|
10mh
|
transferase-DNA |
X-ray (2.55 Å) |
Sheikhnejad G, Brank A, Christman JK, Goddard A,
Alvarez E, Ford Jr H, Marquez VE, Marasco CJ, Sufrin JR,
O'gara M, Cheng X |
(1999) "Mechanism
of inhibition of DNA (cytosine C5)-methyltransferases
by oligodeoxyribonucleotides containing
5,6-dihydro-5-azacytosine." J.Mol.Biol.,
285, 2021-2034. doi: 10.1006/jmbi.1998.2426.
|
Ternary structure of hhai methyltransferase with adohcy
and hemimethylated DNA containing
5,6-dihydro-5-azacytosine at the target . SNAP output
|
|
173d
|
DNA-antibiotic |
X-ray (3.0 Å) |
Kamitori S, Takusagawa F |
(1994) "Multiple Binding Modes of Anticancer Drug
Actinomycin D: X-Ray, Molecular Modeling, and
Spectroscopic Studies of D(Gaagcttc)2-Actinomycin D
Complexes and its Host DNA." J.Am.Chem.Soc.,
116, 4154. doi: 10.1021/JA00089A002.
|
Multiple binding modes of anticancer drug actinomycin
d: x-ray, molecular modeling, and spectroscopic studies
of d(gaagcttc)2-actinomycin d complexes and its host
DNA . SNAP output
|
|
185d
|
DNA-antibiotic |
NMR |
Addess KJ, Feigon J |
(1994) "Sequence
Specificity of Quinoxaline Antibiotics. 1. Solution
Structure of a 1:1 Complex between Triostin a and
[D(Gacgtc)]2 and Comparison with the Solution Structure
of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2
Complex." Biochemistry,
33, 12386. doi: 10.1021/BI00207A005.
|
Sequence specificity of quinoxaline antibiotics. 1.
solution structure of a 1:1 complex between triostin a
and [d(gacgtc)]2 and comparison with the solution
structure of the [n-mecys3,
n-mecys7]tandem-[d(gatatc)]2 complex . SNAP output
|
|
193d
|
DNA-antibiotic |
NMR |
Chen H, Patel DJ |
(1995) "Solution
Structure of a Quinomycin Bisintercalator-DNA
Complex." J.Mol.Biol.,
246, 164. doi: 10.1006/JMBI.1994.0074.
|
Solution structure of a quinomycin bisintercalator-DNA
complex . SNAP
output
|
|
1a02
|
transcription-DNA |
X-ray (2.7 Å) |
Chen L, Glover JN, Hogan PG, Rao A, Harrison SC |
(1998) "Structure
of the DNA-binding domains from NFAT, Fos and Jun bound
specifically to DNA." Nature,
392, 42-48. doi: 10.1038/32100.
|
Structure of the DNA binding domains of nfat, fos and
jun bound to DNA . SNAP
output
|
|
1a0a
|
transcription-DNA |
X-ray (2.8 Å) |
Shimizu T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y,
Ogawa N, Oshima Y, Hakoshima T |
(1997) "Crystal
structure of PHO4 bHLH domain-DNA complex: flanking
base recognition." EMBO J.,
16, 4689-4697. doi: 10.1093/emboj/16.15.4689.
|
Phosphate system positive regulatory protein pho4-DNA
complex . SNAP
output
|
|
1a1f
|
transcription-DNA |
X-ray (2.1 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Dsnr (zif268 variant) zinc finger-DNA complex (gacc
site) . SNAP output
|
|
1a1g
|
transcription-DNA |
X-ray (1.9 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Dsnr (zif268 variant) zinc finger-DNA complex (gcgt
site) . SNAP output
|
|
1a1h
|
transcription-DNA |
X-ray (1.6 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Qgsr (zif268 variant) zinc finger-DNA complex (gcac
site) . SNAP output
|
|
1a1i
|
transcription-DNA |
X-ray (1.6 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Radr (zif268 variant) zinc finger-DNA complex (gcac
site) . SNAP output
|
|
1a1j
|
transcription-DNA |
X-ray (2.0 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Radr (zif268 variant) zinc finger-DNA complex (gcgt
site) . SNAP output
|
|
1a1k
|
transcription-DNA |
X-ray (1.9 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Radr (zif268 variant) zinc finger-DNA complex (gacc
site) . SNAP output
|
|
1a1l
|
transcription-DNA |
X-ray (2.3 Å) |
Elrod-Erickson M, Benson TE, Pabo CO |
(1998) "High-resolution
structures of variant Zif268-DNA complexes:
implications for understanding zinc finger-DNA
recognition." Structure,
6, 451-464. doi: 10.1016/S0969-2126(98)00047-1.
|
Zif268 zinc finger-DNA complex (gcac site) . SNAP output
|
|
1a1v
|
hydrolase-DNA |
X-ray (2.2 Å) |
Kim JL, Morgenstern KA, Griffith JP, Dwyer MD,
Thomson JA, Murcko MA, Lin C, Caron PR |
(1998) "Hepatitis
C virus NS3 RNA helicase domain with a bound
oligonucleotide: the crystal structure provides
insights into the mode of unwinding."
Structure, 6, 89-100. doi:
10.1016/S0969-2126(98)00010-0.
|
Hepatitis c virus ns3 helicase domain complexed with
single stranded sDNA . SNAP output
|
|
1a31
|
isomerase-DNA |
X-ray (2.1 Å) |
Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol
WG |
(1998) "Crystal
structures of human topoisomerase I in covalent and
noncovalent complexes with DNA." Science,
279, 1504-1513. doi: 10.1126/science.279.5356.1504.
|
Human reconstituted DNA topoisomerase i in covalent
complex with a 22 base pair DNA duplex . SNAP output
|
|
1a35
|
isomerase-DNA |
X-ray (2.5 Å) |
Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol
WG |
(1998) "Crystal
structures of human topoisomerase I in covalent and
noncovalent complexes with DNA." Science,
279, 1504-1513. doi: 10.1126/science.279.5356.1504.
|
Human topoisomerase i-DNA complex . SNAP output
|
|
1a36
|
isomerase-DNA |
X-ray (2.8 Å) |
Stewart L, Redinbo MR, Qiu X, Hol WG, Champoux
JJ |
(1998) "A model
for the mechanism of human topoisomerase I."
Science, 279, 1534-1541. doi:
10.1126/science.279.5356.1534.
|
Topoisomerase i-DNA complex . SNAP output
|
|
1a3q
|
transcription-DNA |
X-ray (2.1 Å) |
Cramer P, Larson CJ, Verdine GL, Muller CW |
(1997) "Structure
of the human NF-kappaB p52 homodimer-DNA complex at 2.1
A resolution." EMBO J.,
16, 7078-7090. doi: 10.1093/emboj/16.23.7078.
|
Human nf-kappa-b p52 bound to DNA . SNAP output
|
|
1a66
|
transcription-DNA |
NMR |
Zhou P, Sun LJ, Dotsch V, Wagner G, Verdine GL |
(1998) "Solution
structure of the core NFATC1/DNA complex."
Cell(Cambridge,Mass.), 92,
687-696. doi: 10.1016/S0092-8674(00)81136-8.
|
Solution NMR structure of the core nfatc1-DNA complex,
18 structures . SNAP
output
|
|
1a6b
|
viral protein-DNA |
NMR |
Schuler W, Dong C, Wecker K, Roques BP |
(1999) "NMR
structure of the complex between the zinc finger
protein NCp10 of Moloney murine leukemia virus and the
single-stranded pentanucleotide d(ACGCC): comparison
with HIV-NCp7 complexes." Biochemistry,
38, 12984-12994. doi: 10.1021/bi990378d.
|
NMR structure of the complex between the zinc finger
protein ncp10 of moloney murine leukemia virus and a
sequence of the psi-packaging domain of hiv-1, 20
structures . SNAP
output
|
|
1a6y
|
transcription-DNA |
X-ray (2.3 Å) |
Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA,
Rastinejad F |
(1998) "Structural
elements of an orphan nuclear receptor-DNA
complex." Mol.Cell, 1,
849-861. doi: 10.1016/S1097-2765(00)80084-2.
|
Reverba orphan nuclear receptor-DNA complex . SNAP output
|
|
1a73
|
hydrolase-DNA |
X-ray (1.8 Å) |
Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
binding and cleavage by the nuclear intron-encoded
homing endonuclease I-PpoI." Nature,
394, 96-101. doi: 10.1038/27952.
|
Intron-encoded endonuclease i-ppoi complexed with DNA .
SNAP output
|
|
1a74
|
hydrolase-DNA |
X-ray (2.2 Å) |
Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
binding and cleavage by the nuclear intron-encoded
homing endonuclease I-PpoI." Nature,
394, 96-101. doi: 10.1038/27952.
|
I-ppol homing endonuclease-DNA complex . SNAP output
|
|
1aay
|
transcription-DNA |
X-ray (1.6 Å) |
Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO |
(1996) "Zif268
protein-DNA complex refined at 1.6 A: a model system
for understanding zinc finger-DNA interactions."
Structure, 4, 1171-1180. doi:
10.1016/S0969-2126(96)00125-6.
|
Zif268 zinc finger-DNA complex . SNAP output
|
|
1ahd
|
DNA binding protein-DNA |
NMR |
Billeter M, Qian YQ, Otting G, Muller M, Gehring W,
Wuthrich K |
(1993) "Determination
of the nuclear magnetic resonance solution structure of
an Antennapedia homeodomain-DNA complex."
J.Mol.Biol., 234, 1084-1097.
doi: 10.1006/jmbi.1993.1661.
|
Determination of the NMR solution structure of an
antennapedia homeodomain-DNA complex . SNAP output
|
|
1ais
|
transcription-DNA |
X-ray (2.1 Å) |
Kosa PF, Ghosh G, DeDecker BS, Sigler PB |
(1997) "The 2.1-A
crystal structure of an archaeal preinitiation complex:
TATA-box-binding protein/transcription factor (II)B
core/TATA-box." Proc.Natl.Acad.Sci.USA,
94, 6042-6047. doi: 10.1073/pnas.94.12.6042.
|
Tata-binding protein-transcription factor
(ii)b-tata-box complex from pyrococcus woesei .
SNAP output
|
|
1akh
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Li T, Jin Y, Vershon AK, Wolberger C |
(1998) "Crystal
structure of the MATa1/MATalpha2 homeodomain
heterodimer in complex with DNA containing an
A-tract." Nucleic Acids Res.,
26, 5707-5718. doi: 10.1093/nar/26.24.5707.
|
Mat a1-alpha2-DNA ternary complex . SNAP output
|
|
1am9
|
transcription-DNA |
X-ray (2.3 Å) |
Parraga A, Bellsolell L, Ferre-D'Amare AR, Burley
SK |
(1998) "Co-crystal
structure of sterol regulatory element binding protein
1a at 2.3 A resolution." Structure,
6, 661-672. doi: 10.1016/S0969-2126(98)00067-7.
|
Human srebp-1a bound to ldl receptor promoter .
SNAP output
|
|
1an2
|
transcription-DNA |
X-ray (2.9 Å) |
Ferre-D'Amare AR, Prendergast GC, Ziff EB, Burley
SK |
(1993) "Recognition
by Max of its cognate DNA through a dimeric b/HLH/Z
domain." Nature, 363,
38-45. doi: 10.1038/363038a0.
|
Recognition by max of its cognate DNA through a dimeric
b-hlh-z domain . SNAP
output
|
|
1an4
|
transcription-DNA |
X-ray (2.9 Å) |
Ferre-D'Amare AR, Pognonec P, Roeder RG, Burley
SK |
(1994) "Structure
and function of the b/HLH/Z domain of USF."
EMBO J., 13, 180-189.
|
Structure and function of the b-hlh-z domain of usf .
SNAP output
|
|
1aoi
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond
TJ |
(1997) "Crystal
structure of the nucleosome core particle at 2.8 A
resolution." Nature, 389,
251-260. doi: 10.1038/38444.
|
Complex between nucleosome core particle
(h3,h4,h2a,h2b) and 146 bp long DNA fragment . SNAP output
|
|
1apl
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo
CO |
(1991) "Crystal
structure of a MAT alpha 2 homeodomain-operator complex
suggests a general model for homeodomain-DNA
interactions." Cell(Cambridge,Mass.),
67, 517-528. doi: 10.1016/0092-8674(91)90526-5.
|
Crystal structure of a mat-alpha2 homeodomain-operator
complex suggests a general model for homeodomain-DNA
interactions . SNAP
output
|
|
1au7
|
transcription-DNA |
X-ray (2.3 Å) |
Jacobson EM, Li P, Leon-del-Rio A, Rosenfeld MG,
Aggarwal AK |
(1997) "Structure
of Pit-1 POU domain bound to DNA as a dimer: unexpected
arrangement and flexibility." Genes Dev.,
11, 198-212.
|
Pit-1 mutant-DNA complex . SNAP output
|
|
1awc
|
transcription-DNA |
X-ray (2.15 Å) |
Batchelor AH, Piper DE, de la Brousse FC, McKnight
SL, Wolberger C |
(1998) "The
structure of GABPalpha/beta: an ETS domain- ankyrin
repeat heterodimer bound to DNA." Science,
279, 1037-1041. doi: 10.1126/science.279.5353.1037.
|
Mouse gabp alpha-beta domain bound to DNA . SNAP output
|
|
1az0
|
hydrolase-DNA |
X-ray (2.0 Å) |
Perona JJ, Martin AM |
(1997) "Conformational
transitions and structural deformability of EcoRV
endonuclease revealed by crystallographic
analysis." J.Mol.Biol.,
273, 207-225. doi: 10.1006/jmbi.1997.1315.
|
Ecorv endonuclease-DNA complex . SNAP output
|
|
1azp
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver
JW, Wang AH |
(1998) "The
hyperthermophile chromosomal protein Sac7d sharply
kinks DNA." Nature, 392,
202-205. doi: 10.1038/32455.
|
Hyperthermophile chromosomal protein sac7d bound with
kinked DNA duplex . SNAP
output
|
|
1azq
|
DNA binding protein-DNA |
X-ray (1.94 Å) |
Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver
JW, Wang AH |
(1998) "The
hyperthermophile chromosomal protein Sac7d sharply
kinks DNA." Nature, 392,
202-205. doi: 10.1038/32455.
|
Hyperthermophile chromosomal protein sac7d bound with
kinked DNA duplex . SNAP
output
|
|
1b01
|
gene regulation-DNA |
X-ray (2.56 Å) |
Gomis-Ruth FX, Sola M, Acebo P, Parraga A, Guasch A,
Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll
M |
(1998) "The
structure of plasmid-encoded transcriptional repressor
CopG unliganded and bound to its operator."
EMBO J., 17, 7404-7415. doi:
10.1093/emboj/17.24.7404.
|
Transcriptional repressor copg-DNA complex . SNAP output
|
|
1b3t
|
protein-DNA |
X-ray (2.2 Å) |
Bochkarev A, Bochkareva E, Frappier L, Edwards
AM |
(1998) "The 2.2 A
structure of a permanganate-sensitive DNA site bound by
the Epstein-Barr virus origin binding protein,
EBNA1." J.Mol.Biol., 284,
1273-1278. doi: 10.1006/jmbi.1998.2247.
|
Ebna-1 nuclear protein-DNA complex . SNAP output
|
|
1b69
|
integrase-DNA |
NMR |
Wojciak JM, Connolly KM, Clubb RT |
(1999) "NMR
structure of the Tn916 integrase-DNA complex."
Nat.Struct.Biol., 6, 366-373.
doi: 10.1038/7603.
|
The solution structure of tn916 integrase n-terminal
domain-DNA complex . SNAP output
|
|
1b72
|
protein-DNA |
X-ray (2.35 Å) |
Piper DE, Batchelor AH, Chang CP, Cleary ML,
Wolberger C |
(1999) "Structure
of a HoxB1-Pbx1 heterodimer bound to DNA: role of the
hexapeptide and a fourth homeodomain helix in complex
formation." Cell(Cambridge,Mass.),
96, 587-597. doi: 10.1016/S0092-8674(00)80662-5.
|
Pbx1, homeobox protein hox-b1-DNA ternary complex .
