, Fonseca BD, Ciotti GE, Al-Ashtal HA, Jia JJ, Niklaus MR, Blagden SP, Alain T, Berman AJ |
(2017) "La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs." Elife, 6. doi: 10.7554/eLife.24146. |
Crystal structure of larp1-unique domain dm15 bound 5'top RNA sequence. SNAP output |
| 5v7q |
ribosome |
cryo-EM (3.7 Å) |
Yang K, Chang JY, Cui Z, Li X, Meng R, Duan L, Thongchol J, Jakana J, Huwe CM, Sacchettini JC, Zhang J |
(2017) "Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis." Nucleic Acids Res., 45, 10884-10894. doi: 10.1093/nar/gkx785. |
cryo-EM structure of the large ribosomal subunit from mycobacterium tuberculosis bound with a potent linezolid analog. SNAP output |
| 5vm9 |
hydrolase-RNA |
X-ray (3.28 Å) |
Park MS, Phan HD, Busch F, Hinckley SH, Brackbill JA, Wysocki VH, Nakanishi K |
(2017) "Human Argonaute3 has slicer activity." Nucleic Acids Res., 45, 11867-11877. doi: 10.1093/nar/gkx916. |
Human argonaute3 bound to guide RNA. SNAP output |
| 5voe |
hydrolase-RNA |
X-ray (2.0 Å) |
Gunaratne R, Kumar S, Frederiksen JW, Stayrook S, Lohrmann JL, Perry K, Bompiani KM, Chabata CV, Thalji NK, Ho MD, Arepally G, Camire RM, Krishnaswamy S, Sullenger BA |
(2018) "Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass." Nat. Biotechnol., 36, 606-613. doi: 10.1038/nbt.4153. |
Desgla-xas195a bound to aptamer 11f7t. SNAP output |
| 5vof |
hydrolase-hydrolase inhibitor-RNA |
X-ray (2.25 Å) |
Gunaratne R, Kumar S, Frederiksen JW, Stayrook S, Lohrmann JL, Perry K, Bompiani KM, Chabata CV, Thalji NK, Ho MD, Arepally G, Camire RM, Krishnaswamy S, Sullenger BA |
(2018) "Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass." Nat. Biotechnol., 36, 606-613. doi: 10.1038/nbt.4153. |
Desgla-xas195a bound to aptamer 11f7t and rivaroxaban. SNAP output |
| 5vsu |
splicing |
X-ray (3.1 Å) |
Montemayor EJ, Didychuk AL, Yake AD, Sidhu GK, Brow DA, Butcher SE |
(2018) "Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA." Nat Commun, 9, 1749. doi: 10.1038/s41467-018-04145-4. |
Structure of yeast u6 snrnp with 2'-phosphate terminated u6 RNA. SNAP output |
| 5vt0 |
transcription-RNA |
cryo-EM (3.78 Å) |
Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA |
(2017) "6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase." Mol. Cell, 68, 388-397.e6. doi: 10.1016/j.molcel.2017.09.006. |
Escherichia coli 6s RNA derivative in complex with escherichia coli RNA polymerase sigma70-holoenzyme. SNAP output |
| 5vw1 |
hydrolase |
X-ray (2.598 Å) |
Yang H, Patel DJ |
(2017) "Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9." Mol. Cell, 67, 117-127.e5. doi: 10.1016/j.molcel.2017.05.024. |
Crystal structure of spycas9-sgrna-acriia4 ternary complex. SNAP output |
| 5vzj |
hydrolase-RNA |
X-ray (3.3 Å) |
Wasmuth EV, Zinder JC, Zattas D, Das M, Lima CD |
(2017) "Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase." Elife, 6. doi: 10.7554/eLife.29062. |
Structure of a twelve component mpp6-nuclear RNA exosome complex bound to RNA. SNAP output |
| 5vzl |
immune system-RNA |
cryo-EM (3.9 Å) |
Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA |
(2017) "Disabling Cas9 by an anti-CRISPR DNA mimic." Sci Adv, 3, e1701620. doi: 10.1126/sciadv.1701620. |
cryo-EM structure of the cas9-sgrna-acriia4 anti-crispr complex. SNAP output |
| 5w0m |
transferase-RNA |
X-ray (2.298 Å) |
Faehnle CR, Walleshauser J, Joshua-Tor L |
(2017) "Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis." Nat. Struct. Mol. Biol., 24, 658-665. doi: 10.1038/nsmb.3428. |
Structure of human tut7 catalytic module (cm) in complex with u5 RNA. SNAP output |
| 5w0o |
transferase-RNA |
X-ray (2.488 Å) |
Faehnle CR, Walleshauser J, Joshua-Tor L |
(2017) "Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis." Nat. Struct. Mol. Biol., 24, 658-665. doi: 10.1038/nsmb.3428. |
Structure of human tut7 catalytic module (cm) in complex with dsrna. SNAP output |
| 5w1h |
RNA binding protein-RNA |
X-ray (1.99 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 (24-nt spacer). 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 |
| 5w3v |
antiviral protein-RNA |
X-ray (2.243 Å) |
Bohn JA, Thummar K, York A, Raymond A, Brown WC, Bieniasz PD, Hatziioannou T, Smith JL |
(2017) "APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA." Nat Commun, 8, 1021. doi: 10.1038/s41467-017-01309-6. |
Crystal structure of macaque apobec3h in complex with RNA. SNAP output |
| 5w5h |
RNA binding protein-RNA |
X-ray (2.79 Å) |
Abbas YM, Martinez-Montero S, Cencic R, Pelletier J, Damha MJ, Pawelek PD, Nagar B |
"Structural insights into IFIT1 dimerization and conformational changes associated with mRNA binding." |
Human ifit1 dimer with m7gppp-aaaa. SNAP output |
| 5w5i |
RNA binding protein-RNA |
X-ray (2.65 Å) |
Abbas YM, Martinez-Montero S, Cencic R, Pelletier J, Damha MJ, Pawelek PD, Nagar B |
"Structural insights into IFIT1 dimerization and conformational changes associated with mRNA binding." |
Human ifit1 dimer with ppp-aaaa. SNAP output |
| 5w6v |
gene regulation-RNA |
X-ray (2.828 Å) |
Elkayam E, Faehnle CR, Morales M, Sun J, Li H, Joshua-Tor L |
(2017) "Multivalent Recruitment of Human Argonaute by GW182." Mol. Cell, 67, 646-658.e3. doi: 10.1016/j.molcel.2017.07.007. |
The structure of human argonaute-1 in complex with the hook motif of human gw182. SNAP output |
| 5wea |
hydrolase-RNA |
X-ray (3.12 Å) |
Klum SM, Chandradoss SD, Schirle NT, Joo C, MacRae IJ |
(2018) "Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition." EMBO J., 37, 75-88. doi: 10.15252/embj.201796474. |
Human argonaute2 helix-7 mutant. SNAP output |
| 5wlh |
RNA binding protein-RNA |
X-ray (1.8 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 h328a (c2c2) bound to pre-crrna (24-nt spacer). SNAP output |
| 5wnp |
ribosome |
X-ray (3.3 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wnq |
ribosome |
X-ray (3.5 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wnr |
ribosome |
X-ray (3.5 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wns |
ribosome |
X-ray (3.5 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wnt |
ribosome |
X-ray (3.3 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wnu |
ribosome |
X-ray (3.4 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wnv |
ribosome |
X-ray (3.3 Å) |
Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD |
(2018) "2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation." Nat. Struct. Mol. Biol., 25, 208-216. doi: 10.1038/s41594-018-0030-z. |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 5wqe |
RNA binding protein |
X-ray (3.126 Å) |
Liu L, Chen P, Wang M, Li X, Wang J, Yin M, Wang Y |
(2017) "C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism." Mol. Cell, 65, 310-322. doi: 10.1016/j.molcel.2016.11.040. |
Crystal structure of alicyclobacillus acidoterrestris c2c1 in complex with single-guide RNA at 3.1 angstrom resolution. SNAP output |
| 5ws2 |
hydrolase |
X-ray (2.398 Å) |
Zheng X, Feng N, Li D, Dong X, Li J |
(2017) "New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family." Mol. Microbiol., 106, 351-366. doi: 10.1111/mmi.13769. |
Crystal structure of mpy-rnase j (mutant s247a), an archaeal rnase j from methanolobus psychrophilus r15, complex with RNA. SNAP output |
| 5wsg |
RNA binding protein-RNA |
cryo-EM (4.0 Å) |
Yan C, Wan R, Bai R, Huang G, Shi Y |
(2017) "Structure of a yeast step II catalytically activated spliceosome." Science, 355, 149-155. doi: 10.1126/science.aak9979. |
cryo-EM structure of the catalytic step ii spliceosome (c* complex) at 4.0 angstrom resolution. SNAP output |
| 5wt1 |
transferase-RNA |
X-ray (2.598 Å) |
Wang C, Jia Q, Zeng J, Chen R, Xie W |
(2017) "Structural insight into the methyltransfer mechanism of the bifunctional Trm5." Sci Adv, 3, e1700195. doi: 10.1126/sciadv.1700195. |
Pyrococcus abyssi methyltransferase patrm5a bound by sah and cognate trna. SNAP output |
| 5wt3 |
transferase-RNA |
X-ray (3.204 Å) |
Wang C, Jia Q, Zeng J, Chen R, Xie W |
(2017) "Structural insight into the methyltransfer mechanism of the bifunctional Trm5." Sci Adv, 3, e1700195. doi: 10.1126/sciadv.1700195. |
Pyrococcus abyssi methyltransferase patrm5a bound by mta and cognate trna. SNAP output |
| 5wtk |
hydrolase-RNA |
X-ray (2.651 Å) |
Liu L, Li X, Wang J, Wang M, Chen P, Yin M, Li J, Sheng G, Wang Y |
(2017) "Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities." Cell, 168, 121-134.e12. doi: 10.1016/j.cell.2016.12.031. |
Crystal structure of rnp complex. SNAP output |
| 5wty |
RNA binding protein-RNA |
X-ray (2.785 Å) |
Wang B, Ye K |
(2017) "Nop9 binds the central pseudoknot region of 18S rRNA." Nucleic Acids Res., 45, 3559-3567. doi: 10.1093/nar/gkw1323. |
Structure of nop9 RNA complex. SNAP output |
| 5wwe |
RNA binding protein-RNA |
X-ray (2.4 Å) |
Wu B, Su S, Patil DP, Liu H, Gan J, Jaffrey SR, Ma J |
(2018) "Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1." Nat Commun, 9, 420. doi: 10.1038/s41467-017-02770-z. |
Crystal structure of hnrnpa2b1 in complex with RNA. SNAP output |
| 5wwf |
RNA binding protein-RNA |
X-ray (2.15 Å) |
Wu B, Su S, Patil DP, Liu H, Gan J, Jaffrey SR, Ma J |
(2018) "Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1." Nat Commun, 9, 420. doi: 10.1038/s41467-017-02770-z. |
Crystal structure of hnrnpa2b1 in complex with RNA. SNAP output |
| 5wwg |
RNA binding protein-RNA |
X-ray (2.03 Å) |
Wu B, Su S, Patil DP, Liu H, Gan J, Jaffrey SR, Ma J |
(2018) "Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1." Nat Commun, 9, 420. doi: 10.1038/s41467-017-02770-z. |
Crystal structure of hnrnpa2b1 in complex with aaggacuugc. SNAP output |
| 5wwr |
transferase-RNA |
X-ray (3.096 Å) |
Liu RJ, Long T, Li J, Li H, Wang ED |
(2017) "Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6." Nucleic Acids Res., 45, 6684-6697. doi: 10.1093/nar/gkx473. |
Crystal structure of human nsun6-trna-sfg. SNAP output |
| 5wws |
transferase-RNA |
X-ray (3.247 Å) |
Liu RJ, Long T, Li J, Li H, Wang ED |
(2017) "Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6." Nucleic Acids Res., 45, 6684-6697. doi: 10.1093/nar/gkx473. |
Crystal structure of human nsun6-trna-sam. SNAP output |
| 5wwt |
transferase-RNA |
X-ray (3.197 Å) |
Liu RJ, Long T, Li J, Li H, Wang ED |
(2017) "Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6." Nucleic Acids Res., 45, 6684-6697. doi: 10.1093/nar/gkx473. |
Crystal structure of human nsun6-trna. SNAP output |
| 5www |
RNA binding protein-RNA |
X-ray (1.798 Å) |
Yang L, Wang C, Li F, Zhang J, Nayab A, Wu J, Shi Y, Gong Q |
(2017) "The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity." J. Biol. Chem., 292, 16221-16234. doi: 10.1074/jbc.M117.797746. |
Crystal structure of the kh1 domain of human RNA-binding e3 ubiquitin-protein ligase mex-3c complex with RNA. SNAP output |
| 5wwx |
RNA binding protein-RNA |
X-ray (2.0 Å) |
Yang L, Wang C, Li F, Zhang J, Nayab A, Wu J, Shi Y, Gong Q |
(2017) "The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity." J. Biol. Chem., 292, 16221-16234. doi: 10.1074/jbc.M117.797746. |
Crystal structure of the kh2 domain of human RNA-binding e3 ubiquitin-protein ligase mex-3c complex with RNA. SNAP output |
| 5wzg |
RNA binding protein-RNA |
X-ray (2.55 Å) |
Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y |
(2017) "Structural basis for the specific recognition of 18S rRNA by APUM23." Nucleic Acids Res., 45, 12005-12014. doi: 10.1093/nar/gkx872. |
Structure of apum23-gaauugacgg. SNAP output |
| 5wzh |
RNA binding protein-RNA |
X-ray (2.509 Å) |
Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y |
(2017) "Structural basis for the specific recognition of 18S rRNA by APUM23." Nucleic Acids Res., 45, 12005-12014. doi: 10.1093/nar/gkx872. |
Structure of apum23-ggaauugacgg. SNAP output |
| 5wzi |
RNA binding protein-RNA |
X-ray (2.75 Å) |
Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y |
(2017) "Structural basis for the specific recognition of 18S rRNA by APUM23." Nucleic Acids Res., 45, 12005-12014. doi: 10.1093/nar/gkx872. |
Structure of apum23-ggaguugacgg. SNAP output |
| 5wzj |
RNA binding protein-RNA |
X-ray (2.101 Å) |
Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y |
(2017) "Structural basis for the specific recognition of 18S rRNA by APUM23." Nucleic Acids Res., 45, 12005-12014. doi: 10.1093/nar/gkx872. |
Structure of apum23-ggauuugacgg. SNAP output |
| 5wzk |
RNA binding protein-RNA |
X-ray (2.8 Å) |
Bao H, Wang N, Wang C, Jiang Y, Liu J, Xu L, Wu J, Shi Y |
(2017) "Structural basis for the specific recognition of 18S rRNA by APUM23." Nucleic Acids Res., 45, 12005-12014. doi: 10.1093/nar/gkx872. |
Structure of apum23-deletion-of-insert-region-ggaauugacgg. SNAP output |
| 5x3z |
RNA binding protein-RNA |
NMR |
Iwaoka R, Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, Katahira M |
(2017) "Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA." Molecules, 22. doi: 10.3390/molecules22071207. |
Solution structure of musashi1 rbd2 in complex with RNA. SNAP output |
| 5x6b |
RNA binding protein-RNA |
X-ray (2.596 Å) |
Chen M, Kato K, Kubo Y, Tanaka Y, Liu Y, Long F, Whitman WB, Lill P, Gatsogiannis C, Raunser S, Shimizu N, Shinoda A, Nakamura A, Tanaka I, Yao M |
(2017) "Structural basis for tRNA-dependent cysteine biosynthesis." Nat Commun, 8, 1521. doi: 10.1038/s41467-017-01543-y. |
Crystal structure of sepcyse-sepcyss in complex with trnacys from methanocaldococcus jannaschii. SNAP output |
| 5x70 |
transferase-RNA |
X-ray (3.3 Å) |
Nakamichi Y, Higashiura A, Narita H, Hagiwara K, Uehara-Ichiki T, Omura T, Nakagawa A |
"Crystal structure of capping enzyme from Rice dwarf virus." |
Crystal structure of rice dwarf virus p5 in complex with a ssrna oligomer. SNAP output |
| 5x8r |
ribosome |
cryo-EM (3.7 Å) |
Ahmed T, Shi J, Bhushan S |
(2017) "Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation." Nucleic Acids Res., 45, 8581-8595. doi: 10.1093/nar/gkx499. |
Structure of the 30s small subunit of chloroplast ribosome from spinach. SNAP output |
| 5x8t |
ribosome |
cryo-EM (3.3 Å) |
Ahmed T, Shi J, Bhushan S |
(2017) "Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation." Nucleic Acids Res., 45, 8581-8595. doi: 10.1093/nar/gkx499. |
Structure of the 50s large subunit of chloroplast ribosome from spinach. SNAP output |
| 5xbl |
hydrolase-RNA |
X-ray (3.052 Å) |
Guo M, Wang S, Zhu Y, Wang S, Xiong Z, Yang J, Xu Z, Huang Z |
(2017) "Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein." Nature, 546, 436-439. doi: 10.1038/nature22377. |
Structure of nuclease in complex with associated protein. SNAP output |
| 5xc6 |
hydrolase-RNA |
X-ray (2.9 Å) |
Swarbrick CMD, Basavannacharya C, Chan KWK, Chan SA, Singh D, Wei N, Phoo WW, Luo D, Lescar J, Vasudevan SG |
(2017) "NS3 helicase from dengue virus specifically recognizes viral RNA sequence to ensure optimal replication." Nucleic Acids Res., 45, 12904-12920. doi: 10.1093/nar/gkx1127. |
Dengue virus 4 ns3 helicase in complex with ssrna sla12. SNAP output |
| 5xj2 |
transferase-RNA |
X-ray (2.84 Å) |
Jiang Y, Li F, Wu J, Shi Y, Gong Q |
(2017) "Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD." PLoS ONE, 12, e0185226. doi: 10.1371/journal.pone.0185226. |
Structure of sprlmcd with u747 RNA. SNAP output |
| 5xlo |
immune system-RNA |
cryo-EM (3.8 Å) |
Peng R, Xu Y, Zhu T, Li N, Qi J, Chai Y, Wu M, Zhang X, Shi Y, Wang P, Wang J, Gao N, Gao GF |
(2017) "Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures." Cell Res., 27, 853-864. doi: 10.1038/cr.2017.79. |
Anti-crispr proteins acrf1-2 bound to csy surveillance complex with a 32nt spacer crrna backbone region. SNAP output |
| 5xlp |
immune system-RNA |
cryo-EM (4.2 Å) |
Peng R, Xu Y, Zhu T, Li N, Qi J, Chai Y, Wu M, Zhang X, Shi Y, Wang P, Wang J, Gao N, Gao GF |
(2017) "Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures." Cell Res., 27, 853-864. doi: 10.1038/cr.2017.79. |
Anti-crispr proteins acrf1-2 bound to csy surveillance complex with a 20nt spacer crrna backbone region. SNAP output |
| 5xtm |
RNA binding protein-RNA |
X-ray (2.1 Å) |
Oshima K, Gao X, Hayashi S, Ueda T, Nakashima T, Kimura M |
(2018) "Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif." Acta Crystallogr F Struct Biol Commun, 74, 57-64. doi: 10.1107/S2053230X17018039. |
Crystal structure of phorpp38 bound to a k-turn in p12.2 helix. SNAP output |
| 5xwp |
RNA binding protein-RNA |
X-ray (3.086 Å) |
Liu L, Li X, Ma J, Li Z, You L, Wang J, Wang M, Zhang X, Wang Y |
(2017) "The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a." Cell, 170, 714-726.e10. doi: 10.1016/j.cell.2017.06.050. |
Crystal structure of lbucas13a-crrna-target RNA ternary complex. SNAP output |
| 5xwy |
RNA binding protein-RNA |
cryo-EM (3.2 Å) |
Liu L, Li X, Ma J, Li Z, You L, Wang J, Wang M, Zhang X, Wang Y |
(2017) "The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a." Cell, 170, 714-726.e10. doi: 10.1016/j.cell.2017.06.050. |
Electron cryo-microscopy structure of lbucas13a-crrna binary complex. SNAP output |
| 5xxu |
ribosome |
cryo-EM (3.35 Å) |
Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N |
(2017) "Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii." Cell Res., 27, 1275-1288. doi: 10.1038/cr.2017.104. |
Small subunit of toxoplasma gondii ribosome. SNAP output |
| 5xyi |
ribosome |
cryo-EM (3.35 Å) |
Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N |
(2017) "Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii." Cell Res., 27, 1275-1288. doi: 10.1038/cr.2017.104. |
Small subunit of trichomonas vaginalis ribosome. SNAP output |
| 5xym |
ribosome |
cryo-EM (3.08 Å) |
Li Z, Ge X, Zhang Y, Zheng L, Sanyal S, Gao N |
(2018) "Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers." Protein Cell, 9, 384-388. doi: 10.1007/s13238-017-0456-9. |
Large subunit of mycobacterium smegmatis. SNAP output |
| 5xyu |
ribosome |
cryo-EM (3.45 Å) |
Li Z, Ge X, Zhang Y, Zheng L, Sanyal S, Gao N |
(2018) "Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers." Protein Cell, 9, 384-388. doi: 10.1007/s13238-017-0456-9. |
Small subunit of mycobacterium smegmatis ribosome. SNAP output |
| 5y58 |
RNA binding protein |
X-ray (2.8 Å) |
Chen H, Xue J, Churikov D, Hass EP, Shi S, Lemon LD, Luciano P, Bertuch AA, Zappulla DC, Geli V, Wu J, Lei M |
(2018) "Structural Insights into Yeast Telomerase Recruitment to Telomeres." Cell, 172, 331-343.e13. doi: 10.1016/j.cell.2017.12.008. |
Crystal structure of ku70-80 and tlc1. SNAP output |
| 5y6z |
transferase-RNA |
X-ray (2.5 Å) |
Bi P, Shu B, Gong P |
(2017) "Crystal structure of the coxsackievirus A16 RNA-dependent RNA polymerase elongation complex reveals novel features in motif A dynamics." Virol Sin, 32, 548-552. doi: 10.1007/s12250-017-4066-8. |
Crystal structure of the coxsackievirus a16 polymerase elongation complex. SNAP output |
| 5y7m |
RNA binding protein |
X-ray (3.1 Å) |
Oshima K, Gao X, Hayashi S, Ueda T, Nakashima T, Kimura M |
(2018) "Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif." Acta Crystallogr F Struct Biol Commun, 74, 57-64. doi: 10.1107/S2053230X17018039. |
Crystal structure of phorpp38 bound to a k-turn in p12.1 helix. SNAP output |
| 5y88 |
splicing |
cryo-EM (3.7 Å) |
Wan R, Yan C, Bai R, Lei J, Shi Y |
(2017) "Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae." Cell(Cambridge,Mass.), 171, 120-132. doi: 10.1016/j.cell.2017.08.029. |
cryo-EM structure of the intron-lariat spliceosome ready for disassembly from s.cerevisiae at 3.5 angstrom. SNAP output |
| 5yki |
RNA binding protein-RNA |
X-ray (2.25 Å) |
Zhao YY, Mao MW, Zhang WJ, Wang J, Li HT, Yang Y, Wang Z, Wu JW |
(2018) "Expanding RNA binding specificity and affinity of engineered PUF domains." Nucleic Acids Res., 46, 4771-4782. doi: 10.1093/nar/gky134. |
Crystal structure of the engineered nine-repeat puf domain in complex with cognate 9nt-RNA. SNAP output |
| 5ylz |
splicing |
cryo-EM (3.6 Å) |
Bai R, Yan C, Wan R, Lei J, Shi Y |
(2017) "Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae." Cell, 171, 1589-1598.e8. doi: 10.1016/j.cell.2017.10.038. |
cryo-EM structure of the post-catalytic spliceosome from saccharomyces cerevisiae at 3.6 angstrom. SNAP output |
| 5yts |
RNA binding protein-RNA |
X-ray (1.77 Å) |
Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y |
(2019) "Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA." J.Biol.Chem., 294, 10998-11010. doi: 10.1074/jbc.RA119.007545. |
Crystal structure of yb1 cold-shock domain in complex with ucuucu. SNAP output |
| 5ytt |
RNA binding protein-RNA |
X-ray (1.6 Å) |
Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y |
(2019) "Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA." J.Biol.Chem., 294, 10998-11010. doi: 10.1074/jbc.RA119.007545. |
Crystal structure of yb1 cold-shock domain in complex with ucaugu. SNAP output |
| 5ytv |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y |
(2019) "Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA." J.Biol.Chem., 294, 10998-11010. doi: 10.1074/jbc.RA119.007545. |
Crystal structure of yb1 cold-shock domain in complex with ucaucu. SNAP output |
| 5ytx |
RNA binding protein-RNA |
X-ray (1.551 Å) |
Yang XJ, Zhu H, Mu SR, Wei WJ, Yuan X, Wang M, Liu Y, Hui J, Huang Y |
(2019) "Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA." J.Biol.Chem., 294, 10998-11010. doi: 10.1074/jbc.RA119.007545. |
Crystal structure of yb1 cold-shock domain in complex with ucaacu. SNAP output |
| 5yyn |
ligase-RNA |
X-ray (3.0 Å) |
Zhou M, Ye S, Stephen P, Zhang RG, Wang ED, Giege R, Lin SX |
"Crystal Structures Of E.Coli Arginyl-Trna Synthetase (Argrs) In Complex With Substrates." |
Crystal structures of e.coli arginyl-trna synthetase (argrs) in complex with substrate trna(arg). SNAP output |
| 5z3g |
ribosome |
cryo-EM (3.65 Å) |
Zhou D, Zhu X, Zheng S, Tan D, Dong MQ, Ye K |
(2019) "Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate." Protein Cell, 10, 120-130. doi: 10.1007/s13238-018-0526-7. |
cryo-EM structure of a nucleolar pre-60s ribosome (rpf1-tap). SNAP output |
| 5z4a |
transferase-RNA |
X-ray (1.637 Å) |
Cheng L, Li F, Jiang Y, Yu H, Xie C, Shi Y, Gong Q |
(2019) "Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor." Nucleic Acids Res., 47, 495-508. doi: 10.1093/nar/gky1116. |
Structure of tailor in complex with agu RNA. SNAP output |
| 5z4d |
transferase-RNA |
X-ray (1.803 Å) |
Cheng L, Li F, Jiang Y, Yu H, Xie C, Shi Y, Gong Q |
(2019) "Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor." Nucleic Acids Res., 47, 495-508. doi: 10.1093/nar/gky1116. |
Structure of tailor in complex with aguu RNA. SNAP output |
| 5z4j |
transferase-RNA |
X-ray (1.82 Å) |
Cheng L, Li F, Jiang Y, Yu H, Xie C, Shi Y, Gong Q |
(2019) "Structural insights into a unique preference for 3' terminal guanine of mirtron in Drosophila TUTase tailor." Nucleic Acids Res., 47, 495-508. doi: 10.1093/nar/gky1116. |
Structure of tailor in complex with u4 RNA. SNAP output |
| 5z58 |
splicing |
cryo-EM (4.9 Å) |
Zhang X, Yan C, Zhan X, Li L, Lei J, Shi Y |
(2018) "Structure of the human activated spliceosome in three conformational states." Cell Res., 28, 307-322. doi: 10.1038/cr.2018.14. |
cryo-EM structure of a human activated spliceosome (early bact) at 4.9 angstrom.. 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 |
| 5z9w |
viral protein |
cryo-EM (3.9 Å) |
Sugita Y, Matsunami H, Kawaoka Y, Noda T, Wolf M |
(2018) "Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 angstrom resolution." Nature, 563, 137-140. doi: 10.1038/s41586-018-0630-0. |
Ebola virus nucleoprotein-RNA complex. SNAP output |
| 5z9x |
plant protein-RNA |
X-ray (2.8 Å) |
Chen J, Liu L, You C, Gu J, Ruan W, Zhang L, Gan J, Cao C, Huang Y, Chen X, Ma J |
(2018) "Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1." Nat Commun, 9, 3585. doi: 10.1038/s41467-018-05942-7. |
Arabidopsis small RNA degrading nuclease 1 in complex with an RNA substrate. SNAP output |
| 5zal |
hydrolase-protein binding-RNA |
cryo-EM (4.7 Å) |
Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW |
(2018) "Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate." Cell, 173, 1191-1203.e12. doi: 10.1016/j.cell.2018.03.080. |
cryo-EM structure of human dicer and its complexes with a pre-mirna substrate. SNAP output |
| 5zam |
hydrolase-protein binding-RNA |
cryo-EM (5.7 Å) |
Liu Z, Wang J, Cheng H, Ke X, Sun L, Zhang QC, Wang HW |
(2018) "Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate." Cell, 173, 1191-1203.e12. doi: 10.1016/j.cell.2018.03.080. |
cryo-EM structure of human dicer and its complexes with a pre-mirna substrate. SNAP output |
| 5zc9 |
translation-RNA |
X-ray (2.0 Å) |
Iwasaki S, Iwasaki W, Takahashi M, Sakamoto A, Watanabe C, Shichino Y, Floor SN, Fujiwara K, Mito M, Dodo K, Sodeoka M, Imataka H, Honma T, Fukuzawa K, Ito T, Ingolia NT |
(2019) "The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA." Mol. Cell, 73, 738. doi: 10.1016/j.molcel.2018.11.026. |
Crystal structure of the human eif4a1-atp analog-roca-polypurine RNA complex. SNAP output |
| 5zet |
ribosome |
cryo-EM (3.2 Å) |
Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S |
(2018) "Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA." Sci Rep, 8, 13587. doi: 10.1038/s41598-018-31850-3. |
M. smegmatis p-p state 50s ribosomal subunit. SNAP output |
| 5zeu |
ribosome |
cryo-EM (3.7 Å) |
Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S |
(2018) "Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA." Sci Rep, 8, 13587. doi: 10.1038/s41598-018-31850-3. |
M. smegmatis p-p state 30s ribosomal subunit. SNAP output |
| 5zey |
RNA binding protein-RNA |
cryo-EM (12.5 Å) |
Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S |
(2018) "Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA." Sci Rep, 8, 13587. doi: 10.1038/s41598-018-31850-3. |
M. smegmatis trans-translation state 70s ribosome. SNAP output |
| 5zq0 |
transferase-RNA |
X-ray (2.0 Å) |
Jiang Y, Yu H, Li F, Cheng L, Zhu L, Shi Y, Gong Q |
(2018) "Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD." PLoS Pathog., 14, e1007379. doi: 10.1371/journal.ppat.1007379. |
Crystal structure of sprlmcd with u747loop RNA. SNAP output |
| 5zq1 |
transferase-RNA |
X-ray (3.1 Å) |
Jiang Y, Yu H, Li F, Cheng L, Zhu L, Shi Y, Gong Q |
(2018) "Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD." PLoS Pathog., 14, e1007379. doi: 10.1371/journal.ppat.1007379. |
Crystal structure of sprlmcd with u1939loop RNA at 3.10 angstrom. SNAP output |
| 5zq8 |
transferase-RNA |
X-ray (2.18 Å) |
Jiang Y, Yu H, Li F, Cheng L, Zhu L, Shi Y, Gong Q |
(2018) "Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD." PLoS Pathog., 14, e1007379. doi: 10.1371/journal.ppat.1007379. |
Crystal structure of sprlmcd with u747 stemloop RNA. SNAP output |
| 5zsa |
immune system |
X-ray (2.5 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with imdq and uuuuuu. SNAP output |
| 5zsb |
immune system |
X-ray (2.7 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with imdq and aauuaa. SNAP output |
| 5zsc |
immune system |
X-ray (2.2 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with imdq and ccuucc. SNAP output |
| 5zsd |
immune system |
X-ray (2.603 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with imdq and gguugg. SNAP output |
| 5zse |
immune system |
X-ray (2.201 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with imdq and gguccc. SNAP output |
| 5zsl |
immune system |
X-ray (2.3 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with gguugg. SNAP output |
| 5zsm |
immune system |
X-ray (2.5 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with gguccc. SNAP output |
| 5zsn |
immune system |
X-ray (2.4 Å) |
Shimizu T |
"To be published." |
Crystal structure of monkey tlr7 in complex with aauuaa. SNAP output |
| 5zth |
transferase-RNA |
X-ray (3.24 Å) |
Jiang Y, Yu H, Li F, Cheng L, Zhu L, Shi Y, Gong Q |
(2018) "Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD." PLoS Pathog., 14, e1007379. doi: 10.1371/journal.ppat.1007379. |
Crystal structure of sprlmcd with u1939loop RNA at 3.24 angstrom. SNAP output |
| 5ztm |
hydrolase-RNA |
X-ray (2.899 Å) |
Lv M, Yao Y, Li F, Xu L, Yang L, Gong Q, Xu YZ, Shi Y, Fan YJ, Tang Y |
(2019) "Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila." Nucleic Acids Res., 47, 3142-3157. doi: 10.1093/nar/gky1308. |
Crystal structure of mle dsrbds in complex with rox2 (r2h1). SNAP output |
| 5zuu |
RNA binding protein-RNA |
X-ray (1.95 Å) |
Hou Y, Sun J, Wu B, Gao Y, Nie H, Nie Z, Quan S, Wang Y, Cao X, Li S |
(2021) "CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis." Mol Plant. doi: 10.1016/j.molp.2021.01.013. |
Crystal structure of atcpsf30 yth domain in complex with 10mer m6a-modified RNA. SNAP output |
| 5zw4 |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Ryu H, Grove TL, Almo SC, Kim J |
(2018) "Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine." Nucleic Acids Res., 46, 9160-9169. doi: 10.1093/nar/gky592. |
Crystal structure of trna bound trmr. SNAP output |
| 5zwn |
splicing |
cryo-EM (3.3 Å) |
Bai R, Wan R, Yan C, Lei J, Shi Y |
(2018) "Structures of the fully assembledSaccharomyces cerevisiaespliceosome before activation." Science, 360, 1423-1429. doi: 10.1126/science.aau0325. |
cryo-EM structure of the yeast pre-b complex at an average resolution of 3.3 angstrom (part ii: u1 snrnp region). SNAP output |
| 5zwo |
splicing |
cryo-EM (3.9 Å) |
Bai R, Wan R, Yan C, Lei J, Shi Y |
(2018) "Structures of the fully assembledSaccharomyces cerevisiaespliceosome before activation." Science, 360, 1423-1429. doi: 10.1126/science.aau0325. |
cryo-EM structure of the yeast b complex at average resolution of 3.9 angstrom. SNAP output |
| 6a4e |
hydrolase |
X-ray (2.45 Å) |
Lee CW, Park SH, Jeong CS, Cha SS, Park H, Lee JH |
(2019) "Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H." Sci Rep, 9, 2649. doi: 10.1038/s41598-019-39641-0. |