SNAP output
|
|
1b8i
|
transcription-DNA |
X-ray (2.4 Å) |
Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal
AK |
(1999) "Structure
of a DNA-bound Ultrabithorax-Extradenticle homeodomain
complex." Nature, 397,
714-719. doi: 10.1038/17833.
|
Structure of the homeotic ubx-exd-DNA ternary complex .
SNAP output
|
|
1b94
|
hydrolase-DNA |
X-ray (1.9 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Restriction endonuclease ecorv with calcium . SNAP output
|
|
1b95
|
hydrolase-DNA |
X-ray (2.05 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Analysis of a mutational hot-spot in the ecorv
restriction endonuclease: a catalytic role for a main
chain carbonyl group . SNAP output
|
|
1b96
|
hydrolase-DNA |
X-ray (2.3 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Analysis of a mutational hot-spot in the ecorv
restriction endonuclease: a catalytic role for a main
chain carbonyl group . SNAP output
|
|
1b97
|
hydrolase-DNA |
X-ray (1.9 Å) |
Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin
GS |
(1999) "Structural
analysis of a mutational hot-spot in the EcoRV
restriction endonuclease: a catalytic role for a main
chain carbonyl group." Nucleic Acids Res.,
27, 3438-3445. doi: 10.1093/nar/27.17.3438.
|
Analysis of a mutational hot-spot in the ecorv
restriction endonuclease: a catalytic role for a main
chain carbonyl group . SNAP output
|
|
1bbx
|
DNA binding protein-DNA |
NMR |
Agback P, Baumann H, Knapp S, Ladenstein R, Hard
T |
(1998) "Architecture
of Nonspecific Protein-DNA Interactions in the
Sso7D-DNA Complex." Nat.Struct.Biol.,
5, 579-584. doi: 10.1038/836.
|
Non-specific protein-DNA interactions in the sso7d-DNA
complex, NMR, 1 structure . SNAP output
|
|
1bc7
|
transcription-DNA |
X-ray (2.01 Å) |
Mo Y, Vaessen B, Johnston K, Marmorstein R |
(1998) "Structures
of SAP-1 bound to DNA targets from the E74 and c-fos
promoters: insights into DNA sequence discrimination by
Ets proteins." Mol.Cell,
2, 201-212. doi: 10.1016/S1097-2765(00)80130-6.
|
Serum response factor accessory protein 1a (sap-1)-DNA
complex . SNAP
output
|
|
1bc8
|
transcription-DNA |
X-ray (1.93 Å) |
Mo Y, Vaessen B, Johnston K, Marmorstein R |
(1998) "Structures
of SAP-1 bound to DNA targets from the E74 and c-fos
promoters: insights into DNA sequence discrimination by
Ets proteins." Mol.Cell,
2, 201-212. doi: 10.1016/S1097-2765(00)80130-6.
|
Structures of sap-1 bound to DNA sequences from the e74
and c-fos promoters provide insights into how ets
proteins discriminate between related DNA targets .
SNAP output
|
|
1bdh
|
transcription-DNA |
X-ray (2.7 Å) |
Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan
RG |
(1996) "A Positively Charged Residue Bound in the
Minor Groove Does not Alter the Bending of a DNA Duplex."
J.Am.Chem.Soc., 118,
13073-13074. |
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
|
1bdi
|
transcription-DNA |
X-ray (3.0 Å) |
Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan
RG |
(1996) "A Positively Charged Residue Bound in the
Minor Groove Does not Alter the Bending of a DNA Duplex."
J.Am.Chem.Soc., 118,
13073-13074. |
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
|
1bdt
|
gene regulation-DNA |
X-ray (2.5 Å) |
Schildbach JF, Karzai AW, Raumann BE, Sauer RT |
(1999) "Origins
of DNA-binding specificity: role of protein contacts
with the DNA backbone."
Proc.Natl.Acad.Sci.USA, 96,
811-817. doi: 10.1073/pnas.96.3.811.
|
Wild type gene-regulating protein arc-DNA complex .
SNAP output
|
|
1bdv
|
gene regulation-DNA |
X-ray (2.8 Å) |
Schildbach JF, Karzai AW, Raumann BE, Sauer RT |
(1999) "Origins
of DNA-binding specificity: role of protein contacts
with the DNA backbone."
Proc.Natl.Acad.Sci.USA, 96,
811-817. doi: 10.1073/pnas.96.3.811.
|
Arc fv10 cocrystal . SNAP output
|
|
1bf4
|
DNA-binding protein-DNA |
X-ray (1.6 Å) |
Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L,
McCrary BS, Edmondson SP, Shriver JW, Wang AH |
(1998) "The
crystal structure of the hyperthermophile chromosomal
protein Sso7d bound to DNA."
Nat.Struct.Biol., 5, 782-786.
doi: 10.1038/1822.
|
Chromosomal DNA-binding protein sso7d-d(gcgaacgc)
complex . SNAP
output
|
|
1bf5
|
gene regulation-DNA |
X-ray (2.9 Å) |
Chen X, Vinkemeier U, Zhao Y, Jeruzalmi D, Darnell Jr
JE, Kuriyan J |
(1998) "Crystal
structure of a tyrosine phosphorylated STAT-1 dimer
bound to DNA." Cell(Cambridge,Mass.),
93, 827-839. doi: 10.1016/S0092-8674(00)81443-9.
|
Tyrosine phosphorylated stat-1-DNA complex . SNAP output
|
|
1bg1
|
transcription-DNA |
X-ray (2.25 Å) |
Becker S, Groner B, Muller CW |
(1998) "Three-dimensional
structure of the Stat3beta homodimer bound to DNA."
Nature, 394, 145-151. doi:
10.1038/28101.
|
Transcription factor stat3b-DNA complex . SNAP output
|
|
1bgb
|
hydrolase-DNA |
X-ray (2.0 Å) |
Horton NC, Perona JJ |
(1998) "Recognition
of flanking DNA sequences by EcoRV endonuclease
involves alternative patterns of water-mediated
contacts." J.Biol.Chem.,
273, 21721-21729. doi: 10.1074/jbc.273.34.21721.
|
Ecorv endonuclease complex with 5'-cgggatatccc DNA .
SNAP output
|
|
1bhm
|
hydrolase-DNA |
X-ray (2.2 Å) |
Newman M, Strzelecka T, Dorner LF, Schildkraut I,
Aggarwal AK |
(1995) "Structure
of Bam HI endonuclease bound to DNA: partial folding
and unfolding on DNA binding." Science,
269, 656-663.
|
Restriction endonuclease bamhi complex with DNA .
SNAP output
|
|
1bj6
|
viral protein-DNA |
NMR |
Morellet N, Demene H, Teilleux V, Huynh-Dinh T, de
Rocquigny H, Fournie-Zaluski MC, Roques BP |
(1998) "Structure
of the complex between the HIV-1 nucleocapsid protein
NCp7 and the single-stranded pentanucleotide
d(ACGCC)." J.Mol.Biol.,
283, 419-434. doi: 10.1006/jmbi.1998.2098.
|
1h NMR of (12-53) ncp7-d(acgcc) complex, 10 structures
. SNAP output
|
|
1bl0
|
transcription-DNA |
X-ray (2.3 Å) |
Rhee S, Martin RG, Rosner JL, Davies DR |
(1998) "A novel
DNA-binding motif in MarA: the first structure for an
AraC family transcriptional activator."
Proc.Natl.Acad.Sci.USA, 95,
10413-10418. doi: 10.1073/pnas.95.18.10413.
|
Multiple antibiotic resistance protein (mara)-DNA
complex . SNAP
output
|
|
1bnk
|
hydrolase-DNA |
X-ray (2.7 Å) |
Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger
T |
(1998) "Crystal
structure of a human alkylbase-DNA repair enzyme
complexed to DNA: mechanisms for nucleotide flipping
and base excision." Cell(Cambridge,Mass.),
95, 249-258. doi: 10.1016/S0092-8674(00)81755-9.
|
Human 3-methyladenine DNA glycosylase complexed to DNA
. SNAP output
|
|
1bnz
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L,
McCrary BS, Edmondson SP, Shriver JW, Wang AH |
(1998) "The
crystal structure of the hyperthermophile chromosomal
protein Sso7d bound to DNA."
Nat.Struct.Biol., 5, 782-786.
doi: 10.1038/1822.
|
Sso7d hyperthermophile protein-DNA complex . SNAP output
|
|
1bp7
|
transcription-DNA |
X-ray (3.0 Å) |
Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
recognition and cleavage by the LAGLIDADG homing
endonuclease I-CreI." Mol.Cell,
2, 469-476. doi: 10.1016/S1097-2765(00)80146-X.
|
Group i mobile intron endonuclease i-crei complexed
with homing site DNA . SNAP output
|
|
1bpx
|
transferase-DNA |
X-ray (2.4 Å) |
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier
H |
(1997) "Crystal
structures of human DNA polymerase beta complexed with
gapped and nicked DNA: evidence for an induced fit
mechanism." Biochemistry,
36, 11205-11215. doi: 10.1021/bi9703812.
|
DNA polymerase beta-DNA complex . SNAP output
|
|
1bpy
|
transferase-DNA |
X-ray (2.2 Å) |
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier
H |
(1997) "Crystal
structures of human DNA polymerase beta complexed with
gapped and nicked DNA: evidence for an induced fit
mechanism." Biochemistry,
36, 11205-11215. doi: 10.1021/bi9703812.
|
Human DNA polymerase beta complexed with gapped DNA and
ddctp . SNAP output
|
|
1bpz
|
transferase-DNA |
X-ray (2.6 Å) |
Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier
H |
(1997) "Crystal
structures of human DNA polymerase beta complexed with
gapped and nicked DNA: evidence for an induced fit
mechanism." Biochemistry,
36, 11205-11215. doi: 10.1021/bi9703812.
|
Human DNA polymerase beta complexed with nicked DNA .
SNAP output
|
|
1brn
|
hydrolase-DNA |
X-ray (1.76 Å) |
Buckle AM, Fersht AR |
(1994) "Subsite
binding in an RNase: structure of a
barnase-tetranucleotide complex at 1.76-A
resolution." Biochemistry,
33, 1644-1653. doi: 10.1021/bi00173a005.
|
Subsite binding in an rnase: structure of a
barnase-tetranucleotide complex at 1.76 angstroms
resolution . SNAP
output
|
|
1bss
|
hydrolase-DNA |
X-ray (2.15 Å) |
Horton NC, Newberry KJ, Perona JJ |
(1998) "Metal
ion-mediated substrate-assisted catalysis in type II
restriction endonucleases."
Proc.Natl.Acad.Sci.USA, 95,
13489-13494. doi: 10.1073/pnas.95.23.13489.
|
Ecorv-t93a-DNA-ca2+ . SNAP output
|
|
1bsu
|
hydrolase-DNA |
X-ray (2.0 Å) |
Martin AM, Sam MD, Reich NO, Perona JJ |
(1999) "Structural
and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease." Nat.Struct.Biol.,
6, 269-277. doi: 10.1038/6707.
|
Structural and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease . SNAP
output
|
|
1bua
|
hydrolase-DNA |
X-ray (2.15 Å) |
Martin AM, Sam MD, Reich NO, Perona JJ |
(1999) "Structural
and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease." Nat.Struct.Biol.,
6, 269-276. doi: 10.1038/6707.
|
Structural and energetic origins of indirect readout in
site-specific DNA cleavage by a restriction
endonuclease . SNAP
output
|
|
1bvo
|
complex (transcription factor-DNA) |
X-ray (2.7 Å) |
Cramer P, Varrot A, Barillas-Mury C, Kafatos FC,
Muller CW |
(1999) "Structure
of the specificity domain of the Dorsal homologue
Gambif1 bound to DNA." Structure
Fold.Des., 7, 841-852. doi:
10.1016/S0969-2126(99)80107-5.
|
Dorsal homologue gambif1 bound to DNA . SNAP output
|
|
1by4
|
gene regulation-DNA |
X-ray (2.1 Å) |
Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B,
Rastinejad F |
(2000) "Structural
basis of RXR-DNA interactions."
J.Mol.Biol., 296, 509-520.
doi: 10.1006/jmbi.1999.3457.
|
Structure and mechanism of the homodimeric assembly of
the rxr on DNA . SNAP
output
|
|
1c0w
|
gene regulation-DNA |
X-ray (3.2 Å) |
Pohl E, Holmes RK, Hol WG |
(1999) "Crystal
structure of a cobalt-activated diphtheria toxin
repressor-DNA complex reveals a metal-binding SH3-like
domain." J.Mol.Biol.,
292, 653-667. doi: 10.1006/jmbi.1999.3073.
|
Crystal structure of the cobalt-activated diphtheria
toxin repressor-DNA complex reveals a metal binding
sh-like domain . SNAP
output
|
|
1c7u
|
transcription-DNA |
NMR |
Huang K, Louis JM, Donaldson L, Lim FL, Sharrocks AD,
Clore GM |
(2000) "Solution
structure of the MEF2A-DNA complex: structural basis
for the modulation of DNA bending and specificity by
MADS-box transcription factors." Embo J.,
19, 2615-2628. doi: 10.1093/emboj/19.11.2615.
|
Complex of the DNA binding core domain of the
transcription factor mef2a with a 20mer oligonucleotide
. SNAP output
|
|
1c7y
|
recombination-DNA |
X-ray (3.1 Å) |
Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H,
Morikawa K |
(2000) "Crystal
structure of the holliday junction DNA in complex with
a single RuvA tetramer."
Proc.Natl.Acad.Sci.USA, 97,
8257-8262. doi: 10.1073/pnas.140212997.
|
E.coli ruva-holliday junction complex . SNAP output
|
|
1c8c
|
DNA binding protein-DNA |
X-ray (1.45 Å) |
Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP,
Shriver JW, Wang AH |
(2000) "Crystal
structures of the chromosomal proteins Sso7d/Sac7d
bound to DNA containing T-G mismatched base-pairs."
J.Mol.Biol., 303, 395-403.
doi: 10.1006/jmbi.2000.4112.
|
Crystal structures of the chromosomal proteins
sso7d-sac7d bound to DNA containing t-g mismatched base
pairs . SNAP output
|
|
1c9b
|
transcription-DNA |
X-ray (2.65 Å) |
Tsai FT, Sigler PB |
(2000) "Structural
basis of preinitiation complex assembly on human pol II
promoters." EMBO J., 19,
25-36. doi: 10.1093/emboj/19.1.25.
|
Crystal structure of a human tbp core domain-human
tfiib core domain complex bound to an extended,
modified adenoviral major late promoter (admlp) .
SNAP output
|
|
1ca5
|
structural protein-DNA |
X-ray (2.2 Å) |
Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP,
Shriver JW, Wang AH-J |
(2000) "Crystal
structures of the chromosomal proteins Sso7d/Sac7d
bound to DNA containing T-G mismatched base-pairs."
J.Mol.Biol., 303, 395-403.
doi: 10.1006/jmbi.2000.4112.
|
Intercalation site of hyperthermophile chromosomal
protein sso7d-sac7d bound to DNA . SNAP output
|
|
1ca6
|
structural protein-DNA |
X-ray (2.2 Å) |
Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP,
Shriver JW, Wang AH-J |
(2000) "Crystal
structures of the chromosomal proteins Sso7d/Sac7d
bound to DNA containing T-G mismatched base-pairs."