Two linked uridine bound oligoribonuclease (orn) from colwellia psychrerythraea strain 34h. SNAP output |
| 6a6j |
RNA binding protein-RNA |
X-ray (2.255 Å) |
Yang Y, Wang L, Han X, Yang WL, Zhang M, Ma HL, Sun BF, Li A, Xia J, Chen J, Heng J, Wu B, Chen YS, Xu JW, Yang X, Yao H, Sun J, Lyu C, Wang HL, Huang Y, Sun YP, Zhao YL, Meng A, Ma J, Liu F, Yang YG |
(2019) "RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay." Mol.Cell, 75, 1188-1202.e11. doi: 10.1016/j.molcel.2019.06.033. |
Crystal structure of zebra fish y-box protein1 (yb-1) cold-shock domain in complex with 6mer m5c RNA. SNAP output |
| 6a6l |
RNA binding protein-RNA |
X-ray (1.78 Å) |
Huang Y |
"Crystal structure of the cold shock domain of YB-1 in complex with m5C RNA." |
Crystal structure of the cold shock domain of yb-1 in complex with m5c RNA. SNAP output |
| 6aax |
transferase-RNA |
X-ray (2.994 Å) |
Liu X, Shen S, Wu P, Li F, Liu X, Wang C, Gong Q, Wu J, Yao X, Zhang H, Shi Y |
(2019) "Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function." Nucleic Acids Res., 47, 7648-7665. doi: 10.1093/nar/gkz505. |
Crystal structure of tfb1m and h45 with sam in homo sapiens. SNAP output |
| 6aay |
RNA binding protein-RNA |
X-ray (2.79 Å) |
Zhang B, Ye WW, Ye YM, Zhou H, Saeed AFUH, Chen J, Lin JY, Perculija V, Chen Q, Chen CJ, Chang MX, Choudhary MI, Ouyang SY |
(2018) "Structural insights into Cas13b-guided CRISPR RNA maturation and recognition." Cell Res., 28, 1198-1201. doi: 10.1038/s41422-018-0109-4. |
The cas13b binary complex. SNAP output |
| 6agb |
hydrolase-RNA |
cryo-EM (3.48 Å) |
Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M |
(2018) "Structural insight into precursor tRNA processing by yeast ribonuclease P." Science, 362. doi: 10.1126/science.aat6678. |
cryo-EM structure of yeast ribonuclease p. SNAP output |
| 6ah0 |
splicing |
cryo-EM (5.7 Å) |
Zhan X, Yan C, Zhang X, Lei J, Shi Y |
(2018) "Structures of the human pre-catalytic spliceosome and its precursor spliceosome." Cell Res., 28, 1129-1140. doi: 10.1038/s41422-018-0094-7. |
The cryo-EM structure of the precusor of human pre-catalytic spliceosome (pre-b complex). SNAP output |
| 6ah3 |
hydrolase-RNA |
cryo-EM (3.48 Å) |
Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S, Qiu S, Wang X, Peng X, Cai G, Cheng H, Wu J, Li G, Lei M |
(2018) "Structural insight into precursor tRNA processing by yeast ribonuclease P." Science, 362. doi: 10.1126/science.aat6678. |
cryo-EM structure of yeast ribonuclease p with pre-trna substrate. SNAP output |
| 6ahr |
hydrolase-RNA |
cryo-EM (3.92 Å) |
Wu J, Niu S, Tan M, Huang C, Li M, Song Y, Wang Q, Chen J, Shi S, Lan P, Lei M |
(2018) "Cryo-EM Structure of the Human Ribonuclease P Holoenzyme." Cell, 175, 1393-1404.e11. doi: 10.1016/j.cell.2018.10.003. |
cryo-EM structure of human ribonuclease p. SNAP output |
| 6ahu |
hydrolase-RNA |
cryo-EM (3.66 Å) |
Wu J, Niu S, Tan M, Huang C, Li M, Song Y, Wang Q, Chen J, Shi S, Lan P, Lei M |
(2018) "Cryo-EM Structure of the Human Ribonuclease P Holoenzyme." Cell, 175, 1393-1404.e11. doi: 10.1016/j.cell.2018.10.003. |
cryo-EM structure of human ribonuclease p with mature trna. SNAP output |
| 6ajk |
transferase-RNA |
X-ray (3.001 Å) |
Liu X, Shen S, Wu P, Li F, Liu X, Wang C, Gong Q, Wu J, Yao X, Zhang H, Shi Y |
(2019) "Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function." Nucleic Acids Res., 47, 7648-7665. doi: 10.1093/nar/gkz505. |
Crystal structure of tfb1m and h45 in homo sapiens. SNAP output |
| 6aso |
splicing |
X-ray (2.71 Å) |
Montemayor EJ, Didychuk AL, Yake AD, Sidhu GK, Brow DA, Butcher SE |
(2018) "Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA." Nat Commun, 9, 1749. doi: 10.1038/s41467-018-04145-4. |
Structure of yeast u6 snrnp with 3'-phosphate terminated u6 RNA. SNAP output |
| 6az1 |
ribosome-antibiotic |
cryo-EM (2.7 Å) |
Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G |
(2017) "Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin." Nat Commun, 8, 1589. doi: 10.1038/s41467-017-01664-4. |
cryo-EM structure of the small subunit of leishmania ribosome bound to paromomycin. SNAP output |
| 6b0b |
hydrolase-RNA |
X-ray (3.28 Å) |
Shaban NM, Shi K, Lauer KV, Carpenter MA, Richards CM, Salamango D, Wang J, Lopresti MW, Banerjee S, Levin-Klein R, Brown WL, Aihara H, Harris RS |
(2018) "The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism." Mol. Cell, 69, 75-86.e9. doi: 10.1016/j.molcel.2017.12.010. |
Crystal structure of human apobec3h. SNAP output |
| 6b14 |
immune system-RNA |
X-ray (1.64 Å) |
Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA |
(2018) "Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography." Nucleic Acids Res., 46, 2624-2635. doi: 10.1093/nar/gkx1292. |
Crystal structure of spinach RNA aptamer in complex with fab bl3-6s97n. SNAP output |
| 6b3k |
immune system-RNA |
X-ray (2.09 Å) |
Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA |
(2018) "Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography." Nucleic Acids Res., 46, 2624-2635. doi: 10.1093/nar/gkx1292. |
Crystal structure of mutant spinach RNA aptamer in complex with fab bl3-6. SNAP output |
| 6b45 |
immune system - RNA |
cryo-EM (3.5 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. SNAP output |
| 6b46 |
immune system-hydrolase-RNA |
cryo-EM (3.1 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 anti-crispr protein acrf1. SNAP output |
| 6b47 |
immune system - RNA |
cryo-EM (3.2 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 anti-crispr protein acrf2. SNAP output |
| 6b48 |
immune system - RNA |
cryo-EM (3.6 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 anti-crispr protein acrf10. SNAP output |
| 6bbo |
hydrolase-RNA |
X-ray (3.428 Å) |
Shaban NM, Shi K, Lauer KV, Carpenter MA, Richards CM, Salamango D, Wang J, Lopresti MW, Banerjee S, Levin-Klein R, Brown WL, Aihara H, Harris RS |
(2018) "The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism." Mol. Cell, 69, 75-86.e9. doi: 10.1016/j.molcel.2017.12.010. |
Crystal structure of human apobec3h-RNA complex. SNAP output |
| 6bjg |
RNA binding protein |
X-ray (2.29 Å) |
Foss DV, Schirle NT, MacRae IJ, Pezacki JP |
(2019) "Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs." Febs Open Bio, 9, 1042-1051. doi: 10.1002/2211-5463.12644. |
Cirv p19 mutant t111h in complex with sirna. SNAP output |
| 6bjh |
RNA binding protein |
X-ray (2.58 Å) |
Foss DV, Schirle NT, MacRae IJ, Pezacki JP |
(2019) "Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs." Febs Open Bio, 9, 1042-1051. doi: 10.1002/2211-5463.12644. |
Cirv p19 mutant t111s in complex with sirna. SNAP output |
| 6bjv |
RNA binding protein |
X-ray (2.198 Å) |
Foss DV, Schirle NT, MacRae IJ, Pezacki JP |
(2019) "Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs." Febs Open Bio, 9, 1042-1051. doi: 10.1002/2211-5463.12644. |
Cirv p19 protein in complex with sirna. SNAP output |
| 6bjy |
RNA binding protein-RNA |
X-ray (3.46 Å) |
Gumpper RH, Li W, Castaneda CH, Scuderi MJ, Bashkin JK, Luo M |
(2018) "A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid." J. Virol., 92. doi: 10.1128/JVI.00146-18. |
Vsv nucleocapsid with polyamide bound. SNAP output |
| 6bk8 |
RNA binding protein |
cryo-EM (3.3 Å) |
Liu S, Li X, Zhang L, Jiang J, Hill RC, Cui Y, Hansen KC, Zhou ZH, Zhao R |
(2017) "Structure of the yeast spliceosomal postcatalytic P complex." Science, 358, 1278-1283. doi: 10.1126/science.aar3462. |
S. cerevisiae spliceosomal post-catalytic p complex. SNAP output |
| 6bu9 |
RNA binding protein-RNA |
cryo-EM (6.8 Å) |
Sinha NK, Iwasa J, Shen PS, Bass BL |
(2018) "Dicer uses distinct modules for recognizing dsRNA termini." Science, 359, 329-334. doi: 10.1126/science.aaq0921. |
Drosophila dicer-2 bound to blunt dsrna. SNAP output |
| 6c0f |
ribosome |
cryo-EM (3.7 Å) |
Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S |
(2018) "Modular assembly of the nucleolar pre-60S ribosomal subunit." Nature, 556, 126-129. doi: 10.1038/nature26156. |
Yeast nucleolar pre-60s ribosomal subunit (state 2). SNAP output |
| 6c4h |
ribosomal protein-RNA |
cryo-EM (3.1 Å) |
Zeng F, Jin H |
(2018) "Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination." Sci Rep, 8, 2349. doi: 10.1038/s41598-018-20107-8. |
Conformation of methylated ggq in the peptidyl transferase center during translation termination (ptc region). SNAP output |
| 6c6k |
RNA binding protein-RNA |
X-ray (2.54 Å) |
Johnson B, VanBlargan LA, Xu W, White JP, Shan C, Shi PY, Zhang R, Adhikari J, Gross ML, Leung DW, Diamond MS, Amarasinghe GK |
(2018) "Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability." Immunity, 48, 487-499.e5. doi: 10.1016/j.immuni.2018.01.014. |
Structural basis for preferential recognition of cap 0 RNA by a human ifit1-ifit3 protein complex. SNAP output |
| 6cao |
ribosome |
X-ray (3.45 Å) |
Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Aksit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H |
(2018) "Structure of the 30S ribosomal decoding complex at ambient temperature." RNA, 24, 1667-1676. doi: 10.1261/rna.067660.118. |
Structure of the ribosomal decoding complex at ambient temperature. SNAP output |
| 6cap |
ribosome |
X-ray (3.4 Å) |
DeMirci H |
"Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus in complex with sisomicin. SNAP output |
| 6caq |
ribosome |
X-ray (3.4 Å) |
DeMirci H |
"Crystal Structure of 30S ribosomal subunit from Thermus thermophilus." |
Crystal structure of 30s ribosomal subunit from thermus thermophilus. SNAP output |
| 6car |
ribosome |
X-ray (3.4 Å) |
O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H |
(2018) "Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature." Nucleic Acids Res., 46, 9793-9804. doi: 10.1093/nar/gky693. |
Serial femtosecond x-ray crystal structure of 30s ribosomal subunit from thermus thermophilus in complex with sisomicin. SNAP output |
| 6cas |
ribosome |
X-ray (3.5 Å) |
O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H |
(2018) "Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature." Nucleic Acids Res., 46, 9793-9804. doi: 10.1093/nar/gky693. |
Serial femtosecond x-ray crystal structure of 30s ribosomal subunit from thermus thermophilus in complex with n1ms. SNAP output |
| 6cb1 |
ribosome |
cryo-EM (4.6 Å) |
Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S |
(2018) "Modular assembly of the nucleolar pre-60S ribosomal subunit." Nature, 556, 126-129. doi: 10.1038/nature26156. |
Yeast nucleolar pre-60s ribosomal subunit (state 3). SNAP output |
| 6cbd |
RNA binding protein |
X-ray (2.203 Å) |
Sheu-Gruttadauria J, MacRae IJ |
(2018) "Phase Transitions in the Assembly and Function of Human miRISC." Cell, 173, 946. doi: 10.1016/j.cell.2018.02.051. |
Crystal structure of human argonaute2 bound to three tryptophans. SNAP output |
| 6cf2 |
RNA binding protein-RNA |
X-ray (3.0 Å) |
Dearborn AD, Eren E, Watts NR, Palmer IW, Kaufman JD, Steven AC, Wingfield PT |
(2018) "Structure of an RNA Aptamer that Can Inhibit HIV-1 by Blocking Rev-Cognate RNA (RRE) Binding and Rev-Rev Association." Structure, 26, 1187. doi: 10.1016/j.str.2018.06.001. |
Crystal structure of hiv-1 rev (residues 1-93)-RNA aptamer complex. SNAP output |
| 6cmn |
RNA binding protein-RNA |
X-ray (1.796 Å) |
Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE |
(2018) "Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription." Nucleic Acids Res., 46, 6401-6415. doi: 10.1093/nar/gky529. |
Co-crystal structure of hiv-1 tar bound to lab-evolved rrm tbp6.7. SNAP output |
| 6cyt |
transcription-RNA |
X-ray (3.5 Å) |
Schulze-Gahmen U, Hurley JH |
(2018) "Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex." Proc. Natl. Acad. Sci. U.S.A., 115, 12973-12978. doi: 10.1073/pnas.1806438115. |
Hiv-1 tar loop in complex with tat:aff4:p-tefb. SNAP output |
| 6d06 |
hydrolase-RNA |
X-ray (2.55 Å) |
Monteleone LR, Matthews MM, Palumbo CM, Thomas JM, Zheng Y, Chiang Y, Fisher AJ, Beal PA |
(2019) "A Bump-Hole Approach for Directed RNA Editing." Cell Chem Biol, 26, 269. doi: 10.1016/j.chembiol.2018.10.025. |
Human adar2d e488y mutant complexed with dsrna containing an abasic site opposite the edited base. SNAP output |
| 6d12 |
RNA binding protein-RNA |
X-ray (2.205 Å) |
Eichhorn CD, Yang Y, Repeta L, Feigon J |
(2018) "Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7." Proc. Natl. Acad. Sci. U.S.A., 115, E6457-E6466. doi: 10.1073/pnas.1806276115. |
Crystal structure of c-terminal xrrm domain of human larp7 bound to 7sk stem-loop 4 RNA. SNAP output |
| 6d1v |
isomerase-hydrolase-RNA |
X-ray (1.81 Å) |
Gao A, Vasilyev N, Luciano DJ, Levenson-Palmer R, Richards J, Marsiglia WM, Traaseth NJ, Belasco JG, Serganov A |
(2018) "Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF." Nucleic Acids Res., 46, 6841-6856. doi: 10.1093/nar/gky327. |
Crystal structure of e. coli rpph-dapf complex, monomer bound to RNA. SNAP output |
| 6d2u |
peptide-RNA |
NMR |
Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G |
(2019) "An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb." Nucleic Acids Res., 47, 1523-1531. doi: 10.1093/nar/gky1197. |
Solution structure of a ultra-high affinity macrocycle bound to hiv-1 tar RNA. SNAP output |
| 6d2z |
hydrolase-RNA |
X-ray (1.18 Å) |
Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE |
(2018) "Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1." Nucleic Acids Res., 46, 11488-11501. doi: 10.1093/nar/gky812. |
Structure of human usb1 with uridine-adenosine, inactive h208q mutant. SNAP output |
| 6d30 |
hydrolase-RNA |
X-ray (1.17 Å) |
Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE |
(2018) "Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1." Nucleic Acids Res., 46, 11488-11501. doi: 10.1093/nar/gky812. |
Structure of human usb1 with uridine-uridine, inactive h208q mutant. SNAP output |
| 6db8 |
RNA-immune system |
X-ray (1.87 Å) |
Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA |
(2018) "Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif." Nat Commun, 9, 4542. doi: 10.1038/s41467-018-06942-3. |
Structural basis for promiscuous binding and activation of fluorogenic dyes by dir2s RNA aptamer. SNAP output |
| 6db9 |
RNA-immune system |
X-ray (2.025 Å) |
Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA |
(2018) "Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif." Nat Commun, 9, 4542. doi: 10.1038/s41467-018-06942-3. |
Structural basis for promiscuous binding and activation of fluorogenic dyes by dir2s RNA aptamer. SNAP output |
| 6dcb |
transferase-RNA |
X-ray (1.998 Å) |
Yang Y, Eichhorn CD, Wang Y, Cascio D, Feigon J |
(2019) "Structural basis of 7SK RNA 5'-gamma-phosphate methylation and retention by MePCE." Nat. Chem. Biol., 15, 132-140. doi: 10.1038/s41589-018-0188-z. |
Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7sk RNA. SNAP output |
| 6dcc |
transferase-RNA |
X-ray (2.1 Å) |
Yang Y, Eichhorn CD, Wang Y, Cascio D, Feigon J |
(2019) "Structural basis of 7SK RNA 5'-gamma-phosphate methylation and retention by MePCE." Nat. Chem. Biol., 15, 132-140. doi: 10.1038/s41589-018-0188-z. |
Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7sk RNA. SNAP output |
| 6dcl |
RNA binding protein-RNA |
X-ray (2.497 Å) |
Kooshapur H, Choudhury NR, Simon B, Muhlbauer M, Jussupow A, Fernandez N, Jones AN, Dallmann A, Gabel F, Camilloni C, Michlewski G, Caceres JF, Sattler M |
(2018) "Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1." Nat Commun, 9, 2479. doi: 10.1038/s41467-018-04871-9. |
Crystal structure of up1 bound to pri-mirna-18a terminal loop. SNAP output |
| 6ddd |
ribosome-antibiotic |
cryo-EM (3.1 Å) |
Belousoff MJ, Venugopal H, Wright A, Seoner S, Stuart I, Stubenrauch C, Bamert RS, Lupton DW, Lithgow T |
(2019) "cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria." ChemMedChem, 14, 527-531. doi: 10.1002/cmdc.201900042. |
Structure of the 50s ribosomal subunit from methicillin resistant staphylococcus aureus in complex with the oxazolidinone antibiotic lzd-5. SNAP output |
| 6ddg |
ribosome-antibiotic |
cryo-EM (3.1 Å) |
Belousoff MJ, Venugopal H, Wright A, Seoner S, Stuart I, Stubenrauch C, Bamert RS, Lupton DW, Lithgow T |
(2019) "cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria." ChemMedChem, 14, 527-531. doi: 10.1002/cmdc.201900042. |
Structure of the 50s ribosomal subunit from methicillin resistant staphylococcus aureus in complex with the oxazolidinone antibiotic lzd-6. SNAP output |
| 6dnh |
RNA binding protein-RNA |
cryo-EM (3.4 Å) |
Sun Y, Zhang Y, Hamilton K, Manley JL, Shi Y, Walz T, Tong L |
(2018) "Molecular basis for the recognition of the human AAUAAA polyadenylation signal." Proc. Natl. Acad. Sci. U.S.A., 115, E1419-E1428. doi: 10.1073/pnas.1718723115. |
cryo-EM structure of human cpsf-160-wdr33-cpsf-30-pas RNA complex at 3.4 Å resolution. SNAP output |
| 6dtd |
hydrolase-RNA |
X-ray (1.65 Å) |
Slaymaker IM, Mesa P, Kellner MJ, Kannan S, Brignole E, Koob J, Feliciano PR, Stella S, Abudayyeh OO, Gootenberg JS, Strecker J, Montoya G, Zhang F |
(2019) "High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage." Cell Rep, 26, 3741-3751.e5. doi: 10.1016/j.celrep.2019.02.094. |
High-resolution crystal structure of cas13b from prevotella buccae. SNAP output |
| 6dti |
ribosome |
X-ray (3.54 Å) |
Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy IV FV, Ranganathan SV, Sarachan KL, Agris PF |
(2020) "A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine." J.Mol.Biol., 432, 913-929. doi: 10.1016/j.jmb.2019.12.016. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with an unmodifed anticodon stem loop (asl) of escherichia coli transfer RNA arginine 2 (trnaarg2) bound to an mrna with an cgu-codon in the a-site and paromomycin. SNAP output |
| 6du4 |
transferase-RNA |
X-ray (1.7 Å) |
Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y |
(2018) "Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor." Mol. Cell, 71, 1001-1011.e4. doi: 10.1016/j.molcel.2018.07.025. |
Crystal structure of hmettl16 catalytic domain in complex with mat2a 3'utr hairpin 1. SNAP output |
| 6du5 |
transferase-RNA |
X-ray (3.006 Å) |
Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y |
(2018) "Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor." Mol. Cell, 71, 1001-1011.e4. doi: 10.1016/j.molcel.2018.07.025. |
Crystal structure of hmettl16 catalytic domain in complex with mat2a 3'utr hairpin 6. SNAP output |
| 6duq |
transcription-RNA |
X-ray (3.7 Å) |
Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM |
(2018) "Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein." Mol. Cell, 71, 911-922.e4. doi: 10.1016/j.molcel.2018.07.014. |
Structure of a rho-nusg kow domain complex. SNAP output |
| 6dzk |
ribosome |
cryo-EM (3.6 Å) |
Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK |
(2018) "Zinc depletion induces ribosome hibernation in mycobacteria." Proc. Natl. Acad. Sci. U.S.A., 115, 8191-8196. doi: 10.1073/pnas.1804555115. |
cryo-EM structure of mycobacterium smegmatis c(minus) 30s ribosomal subunit with mpy. SNAP output |
| 6dzp |
ribosome |
cryo-EM (3.42 Å) |
Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK |
(2018) "Zinc depletion induces ribosome hibernation in mycobacteria." Proc. Natl. Acad. Sci. U.S.A., 115, 8191-8196. doi: 10.1073/pnas.1804555115. |
cryo-EM structure of mycobacterium smegmatis c(minus) 50s ribosomal subunit. SNAP output |
| 6e0o |
transferase-RNA |
X-ray (1.25 Å) |
Whiteley AT, Eaglesham JB, de Oliveira Mann CC, Morehouse BR, Lowey B, Nieminen EA, Danilchanka O, King DS, Lee ASY, Mekalanos JJ, Kranzusch PJ |
(2019) "Bacterial cGAS-like enzymes synthesize diverse nucleotide signals." Nature, 567, 194-199. doi: 10.1038/s41586-019-0953-5. |
Structure of elizabethkingia meningoseptica cdne cyclic dinucleotide synthase with pppa[3'-5']pa. SNAP output |
| 6e4p |
RNA binding protein-RNA |
X-ray (1.949 Å) |
Travis B, Shaw PLR, Liu B, Ravindra K, Iliff H, Al-Hashimi HM, Schumacher MA |
(2019) "The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA." Nucleic Acids Res., 47, 2130-2142. doi: 10.1093/nar/gky1259. |
Structure of the t. brucei rrm domain in complex with RNA. SNAP output |
| 6e9e |
RNA binding protein-RNA |
cryo-EM (3.4 Å) |
Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D |
(2018) "Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d." Cell, 175, 212-223.e17. doi: 10.1016/j.cell.2018.09.001. |
Escas13d-crrna binary complex. SNAP output |
| 6e9f |
RNA binding protein-RNA |
cryo-EM (3.3 Å) |
Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D |
(2018) "Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d." Cell, 175, 212-223.e17. doi: 10.1016/j.cell.2018.09.001. |
Escas13d-crrna-target RNA ternary complex. SNAP output |
| 6een |
RNA binding protein-RNA |
X-ray (2.01 Å) |
Schmidberger JW, Bond CS |
"Crystal structure of a designer Pentatrico Peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity." |
Crystal structure of a designer pentatrico peptide RNA binding protein, bound to a complex RNA target and featuring an infinite superhelix and microheterogeneity.. SNAP output |
| 6eml |
ribosome |
cryo-EM (3.6 Å) |
Heuer A, Thomson E, Schmidt C, Berninghausen O, Becker T, Hurt E, Beckmann R |
(2017) "Cryo-EM structure of a late pre-40S ribosomal subunit fromSaccharomyces cerevisiae." Elife, 6. doi: 10.7554/eLife.30189. |
cryo-EM structure of a late pre-40s ribosomal subunit from saccharomyces cerevisiae. SNAP output |
| 6evj |
viral protein |
X-ray (3.9 Å) |
Pflug A, Gaudon S, Resa-Infante P, Lethier M, Reich S, Schulze WM, Cusack S |
(2018) "Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors." Nucleic Acids Res., 46, 956-971. doi: 10.1093/nar/gkx1210. |
Crystal structure of bat influenza a-h17n10 polymerase with viral RNA promoter and capped RNA primer. SNAP output |
| 6evk |
viral protein |
X-ray (2.9 Å) |
Pflug A, Gaudon S, Resa-Infante P, Lethier M, Reich S, Schulze WM, Cusack S |
(2018) "Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors." Nucleic Acids Res., 46, 956-971. doi: 10.1093/nar/gkx1210. |
Crystal structure of bat influenza a-h17n10 polymerase with viral RNA promoter and cap analogue m7gtp. SNAP output |
| 6exn |
splicing |
cryo-EM (3.7 Å) |
Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K |
(2017) "Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection." Science, 358, 1283-1288. doi: 10.1126/science.aar3729. |
Post-catalytic p complex spliceosome with 3' splice site docked. SNAP output |
| 6f3h |
hydrolase |
X-ray (2.703 Å) |
Razew M, Warkocki Z, Taube M, Kolondra A, Czarnocki-Cieciura M, Nowak E, Labedzka-Dmoch K, Kawinska A, Piatkowski J, Golik P, Kozak M, Dziembowski A, Nowotny M |
(2018) "Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components." Nat Commun, 9, 97. doi: 10.1038/s41467-017-02570-5. |
Crystal structure of dss1 exoribonuclease active site mutant d477n from candida glabrata. SNAP output |
| 6f4a |
hydrolase |
X-ray (3.55 Å) |
Razew M, Warkocki Z, Taube M, Kolondra A, Czarnocki-Cieciura M, Nowak E, Labedzka-Dmoch K, Kawinska A, Piatkowski J, Golik P, Kozak M, Dziembowski A, Nowotny M |
(2018) "Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components." Nat Commun, 9, 97. doi: 10.1038/s41467-017-02570-5. |
Yeast mitochondrial RNA degradosome complex mtexo. SNAP output |
| 6f4g |
splicing |
X-ray (1.9 Å) |
Weber G, DeKoster GT, Holton N, Hall KB, Wahl MC |
(2018) "Molecular principles underlying dual RNA specificity in the Drosophila SNF protein." Nat Commun, 9, 2220. doi: 10.1038/s41467-018-04561-6. |
'crystal structure of the drosophila melanogaster snf-u2a'-u2-sl4 complex. SNAP output |
| 6f4h |
splicing |
X-ray (2.0 Å) |
Weber G, DeKoster GT, Holton N, Hall KB, Wahl MC |
(2018) "Molecular principles underlying dual RNA specificity in the Drosophila SNF protein." Nat Commun, 9, 2220. doi: 10.1038/s41467-018-04561-6. |
Crystal structure of the drosophila melanogaster snf-u1-sl2 complex. SNAP output |
| 6f5o |
viral protein |
cryo-EM (9.8 Å) |
Serna Martin I, Hengrung N, Renner M, Sharps J, Martinez-Alonso M, Masiulis S, Grimes JM, Fodor E |
(2018) "A Mechanism for the Activation of the Influenza Virus Transcriptase." Mol. Cell, 70, 1101-1110.e4. doi: 10.1016/j.molcel.2018.05.011. |
A mechanism for the activation of the influenza virus transcriptase. SNAP output |
| 6fai |
ribosome |
cryo-EM (3.4 Å) |
Scaiola A, Pena C, Weisser M, Bohringer D, Leibundgut M, Klingauf-Nerurkar P, Gerhardy S, Panse VG, Ban N |
(2018) "Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit." EMBO J., 37. doi: 10.15252/embj.201798499. |
Structure of a eukaryotic cytoplasmic pre-40s ribosomal subunit. SNAP output |
| 6fbs |
RNA binding protein |
cryo-EM (3.07 Å) |
Clerici M, Faini M, Muckenfuss LM, Aebersold R, Jinek M |
(2018) "Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex." Nat. Struct. Mol. Biol., 25, 135-138. doi: 10.1038/s41594-017-0020-6. |
cryo-EM structure of the human cpsf160-wdr33-cpsf30 complex bound to the pas aauaaa motif at 3.1 angstrom resolution. SNAP output |
| 6ff4 |
splicing |
cryo-EM (3.4 Å) |
Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luhrmann R, Stark H |
(2018) "Structure and Conformational Dynamics of the Human Spliceosomal BactComplex." Cell, 172, 454-464.e11. doi: 10.1016/j.cell.2018.01.010. |
Human bact spliceosome core structure. SNAP output |
| 6ff7 |
splicing |
cryo-EM (4.5 Å) |
Haselbach D, Komarov I, Agafonov DE, Hartmuth K, Graf B, Dybkov O, Urlaub H, Kastner B, Luhrmann R, Stark H |
(2018) "Structure and Conformational Dynamics of the Human Spliceosomal BactComplex." Cell, 172, 454-464.e11. doi: 10.1016/j.cell.2018.01.010. |
Human bact spliceosome core structure. SNAP output |
| 6fhh |
viral protein |
X-ray (2.7 Å) |
Claron M, Lukarska M, Uhrig U, Sehr P, Drncova P, Lewis JD, Will DW, Cusack S |
"Towards New Anti-Influenza Therapeutics: Structure-Activity Relationships in the Interaction between Heterotrimeric Influenza Polymerase and Pol II C-terminal domain." |
Crystal structure of bat influenza a-h17n10 polymerase with viral RNA promoter bound to a 22-mer modified pol ii ctd peptide with serine 5 thiophosphorylated.. SNAP output |
| 6fhi |
viral protein |
X-ray (2.8 Å) |
Claron M, Lukarska M, Uhrig U, Sehr P, Drncova P, Lewis JD, Will DW, Cusack S |
"Towards New Anti-Influenza Therapeutics: Structure-Activity Relationships in the Interaction between Heterotrimeric Influenza Polymerase and Pol II C-terminal domain." |
Crystal structure of bat influenza a-h17n10 polymerase with viral RNA promoter bound to a 19-mer serine 5 phosphorylated pol ii ctd peptide with a truncated linker.. SNAP output |
| 6fpq |
RNA binding protein |
X-ray (1.42 Å) |
Stowell JAW, Wagstaff JL, Hill CH, Yu M, McLaughlin SH, Freund SMV, Passmore LA |
(2018) "A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding." J. Biol. Chem., 293, 9210-9222. doi: 10.1074/jbc.RA118.002291. |
Structure of s. pombe mmi1 in complex with 7-mer RNA. SNAP output |
| 6fpx |
RNA binding protein |
X-ray (1.97 Å) |
Stowell JAW, Wagstaff JL, Hill CH, Yu M, McLaughlin SH, Freund SMV, Passmore LA |
(2018) "A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding." J. Biol. Chem., 293, 9210-9222. doi: 10.1074/jbc.RA118.002291. |
Structure of s. pombe mmi1 in complex with 11-mer RNA. SNAP output |
| 6fq3 |
RNA binding protein |
X-ray (1.901 Å) |
Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Grosshans H, Ciosk R |
(2018) "Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition." Nat Commun, 9, 1549. doi: 10.1038/s41467-018-03920-7. |
Crystal structure of danio rerio lin41 filamin-nhl domains in complex with lin-29a 5'utr 13mer RNA. SNAP output |
| 6fql |
RNA binding protein |
X-ray (2.349 Å) |
Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Grosshans H, Ciosk R |
(2018) "Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition." Nat Commun, 9, 1549. doi: 10.1038/s41467-018-03920-7. |
Crystal structure of danio rerio lin41 filamin-nhl domains in complex with mab-10 3'utr 13mer RNA. SNAP output |
| 6fqr |
RNA binding protein |
X-ray (2.1 Å) |
Jia M, Gut H, Chao JA |
(2018) "Structural basis of IMP3 RRM12 recognition of RNA." RNA, 24, 1659-1666. doi: 10.1261/rna.065649.118. |
Crystal structure of imp3 rrm12 in complex with RNA (cccc). SNAP output |
| 6fuw |
RNA binding protein |
cryo-EM (3.07 Å) |
Clerici M, Faini M, Muckenfuss LM, Aebersold R, Jinek M |
(2018) "Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex." Nat. Struct. Mol. Biol., 25, 135-138. doi: 10.1038/s41594-017-0020-6. |
cryo-EM structure of the human cpsf160-wdr33-cpsf30 complex bound to the pas aauaaa motif at 3.1 angstrom resolution. SNAP output |
| 6g18 |
ribosome |
cryo-EM (3.6 Å) |
Ameismeier M, Cheng J, Berninghausen O, Beckmann R |
(2018) "Visualizing late states of human 40S ribosomal subunit maturation." Nature, 558, 249-253. doi: 10.1038/s41586-018-0193-0. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state c. SNAP output |
| 6g19 |
immune system |
cryo-EM (3.68 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament with 74-degree helical twist. SNAP output |
| 6g1s |
immune system |
cryo-EM (3.93 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament with 87-degree helical twist. SNAP output |
| 6g1x |
immune system |
cryo-EM (3.93 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament with 91-degree helical twist. SNAP output |
| 6g2k |
RNA binding protein |
X-ray (2.01 Å) |
Pabis M, Popowicz GM, Stehle R, Fernandez-Ramos D, Asami S, Warner L, Garcia-Maurino SM, Schlundt A, Martinez-Chantar ML, Diaz-Moreno I, Sattler M |
(2019) "HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs." Nucleic Acids Res., 47, 1011-1029. doi: 10.1093/nar/gky1138. |
Structure of hur rrm3 in complex with RNA (uuuuuu). SNAP output |
| 6g5h |
ribosome |
cryo-EM (3.6 Å) |
Ameismeier M, Cheng J, Berninghausen O, Beckmann R |
(2018) "Visualizing late states of human 40S ribosomal subunit maturation." Nature, 558, 249-253. doi: 10.1038/s41586-018-0193-0. |
cryo-EM structure of a late human pre-40s ribosomal subunit - mature. SNAP output |
| 6g5i |
ribosome |
cryo-EM (3.5 Å) |
Ameismeier M, Cheng J, Berninghausen O, Beckmann R |
(2018) "Visualizing late states of human 40S ribosomal subunit maturation." Nature, 558, 249-253. doi: 10.1038/s41586-018-0193-0. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state r. SNAP output |
| 6g63 |
RNA binding protein |
X-ray (3.95 Å) |
Bandyra KJ, Wandzik JM, Luisi BF |
(2018) "Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E." Mol. Cell, 72, 275-285.e4. doi: 10.1016/j.molcel.2018.08.039. |
Rnase e in complex with srna rrpa. SNAP output |
| 6g90 |
splicing |
cryo-EM (4.0 Å) |
Plaschka C, Lin PC, Charenton C, Nagai K |
(2018) "Prespliceosome structure provides insights into spliceosome assembly and regulation." Nature, 559, 419-422. doi: 10.1038/s41586-018-0323-8. |
Prespliceosome structure provides insight into spliceosome assembly and regulation (map a2). SNAP output |
| 6g99 |
RNA binding protein |
NMR |
Loughlin FE, Lukavsky PJ, Kazeeva T, Reber S, Hock EM, Colombo M, Von Schroetter C, Pauli P, Clery A, Muhlemann O, Polymenidou M, Ruepp MD, Allain FH |
(2019) "The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity." Mol. Cell, 73, 490-504.e6. doi: 10.1016/j.molcel.2018.11.012. |
Solution structure of fus-znf bound to uggug. SNAP output |
| 6gbm |
RNA binding protein |
NMR |
Loughlin FE, Lukavsky PJ, Kazeeva T, Reber S, Hock EM, Colombo M, Von Schroetter C, Pauli P, Clery A, Muhlemann O, Polymenidou M, Ruepp MD, Allain FH |
(2019) "The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity." Mol. Cell, 73, 490-504.e6. doi: 10.1016/j.molcel.2018.11.012. |
Solution structure of fus-rrm bound to stem-loop RNA. SNAP output |
| 6gbz |
ribosome |
cryo-EM (3.8 Å) |
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT |
(2018) "Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution." Mol. Cell, 70, 881-893.e3. doi: 10.1016/j.molcel.2018.05.003. |
50s ribosomal subunit assembly intermediate state 5. SNAP output |
| 6gc0 |
ribosome |
cryo-EM (3.8 Å) |
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT |
(2018) "Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution." Mol. Cell, 70, 881-893.e3. doi: 10.1016/j.molcel.2018.05.003. |
50s ribosomal subunit assembly intermediate state 4. SNAP output |
| 6gc4 |
ribosome |
cryo-EM (4.3 Å) |
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT |
(2018) "Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution." Mol. Cell, 70, 881-893.e3. doi: 10.1016/j.molcel.2018.05.003. |
50s ribosomal subunit assembly intermediate state 3. SNAP output |
| 6gc5 |
RNA binding protein |
X-ray (1.9 Å) |
Ripin N, Boudet J, Duszczyk MM, Hinniger A, Faller M, Krepl M, Gadi A, Schneider RJ, Sponer J, Meisner-Kober NC, Allain FH |
(2019) "Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM." Proc. Natl. Acad. Sci. U.S.A., 116, 2935-2944. doi: 10.1073/pnas.1808696116. |
Molecular basis for au-rich element recognition and dimerization by the hur c-terminal rrm. SNAP output |
| 6gc6 |
ribosome |
cryo-EM (4.3 Å) |
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT |
(2018) "Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution." Mol. Cell, 70, 881-893.e3. doi: 10.1016/j.molcel.2018.05.003. |
50s ribosomal subunit assembly intermediate state 2. SNAP output |
| 6gc7 |
ribosome |
cryo-EM (4.3 Å) |
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT |
(2018) "Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution." Mol. Cell, 70, 881-893.e3. doi: 10.1016/j.molcel.2018.05.003. |
50s ribosomal subunit assembly intermediate state 1. SNAP output |
| 6gc8 |
ribosome |
cryo-EM (3.8 Å) |
Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT |
(2018) "Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution." Mol. Cell, 70, 881-893.e3. doi: 10.1016/j.molcel.2018.05.003. |
50s ribosomal subunit assembly intermediate - 50s rec*. SNAP output |
| 6gd2 |
RNA binding protein |
X-ray (1.9 Å) |
Pabis M, Popowicz GM, Stehle R, Fernandez-Ramos D, Asami S, Warner L, Garcia-Maurino SM, Schlundt A, Martinez-Chantar ML, Diaz-Moreno I, Sattler M |
(2019) "HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs." Nucleic Acids Res., 47, 1011-1029. doi: 10.1093/nar/gky1138. |
Structure of hur rrm3 in complex with RNA. SNAP output |
| 6gd3 |
RNA binding protein |
X-ray (1.35 Å) |
Pabis M, Popowicz GM, Stehle R, Fernandez-Ramos D, Asami S, Warner L, Garcia-Maurino SM, Schlundt A, Martinez-Chantar ML, Diaz-Moreno I, Sattler M |
(2019) "HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs." Nucleic Acids Res., 47, 1011-1029. doi: 10.1093/nar/gky1138. |
Structure of hur rrm3 in complex with RNA (uauuua). SNAP output |
| 6gjz |
immune system |
cryo-EM (4.06 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament in complex with amppnp. SNAP output |
| 6gkh |
immune system |
cryo-EM (4.06 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament in complex with adp-alf4. SNAP output |
| 6gkm |
immune system |
cryo-EM (3.87 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament in complex with atp (10 mm). SNAP output |
| 6gpg |
antiviral protein |
X-ray (2.894 Å) |
Lassig C, Lammens K, Gorenflos Lopez JL, Michalski S, Fettscher O, Hopfner KP |
(2018) "Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants." Elife, 7. doi: 10.7554/eLife.38958. |
Structure of the rig-i singleton-merten syndrome variant c268f. SNAP output |
| 6gv4 |
virus |
cryo-EM (2.8 Å) |
Domanska A, Flatt JW, Jukonen JJJ, Geraets JA, Butcher SJ |
(2019) "A 2.8-Angstrom-Resolution Cryo-Electron Microscopy Structure of Human Parechovirus 3 in Complex with Fab from a Neutralizing Antibody." J.Virol., 93. doi: 10.1128/JVI.01597-18. |
High-resolution cryo-EM of fab-labeled human parechovirus 3. SNAP output |
| 6gvy |
viral protein |
X-ray (2.2 Å) |
de la Higuera I, Ferrer-Orta C, Moreno E, de Avila AI, Soria ME, Singh K, Caridi F, Sobrino F, Sarafianos SG, Perales C, Verdaguer N, Domingo E |
(2018) "Contribution of a Multifunctional Polymerase Region of Foot-and-Mouth Disease Virus to Lethal Mutagenesis." J. Virol., 92. doi: 10.1128/JVI.01119-18. |
Mutant m16a of RNA dependent RNA polymerase 3d from foot-and-mouth disease virus complexed with an template -primer RNA. SNAP output |
| 6gx6 |
RNA binding protein |
X-ray (2.0 Å) |
Jia M, Gut H, Chao JA |
(2018) "Structural basis of IMP3 RRM12 recognition of RNA." RNA, 24, 1659-1666. doi: 10.1261/rna.065649.118. |
Crystal structure of imp3 rrm12 in complex with RNA (acac). SNAP output |
| 6h25 |
RNA binding protein |
cryo-EM (3.8 Å) |
Gerlach P, Schuller JM, Bonneau F, Basquin J, Reichelt P, Falk S, Conti E |
(2018) "Distinct and evolutionary conserved structural features of the human nuclear exosome complex." Elife, 7. doi: 10.7554/eLife.38686. |
Human nuclear RNA exosome exo-10-mpp6 complex. SNAP output |
| 6h5q |
viral protein |
cryo-EM (3.3 Å) |
Desfosses A, Milles S, Jensen MR, Guseva S, Colletier JP, Maurin D, Schoehn G, Gutsche I, Ruigrok RWH, Blackledge M |
(2019) "Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication." Proc.Natl.Acad.Sci.USA, 116, 4256-4264. doi: 10.1073/pnas.1816417116. |
cryo-EM structure of in vitro assembled measles virus n into nucleocapsid-like particles (nclps) bound to polya RNA hexamers.. SNAP output |
| 6h5s |
viral protein |
cryo-EM (3.3 Å) |
Desfosses A, Milles S, Jensen MR, Guseva S, Colletier JP, Maurin D, Schoehn G, Gutsche I, Ruigrok RWH, Blackledge M |
(2019) "Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication." Proc.Natl.Acad.Sci.USA, 116, 4256-4264. doi: 10.1073/pnas.1816417116. |
cryo-EM map of in vitro assembled measles virus n into nucleocapsid-like particles (nclps) bound to viral genomic 5-prime RNA hexamers.. SNAP output |
| 6h61 |
immune system |
cryo-EM (4.02 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament with 89 degree twist and without nucleotide. SNAP output |
| 6h66 |
immune system |
cryo-EM (4.16 Å) |
Yu Q, Qu K, Modis Y |
(2018) "Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis." Mol. Cell, 72, 999-1012.e6. doi: 10.1016/j.molcel.2018.10.012. |
Cryoem structure of the mda5-dsrna filament with 93 degree twist and without nucleotide. SNAP output |
| 6h9h |
RNA binding protein |
X-ray (1.75 Å) |
Ozcan A, Pausch P, Linden A, Wulf A, Schuhle K, Heider J, Urlaub H, Heimerl T, Bange G, Randau L |
(2019) "Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum." Nat Microbiol, 4, 89-96. doi: 10.1038/s41564-018-0274-8. |
Csf5, crispr-cas type iv cas6 crrna endonuclease. SNAP output |
| 6h9i |
RNA binding protein |
X-ray (2.29 Å) |
Ozcan A, Pausch P, Linden A, Wulf A, Schuhle K, Heider J, Urlaub H, Heimerl T, Bange G, Randau L |
(2019) "Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum." Nat Microbiol, 4, 89-96. doi: 10.1038/s41564-018-0274-8. |
Csf5, crispr-cas type iv cas6 crrna endonuclease. SNAP output |
| 6hak |
transcription |
X-ray (3.95 Å) |
Das K, Martinez SE, DeStefano JJ, Arnold E |
(2019) "Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation." Proc.Natl.Acad.Sci.USA, 116, 7308-7313. doi: 10.1073/pnas.1814170116. |
Crystal structure of hiv-1 reverse transcriptase (rt) in complex with a double stranded RNA represents the rt transcription initiation complex prior to nucleotide incorporation. SNAP output |
| 6hau |
RNA binding protein |
X-ray (1.86 Å) |
Tunnicliffe RB, Levy C, Ruiz Nivia HD, Sandri-Goldin RM, Golovanov AP |
(2019) "Structural identification of conserved RNA binding sites in herpesvirus ORF57 homologs: implications for PAN RNA recognition." Nucleic Acids Res., 47, 1987-2001. doi: 10.1093/nar/gky1181. |
Kshv pan RNA mta-response element fragment complexed with the globular domain of herpesvirus saimiri orf57. SNAP output |
| 6hct |
RNA |
X-ray (3.091 Å) |
Huang L, Ashraf S, Lilley DMJ |
(2019) "The role of RNA structure in translational regulation by L7Ae protein in archaea." RNA, 25, 60-69. doi: 10.1261/rna.068510.118. |
Crystal structure of archeoglobus fulgidus l7ae bound to its cognate utr k-turn. SNAP output |
| 6hma |
ribosome |
cryo-EM (2.65 Å) |
Eyal Z, Cimicata G |
"Improved model derived from cryo-EM map of Staphylococcus aureus large ribosomal subunit." |
Improved model derived from cryo-EM map of staphylococcus aureus large ribosomal subunit. SNAP output |
| 6hpj |
RNA binding protein |
NMR |
Clery A, Krepl M, Nguyen CKX, Moursy A, Jorjani H, Katsantoni M, Okoniewski M, Mittal N, Zavolan M, Sponer J, Allain FH |
(2021) "Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing." Nat Commun, 12, 428. doi: 10.1038/s41467-020-20481-w. |
Structure of human srsf1 rrm1 bound to aacaaa RNA. SNAP output |
| 6htu |
RNA binding protein |
X-ray (2.888 Å) |
Lazzaretti D, Bandholz-Cajamarca L, Emmerich C, Schaaf K, Basquin C, Irion U, Bono F |
(2018) "The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity." Life Sci Alliance, 1, e201800187. doi: 10.26508/lsa.201800187. |
Structure of hstau1 dsrbd3-4 in complex with arf1 RNA. SNAP output |
| 6i0t |
transferase |
X-ray (2.0 Å) |
Kroupova A, Ivascu A, Reimao-Pinto MM, Ameres SL, Jinek M |
(2019) "Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor." Nucleic Acids Res., 47, 1030-1042. doi: 10.1093/nar/gky1164. |
Crystal structure of dmtailor in complex with gpu. SNAP output |
| 6i0u |
transferase |
X-ray (2.001 Å) |
Kroupova A, Ivascu A, Reimao-Pinto MM, Ameres SL, Jinek M |
(2019) "Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor." Nucleic Acids Res., 47, 1030-1042. doi: 10.1093/nar/gky1164. |
Crystal structure of dmtailor in complex with u6 RNA. SNAP output |
| 6i0v |
transferase |
X-ray (1.851 Å) |
Kroupova A, Ivascu A, Reimao-Pinto MM, Ameres SL, Jinek M |
(2019) "Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor." Nucleic Acids Res., 47, 1030-1042. doi: 10.1093/nar/gky1164. |
Crystal structure of dmtailor in complex with cacagu RNA. SNAP output |
| 6i0y |
ribosome |
cryo-EM (3.2 Å) |
Tian P, Steward A, Kudva R, Su T, Shilling PJ, Nickson AA, Hollins JJ, Beckmann R, von Heijne G, Clarke J, Best RB |
(2018) "Folding pathway of an Ig domain is conserved on and off the ribosome." Proc. Natl. Acad. Sci. U.S.A., 115, E11284-E11293. doi: 10.1073/pnas.1810523115. |
Tnac-stalled ribosome complex with the titin i27 domain folding close to the ribosomal exit tunnel. SNAP output |
| 6i2n |
viral protein |
cryo-EM (3.3 Å) |
Arragain B, Reguera J, Desfosses A, Gutsche I, Schoehn G, Malet H |
(2019) "High resolution cryo-EM structure of the helical RNA-bound Hantaan virus nucleocapsid reveals its assembly mechanisms." Elife, 8. doi: 10.7554/eLife.43075. |
Helical RNA-bound hantaan virus nucleocapsid. SNAP output |
| 6i3p |
hydrolase |
X-ray (2.75 Å) |
Hamann F, Enders M, Ficner R |
(2019) "Structural basis for RNA translocation by DEAH-box ATPases." Nucleic Acids Res., 47, 4349-4362. doi: 10.1093/nar/gkz150. |
Crystal structure of deah-box atpase prp22 with bound ssrna. SNAP output |
| 6icz |
splicing |
cryo-EM (3.0 Å) |
Zhang X, Zhan X, Yan C, Zhang W, Liu D, Lei J, Shi Y |
(2019) "Structures of the human spliceosomes before and after release of the ligated exon." Cell Res., 29, 274-285. doi: 10.1038/s41422-019-0143-x. |
cryo-EM structure of a human post-catalytic spliceosome (p complex) at 3.0 angstrom. SNAP output |
| 6id0 |
splicing |
cryo-EM (2.9 Å) |
Zhang X, Zhan X, Yan C, Zhang W, Liu D, Lei J, Shi Y |
(2019) "Structures of the human spliceosomes before and after release of the ligated exon." Cell Res., 29, 274-285. doi: 10.1038/s41422-019-0143-x. |
cryo-EM structure of a human intron lariat spliceosome prior to prp43 loaded (ils1 complex) at 2.9 angstrom resolution. SNAP output |
| 6id1 |
splicing |
cryo-EM (2.86 Å) |
Zhang X, Zhan X, Yan C, Zhang W, Liu D, Lei J, Shi Y |
(2019) "Structures of the human spliceosomes before and after release of the ligated exon." Cell Res., 29, 274-285. doi: 10.1038/s41422-019-0143-x. |
cryo-EM structure of a human intron lariat spliceosome after prp43 loaded (ils2 complex) at 2.9 angstrom resolution. SNAP output |
| 6ifk |
RNA binding protein |
cryo-EM (3.2 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
cryo-EM structure of type iii-a csm-ctr1 complex, amppnp bound. SNAP output |
| 6ifl |
RNA binding protein |
cryo-EM (3.16 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
cryo-EM structure of type iii-a csm-ntr complex. SNAP output |
| 6ifn |
RNA binding protein |
X-ray (2.9 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
Crystal structure of type iii-a crispr csm complex. SNAP output |
| 6ifo |
RNA binding protein-RNA |
X-ray (3.313 Å) |
Liu L, Yin M, Wang M, Wang Y |
(2019) "Phage AcrIIA2 DNA Mimicry: Structural Basis of the CRISPR and Anti-CRISPR Arms Race." Mol. Cell, 73, 611-620.e3. doi: 10.1016/j.molcel.2018.11.011. |
Crystal structure of acriia2-spycas9-sgrna ternary complex. SNAP output |
| 6ifr |
RNA binding protein |
cryo-EM (3.4 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
Type iii-a csm complex, cryo-EM structure of csm-ntr, atp bound. SNAP output |
| 6ifu |
RNA binding protein |
cryo-EM (3.6 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
cryo-EM structure of type iii-a csm-ctr2-dsDNA complex. SNAP output |
| 6ify |
RNA binding protein |
cryo-EM (3.8 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
Type iii-a csm complex, cryo-EM structure of csm-ctr1. SNAP output |
| 6ifz |
RNA binding protein |
cryo-EM (3.58 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
Type iii-a csm complex, cryo-EM structure of csm-ctr2-ssDNA complex. SNAP output |
| 6ig0 |
RNA binding protein |
cryo-EM (3.37 Å) |
You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y |
(2019) "Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference." Cell, 176, 239-253.e16. doi: 10.1016/j.cell.2018.10.052. |
Type iii-a csm complex, cryo-EM structure of csm-ctr1, atp bound. SNAP output |
| 6ij2 |
hydrolase |
X-ray (1.7 Å) |
Yadav M, Pal K, Sen U |
(2019) "Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication." Biochem.J., 476, 3333-3353. doi: 10.1042/BCJ20190399. |
Crystal structure of a standalone versatile eal protein from vibrio cholerae o395 - 5'-pgpg bound form. SNAP output |
| 6iqw |
RNA binding protein-RNA |
cryo-EM (3.35 Å) |
Huo Y, Li T, Wang N, Dong Q, Wang X, Jiang T |
(2018) "Cryo-EM structure of Type III-A CRISPR effector complex." Cell Res., 28, 1195-1197. doi: 10.1038/s41422-018-0115-6. |
cryo-EM structure of csm effector complex. SNAP output |
| 6is0 |
transferase-RNA |
X-ray (1.8 Å) |
Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, Sugita A, Hirose Y, Iwasaki S, Nureki O, Suzuki T |
(2019) "Cap-specific terminalN6-methylation of RNA by an RNA polymerase II-associated methyltransferase." Science, 363. doi: 10.1126/science.aav0080. |
Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to sah and m7g-capped RNA. SNAP output |
| 6iv6 |
immune system-RNA |
cryo-EM (3.6 Å) |
Dong L, Guan X, Li N, Zhang F, Zhu Y, Ren K, Yu L, Zhou F, Han Z, Gao N, Huang Z |
(2019) "An anti-CRISPR protein disables type V Cas12a by acetylation." Nat. Struct. Mol. Biol., 26, 308-314. doi: 10.1038/s41594-019-0206-1. |
cryo-EM structure of acrva5-acetylated mbcas12a in complex with crrna. SNAP output |
| 6iv8 |
RNA binding protein-RNA |
X-ray (2.15 Å) |
Zhang B, Ye Y, Ye W, Perculija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S |
(2019) "Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d." Nat Commun, 10, 2544. doi: 10.1038/s41467-019-10507-3. |
The selenomethionine(semet)-derived cas13d binary complex. SNAP output |
| 6iv9 |
RNA binding protein-RNA |
X-ray (1.86 Å) |
Zhang B, Ye Y, Ye W, Perculija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S |
(2019) "Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d." Nat Commun, 10, 2544. doi: 10.1038/s41467-019-10507-3. |
The cas13d binary complex. SNAP output |
| 6j6g |
splicing |
cryo-EM (3.2 Å) |
Wan R, Bai R, Yan C, Lei J, Shi Y |
(2019) "Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching." Cell, 177, 339-351.e13. doi: 10.1016/j.cell.2019.02.006. |
cryo-EM structure of the yeast b*-a2 complex at an average resolution of 3.2 angstrom. SNAP output |
| 6j6h |
splicing |
cryo-EM (3.6 Å) |
Wan R, Bai R, Yan C, Lei J, Shi Y |
(2019) "Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching." Cell, 177, 339-351.e13. doi: 10.1016/j.cell.2019.02.006. |
cryo-EM structure of the yeast b*-a1 complex at an average resolution of 3.6 angstrom. SNAP output |
| 6j6n |
splicing |
cryo-EM (3.86 Å) |
Wan R, Bai R, Yan C, Lei J, Shi Y |
(2019) "Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching." Cell, 177, 339-351.e13. doi: 10.1016/j.cell.2019.02.006. |
cryo-EM structure of the yeast b*-b1 complex at an average resolution of 3.86 angstrom. SNAP output |
| 6j6q |
splicing |
cryo-EM (3.7 Å) |
Wan R, Bai R, Yan C, Lei J, Shi Y |
(2019) "Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching." Cell, 177, 339-351.e13. doi: 10.1016/j.cell.2019.02.006. |
cryo-EM structure of the yeast b*-b2 complex at an average resolution of 3.7 angstrom. SNAP output |
| 6j7z |
hydrolase |
X-ray (2.005 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 RNA. SNAP output |
| 6jc3 |
nuclear protein-RNA |
cryo-EM (4.8 Å) |
Song X, Shan H, Zhu Y, Hu S, Xue L, Chen Y, Ding W, Niu T, Gu J, Ouyang S, Shen QT, Liu ZJ |
(2019) "Self-capping of nucleoprotein filaments protects the Newcastle disease virus genome." Elife, 8. doi: 10.7554/eLife.45057. |
The cryo-EM structure of nucleoprotein-RNA complex of newcastle disease virus. SNAP output |
| 6jdq |
hydrolase-RNA |
X-ray (2.95 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. SNAP output |
| 6je9 |
hydrolase-hydrolase inhibitor-RNA |
X-ray (3.46 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 dimer mediated by double protein inhibitor acriic3 monomers. SNAP output |
| 6jim |
viral protein-RNA |
X-ray (2.0 Å) |
Law YS, Utt A, Tan YB, Zheng J, Wang S, Chen MW, Griffin PR, Merits A, Luo D |
(2019) "Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase." Proc.Natl.Acad.Sci.USA, 116, 9558-9567. doi: 10.1073/pnas.1900656116. |
Viral helicase protein. SNAP output |
| 6jvx |
RNA binding protein-RNA |
X-ray (2.301 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 RNA. SNAP output |
| 6k0a |
RNA binding protein-RNA |
cryo-EM (4.6 Å) |
Wan F, Wang Q, Tan J, Tan M, Chen J, Shi S, Lan P, Wu J, Lei M |
(2019) "Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme." Nat Commun, 10, 2617. doi: 10.1038/s41467-019-10496-3. |
cryo-EM structure of an archaeal ribonuclease p. SNAP output |
| 6k0b |
RNA binding protein-RNA |
cryo-EM (4.3 Å) |
Wan F, Wang Q, Tan J, Tan M, Chen J, Shi S, Lan P, Wu J, Lei M |
(2019) "Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme." Nat Commun, 10, 2617. doi: 10.1038/s41467-019-10496-3. |
cryo-EM structure of archaeal ribonuclease p with mature trna. SNAP output |
| 6k32 |
viral protein-RNA |
cryo-EM (3.2 Å) |
Li X, Wang L, Wang X, Chen W, Yang T, Song J, Liu H, Cheng L |
(2020) "Structure of RdRps Within a Transcribing dsRNA Virus Provides Insights Into the Mechanisms of RNA Synthesis." J.Mol.Biol., 432, 358-366. doi: 10.1016/j.jmb.2019.09.015. |
Rdrp complex. SNAP output |
| 6kl9 |
RNA binding protein-RNA |
cryo-EM (3.25 Å) |
Peng R, Li Z, Xu Y, He S, Peng Q, Wu LA, Wu Y, Qi J, Wang P, Shi Y, Gao GF |
(2019) "Structural insight into multistage inhibition of CRISPR-Cas12a by AcrVA4." Proc.Natl.Acad.Sci.USA, 116, 18928-18936. doi: 10.1073/pnas.1909400116. |
Structure of lbcas12a-crrna complex bound to acrva4 (form a complex). SNAP output |
| 6klb |
RNA binding protein-RNA |
cryo-EM (4.1 Å) |
Peng R, Li Z, Xu Y, He S, Peng Q, Wu LA, Wu Y, Qi J, Wang P, Shi Y, Gao GF |
(2019) "Structural insight into multistage inhibition of CRISPR-Cas12a by AcrVA4." Proc.Natl.Acad.Sci.USA, 116, 18928-18936. doi: 10.1073/pnas.1909400116. |
Structure of lbcas12a-crrna complex bound to acrva4 (form b complex). SNAP output |
| 6kle |
viral protein-RNA |
cryo-EM (4.5 Å) |
Peng R, Xu X, Jing J, Wang M, Peng Q, Liu S, Wu Y, Bao X, Wang P, Qi J, Gao GF, Shi Y |
(2020) "Structural insight into arenavirus replication machinery." Nature, 579, 615-619. doi: 10.1038/s41586-020-2114-2. |
Monomeric structure of machupo virus polymerase bound to vrna promoter. SNAP output |
| 6klh |
viral protein-RNA |
cryo-EM (3.7 Å) |
Peng R, Xu X, Jing J, Wang M, Peng Q, Liu S, Wu Y, Bao X, Wang P, Qi J, Gao GF, Shi Y |
(2020) "Structural insight into arenavirus replication machinery." Nature, 579, 615-619. doi: 10.1038/s41586-020-2114-2. |
Dimeric structure of machupo virus polymerase bound to vrna promoter. SNAP output |
| 6kr6 |
RNA binding protein-RNA |
X-ray (2.9 Å) |
Yamaguchi S, Oe A, Nishida KM, Yamashita K, Kajiya A, Hirano S, Matsumoto N, Dohmae N, Ishitani R, Saito K, Siomi H, Nishimasu H, Siomi MC, Nureki O |
(2020) "Crystal structure of Drosophila Piwi." Nat Commun, 11, 858. doi: 10.1038/s41467-020-14687-1. |
Crystal structure of drosophila piwi. SNAP output |
| 6ktc |
RNA binding protein-RNA |
X-ray (2.008 Å) |
Zou F, Tu R, Duan B, Yang Z, Ping Z, Song X, Chen S, Price A, Li H, Scott A, Perera A, Li S, Xie T |
(2020) "DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs." Proc.Natl.Acad.Sci.USA, 117, 3603-3609. doi: 10.1073/pnas.1910862117. |
Crystal structure of ybx1 csd with m5c RNA. SNAP output |
| 6kug |
RNA binding protein-RNA |
X-ray (1.4 Å) |
Zou F, Tu R, Duan B, Yang Z, Ping Z, Song X, Chen S, Price A, Li H, Scott A, Perera A, Li S, Xie T |
(2020) "DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs." Proc.Natl.Acad.Sci.USA, 117, 3603-3609. doi: 10.1073/pnas.1910862117. |
Crystal structure of ybx1 csd with RNA. SNAP output |
| 6kuj |
viral protein-RNA |
cryo-EM (3.4 Å) |
Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y |
(2019) "Structure of influenza D virus polymerase bound to cRNA promoter in Mode A conformation." NAT NANOTECHNOL. doi: 10.1038/s41564-019-0487-5. |
Structure of influenza d virus polymerase bound to crna promoter in class 1. SNAP output |
| 6kuk |
viral protein-RNA |
cryo-EM (3.9 Å) |
Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y |
(2019) "Structural insight into RNA synthesis by influenza D polymerase." Nat Microbiol, 4, 1750-1759. doi: 10.1038/s41564-019-0487-5. |
Structure of influenza d virus polymerase bound to vrna promoter in mode a conformation (class a1). SNAP output |
| 6kup |
viral protein-RNA |
cryo-EM (4.3 Å) |
Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y |
(2019) "Structural insight into RNA synthesis by influenza D polymerase." Nat Microbiol, 4, 1750-1759. doi: 10.1038/s41564-019-0487-5. |
Structure of influenza d virus polymerase bound to vrna promoter in mode a conformation(class a2). SNAP output |
| 6kur |
viral protein-RNA |
cryo-EM (3.7 Å) |
Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y |
(2019) "Structural insight into RNA synthesis by influenza D polymerase." Nat Microbiol, 4, 1750-1759. doi: 10.1038/s41564-019-0487-5. |
Structure of influenza d virus polymerase bound to vrna promoter in mode b conformation (class b1). SNAP output |
| 6kut |
viral protein-RNA |
cryo-EM (4.1 Å) |
Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y |
(2019) "Structural insight into RNA synthesis by influenza D polymerase." Nat Microbiol, 4, 1750-1759. doi: 10.1038/s41564-019-0487-5. |
Structure of influenza d virus polymerase bound to vrna promoter in mode b conformation (class b2). SNAP output |
| 6kuu |
viral protein-RNA |
cryo-EM (4.0 Å) |
Peng Q, Peng R, Qi J, Gao GF, Shi Y |
"Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B3)." |
Structure of influenza d virus polymerase bound to vrna promoter in mode b conformation (class b3). SNAP output |
| 6kuv |
viral protein-RNA |
cryo-EM (4.1 Å) |
Peng Q, Liu Y, Peng R, Wang M, Yang W, Song H, Chen Y, Liu S, Han M, Zhang X, Wang P, Yan J, Zhang B, Qi J, Deng T, Gao GF, Shi Y |
(2019) "Structural insight into RNA synthesis by influenza D polymerase." Nat Microbiol, 4, 1750-1759. doi: 10.1038/s41564-019-0487-5. |
Structure of influenza d virus polymerase bound to crna promoter in class 2. SNAP output |
| 6kwq |
transferase-RNA |
X-ray (1.76 Å) |
Shi W, Ye HQ, Deng CL, Li R, Zhang B, Gong P |
(2020) "A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability." Nucleic Acids Res., 48, 1392-1405. doi: 10.1093/nar/gkz1170. |
Crystal structure of enterovirus 71 polymerase elongation complex (native form). SNAP output |
| 6kwr |
transferase-RNA |
X-ray (2.5 Å) |
Shi W, Ye HQ, Deng CL, Li R, Zhang B, Gong P |
(2020) "A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability." Nucleic Acids Res., 48, 1392-1405. doi: 10.1093/nar/gkz1170. |
Crystal structure of enterovirus 71 polymerase elongation complex (ddctp form). SNAP output |
| 6kyv |
immune system |
X-ray (3.0 Å) |
Kim KH, Hwang J, Kim JH, Son KP, Jang Y, Kim M, Kang SJ, Lee JO, Kang JY, Choi BS |
(2020) "Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs." Rna Biol., 17, 325-334. doi: 10.1080/15476286.2019.1700034. |
Crystal structure of rig-i and hairpin RNA with g-u wobble base pairs. SNAP output |
| 6l1w |
RNA binding protein-RNA |
X-ray (2.194 Å) |
Luo X, Wang X, Gao Y, Zhu J, Liu S, Gao G, Gao P |
(2020) "Molecular Mechanism of RNA Recognition by Zinc-Finger Antiviral Protein." Cell Rep, 30, 46-52.e4. doi: 10.1016/j.celrep.2019.11.116. |
Zinc-finger antiviral protein (zap) bound to RNA. SNAP output |
| 6l5n |
RNA binding protein-RNA |
X-ray (2.242 Å) |
Chen Z, Li Z, Hu X, Xie F, Kuang S, Zhan B, Gao W, Chen X, Gao S, Li Y, Wang Y, Qian F, Ding C, Gan J, Ji C, Xu X, Zhou Z, Huang J, He HH, Li J |
(2020) "Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation." Adv Sci, 7, 2000532. doi: 10.1002/advs.202000532. |
Crystal structure of human dead-box RNA helicase ddx21 at post-unwound state. SNAP output |
| 6las |
RNA |
X-ray (2.708 Å) |
Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A |
(2019) "SAM-VI riboswitch structure and signature for ligand discrimination." Nat Commun, 10, 5728. doi: 10.1038/s41467-019-13600-9. |
The wildtype sam-vi riboswitch bound to sam. SNAP output |
| 6lau |
RNA |
X-ray (3.109 Å) |
Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A |
(2019) "SAM-VI riboswitch structure and signature for ligand discrimination." Nat Commun, 10, 5728. doi: 10.1038/s41467-019-13600-9. |
The wildtype sam-vi riboswitch bound to sah. SNAP output |
| 6lax |
RNA |
X-ray (2.7 Å) |
Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A |
(2019) "SAM-VI riboswitch structure and signature for ligand discrimination." Nat Commun, 10, 5728. doi: 10.1038/s41467-019-13600-9. |
The mutant sam-vi riboswitch (u6c) bound to sam. SNAP output |
| 6laz |
RNA |
X-ray (2.76 Å) |
Sun A, Gasser C, Li F, Chen H, Mair S, Krasheninina O, Micura R, Ren A |
(2019) "SAM-VI riboswitch structure and signature for ligand discrimination." Nat Commun, 10, 5728. doi: 10.1038/s41467-019-13600-9. |
The wildtype sam-vi riboswitch bound to a n-mustard sam analog m1. SNAP output |
| 6llb |
RNA binding protein-RNA |
X-ray (2.6 Å) |
Li J, Hou Y, Gu X, Yue L, Guo L, Li D, Dong X |
(2020) "A newly identified duplex RNA unwinding activity of archaeal RNase J depends on processive exoribonucleolysis coupled steric occlusion by its structural archaeal loops." Rna Biol., 17, 1480-1491. doi: 10.1080/15476286.2020.1777379. |
Crystal structure of mpy-rnase j (mutant s247a), an archaeal rnase j from methanolobus psychrophilus r15, in complex with 6 nt RNA. SNAP output |
| 6lnc |
immune system |