J.Mol.Biol., 303, 395-403.
doi: 10.1006/jmbi.2000.4112.
|
Intercalation site of hyperthermophile chromosomal
protein sso7d-sac7d bound to DNA . SNAP output
|
|
1cbv
|
immune system-DNA |
X-ray (2.66 Å) |
Herron JN, He XM, Ballard DW, Blier PR, Pace PE,
Bothwell AL, Voss Jr EW, Edmundson AB |
(1991) "An
autoantibody to single-stranded DNA: comparison of the
three-dimensional structures of the unliganded Fab and
a deoxynucleotide-Fab complex." Proteins,
11, 159-175. doi: 10.1002/prot.340110302.
|
An autoantibody to single-stranded DNA: comparison of
the three-dimensional structures of the unliganded fab
and a deoxynucleotide-fab complex . SNAP output
|
|
1cdw
|
transcription-DNA |
X-ray (1.9 Å) |
Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG,
Burley SK |
(1996) "Crystal
structure of a human TATA box-binding protein/TATA
element complex." Proc.Natl.Acad.Sci.USA,
93, 4862-4867. doi: 10.1073/pnas.93.10.4862.
|
Human tbp core domain complexed with DNA . SNAP output
|
|
1cez
|
transferase-DNA |
X-ray (2.4 Å) |
Cheetham GM, Jeruzalmi D, Steitz TA |
(1999) "Structural
basis for initiation of transcription from an RNA
polymerase-promoter complex." Nature,
399, 80-83. doi: 10.1038/19999.
|
Crystal structure of a t7 RNA polymerase-t7 promoter
complex . SNAP
output
|
|
1cf7
|
transcription-DNA |
X-ray (2.6 Å) |
Zheng N, Fraenkel E, Pabo CO, Pavletich NP |
(1999) "Structural
basis of DNA recognition by the heterodimeric cell
cycle transcription factor E2F-DP." Genes
Dev., 13, 666-674.
|
Structural basis of DNA recognition by the
heterodimeric cell cycle transcription factor e2f-dp .
SNAP output
|
|
1cgp
|
transcription-DNA |
X-ray (3.0 Å) |
Schultz SC, Shields GC, Steitz TA |
(1991) "Crystal
structure of a CAP-DNA complex: the DNA is bent by 90
degrees." Science, 253,
1001-1007.
|
Catabolite gene activator protein (cap)-DNA complex +
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
|
1cit
|
transcription-DNA |
X-ray (2.7 Å) |
Meinke G, Sigler PB |
(1999) "DNA-binding
mechanism of the monomeric orphan nuclear receptor
NGFI-B." Nat.Struct.Biol.,
6, 471-477. doi: 10.1038/8276.
|
DNA-binding mechanism of the monomeric orphan nuclear
receptor ngfi-b . SNAP
output
|
|
1cjg
|
transcription-DNA |
NMR |
Spronk CA, Bonvin AM, Radha PK, Melacini G, Boelens
R, Kaptein R |
(1999) "The
solution structure of Lac repressor headpiece 62
complexed to a symmetrical lac operator."
Structure Fold.Des., 7,
1483-1492. doi: 10.1016/S0969-2126(00)88339-2.
|
NMR structure of lac repressor hp62-DNA complex .
SNAP output
|
|
1ckq
|
protein-DNA |
X-ray (1.85 Å) |
Horvath M, Choi J, Kim Y, Wilkosz PA, Chandrasekhar
K, Rosenberg JM |
"The Integration of Recognition and Cleavage: X-Ray
Structures of Pre- Transition State and Post-Reactive
DNA-Eco Ri Endonuclease Complexes." |
Pre-transition state eco ri endonuclease-cognate DNA
(tcgcgaattcgcg) complex . SNAP output
|
|
1ckt
|
gene regulation-DNA |
X-ray (2.5 Å) |
Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ |
(1999) "Basis
for recognition of cisplatin-modified DNA by
high-mobility-group proteins." Nature,
399, 708-712. doi: 10.1038/21460.
|
Crystal structure of hmg1 domain a bound to a
cisplatin-modified DNA duplex . SNAP output
|
|
1cl8
|
protein-DNA |
X-ray (1.8 Å) |
Horvath M, Rosenberg JM |
"Iap (Inner-Adenine to Purine): A Cognate EcoRI-DNA
Base Analog Complex." |
A pre-transition state eco ri endonuclease-cognate DNA
(tcgcgapttcgcg) complex with DNA base analog purine (p)
. SNAP output
|
|
1clq
|
transferase-DNA |
X-ray (2.7 Å) |
Shamoo Y, Steitz TA |
(1999) "Building
a replisome from interacting pieces: sliding clamp
complexed to a peptide from DNA polymerase and a
polymerase editing complex."
Cell(Cambridge,Mass.), 99,
155-166. doi: 10.1016/S0092-8674(00)81647-5.
|
Crystal structure of a replication fork DNA polymerase
editing complex at 2.7 Å resolution . SNAP output
|
|
1cma
|
transcription-DNA |
X-ray (2.8 Å) |
Somers WS, Phillips SE |
(1992) "Crystal
structure of the met repressor-operator complex at 2.8
A resolution reveals DNA recognition by
beta-strands." Nature,
359, 387-393. doi: 10.1038/359387a0.
|
Met repressor-DNA complex + s-adenosyl-methionine .
SNAP output
|
|
1co0
|
transcription |
NMR |
Brocchieri L, Zhou GP, Jardetzky O |
(2002) "Allostery and Induced Fit, NMR and Molecular
Modeling Study of the trp-repressor - mtr DNA complex."
Structures and Mechanisms, ACS Symposium Series,
827, 340-366. |
NMR study of trp repressor-mtr operator DNA complex .
SNAP output
|
|
1cqt
|
gene regulation-DNA |
X-ray (3.2 Å) |
Chasman D, Cepek K, Sharp PA, Pabo CO |
(1999) "Crystal
structure of an OCA-B peptide bound to an Oct-1 POU
domain/octamer DNA complex: specific recognition of a
protein-DNA interface." Genes Dev.,
13, 2650-2657. doi: 10.1101/gad.13.20.2650.
|
Crystal structure of a ternary complex containing an
oca-b peptide, the oct-1 pou domain, and an octamer
element . SNAP
output
|
|
1crx
|
replication-DNA |
X-ray (2.4 Å) |
Guo F, Gopaul DN, van Duyne GD |
(1997) "Structure
of Cre recombinase complexed with DNA in a
site-specific recombination synapse."
Nature, 389, 40-46. doi:
10.1038/37925.
|
Cre recombinase-DNA complex reaction intermediate i .
SNAP output
|
|
1cw0
|
hydrolase-DNA |
X-ray (2.3 Å) |
Tsutakawa SE, Jingami H, Morikawa K |
(1999) "Recognition
of a TG mismatch: the crystal structure of very short
patch repair endonuclease in complex with a DNA
duplex." Cell(Cambridge,Mass.),
99, 615-623. doi: 10.1016/S0092-8674(00)81550-0.
|
Crystal structure analysis of very short patch repair
(vsr) endonuclease in complex with a duplex DNA .
SNAP output
|
|
1cyq
|
hydrolase-DNA |
X-ray (1.93 Å) |
Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE,
Monnat Jr RJ, Stoddard BL |
(1999) "A novel
endonuclease mechanism directly visualized for
I-PpoI." Nat.Struct.Biol.,
6, 1096-1099. doi: 10.1038/70027.
|
Intron encoded homing endonuclease i-ppoi (h98a)-DNA
homing site complex . SNAP output
|
|
1cz0
|
hydrolase-DNA |
X-ray (2.1 Å) |
Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE,
Monnat Jr RJ, Stoddard BL |
(1999) "A novel
endonuclease mechanism directly visualized for
I-PpoI." Nat.Struct.Biol.,
6, 1096-1099. doi: 10.1038/70027.
|
Intron encoded homing endonuclease i-ppoi-DNA complex
lacking catalytic metal ion . SNAP output
|
|
1d02
|
hydrolase-DNA |
X-ray (1.7 Å) |
Deibert M, Grazulis S, Janulaitis A, Siksnys V, Huber
R |
(1999) "Crystal
structure of MunI restriction endonuclease in complex
with cognate DNA at 1.7 A resolution." EMBO
J., 18, 5805-5816. doi: 10.1093/emboj/18.21.5805.
|
Crystal structure of muni restriction endonuclease in
complex with cognate DNA . SNAP output
|
|
1d0e
|
transferase-DNA |
X-ray (3.0 Å) |
Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP,
Gu J, Georgiadis MM |
(2000) "Crystal
structures of an N-terminal fragment from Moloney
murine leukemia virus reverse transcriptase complexed
with nucleic acid: functional implications for
template-primer binding to the fingers domain."
J.Mol.Biol., 296, 613-632.
doi: 10.1006/jmbi.1999.3477.
|
Crystal structures of the n-terminal fragment from
moloney murine leukemia virus reverse transcriptase
complexed with nucleic acid: functional implications
for template-primer binding to the fingers domain .
SNAP output
|
|
1d1u
|
hydrolase-DNA |
X-ray (2.3 Å) |
Cote ML, Yohannan SJ, Georgiadis MM |
(2000) "Use of
an N-terminal fragment from moloney murine leukemia
virus reverse transcriptase to facilitate
crystallization and analysis of a pseudo-16-mer DNA
molecule containing G-A mispairs." Acta
Crystallogr.,Sect.D, 56,
1120-1131. doi: 10.1107/S0907444900008246.
|
Use of an n-terminal fragment from moloney murine
leukemia virus reverse transcriptase to facilitate
crystallization and analysis of a pseudo-16-mer DNA
molecule containing g-a mispairs . SNAP output
|
|
1d2i
|
hydrolase-DNA |
X-ray (1.7 Å) |
Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK |
(2000) "Understanding
the immutability of restriction enzymes: crystal
structure of BglII and its DNA substrate at 1.5 A
resolution." Nat.Struct.Biol.,
7, 134-140. doi: 10.1038/72405.
|
Crystal structure of restriction endonuclease bglii
complexed with DNA 16-mer . SNAP output
|
|
1d3u
|
gene regulation-DNA |
X-ray (2.4 Å) |
Littlefield O, Korkhin Y, Sigler PB |
(1999) "The
structural basis for the oriented assembly of a
TBP/TFB/promoter complex."
Proc.Natl.Acad.Sci.USA, 96,
13668-13673. doi: 10.1073/pnas.96.24.13668.
|
Tata-binding protein-transcription factor
(ii)b-bre+tata-box complex from pyrococcus woesei .
SNAP output
|
|
1d5y
|
transcription-DNA |
X-ray (2.7 Å) |
Kwon HJ, Bennik MH, Demple B, Ellenberger T |
(2000) "Crystal
structure of the Escherichia coli Rob transcription
factor in complex with DNA."
Nat.Struct.Biol., 7, 424-430.
doi: 10.1038/75213.
|
Crystal structure of the e. coli rob transcription
factor in complex with DNA . SNAP output
|
|
1d66
|
transcription-DNA |
X-ray (2.7 Å) |
Marmorstein R, Carey M, Ptashne M, Harrison SC |
(1992) "DNA
recognition by GAL4: structure of a protein-DNA
complex." Nature, 356,
408-414. doi: 10.1038/356408a0.
|
DNA recognition by gal4: structure of a protein-DNA
complex . SNAP
output
|
|
1d8y
|
transferase-DNA |
X-ray (2.08 Å) |
Teplova M, Wallace ST, Tereshko V, Minasov G, Symons
AM, Cook PD, Manoharan M, Egli M |
(1999) "Structural
origins of the exonuclease resistance of a zwitterionic
RNA." Proc.Natl.Acad.Sci.USA,
96, 14240-14245. doi: 10.1073/pnas.96.25.14240.
|
Crystal structure of the complex of DNA polymerase i
klenow fragment with DNA . SNAP output
|
|
1dc1
|
hydrolase-DNA |
X-ray (1.7 Å) |
van der Woerd MJ, Pelletier JJ, Xu S, Friedman
AM |
(2001) "Restriction
enzyme BsoBI-DNA complex: a tunnel for recognition of
degenerate DNA sequences and potential histidine
catalysis." Structure, 9,
133-144. doi: 10.1016/S0969-2126(01)00564-0.
|
Restriction enzyme bsobi-DNA complex structure:
encirclement of the DNA and histidine-catalyzed
hydrolysis within a canonical restriction enzyme fold .
SNAP output
|
|
1dct
|
transferase-DNA |
X-ray (2.8 Å) |
Reinisch KM, Chen L, Verdine GL, Lipscomb WN |
(1995) "The
crystal structure of HaeIII methyltransferase
convalently complexed to DNA: an extrahelical cytosine
and rearranged base pairing."
Cell(Cambridge,Mass.), 82,
143-153. doi: 10.1016/0092-8674(95)90060-8.
|
DNA (cytosine-5) methylase from haeiii covalently bound
to DNA . SNAP output
|
|
1ddn
|
gene regulation-DNA |
X-ray (3.0 Å) |
White A, Ding X, vanderSpek JC, Murphy JR, Ringe
D |
(1998) "Structure
of the metal-ion-activated diphtheria toxin
repressor/tox operator complex." Nature,
394, 502-506. doi: 10.1038/28893.
|
Diphtheria tox repressor (c102d mutant)-tox DNA
operator complex . SNAP
output
|
|
1de8
|
lyase-DNA |
X-ray (2.95 Å) |
Mol CD, Izumi T, Mitra S, Tainer JA |
(2000) "DNA-bound
structures and mutants reveal abasic DNA binding by
APE1 and DNA repair coordination [corrected."
Nature, 403, 451-456. doi:
10.1038/35000249.
|
Human apurinic-apyrimidinic endonuclease-1 (ape1) bound
to abasic DNA . SNAP
output
|
|
1de9
|
lyase-DNA |
X-ray (3.0 Å) |
Mol CD, Izumi T, Mitra S, Tainer JA |
(2000) "DNA-bound
structures and mutants reveal abasic DNA binding by
APE1 and DNA repair coordination." Nature,
403, 451-456. doi: 10.1038/35000249.
|
Human ape1 endonuclease with bound abasic DNA and mn2+
ion . SNAP output
|
|
1dew
|
lyase-DNA |
X-ray (2.65 Å) |
Mol CD, Izumi T, Mitra S, Tainer JA |
(2000) "DNA-bound
structures and mutants reveal abasic DNA binding by
APE1 and DNA repair coordination." Nature,
403, 451-456. doi: 10.1038/35000249.
|
Crystal structure of human ape1 bound to abasic DNA .
SNAP output
|
|
1dfm
|
hydrolase-DNA |
X-ray (1.5 Å) |
Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK |
(2000) "Understanding
the immutability of restriction enzymes: crystal
structure of BglII and its DNA substrate at 1.5 A
resolution." Nat.Struct.Biol.,
7, 134-140. doi: 10.1038/72405.
|
Crystal structure of restriction endonuclease bglii
complexed with DNA 16-mer . SNAP output
|
|
1dgc
|
transcription-DNA |
X-ray (3.0 Å) |
Konig P, Richmond TJ |
(1993) "The X-ray
structure of the GCN4-bZIP bound to ATF/CREB site DNA
shows the complex depends on DNA flexibility."
J.Mol.Biol., 233, 139-154.
doi: 10.1006/jmbi.1993.1490.
|
The x-ray structure of the gcn4-bzip bound to atf-creb
site DNA shows the complex depends on DNA flexibility .
SNAP output
|
|
1dh3
|
transcription-DNA |
X-ray (3.0 Å) |
Schumacher MA, Goodman RH, Brennan RG |
(2000) "The
structure of a CREB bZIP.somatostatin CRE complex
reveals the basis for selective dimerization and
divalent cation-enhanced DNA binding."
J.Biol.Chem., 275,
35242-35247. doi: 10.1074/jbc.M007293200.
|
Crystal structure of a creb bzip-cre complex reveals
the basis for creb faimly selective dimerization and
DNA binding . SNAP
output
|
|
1diz
|
hydrolase-DNA |
X-ray (2.5 Å) |
Hollis T, Ichikawa Y, Ellenberger T |
(2000) "DNA
bending and a flip-out mechanism for base excision by
the helix-hairpin-helix DNA glycosylase, Escherichia
coli AlkA." EMBO J., 19,
758-766. doi: 10.1093/emboj/19.4.758.
|
Crystal structure of e. coli 3-methyladenine DNA
glycosylase (alka) complexed with DNA . SNAP output
|
|
1dmu
|
hydrolase-DNA |
X-ray (2.2 Å) |
Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I,
Phillips SE |
(1998) "Crystal
structure of restriction endonuclease BglI bound to its
interrupted DNA recognition sequence." EMBO
J., 17, 5466-5476. doi: 10.1093/emboj/17.18.5466.
|
Crystal structure of the restriction endonuclease bgli
(e.c.3.1.21.4) bound to its DNA recognition sequence .
SNAP output
|
|
1dnk
|
hydrolase-DNA |
X-ray (2.3 Å) |
Weston SA, Lahm A, Suck D |
(1992) "X-ray
structure of the DNase I-d(GGTATACC)2 complex at 2.3 A
resolution." J.Mol.Biol.,
226, 1237-1256. doi: 10.1016/0022-2836(92)91064-V.
|
The x-ray structure of the dnase i-d(ggtatacc)2 complex
at 2.3 angstroms resolution . SNAP output
|
|
1dp7
|
transcription-DNA |
X-ray (1.5 Å) |
Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W,
Mach B, Burley SK |
(2000) "Structure
of the winged-helix protein hRFX1 reveals a new mode of
DNA binding." Nature,
403, 916-921. doi: 10.1038/35002634.
|
Cocrystal structure of rfx-dbd in complex with its
cognate x-box binding site . SNAP output
|
|
1drg
|
hydrolase, ligase-DNA |
X-ray (2.55 Å) |
Woods KC, Martin SS, Chu VC, Baldwin EP |
(2001) "Quasi-equivalence
in site-specific recombinase structure and function:
crystal structure and activity of trimeric Cre
recombinase bound to a three-way Lox DNA junction."
J.Mol.Biol., 313, 49-69. doi:
10.1006/jmbi.2001.5012.
|
Crystal structure of trimeric cre recombinase-lox
complex . SNAP
output
|
|
1dsc
|
DNA-antibiotic |
NMR |
Lian C, Robinson H, Wang AH-J |
(1996) "Structure of Actinomycin D Bound with
(Gaagcttc)2 and (Gatgcttc)2 and its Binding to the
(Cag)N:(Ctg)N Triplet Sequence by NMR Analysis."
J.Am.Chem.Soc., 118, 8791.
doi: 10.1021/JA961631P.
|
NMR study of DNA (5'-d(*gp*ap*ap*gp*cp*tp*tp*c)-3')
self-complementary duplex complexed with actinomycin d,
minimized average structure . SNAP output
|
|
1dsd
|
DNA-antibiotic |
NMR |
Lian C, Robinson H, Wang AH-J |
(1996) "Structure of Actinomycin D Bound with
(Gaagcttc)2 and (Gatgcttc)2 and its Binding to the
(Cag)N:(Ctg)N Triplet Sequence by NMR Analysis."
J.Am.Chem.Soc., 118, 8791.
doi: 10.1021/JA961631P.
|
NMR study of DNA (5'-d(*gp*ap*tp*gp*cp*tp*tp*c)-3') t:t
mismatched duplex complexed with actinomycin d,
minimized average structure . SNAP output
|
|
1dsz
|
transcription-DNA |
X-ray (1.7 Å) |
Rastinejad F, Wagner T, Zhao Q, Khorasanizadeh S |
(2000) "Structure
of the RXR-RAR DNA-binding complex on the retinoic acid
response element DR1." EMBO J.,
19, 1045-1054. doi: 10.1093/emboj/19.5.1045.
|
Structure of the rxr-rar DNA-binding domain heterodimer
in complex with the retinoic acid response element dr1
. SNAP output
|
|
1du0
|
transcription-DNA |
X-ray (2.0 Å) |
Grant RA, Rould MA, Klemm JD, Pabo CO |
(2000) "Exploring
the role of glutamine 50 in the homeodomain-DNA
interface: crystal structure of engrailed (Gln50 -->
ala) complex at 2.0 A." Biochemistry,
39, 8187-8192. doi: 10.1021/bi000071a.
|
Engrailed homeodomain q50a variant DNA complex .
SNAP output
|
|
1dux
|
transcription-DNA |
X-ray (2.1 Å) |
Mo Y, Vaessen B, Johnston K, Marmorstein R |
(2000) "Structure
of the elk-1-DNA complex reveals how DNA-distal
residues affect ETS domain recognition of DNA."
Nat.Struct.Biol., 7, 292-297.
doi: 10.1038/74055.
|
Elk-1-DNA structure reveals how residues distal from
DNA-binding surface affect DNA-recognition . SNAP output
|
|
1e3m
|
DNA binding |
X-ray (2.2 Å) |
Lamers MH, Perrakis A, Enzlin JH, Winterwerp HHK, De
Wind N, Sixma TK |
(2000) "The
Crystal Structure of DNA Mismatch Repair Protein Muts
Binding to a G X T Mismatch." Nature,
407, 711. doi: 10.1038/35037523.
|
The crystal structure of e. coli muts binding to DNA
with a g:t mismatch . SNAP output
|
|
1e3o
|
transcription |
X-ray (1.9 Å) |
Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A,
Reinbold R, Scholer HR, Wilmanns M |
(2001) "Differential
Dimer Activities of the Transcription Factor Oct-1 by
DNA-Induced Interface Swapping." Mol.Cell,
8, 569. doi: 10.1016/S1097-2765(01)00336-7.
|
Crystal structure of oct-1 pou dimer bound to more .
SNAP output
|
|
1ea4
|
gene regulation-DNA |
X-ray (2.95 Å) |
Costa M, Sola M, Del G, Eritja R, Hernaindez-Arriaga
AM, Espinosa M, Gomis-Rueth FX, Coll M |
(2001) "Plasmid
Transcriptional Repressor Copg Oligomerises to Render
Helical Superstructures Unbound and in Complexes with
Oligonucleotides." J.Mol.Biol.,
310, 403. doi: 10.1006/JMBI.2001.4760.
|
Transcriptional repressor copg-22bp dsDNA complex .
SNAP output
|
|
1ebm
|
lyase-DNA |
X-ray (2.1 Å) |
Bruner SD, Norman DP, Verdine GL |
(2000) "Structural
basis for recognition and repair of the endogenous
mutagen 8-oxoguanine in DNA." Nature,
403, 859-866. doi: 10.1038/35002510.
|
Crystal structure of the human 8-oxoguanine glycosylase
(hogg1) bound to a substrate oligonucleotide . SNAP output
|
|
1ecr
|
replication-DNA |
X-ray (2.7 Å) |
Kamada K, Horiuchi T, Ohsumi K, Shimamoto N, Morikawa
K |
(1996) "Structure
of a replication-terminator protein complexed with
DNA." Nature, 383,
598-603. doi: 10.1038/383598a0.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA . SNAP output
|
|
1efa
|
transcription-DNA |
X-ray (2.6 Å) |
Bell CE, Lewis M |
(2000) "A closer
view of the conformation of the Lac repressor bound to
operator." Nat.Struct.Biol.,
7, 209-214. doi: 10.1038/78907.
|
Crystal structure of the lac repressor dimer bound to
operator and the anti-inducer onpf . SNAP output
|
|
1egw
|
transcription-DNA |
X-ray (1.5 Å) |
Santelli E, Richmond TJ |
(2000) "Crystal
structure of MEF2A core bound to DNA at 1.5 A
resolution." J.Mol.Biol.,
297, 437-449. doi: 10.1006/jmbi.2000.3568.
|
Crystal structure of mef2a core bound to DNA . SNAP output
|
|
1ehl
|
immune system |
X-ray (2.4 Å) |
Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka
E, Nikaido O |
(2000) "Crystal
structure of the 64M-2 antibody Fab fragment in complex
with a DNA dT(6-4)T photoproduct formed by ultraviolet
radiation." J.Mol.Biol.,
299, 711-723. doi: 10.1006/jmbi.2000.3772.
|
64m-2 antibody fab complexed with d(5ht)(6-4)t .
SNAP output
|
|
1ej9
|
isomerase-DNA |
X-ray (2.6 Å) |
Redinbo MR, Champoux JJ, Hol WG |
(2000) "Novel
insights into catalytic mechanism from a crystal
structure of human topoisomerase I in complex with
DNA." Biochemistry, 39,
6832-6840. doi: 10.1021/bi992690t.
|
Crystal structure of human topoisomerase i DNA complex
. SNAP output
|
|
1emh
|
hydrolase-DNA |
X-ray (1.8 Å) |
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan
HE, Blackburn GM, Tainer JA |
(2000) "Uracil-DNA
glycosylase-DNA substrate and product structures:
conformational strain promotes catalytic efficiency by
coupled stereoelectronic effects."
Proc.Natl.Acad.Sci.USA, 97,
5083-5088. doi: 10.1073/pnas.97.10.5083.
|
Crystal structure of human uracil-DNA glycosylase bound
to uncleaved substrate-containing DNA . SNAP output
|
|
1emj
|
hydrolase-DNA |
X-ray (2.0 Å) |
Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan
HE, Blackburn GM, Tainer JA |
(2000) "Uracil-DNA
glycosylase-DNA substrate and product structures:
conformational strain promotes catalytic efficiency by
coupled stereoelectronic effects."
Proc.Natl.Acad.Sci.USA, 97,
5083-5088. doi: 10.1073/pnas.97.10.5083.
|
Uracil-DNA glycosylase bound to DNA containing a
4'-thio-2'deoxyuridine analog product . SNAP output
|
|
1eo3
|
hydrolase-DNA |
X-ray (2.0 Å) |
Horton NC, Connolly BA, Perona JJ |
(2000) "Inhibition of EcoRV Endonuclease by
Deoxyribo-3'-S-phosphorothiolates: A High-Resolution
X-ray Crystallographic Study." J.Am.Chem.Soc.,
122, 3314-3324. doi: 10.1021/ja993719j.
|
Inhibition of ecorv endonuclease by
deoxyribo-3'-s-phosphorothiolates: a high resolution
x-ray crystallographic study . SNAP output
|
|
1eo4
|
hydrolase-DNA |
X-ray (1.9 Å) |
Horton NC, Connolly BA, Perona JJ |
(2000) "Inhibition of EcoRV Endonuclease by
Deoxyribo-3'-S-phosphorothiolates: A High-Resolution
X-ray Crystallographic Study." J.Am.Chem.Soc.,
122, 3314-3324. doi: 10.1021/ja993719j.
|
Ecorv bound to mn2+ and cognate DNA containing a 3's
substition at the cleavage site . SNAP output
|
|
1eon
|
hydrolase-DNA |
X-ray (1.6 Å) |
Horton NC, Connolly BA, Perona JJ |
(2000) "Inhibition of EcoRV Endonuclease by
Deoxyribo-3'-S-phosphorothiolates: A High-Resolution
X-ray Crystallographic Study." J.Am.Chem.Soc.,
122, 3314-3324. doi: 10.1021/ja993719j.
|
Ecorv bound to 3'-s-phosphorothiolate DNA and ca2+ .
SNAP output
|
|
1eoo
|
hydrolase-DNA |
X-ray (2.16 Å) |
Horton NC, Perona JJ |
(2000) "Crystallographic
snapshots along a protein-induced DNA-bending
pathway." Proc.Natl.Acad.Sci.USA,
97, 5729-5734. doi: 10.1073/pnas.090370797.
|
Ecorv bound to cognate DNA . SNAP output
|
|
1eop
|
hydrolase-DNA |
X-ray (2.6 Å) |
Horton NC, Perona JJ |
(2000) "Crystallographic
snapshots along a protein-induced DNA-bending
pathway." Proc.Natl.Acad.Sci.USA,
97, 5729-5734. doi: 10.1073/pnas.090370797.
|
Ecorv bound to cognate DNA . SNAP output
|
|
1eqz
|
structural protein-DNA |
X-ray (2.5 Å) |
Harp JM, Hanson BL, Timm DE, Bunick GJ |
(2000) "Asymmetries
in the nucleosome core particle at 2.5 A
resolution." Acta Crystallogr.,Sect.D,
56, 1513-1534. doi: 10.1107/S0907444900011847.
|
X-ray structure of the nucleosome core particle at 2.5
Å resolution . SNAP
output
|
|
1eri
|
hydrolase-DNA |
X-ray (2.5 Å) |
Kim YC, Grable JC, Love R, Greene PJ, Rosenberg
JM |
(1990) "Refinement
of Eco RI endonuclease crystal structure: a revised
protein chain tracing." Science,
249, 1307-1309.
|
X-ray structure of the DNA-eco ri endonuclease-DNA
recognition complex: the recognition network and the
integration of recognition and cleavage . SNAP output
|
|
1esg
|
hydrolase-DNA |
X-ray (1.9 Å) |
Viadiu H, Aggarwal AK |
(2000) "Structure
of BamHI bound to nonspecific DNA: a model for DNA
sliding." Mol.Cell, 5,
889-895. doi: 10.1016/S1097-2765(00)80329-9.
|
Restriction endonuclease bamhi bound to a non-specific
DNA. . SNAP output
|
|
1evw
|
hydrolase-DNA |
X-ray (3.1 Å) |
Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho
D, Tang W, Monnat Jr RJ, Stoddard BL |
(2000) "Conformational
changes and cleavage by the homing endonuclease I-PpoI:
a critical role for a leucine residue in the active
site." J.Mol.Biol., 300,
877-887. doi: 10.1006/jmbi.2000.3874.
|
L116a mutant of the homing endonuclease i-ppoi
complexed to homing site DNA. . SNAP output
|
|
1ewn
|
hydrolase-DNA |
X-ray (2.1 Å) |
Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger
T |
(2000) "Molecular
basis for discriminating between normal and damaged
bases by the human alkyladenine glycosylase, AAG."
Proc.Natl.Acad.Sci.USA, 97,
13573-13578. doi: 10.1073/pnas.97.25.13573.
|
Crystal structure of the human aag DNA repair
glycosylase complexed with 1,n6-ethenoadenine-DNA .
SNAP output
|
|
1ewq
|
replication-DNA |
X-ray (2.2 Å) |
Obmolova G, Ban C, Hsieh P, Yang W |
(2000) "Crystal
structures of mismatch repair protein MutS and its
complex with a substrate DNA." Nature,
407, 703-710. doi: 10.1038/35037509.
|
Crystal structure taq muts complexed with a
heteroduplex DNA at 2.2 Å resolution . SNAP output
|
|
1exi
|
transcription-DNA |
X-ray (3.12 Å) |
Heldwein EE, Brennan RG |
(2001) "Crystal
structure of the transcription activator BmrR bound to
DNA and a drug." Nature,
409, 378-382. doi: 10.1038/35053138.
|
Crystal structure of transcription activator bmrr, from
b. subtilis, bound to 21 base pair bmr operator and
tpsb . SNAP output
|
|
1exj
|
transcription-DNA |
X-ray (3.0 Å) |
Heldwein EE, Brennan RG |
(2001) "Crystal
structure of the transcription activator BmrR bound to
DNA and a drug." Nature,
409, 378-382. doi: 10.1038/35053138.
|
Crystal structure of transcription activator bmrr, from
b. subtilis, bound to 21 base pair bmr operator and tpp
. SNAP output
|
|
1eyg
|
replication-DNA |
X-ray (2.8 Å) |
Raghunathan S, Kozlov AG, Lohman TM, Waksman G |
(2000) "Structure
of the DNA binding domain of E. coli SSB bound to
ssDNA." Nat.Struct.Biol.,
7, 648-652. doi: 10.1038/77943.
|
Crystal structure of chymotryptic fragment of e. coli
ssb bound to two 35-mer single strand dnas . SNAP output
|
|
1eyu
|
hydrolase-DNA |
X-ray (1.78 Å) |
Horton JR, Cheng X |
(2000) "PvuII
endonuclease contains two calcium ions in active
sites." J.Mol.Biol., 300,
1049-1056. doi: 10.1006/jmbi.2000.3938.
|
High resolution structure of the pvuii
endonculease-cognate DNA complex at ph 4.6 . SNAP output
|
|
1f0o
|
hydrolase-DNA |
X-ray (2.5 Å) |
Horton JR, Cheng X |
(2000) "PvuII
endonuclease contains two calcium ions in active
sites." J.Mol.Biol., 300,
1049-1056. doi: 10.1006/jmbi.2000.3938.
|
Pvuii endonuclease-cognate DNA complex
(glutaraldehyde-crosslinked crystal) at ph 7.5 with two
calcium ions at each active site . SNAP output
|
|
1f0v
|
hydrolase-DNA |
X-ray (1.7 Å) |
Liu YS, Gotte G, Libonati M, Eisenberg DS |
(2001) "A
domain-swapped RNase A dimer with implications for
amyloid formation." Nat.Struct.Biol.,
8, 211-214. doi: 10.1038/84941.
|
Crystal structure of an rnase a dimer displaying a new
type of 3d domain swapping . SNAP output
|
|
1f2i
|
transcription-DNA |
X-ray (2.35 Å) |
Wang BS, Grant RA, Pabo CO |
(2001) "Selected
peptide extension contacts hydrophobic patch on
neighboring zinc finger and mediates dimerization on
DNA." Nat.Struct.Biol.,
8, 589-593. doi: 10.1038/89617.
|
Cocrystal structure of selected zinc finger dimer bound
to DNA . SNAP output
|
|
1f44
|
hydrolase, ligase-DNA |
X-ray (2.05 Å) |
Woods KC, Martin SS, Chu VC, Baldwin EP |
(2001) "Quasi-equivalence
in site-specific recombinase structure and function:
crystal structure and activity of trimeric Cre
recombinase bound to a three-way Lox DNA junction."