cryo-EM (3.21 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 complex. SNAP output |
| 6lse |
transferase-RNA |
X-ray (2.25 Å) |
Wang M, Li R, Shu B, Jing X, Ye HQ, Gong P |
(2020) "Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures." Nat Commun, 11, 2605. doi: 10.1038/s41467-020-16234-4. |
Crystal structure of the enterovirus 71 polymerase elongation complex (c3s6a-c3s6b form). SNAP output |
| 6lsf |
transferase-DNA |
X-ray (2.152 Å) |
Wang M, Li R, Shu B, Jing X, Ye HQ, Gong P |
(2020) "Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures." Nat Commun, 11, 2605. doi: 10.1038/s41467-020-16234-4. |
Crystal structure of the enterovirus 71 polymerase elongation complex (c2s6ra-c2s6rb form). SNAP output |
| 6lsg |
transferase-RNA |
X-ray (2.14 Å) |
Wang M, Li R, Shu B, Jing X, Ye HQ, Gong P |
(2020) "Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures." Nat Commun, 11, 2605. doi: 10.1038/s41467-020-16234-4. |
Crystal structure of the enterovirus 71 polymerase elongation complex (c0s6m form). SNAP output |
| 6lsh |
transferase-RNA |
X-ray (2.231 Å) |
Wang M, Li R, Shu B, Jing X, Ye HQ, Gong P |
(2020) "Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures." Nat Commun, 11, 2605. doi: 10.1038/s41467-020-16234-4. |
Crystal structure of the enterovirus 71 polymerase elongation complex (c2s6m form). SNAP output |
| 6lt7 |
hydrolase-RNA |
X-ray (2.7 Å) |
Yin C, Bai G, Zhang Y, Huang J |
(2021) "Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP." J.Struct.Biol., 213, 107704. doi: 10.1016/j.jsb.2021.107704. |
Crystal structure of human rpp20-rpp25 proteins in complex with the p3 domain of lncrna rmrp. SNAP output |
| 6ltp |
hydrolase-RNA |
X-ray (3.4 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 binary complex. SNAP output |
| 6lvr |
RNA binding protein |
X-ray (2.85 Å) |
Teramoto T, Kaitany KJ, Kakuta Y, Kimura M, Fierke CA, Hall TMT |
(2020) "Pentatricopeptide repeats of protein-only RNase P use a distinct mode to recognize conserved bases and structural elements of pre-tRNA." Nucleic Acids Res., 48, 11815-11826. doi: 10.1093/nar/gkaa627. |
Crystal structure of the ppr domain of arabidopsis thaliana protein-only rnase p 1 (prorp1) in complex with trna. SNAP output |
| 6lxd |
hydrolase-RNA binding protein-RNA |
cryo-EM (3.9 Å) |
Jin W, Wang J, Liu CP, Wang HW, Xu RM |
(2020) "Structural Basis for pri-miRNA Recognition by Drosha." Mol.Cell, 78, 423. doi: 10.1016/j.molcel.2020.02.024. |
Pri-mirna bound drosha-dgcr8 complex. SNAP output |
| 6m6r |
RNA binding protein-RNA |
X-ray (1.89 Å) |
Li K, Zheng J, Wirawan M, Xiong Z, Fedorova O, Griffin P, Plyle A, Luo D |
"Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain." |
Crystal structure of caenorhabditis elegans dicer-related helicase 3 (drh-3) c-terminal domain with 5'-ppp 8-mer ssrna. SNAP output |
| 6m6s |
RNA binding protein-RNA |
X-ray (1.6 Å) |
Li K, Zheng J, Wirawan M, Xiong Z, Fedorova O, Griffin P, Plyle A, Luo D |
"Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain." |
Crystal structure of caenorhabditis elegans dicer-related helicase 3 (drh-3) c-terminal domain with 5'-ppp 12-mer dsrna. SNAP output |
| 6m6v |
antitoxin |
X-ray (3.08 Å) |
Yao J, Zhen X, Tang K, Liu T, Xu X, Chen Z, Guo Y, Liu X, Wood TK, Ouyang S, Wang X |
(2020) "Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system." Nucleic Acids Res., 48, 11054-11067. doi: 10.1093/nar/gkaa855. |
Crystal structure the toxin-antitoxin mnta-hept. SNAP output |
| 6m7d |
nuclear protein-RNA |
cryo-EM (2.9 Å) |
Shen Q, Shan H, Zhang N |
"structure of the nucleocapsid of sendai virus at 2.9 Angstroms resolution." |
Structure of ncleoprotein of sendai virus. SNAP output |
| 6m7k |
oxidoreductase |
X-ray (1.1 Å) |
Whiteley AT, Eaglesham JB, de Oliveira Mann CC, Morehouse BR, Lowey B, Nieminen EA, Danilchanka O, King DS, Lee ASY, Mekalanos JJ, Kranzusch PJ |
(2019) "Bacterial cGAS-like enzymes synthesize diverse nucleotide signals." Nature, 567, 194-199. doi: 10.1038/s41586-019-0953-5. |
Structure of mouse recon (akr1c13) in complex with cyclic amp-amp-gmp (caag). SNAP output |
| 6mcb |
hydrolase-RNA-viral protein |
cryo-EM (3.4 Å) |
Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA |
(2019) "Temperature-Responsive Competitive Inhibition of CRISPR-Cas9." Mol. Cell, 73, 601. doi: 10.1016/j.molcel.2018.11.016. |
Cryoem structure of acriia2 in complex with crispr-cas9. SNAP output |
| 6mcc |
hydrolase-RNA-viral protein |
cryo-EM (3.9 Å) |
Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA |
(2019) "Temperature-Responsive Competitive Inhibition of CRISPR-Cas9." Mol. Cell, 73, 601. doi: 10.1016/j.molcel.2018.11.016. |
Cryoem structure of acriia2 homolog in complex with crispr-cas9. SNAP output |
| 6mce |
transcription |
NMR |
Pham VV, Salguero C, Khan SN, Meagher JL, Brown WC, Humbert N, de Rocquigny H, Smith JL, D'Souza VM |
(2018) "HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry." Nat Commun, 9, 4266. doi: 10.1038/s41467-018-06591-6. |
Solution structure of hiv-1 tar with tat RNA binding domain. SNAP output |
| 6mcf |
transcription |
NMR |
Pham VV, Salguero C, Khan SN, Meagher JL, Brown WC, Humbert N, de Rocquigny H, Smith JL, D'Souza VM |
(2018) "HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry." Nat Commun, 9, 4266. doi: 10.1038/s41467-018-06591-6. |
Solution structure of 7sk stem-loop 1 with hiv-1 tat RNA binding domain. 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 |
| 6mfn |
hydrolase-RNA |
X-ray (2.5 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. doi: 10.1016/j.molcel.2019.06.019. |
Human argonaute2-mir-27a bound to hsur1 target RNA. 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 |
| 6mkn |
ribosome |
X-ray (3.46 Å) |
Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy IV FV, Ranganathan SV, Sarachan KL, Agris PF |
(2020) "A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine." J.Mol.Biol., 432, 913-929. doi: 10.1016/j.jmb.2019.12.016. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with an inosine (i34) modified anticodon stem loop (asl) of escherichia coli transfer RNA arginine 2 (trnaarg2) bound to an mrna with an cgu-codon in the a-site and paromomycin. SNAP output |
| 6mpf |
ribosome |
X-ray (3.33 Å) |
Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy IV FV, Ranganathan SV, Sarachan KL, Agris PF |
(2020) "A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine." J.Mol.Biol., 432, 913-929. doi: 10.1016/j.jmb.2019.12.016. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a 2-thiocytidine (s2c32) and inosine (i34) modified anticodon stem loop (asl) of escherichia coli transfer RNA arginine 1 (trnaarg1) bound to an mrna with an cgc-codon in the a-site and paromomycin. SNAP output |
| 6mpi |
ribosome |
X-ray (3.33 Å) |
Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy IV FV, Ranganathan SV, Sarachan KL, Agris PF |
(2020) "A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine." J.Mol.Biol., 432, 913-929. doi: 10.1016/j.jmb.2019.12.016. |
Structure of the thermus thermophilus 30s ribosomal subunit complexed with a 2-thiocytidine (s2c32) and inosine (i34) modified anticodon stem loop (asl) of escherichia coli transfer RNA arginine 1 (trnaarg1) bound to an mrna with an cgu-codon in the a-site and paromomycin. SNAP output |
| 6msf |
virus-RNA |
X-ray (2.8 Å) |
Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SE, Stockley PG |
(1998) "Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution." Nat.Struct.Biol., 5, 133-139. doi: 10.1038/nsb0298-133. |
F6 aptamer ms2 coat protein complex. SNAP output |
| 6mur |
RNA binding protein-RNA |
cryo-EM (3.1 Å) |
Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ |
(2019) "Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity." Mol. Cell, 73, 264. doi: 10.1016/j.molcel.2018.11.007. |
cryo-EM structure of csm-crrna-target RNA ternary complex in type iii-a crispr-cas system. SNAP output |
| 6mus |
RNA binding protein-RNA |
cryo-EM (3.6 Å) |
Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ |
(2019) "Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity." Mol. Cell, 73, 264. doi: 10.1016/j.molcel.2018.11.007. |
cryo-EM structure of larger csm-crrna-target RNA ternary complex in type iii-a crispr-cas system. SNAP output |
| 6mut |
RNA binding protein-RNA |
cryo-EM (3.1 Å) |
Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ |
(2019) "Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity." Mol. Cell, 73, 264. doi: 10.1016/j.molcel.2018.11.007. |
cryo-EM structure of ternary csm-crrna-target RNA with anti-tag sequence complex in type iii-a crispr-cas system. SNAP output |
| 6muu |
RNA binding protein-RNA |
cryo-EM (3.0 Å) |
Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ |
(2019) "Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity." Mol. Cell, 73, 264. doi: 10.1016/j.molcel.2018.11.007. |
cryo-EM structure of csm-crrna binary complex in type iii-a crispr-cas system. SNAP output |
| 6mwn |
RNA-immune system |
X-ray (2.838 Å) |
Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA |
(2019) "A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites." Nat Commun, 10, 3629. doi: 10.1038/s41467-019-11585-z. |
Crystal structure of hepatitis a virus ires domain v in complex with fab havx. SNAP output |
| 6n4o |
RNA binding protein-RNA |
X-ray (2.899 Å) |
Sheu-Gruttadauria J, Xiao Y, Gebert LF, MacRae IJ |
(2019) "Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2." Embo J., 38, e101153. doi: 10.15252/embj.2018101153. |
Human argonaute2-mir-122 bound to a seed and supplementary paired target. SNAP output |
| 6n6a |
RNA binding protein-RNA |
X-ray (1.5 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to pgg. SNAP output |
| 6n6c |
RNA binding protein-RNA |
X-ray (1.619 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to paa. SNAP output |
| 6n6d |
RNA binding protein-RNA |
X-ray (1.534 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to pag. SNAP output |
| 6n6e |
RNA binding protein-RNA |
X-ray (1.578 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to pga. SNAP output |
| 6n6f |
RNA binding protein-RNA |
X-ray (1.735 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to pgc. SNAP output |
| 6n6g |
RNA binding protein-RNA |
X-ray (2.018 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to pcg. SNAP output |
| 6n6h |
RNA binding protein-RNA |
X-ray (1.757 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Vibrio cholerae oligoribonuclease bound to pcpu. SNAP output |
| 6n6i |
RNA binding protein-RNA |
X-ray (1.431 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Human rexo2 bound to pgg. SNAP output |
| 6n6j |
RNA binding protein-RNA |
X-ray (1.317 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Human rexo2 bound to paa. SNAP output |
| 6n6k |
RNA binding protein-RNA |
X-ray (1.418 Å) |
Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT |
(2019) "A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation." Elife, 8. doi: 10.7554/eLife.46313. |
Human rexo2 bound to pag. SNAP output |
| 6n7p |
RNA binding protein |
cryo-EM (3.6 Å) |
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R |
(2019) "A unified mechanism for intron and exon definition and back-splicing." Nature, 573, 375-380. doi: 10.1038/s41586-019-1523-6. |
S. cerevisiae spliceosomal e complex (ubc4). SNAP output |
| 6n7r |
RNA binding protein |
cryo-EM (3.2 Å) |
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R |
(2019) "A unified mechanism for intron and exon definition and back-splicing." Nature, 573, 375-380. doi: 10.1038/s41586-019-1523-6. |
Saccharomyces cerevisiae spliceosomal e complex (act1). SNAP output |
| 6n7x |
RNA binding protein-RNA |
cryo-EM (3.6 Å) |
Li X, Liu S, Jiang J, Zhang L, Espinosa S, Hill RC, Hansen KC, Zhou ZH, Zhao R |
(2017) "CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing." Nat Commun, 8, 1035. doi: 10.1038/s41467-017-01241-9. |
S. cerevisiae u1 snrnp. SNAP output |
| 6nd4 |
ribosome |
cryo-EM (4.3 Å) |
Hunziker M, Barandun J, Buzovetsky O, Steckler C, Molina H, Klinge S |
(2019) "Conformational switches control early maturation of the eukaryotic small ribosomal subunit." Elife, 8. doi: 10.7554/eLife.45185. |
Conformational switches control early maturation of the eukaryotic small ribosomal subunit. SNAP output |
| 6neq |
ribosomal protein |
cryo-EM (3.32 Å) |
Koripella RK, Sharma MR, Haque ME, Risteff P, Spremulli LL, Agrawal RK |
(2019) "Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit." iScience, 12, 76-86. doi: 10.1016/j.isci.2018.12.030. |
Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit-class-ii. SNAP output |
| 6nf8 |
ribosomal protein |
cryo-EM (3.48 Å) |
Koripella RK, Sharma MR, Haque ME, Risteff P, Spremulli LL, Agrawal RK |
(2019) "Structure of Human Mitochondrial Translation Initiation Factor 3 Bound to the Small Ribosomal Subunit." iScience, 12, 76-86. doi: 10.1016/j.isci.2018.12.030. |
Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit -class i. 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 |
| 6nm9 |
unknown function-RNA |
cryo-EM (3.38 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 dimer. SNAP output |
| 6nma |
unknown function-RNA |
cryo-EM (3.38 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 complex. SNAP output |
| 6nmc |
unknown function-RNA |
cryo-EM (4.24 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-2xacrva1 complex. SNAP output |
| 6nmd |
unknown function-RNA |
cryo-EM (3.49 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. |
cryo-EM structure of the lbcas12a-crrna-acrva1 complex. SNAP output |
| 6nme |
unknown function-RNA |
cryo-EM (5.67 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. |
Structure of lbcas12a-crrna. SNAP output |
| 6noc |
RNA binding protein-RNA |
X-ray (2.849 Å) |
Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT |
(2019) "Engineering a conserved RNA regulatory protein repurposes its biological functionin vivo." Elife, 8. doi: 10.7554/eLife.43788. |
Crystal structure of fbf-2 repeat 5 mutant (c363a, r364y) in complex with 8-nt RNA. SNAP output |
| 6nod |
RNA binding protein-RNA |
X-ray (2.547 Å) |
Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT |
(2019) "Engineering a conserved RNA regulatory protein repurposes its biological functionin vivo." Elife, 8. doi: 10.7554/eLife.43788. |
Crystal structure of c. elegans puf-8 in complex with RNA. SNAP output |
| 6nof |
RNA binding protein-RNA |
X-ray (2.251 Å) |
Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT |
(2019) "Engineering a conserved RNA regulatory protein repurposes its biological functionin vivo." Elife, 8. doi: 10.7554/eLife.43788. |
Crystal structure of fbf-2 repeat 5 mutant (c363a, r364y, q367s) in complex with 8-nt RNA. SNAP output |
| 6noh |
RNA binding protein-RNA |
X-ray (2.249 Å) |
Bhat VD, McCann KL, Wang Y, Fonseca DR, Shukla T, Alexander JC, Qiu C, Wickens M, Lo TW, Tanaka Hall TM, Campbell ZT |
(2019) "Engineering a conserved RNA regulatory protein repurposes its biological functionin vivo." Elife, 8. doi: 10.7554/eLife.43788. |
Crystal structure of fbf-2 repeat 5 mutant (c363s, r364y, q367s) in complex with 8-nt RNA. SNAP output |
| 6nqb |
ribosome |
cryo-EM (3.8 Å) |
Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Guarne A, Woodson SA, Williamson JR, Ortega J |
(2019) "Role of Era in assembly and homeostasis of the ribosomal small subunit." Nucleic Acids Res., 47, 8301-8317. doi: 10.1093/nar/gkz571. |
Role of era in assembly and homeostasis of the ribosomal small subunit. SNAP output |
| 6nud |
hydrolase,transferase-RNA |
cryo-EM (3.5 Å) |
Guo M, Zhang K, Zhu Y, Pintilie GD, Guan X, Li S, Schmid MF, Ma Z, Chiu W, Huang Z |
(2019) "Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry." Cell Res., 29, 305-312. doi: 10.1038/s41422-019-0151-x. |
Small conformation of ssrna-bound crispr_csm complex. SNAP output |
| 6nue |
hydrolase,transferase-RNA |
cryo-EM (3.3 Å) |
Guo M, Zhang K, Zhu Y, Pintilie GD, Guan X, Li S, Schmid MF, Ma Z, Chiu W, Huang Z |
(2019) "Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry." Cell Res., 29, 305-312. doi: 10.1038/s41422-019-0151-x. |
Small conformation of apo crispr_csm complex. SNAP output |
| 6nut |
viral protein-RNA |
cryo-EM (3.1 Å) |
Kirchdoerfer RN, Saphire EO, Ward AB |
(2019) "Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex." Acta Crystallogr.,Sect.F, 75, 340-347. doi: 10.1107/S2053230X19004424. |
Ebola virus nucleoprotein - RNA complex. SNAP output |
| 6ny5 |
RNA binding protein-RNA |
X-ray (3.002 Å) |
Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TMT |
(2019) "Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity." Nucleic Acids Res., 47, 8770-8784. doi: 10.1093/nar/gkz583. |
Crystal structure of the pum-hd domain of s. pombe puf1 in complex with RNA. SNAP output |
| 6ny6 |
ribosome |
X-ray (3.74 Å) |
Pavelich IJ, Maehigashi T, Hoffer ED, Ruangprasert A, Miles SJ, Dunham CM |
(2019) "Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability." Nucleic Acids Res., 47, 10400-10413. doi: 10.1093/nar/gkz760. |
Structure of dimeric escherichia coli toxin yoeb bound to the thermus thermophilus 30s ribosome. SNAP output |
| 6o16 |
hydrolase-RNA |
X-ray (2.875 Å) |
Boneberg FM, Brandmann T, Kobel L, van den Heuvel J, Bargsten K, Bammert L, Kutay U, Jinek M |
(2019) "Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis." Rna, 25, 685-701. doi: 10.1261/rna.069609.118. |
Crystal structure of murine dhx37 in complex with RNA. SNAP output |
| 6o1k |
RNA binding protein-RNA-hydrolase |
cryo-EM (3.13 Å) |
Pei XY, Dendooven T, Sonnleitner E, Chen S, Blasi U, Luisi BF |
(2019) "Architectural principles for Hfq/Crc-mediated regulation of gene expression." Elife, 8. doi: 10.7554/eLife.43158. |
Architectural principles for hfq-crc-mediated regulation of gene expression. hfq-crc-amie 2:2:2 complex (core complex). SNAP output |
| 6o1l |
RNA binding protein-RNA-hydrolase |
cryo-EM (3.37 Å) |
Pei XY, Dendooven T, Sonnleitner E, Chen S, Blasi U, Luisi BF |
(2019) "Architectural principles for Hfq/Crc-mediated regulation of gene expression." Elife, 8. doi: 10.7554/eLife.43158. |
Architectural principles for hfq-crc-mediated regulation of gene expression hfq-crc-amie 2:3:2 complex. SNAP output |
| 6o1m |
RNA binding protein-RNA-hydrolase |
cryo-EM (3.15 Å) |
Pei XY, Dendooven T, Sonnleitner E, Chen S, Blasi U, Luisi BF |
(2019) "Architectural principles for Hfq/Crc-mediated regulation of gene expression." Elife, 8. doi: 10.7554/eLife.43158. |
Architectural principles for hfq-crc-mediated regulation of gene expression. hfq-crc-amie 2:4:2 complex. SNAP output |
| 6o1o |
RNA binding protein-RNA |
cryo-EM (3.8 Å) |
Liu TY, Liu JJ, Aditham AJ, Nogales E, Doudna JA |
(2019) "Target preference of Type III-A CRISPR-Cas complexes at the transcription bubble." Nat Commun, 10, 3001. doi: 10.1038/s41467-019-10780-2. |
cryo-EM structure of the t. thermophilus csm complex bound to target ssrna. SNAP output |
| 6o5f |
hydrolase-RNA |
X-ray (2.504 Å) |
Song H, Ji X |
(2019) "The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X." Nat Commun, 10, 3085. doi: 10.1038/s41467-019-11083-2. |
Crystal structure of dead-box RNA helicase ddx3x at pre-unwound state. SNAP output |
| 6o6v |
immune system-RNA |
X-ray (2.35 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 ca4 by soaking ca4 into csm6. SNAP output |
| 6o6x |
immune system-RNA |
X-ray (2.11 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 w14a-e337a mutant in complex with ca4 by cocrystallization. SNAP output |
| 6o75 |
immune system-RNA |
X-ray (2.6 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
Crystal structure of csm1-csm4 cassette in complex with pppapa. SNAP output |
| 6o78 |
immune system-RNA |
X-ray (2.8 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
Crystal structure of csm1-csm4 cassette in complex with pppapapa. SNAP output |
| 6o79 |
immune sytem-RNA |
X-ray (3.0 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
Crystal structure of csm1-csm4 cassette in complex with ca3. SNAP output |
| 6o7b |
immune system-RNA |
X-ray (2.4 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
Crystal structure of csm1-csm4 cassette in complex with ca4. SNAP output |
| 6o7e |
immune system-RNA |
cryo-EM (3.2 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
cryo-EM structure of csm-crrna-target RNA ternary complex in complex with amppnp in type iii-a crispr-cas system. SNAP output |
| 6o7h |
immune system-RNA-DNA |
cryo-EM (2.9 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
cryo-EM structure of csm-crrna-target RNA ternary complex in complex with ca4 in type iii-a crispr-cas system. SNAP output |
| 6o7i |
immune system-RNA |
cryo-EM (3.2 Å) |
Jia N, Jones R, Sukenick G, Patel DJ |
(2019) "Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path." Mol.Cell, 75, 933-943.e6. doi: 10.1016/j.molcel.2019.06.013. |
cryo-EM structure of csm-crrna-target RNA ternary bigger complex in complex with ca4 in type iii-a crispr-cas system. SNAP output |
| 6o7k |
ribosome |
cryo-EM (4.2 Å) |
Kaledhonkar S, Fu Z, Caban K, Li W, Chen B, Sun M, Gonzalez Jr RL, Frank J |
(2019) "Late steps in bacterial translation initiation visualized using time-resolved cryo-EM." Nature, 570, 400-404. doi: 10.1038/s41586-019-1249-5. |
30s initiation complex. SNAP output |
| 6ogy |
viral protein-transferase-RNA |
cryo-EM (3.4 Å) |
Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH |
(2019) "In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release." Nat Commun, 10, 2216. doi: 10.1038/s41467-019-10236-7. |
In situ structure of rotavirus RNA-dependent RNA polymerase at duplex-open state. SNAP output |
| 6ogz |
viral protein-RNA-transferase |
cryo-EM (3.6 Å) |
Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH |
(2019) "In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release." Nat Commun, 10, 2216. doi: 10.1038/s41467-019-10236-7. |
In situ structure of rotavirus RNA-dependent RNA polymerase at transcript-elongated state. SNAP output |
| 6okk |
ribosome-inhibitor |
cryo-EM (3.3 Å) |
Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SH |
(2014) "Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine." Elife, 3. doi: 10.7554/eLife.03080. |
cryo-EM structure of the plasmodium falciparum 80s ribosome bound to the anti-protozoan drug emetine, small subunit. SNAP output |
| 6oon |
hydrolase-RNA |
X-ray (1.9 Å) |
Park MS, Araya-Secchi R, Brackbill JA, Phan HD, Kehling AC, Abd El-Wahab EW, Dayeh DM, Sotomayor M, Nakanishi K |
(2019) "Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters." Mol.Cell, 75, 725-740.e6. doi: 10.1016/j.molcel.2019.06.011. |
RNA-binding protein. SNAP output |
| 6ov0 |
immune system-RNA |
X-ray (2.8 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 a4>p by soaking a4>p into csm6. SNAP output |
| 6ozj |
hydrolase |
X-ray (2.247 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine in the absence of divalent cation. SNAP output |
| 6ozk |
hydrolase |
X-ray (2.104 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after 68h soak in ca2+. SNAP output |
| 6ozl |
hydrolase |
X-ray (2.1 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 2 min soak in mn2+. SNAP output |
| 6ozm |
hydrolase-RNA |
X-ray (2.15 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 10 min soak in 10 mm mn2+. SNAP output |
| 6ozn |
hydrolase-RNA |
X-ray (1.9 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mm mn2+. SNAP output |
| 6ozo |
hydrolase-RNA |
X-ray (2.235 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 30 min soak in 10 mm mn2+. SNAP output |
| 6ozp |
hydrolase-RNA |
X-ray (1.96 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mm mn2+. SNAP output |
| 6ozq |
hydrolase |
X-ray (2.153 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 mus musculus (mm) endonuclease v (k155m) in complex with a 23mer RNA oligo containing an inosine after a 100 min soak in 10 mm mn2+ and k+. SNAP output |
| 6ozr |
hydrolase |
X-ray (2.15 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mm mg2+. SNAP output |
| 6ozs |
hydrolase-RNA |
X-ray (2.41 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 mus musculus (mm) endonuclease v in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mm mg2+. SNAP output |
| 6p4g |
ribosome |
cryo-EM (3.1 Å) |
Acosta-Reyes F, Neupane R, Frank J, Fernandez IS |
(2019) "The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs." Embo J., 38, e102226. doi: 10.15252/embj.2019102226. |
Structure of a mammalian small ribosomal subunit in complex with the israeli acute paralysis virus ires (class 1). SNAP output |
| 6p4h |
ribosome |
cryo-EM (3.2 Å) |
Acosta-Reyes F, Neupane R, Frank J, Fernandez IS |
(2019) "The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs." Embo J., 38, e102226. doi: 10.15252/embj.2019102226. |
Structure of a mammalian small ribosomal subunit in complex with the israeli acute paralysis virus ires (class 2). SNAP output |
| 6p7m |
RNA binding protein-RNA |
cryo-EM (3.0 Å) |
Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA |
(2019) "Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a." Elife, 8. doi: 10.7554/eLife.49110. |
cryo-EM structure of lbcas12a-crrna: acrva4 (1:2 complex). SNAP output |
| 6p7n |
RNA binding protein-RNA |
cryo-EM (4.9 Å) |
Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA |
(2019) "Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a." Elife, 8. doi: 10.7554/eLife.49110. |
cryo-EM structure of lbcas12a-crrna: acrva4 (2:2 complex). SNAP output |
| 6p7p |
DNA binding protein |
X-ray (1.665 Å) |
Lau RK, Ye Q, Birkholz EA, Berg KR, Patel L, Mathews IT, Watrous JD, Ego K, Whiteley AT, Lowey B, Mekalanos JJ, Kranzusch PJ, Jain M, Pogliano J, Corbett KD |
(2020) "Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity." Mol.Cell, 77, 723. doi: 10.1016/j.molcel.2019.12.010. |
Structure of e. coli ms115-1 nucc, caaa-bound form. SNAP output |
| 6p7q |
DNA binding protein |
X-ray (1.66 Å) |
Lau RK, Ye Q, Birkholz EA, Berg KR, Patel L, Mathews IT, Watrous JD, Ego K, Whiteley AT, Lowey B, Mekalanos JJ, Kranzusch PJ, Jain M, Pogliano J, Corbett KD |
(2020) "Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity." Mol.Cell, 77, 723. doi: 10.1016/j.molcel.2019.12.010. |
Structure of e. coli ms115-1 nucc, 5'-papa bound form. SNAP output |
| 6pc5 |
ribosome |
cryo-EM (2.7 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compounds 46 and vs1. SNAP output |
| 6pc6 |
ribosome |
cryo-EM (2.5 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 47. SNAP output |
| 6pc7 |
ribosome |
cryo-EM (2.5 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 46. SNAP output |
| 6pc8 |
ribosome |
cryo-EM (2.9 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 40q. SNAP output |
| 6pch |
ribosome |
cryo-EM (2.9 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 21. SNAP output |
| 6pcq |
ribosome |
cryo-EM (2.6 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to vm2. SNAP output |
| 6pcr |
ribosome |
cryo-EM (2.5 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 40o. SNAP output |
| 6pcs |
ribosome |
cryo-EM (2.8 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 40e. SNAP output |
| 6pct |
ribosome |
cryo-EM (2.8 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compound 41q. SNAP output |
| 6pif |
RNA binding protein-RNA |
cryo-EM (3.6 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. |
V. cholerae tniq-cascade complex, open conformation. SNAP output |
| 6pig |
RNA binding protein-RNA |
cryo-EM (3.5 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. |
V. cholerae tniq-cascade complex, closed conformation. SNAP output |
| 6ppf |
ribosome |
cryo-EM (3.4 Å) |
Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA, Ortega J |
(2019) "Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate." Nucleic Acids Res., 47, 10414-10425. doi: 10.1093/nar/gkz770. |
Bacterial 45srbga ribosomal particle class b. SNAP output |
| 6ppk |
ribosome |
cryo-EM (4.4 Å) |
Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA, Ortega J |
(2019) "Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate." Nucleic Acids Res., 47, 10414-10425. doi: 10.1093/nar/gkz770. |
Rbga+45srbga complex. SNAP output |
| 6ppn |
RNA binding protein-RNA |
X-ray (1.91 Å) |
Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE |
(2020) "Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes." Rna, 26, 1400-1413. doi: 10.1261/rna.075879.120. |
Structure of s. pombe lsm2-8 with unprocessed u6 snrna. SNAP output |
| 6ppp |
RNA binding protein-RNA |
X-ray (2.33 Å) |
Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE |
(2020) "Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes." Rna, 26, 1400-1413. doi: 10.1261/rna.075879.120. |
Structure of s. pombe lsm2-8 with processed u6 snrna. SNAP output |
| 6ppq |
RNA binding protein-RNA |
X-ray (1.81 Å) |
Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE |
(2020) "Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes." Rna, 26, 1400-1413. doi: 10.1261/rna.075879.120. |
Structure of s. pombe lsm1-7 with RNA, polyuridine with 3' adenosine. SNAP output |
| 6ppv |
RNA binding protein-RNA |
X-ray (2.05 Å) |
Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE |
(2020) "Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes." Rna, 26, 1400-1413. doi: 10.1261/rna.075879.120. |
Structure of s. pombe lsm1-7 with RNA, polyuridine with 3' guanosine. SNAP output |
| 6pun |
RNA binding protein-RNA |
X-ray (2.099 Å) |
Qiu C, Bhat VD, Rajeev S, Zhang C, Lasley AE, Wine RN, Campbell ZT, Tanaka Hall TMT |
(2019) "A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity." Elife, 8. doi: 10.7554/eLife.48968. |
Crystal structure of a ternary complex of fbf-2 with lst-1 (site b) and compact fbe RNA. SNAP output |
| 6pvk |
ribosome |
cryo-EM (3.4 Å) |
Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA, Ortega J |
(2019) "Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate." Nucleic Acids Res., 47, 10414-10425. doi: 10.1093/nar/gkz770. |
Bacterial 45srbga ribosomal particle class a. SNAP output |
| 6pzq |
metal binding protein-RNA |
X-ray (2.703 Å) |
Gao Y, Cao D, Pawnikar S, John KP, Ahn HM, Hill S, Ha JM, Parikh P, Ogilvie C, Swain A, Yang A, Bell A, Salazar A, Miao Y, Liang B |
(2020) "Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA." Structure, 28, 979. doi: 10.1016/j.str.2020.07.001. |
Structure of the human respiratory syncytial virus m2-1 protein in complex with a short positive-sense gene-end RNA. SNAP output |
| 6q1h |
DNA binding protein-RNA |
X-ray (1.45 Å) |
Lau RK, Ye Q, Birkholz EA, Berg KR, Patel L, Mathews IT, Watrous JD, Ego K, Whiteley AT, Lowey B, Mekalanos JJ, Kranzusch PJ, Jain M, Pogliano J, Corbett KD |
(2020) "Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity." Mol.Cell, 77, 723. doi: 10.1016/j.molcel.2019.12.010. |
Structure of p. aeruginosa atcc27853 nucc, caaa-bound form. SNAP output |
| 6q8u |
RNA |
X-ray (1.99 Å) |
Ashraf S, Huang L, Lilley DMJ |
(2019) "Effect of methylation of adenine N6on kink turn structure depends on location." Rna Biol., 16, 1377-1385. doi: 10.1080/15476286.2019.1630797. |
Structure of the standard kink turn hmkt-7 variant a2bm6a bound with afl7ae protein. SNAP output |
| 6qcs |
viral protein |
cryo-EM (3.1 Å) |
Kouba T, Drncova P, Cusack S |
(2019) "Structural snapshots of actively transcribing influenza polymerase." Nat.Struct.Mol.Biol., 26, 460-470. doi: 10.1038/s41594-019-0232-z. |
Influenza b polymerase pre-initiation complex. SNAP output |
| 6qct |
viral protein |
cryo-EM (3.2 Å) |
Kouba T, Drncova P, Cusack S |
(2019) "Structural snapshots of actively transcribing influenza polymerase." Nat.Struct.Mol.Biol., 26, 460-470. doi: 10.1038/s41594-019-0232-z. |
Influenza b polymerase elongation complex. SNAP output |
| 6qcv |
viral protein |
X-ray (3.24 Å) |
Kouba T, Drncova P, Cusack S |
(2019) "Structural snapshots of actively transcribing influenza polymerase." Nat.Struct.Mol.Biol., 26, 460-470. doi: 10.1038/s41594-019-0232-z. |
Crystal structure of influenza b polymerase initiation state with capped 14-mer RNA primer and ctp. SNAP output |
| 6qcw |
viral protein |
X-ray (2.88 Å) |
Kouba T, Drncova P, Cusack S |
(2019) "Structural snapshots of actively transcribing influenza polymerase." Nat.Struct.Mol.Biol., 26, 460-470. doi: 10.1038/s41594-019-0232-z. |
Crystal structure of influenza b polymerase initiation state with capped 14-mer RNA primer. SNAP output |
| 6qcx |
viral protein |
X-ray (3.08 Å) |
Kouba T, Drncova P, Cusack S |
(2019) "Structural snapshots of actively transcribing influenza polymerase." Nat.Struct.Mol.Biol., 26, 460-470. doi: 10.1038/s41594-019-0232-z. |
Crystal structure of influenza b polymerase initiation state with capped 15-mer RNA primer. SNAP output |
| 6qdw |
ribosome |
cryo-EM (2.83 Å) |
Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H |
(2020) "Cysteine oxidation and disulfide formation in the ribosomal exit tunnel." Nat Commun, 11, 5569. doi: 10.1038/s41467-020-19372-x. |
cryo-EM structure of the 50s ribosomal subunit at 2.83 angstroms with modeled gbc secm peptide. SNAP output |
| 6qic |
hydrolase |
X-ray (2.7 Å) |
Hamann F, Enders M, Ficner R |
(2019) "Structural basis for RNA translocation by DEAH-box ATPases." Nucleic Acids Res., 47, 4349-4362. doi: 10.1093/nar/gkz150. |
Crystal structure of deah-box atpase prp22-s837a with bound ssrna. SNAP output |
| 6qkl |
ribosome |
cryo-EM (3.3 Å) |
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ |
(2015) "Mechanism of eIF6 release from the nascent 60S ribosomal subunit." Nat.Struct.Mol.Biol., 22, 914-919. doi: 10.1038/nsmb.3112. |
Mechanism of eif6 release from the nascent 60s ribosomal subunit. SNAP output |
| 6qul |
antibiotic |
cryo-EM (3.0 Å) |
Scaiola A, Leibundgut M, Boehringer D, Caspers P, Bur D, Locher HH, Rueedi G, Ritz D |
(2019) "Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic." Sci Rep, 9, 5634. doi: 10.1038/s41598-019-42155-4. |
Structure of a bacterial 50s ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid. SNAP output |
| 6qwl |
RNA binding protein |
cryo-EM (4.1 Å) |
Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E |
(2019) "Structures of influenza A virus RNA polymerase offer insight into viral genome replication." Nature, 573, 287-290. doi: 10.1038/s41586-019-1530-7. |
Influenza b virus (b-panama-45) polymerase hetermotrimer in complex with 3'5' crna promoter. SNAP output |
| 6qx3 |
RNA binding protein |
cryo-EM (3.79 Å) |
Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E |
(2019) "Structures of influenza A virus RNA polymerase offer insight into viral genome replication." Nature, 573, 287-290. doi: 10.1038/s41586-019-1530-7. |
Influenza a virus (a-nt-60-1968) polymerase hetermotrimer in complex with 3'5' crna promoter and nb8205. SNAP output |
| 6qx8 |
RNA binding protein |
cryo-EM (4.07 Å) |
Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E |
(2019) "Structures of influenza A virus RNA polymerase offer insight into viral genome replication." Nature, 573, 287-290. doi: 10.1038/s41586-019-1530-7. |
Influenza a virus (a-nt-60-1968) polymerase dimer of heterotrimer in complex with 5' crna promoter. SNAP output |
| 6qxe |
RNA binding protein |
cryo-EM (4.15 Å) |
Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E |
(2019) "Structures of influenza A virus RNA polymerase offer insight into viral genome replication." Nature, 573, 287-290. doi: 10.1038/s41586-019-1530-7. |
Influenza a virus (a-nt-60-1968) polymerase dimer of hetermotrimer in complex with 3'5' crna promoter and nb8205. SNAP output |
| 6r5k |
RNA binding protein |
cryo-EM (4.8 Å) |
Schafer IB, Yamashita M, Schuller JM, Schussler S, Reichelt P, Strauss M, Conti E |
(2019) "Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase." Cell, 177, 1619. doi: 10.1016/j.cell.2019.04.013. |
cryo-EM structure of a poly(a) rnp bound to the pan2-pan3 deadenylase. SNAP output |
| 6r7b |
RNA binding protein |
X-ray (3.12 Å) |
Molina R, Stella S, Feng M, Sofos N, Jauniskis V, Pozdnyakova I, Lopez-Mendez B, She Q, Montoya G |
(2019) "Structure of Csx1-cOA4complex reveals the basis of RNA decay in Type III-B CRISPR-Cas." Nat Commun, 10, 4302. doi: 10.1038/s41467-019-12244-z. |
Crystal structure of csx1 in complex with cyclic oligoadenylate coa4 conformation 1. SNAP output |
| 6r7g |
virus |
cryo-EM (2.2 Å) |
Grinzato A, Kandiah E, Lico C, Betti C, Baschieri S, Zanotti G |
(2020) "Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family." Nat.Chem.Biol., 16, 564-569. doi: 10.1038/s41589-020-0502-4. |
Atomic structure of potato virus x, the prototype of the alphaflexiviridae family. SNAP output |
| 6r9j |
hydrolase |
X-ray (3.326 Å) |
Tang TTL, Stowell JAW, Hill CH, Passmore LA |
(2019) "The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases." Nat.Struct.Mol.Biol., 26, 433-442. doi: 10.1038/s41594-019-0227-9. |
Structure of saccharomyces cerevisiae apo pan2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with a7 RNA. SNAP output |
| 6r9m |
hydrolase |
X-ray (3.329 Å) |
Tang TTL, Stowell JAW, Hill CH, Passmore LA |
(2019) "The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases." Nat.Struct.Mol.Biol., 26, 433-442. doi: 10.1038/s41594-019-0227-9. |
Structure of saccharomyces cerevisiae apo pan2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aaggaa RNA. SNAP output |
| 6r9o |
hydrolase |
X-ray (3.319 Å) |
Tang TTL, Stowell JAW, Hill CH, Passmore LA |
(2019) "The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases." Nat.Struct.Mol.Biol., 26, 433-442. doi: 10.1038/s41594-019-0227-9. |
Structure of saccharomyces cerevisiae apo pan2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aagga RNA. SNAP output |
| 6r9p |
hydrolase |
X-ray (2.98 Å) |
Tang TTL, Stowell JAW, Hill CH, Passmore LA |
(2019) "The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases." Nat.Struct.Mol.Biol., 26, 433-442. doi: 10.1038/s41594-019-0227-9. |
Structure of saccharomyces cerevisiae apo pan2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aauuaa RNA. SNAP output |
| 6r9q |
hydrolase |
X-ray (3.079 Å) |
Tang TTL, Stowell JAW, Hill CH, Passmore LA |
(2019) "The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases." Nat.Struct.Mol.Biol., 26, 433-442. doi: 10.1038/s41594-019-0227-9. |
Structure of saccharomyces cerevisiae apo pan2 pseudoubiquitin hydrolase-RNA exonuclease (uch-exo) module in complex with aaccaa RNA. SNAP output |
| 6r9r |
RNA binding protein |
X-ray (2.7 Å) |
Molina R, Stella S, Feng M, Sofos N, Jauniskis V, Pozdnyakova I, Lopez-Mendez B, She Q, Montoya G |
(2019) "Structure of Csx1-cOA4complex reveals the basis of RNA decay in Type III-B CRISPR-Cas." Nat Commun, 10, 4302. doi: 10.1038/s41467-019-12244-z. |
Crystal structure of csx1 in complex with cyclic oligoadenylate coa4 conformation 2. SNAP output |
| 6ra4 |
RNA binding protein |
X-ray (1.9 Å) |
Greenidge PA, Blommers MJJ, Priestle JP, Hunziker J |
(2019) "How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection." J.Chem.Inf.Model., 59, 1897-1908. doi: 10.1021/acs.jcim.8b00892. |
Human argonaute-2 paz domain (214-347) in complex with cgugacucu. SNAP output |
| 6rbd |
ribosome |
cryo-EM (3.47 Å) |
Mitterer V, Shayan R, Ferreira-Cerca S, Murat G, Enne T, Rinaldi D, Weigl S, Omanic H, Gleizes PE, Kressler D, Plisson-Chastang C, Pertschy B |
(2019) "Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism." Nat Commun, 10, 2754. doi: 10.1038/s41467-019-10678-z. |
State 1 of yeast tsr1-tap rps20-deltaloop pre-40s particles. SNAP output |
| 6rbe |
ribosome |
cryo-EM (3.8 Å) |
Mitterer V, Shayan R, Ferreira-Cerca S, Murat G, Enne T, Rinaldi D, Weigl S, Omanic H, Gleizes PE, Kressler D, Plisson-Chastang C, Pertschy B |
(2019) "Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism." Nat Commun, 10, 2754. doi: 10.1038/s41467-019-10678-z. |
State 2 of yeast tsr1-tap rps20-deltaloop pre-40s particles. SNAP output |
| 6rcl |
hydrolase |
X-ray (1.97 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-aa. SNAP output |
| 6rfl |
viral protein |
cryo-EM (2.76 Å) |
Grimm C, Hillen HS, Bedenk K, Bartuli J, Neyer S, Zhang Q, Huttenhofer A, Erlacher M, Dienemann C, Schlosser A, Urlaub H, Bottcher B, Szalay AA, Cramer P, Fischer U |
(2019) "Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes." Cell, 179, 1537-1550.e19. doi: 10.1016/j.cell.2019.11.024. |
Structure of the complete vaccinia DNA-dependent RNA polymerase complex. SNAP output |
| 6rr7 |
RNA binding protein |
cryo-EM (3.01 Å) |
Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E |
(2019) "Structures of influenza A virus RNA polymerase offer insight into viral genome replication." Nature, 573, 287-290. doi: 10.1038/s41586-019-1530-7. |
Influenza a virus (a-nt-60-1968) polymerase heterotrimer bound to 3'5' vrna promoter and capped RNA primer. 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 |
| 6rti |
hydrolase |
X-ray (2.2 Å) |
Ptacek J, Zhang D, Qiu L, Kruspe S, Motlova L, Kolenko P, Novakova Z, Shubham S, Havlinova B, Baranova P, Chen SJ, Zou X, Giangrande P, Barinka C |
(2020) "Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer." Nucleic Acids Res., 48, 11130-11145. doi: 10.1093/nar/gkaa494. |
X-ray structure of human glutamate carboxypeptidase ii (gcpii) in complex with aptamer a9g. SNAP output |
| 6s0k |
ribosome |
cryo-EM (3.1 Å) |
Wang S, Jomaa A, Jaskolowski M, Yang CI, Ban N, Shan SO |
(2019) "The molecular mechanism of cotranslational membrane protein recognition and targeting by SecA." Nat.Struct.Mol.Biol., 26, 919-929. doi: 10.1038/s41594-019-0297-8. |
Ribosome nascent chain in complex with seca. SNAP output |
| 6s0m |
RNA binding protein |
X-ray (2.0 Å) |
Calvanese L, Squeglia F, Romano M, D'Auria G, Falcigno L, Berisio R |
(2020) "Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence." J.Biomol.Struct.Dyn., 38, 2455-2467. doi: 10.1080/07391102.2019.1643786. |
Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence. SNAP output |
| 6s6b |
antiviral protein |
cryo-EM (2.75 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
Type iii-b cmr-beta cryo-EM structure of the apo state. SNAP output |
| 6s8b |
antiviral protein |
cryo-EM (2.41 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
cryo-EM structure of the type iii-b cmr-beta bound to cognate target RNA and amppnp, state 1. SNAP output |
| 6s8e |
antiviral protein |
cryo-EM (3.1 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
cryo-EM structure of the type iii-b cmr-beta complex bound to non-cognate target RNA. SNAP output |
| 6s91 |
antiviral protein |
cryo-EM (2.68 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
cryo-EM structure of the type iii-b cmr-beta bound to cognate target RNA and amppnp, state 2. SNAP output |
| 6sae |
virus |
cryo-EM (1.9 Å) |
Weis F, Beckers M, von der Hocht I, Sachse C |
(2019) "Elucidation of the viral disassembly switch of tobacco mosaic virus." Embo Rep., 20, e48451. doi: 10.15252/embr.201948451. |
cryo-EM structure of tmv in water. SNAP output |
| 6sag |
virus |
cryo-EM (2.0 Å) |
Weis F, Beckers M, von der Hocht I, Sachse C |
(2019) "Elucidation of the viral disassembly switch of tobacco mosaic virus." Embo Rep., 20, e48451. doi: 10.15252/embr.201948451. |
cryo-EM structure of tmv with ca2+ at low ph. SNAP output |
| 6sce |
DNA |
X-ray (1.83 Å) |
McMahon SA, Zhu W, Graham S, Rambo R, White MF, Gloster TM |
(2020) "Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate." Nat Commun, 11, 500. doi: 10.1038/s41467-019-14222-x. |
Structure of a type iii crispr defence DNA nuclease activated by cyclic oligoadenylate. SNAP output |
| 6scf |
DNA |
X-ray (1.55 Å) |
Athukoralage JS, McMahon SA, Zhang C, Gruschow S, Graham S, Krupovic M, Whitaker RJ, Gloster TM, White MF |
(2020) "An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity." Nature, 577, 572-575. doi: 10.1038/s41586-019-1909-5. |
A viral anti-crispr subverts type iii crispr immunity by rapid degradation of cyclic oligoadenylate. SNAP output |
| 6sdw |
RNA binding protein |
NMR |
Yadav DK, Zigackova D, Zlobina M, Klumpler T, Beaumont C, Kubickova M, Vanacova S, Lukavsky PJ |
(2020) "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition." Nucleic Acids Res., 48, 2091-2106. doi: 10.1093/nar/gkz1163. |
Solution structure of staufen1 dsrbd3+4 - harf1 sbs dsrna complex.. SNAP output |
| 6sdy |
RNA binding protein |
NMR |
Yadav DK, Zigackova D, Zlobina M, Klumpler T, Beaumont C, Kubickova M, Vanacova S, Lukavsky PJ |
(2020) "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition." Nucleic Acids Res., 48, 2091-2106. doi: 10.1093/nar/gkz1163. |
Solution structure of staufen1 dsrbd4 - harf1 sbs dsrna complex.. SNAP output |
| 6sh8 |
antiviral protein |
cryo-EM (3.14 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
cryo-EM structure of the type iii-b cmr-beta bound to cognate target RNA and amppnp, state 2, in the presence of ssDNA. SNAP output |
| 6shb |
antiviral protein |
cryo-EM (3.07 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
cryo-EM structure of the type iii-b cmr-beta bound to cognate target RNA and amppnp, state 1, in the presence of ssDNA. SNAP output |
| 6sic |
antiviral protein |
cryo-EM (3.52 Å) |
Sofos N, Feng M, Stella S, Pape T, Fuglsang A, Lin J, Huang Q, Li Y, She Q, Montoya G |
(2020) "Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas." Mol.Cell, 79, 741-757.e7. doi: 10.1016/j.molcel.2020.07.008. |
cryo-EM structure of the type iii-b cmr-beta bound to cognate target RNA. SNAP output |
| 6sj6 |
ribosome |
cryo-EM (3.23 Å) |
Khusainov I, Fatkhullin B, Pellegrino S, Bikmullin A, Liu WT, Gabdulkhakov A, Shebel AA, Golubev A, Zeyer D, Trachtmann N, Sprenger GA, Validov S, Usachev K, Yusupova G, Yusupov M |
(2020) "Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach." Nat Commun, 11, 1656. doi: 10.1038/s41467-020-15517-0. |
cryo-EM structure of 50s-rsfs complex from staphylococcus aureus. SNAP output |
| 6sjd |
RNA binding protein |
X-ray (3.29 Å) |
Jolma A, Zhang J, Mondragon E, Morgunova E, Kivioja T, Laverty KU, Yin Y, Zhu F, Bourenkov G, Morris Q, Hughes TR, Maher 3rd LJ, Taipale J |
(2020) "Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences." Genome Res., 30, 962-973. doi: 10.1101/gr.258848.119. |
Zc3h12b-ribonuclease domain bound to RNA. SNAP output |
| 6snj |
splicing |
NMR |
Jutzi D, Campagne S, Schmidt R, Reber S, Mechtersheimer J, Gypas F, Schweingruber C, Colombo M, von Schroetter C, Loughlin FE, Devoy A, Hedlund E, Zavolan M, Allain FH, Ruepp MD |
(2020) "Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis." Nat Commun, 11, 6341. doi: 10.1038/s41467-020-20191-3. |
Solution structure of the fus-tls RNA recognition motif in complex with u1 snrna stem loop iii. SNAP output |
| 6so9 |
RNA binding protein |
NMR |
Upadhyay SK, Mackereth CD |
(2020) "Structural basis of UCUU RNA motif recognition by splicing factor RBM20." Nucleic Acids Res., 48, 4538-4550. doi: 10.1093/nar/gkaa168. |
Mouse rbm20 rrm domain in complex with aucuua RNA. SNAP output |
| 6spb |
ribosome |
cryo-EM (2.82 Å) |
Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A |
(2019) "Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate." Proc.Natl.Acad.Sci.USA, 116, 22275-22281. doi: 10.1073/pnas.1909831116. |
Pseudomonas aeruginosa 50s ribosome from a clinical isolate with a mutation in ul6. SNAP output |
| 6spc |
ribosome |
cryo-EM (2.95 Å) |
Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A |
(2019) "Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate." Proc.Natl.Acad.Sci.USA, 116, 22275-22281. doi: 10.1073/pnas.1909831116. |
Pseudomonas aeruginosa 30s ribosome from an aminoglycoside resistant clinical isolate. SNAP output |
| 6spd |
ribosome |
cryo-EM (3.28 Å) |
Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A |
(2019) "Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate." Proc.Natl.Acad.Sci.USA, 116, 22275-22281. doi: 10.1073/pnas.1909831116. |
Pseudomonas aeruginosa 50s ribosome from a clinical isolate. SNAP output |
| 6spe |
ribosome |
cryo-EM (3.6 Å) |
Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A |
(2019) "Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate." Proc.Natl.Acad.Sci.USA, 116, 22275-22281. doi: 10.1073/pnas.1909831116. |
Pseudomonas aeruginosa 30s ribosome from a clinical isolate. SNAP output |
| 6sqn |
RNA binding protein |
X-ray (2.05 Å) |
Rosenbach H, Victor J, Borggrafe J, Biehl R, Steger G, Etzkorn M, Span I |
(2020) "Expanding crystallization tools for nucleic acid complexes using U1A protein variants." J.Struct.Biol., 210, 107480. doi: 10.1016/j.jsb.2020.107480. |
Structure of the u1a variant a1-98 y31h-q36r-f56w triple mutant co-crystallized with RNA. SNAP output |
| 6sty |
RNA binding protein |
X-ray (3.15 Å) |
Szewczyk M, Malik D, Borowski LS, Czarnomska SD, Kotrys AV, Klosowska-Kosicka K, Nowotny M, Szczesny RJ |
(2020) "Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA." Nucleic Acids Res., 48, 5572-5590. doi: 10.1093/nar/gkaa302. |
Human rexo2 exonuclease in complex with RNA.. SNAP output |
| 6sw9 |
ribosome |
cryo-EM (4.2 Å) |
Coureux PD, Lazennec-Schurdevin C, Bourcier S, Mechulam Y, Schmitt E |
(2020) "Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation." Commun Biol, 3, 58. doi: 10.1038/s42003-020-0780-0. |
Ic2a model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi. SNAP output |
| 6swc |
ribosome |
cryo-EM (3.3 Å) |
Coureux PD, Lazennec-Schurdevin C, Bourcier S, Mechulam Y, Schmitt E |
(2020) "Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation." Commun Biol, 3, 58. doi: 10.1038/s42003-020-0780-0. |
Ic2b model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi. SNAP output |
| 6swd |
ribosome |
cryo-EM (3.2 Å) |
Coureux PD, Lazennec-Schurdevin C, Bourcier S, Mechulam Y, Schmitt E |
(2020) "Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation." Commun Biol, 3, 58. doi: 10.1038/s42003-020-0780-0. |
Ic2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi. SNAP output |
| 6swe |
ribosome |
cryo-EM (3.1 Å) |
Coureux PD, Lazennec-Schurdevin C, Bourcier S, Mechulam Y, Schmitt E |
(2020) "Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation." Commun Biol, 3, 58. doi: 10.1038/s42003-020-0780-0. |
Ic2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aif1 in p. abyssi. SNAP output |
| 6sx0 |
viral protein |
X-ray (1.75 Å) |
Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D |
(2020) "Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1." Viruses, 12. doi: 10.3390/v12090947. |
Specific dsrna recognition by wild type h7n1 ns1 RNA-binding domain. SNAP output |
| 6sx2 |
viral protein |
X-ray (1.9 Å) |
Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D |
(2020) "Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1." Viruses, 12. doi: 10.3390/v12090947. |
Dsrna recognition by r38ak41a mutant of h7n1 ns1 RNA binding domain. SNAP output |
| 6sy4 |
DNA binding protein |
X-ray (2.695 Å) |
Grau FC, Jaeger J, Groher F, Suess B, Muller YA |
(2020) "The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex." Nucleic Acids Res., 48, 3366-3378. doi: 10.1093/nar/gkaa083. |
Tetr in complex with the tetr-binding RNA-aptamer k1. SNAP output |
| 6sy6 |
DNA binding protein |
X-ray (2.9 Å) |
Grau FC, Jaeger J, Groher F, Suess B, Muller YA |
(2020) "The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex." Nucleic Acids Res., 48, 3366-3378. doi: 10.1093/nar/gkaa083. |
Tetr in complex with the tetr-binding RNA-aptamer k2. SNAP output |
| 6szu |
viral protein |
cryo-EM (2.41 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase pre-termination complex with pyrophosphate using 44-mer vrna template with mutated oligo(u) sequence. SNAP output |
| 6szv |
viral protein |
cryo-EM (2.5 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase elongation complex with incoming utp analogue (core + endonuclease only). SNAP output |
| 6t0n |
viral protein |
cryo-EM (2.54 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase pre-initiation complex. SNAP output |
| 6t0r |
viral protein |
cryo-EM (2.82 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase product dissociation complex using 44-mer vrna template with mutated oligo(u) sequence. SNAP output |
| 6t0s |
viral protein |
cryo-EM (3.04 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase stuttering complex using 44-mer vrna template with intact oligo(u) sequence. SNAP output |
| 6t0u |
viral protein |
cryo-EM (3.12 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase product dissociation complex using 44-mer vrna template with intact oligo(u) sequence. SNAP output |
| 6t0v |
viral protein |
cryo-EM (3.02 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase elongation complex with incoming utp analogue (complete polymerase). SNAP output |
| 6t0w |
viral protein |
cryo-EM (3.18 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Human influenza b polymerase recycling complex. SNAP output |
| 6t2c |
viral protein |
cryo-EM (3.52 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell, 181, 877. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase recycling complex. SNAP output |
| 6t34 |
virus |
cryo-EM (5.2 Å) |
Cuesta R, Yuste-Calvo C, Gil-Carton D, Sanchez F, Ponz F, Valle M |
(2019) "Structure of Turnip mosaic virus and its viral-like particles." Sci Rep, 9, 15396. doi: 10.1038/s41598-019-51823-4. |
Atomic model for turnip mosaic virus (tumv). SNAP output |
| 6thn |
virus |
cryo-EM (2.6 Å) |
Chandler-Bostock R, Mata CP, Bingham RJ, Dykeman EC, Meng B, Tuthill TJ, Rowlands DJ, Ranson NA, Twarock R, Stockley PG |
(2020) "Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts." Plos Pathog., 16, e1009146. doi: 10.1371/journal.ppat.1009146. |
Multiple genomic RNA-coat protein contacts play vital roles in the assembly of infectious enterovirus-e symmetry expansion+2fold focused classification. SNAP output |
| 6tmf |
ribosome |
cryo-EM (2.8 Å) |
Nurenberg-Goloub E, Kratzat H, Heinemann H, Heuer A, Kotter P, Berninghausen O, Becker T, Tampe R, Beckmann R |
(2020) "Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex." Embo J., 39, e103788. doi: 10.15252/embj.2019103788. |
Structure of an archaeal abce1-bound ribosomal post-splitting complex. SNAP output |
| 6tnn |
ribosomal protein |
cryo-EM (3.07 Å) |
Oerum S, Dendooven T, Catala M, Gilet L, Degut C, Trinquier A, Bourguet M, Barraud P, Cianferani S, Luisi BF, Condon C, Tisne C |
(2020) "Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs." Mol.Cell, 80, 227. doi: 10.1016/j.molcel.2020.09.008. |
Mini-rnase iii (mini-iii) bound to 50s ribosome with precursor 23s rrna. SNAP output |
| 6tph |
RNA |
NMR |
Ahmed M, Marchanka A, Carlomagno T |
(2020) "Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy." Angew.Chem.Int.Ed.Engl., 59, 6866-6873. doi: 10.1002/anie.201915465. |
Structure of a protein-RNA complex by ssnmr. SNAP output |
| 6tpq |
ribosomal protein |
cryo-EM (3.07 Å) |
Oerum S, Dendooven T, Catala M, Gilet L, Degut C, Trinquier A, Bourguet M, Barraud P, Cianferani S, Luisi BF, Condon C, Tisne C |
(2020) "Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs." Mol.Cell, 80, 227. doi: 10.1016/j.molcel.2020.09.008. |
Rnase m5 bound to 50s ribosome with precursor 5s rrna. SNAP output |
| 6tqa |
RNA binding protein |
X-ray (2.4 Å) |
Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A |
(2020) "Structural basis for the recognition of transiently structured AU-rich elements by Roquin." Nucleic Acids Res., 48, 7385-7403. doi: 10.1093/nar/gkaa465. |
X-ray structure of roquin roq domain in complex with a ucp3 cde2 sl RNA motif. SNAP output |
| 6tqb |
RNA binding protein |
X-ray (1.6 Å) |
Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A |
(2020) "Structural basis for the recognition of transiently structured AU-rich elements by Roquin." Nucleic Acids Res., 48, 7385-7403. doi: 10.1093/nar/gkaa465. |
X-ray structure of roquin roq domain in complex with a ucp3 cde1 sl RNA motif. SNAP output |
| 6tw1 |
viral protein |
cryo-EM (2.7 Å) |
Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S |
(2020) "A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase." Cell. doi: 10.1016/j.cell.2020.03.061. |
Bat influenza a polymerase termination complex with pyrophosphate using 44-mer vrna template with mutated oligo(u) sequence. SNAP output |
| 6ty9 |
viral protein, transferase-RNA |
cryo-EM (2.9 Å) |
Cui Y, Zhang Y, Zhou K, Sun J, Zhou ZH |
(2019) "Conservative transcription in three steps visualized in a double-stranded RNA virus." Nat.Struct.Mol.Biol., 26, 1023-1034. doi: 10.1038/s41594-019-0320-0. |
In situ structure of bmcpv RNA dependent RNA polymerase at initiation state. SNAP output |
| 6tz1 |
viral protein, transferase-RNA |
cryo-EM (3.4 Å) |
Cui Y, Zhang Y, Zhou K, Sun J, Zhou ZH |
(2019) "Conservative transcription in three steps visualized in a double-stranded RNA virus." Nat.Struct.Mol.Biol., 26, 1023-1034. doi: 10.1038/s41594-019-0320-0. |
In situ structure of bmcpv RNA-dependent RNA polymerase at early-elongation state. SNAP output |
| 6tz2 |
viral protein, transferase-RNA |
cryo-EM (3.5 Å) |
Cui Y, Zhang Y, Zhou K, Sun J, Zhou ZH |
(2019) "Conservative transcription in three steps visualized in a double-stranded RNA virus." Nat.Struct.Mol.Biol., 26, 1023-1034. doi: 10.1038/s41594-019-0320-0. |
In situ structure of bmcpv RNA-dependent RNA polymerase at elongation state. SNAP output |
| 6u6y |
hydrolase |
X-ray (2.47 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 ribo(cgccu)-oligonucleotide. SNAP output |
| 6u8d |
RNA-immune system |
X-ray (1.807 Å) |
Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA |
(2020) "Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation." Acs Chem.Biol., 15, 205-216. doi: 10.1021/acschembio.9b00785. |
Crystal structure of hepatitis c virus ires junction iiiabc in complex with fab hcv2. SNAP output |
| 6u8k |
RNA-immune system |
X-ray (2.75 Å) |
Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA |
(2020) "Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation." Acs Chem.Biol., 15, 205-216. doi: 10.1021/acschembio.9b00785. |
Crystal structure of hepatitis c virus ires junction iiiabc in complex with fab hcv3. SNAP output |
| 6u9x |
RNA binding protein-RNA |
X-ray (2.6 Å) |
Schumacher MA, Henderson M, Zeng W |
(2020) "Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inTrypanosoma brucei." Rna, 26, 69-82. doi: 10.1261/rna.072231.119. |
Structure of t. brucei mers1-RNA complex. SNAP output |
| 6uej |
antiviral protein |
X-ray (2.21 Å) |
Meagher JL, Takata M, Goncalves-Carneiro D, Keane SC, Rebendenne A, Ong H, Orr VK, MacDonald MR, Stuckey JA, Bieniasz PD, Smith JL |
(2019) "Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences." Proc.Natl.Acad.Sci.USA, 116, 24303-24309. doi: 10.1073/pnas.1913232116. |
Crystal structure of human zinc finger antiviral protein bound to RNA. SNAP output |
| 6uro |
RNA binding protein-RNA |
cryo-EM (3.6 Å) |
Zhang Y, Sun Y, Shi Y, Walz T, Tong L |
(2020) "Structural Insights into the Human Pre-mRNA 3'-End Processing Machinery." Mol.Cell, 77, 800. doi: 10.1016/j.molcel.2019.11.005. |
cryo-EM structure of human cpsf160-wdr33-cpsf30-pas RNA-cstf77 complex. SNAP output |
| 6uv1 |
RNA binding protein-RNA |
X-ray (2.307 Å) |
Ngo TD, Partin AC, Nam Y |
(2019) "RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis." Cell Rep, 29, 4024-4035.e5. doi: 10.1016/j.celrep.2019.11.059. |
Crystal structure of RNA helicase ddx17 in complex of ru10 RNA. SNAP output |
| 6uv2 |
RNA binding protein-RNA |
X-ray (1.894 Å) |
Ngo TD, Partin AC, Nam Y |
(2019) "RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis." Cell Rep, 29, 4024-4035.e5. doi: 10.1016/j.celrep.2019.11.059. |