J.Mol.Biol., 313, 49-69. doi:
10.1006/jmbi.2001.5012.
|
Crystal structure of trimeric cre recombinase-lox
complex . SNAP
output
|
|
1f4k
|
replication-DNA |
X-ray (2.5 Å) |
Wilce JA, Vivian JP, Hastings AF, Otting G, Folmer
RH, Duggin IG, Wake RG, Wilce MC |
(2001) "Structure
of the RTP-DNA complex and the mechanism of polar
replication fork arrest."
Nat.Struct.Biol., 8, 206-210.
doi: 10.1038/84934.
|
Crystal structure of the replication terminator
protein-b-site DNA complex . SNAP output
|
|
1f4r
|
hydrolase-DNA |
X-ray (2.4 Å) |
Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger
T |
(2000) "Molecular
basis for discriminating between normal and damaged
bases by the human alkyladenine glycosylase, AAG."
Proc.Natl.Acad.Sci.USA, 97,
13573-13578. doi: 10.1073/pnas.97.25.13573.
|
Crystal structure of the human aag DNA repair
glycosylase complexed with 1,n6-ethenoadenine-DNA .
SNAP output
|
|
1f4s
|
transcription-DNA |
NMR |
Cahuzac B, Cerdan R, Felenbok B, Guittet E |
(2001) "The
solution structure of an AlcR-DNA complex sheds light
onto the unique tight and monomeric DNA binding of a
Zn(2)Cys(6) protein." Structure,
9, 827-836. doi: 10.1016/S0969-2126(01)00640-2.
|
Structure of transcriptional factor alcr in complex
with a target DNA . SNAP
output
|
|
1f5e
|
transcription-DNA |
NMR |
Cahuzac B, Cerdan R, Felenbok B, Guittet E |
(2001) "The
solution structure of an AlcR-DNA complex sheds light
onto the unique tight and monomeric DNA binding of a
Zn(2)Cys(6) protein." Structure,
9, 827-836. doi: 10.1016/S0969-2126(01)00640-2.
|
Structure of transcriptional factor alcr in complex
with a target DNA . SNAP
output
|
|
1f5t
|
transcription-DNA |
X-ray (3.0 Å) |
Chen CS, White A, Love J, Murphy JR, Ringe D |
(2000) "Methyl
groups of thymine bases are important for nucleic acid
recognition by DtxR." Biochemistry,
39, 10397-10407. doi: 10.1021/bi0009284.
|
Diphtheria tox repressor (c102d mutant) complexed with
nickel and dtxr consensus binding sequence . SNAP output
|
|
1f66
|
structural protein-DNA |
X-ray (2.6 Å) |
Suto RK, Clarkson MJ, Tremethick DJ, Luger K |
(2000) "Crystal
structure of a nucleosome core particle containing the
variant histone H2A.Z." Nat.Struct.Biol.,
7, 1121-1124. doi: 10.1038/81971.
|
2.6 a crystal structure of a nucleosome core particle
containing the variant histone h2a.z . SNAP output
|
|
1f6o
|
hydrolase-DNA |
X-ray (2.4 Å) |
Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger
T |
(2000) "Molecular
basis for discriminating between normal and damaged
bases by the human alkyladenine glycosylase, AAG."
Proc.Natl.Acad.Sci.USA, 97,
13573-13578. doi: 10.1073/pnas.97.25.13573.
|
Crystal structure of the human aag DNA repair
glycosylase complexed with DNA . SNAP output
|
|
1fiu
|
hydrolase-DNA |
X-ray (1.6 Å) |
Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber
R |
(2000) "Structure
of the tetrameric restriction endonuclease NgoMIV in
complex with cleaved DNA."
Nat.Struct.Biol., 7, 792-799.
doi: 10.1038/79032.
|
Tetrameric restriction endonuclease ngomiv in complex
with cleaved DNA . SNAP
output
|
|
1fja
|
DNA-antibiotic |
NMR |
Chen H, Liu X, Patel DJ |
(1996) "DNA
Bending and Unwinding Associated with Actinomycin D
Antibiotics Bound to Partially Overlapping Sites on
DNA." J.Mol.Biol., 258,
457. doi: 10.1006/JMBI.1996.0262.
|
NMR study of deoxyribonucleic acid complexed with
actinomycin d . SNAP
output
|
|
1fjl
|
transcription-DNA |
X-ray (2.0 Å) |
Wilson DS, Guenther B, Desplan C, Kuriyan J |
(1995) "High
resolution crystal structure of a paired (Pax) class
cooperative homeodomain dimer on DNA."
Cell(Cambridge,Mass.), 82,
709-719. doi: 10.1016/0092-8674(95)90468-9.
|
Homeodomain from the drosophila paired protein bound to
a DNA oligonucleotide . SNAP output
|
|
1fjx
|
transferase-DNA |
X-ray (2.26 Å) |
Vilkaitis G, Dong A, Weinhold E, Cheng X,
Klimasauskas S |
(2000) "Functional
roles of the conserved threonine 250 in the target
recognition domain of HhaI DNA methyltransferase."
J.Biol.Chem., 275,
38722-38730.
|
Structure of ternary complex of hhai methyltransferase
mutant (t250g) in complex with DNA and adohcy .
SNAP output
|
|
1flo
|
ligase, lyase-DNA |
X-ray (2.65 Å) |
Chen Y, Narendra U, Iype LE, Cox MM, Rice PA |
(2000) "Crystal
structure of a Flp recombinase-Holliday junction
complex: assembly of an active oligomer by helix
swapping." Mol.Cell, 6,
885-897. doi: 10.1016/S1097-2765(00)00086-1.
|
Flp recombinase-holliday junction complex i . SNAP output
|
|
1fn7
|
hydrolase-DNA |
X-ray (2.6 Å) |
Norman DP, Bruner SD, Verdine GL |
(2001) "Coupling
of substrate recognition and catalysis by a human
base-excision DNA repair protein."
J.Am.Chem.Soc., 123, 359-360.
doi: 10.1021/ja003144m.
|
Coupling of damage recognition and catalysis by a human
base-excision DNA repair protein . SNAP output
|
|
1fok
|
hydrolase-DNA |
X-ray (2.8 Å) |
Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal
AK |
(1997) "Structure
of the multimodular endonuclease FokI bound to
DNA." Nature, 388,
97-100. doi: 10.1038/40446.
|
Structure of restriction endonuclease foki bound to DNA
. SNAP output
|
|
1fos
|
transcription-DNA |
X-ray (3.05 Å) |
Glover JN, Harrison SC |
(1995) "Crystal
structure of the heterodimeric bZIP transcription
factor c-Fos-c-Jun bound to DNA." Nature,
373, 257-261. doi: 10.1038/373257a0.
|
Two human c-fos:c-jun:DNA complexes . SNAP output
|
|
1fw6
|
replication-DNA |
X-ray (2.7 Å) |
Junop MS, Obmolova G, Rausch K, Hsieh P, Yang W |
(2001) "Composite
active site of an ABC ATPase: MutS uses ATP to verify
mismatch recognition and authorize DNA repair."
Mol.Cell, 7, 1-12. doi:
10.1016/S1097-2765(01)00149-6.
|
Crystal structure of a taq muts-DNA-adp ternary complex
. SNAP output
|
|
1fyl
|
transcription-DNA |
X-ray (2.1 Å) |
Littlefield O, Nelson HC |
(2001) "Crystal
packing interaction that blocks crystallization of a
site-specific DNA binding protein-DNA complex."
Proteins, 45, 219-228. doi:
10.1002/prot.1142.
|
Serendipitous crystal structure containing the heat
shock transcription factor's DNA binding domain and
cognate DNA in a head-to-head orientation . SNAP output
|
|
1fym
|
transcription-DNA |
X-ray (2.2 Å) |
Littlefield O, Nelson HC |
(2001) "Crystal
packing interaction that blocks crystallization of a
site-specific DNA binding protein-DNA complex."
Proteins, 45, 219-228. doi:
10.1002/prot.1142.
|
Serendipitous crystal structure containing the heat
shock transcription factor's DNA binding domain and
cognate DNA in a tail-to-tail orientation . SNAP output
|
|
1g2d
|
transcription-DNA |
X-ray (2.2 Å) |
Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO |
(2001) "Beyond
the "recognition code": structures of two Cys2His2 zinc
finger/TATA box complexes." Structure,
9, 717-723. doi: 10.1016/S0969-2126(01)00632-3.
|
Structure of a cys2his2 zinc finger-tata box complex
(clone #2) . SNAP
output
|
|
1g2f
|
transcription-DNA |
X-ray (2.0 Å) |
Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO |
(2001) "Beyond
the "recognition code": structures of two Cys2His2 zinc
finger/TATA box complexes." Structure,
9, 717-723. doi: 10.1016/S0969-2126(01)00632-3.
|
Structure of a cys2his2 zinc finger-tata box complex
(tatazf;clone #6) . SNAP
output
|
|
1g38
|
transferase-DNA |
X-ray (2.0 Å) |
Goedecke K, Pignot M, Goody RS, Scheidig AJ, Weinhold
E |
(2001) "Structure
of the N6-adenine DNA methyltransferase M.TaqI in
complex with DNA and a cofactor analog."
Nat.Struct.Biol., 8, 121-125.
doi: 10.1038/84104.
|
Adenine-specific methyltransferase m. taq i-DNA complex
. SNAP output
|
|
1g3x
|
DNA |
X-ray (2.7 Å) |
Malinina L, Soler-Lopez M, Aymami J, Subirana JA |
(2002) "Intercalation
of an acridine-peptide drug in an AA/TT base step in
the crystal structure of [d(CGCGAATTCGCG)](2) with six
duplexes and seven Mg(2+) ions in the asymmetric
unit." Biochemistry, 41,
9341-9348. doi: 10.1021/bi020135c.
|
Intercalation of an 9acridine-peptide drug in a DNA
dodecamer . SNAP
output
|
|
1g4d
|
viral protein-DNA |
NMR |
Wojciak JM, Iwahara J, Clubb RT |
(2001) "The Mu
repressor-DNA complex contains an immobilized 'wing'
within the minor groove."
Nat.Struct.Biol., 8, 84-90.
doi: 10.1038/89582.
|
NMR structure of the mu bacteriophage repressor
DNA-binding domain-DNA complex . SNAP output
|
|
1g9y
|
hydrolase-DNA |
X-ray (2.05 Å) |
Chevalier BS, Monnat Jr RJ, Stoddard BL |
(2001) "The
homing endonuclease I-CreI uses three metals, one of
which is shared between the two active sites."
Nat.Struct.Biol., 8, 312-316.
doi: 10.1038/86181.
|
Homing endonuclease i-crei - DNA substrate complex with
calcium . SNAP
output
|
|
1g9z
|
hydrolase-DNA |
X-ray (1.8 Å) |
Chevalier BS, Monnat Jr RJ, Stoddard BL |
(2001) "The
homing endonuclease I-CreI uses three metals, one of
which is shared between the two active sites."
Nat.Struct.Biol., 8, 312-316.
doi: 10.1038/86181.
|
Laglidadg homing endonuclease i-crei - DNA product
complex with magnesium . SNAP output
|
|
1ga5
|
transcription-DNA |
X-ray (2.4 Å) |
Sierk ML, Zhao Q, Rastinejad F |
(2001) "DNA
Deformability as a Recognition Feature in the RevErb
Response Element." Biochemistry,
40, 12833-12843. doi: 10.1021/bi011086r.
|
Crystal structure of the orphan nuclear receptor
rev-erb(alpha) DNA-binding domain bound to its cognate
response element . SNAP
output
|
|
1gat
|
transcription-DNA |
NMR |
Omichinski JG, Clore GM, Schaad O, Felsenfeld G,
Trainor C, Appella E, Stahl SJ, Gronenborn AM |
(1993) "NMR
structure of a specific DNA complex of Zn-containing
DNA binding domain of GATA-1." Science,
261, 438-446. doi: 10.1021/bi00131a004.
|
Solution structure of the specific DNA complex of the
zinc containing DNA binding domain of the erythroid
transcription factor gata-1 by multidimensional NMR .
SNAP output
|
|
1gau
|
transcription-DNA |
NMR |
Omichinski JG, Clore GM, Schaad O, Felsenfeld G,
Trainor C, Appella E, Stahl SJ, Gronenborn AM |
(1993) "NMR
structure of a specific DNA complex of Zn-containing
DNA binding domain of GATA-1." Science,
261, 438-446. doi: 10.1021/bi00131a004.
|
Solution structure of the specific DNA complex of the
zinc containing DNA binding domain of the erythroid
transcription factor gata-1 by multidimensional NMR .
SNAP output
|
|
1gcc
|
transcription-DNA |
NMR |
Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki
M |
(1998) "A novel
mode of DNA recognition by a beta-sheet revealed by the
solution structure of the GCC-box binding domain in
complex with DNA." EMBO J.,
17, 5484-5496. doi: 10.1093/emboj/17.18.5484.
|
Solution NMR structure of the complex of gcc-box
binding domain of aterf1 and gcc-box DNA, minimized
average structure . SNAP
output
|
|
1gd2
|
transcription-DNA |
X-ray (2.0 Å) |
Fujii Y, Shimizu T, Toda T, Yanagida M, Hakoshima
T |
(2000) "Structural
basis for the diversity of DNA recognition by bZIP
transcription factors." Nat.Struct.Biol.,
7, 889-893. doi: 10.1038/82822.
|
Crystal structure of bzip transcription factor pap1
bound to DNA . SNAP
output
|
|
1gdt
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Yang W, Steitz TA |
(1995) "Crystal
structure of the site-specific recombinase gamma delta
resolvase complexed with a 34 bp cleavage site."
Cell(Cambridge,Mass.), 82,
193-207. doi: 10.1016/0092-8674(95)90307-0.
|
Crystal structure of a site-specific recombinase,
gamma-delta resolvase complexed with a 34 bp cleavage
site . SNAP output
|
|
1gji
|
transcription-DNA |
X-ray (2.85 Å) |
Huang DB, Chen YQ, Ruetsche M, Phelps CB, Ghosh
G |
(2001) "X-ray
crystal structure of proto-oncogene product c-Rel bound
to the CD28 response element of IL-2."
Structure, 9, 669-678. doi:
10.1016/S0969-2126(01)00635-9.
|
Crystal structure of c-rel bound to DNA . SNAP output
|
|
1glu
|
transcription-DNA |
X-ray (2.9 Å) |
Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto
KR, Sigler PB |
(1991) "Crystallographic
analysis of the interaction of the glucocorticoid
receptor with DNA." Nature,
352, 497-505. doi: 10.1038/352497a0.
|
Crystallographic analysis of the interaction of the
glucocorticoid receptor with DNA . SNAP output
|
|
1gm5
|
helicase |
X-ray (3.24 Å) |
Singleton MR, Scaife S, Wigley DB |
(2001) "Structural
Analysis of DNA Replication Fork Reversal by Recg."