Crystal structure of the core domain of RNA helicase ddx17 with RNA pri-125a-oligo1. SNAP output |
| 6uv3 |
RNA binding protein-RNA |
X-ray (1.597 Å) |
Ngo TD, Partin AC, Nam Y |
(2019) "RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis." Cell Rep, 29, 4024-4035.e5. doi: 10.1016/j.celrep.2019.11.059. |
Crystal structure of the core domain of RNA helicase ddx17 with RNA pri-125a-oligo2. SNAP output |
| 6uv4 |
RNA binding protein-RNA |
X-ray (1.7 Å) |
Ngo TD, Partin AC, Nam Y |
(2019) "RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis." Cell Rep, 29, 4024-4035.e5. doi: 10.1016/j.celrep.2019.11.059. |
Crystal structure of the core domain of RNA helicase ddx17 with RNA pri-18a-oligo1. 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 |
| 6v4x |
RNA binding protein-RNA |
cryo-EM (3.2 Å) |
Sun Y, Zhang Y, Aik WS, Yang XC, Marzluff WF, Walz T, Dominski Z, Tong L |
(2020) "Structure of an active human histone pre-mRNA 3'-end processing machinery." Science, 367, 700-703. doi: 10.1126/science.aaz7758. |
cryo-EM structure of an active human histone pre-mrna 3'-end processing machinery at 3.2 angstrom resolution. SNAP output |
| 6v5b |
RNA binding protein-RNA |
cryo-EM (3.7 Å) |
Partin AC, Zhang K, Jeong BC, Herrell E, Li S, Chiu W, Nam Y |
(2020) "Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA." Mol.Cell, 78, 411. doi: 10.1016/j.molcel.2020.02.016. |
Human drosha and dgcr8 in complex with primary microrna (mp-RNA complex) - active state. SNAP output |
| 6v5c |
RNA binding protein-RNA |
cryo-EM (4.4 Å) |
Partin AC, Zhang K, Jeong BC, Herrell E, Li S, Chiu W, Nam Y |
(2020) "Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA." Mol.Cell, 78, 411. doi: 10.1016/j.molcel.2020.02.016. |
Human drosha and dgcr8 in complex with primary microrna (mp-RNA complex) - partially docked state. SNAP output |
| 6v9q |
immune system |
cryo-EM (2.9 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 binary complex. SNAP output |
| 6vff |
hydrolase-RNA |
X-ray (2.8 Å) |
Thuy-Boun AS, Thomas JM, Grajo HL, Palumbo CM, Park S, Nguyen LT, Fisher AJ, Beal PA |
(2020) "Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition." Nucleic Acids Res., 48, 7958-7972. doi: 10.1093/nar/gkaa532. |
Dimer of human adenosine deaminase acting on dsrna (adar2) mutant e488q bound to dsrna sequence derived from human gli1 gene. SNAP output |
| 6vm6 |
hydrolase |
X-ray (2.1 Å) |
Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ |
(2020) "CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection." Cell, 182, 38. doi: 10.1016/j.cell.2020.05.019. |
Structure of acinetobacter baumannii cap4 saved-carf-domain containing receptor with the cyclic trinucleotide 2'3'3'-caaa. SNAP output |
| 6vqv |
RNA binding protein-RNA-inhibitor |
cryo-EM (2.57 Å) |
Zhang K, Wang S, Li S, Zhu Y, Pintilie GD, Mou TC, Schmid MF, Huang Z, Chiu W |
(2020) "Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM." Proc.Natl.Acad.Sci.USA, 117, 7176-7182. doi: 10.1073/pnas.1922638117. |
Type i-f crispr-csy complex with its inhibitor acrf9. SNAP output |
| 6vqw |
RNA binding protein-RNA-inhibitor |
cryo-EM (3.42 Å) |
Zhang K, Wang S, Li S, Zhu Y, Pintilie GD, Mou TC, Schmid MF, Huang Z, Chiu W |
(2020) "Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM." Proc.Natl.Acad.Sci.USA, 117, 7176-7182. doi: 10.1073/pnas.1922638117. |
Type i-f crispr-csy complex with its inhibitor acrf8. SNAP output |
| 6vqx |
RNA binding protein-RNA-inhibitor |
cryo-EM (3.15 Å) |
Zhang K, Wang S, Li S, Zhu Y, Pintilie GD, Mou TC, Schmid MF, Huang Z, Chiu W |
(2020) "Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM." Proc.Natl.Acad.Sci.USA, 117, 7176-7182. doi: 10.1073/pnas.1922638117. |
Type i-f crispr-csy complex with its inhibitor acrf6. SNAP output |
| 6vrb |
immune system |
cryo-EM (3.0 Å) |
Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA |
(2020) "A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity." Science, 369, 54-59. doi: 10.1126/science.abb6151. |
cryo-EM structure of acrvia1-cas13(crrna) complex. SNAP output |
| 6vrc |
immune system |
cryo-EM (3.2 Å) |
Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA |
(2020) "A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity." Science, 369, 54-59. doi: 10.1126/science.abb6151. |
cryo-EM structure of cas13(crrna). SNAP output |
| 6w11 |
transcription |
X-ray (2.46 Å) |
Charbonneau AA, Eckert DM, Gauvin CC, Lintner NG, Lawrence CM |
(2021) "Cyclic Tetra-Adenylate (cA 4 ) Recognition by Csa3; Implications for an Integrated Class 1 CRISPR-Cas Immune Response in Saccharolobus solfataricus." Biomolecules, 11. doi: 10.3390/biom11121852. |
The structure of sulfolobus solfataricus csa3 in complex with cyclic tetraadenylate (ca4). SNAP output |
| 6w1x |
immune system-RNA |
cryo-EM (3.9 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-EM structure of anti-crispr acrif9, bound to the type i-f crrna-guided crispr surveillance complex. SNAP output |
| 6w62 |
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 complex. SNAP output |
| 6w6k |
ribosome |
cryo-EM (3.6 Å) |
Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J |
(2020) "Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy." Rna, 26, 2017-2030. doi: 10.1261/rna.075846.120. |
30s-activated-high-mg2+. SNAP output |
| 6w6v |
hydrolase |
cryo-EM (3.0 Å) |
Perederina A, Li D, Lee H, Bator C, Berezin I, Hafenstein SL, Krasilnikov AS |
(2020) "Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP." Nat Commun, 11, 3474. doi: 10.1038/s41467-020-17308-z. |
Structure of yeast rnase mrp holoenzyme. SNAP output |
| 6w77 |
ribosome |
cryo-EM (3.6 Å) |
Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J |
(2020) "Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy." Rna, 26, 2017-2030. doi: 10.1261/rna.075846.120. |
30s-inactivated-high-mg2+ class a. SNAP output |
| 6w7m |
ribosome |
cryo-EM (3.8 Å) |
Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J |
(2020) "Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy." Rna, 26, 2017-2030. doi: 10.1261/rna.075846.120. |
30s-inactive-high-mg2+ + carbon layer. SNAP output |
| 6w7n |
ribosome |
cryo-EM (3.4 Å) |
Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J |
(2020) "Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy." Rna, 26, 2017-2030. doi: 10.1261/rna.075846.120. |
30s-inactive-low-mg2+ class a. SNAP output |
| 6w7w |
ribosome |
cryo-EM (3.9 Å) |
Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, Ortega J |
(2020) "Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy." Rna, 26, 2017-2030. doi: 10.1261/rna.075846.120. |
30s-inactive-low-mg2+ class b. SNAP output |
| 6wan |
hydrolase |
X-ray (2.4 Å) |
Lowey B, Whiteley AT, Keszei AFA, Morehouse BR, Mathews IT, Antine SP, Cabrera VJ, Kashin D, Niemann P, Jain M, Schwede F, Mekalanos JJ, Shao S, Lee ASY, Kranzusch PJ |
(2020) "CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection." Cell, 182, 38. doi: 10.1016/j.cell.2020.05.019. |
Structure of acinetobacter baumannii cap4 saved-carf-domain containing receptor with the cyclic trinucleotide 3'3'3'-caaa. SNAP output |
| 6wdr |
ribosome |
cryo-EM (3.7 Å) |
Rai J, Parker MD, Huang H, Choy S, Ghalei H, Johnson MC, Karbstein K, Stroupe ME |
(2021) "An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7." Rna, 27, 221-233. doi: 10.1261/rna.077610.120. |
Subunit joining exposes nascent pre-40s rrna for processing and quality control. SNAP output |
| 6wlh |
transcription |
NMR |
Nishikawa T, Wojciak JM, Dyson HJ, Wright PE |
(2020) "RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1." Biochemistry, 59, 3889-3901. doi: 10.1021/acs.biochem.0c00602. |
RNA complex of wt1 zinc finger transcription factor. SNAP output |
| 6wnt |
ribosome |
cryo-EM (3.1 Å) |
Huang S, Aleksashin NA, Loveland AB, Klepacki D, Reier K, Kefi A, Szal T, Remme J, Jaeger L, Vazquez-Laslop N, Korostelev AA, Mankin AS |
(2020) "Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly." Nat Commun, 11, 2900. doi: 10.1038/s41467-020-16694-8. |
50s ribosomal subunit without free 5s rrna and perturbed ptc. SNAP output |
| 6wpi |
RNA binding protein-RNA |
X-ray (3.02 Å) |
Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Tanaka Hall TM |
(2020) "Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA." Rna, 26, 1049-1059. doi: 10.1261/rna.075416.120. |
Crystal structure of nop9 in complex with its1 RNA. SNAP output |
| 6wqn |
ribosome |
cryo-EM (2.9 Å) |
Wright A, Deane-Alder K, Marschall E, Bamert R, Venugopal H, Lithgow T, Lupton DW, Belousoff MJ |
(2020) "Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM." Acs Pharmacol Transl Sci, 3, 425-432. doi: 10.1021/acsptsci.0c00041. |
Structure of the 50s subunit of the ribosome from methicillin resistant staphylococcus aureus in complex with the antibiotic, contezolid. SNAP output |
| 6wqq |
ribosome |
cryo-EM (3.1 Å) |
Wright A, Deane-Alder K, Marschall E, Bamert R, Venugopal H, Lithgow T, Lupton DW, Belousoff MJ |
(2020) "Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM." Acs Pharmacol Transl Sci, 3, 425-432. doi: 10.1021/acsptsci.0c00041. |
Structure of the 50s subunit of the ribosome from methicillin resistant staphylococcus aureus in complex with the antibiotic, radezolid. SNAP output |
| 6wre |
hydrolase |
X-ray (2.0 Å) |
Doamekpor SK, Gozdek A, Kwasnik A, Kufel J, Tong L |
(2020) "A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes." Nucleic Acids Res., 48, 349-358. doi: 10.1093/nar/gkz1107. |
Crystal structure of mouse dxo in complex with 5'-oh RNA substrate mimic and calcium ion. SNAP output |
| 6wrs |
ribosome |
cryo-EM (3.2 Å) |
Wright A, Deane-Alder K, Marschall E, Bamert R, Venugopal H, Lithgow T, Lupton DW, Belousoff MJ |
(2020) "Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM." Acs Pharmacol Transl Sci, 3, 425-432. doi: 10.1021/acsptsci.0c00041. |
Structure of the 50s subunit of the ribosome from methicillin resistant staphylococcus aureus in complex with the antibiotic, tedizolid. SNAP output |
| 6wru |
ribosome |
cryo-EM (3.1 Å) |
Wright A, Deane-Alder K, Marschall E, Bamert R, Venugopal H, Lithgow T, Lupton DW, Belousoff MJ |
(2020) "Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM." Acs Pharmacol Transl Sci, 3, 425-432. doi: 10.1021/acsptsci.0c00041. |
Structure of the 50s subunit of the ribosome from methicillin resistant staphylococcus aureus in complex with an isomer of the tedizolid. SNAP output |
| 6wu9 |
ribosome |
cryo-EM (2.9 Å) |
Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G |
(2020) "Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis." Sci Rep, 10, 16301. doi: 10.1038/s41598-020-73199-6. |
50s subunit of 70s ribosome enterococcus faecalis multibody refinement. SNAP output |
| 6wua |
ribosome |
cryo-EM (3.2 Å) |
Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G |
(2020) "Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis." Sci Rep, 10, 16301. doi: 10.1038/s41598-020-73199-6. |
30s subunit (head) of 70s ribosome enterococcus faecalis multibody refinement. SNAP output |
| 6wub |
ribosome |
cryo-EM (3.2 Å) |
Murphy EL, Singh KV, Avila B, Kleffmann T, Gregory ST, Murray BE, Krause KL, Khayat R, Jogl G |
(2020) "Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis." Sci Rep, 10, 16301. doi: 10.1038/s41598-020-73199-6. |
30s subunit (head) of 70s ribosome enterococcus faecalis multibody refinement. SNAP output |
| 6ww6 |
RNA binding protein-RNA |
X-ray (3.8 Å) |
Ataide SF, Walshe JL |
"One by one: Structural characterisation of an RNA bound anti-terminator protein reveals a successive binding mode." |
Crystal structure of eutv bound to RNA. SNAP output |
| 6wxq |
transcription |
X-ray (2.05 Å) |
Xia P, Dutta A, Gupta K, Batish M, Parashar V |
(2022) "Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems." J.Biol.Chem., 298, 101591. doi: 10.1016/j.jbc.2022.101591. |
Crystal structure of crispr-associated transcription factor csa3 complexed with ca4. SNAP output |
| 6wxx |
DNA binding protein-RNA |
X-ray (3.0 Å) |
Rostol JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA |
(2021) "The Card1 nuclease provides defence during type III CRISPR immunity." Nature, 590, 624-629. doi: 10.1038/s41586-021-03206-x. |
Crystal structure of ca4-activated card1. SNAP output |
| 6wxy |
DNA binding protein-RNA |
X-ray (2.1 Å) |
Rostol JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA |
(2021) "The Card1 nuclease provides defence during type III CRISPR immunity." Nature, 590, 624-629. doi: 10.1038/s41586-021-03206-x. |
Crystal structure of ca6-bound card1. SNAP output |
| 6wyv |
ribosome |
cryo-EM (2.75 Å) |
Li Q, Pellegrino J, Lee DJ, Tran AA, Chaires HA, Wang R, Park JE, Ji K, Chow D, Zhang N, Brilot AF, Biel JT, van Zundert G, Borrelli K, Shinabarger D, Wolfe C, Murray B, Jacobson MP, Muhle E, Chesneau O, Fraser JS, Seiple IB |
(2020) "Synthetic group A streptogramin antibiotics that overcome Vat resistance." Nature, 586, 145-150. doi: 10.1038/s41586-020-2761-3. |
E. coli 50s ribosome bound to compounds 47 and vs1. SNAP output |
| 6x1b |
viral protein |
X-ray (1.97 Å) |
Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R, Wilamowski M, Kang S, Nicolaescu V, Randall G, Michalska K, Joachimiak A |
(2021) "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2." Commun Biol, 4, 193. doi: 10.1038/s42003-021-01735-9. |
Crystal structure of nsp15 endoribonuclease from sars cov-2 in the complex with the product nucleotide gpu.. SNAP output |
| 6x5m |
immune system-RNA |
X-ray (2.5 Å) |
Swain M, Ageeli AA, Kasprzak WK, Li M, Miller JT, Sztuba-Solinska J, Schneekloth JS, Koirala D, Piccirili J, Fraboni AJ, Murelli RP, Wlodawer A, Shapiro BA, Baird N, Le Grice SFJ |
(2021) "Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands." Nucleic Acids Res., 49, 13179-13193. doi: 10.1093/nar/gkab1170. |
Crystal structure of a stabilized pan ene bimolecular triplex with a gc-clamped polya tail, in complex with fab-bl-3,6.. SNAP output |
| 6x5n |
immune system-RNA |
X-ray (3.3 Å) |
Swain M, Ageeli AA, Kasprzak WK, Li M, Miller JT, Sztuba-Solinska J, Schneekloth JS, Koirala D, Piccirili J, Fraboni AJ, Murelli RP, Wlodawer A, Shapiro BA, Baird N, Le Grice SFJ |
(2021) "Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands." Nucleic Acids Res., 49, 13179-13193. doi: 10.1093/nar/gkab1170. |
Crystal structure of a stabilized pan ene bimolecular triplex with a gc-clamped polya tail, in complex with fab-bl-3,6. SNAP output |
| 6xe0 |
ribosome |
cryo-EM (6.8 Å) |
Washburn RS, Zuber PK, Sun M, Hashem Y, Shen B, Li W, Harvey S, Acosta Reyes FJ, Gottesman ME, Knauer SH, Frank J |
(2020) "Escherichia coli NusG Links the Lead Ribosome with the Transcription Elongation Complex." Iscience, 23, 101352. doi: 10.1016/j.isci.2020.101352. |
cryo-EM structure of nusg-ctd bound to 70s ribosome (30s: nusg-ctd fragment). SNAP output |
| 6xez |
transferase-hydrolase-RNA |
cryo-EM (3.5 Å) |
Chen J, Malone B, Llewellyn E, Grasso M, Shelton PMM, Olinares PDB, Maruthi K, Eng ET, Vatandaslar H, Chait BT, Kapoor TM, Darst SA, Campbell EA |
(2020) "Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex." Cell, 182, 1560-1573.e13. doi: 10.1016/j.cell.2020.07.033. |
Structure of sars-cov-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-rtc. SNAP output |
| 6xh0 |
RNA binding protein-RNA |
X-ray (3.1 Å) |
Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE |
(2020) "Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors." J.Biol.Chem., 295, 16470-16486. doi: 10.1074/jbc.RA120.015444. |
Co-crystal structure of hiv-1 tar RNA in complex with lab-evolved rrm tbp6.9. SNAP output |
| 6xh1 |
RNA binding protein-RNA |
X-ray (2.601 Å) |
Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE |
(2020) "Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors." J.Biol.Chem., 295, 16470-16486. doi: 10.1074/jbc.RA120.015444. |
Co-crystal structure of hiv-1 tar RNA in complex with lab-evolved rrm tbp6.7 mutant. SNAP output |
| 6xh2 |
RNA binding protein-RNA |
X-ray (1.71 Å) |
Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE |
(2020) "Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors." J.Biol.Chem., 295, 16470-16486. doi: 10.1074/jbc.RA120.015444. |
Co-crystal structure of hiv-1 tar RNA in complex with lab-evolved rrm 6.6. SNAP output |
| 6xh3 |
RNA binding protein-RNA |
X-ray (2.353 Å) |
Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE |
(2020) "Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors." J.Biol.Chem., 295, 16470-16486. doi: 10.1074/jbc.RA120.015444. |
Co-crystal structure of hiv-1 tar RNA in complex with lab-evolved rrm tbp6.3. SNAP output |
| 6xjq |
RNA-immune system |
X-ray (1.708 Å) |
Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA |
(2022) "Structural basis for substrate binding and catalysis by a self-alkylating ribozyme." Nat.Chem.Biol., 18, 376-384. doi: 10.1038/s41589-021-00950-z. |
Crystal structure of a self-alkylating ribozyme - alkylated form with biotinylated epoxide substrate. SNAP output |
| 6xjw |
RNA-immune system |
X-ray (1.918 Å) |
Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA |
(2022) "Structural basis for substrate binding and catalysis by a self-alkylating ribozyme." Nat.Chem.Biol., 18, 376-384. doi: 10.1038/s41589-021-00950-z. |
Crystal structure of a self-alkylating ribozyme - alkylated form without biotin moiety. SNAP output |
| 6xjy |
RNA-immune system |
X-ray (2.156 Å) |
Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA |
(2022) "Structural basis for substrate binding and catalysis by a self-alkylating ribozyme." Nat.Chem.Biol., 18, 376-384. doi: 10.1038/s41589-021-00950-z. |
Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate. SNAP output |
| 6xjz |
RNA-immune system |
X-ray (2.488 Å) |
Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA |
(2022) "Structural basis for substrate binding and catalysis by a self-alkylating ribozyme." Nat.Chem.Biol., 18, 376-384. doi: 10.1038/s41589-021-00950-z. |
Crystal structure of a self-alkylating ribozyme - apo form. SNAP output |
| 6xki |
translation-RNA-inhibitor |
X-ray (2.87 Å) |
Naineni SK, Liang J, Hull K, Cencic R, Zhu M, Northcote P, Teesdale-Spittle P, Romo D, Nagar B, Pelletier J |
(2021) "Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A." Cell Chem Biol, 28, 825. doi: 10.1016/j.chembiol.2020.12.006. |
Crystal structure of eif4a-i in complex with RNA bound to des-mepatea, a pateamine a analog. SNAP output |
| 6xl1 |
DNA binding protein-RNA |
X-ray (1.95 Å) |
Rostol JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA |
(2021) "The Card1 nuclease provides defence during type III CRISPR immunity." Nature, 590, 624-629. doi: 10.1038/s41586-021-03206-x. |
Crystal structure of ca4-activated card1(d294n). SNAP output |
| 6xmf |
hydrolase-RNA |
cryo-EM (3.1 Å) |
Li Z, Zhang H, Xiao R, Han R, Chang L |
(2021) "Cryo-EM structure of the RNA-guided ribonuclease Cas12g." Nat.Chem.Biol., 17, 387-393. doi: 10.1038/s41589-020-00721-2. |
cryo-EM structure of cas12g binary complex. SNAP output |
| 6xmg |
hydrolase-RNA |
cryo-EM (4.8 Å) |
Li Z, Zhang H, Xiao R, Han R, Chang L |
(2021) "Cryo-EM structure of the RNA-guided ribonuclease Cas12g." Nat.Chem.Biol., 17, 387-393. doi: 10.1038/s41589-020-00721-2. |
cryo-EM structure of cas12g ternary complex. SNAP output |
| 6xn3 |
RNA binding protein-RNA |
cryo-EM (3.0 Å) |
Sridhara S, Rai J, Whyms C, Goswami H, He H, Woodside W, Terns MP, Li H |
(2022) "Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex." Commun Biol, 5, 279. doi: 10.1038/s42003-022-03187-1. |
Structure of the lactococcus lactis csm ctr_4:3 crispr-cas complex. SNAP output |
| 6xn4 |
RNA binding protein-RNA |
cryo-EM (3.35 Å) |
Sridhara S, Rai J, Whyms C, Goswami H, He H, Woodside W, Terns MP, Li H |
(2022) "Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex." Commun Biol, 5, 279. doi: 10.1038/s42003-022-03187-1. |
Structure of the lactococcus lactis csm ctr_3:2 crispr-cas complex. SNAP output |
| 6xn5 |
RNA binding protein-RNA |
cryo-EM (2.97 Å) |
Sridhara S, Rai J, Whyms C, Goswami H, He H, Woodside W, Terns MP, Li H |
(2022) "Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex." Commun Biol, 5, 279. doi: 10.1038/s42003-022-03187-1. |
Structure of the lactococcus lactis csm apo- crispr-cas complex. SNAP output |
| 6xn7 |
RNA binding protein-RNA |
cryo-EM (3.47 Å) |
Sridhara S, Rai J, Whyms C, Goswami H, He H, Woodside W, Terns MP, Li H |
(2022) "Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex." Commun Biol, 5, 279. doi: 10.1038/s42003-022-03187-1. |
Structure of the lactococcus lactis csm ntr crispr-cas complex. SNAP output |
| 6xqb |
viral protein, transferase-hydrolase |
cryo-EM (3.4 Å) |
Liu B, Shi W, Yang Y |
"Structure of SARS-CoV-2 RdRp/RNA complex at 3.4 Angstroms resolution." |
Sars-cov-2 rdrp-RNA complex. SNAP output |
| 6xz7 |
ribosome |
cryo-EM (2.1 Å) |
Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL |
(2020) "Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to theE. coli70S ribosome." Rna, 26, 715-723. doi: 10.1261/rna.073817.119. |
E. coli 50s ribosomal subunit in complex with dirithromycin, fmet-phe-trna(phe) and deacylated trna(imet).. SNAP output |
| 6xzq |
viral protein |
cryo-EM (3.6 Å) |
Carrique L, Fan H, Walker AP, Keown JR, Sharps J, Staller E, Barclay WS, Fodor E, Grimes JM |
(2020) "Host ANP32A mediates the assembly of the influenza virus replicase." Nature, 587, 638-643. doi: 10.1038/s41586-020-2927-z. |
Influenza c virus polymerase in complex with human anp32a - subclass 1. SNAP output |
| 6y4b |
RNA binding protein |
X-ray (5.0 Å) |
Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E |
(2020) "Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates." Rna, 26, 1589-1602. doi: 10.1261/rna.075184.120. |
Structure of cyclodipeptide synthase from candidatus glomeribacter gigasporarum bound to phe-trnaphe. SNAP output |
| 6y50 |
splicing |
cryo-EM (4.1 Å) |
Zhang Z, Will CL, Bertram K, Dybkov O, Hartmuth K, Agafonov DE, Hofele R, Urlaub H, Kastner B, Luhrmann R, Stark H |
(2020) "Molecular architecture of the human 17S U2 snRNP." Nature, 583, 310-313. doi: 10.1038/s41586-020-2344-3. |
5'domain of human 17s u2 snrnp. SNAP output |
| 6y53 |
splicing |
cryo-EM (7.1 Å) |
Zhang Z, Will CL, Bertram K, Dybkov O, Hartmuth K, Agafonov DE, Hofele R, Urlaub H, Kastner B, Luhrmann R, Stark H |
(2020) "Molecular architecture of the human 17S U2 snRNP." Nature, 583, 310-313. doi: 10.1038/s41586-020-2344-3. |
Human 17s u2 snrnp low resolution part. SNAP output |
| 6y5q |
splicing |
cryo-EM (7.1 Å) |
Zhang Z, Will CL, Bertram K, Dybkov O, Hartmuth K, Agafonov DE, Hofele R, Urlaub H, Kastner B, Luhrmann R, Stark H |
(2020) "Molecular architecture of the human 17S U2 snRNP." Nature, 583, 310-313. doi: 10.1038/s41586-020-2344-3. |
Human 17s u2 snrnp. SNAP output |
| 6y7c |
ribosome |
cryo-EM (3.8 Å) |
Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssie D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C |
(2020) "Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy." Molecules, 25. doi: 10.3390/molecules25051125. |
Early cytoplasmic yeast pre-40s particle (purified with tsr1 as bait). SNAP output |
| 6yal |
translation |
cryo-EM (3.0 Å) |
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y |
(2020) "Structural Insights into the Mammalian Late-Stage Initiation Complexes." Cell Rep, 31, 107497. doi: 10.1016/j.celrep.2020.03.061. |
Mammalian 48s late-stage initiation complex with beta-globin mrna. SNAP output |
| 6yan |
translation |
cryo-EM (3.48 Å) |
Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y |
(2020) "Structural Insights into the Mammalian Late-Stage Initiation Complexes." Cell Rep, 31, 107497. doi: 10.1016/j.celrep.2020.03.061. |
Mammalian 48s late-stage translation initiation complex with histone 4 mrna. SNAP output |
| 6ybs |
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 - head. SNAP output |
| 6ybv |
translation |
cryo-EM (3.8 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 - eif2-tc. SNAP output |
| 6yhs |
ribosome |
cryo-EM (2.7 Å) |
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA |
(2020) "Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics." Structure, 28, 1087-1100.e3. doi: 10.1016/j.str.2020.08.004. |
Acinetobacter baumannii ribosome-amikacin complex - 50s subunit. SNAP output |
| 6ypu |
ribosome |
cryo-EM (2.9 Å) |
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA |
(2020) "Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics." Structure, 28, 1087-1100.e3. doi: 10.1016/j.str.2020.08.004. |
Acinetobacter baumannii ribosome-amikacin complex - 30s subunit body. 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 |
| 6yrq |
viral protein |
X-ray (1.902 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 4.6. SNAP output |
| 6ys3 |
ribosome |
cryo-EM (2.58 Å) |
Schulte L, Reitz J, Mao J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer J, Blackledge M, Glaubitz C, Frangakis A, Schwalbe H |
(2020) "Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM peptide." Nat Commun. |
cryo-EM structure of the 50s ribosomal subunit at 2.58 angstroms with modeled gbc secm peptide. SNAP output |
| 6ys5 |
ribosome |
cryo-EM (3.0 Å) |
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA |
(2020) "Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics." Structure, 28, 1087-1100.e3. doi: 10.1016/j.str.2020.08.004. |
Acinetobacter baumannii ribosome-amikacin complex - 30s subunit head. SNAP output |
| 6ysi |
ribosome |
cryo-EM (2.5 Å) |
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA |
(2020) "Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics." Structure, 28, 1087-1100.e3. doi: 10.1016/j.str.2020.08.004. |
Acinetobacter baumannii ribosome-tigecycline complex - 50s subunit. SNAP output |
| 6yt9 |
ribosome |
cryo-EM (2.7 Å) |
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA |
(2020) "Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics." Structure, 28, 1087-1100.e3. doi: 10.1016/j.str.2020.08.004. |
Acinetobacter baumannii ribosome-tigecycline complex - 30s subunit body. SNAP output |
| 6ytf |
ribosome |
cryo-EM (3.0 Å) |
Nicholson D, Edwards TA, O'Neill AJ, Ranson NA |
(2020) "Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics." Structure, 28, 1087-1100.e3. doi: 10.1016/j.str.2020.08.004. |
Acinetobacter baumannii ribosome-tigecycline complex - 30s subunit head. SNAP output |
| 6yud |
RNA binding protein |
X-ray (1.84 Å) |
Athukoralage JS, McQuarrie S, Gruschow S, Graham S, Gloster TM, White MF |
(2020) "Tetramerisation of the CRISPR ring nuclease Crn3/Csx3 facilitates cyclic oligoadenylate cleavage." Elife, 9. doi: 10.7554/eLife.57627. |
Structure of csx3-crn3 from archaeoglobus fulgidus in complex with cyclic tetra-adenylate (ca4). SNAP output |
| 6ywo |
RNA binding protein |
X-ray (1.9 Å) |
Malik D, Kobylecki K, Krawczyk P, Poznanski J, Jakielaszek A, Napiorkowska A, Dziembowski A, Tomecki R, Nowotny M |
(2020) "Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine." Nucleic Acids Res., 48, 9387-9405. doi: 10.1093/nar/gkaa647. |
Cuta in complex with a3 RNA. SNAP output |
| 6yym |
RNA binding protein |
X-ray (2.63 Å) |
Andric V, Nevers A, Hazra D, Auxilien S, Menant A, Graille M, Palancade B, Rougemaille M |
(2021) "A scaffold lncRNA shapes the mitosis to meiosis switch." Nat Commun, 12, 770. doi: 10.1038/s41467-021-21032-7. |
Structure of s. pombe mei2 rrm3 domain bound to RNA. SNAP output |
| 6yyt |
viral protein |
cryo-EM (2.9 Å) |
Hillen HS, Kokic G, Farnung L, Dienemann C, Tegunov D, Cramer P |
(2020) "Structure of replicating SARS-CoV-2 polymerase." Nature, 584, 154-156. doi: 10.1038/s41586-020-2368-8. |
Structure of replicating sars-cov-2 polymerase. SNAP output |
| 6z6g |
replication |
cryo-EM (3.06 Å) |
Arragain B, Effantin G, Gerlach P, Reguera J, Schoehn G, Cusack S, Malet H |
(2020) "Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes." Nat Commun, 11, 3590. doi: 10.1038/s41467-020-17349-4. |
cryo-EM structure of la crosse virus polymerase at pre-initiation stage. SNAP output |
| 6z8k |
replication |
cryo-EM (3.02 Å) |
Arragain B, Effantin G, Gerlach P, Reguera J, Schoehn G, Cusack S, Malet H |
(2020) "Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes." Nat Commun, 11, 3590. doi: 10.1038/s41467-020-17349-4. |
La crosse virus polymerase at elongation mimicking stage. SNAP output |
| 6zce |
ribosome |
cryo-EM (5.3 Å) |
Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R |
(2020) "A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes." Embo J., e105179. doi: 10.15252/embj.2020105179. |
Structure of a yeast abce1-bound 43s pre-initiation complex. SNAP output |
| 6zdp |
replication |
X-ray (2.85 Å) |
Zhai LT, Rety S, Chen WF, Song ZY, Auguin D, Sun B, Dou SX, Xi XG |
(2021) "Crystal structures of N-terminally truncated telomerase reverse transcriptase from fungi‡." Nucleic Acids Res., 49, 4768-4781. doi: 10.1093/nar/gkab261. |
Structure of telomerase from candida tropicalis in complexe with twj fragment of telomeric RNA. SNAP output |
| 6zdq |
replication |
X-ray (2.98 Å) |
Zhai LT, Rety S, Chen WF, Song ZY, Auguin D, Sun B, Dou SX, Xi XG |
(2021) "Crystal structures of N-terminally truncated telomerase reverse transcriptase from fungi‡." Nucleic Acids Res., 49, 4768-4781. doi: 10.1093/nar/gkab261. |
Structure of telomerase from candida albicans in complexe with twj fragment of telomeric RNA. SNAP output |
| 6zdu |
replication |
X-ray (3.45 Å) |
Zhai LT, Rety S, Chen WF, Song ZY, Auguin D, Sun B, Dou SX, Xi XG |
(2021) "Crystal structures of N-terminally truncated telomerase reverse transcriptase from fungi‡." Nucleic Acids Res., 49, 4768-4781. doi: 10.1093/nar/gkab261. |
Structure of telomerase from candida albicans in complexe with twj fragment of telomeric RNA. SNAP output |
| 6zlc |
viral protein |