Cell(Cambridge,Mass.), 107,
79. doi: 10.1016/S0092-8674(01)00501-3.
|
Structure of recg bound to three-way DNA junction .
SNAP output
|
|
1gt0
|
transcription |
X-ray (2.6 Å) |
Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR,
Wilmanns M |
(2003) "Crystal
Structure of a POU/Hmg/DNA Ternary Complex Suggests
Differential Assembly of Oct4 and Sox2 on Two
Enhancers." Genes Dev.,
17, 2048. doi: 10.1101/GAD.269303.
|
Crystal structure of a pou-hmg-DNA ternary complex .
SNAP output
|
|
1gtw
|
transcription-DNA |
X-ray (1.85 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata
K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer bound to
a DNA fragment from the tom-1a promoter . SNAP output
|
|
1gu4
|
transcription-DNA |
X-ray (1.8 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata
K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer bound to
a high affinity DNA fragment . SNAP output
|
|
1gu5
|
transcription-DNA |
X-ray (2.1 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata
K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer bound to
a DNA fragment from the mim-1 promoter . SNAP output
|
|
1gxp
|
transcriptional activator |
X-ray (2.5 Å) |
Blanco AG, Sola M, Gomis-Ruth FX, Coll M |
(2002) "Tandem
DNA Recognition by Two-Component Signal Transduction
Transcriptional Activator Phob."
Structure, 10, 701. doi:
10.1016/S0969-2126(02)00761-X.
|
Phob effector domain in complex with pho box DNA. .
SNAP output
|
|
1h0m
|
transcription-DNA |
X-ray (3.0 Å) |
Vannini A, Volpari C, Gargioli C, Muraglia E, Cortese
R, De Francesco R, Neddermann P, Di Marco S |
(2002) "The
Crystal Structure of the Quorum Sensing Protein Trar
Bound to its Autoinducer and Target DNA." Embo
J., 21, 4393. doi: 10.1093/EMBOJ/CDF459.
|
Three-dimensional structure of the quorum sensing
protein trar bound to its autoinducer and to its target
DNA . SNAP output
|
|
1h38
|
transferase |
X-ray (2.9 Å) |
Tahirov TH, Temiakov D, Anikin M, Patlan V,
Mcallister WT, Vassylyev DG, Yokoyama S |
(2002) "Structure
of a T7 RNA Polymerase Elongation Complex at 2.9 A
Resolution." Nature, 420,
43. doi: 10.1038/NATURE01129.
|
Structure of a t7 RNA polymerase elongation complex at
2.9a resolution . SNAP
output
|
|
1h6f
|
transcription factor |
X-ray (1.7 Å) |
Coll M, Seidman JG, Muller CW |
(2002) "Structure
of the DNA-Bound T-Box Domain of Human Tbx3, a
Transcription Factor Responsible for Ulnar- Mammary
Syndrome." Structure, 10,
343. doi: 10.1016/S0969-2126(02)00722-0.
|
Human tbx3, a transcription factor responsible for
ulnar-mammary syndrome, bound to a palindromic DNA site
. SNAP output
|
|
1h88
|
transcription-DNA |
X-ray (2.8 Å) |
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M,
Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A,
Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K |
(2002) "Mechanism
of C-Myb-C/Ebpbeta Cooperation from Separated Sites on
a Promoter." Cell(Cambridge,Mass.),
108, 57. doi: 10.1016/S0092-8674(01)00636-5.
|
Crystal structure of ternary protein-DNA complex1 .
SNAP output
|
|
1h89
|
transcription-DNA |
X-ray (2.45 Å) |
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M,
Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A,
Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K |
(2002) "Mechanism
of C-Myb-C/Ebpbeta Cooperation from Separated Sites on
a Promoter." Cell(Cambridge,Mass.),
108, 57. doi: 10.1016/S0092-8674(01)00636-5.
|
Crystal structure of ternary protein-DNA complex2 .
SNAP output
|
|
1h8a
|
transcription-DNA |
X-ray (2.23 Å) |
Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M,
Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A,
Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K |
(2002) "Mechanism
of C-Myb-C/Ebpbeta Cooperation from Separated Sites on
a Promoter." Cell(Cambridge,Mass.),
108, 57. doi: 10.1016/S0092-8674(01)00636-5.
|
Crystal structure of ternary protein-DNA complex3 .
SNAP output
|
|
1h9d
|
transcription factor |
X-ray (2.6 Å) |
Bravo J, Li Z, Speck NA, Warren AJ |
(2001) "The
Leukemia-Associated Aml1 (Runx1)-Cbfbeta Complex
Functions as a DNA-Induced Molecular Clamp."
Nat.Struct.Biol., 8, 371.
doi: 10.1038/86264.
|
Aml1-cbf-beta-DNA complex . SNAP output
|
|
1h9t
|
transcriptional regulation |
X-ray (3.25 Å) |
Van Aalten DMF, Dirusso CC, Knudsen J |
(2001) "The
Structural Basis of Acyl Coenzyme A-Dependent
Regulation of the Transcription Factor Fadr."
Embo J., 20, 2041. doi:
10.1093/EMBOJ/20.8.2041.
|
Fadr, fatty acid responsive transcription factor from
e. coli in complex with fadb operator . SNAP output
|
|
1hao
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.8 Å) |
Padmanabhan K, Tulinsky A |
(1996) "An
ambiguous structure of a DNA 15-mer thrombin
complex." Acta Crystallogr.,Sect.D,
52, 272-282. doi: 10.1107/S0907444995013977.
|
Complex of human alpha-thrombin with a 15mer
oligonucleotide ggttggtgtggttgg (based on NMR model of
DNA) . SNAP output
|
|
1hap
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.8 Å) |
Padmanabhan K, Tulinsky A |
(1996) "An
ambiguous structure of a DNA 15-mer thrombin
complex." Acta Crystallogr.,Sect.D,
52, 272-282. doi: 10.1107/S0907444995013977.
|
Complex of human alpha-thrombin with a 15mer
oligonucleotide ggttggtgtggttgg (based on x-ray model
of DNA) . SNAP
output
|
|
1hbx
|
gene regulation |
X-ray (3.15 Å) |
Hassler M, Richmond TJ |
(2001) "The
B-Box Dominates Sap-1/Srf Interactions in the Structure
of the Ternary Complex." Embo J.,
20, 3018. doi: 10.1093/EMBOJ/20.12.3018.
|
Ternary complex of sap-1 and srf with specific sre DNA
. SNAP output
|
|
1hcq
|
transcription-DNA |
X-ray (2.4 Å) |
Schwabe JW, Chapman L, Finch JT, Rhodes D |
(1993) "The
crystal structure of the estrogen receptor DNA-binding
domain bound to DNA: how receptors discriminate between
their response elements."
Cell(Cambridge,Mass.), 75,
567-578. doi: 10.1016/0092-8674(93)90390-C.
|
The crystal structure of the estrogen receptor
DNA-binding domain bound to DNA: how receptors
discriminate between their response elements . SNAP output
|
|
1hcr
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Feng JA, Johnson RC, Dickerson RE |
(1994) "Hin
recombinase bound to DNA: the origin of specificity in
major and minor groove interactions."
Science, 263, 348-355.
|
Hin recombinase bound to DNA: the origin of specificity
in major and minor groove interactions . SNAP output
|
|
1hdd
|
transcription-DNA |
X-ray (2.8 Å) |
Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB,
Pabo CO |
(1990) "Crystal
structure of an engrailed homeodomain-DNA complex at
2.8 A resolution: a framework for understanding
homeodomain-DNA interactions."
Cell(Cambridge,Mass.), 63,
579-590. doi: 10.1016/0092-8674(90)90453-L.
|
Crystal structure of an engrailed homeodomain-DNA
complex at 2.8 angstroms resolution: a framework for
understanding homeodomain-DNA interactions . SNAP output
|
|
1hf0
|
transcription |
X-ray (2.7 Å) |
Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A,
Reinbold R, Scholer HR, Wilmanns M |
(2001) "Differential
Dimer Activities of the Transcription Factor Oct-1 by
DNA-Induced Interface Swapping." Mol.Cell,
8, 569. doi: 10.1016/S1097-2765(01)00336-7.
|
Crystal structure of the DNA-binding domain of oct-1
bound to DNA as a dimer . SNAP output
|
|
1hht
|
RNA polymerase |
X-ray (2.9 Å) |
Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart
DI |
(2001) "A
Mechanism for Initiating RNA-Dependent RNA
Polymerization." Nature,
410, 235. doi: 10.1038/35065653.
|
RNA dependent RNA polymerase from dsrna bacteriophage
phi6 plus template . SNAP output
|
|
1hi0
|
RNA polymerase |
X-ray (3.0 Å) |
Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart
DI |
(2001) "A
Mechanism for Initiating RNA-Dependent RNA
Polymerization." Nature,
410, 235. doi: 10.1038/35065653.
|
RNA dependent RNA polymerase from dsrna bacteriophage
phi6 plus initiation complex . SNAP output
|
|
1hjb
|
transcription-DNA |
X-ray (3.0 Å) |
Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A,
Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T,
Yamamoto M, Ishii S, Ogata K |
(2001) "Structural
Analyses of DNA Recognition by the Aml1/Runx-1 Runt
Domain and its Allosteric Control by Cbfbeta."
Cell(Cambridge,Mass.), 104,
755. doi: 10.1016/S0092-8674(01)00271-9.
|
Crystal structure of runx-1-aml1-cbfalpha runt domain
and c-ebpbeta bzip homodimer bound to a DNA fragment
from the csf-1r promoter . SNAP output
|
|
1hjc
|
transcription-DNA |
X-ray (2.65 Å) |
Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A,
Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T,
Yamamoto M, Ishii S, Ogata K |
(2001) "Structural
Analyses of DNA Recognition by the Aml1/Runx-1 Runt
Domain and its Allosteric Control by Cbfbeta."
Cell(Cambridge,Mass.), 104,
755. doi: 10.1016/S0092-8674(01)00271-9.
|
Crystal structure of runx-1-aml1-cbfalpha runt domain
bound to a DNA fragment from the csf-1r promoter .
SNAP output
|
|
1hlo
|
transcription-DNA |
X-ray (2.8 Å) |
Brownlie P, Ceska T, Lamers M, Romier C, Stier G, Teo
H, Suck D |
(1997) "The
crystal structure of an intact human Max-DNA complex:
new insights into mechanisms of transcriptional
control." Structure, 5,
509-520. doi: 10.1016/S0969-2126(97)00207-4.
|
The crystal structure of an intact human max-DNA
complex: new insights into mechanisms of
transcriptional control . SNAP output
|
|
1hlv
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi
S, Ikuta M, Iwahara J, Okazaki T, Yokoyama S |
(2001) "Crystal
structure of the CENP-B protein-DNA complex: the
DNA-binding domains of CENP-B induce kinks in the
CENP-B box DNA." EMBO J.,
20, 6612-6618. doi: 10.1093/emboj/20.23.6612.
|
Crystal structure of cenp-b(1-129) complexed with the
cenp-b box DNA . SNAP
output
|
|
1hlz
|
transcription-DNA |
X-ray (2.8 Å) |
Sierk ML, Zhao Q, Rastinejad F |
(2001) "DNA
Deformability as a Recognition Feature in the RevErb
Response Element." Biochemistry,
40, 12833-12843. doi: 10.1021/bi011086r.
|
Crystal structure of the orphan nuclear receptor
rev-erb(alpha) DNA-binding domain bound to its cognate
response element . SNAP
output
|
|
1hry
|
DNA binding protein-DNA |
NMR |
Werner MH, Huth JR, Gronenborn AM, Clore GM |
(1995) "Molecular
basis of human 46X,Y sex reversal revealed from the
three-dimensional solution structure of the human
SRY-DNA complex." Cell(Cambridge,Mass.),
81, 704-705. doi: 10.1016/0092-8674(95)90532-4.
|
The 3d structure of the human sry-DNA complex solved by
multid-dimensional heteronuclear-edited and-filtered
NMR . SNAP output
|
|
1hrz
|
DNA binding protein-DNA |
NMR |
Werner MH, Huth JR, Gronenborn AM, Clore GM |
(1995) "Molecular
basis of human 46X,Y sex reversal revealed from the
three-dimensional solution structure of the human
SRY-DNA complex." Cell(Cambridge,Mass.),
81, 704-705. doi: 10.1016/0092-8674(95)90532-4.
|
The 3d structure of the human sry-DNA complex solved by
multi-dimensional heteronuclear-edited and-filtered NMR
. SNAP output
|
|
1hu0
|
hydrolase-DNA |
X-ray (2.35 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in base-excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Crystal structure of an hogg1-DNA borohydride trapped
intermediate complex . SNAP output
|
|
1huo
|
transferase-DNA |
X-ray (2.6 Å) |
Arndt JW, Gong W, Zhong X, Showalter AK, Liu J,
Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK |
(2001) "Insight
into the catalytic mechanism of DNA polymerase beta:
structures of intermediate complexes."
Biochemistry, 40, 5368-5375.
doi: 10.1021/bi002176j.
|
Crystal structure of DNA polymerase beta complexed with
DNA and cr-tmppcp . SNAP
output
|
|
1hut
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.9 Å) |
Padmanabhan K, Padmanabhan KP, Ferrara JD, Sadler JE,
Tulinsky A |
(1993) "The
structure of alpha-thrombin inhibited by a 15-mer
single-stranded DNA aptamer."
J.Biol.Chem., 268,
17651-17654.
|
The structure of alpha-thrombin inhibited by a 15-mer
single-stranded DNA aptamer . SNAP output
|
|
1huz
|
transferase-DNA |
X-ray (2.6 Å) |
Arndt JW, Gong W, Zhong X, Showalter AK, Liu J,
Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK |
(2001) "Insight
into the catalytic mechanism of DNA polymerase beta:
structures of intermediate complexes."
Biochemistry, 40, 5368-5375.
doi: 10.1021/bi002176j.
|
Crystal structure of DNA polymerase complexed with DNA
and cr-pcp . SNAP
output
|
|
1hvn
|
viral protein-DNA |
NMR |
South TL, Summers MF |
(1993) "Zinc- and
sequence-dependent binding to nucleic acids by the
N-terminal zinc finger of the HIV-1 nucleocapsid
protein: NMR structure of the complex with the Psi-site
analog, dACGCC." Protein Sci.,
2, 3.
|
Zinc-and sequence-dependent binding to nucleic acids by
the n-terminal zinc finger domain of the hiv-1
nucleocapsid protein: NMR structure of the complex with
the psi-site analog, d-acgcc . SNAP output
|
|
1hvo
|
viral protein-DNA |
NMR |
South TL, Summers MF |
(1993) "Zinc- and
sequence-dependent binding to nucleic acids by the
N-terminal zinc finger of the HIV-1 nucleocapsid
protein: NMR structure of the complex with the Psi-site
analog, dACGCC." Protein Sci.,
2, 3.
|
Zinc-and sequence-dependent binding to nucleic acids by
the n-terminal zinc finger domain of the hiv-1
nucleocapsid protein: NMR structure of the complex with
the psi-site analog, d-acgcc . SNAP output
|
|
1hw2
|
transcription-DNA |
X-ray (3.25 Å) |
Xu Y, Heath RJ, Li Z, Rock CO, White SW |
(2001) "The
FadR.DNA complex. Transcriptional control of fatty acid
metabolism in Escherichia coli."
J.Biol.Chem., 276,
17373-17379. doi: 10.1074/jbc.M100195200.
|
Fadr-DNA complex: transcriptional control of fatty acid
metabolism in echerichia coli . SNAP output
|
|
1hwt
|
gene regulation-DNA |
X-ray (2.5 Å) |
King DA, Zhang L, Guarente L, Marmorstein R |
(1999) "Structure
of a HAP1-DNA complex reveals dramatically asymmetric
DNA binding by a homodimeric protein."
Nat.Struct.Biol., 6, 64-71.
doi: 10.1038/4940.
|
Structure of a hap1-DNA complex reveals dramatically
asymmetric DNA binding by a homodimeric protein .