X-ray (2.3 Å) |
Wacquiez A, Coste F, Kut E, Gaudon V, Trapp S, Castaing B, Marc D |
(2020) "Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1." Viruses, 12. doi: 10.3390/v12090947. |
Non-specific dsrna recognition by wildtype h7n1 RNA-binding domain. SNAP output |
| 6zlw |
viral protein |
cryo-EM (2.6 Å) |
Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Straub JH, Sturzel CM, Frohlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R |
(2020) "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2." Science, 369, 1249-1255. doi: 10.1126/science.abc8665. |
Sars-cov-2 nsp1 bound to the human 40s ribosomal subunit. SNAP output |
| 6zm2 |
hydrolase |
X-ray (2.1 Å) |
Hamann F, Zimmerningkat LC, Becker RA, Garbers TB, Neumann P, Hub JS, Ficner R |
(2021) "The structure of Prp2 bound to RNA and ADP-BeF 3 - reveals structural features important for RNA unwinding by DEAH-box ATPases." Acta Crystallogr D Struct Biol, 77, 496-509. doi: 10.1107/S2059798321001194. |
Crystal structure of the deah-box atpase prp2 in complex with adp-bef3 and ssrna. SNAP output |
| 6zmt |
viral protein |
cryo-EM (3.0 Å) |
Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Straub JH, Sturzel CM, Frohlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R |
(2020) "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2." Science, 369, 1249-1255. doi: 10.1126/science.abc8665. |
Sars-cov-2 nsp1 bound to a pre-40s-like ribosome complex. SNAP output |
| 6zn5 |
viral protein |
cryo-EM (3.2 Å) |
Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Straub JH, Sturzel CM, Frohlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R |
(2020) "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2." Science, 369, 1249-1255. doi: 10.1126/science.abc8665. |
Sars-cov-2 nsp1 bound to a pre-40s-like ribosome complex - state 2. SNAP output |
| 6zoj |
translation |
cryo-EM (2.8 Å) |
Schubert K, Karousis ED, Jomaa A, Scaiola A, Echeverria B, Gurzeler LA, Leibundgut M, Thiel V, Muhlemann O, Ban N |
(2020) "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation." Nat.Struct.Mol.Biol., 27, 959-966. doi: 10.1038/s41594-020-0511-8. |
Sars-cov-2-nsp1-40s complex, composite map. SNAP output |
| 6zok |
translation |
cryo-EM (2.8 Å) |
Schubert K, Karousis ED, Jomaa A, Scaiola A, Echeverria B, Gurzeler LA, Leibundgut M, Thiel V, Muhlemann O, Ban N |
(2020) "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation." Nat.Struct.Mol.Biol., 27, 959-966. doi: 10.1038/s41594-020-0511-8. |
Sars-cov-2-nsp1-40s complex, focused on body. SNAP output |
| 6zol |
translation |
cryo-EM (2.8 Å) |
Schubert K, Karousis ED, Jomaa A, Scaiola A, Echeverria B, Gurzeler LA, Leibundgut M, Thiel V, Muhlemann O, Ban N |
(2020) "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation." Nat.Struct.Mol.Biol., 27, 959-966. doi: 10.1038/s41594-020-0511-8. |
Sars-cov-2-nsp1-40s complex, focused on head. SNAP output |
| 6zot |
RNA binding protein |
X-ray (2.7 Å) |
Li Y, Bedi RK, Moroz-Omori EV, Caflisch A |
(2020) "Structural and Dynamic Insights into Redundant Function of YTHDF Proteins." J.Chem.Inf.Model., 60, 5932-5935. doi: 10.1021/acs.jcim.0c01029. |
Crystal structure of ythdf3 yth domain in complex with m6a RNA. SNAP output |
| 6zu9 |
ribosome |
cryo-EM (6.2 Å) |
Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R |
(2020) "A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes." Embo J., e105179. doi: 10.15252/embj.2020105179. |
Structure of a yeast abce1-bound 48s initiation complex. SNAP output |
| 6zuo |
ribosome |
cryo-EM (3.1 Å) |
Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C |
(2021) "The final step of 40S ribosomal subunit maturation is controlled by a dual key lock." Elife, 10. doi: 10.7554/eLife.61254. |
Human rio1(kd)-stha late pre-40s particle, structural state a (pre 18s rrna cleavage). SNAP output |
| 6zv6 |
ribosome |
cryo-EM (2.9 Å) |
Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C |
(2021) "The final step of 40S ribosomal subunit maturation is controlled by a dual key lock." Elife, 10. doi: 10.7554/eLife.61254. |
Human rio1(kd)-stha late pre-40s particle, structural state b (post 18s rrna cleavage). SNAP output |
| 6zvi |
ribosome |
cryo-EM (3.0 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. |
Mbf1-ribosome complex. SNAP output |
| 6zww |
RNA binding protein |
X-ray (3.16 Å) |
Grass LM, Wollenhaupt J, Barthel T, Parfentev I, Urlaub H, Loll B, Klauck E, Antelmann H, Wahl MC |
(2021) "Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2100370118. |
Crystal structure of e. coli RNA helicase hrpa in complex with RNA. SNAP output |
| 6zxd |
ribosome |
cryo-EM (3.2 Å) |
Ameismeier M, Zemp I, van den Heuvel J, Thoms M, Berninghausen O, Kutay U, Beckmann R |
(2020) "Structural basis for the final steps of human 40S ribosome maturation." Nature, 587, 683-687. doi: 10.1038/s41586-020-2929-x. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state f1. SNAP output |
| 6zxe |
ribosome |
cryo-EM (3.0 Å) |
Ameismeier M, Zemp I, van den Heuvel J, Thoms M, Berninghausen O, Kutay U, Beckmann R |
(2020) "Structural basis for the final steps of human 40S ribosome maturation." Nature, 587, 683-687. doi: 10.1038/s41586-020-2929-x. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state f2. SNAP output |
| 6zxf |
ribosome |
cryo-EM (3.7 Å) |
Ameismeier M, Zemp I, van den Heuvel J, Thoms M, Berninghausen O, Kutay U, Beckmann R |
(2020) "Structural basis for the final steps of human 40S ribosome maturation." Nature, 587, 683-687. doi: 10.1038/s41586-020-2929-x. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state g. SNAP output |
| 6zxg |
ribosome |
cryo-EM (2.6 Å) |
Ameismeier M, Zemp I, van den Heuvel J, Thoms M, Berninghausen O, Kutay U, Beckmann R |
(2020) "Structural basis for the final steps of human 40S ribosome maturation." Nature, 587, 683-687. doi: 10.1038/s41586-020-2929-x. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state h1. SNAP output |
| 6zxh |
ribosome |
cryo-EM (2.7 Å) |
Ameismeier M, Zemp I, van den Heuvel J, Thoms M, Berninghausen O, Kutay U, Beckmann R |
(2020) "Structural basis for the final steps of human 40S ribosome maturation." Nature, 587, 683-687. doi: 10.1038/s41586-020-2929-x. |
cryo-EM structure of a late human pre-40s ribosomal subunit - state h2. SNAP output |
| 6zym |
splicing |
cryo-EM (3.4 Å) |
Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R |
(2020) "Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome." Mol.Cell, 80, 127-139.e6. doi: 10.1016/j.molcel.2020.09.012. |
Human c complex spliceosome - high-resolution core. SNAP output |
| 7a0r |
antibiotic |
X-ray (3.3 Å) |
Breiner-Goldstein E, Eyal Z, Matzov D, Halfon Y, Cimicata G, Baum M, Rokney A, Ezernitchi AV, Lowell AN, Schmidt JJ, Rozenberg H, Zimmerman E, Bashan A, Valinsky L, Anzai Y, Sherman DH, Yonath A |
(2021) "Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida." Nucleic Acids Res., 49, 9560-9573. doi: 10.1093/nar/gkab684. |
50s deinococcus radiodurans ribosome bounded with mycinamicin i. SNAP output |
| 7a0s |
antibiotic |
X-ray (3.22 Å) |
Breiner-Goldstein E, Eyal Z, Matzov D, Halfon Y, Cimicata G, Baum M, Rokney A, Ezernitchi AV, Lowell AN, Schmidt JJ, Rozenberg H, Zimmerman E, Bashan A, Valinsky L, Anzai Y, Sherman DH, Yonath A |
(2021) "Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida." Nucleic Acids Res., 49, 9560-9573. doi: 10.1093/nar/gkab684. |
50s deinococcus radiodurans ribosome bounded with mycinamicin i. SNAP output |
| 7a18 |
antibiotic |
X-ray (3.4 Å) |
Breiner-Goldstein E, Eyal Z, Matzov D, Halfon Y, Cimicata G, Baum M, Rokney A, Ezernitchi AV, Lowell AN, Schmidt JJ, Rozenberg H, Zimmerman E, Bashan A, Valinsky L, Anzai Y, Sherman DH, Yonath A |
(2021) "Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida." Nucleic Acids Res., 49, 9560-9573. doi: 10.1093/nar/gkab684. |
50s deinococcus radiodurans ribosome bounded with mycinamicin iv. SNAP output |
| 7a1g |
ribosome |
cryo-EM (3.0 Å) |
Kratzat H, Mackens-Kiani T, Ameismeier M, Potocnjak M, Cheng J, Dacheux E, Namane A, Berninghausen O, Herzog F, Fromont-Racine M, Becker T, Beckmann R |
(2020) "A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes." Embo J., e105179. doi: 10.15252/embj.2020105179. |
Structure of a crosslinked yeast abce1-bound 43s pre-initiation complex. SNAP output |
| 7a5p |
splicing |
cryo-EM (5.0 Å) |
Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R |
(2020) "Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome." Mol.Cell, 80, 127-139.e6. doi: 10.1016/j.molcel.2020.09.012. |
Human c complex spliceosome - medium-resolution periphery. SNAP output |
| 7a9w |
RNA binding protein |
X-ray (2.55 Å) |
Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M |
(2021) "The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2009329118. |
Structure of yeast rmd9p in complex with 20nt target RNA. SNAP output |
| 7a9x |
RNA binding protein |
X-ray (2.45 Å) |
Hillen HS, Markov DA, Wojtas ID, Hofmann KB, Lidschreiber M, Cowan AT, Jones JL, Temiakov D, Cramer P, Anikin M |
(2021) "The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2009329118. |
Structure of yeast rmd9p in complex with 16nt target RNA. SNAP output |
| 7aap |
viral protein |
cryo-EM (2.5 Å) |
Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Lowe J, Barford D, Russo CJ |
(2021) "Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2021946118. |
Nsp7-nsp8-nsp12 sars-cov2 RNA-dependent RNA polymerase in complex with template:primer dsrna and favipiravir-rtp. SNAP output |
| 7aav |
splicing |
cryo-EM (4.2 Å) |
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R |
(2020) "Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation." Science, 370. doi: 10.1126/science.abc3753. |
Human pre-bact-2 spliceosome core structure. SNAP output |
| 7abh |
splicing |
cryo-EM (4.5 Å) |
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R |
(2020) "Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation." Science, 370. doi: 10.1126/science.abc3753. |
Human pre-bact-2 spliceosome (sf3b-u2 snrnp portion). SNAP output |
| 7abi |
splicing |
cryo-EM (8.0 Å) |
Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Luhrmann R |
(2020) "Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation." Science, 370. doi: 10.1126/science.abc3753. |
Human pre-bact-2 spliceosome. SNAP output |
| 7acs |
viral protein |
NMR |
Dinesh DC, Chalupska D, Silhan J, Koutna E, Nencka R, Veverka V, Boura E |
(2020) "Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein." Plos Pathog., 16, e1009100. doi: 10.1371/journal.ppat.1009100. |
The sars-cov-2 nucleocapsid phosphoprotein n-terminal domain in complex with 7mer dsrna. SNAP output |
| 7act |
viral protein |
NMR |
Dinesh DC, Chalupska D, Silhan J, Koutna E, Nencka R, Veverka V, Boura E |
(2020) "Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein." Plos Pathog., 16, e1009100. doi: 10.1371/journal.ppat.1009100. |
The sars-cov-2 nucleocapsid phosphoprotein n-terminal domain in complex with 10mer ssrna. SNAP output |
| 7af3 |
ribosome |
cryo-EM (2.82 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state m (head domain). SNAP output |
| 7af5 |
ribosome |
cryo-EM (2.96 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state i (head domain). SNAP output |
| 7af8 |
ribosome |
cryo-EM (2.75 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state e (head domain). SNAP output |
| 7afa |
ribosome |
cryo-EM (2.95 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state f (head domain). SNAP output |
| 7afd |
ribosome |
cryo-EM (3.44 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state a (head domain). SNAP output |
| 7afh |
ribosome |
cryo-EM (3.59 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state c (head domain). SNAP output |
| 7afi |
ribosome |
cryo-EM (3.53 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state c (body domain). SNAP output |
| 7afk |
ribosome |
cryo-EM (4.9 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state d (head domain). SNAP output |
| 7afl |
ribosome |
cryo-EM (4.2 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state d (multibody refinement for body domain of 30s ribosome). SNAP output |
| 7afn |
ribosome |
cryo-EM (3.86 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state b (head domain). SNAP output |
| 7afo |
ribosome |
cryo-EM (3.93 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state b (body domain). SNAP output |
| 7aqc |
ribosome |
cryo-EM (2.99 Å) |
Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S |
(2021) "Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC." Mol.Cell, 81, 104. doi: 10.1016/j.molcel.2020.11.001. |
Structure of the bacterial rqc complex (decoding state). SNAP output |
| 7aqd |
ribosome |
cryo-EM (3.1 Å) |
Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S |
(2021) "Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC." Mol.Cell, 81, 104. doi: 10.1016/j.molcel.2020.11.001. |
Structure of the bacterial rqc complex (translocating state). SNAP output |
| 7as8 |
translation |
cryo-EM (2.9 Å) |
Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V |
(2021) "Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP." Mol.Cell, 81, 115. doi: 10.1016/j.molcel.2020.11.002. |
Bacillus subtilis ribosome quality control complex state b. ribosomal 50s subunit with p-trna, rqch, and rqcp-yabo. SNAP output |
| 7as9 |
translation |
cryo-EM (3.5 Å) |
Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V |
(2021) "Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP." Mol.Cell, 81, 115. doi: 10.1016/j.molcel.2020.11.002. |
Bacillus subtilis ribosome-associated quality control complex state a. ribosomal 50s subunit with peptidyl trna in the a-p position and rqch.. SNAP output |
| 7asa |
translation |
cryo-EM (3.5 Å) |
Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V |
(2021) "Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP." Mol.Cell, 81, 115. doi: 10.1016/j.molcel.2020.11.002. |
Bacillus subtilis ribosome-associated quality control complex state b, multibody refinement focussed on rqch. ribosomal 50s subunit with p-trna, rqch, and rqcp-yabo. SNAP output |
| 7asm |
ribosome |
cryo-EM (2.48 Å) |
Cimicata G, Bashan A, Yonath A |
"Staphylococcus aureus 50S after 30 minutes incubation a 37C." |
Staphylococcus aureus 50s after 30 minutes incubation at 37c. SNAP output |
| 7asn |
ribosome |
cryo-EM (2.73 Å) |
Cimicata G, Bashan A, Yonath A |
"Staphylococcus aureus 50S after 30 minutes incubation a 37C." |
Staphylococcus aureus 50s after 30 minutes incubation a 37c. SNAP output |
| 7b3b |
viral protein |
cryo-EM (3.1 Å) |
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P |
(2021) "Mechanism of SARS-CoV-2 polymerase stalling by remdesivir." Nat Commun, 12, 279. doi: 10.1038/s41467-020-20542-0. |
Structure of elongating sars-cov-2 RNA-dependent RNA polymerase with remdesivir at position -3 (structure 1). SNAP output |
| 7b3c |
viral protein |
cryo-EM (3.4 Å) |
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P |
(2021) "Mechanism of SARS-CoV-2 polymerase stalling by remdesivir." Nat Commun, 12, 279. doi: 10.1038/s41467-020-20542-0. |
Structure of elongating sars-cov-2 RNA-dependent RNA polymerase with remdesivir at position -4 (structure 2). SNAP output |
| 7b3d |
viral protein |
cryo-EM (2.8 Å) |
Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F, Schmitzova J, Farnung L, Siewert A, Hobartner C, Cramer P |
(2021) "Mechanism of SARS-CoV-2 polymerase stalling by remdesivir." Nat Commun, 12, 279. doi: 10.1038/s41467-020-20542-0. |
Structure of elongating sars-cov-2 RNA-dependent RNA polymerase with amp at position -4 (structure 3). SNAP output |
| 7bah |
immune system |
X-ray (1.89 Å) |
de Regt AK, Anand K, Gatterdam K, Hagelueken G, Hartmann G, Geyer M, Schlee M |
"A conserved isoleucine in the RNA sensor RIG-I controls immune tolerance to mitochondrial RNA." |
Structure of rig-i ctd bound to oh-RNA. SNAP output |
| 7bai |
immune system |
X-ray (3.4 Å) |
de Regt AK, Anand K, Gatterdam K, Hagelueken G, Hartmann G, Geyer M, Schlee M |
"A conserved isoleucine in the RNA sensor RIG-I controls immune tolerance to mitochondrial RNA." |
Structure of rig-i ctd (i875a) bound to p-RNA. SNAP output |
| 7bdv |
DNA binding protein |
X-ray (2.02 Å) |
Zhu W, McQuarrie S, Gruschow S, McMahon SA, Graham S, Gloster TM, White MF |
(2021) "The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence." Nucleic Acids Res., 49, 2777-2789. doi: 10.1093/nar/gkab073. |
Structure of can2 from sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (ca4). SNAP output |
| 7bg6 |
virus |
cryo-EM (2.6 Å) |
Hrebik D, Fuzik T, Gondova M, Smerdova L, Adamopoulos A, Sedo O, Zdrahal Z, Plevka P |
(2021) "ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2024251118. |
Hrv14 native particle solved by cryoem. SNAP output |
| 7bgb |
RNA binding protein |
cryo-EM (3.39 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 h-aca rnp lobe of human telomerase. SNAP output |
| 7bgd |
ribosome |
cryo-EM (3.2 Å) |
Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y |
(2021) "Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus." Front Mol Biosci, 8, 1022. |
Staphylococcus aureus 30s ribosomal subunit in presence of spermidine (body only). SNAP output |
| 7bge |
ribosome |
cryo-EM (3.6 Å) |
Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y |
(2021) "Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus." Front Mol Biosci, 8, 1022. |
Staphylococcus aureus 30s ribosomal subunit in presence of spermidine (head only). SNAP output |
| 7bkp |
immune system |
cryo-EM (2.8 Å) |
Yu Q, Herrero Del Valle A, Singh R, Modis Y |
(2021) "MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA." Nat Commun, 12, 6668. doi: 10.1038/s41467-021-27062-5. |
Cryoem structure of disease related m854k mda5-dsrna filament in complex with atp. SNAP output |
| 7bkq |
immune system |
cryo-EM (3.4 Å) |
Yu Q, Herrero Del Valle A, Singh R, Modis Y |
(2021) "MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA." Nat Commun, 12, 6668. doi: 10.1038/s41467-021-27062-5. |
Cryoem structure of mda5-dsrna filament in complex with adp with 92-degree helical twist. SNAP output |
| 7bl4 |
ribosome |
cryo-EM (2.4 Å) |
Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Burger J, Loerke J, Amikura K, Flugel T, Ueda T, Selbach M, Deuerling E, Spahn CMT |
(2021) "Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization." Mol.Cell, 81, 1200-1215.e9. doi: 10.1016/j.molcel.2021.02.006. |
In vitro reconstituted 50s-obge-gmppnp-rsfs particle. SNAP output |
| 7bl5 |
ribosome |
cryo-EM (3.3 Å) |
Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Burger J, Loerke J, Amikura K, Flugel T, Ueda T, Selbach M, Deuerling E, Spahn CMT |
(2021) "Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization." Mol.Cell, 81, 1200-1215.e9. doi: 10.1016/j.molcel.2021.02.006. |
Pre-50s-obge particle. SNAP output |
| 7bl6 |
ribosome |
cryo-EM (4.0 Å) |
Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Burger J, Loerke J, Amikura K, Flugel T, Ueda T, Selbach M, Deuerling E, Spahn CMT |
(2021) "Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization." Mol.Cell, 81, 1200-1215.e9. doi: 10.1016/j.molcel.2021.02.006. |
50s-obge-gmppnp particle. SNAP output |
| 7bod |
ribosome |
cryo-EM (2.88 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state m (body domain). SNAP output |
| 7boe |
ribosome |
cryo-EM (2.9 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state m (consensus refinement). SNAP output |
| 7bof |
ribosome |
cryo-EM (2.92 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state i (body domain). SNAP output |
| 7bog |
ribosome |
cryo-EM (2.75 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state e (body domain). SNAP output |
| 7boh |
ribosome |
cryo-EM (2.82 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Complete bacterial 30s ribosomal subunit assembly complex state e (+rbfa)(consensus refinement). SNAP output |
| 7boi |
ribosome |
cryo-EM (2.98 Å) |
Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, Lopez-Alonso JP, Lavin JL, Kaminishi T, Capuni R, Dhimole N, de Astigarraga E, Gil-Carton D, Fucini P, Connell SR |
(2021) "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Sci Adv, 7. doi: 10.1126/sciadv.abf7547. |
Bacterial 30s ribosomal subunit assembly complex state f (multibody refinement for body domain of 30s ribosome). SNAP output |
| 7bv2 |
viral protein |
cryo-EM (2.5 Å) |
Yin W, Mao C, Luan X, Shen DD, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S, Xie YC, Tian G, Jiang HW, Tao SC, Shen J, Jiang Y, Jiang H, Xu Y, Zhang S, Zhang Y, Xu HE |
(2020) "Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir." Science, 368, 1499-1504. doi: 10.1126/science.abc1560. |
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of remdesivir(rtp). SNAP output |
| 7bv8 |
ribosome |
cryo-EM (3.14 Å) |
Wang W, Li W, Ge X, Yan K, Mandava CS, Sanyal S, Gao N |
(2020) "Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation." Proc.Natl.Acad.Sci.USA, 117, 15609-15619. doi: 10.1073/pnas.1914323117. |
Mature 50s ribosomal subunit from rrmj knock out e.coli strain. SNAP output |
| 7bzf |
viral protein-RNA |
cryo-EM (3.26 Å) |
Wang Q, Wu J, Wang H, Gao Y, Liu Q, Mu A, Ji W, Yan L, Zhu Y, Zhu C, Fang X, Yang X, Huang Y, Gao H, Liu F, Ge J, Sun Q, Yang X, Xu W, Liu Z, Yang H, Lou Z, Jiang B, Guddat LW, Gong P, Rao Z |
(2020) "Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase." Cell, 182, 417-428.e13. doi: 10.1016/j.cell.2020.05.034. |
Covid-19 RNA-dependent RNA polymerase post-translocated catalytic complex. SNAP output |
| 7c06 |
splicing-RNA |
X-ray (3.02 Å) |
Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E |
(2020) "Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1." Nat Commun, 11, 4744. doi: 10.1038/s41467-020-18559-6. |
Crystal structure of yeast u2af1 complex bound to 3' splice site RNA, 5'-uaggu.. SNAP output |
| 7c07 |
splicing-RNA |
X-ray (3.2 Å) |
Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E |
(2020) "Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1." Nat Commun, 11, 4744. doi: 10.1038/s41467-020-18559-6. |
Crystal structure of yeast u2af1 complex bound to 5'-aaggu RNA.. SNAP output |
| 7c08 |
splicing-RNA |
X-ray (3.35 Å) |
Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E |
(2020) "Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1." Nat Commun, 11, 4744. doi: 10.1038/s41467-020-18559-6. |
Crystal structure of s34y mutant of yeast u2af1 complex bound to 3' splice site RNA, 5'-uaggu.. SNAP output |
| 7c2k |
viral protein-RNA |
cryo-EM (2.93 Å) |
Wang Q, Wu J, Wang H, Gao Y, Liu Q, Mu A, Ji W, Yan L, Zhu Y, Zhu C, Fang X, Yang X, Huang Y, Gao H, Liu F, Ge J, Sun Q, Yang X, Xu W, Liu Z, Yang H, Lou Z, Jiang B, Guddat LW, Gong P, Rao Z |
(2020) "Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase." Cell, 182, 417-428.e13. doi: 10.1016/j.cell.2020.05.034. |
Covid-19 RNA-dependent RNA polymerase pre-translocated catalytic complex. SNAP output |
| 7c45 |
RNA binding protein-RNA |
X-ray (1.769 Å) |
Gao Y, Liu H, Zhang C, Su S, Chen Y, Chen X, Li Y, Shao Z, Zhang Y, Shao Q, Li J, Huang Z, Ma J, Gan J |
(2021) "Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei." Nucleic Acids Res., 49, 568-583. doi: 10.1093/nar/gkaa1197. |
The crystal structure of trypanosoma brucei rnase d complex with RNA u12. SNAP output |
| 7c79 |
RNA binding protein |
cryo-EM (2.5 Å) |
Lan P, Zhou B, Tan M, Li S, Cao M, Wu J, Lei M |
(2020) "Structural insight into precursor ribosomal RNA processing by ribonuclease MRP." Science, 369, 656-663. doi: 10.1126/science.abc0149. |
cryo-EM structure of yeast ribonuclease mrp. SNAP output |
| 7c7a |
RNA binding protein |
cryo-EM (2.8 Å) |
Lan P, Zhou B, Tan M, Li S, Cao M, Wu J, Lei M |
(2020) "Structural insight into precursor ribosomal RNA processing by ribonuclease MRP." Science, 369, 656-663. doi: 10.1126/science.abc0149. |
cryo-EM structure of yeast ribonuclease mrp with substrate its1. SNAP output |
| 7cgf |
RNA binding protein |
X-ray (1.7 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgg |
RNA binding protein |
X-ray (2.7 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgh |
RNA binding protein |
X-ray (2.4 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgi |
RNA binding protein |
X-ray (2.796 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgj |
RNA binding protein |
X-ray (2.546 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgk |
RNA binding protein |
X-ray (2.4 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgl |
RNA binding protein |
X-ray (2.5 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7cgm |
RNA binding protein |
X-ray (2.6 Å) |
Xu Z, Zhao J, Hong M, Zeng C, Guang S, Shi Y |
(2021) "Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans." Nucleic Acids Res., 49, 10082-10097. doi: 10.1093/nar/gkab754. |
Crystal structure of puf-8 in complex with pbe-RNA. SNAP output |
| 7chd |
transferase |
X-ray (3.804 Å) |
Yashiro Y, Sakaguchi Y, Suzuki T, Tomita K |
(2020) "Mechanism of aminoacyl-tRNA acetylation by an aminoacyl-tRNA acetyltransferase AtaT from enterohemorrhagic E. coli." Nat Commun, 11, 5438. doi: 10.1038/s41467-020-19281-z. |
Atat complexed with acetyl-methionyl-trnafmet. SNAP output |
| 7ctt |
viral protein |
cryo-EM (3.2 Å) |
Peng Q, Peng R, Yuan B, Wang M, Zhao J, Fu L, Qi J, Shi Y |
(2021) "Structural Basis of SARS-CoV-2 Polymerase Inhibition by Favipiravir." Innovation (N Y), 2, 100080. doi: 10.1016/j.xinn.2021.100080. |
cryo-EM structure of favipiravir bound to replicating polymerase complex of sars-cov-2 in the pre-catalytic state.. SNAP output |
| 7cxm |
viral protein-RNA |
cryo-EM (2.9 Å) |
Yan L, Zhang Y, Ge J, Zheng L, Gao Y, Wang T, Jia Z, Wang H, Huang Y, Li M, Wang Q, Rao Z, Lou Z |
(2020) "Architecture of a SARS-CoV-2 mini replication and transcription complex." Nat Commun, 11, 5874. doi: 10.1038/s41467-020-19770-1. |
Architecture of a sars-cov-2 mini replication and transcription complex. SNAP output |
| 7cxn |
viral protein-RNA |
cryo-EM (3.84 Å) |
Yan L, Zhang Y, Ge J, Zheng L, Gao Y, Wang T, Jia Z, Wang H, Huang Y, Li M, Wang Q, Rao Z, Lou Z |
(2020) "Architecture of a SARS-CoV-2 mini replication and transcription complex." Nat Commun, 11, 5874. doi: 10.1038/s41467-020-19770-1. |
Architecture of a sars-cov-2 mini replication and transcription complex. SNAP output |
| 7cyq |
viral protein-RNA |
cryo-EM (2.83 Å) |
Yan L, Ge J, Zheng L, Zhang Y, Gao Y, Wang T, Huang Y, Yang Y, Gao S, Li M, Liu Z, Wang H, Li Y, Chen Y, Guddat LW, Wang Q, Rao Z, Lou Z |
(2021) "Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis." Cell, 184, 184-193.e10. doi: 10.1016/j.cell.2020.11.016. |
cryo-EM structure of an extended sars-cov-2 replication and transcription complex reveals an intermediate state in cap synthesis. SNAP output |
| 7d0f |
transferase-RNA |
cryo-EM (5.0 Å) |
Liu N, Dong X, Hu C, Zeng J, Wang J, Wang J, Wang HW, Belfort M |
(2020) "Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing." Nucleic Acids Res., 48, 11185-11198. doi: 10.1093/nar/gkaa773. |
cryo-EM structure of a pre-catalytic group ii intron rnp. SNAP output |
| 7d0g |
transferase-RNA |
cryo-EM (5.0 Å) |
Liu N, Dong X, Hu C, Zeng J, Wang J, Wang J, Wang HW, Belfort M |
(2020) "Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing." Nucleic Acids Res., 48, 11185-11198. doi: 10.1093/nar/gkaa773. |
cryo-EM structure of a pre-catalytic group ii intron. SNAP output |
| 7d1a |
transferase-RNA |
cryo-EM (3.8 Å) |
Liu N, Dong X, Hu C, Zeng J, Wang J, Wang J, Wang HW, Belfort M |
(2020) "Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing." Nucleic Acids Res., 48, 11185-11198. doi: 10.1093/nar/gkaa773. |
cryo-EM structure of a group ii intron rnp complexed with its reverse transcriptase. SNAP output |
| 7d7v |
RNA |
X-ray (2.8 Å) |
Chen H, Egger M, Xu X, Flemmich L, Krasheninina O, Sun A, Micura R, Ren A |
(2020) "Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding." Nucleic Acids Res., 48, 12394-12406. doi: 10.1093/nar/gkaa1029. |
Crystal structure of the domain1 of nad+ riboswitch with nicotinamide adenine dinucleotide (nad+) and u1a protein. SNAP output |
| 7d8c |
RNA binding protein |
X-ray (3.6 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-crrna binary complex. SNAP output |
| 7d8o |
toxin-RNA |
X-ray (2.097 Å) |
Manikandan P, Sandhya S, Nadig K, Paul S, Srinivasan N, Rothweiler U, Singh M |
(2022) "Identification, functional characterization, assembly and structure of ToxIN type III toxin-antitoxin complex from E. coli." Nucleic Acids Res., 50, 1687-1700. doi: 10.1093/nar/gkab1264. |
Crystal structure of e. coli toxin type iii toxin-antitoxin complex. SNAP output |
| 7dd3 |
splicing |
cryo-EM (3.2 Å) |
Bai R, Wan R, Yan C, Jia Q, Lei J, Shi Y |
(2021) "Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2." Science, 371. doi: 10.1126/science.abe8863. |
cryo-EM structure of the pre-mrna-loaded deah-box atpase-helicase prp2 in complex with spp2. SNAP output |
| 7dfg |
viral protein-RNA |
cryo-EM (2.7 Å) |
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H |
"Structural basis for repurpose and design of nucleotide drugs for treating COVID-19." |
Structure of covid-19 RNA-dependent RNA polymerase bound to favipiravir. SNAP output |
| 7dfh |
viral protein-RNA |
cryo-EM (2.97 Å) |
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H |
"Structural basis for repurpose and design of nucleotide drugs for treating COVID-19." |
Structure of covid-19 RNA-dependent RNA polymerase bound to ribavirin. SNAP output |
| 7dic |
hydrolase-RNA |
X-ray (2.242 Å) |
Abula A, Li X, Quan X, Yang T, Liu Y, Guo H, Li T, Ji X |
(2021) "Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation." Nucleic Acids Res., 49, 4738-4749. doi: 10.1093/nar/gkab202. |
Mycoplasma genitalium rnase r in complex with single-stranded RNA. SNAP output |
| 7did |
hydrolase-RNA |
X-ray (1.9 Å) |
Abula A, Li X, Quan X, Yang T, Liu Y, Guo H, Li T, Ji X |
(2021) "Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation." Nucleic Acids Res., 49, 4738-4749. doi: 10.1093/nar/gkab202. |
Mycoplasma genitalium rnase r in complex with ribose methylated single-stranded RNA. SNAP output |
| 7dkg |
viral protein-RNA |
X-ray (3.0 Å) |
Tang YS, Xu S, Chen YW, Wang JH, Shaw PC |
(2021) "Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction." Nucleic Acids Res., 49, 4144-4154. doi: 10.1093/nar/gkab203. |
Influenza h5n1 nucleoprotein (truncated) in complex with nucleotides. SNAP output |
| 7dlz |
transferase-RNA |
X-ray (3.002 Å) |
Jiang HY, Gao YQ, Zhang L, Chen DR, Gan JH, Murchie AIH |
(2021) "The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences." Nat Catal, 4, 872-881. doi: 10.1038/s41929-021-00685-z. |
Crystal structure of methyltransferase ribozyme. SNAP output |
| 7dmq |
immune system-RNA |
cryo-EM (3.06 Å) |
Wang B, Zhang T, Yin J, Yu Y, Xu W, Ding J, Patel DJ, Yang H |
(2021) "Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems." Mol.Cell, 81, 1100. doi: 10.1016/j.molcel.2020.12.033. |
cryo-EM structure of lshcas13a-crrna-anti-tag RNA complex. SNAP output |
| 7doi |
viral protein |
cryo-EM (2.6 Å) |
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H |
"Structural basis for repurpose and design of nucleotide drugs for treating COVID-19." |
Structure of covid-19 RNA-dependent RNA polymerase bound to penciclovir.. SNAP output |
| 7dok |
viral protein |
cryo-EM (2.73 Å) |
Yin W, Luan X, Li Z, Xie Y, Zhou Z, Liu J, Gao M, Wang X, Zhou F, Wang Q, Wang Q, Shen D, Zhang Y, Tian G, Aisa H, Wei D, Jiang Y, Xiao G, Jiang H, Zhang L, Yu X, Shen J, Zhang S, Xu H |
"Structural basis for repurpose and design of nucleotide drugs for treating COVID-19." |
Structure of covid-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir. SNAP output |
| 7dol |
hydrolase-RNA |
X-ray (2.002 Å) |
Abula A, Li X, Quan X, Yang T, Liu Y, Guo H, Li T, Ji X |
(2021) "Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation." Nucleic Acids Res., 49, 4738-4749. doi: 10.1093/nar/gkab202. |
Mycoplasma genitalium rnase r in complex with double-stranded RNA. SNAP output |
| 7dte |
viral protein-RNA |
cryo-EM (3.0 Å) |
Wang Q, Gong P |
"SARS-CoV-2 RdRP catalytic complex with T33-1 RNA." |
Sars-cov-2 rdrp catalytic complex with t33-1 RNA. SNAP output |
| 7dug |
ribosome |
X-ray (3.75 Å) |
Demirci H |
"Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''TFMS bound." |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with mrna and cognate transfer RNA anticodon stem-loop and sisomicin derivative n1''tfms bound. SNAP output |
| 7duh |
ribosome |
X-ray (3.75 Å) |
Demirci H |
"Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC bound." |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with mrna and cognate transfer RNA anticodon stem-loop and sisomicin derivative n1''ac bound. SNAP output |
| 7dui |
ribosome |
X-ray (3.62 Å) |
Demirci H |
"Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''PyrS bound." |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with mrna and cognate transfer RNA anticodon stem-loop and sisomicin derivative n1''pyrs bound. SNAP output |
| 7duj |
ribosome |
X-ray (3.75 Å) |
Demirci H |
"Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''Bz bound." |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with mrna and cognate transfer RNA anticodon stem-loop and sisomicin derivative n1,3''bz bound. SNAP output |
| 7duk |
ribosome |
X-ray (3.6 Å) |
Demirci H |
"Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''MS bound." |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with mrna and cognate transfer RNA anticodon stem-loop and sisomicin derivative n1,3''ms bound. SNAP output |
| 7dul |
ribosome |
X-ray (3.62 Å) |
DeMirci H, Destan E |
"Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N3''MS bound." |
Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with mrna and cognate transfer RNA anticodon stem-loop and sisomicin derivative n3''ms bound. SNAP output |
| 7dvq |
splicing |
cryo-EM (2.89 Å) |
Bai R, Wan R, Wang L, Xu K, Zhang Q, Lei J, Shi Y |
(2021) "Structure of the activated human minor spliceosome." Science, 371. doi: 10.1126/science.abg0879. |
cryo-EM structure of the activated human minor spliceosome (minor bact complex). SNAP output |
| 7dwh |
transferase-RNA |
X-ray (3.1 Å) |
Jiang HY, Gao YQ, Zhang L, Chen DR, Gan JH, Murchie AIH |
(2021) "The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences." Nat Catal, 4, 872-881. doi: 10.1038/s41929-021-00685-z. |
Complex structure of sam-dependent methyltransferase ribozyme. SNAP output |
| 7dxp |
viral protein-RNA |
X-ray (2.3 Å) |
Tang YS, Xu S, Chen YW, Wang JH, Shaw PC |
(2021) "Crystal structures of influenza nucleoprotein complexed with nucleic acid provide insights into the mechanism of RNA interaction." Nucleic Acids Res., 49, 4144-4154. doi: 10.1093/nar/gkab203. |
Influenza h5n1 nucleoprotein in complex with nucleotides. SNAP output |
| 7e8o |
hydrolase |
X-ray (2.804 Å) |
Li YY, Gan JH |
"Crystal structure of proteinaceous RNase P(PRORP) from Planctomycetes bacterium GWF2_40_8 complexed with Escherichia coli histidine pre-tRNA." |
Crystal structure of proteinaceous rnase p(prorp) from planctomycetes bacterium gwf2_40_8 complexed with escherichia coli histidine pre-trna. SNAP output |
| 7ecv |
immune system-RNA |
cryo-EM (3.43 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 complex. SNAP output |
| 7ed5 |
viral protein |
cryo-EM (2.98 Å) |
Shannon A, Fattorini V, Sama B, Selisko B, Feracci M, Falcou C, Gauffre P, El Kazzi P, Delpal A, Decroly E, Alvarez K, Eydoux C, Guillemot JC, Moussa A, Good SS, La Colla P, Lin K, Sommadossi JP, Zhu Y, Yan X, Shi H, Ferron F, Canard B |
(2022) "A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase." Nat Commun, 13, 621. doi: 10.1038/s41467-022-28113-1. |
A dual mechanism of action of at-527 against sars-cov-2 polymerase. SNAP output |
| 7egq |
viral protein-RNA |
cryo-EM (3.35 Å) |
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z |
(2021) "Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading." Cell, 184, 3474-3485.e11. doi: 10.1016/j.cell.2021.05.033. |
Co-transcriptional capping machineries in sars-cov-2 rtc: coupling of n7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading. SNAP output |
| 7eiu |
RNA binding protein |
X-ray (2.349 Å) |
Shen S, Jian Y, Cai Z, Li F, Lv M, Liu Y, Wu J, Fu C, Shi Y |
(2022) "Structural insights reveal the specific recognition of meiRNA by the Mei2 protein." J Mol Cell Biol. doi: 10.1093/jmcb/mjac029. |
Crystal structure of mei2 rrm3 in complex with 8mer meirna. SNAP output |
| 7eiz |
viral protein-RNA |
cryo-EM |
Yan L, Yang Y, Li M, Zhang Y, Zheng L, Ge J, Huang YC, Liu Z, Wang T, Gao S, Zhang R, Huang YY, Guddat LW, Gao Y, Rao Z, Lou Z |
(2021) "Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading." Cell, 184, 3474-3485.e11. doi: 10.1016/j.cell.2021.05.033. |
Coupling of n7-methyltransferase and 3'-5' exoribonuclease with sars-cov-2 polymerase reveals mechanisms for capping and proofreading. SNAP output |
| 7el9 |
viral protein-RNA |
cryo-EM (3.2 Å) |
Xu X, Peng R, Peng Q, Wang M, Xu Y, Liu S, Tian X, Deng H, Tong Y, Hu X, Zhong J, Wang P, Qi J, Gao GF, Shi Y |
(2021) "Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals." Nat Microbiol, 6, 921-931. doi: 10.1038/s41564-021-00916-w. |
Structure of machupo virus l polymerase in complex with z protein and 3'-vrna (dimeric complex). SNAP output |
| 7ela |
viral protein-RNA |
cryo-EM (3.4 Å) |
Xu X, Peng R, Peng Q, Wang M, Xu Y, Liu S, Tian X, Deng H, Tong Y, Hu X, Zhong J, Wang P, Qi J, Gao GF, Shi Y |
(2021) "Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals." Nat Microbiol, 6, 921-931. doi: 10.1038/s41564-021-00916-w. |
Structure of lassa virus polymerase in complex with 3'-vrna and z mutant (f36a). SNAP output |
| 7elc |
viral protein-RNA |
cryo-EM (3.1 Å) |
Xu X, Peng R, Peng Q, Wang M, Xu Y, Liu S, Tian X, Deng H, Tong Y, Hu X, Zhong J, Wang P, Qi J, Gao GF, Shi Y |
(2021) "Cryo-EM structures of Lassa and Machupo virus polymerases complexed with cognate regulatory Z proteins identify targets for antivirals." Nat Microbiol, 6, 921-931. doi: 10.1038/s41564-021-00916-w. |
Structure of monomeric complex of macv l bound to z and 3'-vrna. SNAP output |
| 7eld |
hydrolase |
cryo-EM (4.6 Å) |
Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y |
(2021) "Structural basis of microRNA processing by Dicer-like 1." Nat.Plants, 7, 1389-1396. doi: 10.1038/s41477-021-01000-1. |
cryo-EM structure of arabidopsis dcl1 in complex with pri-mirna 166f. SNAP output |
| 7ele |
hydrolase |
cryo-EM (4.9 Å) |
Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y |
(2021) "Structural basis of microRNA processing by Dicer-like 1." Nat.Plants, 7, 1389-1396. doi: 10.1038/s41477-021-01000-1. |
cryo-EM structure of arabidopsis dcl1 in complex with pre-mirna 166f. SNAP output |
| 7elm |
immune system-RNA |
cryo-EM (2.88 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. SNAP output |
| 7eni |
viral protein-RNA |
X-ray (2.632 Å) |
Wang Y, Li X |
"Crystal structure of cas and anti-cas protein complex." |
Crystal structure of cas and anti-cas protein complex. SNAP output |
| 7enr |
viral protein-RNA |
X-ray (4.205 Å) |
Wang Y, Li X |
"Crystal structure of cas and anti-cas protein complex." |
Crystal structure of cas and anti-cas protein complex. SNAP output |
| 7ewq |
nuclear protein |
cryo-EM (3.5 Å) |
Su X, Shen Q, Shan H |
"Structural plasticity of mumps virus nucleocapsids
for genome protection and condensation." |
Structure of mumps virus nucleocapsid ring. SNAP output |
| 7f1m |
viral protein |
cryo-EM (3.1 Å) |
Fujita-Fujiharu Y, Sugita Y, Takamatsu Y, Houri K, Igarashi M, Muramoto Y, Nakano M, Tsunoda Y, Taniguchi I, Becker S, Noda T |
(2022) "Structural insight into Marburg virus nucleoprotein-RNA complex formation." Nat Commun, 13, 1191. doi: 10.1038/s41467-022-28802-x. |
Marburg virus nucleoprotein-RNA complex. SNAP output |
| 7f36 |
transferase |
X-ray (3.098 Å) |
Yashiro Y, Zhang C, Sakaguchi Y, Suzuki T, Tomita K |
(2021) "Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium." Cell Rep, 37, 110130. doi: 10.1016/j.celrep.2021.110130. |
Tact complexed with acetyl-glycyl-trnagly. SNAP output |
| 7f49 |
blood clotting |
X-ray (2.09 Å) |
Zhu S, Gilbert CJ |
(2020) "The development and characterization of a long acting anti-thrombotic von Willebrand factor (VWF) aptamer." J Thromb Haemost., 18, 1113-1123. doi: 10.1111/jth.14755. |
Von willebrand factor (vwf) a1 domain with bt-100 aptamer RNA. SNAP output |
| 7jhy |
immune system-RNA |
cryo-EM (3.9 Å) |
Zhou Y, Bravo JPK, Taylor HN, Steens JA, Jackson RN, Staals RHJ, Taylor DW |
(2021) "Structure of a type IV CRISPR-Cas ribonucleoprotein complex." Iscience, 24, 102201. doi: 10.1016/j.isci.2021.102201. |
Type iv-b crispr complex. SNAP output |
| 7jl0 |
hydrolase-immune system-RNA |
cryo-EM (4.3 Å) |
Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S |
(2021) "Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases." Mol.Cell, 81, 599-613.e8. doi: 10.1016/j.molcel.2020.11.047. |
cryo-EM structure of mda5-dsrna in complex with trim65 pspry domain (monomer). SNAP output |
| 7jl1 |
hydrolase-transferase-RNA |
cryo-EM (3.9 Å) |
Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S |
(2021) "Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases." Mol.Cell, 81, 599-613.e8. doi: 10.1016/j.molcel.2020.11.047. |
cryo-EM structure of rig-i:dsrna in complex with riplet pryspry domain (monomer). SNAP output |
| 7jl2 |
hydrolase-immune system-RNA |
cryo-EM (4.3 Å) |
Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S |
(2021) "Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases." Mol.Cell, 81, 599-613.e8. doi: 10.1016/j.molcel.2020.11.047. |
cryo-EM structure of mda5-dsrna filament in complex with trim65 pspry domain (trimer). SNAP output |
| 7jl3 |
hydrolase-transferase-RNA |
cryo-EM (4.2 Å) |
Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S |
(2021) "Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases." Mol.Cell, 81, 599-613.e8. doi: 10.1016/j.molcel.2020.11.047. |
cryo-EM structure of rig-i:dsrna filament in complex with riplet pryspry domain (trimer). SNAP output |
| 7jqb |
ribosome-viral protein |
cryo-EM (2.7 Å) |
Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y |
(2020) "Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA." Mol.Cell, 80, 1055-1066.e6. doi: 10.1016/j.molcel.2020.10.034. |
Sars-cov-2 nsp1 and rabbit 40s ribosome complex. SNAP output |
| 7jqc |
ribosome-viral protein |
cryo-EM (3.3 Å) |
Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y |
(2020) "Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA." Mol.Cell, 80, 1055-1066.e6. doi: 10.1016/j.molcel.2020.10.034. |
Sars-cov-2 nsp1, crpv ires and rabbit 40s ribosome complex. SNAP output |
| 7jyy |
viral protein-RNA |
X-ray (2.05 Å) |
Minasov G, Rosas-Lemus M, Shuvalova L, Inniss NL, Brunzelle JS, Daczkowski CM, Hoover P, Mesecar AD, Satchell KJF |
(2021) "Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16." Sci.Signal., 14. doi: 10.1126/scisignal.abh2071. |
Crystal structure of sars-cov-2 nsp16-10 heterodimer in complex with (m7gpppa)pupupapapa (cap-0) and s-adenosylmethionine (sam).. SNAP output |
| 7jz0 |
viral protein-RNA |
X-ray (2.15 Å) |
Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Brunzelle J, Satchell KJF |
(2020) "High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design." Sci.Signal., 13. doi: 10.1126/scisignal.abe1202. |
Crystal structure of sars-cov-2 nsp16-10 heterodimer in complex with (m7gpppa2m)pupupapapa (cap-1) and s-adenosyl-l-homocysteine (sah).. SNAP output |
| 7jzw |
hydrolase |
cryo-EM (3.2 Å) |
Gabel C, Li Z, Zhang H, Chang L |
(2021) "Structural basis for inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14." Nucleic Acids Res., 49, 584-594. doi: 10.1093/nar/gkaa1199. |
cryo-EM structure of crispr-cas surveillance complex with acrif4. SNAP output |
| 7jzx |
hydrolase-RNA |
cryo-EM (3.4 Å) |
Gabel C, Li Z, Zhang H, Chang L |
(2021) "Structural basis for inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14." Nucleic Acids Res., 49, 584-594. doi: 10.1093/nar/gkaa1199. |
cryo-EM structure of crispr-cas surveillance complex with acrif7. SNAP output |
| 7jzy |
hydrolase-RNA |
cryo-EM (3.6 Å) |
Chang L, Li Z, Gabel C |
"CryoEM structure of a CRISPR-Cas complex." |
Cryoem structure of a crispr-cas complex. SNAP output |
| 7jzz |
hydrolase-RNA |
cryo-EM (3.2 Å) |
Gabel C, Li Z, Zhang H, Chang L |
(2021) "Structural basis for inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14." Nucleic Acids Res., 49, 584-594. doi: 10.1093/nar/gkaa1199. |
cryo-EM structure of crispr-cas surveillance complex with acrif14. SNAP output |
| 7k5i |
ribosome-viral protein |
cryo-EM (2.9 Å) |
Shi M, Wang L, Fontana P, Vora S, Zhang Y, Fu TM, Lieberman J, Wu H |
(2020) "SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism." Biorxiv. doi: 10.1101/2020.09.18.302901. |
Sars-cov-2 nsp1 in complex with human 40s ribosome. SNAP output |
| 7k5l |
viral protein |
X-ray (1.38 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 an RNA oligonucleotide. SNAP output |
| 7k98 |
ligase-RNA |
X-ray (2.19 Å) |
Michalska K, Jedrzejczak R, Wower J, Chang C, Baragana B, Gilbert IH, Forte B, Joachimiak A |
(2021) "Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation." Nucleic Acids Res., 49, 5351-5368. doi: 10.1093/nar/gkab272. |
Preaminoacylation complex of m. tuberculosis phers with cognate precursor trna and 5'-o-(n-phenylalanyl)sulfamoyl-adenosine (f-ams). SNAP output |
| 7k9d |
RNA-binding protein-RNA |
X-ray (2.098 Å) |
Yang Y, Harris KA, Widner DL, Breaker RR |
(2021) "Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2020393118. |
Crystal structure of bacillus halodurans oapb in complex with its ole RNA target (crystal form i). SNAP output |
| 7k9e |
RNA-binding protein-RNA |
X-ray (2.1 Å) |
Yang Y, Harris KA, Widner DL, Breaker RR |
(2021) "Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2020393118. |
Crystal structure of bacillus halodurans oapb in complex with its ole RNA target (crystal form ii). SNAP output |
| 7k9m |
ligase-RNA |
X-ray (2.5 Å) |
Michalska K, Jedrzejczak R, Wower J, Chang C, Baragana B, Gilbert IH, Forte B, Joachimiak A |
(2021) "Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation." Nucleic Acids Res., 49, 5351-5368. doi: 10.1093/nar/gkab272. |
Crystal structure of the complex of m. tuberculosis phers with cognate precursor trna and 5'-o-(n-phenylalanyl)sulfamoyl-adenosine. SNAP output |
| 7ka0 |
ligase-RNA |
X-ray (2.4 Å) |
Michalska K, Jedrzejczak R, Wower J, Chang C, Baragana B, Gilbert IH, Forte B, Joachimiak A |
(2021) "Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation." Nucleic Acids Res., 49, 5351-5368. doi: 10.1093/nar/gkab272. |
Crystal structure of the complex of m. tuberculosis phers with cognate precursor trna and phenylalanine. SNAP output |
| 7kab |
ligase-RNA |
X-ray (2.5 Å) |
Michalska K, Jedrzejczak R, Wower J, Chang C, Baragana B, Gilbert IH, Forte B, Joachimiak A |
(2021) "Mycobacterium tuberculosis Phe-tRNA synthetase: structural insights into tRNA recognition and aminoacylation." Nucleic Acids Res., 49, 5351-5368. doi: 10.1093/nar/gkab272. |
M. tuberculosis phers complex with cognate precursor trna and phenylalanine. SNAP output |
| 7kfn |
RNA binding protein-RNA |
X-ray (2.5 Å) |
Doherty EE, Wilcox XE, van Sint Fiet L, Kemmel C, Turunen JJ, Klein B, Tantillo DJ, Fisher AJ, Beal PA |
(2021) "Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position." J.Am.Chem.Soc., 143, 6865-6876. doi: 10.1021/jacs.0c13319. |
Structure of human adenosine deaminase acting on dsrna (adar2) bound to dsrna containing a 2'-deoxy benner's base z opposite the edited base. SNAP output |
| 7kha |
RNA binding protein-RNA |
cryo-EM (3.13 Å) |
O'Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor DW |
(2020) "Structural basis for assembly of non-canonical small subunits into type I-C Cascade." Nat Commun, 11, 5931. doi: 10.1038/s41467-020-19785-8. |
cryo-EM structure of the desulfovibrio vulgaris type i-c apo cascade. SNAP output |
| 7ki3 |
hydrolase-RNA |
X-ray (3.0 Å) |
Gebert LFR, Law M, MacRae IJ |
(2021) "A structured RNA motif locks Argonaute2:miR-122 onto the 5' end of the HCV genome." Nat Commun, 12, 6836. doi: 10.1038/s41467-021-27177-9. |
Human argonaute2:mir-122 bound to the hcv genotype 1a site-1 RNA. SNAP output |
| 7kjt |
RNA binding protein-RNA |
X-ray (3.34 Å) |
Beenstock J, Ona SM, Porat J, Orlicky S, Wan LCK, Ceccarelli DF, Maisonneuve P, Szilard RK, Yin Z, Setiaputra D, Mao DYL, Khan M, Raval S, Schriemer DC, Bayfield MA, Durocher D, Sicheri F |
(2020) "A substrate binding model for the KEOPS tRNA modifying complex." Nat Commun, 11, 6233. doi: 10.1038/s41467-020-19990-5. |
Keops trna modifying sub-complex of archaeal cgi121 and trna. SNAP output |
| 7kjv |
viral protein-RNA |
cryo-EM (2.8 Å) |
Ha B, Larsen KP, Zhang J, Fu Z, Montabana E, Jackson LN, Chen DH, Puglisi EV |
(2021) "High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs." Nat Commun, 12, 2500. doi: 10.1038/s41467-021-22628-9. |
Structure of hiv-1 reverse transcriptase initiation complex core. SNAP output |
| 7kjw |
viral protein-RNA |
cryo-EM (2.9 Å) |
Ha B, Larsen KP, Zhang J, Fu Z, Montabana E, Jackson LN, Chen DH, Puglisi EV |
(2021) "High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs." Nat Commun, 12, 2500. doi: 10.1038/s41467-021-22628-9. |
Structure of hiv-1 reverse transcriptase initiation complex core with efavirenz. SNAP output |
| 7kjx |
viral protein-RNA |
cryo-EM (3.1 Å) |
Ha B, Larsen KP, Zhang J, Fu Z, Montabana E, Jackson LN, Chen DH, Puglisi EV |
(2021) "High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs." Nat Commun, 12, 2500. doi: 10.1038/s41467-021-22628-9. |
Structure of hiv-1 reverse transcriptase initiation complex core with nevirapine. SNAP output |
| 7kkv |
RNA-binding protein-RNA |
X-ray (2.0 Å) |
Yang Y, Harris KA, Widner DL, Breaker RR |
(2021) "Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2020393118. |
Crystal structure of bacillus halodurans oapb in complex with its ole RNA target (native, crystal form i). SNAP output |
| 7kl3 |
viral protein-RNA |
X-ray (1.99 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 RNA oligomer ag*cauc (*uncleaveable bond, -uc disordered). SNAP output |
| 7krn |
transferase-hydrolase-RNA |
cryo-EM (3.4 Å) |
Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA |
(2021) "Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2102516118. |
Structure of sars-cov-2 backtracked complex bound to nsp13 helicase - nsp13(1)-btc. SNAP output |
| 7kro |
transferase-hydrolase-RNA |
cryo-EM (3.6 Å) |
Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA |
(2021) "Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2102516118. |
Structure of sars-cov-2 backtracked complex complex bound to nsp13 helicase - nsp13(2)-btc. SNAP output |
| 7krp |
transferase-RNA |
cryo-EM (3.2 Å) |
Malone B, Chen J, Wang Q, Llewellyn E, Choi YJ, Olinares PDB, Cao X, Hernandez C, Eng ET, Chait BT, Shaw DE, Landick R, Darst SA, Campbell EA |
(2021) "Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex." Proc.Natl.Acad.Sci.USA, 118. doi: 10.1073/pnas.2102516118. |
Structure of sars-cov-2 backtracked complex complex bound to nsp13 helicase - btc (local refinement). SNAP output |
| 7kwg |
ribosome |
cryo-EM (3.75 Å) |
Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y |
(2021) "Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus ." Front Mol Biosci, 8, 738752. doi: 10.3389/fmolb.2021.738752. |
Staphylococcus aureus 30s ribosomal subunit in presence of spermidine. SNAP output |
| 7kx7 |
hydrolase,RNA binding protein-RNA |
cryo-EM (3.8 Å) |
Anzelon TA, Chowdhury S, Hughes SM, Xiao Y, Lander GC, MacRae IJ |
(2021) "Structural basis for piRNA targeting." Nature, 597, 285-289. doi: 10.1038/s41586-021-03856-x. |
cryo-EM structure of ephydatia fluviatilis piwia-pirna complex. SNAP output |
| 7kx9 |
hydrolase,RNA binding protein-RNA |
cryo-EM (3.5 Å) |
Anzelon TA, Chowdhury S, Hughes SM, Xiao Y, Lander GC, MacRae IJ |
(2021) "Structural basis for piRNA targeting." Nature, 597, 285-289. doi: 10.1038/s41586-021-03856-x. |
cryo-EM structure of ephydatia fluviatilis piwia-pirna-target complex. SNAP output |
| 7l1f |
viral protein-RNA |
cryo-EM (3.89 Å) |
Bravo JPK, Dangerfield TL, Taylor DW, Johnson KA |
(2021) "Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication." Mol.Cell, 81, 1548-1552.e4. doi: 10.1016/j.molcel.2021.01.035. |
Sars-cov-2 rdrp in complex with 4 remdesivir monophosphate. SNAP output |
| 7l48 |
RNA binding protein-RNA |
cryo-EM (3.9 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 a crispr-cas12f binary complex. SNAP output |
| 7l6r |
viral protein-RNA |
X-ray (1.98 Å) |
Minasov G, Rosas-Lemus M, Shuvalova L, Inniss NL, Brunzelle JS, Daczkowski CM, Hoover P, Mesecar AD, Satchell KJF |
(2021) "Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16." Sci.Signal., 14. doi: 10.1126/scisignal.abh2071. |
Crystal structure of sars-cov-2 nsp16-10 heterodimer in complex with (m7gpppa2m)pupupapapa (cap-1), s-adenosyl-l-homocysteine (sah) and manganese (mn).. SNAP output |
| 7l6t |
viral protein-RNA |
X-ray (1.78 Å) |
Minasov G, Rosas-Lemus M, Shuvalova L, Inniss NL, Brunzelle JS, Daczkowski CM, Hoover P, Mesecar AD, Satchell KJF |
(2021) "Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16." Sci.Signal., 14. doi: 10.1126/scisignal.abh2071. |
Crystal structure of sars-cov-2 nsp16-10 heterodimer in complex with (m7gpppa2m)pupupapapa (cap-1), s-adenosyl-l-homocysteine (sah) and two magnesium (mg) ions.. SNAP output |
| 7ld5 |
transferase-RNA |
cryo-EM (3.07 Å) |
Unciuleac MC, Ghosh S, de la Cruz MJ, Goldgur Y, Shuman S |
(2021) "Structure and mechanism of Mycobacterium smegmatis polynucleotide phosphorylase." Rna. doi: 10.1261/rna.078822.121. |
Polynucleotide phosphorylase. SNAP output |
| 7lj3 |
virus |
cryo-EM (2.9 Å) |
Liu YT, Strugatsky D, Liu W, Zhou ZH |
(2021) "Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150." Nat Commun, 12, 5513. doi: 10.1038/s41467-021-25791-1. |
Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus. SNAP output |
| 7m4u |
ribosome |
cryo-EM (2.71 Å) |
Zhang Z, Morgan CE, Bonomo RA, Yu EW |
(2021) "Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii." Mbio, e0103121. doi: 10.1128/mBio.01031-21. |
A. baumannii ribosome-eravacycline complex: 30s. SNAP output |
| 7m4v |
ribosome |
cryo-EM (2.54 Å) |
Zhang Z, Morgan CE, Bonomo RA, Yu EW |
(2021) "Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii." Mbio, e0103121. doi: 10.1128/mBio.01031-21. |
A. baumannii ribosome-eravacycline complex: 50s. SNAP output |
| 7m5o |
viral protein-RNA |
cryo-EM (3.54 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. SNAP output |
| 7mjv |
transferase-RNA |
X-ray (2.24 Å) |
Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ |
(2021) "Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB." Nature, 597, 566-570. doi: 10.1038/s41586-021-03904-6. |
Miab in the complex with s-adenosylmethionine and RNA. SNAP output |
| 7mjw |
transferase-RNA |
X-ray (1.4 Å) |
Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ |
(2021) "Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB." Nature, 597, 566-570. doi: 10.1038/s41586-021-03904-6. |
Methylated miab in the complex with 5'-deoxyadenosine, methionine and RNA. SNAP output |
| 7mjx |
transferase-RNA |
X-ray (1.5 Å) |
Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ |
(2021) "Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB." Nature, 597, 566-570. doi: 10.1038/s41586-021-03904-6. |
Miab in the complex with 5'-deoxyadenosine, methionine and RNA. SNAP output |
| 7mjy |
transferase-RNA |
X-ray (1.86 Å) |
Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ |
(2021) "Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB." Nature, 597, 566-570. doi: 10.1038/s41586-021-03904-6. |
Miab in the complex with s-adenosyl-l-homocysteine and RNA. SNAP output |
| 7mlx |
RNA-immune system |
X-ray (2.09 Å) |
Roman C, Lewicka A, Koirala D, Li NS, Piccirilli JA |
(2021) "The SARS-CoV-2 Programmed -1 Ribosomal Frameshifting Element Crystal Structure Solved to 2.09 angstrom Using Chaperone-Assisted RNA Crystallography." Acs Chem.Biol., 16, 1469-1481. doi: 10.1021/acschembio.1c00324. |
Sars-cov-2 programmed -1 frameshifting element three stem h-type pseudoknot. SNAP output |
| 7mpl |
RNA binding protein-RNA |
X-ray (1.8 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc bound to pgg. SNAP output |
| 7mpm |
RNA binding protein-RNA |
X-ray (1.95 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc bound to paa. SNAP output |
| 7mpn |
RNA binding protein-RNA |
X-ray (1.94 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc bound to pgc. SNAP output |
| 7mpq |
RNA binding protein |
X-ray (2.35 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc cleaving pgg in the presence of mn2+. SNAP output |
| 7mpu |
RNA binding protein-RNA |
X-ray (1.72 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Brucella melitensis nrnc bound to pgg. SNAP output |
| 7mqb |
RNA binding protein-RNA |
cryo-EM (3.25 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc bound to pgg. d4 symmetry. SNAP output |
| 7mqc |
RNA binding protein-RNA |
cryo-EM (3.64 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc bound to pgg. c1 reconstruction.. SNAP output |
| 7mqd |
RNA binding protein-RNA |
cryo-EM (3.25 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc complexed with pagg. d4 symmetry.. SNAP output |
| 7mqe |
RNA binding protein-RNA |
cryo-EM (3.69 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc complexed with pagg. c1 reconstruction.. SNAP output |
| 7mqf |
RNA binding protein-RNA |
cryo-EM (2.88 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc complexed with paaagg. d4 symmetry.. SNAP output |
| 7mqg |
RNA binding protein-RNA |
cryo-EM (3.25 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc complexed with paaagg. c1 reconstruction.. SNAP output |
| 7mqh |
RNA binding protein-RNA |
cryo-EM (3.1 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc complexed with paaagg in the presence of ca2+. d4 symmetry.. SNAP output |
| 7mqi |
RNA binding protein-RNA |
cryo-EM (3.21 Å) |
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H |
(2021) "Structural characterization of NrnC identifies unifying features of dinucleotidases." Elife, 10. doi: 10.7554/eLife.70146. |
Bartonella henselae nrnc complexed with paaagg in the presence of ca2+. c1 reconstruction.. SNAP output |
| 7mrl |
viral protein-RNA |
X-ray (3.15 Å) |
Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R, Summers MF, Bieniasz PD, Zhang J |
(2021) "HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization." Cell Host Microbe, 29, 1421. doi: 10.1016/j.chom.2021.07.006. |
Structure of hiv-1 matrix domain bound to human trnalys3. SNAP output |
| 7msf |
virus-RNA |
X-ray (2.8 Å) |
Rowsell S, Stonehouse NJ, Convery MA, Adams CJ, Ellington AD, Hirao I, Peabody DS, Stockley PG, Phillips SE |
(1998) "Crystal structures of a series of RNA aptamers complexed to the same protein target." Nat.Struct.Biol., 5, 970-975. doi: 10.1038/2946. |
Ms2 protein capsid-RNA complex. SNAP output |
| 7mw8 |
hydrolase |
X-ray (1.9 Å) |
Fernandez D, Li L, Brown JA |
"Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase." |
Crystal structure analysis of xac nucleotide pyrophosphatase-phosphodiesterase. SNAP output |