SNAP output
|
|
1hys
|
transferase-DNA-RNA hybrid |
X-ray (3.0 Å) |
Sarafianos SG, Das K, Tantillo C, Clark Jr AD, Ding
J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E |
(2001) "Crystal
structure of HIV-1 reverse transcriptase in complex
with a polypurine tract RNA:DNA." EMBO J.,
20, 1449-1461. doi: 10.1093/emboj/20.6.1449.
|
Crystal structure of hiv-1 reverse transcriptase in
complex with a polypurine tract RNA:DNA . SNAP output
|
|
1i3j
|
hydrolase-DNA |
X-ray (2.2 Å) |
Van Roey P, Waddling CA, Fox KM, Belfort M,
Derbyshire V |
(2001) "Intertwined
structure of the DNA-binding domain of intron
endonuclease I-TevI with its substrate." EMBO
J., 20, 3631-3637. doi: 10.1093/emboj/20.14.3631.
|
Crystal structure of the DNA-binding domain of intron
endonuclease i-tevi with its substrate . SNAP output
|
|
1i3w
|
DNA-antibiotic |
X-ray (1.7 Å) |
Robinson H, Gao YG, Yang X, Sanishvili R, Joachimiak
A, Wang AH |
(2001) "Crystallographic
Analysis of a Novel Complex of Actinomycin D Bound to
the DNA Decamer Cgatcgatcg." Biochemistry,
40, 5587. doi: 10.1021/BI002859Z.
|
Actinomycin d binding to cgatcgatcg . SNAP output
|
|
1i6h
|
transcription-DNA-RNA hybrid |
X-ray (3.3 Å) |
Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg
RD |
(2001) "Structural
basis of transcription: an RNA polymerase II elongation
complex at 3.3 A resolution." Science,
292, 1876-1882. doi: 10.1126/science.1059495.
|
RNA polymerase ii elongation complex . SNAP output
|
|
1i6j
|
transferase-DNA |
X-ray (2.0 Å) |
Cote ML, Georgiadis MM |
(2001) "Structure
of a pseudo-16-mer DNA with stacked guanines and two
G-A mispairs complexed with the N-terminal fragment of
Moloney murine leukemia virus reverse
transcriptase." Acta Crystallogr.,Sect.D,
57, 1238-1250. doi: 10.1107/S090744490100943X.
|
Crystal structure of a pseudo-16-mer DNA with stacked
guanines and two g-a mispairs complexed with the
n-terminal fragment of moloney murine leukemia virus
reverse transcriptase . SNAP output
|
|
1i7d
|
isomerase-DNA |
X-ray (2.05 Å) |
Changela A, DiGate RJ, Mondragon A |
(2001) "Crystal
structure of a complex of a type IA DNA topoisomerase
with a single-stranded DNA molecule."
Nature, 411, 1077-1081. doi:
10.1038/35082615.
|
Noncovalent complex of e.coli DNA topoisomerase iii
with an 8-base single-stranded DNA oligonucleotide .
SNAP output
|
|
1i8m
|
immune system-DNA |
X-ray (2.1 Å) |
Tanner JJ, Komissarov AA, Deutscher SL |
(2001) "Crystal
Structure of an Antigen-Binding Fragment Bound to
Single-Stranded DNA." J.Mol.Biol.,
314, 807-822. doi: 10.1006/jmbi.2001.5178.
|
Crystal structure of a recombinant anti-single-stranded
DNA antibody fragment complexed with dt5 . SNAP output
|
|
1iaw
|
hydrolase-DNA |
X-ray (2.4 Å) |
Huai Q, Colandene JD, Topal MD, Ke H |
(2001) "Structure
of NaeI-DNA complex reveals dual-mode DNA recognition
and complete dimer rearrangement."
Nat.Struct.Biol., 8, 665-669.
doi: 10.1038/90366.
|
Crystal structure of naei complexed with 17mer DNA .
SNAP output
|
|
1ic8
|
transcription-DNA |
X-ray (2.6 Å) |
Chi Y-I, Frantz JD, Oh B-C, Hansen L, Dhe-Paganon S,
Shoelson SE |
(2002) "Diabetes
mutations delineate an atypical POU domains in
HNF1-Alpha." Mol.Cell,
10, 1129-1137. doi: 10.1016/S1097-2765(02)00704-9.
|
Hepatocyte nuclear factor 1a bound to DNA : mody3 gene
product . SNAP
output
|
|
1id3
|
structural protein-DNA |
X-ray (3.1 Å) |
White CL, Suto RK, Luger K |
(2001) "Structure
of the yeast nucleosome core particle reveals
fundamental changes in internucleosome
interactions." EMBO J.,
20, 5207-5218. doi: 10.1093/emboj/20.18.5207.
|
Crystal structure of the yeast nucleosome core particle
reveals fundamental differences in inter-nucleosome
interactions . SNAP
output
|
|
1if1
|
transcription-DNA |
X-ray (3.0 Å) |
Escalante CR, Yie J, Thanos D, Aggarwal AK |
(1998) "Structure
of IRF-1 with bound DNA reveals determinants of
interferon regulation." Nature,
391, 103-106. doi: 10.1038/34224.
|
Interferon regulatory factor 1 (irf-1) complex with DNA
. SNAP output
|
|
1ig4
|
transcription-DNA |
NMR |
Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T,
Nakao M, Shirakawa M |
(2001) "Solution
structure of the methyl-CpG binding domain of human
MBD1 in complex with methylated DNA."
Cell(Cambridge,Mass.), 105,
487-497. doi: 10.1016/S0092-8674(01)00324-5.
|
Solution structure of the methyl-cpg-binding domain of
human mbd1 in complex with methylated DNA . SNAP output
|
|
1ig7
|
transcription-DNA |
X-ray (2.2 Å) |
Hovde S, Abate-Shen C, Geiger JH |
(2001) "Crystal
structure of the Msx-1 homeodomain/DNA complex."
Biochemistry, 40,
12013-12021. doi: 10.1021/bi0108148.
|
Msx-1 homeodomain-DNA complex structure . SNAP output
|
|
1ig9
|
transferase-DNA |
X-ray (2.6 Å) |
Franklin MC, Wang J, Steitz TA |
(2001) "Structure
of the Replicating Complex of a Pol Alpha Family DNA
Polymerase." Cell(Cambridge,Mass.),
105, 657-667. doi: 10.1016/S0092-8674(01)00367-1.
|
Structure of the replicating complex of a pol alpha
family DNA polymerase . SNAP output
|
|
1ign
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Konig P, Giraldo R, Chapman L, Rhodes D |
(1996) "The
crystal structure of the DNA-binding domain of yeast
RAP1 in complex with telomeric DNA."
Cell(Cambridge,Mass.), 85,
125-136. doi: 10.1016/S0092-8674(00)81088-0.
|
DNA-binding domain of rap1 in complex with telomeric
DNA site . SNAP
output
|
|
1ihf
|
transcription-DNA |
X-ray (2.5 Å) |
Rice PA, Yang S, Mizuuchi K, Nash HA |
(1996) "Crystal
structure of an IHF-DNA complex: a protein-induced DNA
U-turn." Cell(Cambridge,Mass.),
87, 1295-1306. doi: 10.1016/S0092-8674(00)81824-3.
|
Integration host factor-DNA complex . SNAP output
|
|
1ijs
|
virus-DNA |
X-ray (3.25 Å) |
Llamas-Saiz AL, Agbandje-McKenna M, Parker JS, Wahid
AT, Parrish CR, Rossmann MG |
(1996) "Structural
analysis of a mutation in canine parvovirus which
controls antigenicity and host range."
Virology, 225, 65-71. doi:
10.1006/viro.1996.0575.
|
Cpv (strain d) mutant a300d, complex (viral coat-DNA),
vp2, ph=7.5, t=4 degrees c . SNAP output
|
|
1ijw
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations. . SNAP output
|
|
1imh
|
transcription-DNA |
X-ray (2.86 Å) |
Stroud JC, Lopez-Rodriguez C, Rao A, Chen L |
(2002) "Structure
of a TonEBP-DNA complex reveals DNA encircled by a
transcription factor." Nat.Struct.Biol.,
9, 90-94. doi: 10.1038/nsb749.
|
Tonebp-DNA complex . SNAP output
|
|
1io4
|
transcription-DNA |
X-ray (3.0 Å) |
Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A,
Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T,
Yamamoto M, Ishii S, Ogata K |
(2001) "Structural
analyses of DNA recognition by the AML1/Runx-1 Runt
domain and its allosteric control by CBFbeta."
Cell(Cambridge,Mass.), 104,
755-767. doi: 10.1016/S0092-8674(01)00271-9.
|
Crystal structure of runx-1-aml1-cbfalpha runt
domain-cbfbeta core domain heterodimer and c-ebpbeta
bzip homodimer bound to a DNA fragment from the csf-1r
promoter . SNAP
output
|
|
1ipp
|
transcription-DNA |
X-ray (2.2 Å) |
Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL |
(1998) "DNA
binding and cleavage by the nuclear intron-encoded
homing endonuclease I-PpoI." Nature,
394, 96-101. doi: 10.1038/27952.
|
Homing endonuclease-DNA complex . SNAP output
|
|
1iu3
|
replication inhibitor-DNA |
X-ray (3.0 Å) |
Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe
M, Hiraga S, Yokoyama S |
(2004) "Structural
and biochemical analyses of hemimethylated DNA binding
by the SeqA protein." Nucleic Acids Res.,
32, 82-92. doi: 10.1093/nar/gkh173.
|
Crystal structure of the e.coli seqa protein complexed
with hemimethylated DNA . SNAP output
|
|
1iv6
|
DNA binding protein-DNA |
NMR |
Nishikawa T, Okamura H, Nagadoi A, Konig P, Rhodes D,
Nishimura Y |
(2001) "Solution
structure of a telomeric DNA complex of human
TRF1." Structure, 9,
1237-1251. doi: 10.1016/S0969-2126(01)00688-8.
|
Solution structure of the DNA complex of human trf1 .
SNAP output
|
|
1ixy
|
transferase-DNA |
X-ray (2.5 Å) |
Lariviere L, Morera S |
(2002) "A
Base-flipping Mechanism for the T4 Phage
beta-Glucosyltransferase and Identification of a
Transition-state Analog." J.Mol.Biol.,
324, 483-490. doi: 10.1016/S0022-2836(02)01091-4.
|
Ternary complex of t4 phage bgt with udp and a 13 mer
DNA duplex . SNAP
output
|
|
1j1v
|
replication-DNA |
X-ray (2.1 Å) |
Fujikawa N, Kurumizaka H, Nureki O, Terada T,
Shirouzu M, Katayama T, Yokoyama S |
(2003) "Structural
basis of replication origin recognition by the DnaA
protein." NUCLEIC ACIDS RES.,
31, 2077-2086. doi: 10.1093/nar/gkg309.
|
Crystal structure of dnaa domainiv complexed with
dnaabox DNA . SNAP
output
|
|
1j3e
|
replication-DNA |
X-ray (2.5 Å) |
Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe
M, Hiraga S, Yokoyama S |
(2004) "Structural
and biochemical analyses of hemimethylated DNA binding
by the SeqA protein." Nucleic Acids Res.,
32, 82-92. doi: 10.1093/nar/gkh173.
|
Crystal structure of the e.coli seqa protein complexed
with n6-methyladenine- guanine mismatch DNA . SNAP output
|
|
1j46
|
transcription-DNA |
NMR |
Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore
GM |
(2001) "Structural
basis for SRY-dependent 46-X,Y sex reversal: modulation
of DNA bending by a naturally occurring point
mutation." J.Mol.Biol.,
312, 481-499. doi: 10.1006/jmbi.2001.4977.
|
3d solution NMR structure of the wild type hmg-box
domain of the human male sex determining factor sry
complexed to DNA . SNAP
output
|
|
1j47
|
transcription-DNA |
NMR |
Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore
GM |
(2001) "Structural
basis for SRY-dependent 46-X,Y sex reversal: modulation
of DNA bending by a naturally occurring point
mutation." J.Mol.Biol.,
312, 481-499. doi: 10.1006/jmbi.2001.4977.
|
3d solution NMR structure of the m9i mutant of the
hmg-box domain of the human male sex determining factor
sry complexed to DNA . SNAP output
|
|
1j4w
|
transcription-DNA |
NMR |
Braddock DT, Louis JM, Baber JL, Levens D, Clore
GM |
(2002) "Structure
and dynamics of KH domains from FBP bound to
single-stranded DNA." Nature,
415, 1051-1056. doi: 10.1038/4151051a.
|
Complex of the kh3 and kh4 domains of fbp with a
single_stranded 29mer DNA oligonucleotide from the fuse
element of the c-myc oncogene . SNAP output
|
|
1j59
|
gene regulation-DNA |
X-ray (2.5 Å) |
Parkinson G, Wilson C, Gunasekera A, Ebright YW,
Ebright RE, Berman HM |
(1996) "Structure
of the CAP-DNA complex at 2.5 angstroms resolution: a
complete picture of the protein-DNA interface."
J.Mol.Biol., 260, 395-408.
doi: 10.1006/jmbi.1996.0409.
|
Catabolite gene activator protein (cap)-DNA complex +
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
|
1j5k
|
transcription-DNA |
NMR |
Braddock DT, Baber JL, Levens D, Clore GM |
(2002) "Molecular
basis of sequence-specific single-stranded DNA
recognition by KH domains: solution structure of a
complex between hnRNP K KH3 and single-stranded
DNA." EMBO J., 21,
3476-3485. doi: 10.1093/emboj/cdf352.
|
Complex of the kh3 domain of hnrnp k with a
single_stranded 10mer DNA oligonucleotide . SNAP output
|
|
1j5n
|
DNA binding protein-DNA |
NMR |
Masse JE, Wong B, Yen Y-M, Allain FH-T, Johnson RC,
Feigon J |
(2002) "The S.
cerevisiae architectural HMGB protein NHP6A complexed
with DNA: DNA and protein conformational changes upon
binding." J.Mol.Biol.,
323, 263-284. doi: 10.1016/S0022-2836(02)00938-5.
|
Solution structure of the non-sequence-specific hmgb
protein nhp6a in complex with sry DNA . SNAP output
|
|
1j5o
|
transferase-immune system-DNA |
X-ray (3.5 Å) |
Sarafianos SG, Das K, Clark Jr AD, Ding J, Boyer PL,
Hughes SH, Arnold E |
(1999) "Lamivudine
(3TC) resistance in HIV-1 reverse transcriptase
involves steric hindrance with beta-branched amino
acids." Proc.Natl.Acad.Sci.USA,
96, 10027-10032. doi: 10.1073/pnas.96.18.10027.
|
Crystal structure of met184ile mutant of hiv-1 reverse
transcriptase in complex with double stranded DNA
template-primer . SNAP
output
|
|
1j75
|
immune system-DNA |
X-ray (1.85 Å) |
Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich
A |
(2001) "Structure
of the DLM-1-Z-DNA complex reveals a conserved family
of Z-DNA-binding proteins."
Nat.Struct.Biol., 8, 761-765.
doi: 10.1038/nsb0901-761.
|
Crystal structure of the DNA-binding domain zalpha of
dlm-1 bound to z-DNA . SNAP output
|
|
1j9n
|
DNA binding protein-DNA |
NMR |
Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez
C |
(2003) "Solution
structure and stability of tryptophan-containing
nucleopeptide duplexes." Chembiochem,
4, 40-49. doi: 10.1002/cbic.200390012.
|
Solution structure of the nucleopeptide
[ac-lys-trp-lys-hse(p3*dgcatcg)-ala]-[p5*dcgtagc] .
SNAP output
|
|
1jb7
|
DNA-binding protein-DNA |
X-ray (1.86 Å) |
Horvath MP, Schultz SC |
(2001) "DNA
G-quartets in a 1.86 A resolution structure of an
Oxytricha nova telomeric protein-DNA complex."
J.Mol.Biol., 310, 367-377.
doi: 10.1006/jmbi.2001.4766.
|
DNA g-quartets in a 1.86 Å resolution structure of an
oxytricha nova telomeric protein-DNA complex . SNAP output
|
|
1je8
|
transcription-DNA |
X-ray (2.12 Å) |
Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR,
Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson
RE |
(2002) "Dimerization
allows DNA target site recognition by the NarL response
regulator." Nat.Struct.Biol.,
9, 771-778. doi: 10.1038/nsb845.
|
Two-component response regulator narl-DNA complex: DNA
bending found in a high affinity site . SNAP output
|
|
1jey
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Walker JR, Corpina RA, Goldberg J |
(2001) "Structure
of the Ku heterodimer bound to DNA and its implications
for double-strand break repair." Nature,
412, 607-614. doi: 10.1038/35088000.
|
Crystal structure of the ku heterodimer bound to DNA .
SNAP output
|
|
1jfi
|
transcription-DNA |
X-ray (2.62 Å) |
Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder
RG, Meisterernst M, Burley SK |
(2001) "Crystal
structure of negative cofactor 2 recognizing the
TBP-DNA transcription complex."
Cell(Cambridge,Mass.), 106,
71-81. doi: 10.1016/S0092-8674(01)00417-2.
|
Crystal structure of the nc2-tbp-DNA ternary complex .
SNAP output
|
|
1jfs
|
transcription-DNA |
X-ray (2.9 Å) |
Huffman JL, Lu F, Zalkin H, Brennan RG |
(2002) "Role of
residue 147 in the gene regulatory function of the
Escherichia coli purine repressor."
Biochemistry, 41, 511-520.
doi: 10.1021/bi0156660.
|
Purine repressor mutant-hypoxanthine-purf operator
complex . SNAP
output
|
|
1jft
|
transcription-DNA |
X-ray (2.5 Å) |
Huffman JL, Lu F, Zalkin H, Brennan RG |
(2002) "Role of
residue 147 in the gene regulatory function of the
Escherichia coli purine repressor."
Biochemistry, 41, 511-520.
doi: 10.1021/bi0156660.
|
Purine repressor mutant-hypoxanthine-purf operator
complex . SNAP
output
|
|
1jgg
|
transcription-DNA |
X-ray (2.0 Å) |
Hirsch JA, Aggarwal AK |
(1995) "Structure
of the even-skipped homeodomain complexed to AT-rich
DNA: new perspectives on homeodomain specificity."
EMBO J., 14, 6280-6291.
|
Even-skipped homeodomain complexed to at-rich DNA .
SNAP output
|
|
1jh9
|
transcription-DNA |
X-ray (2.55 Å) |
Huffman JL, Lu F, Zalkin H, Brennan RG |
(2002) "Role of
residue 147 in the gene regulatory function of the
Escherichia coli purine repressor."
Biochemistry, 41, 511-520.
doi: 10.1021/bi0156660.
|
Purine repressor mutant-hypoxanthine-purf operator
complex . SNAP
output
|
|
1jj4
|
transcription-DNA |
X-ray (2.4 Å) |
Kim SS, Tam JK, Wang AF, Hegde RS |
(2000) "The
structural basis of DNA target discrimination by
papillomavirus E2 proteins." J.Biol.Chem.,
275, 31245-31254. doi: 10.1074/jbc.M004541200.
|
Human papillomavirus type 18 e2 DNA-binding domain
bound to its DNA target . SNAP output
|
|
1jj6
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations. . SNAP output
|
|
1jj8
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
|
1jk1
|
transcription-DNA |
X-ray (1.9 Å) |
Miller JC, Pabo CO |
(2001) "Rearrangement
of side-chains in a Zif268 mutant highlights the
complexities of zinc finger-DNA recognition."
J.Mol.Biol., 313, 309-315.
doi: 10.1006/jmbi.2001.4975.
|
Zif268 d20a mutant bound to wt DNA site . SNAP output
|
|
1jk2
|
transcription-DNA |
X-ray (1.65 Å) |
Miller JC, Pabo CO |
(2001) "Rearrangement
of side-chains in a Zif268 mutant highlights the
complexities of zinc finger-DNA recognition."
J.Mol.Biol., 313, 309-315.
doi: 10.1006/jmbi.2001.4975.
|
Zif268 d20a mutant bound to the gct DNA site . SNAP output
|
|
1jko
|
DNA binding protein-DNA |
X-ray (2.24 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
|
1jkp
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
|
1jkq
|
DNA binding protein-DNA |
X-ray (2.86 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
|
1jkr
|
DNA binding protein-DNA |
X-ray (2.28 Å) |
Chiu TK, Sohn C, Dickerson RE, Johnson RC |
(2002) "Testing
water-mediated DNA recognition by the Hin
recombinase." EMBO J.,
21, 801-814. doi: 10.1093/emboj/21.4.801.
|
Testing the water-mediated hin recombinase DNA
recognition by systematic mutations . SNAP output
|
|
1jmc
|
replication-DNA |
X-ray (2.4 Å) |
Bochkarev A, Pfuetzner RA, Edwards AM, Frappier
L |
(1997) "Structure
of the single-stranded-DNA-binding domain of
replication protein A bound to DNA."
Nature, 385, 176-181. doi:
10.1038/385176a0.
|
Single stranded DNA-binding domain of human replication
protein a bound to single stranded DNA, rpa70 subunit,
residues 183-420 . SNAP
output
|
|
1jnm
|
transcription-DNA |
X-ray (2.2 Å) |
Kim Y, Podust LM |
"Crystal Structure of the Jun bZIP homodimer
complexed with CRE." |
Crystal structure of the jun-cre complex . SNAP output
|
|
1jt0
|
transcription-DNA |
X-ray (2.9 Å) |
Schumacher MA, Miller MC, Grkovic S, Brown MH,
Skurray RA, Brennan RG |
(2002) "Structural
basis for cooperative DNA binding by two dimers of the
multidrug-binding protein QacR." EMBO J.,
21, 1210-1218. doi: 10.1093/emboj/21.5.1210.
|
Crystal structure of a cooperative qacr-DNA complex .
SNAP output
|
|
1jwl
|
transcription-DNA |
X-ray (4.0 Å) |
Bell CE, Lewis M |
(2001) "Crystallographic
analysis of Lac repressor bound to natural operator
O1." J.Mol.Biol., 312,
921-926. doi: 10.1006/jmbi.2001.5024.
|
Structure of the dimeric lac repressor-operator o1-onpf
complex . SNAP
output
|
|
1jx4
|
transferase-DNA |
X-ray (1.7 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2001) "Crystal
structure of a Y-family DNA polymerase in action: a
mechanism for error-prone and lesion-bypass
replication." Cell(Cambridge,Mass.),
107, 91-102. doi: 10.1016/S0092-8674(01)00515-3.
|
Crystal structure of a y-family DNA polymerase in a
ternary complex with DNA substrates and an incoming
nucleotide . SNAP
output
|
|
1jxl
|
transferase-DNA |
X-ray (2.1 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2001) "Crystal
structure of a Y-family DNA polymerase in action: a
mechanism for error-prone and lesion-bypass
replication." Cell(Cambridge,Mass.),
107, 91-102. doi: 10.1016/S0092-8674(01)00515-3.
|
Crystal structure of a y-family DNA polymerase in a
ternary complex with DNA substrates and an incoming
nucleotide . SNAP
output
|
|
1k3w
|
hydrolase-DNA |
X-ray (1.42 Å) |
Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman
SE, Kycia JH, Rieger RA, Grollman AP, Shoham G |
(2002) "Structural
analysis of an Escherichia coli endonuclease VIII
covalent reaction intermediate." EMBO J.,
21, 789-800. doi: 10.1093/emboj/21.4.789.
|
Crystal structure of a trapped reaction intermediate of
the DNA repair enzyme endonuclease viii with DNA .
SNAP output
|
|
1k3x
|
hydrolase-DNA |
X-ray (1.25 Å) |
Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman
SE, Kycia JH, Rieger RA, Grollman AP, Shoham G |
(2002) "Structural
analysis of an Escherichia coli endonuclease VIII
covalent reaction intermediate." EMBO J.,
21, 789-800. doi: 10.1093/emboj/21.4.789.
|
Crystal structure of a trapped reaction intermediate of
the DNA repair enzyme endonuclease viii with
brominated-DNA . SNAP
output
|
|
1k4s
|
isomerase-DNA |
X-ray (3.2 Å) |
Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr
AB, Stewart LJ |
(2002) "The
mechanism of topoisomerase I poisoning by a
camptothecin analog."
Proc.Natl.Acad.Sci.USA, 99,
15387-15392. doi: 10.1073/pnas.242259599.
|
Human DNA topoisomerase i in covalent complex with a 22
base pair DNA duplex . SNAP output
|
|
1k4t
|
isomerase-DNA |
X-ray (2.1 Å) |
Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr
AB, Stewart LJ |
(2002) "The
mechanism of topoisomerase I poisoning by a
camptothecin analog."
Proc.Natl.Acad.Sci.USA, 99,
15387-15392. doi: 10.1073/pnas.242259599.
|
Human DNA topoisomerase i (70 kda) in complex with the
poison topotecan and covalent complex with a 22 base
pair DNA duplex . SNAP
output
|
|
1k61
|
transcription-DNA |
X-ray (2.1 Å) |
Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T,
Wolberger C |
(2002) "A
Hoogsteen base pair embedded in undistorted B-DNA."
NUCLEIC ACIDS RES., 30,
5244-5252. doi: 10.1093/nar/gkf661.
|
Matalpha2 homeodomain bound to DNA . SNAP output
|
|
1k6o
|
transcription-DNA |
X-ray (3.19 Å) |
Mo Y, Ho W, Johnston K, Marmorstein R |
(2001) "Crystal
structure of a ternary SAP-1/SRF/c-fos SRE DNA
complex." J.Mol.Biol.,
314, 495-506. doi: 10.1006/jmbi.2001.5138.
|
Crystal structure of a ternary sap-1-srf-c-fos sre DNA
complex . SNAP
output
|
|
1k78
|
transcription-DNA |
X-ray (2.25 Å) |
Garvie CW, Hagman J, Wolberger C |
(2001) "Structural
studies of Ets-1/Pax5 complex formation on DNA."
Mol.Cell, 8, 1267-1276. doi:
10.1016/S1097-2765(01)00410-5.
|
Pax5(1-149)+ets-1(331-440)+DNA . SNAP output
|
|
1k79
|
transcription-DNA |
X-ray (2.4 Å) |
Garvie CW, Hagman J, Wolberger C |
(2001) "Structural
studies of Ets-1/Pax5 complex formation on DNA."
Mol.Cell, 8, 1267-1276. doi:
10.1016/S1097-2765(01)00410-5.
|
Ets-1(331-440)+ggaa duplex . SNAP output
|
|
1k7a
|
transcription-DNA |
X-ray (2.8 Å) |
Garvie CW, Hagman J, Wolberger C |
(2001) "Structural
studies of Ets-1/Pax5 complex formation on DNA."
Mol.Cell, 8, 1267-1276. doi:
10.1016/S1097-2765(01)00410-5.
|
Ets-1(331-440)+ggag duplex . SNAP output
|
|
1k82
|
hydrolase-DNA |
X-ray (2.1 Å) |
Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman
SE, Matz E, Kycia JH, Grollman AP, Shoham G |
(2002) "Structure
of formamidopyrimidine-DNA glycosylase covalently
complexed to DNA." J.Biol.Chem.,
277, 19811-19816. doi: 10.1074/jbc.M202058200.
|
Crystal structure of e.coli formamidopyrimidine-DNA
glycosylase (fpg) covalently trapped with DNA .
SNAP output
|
|
1k8g
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Classen S, Ruggles JA, Schultz SC |
(2001) "Crystal
structure of the N-terminal domain of Oxytricha nova
telomere end-binding protein alpha subunit both
uncomplexed and complexed with telomeric ssDNA."
J.Mol.Biol., 314, 1113-1125.
doi: 10.1006/jmbi.2000.5191.
|
Crystal structure of the n-terminal domain of oxytricha
nova telomere end binding protein alpha subunit both
uncomplexed and complexed with telomeric ssDNA .
SNAP output
|
|
1kb2
|
transcription-DNA |
X-ray (2.7 Å) |
Shaffer PL, Gewirth DT |
(2002) "Structural
basis of VDR-DNA interactions on direct repeat response
elements." EMBO J., 21,
2242-2252. doi: 10.1093/emboj/21.9.2242.
|
Crystal structure of vdr DNA-binding domain bound to
mouse osteopontin (spp) response element . SNAP output
|
|
1kb4
|
transcription-DNA |
X-ray (2.8 Å) |
Shaffer PL, Gewirth DT |
(2002) "Structural
basis of VDR-DNA interactions on direct repeat response
elements." EMBO J., 21,
2242-2252. doi: 10.1093/emboj/21.9.2242.
|
Crystal structure of vdr DNA-binding domain bound to a
canonical direct repeat with three base pair spacer
(dr3) response element . SNAP output
|
|
1kb6
|
transcription-DNA |
X-ray (2.7 Å) |
Shaffer PL, Gewirth DT |
(2002) "Structural
basis of VDR-DNA interactions on direct repeat response
elements." EMBO J., 21,
2242-2252. doi: 10.1093/emboj/21.9.2242.
|
Crystal structure of vdr DNA-binding domain bound to
rat osteocalcin (oc) response element . SNAP output
|
|
1kbu
|
hydrolase, ligase-DNA |
X-ray (2.2 Å) |
Martin SS, Pulido E, Chu VC, Lechner TS, Baldwin
EP |
(2002) "The
Order of Strand Exchanges in Cre-LoxP Recombination and
its Basis Suggested by the Crystal Structure of a
Cre-LoxP Holliday Junction Complex."
J.Mol.Biol., 319, 107-127.
doi: 10.1016/S0022-2836(02)00246-2.
|
Cre recombinase bound to a loxp holliday junction .
SNAP output
|
|
1kc6
|
hydrolase-DNA |
X-ray (2.6 Å) |
Horton NC, Dorner LF, Perona JJ |
(2002) "Sequence
selectivity and degeneracy of a restriction
endonuclease mediated by DNA intercalation."
Nat.Struct.Biol., 9, 42-47.
doi: 10.1038/nsb741.
|
Hincii bound to cognate DNA . SNAP output
|
|
1kc8
|
ribosome |
X-ray (3.01 Å) |
Hansen J, Moore PB, Steitz TA |
(2003) "Structures
of Five Antibiotics Bound at the Peptidyl Transferase
Center of the Large Ribosomal Subunit."
J.Mol.Biol., 330, 1061-1075.
doi: 10.1016/S0022-2836(03)00668-5.
|
Co-crystal structure of blasticidin s bound to the 50s
ribosomal subunit . SNAP
output
|
|
1kdh
|
transferase-DNA |
X-ray (3.0 Å) |
Delarue M, Boule JB, Lescar J, Expert-Bezancon N,
Jourdan N, Sukumar N, Rougeon F, Papanicolaou C |
(2002) "Crystal
structures of a template-independent DNA polymerase:
murine terminal deoxynucleotidyltransferase."
EMBO J., 21, 427-439. doi:
10.1093/emboj/21.3.427.
|
Binary complex of murine terminal deoxynucleotidyl
transferase with a primer single stranded DNA .
SNAP output
|
|
1keg
|
immune system-DNA |
X-ray (2.4 Å) |
Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y,
Ohtsuka E, Nikaido O |
(2012) "Structure
of the DNA (6-4) photoproduct dTT(6-4)TT in complex
with the 64M-2 antibody Fab fragment implies increased
antibody-binding affinity by the flanking
nucleotides." Acta Crystallogr.,Sect.D,
68, 232-238. doi: 10.1107/S0907444912000327.
|
Antibody 64m-2 fab complexed with dtt(6-4)tt . SNAP output
|
|
1kfs
|
transferase-DNA |
X-ray (2.1 Å) |
Brautigam CA, Steitz TA |
(1998) "Structural
principles for the inhibition of the 3'-5' exonuclease
activity of Escherichia coli DNA polymerase I by
phosphorothioates." J.Mol.Biol.,
277, 363-377. doi: 10.1006/jmbi.1997.1586.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
|
1kfv
|
hydrolase-DNA |
X-ray (2.55 Å) |
Serre L, Pereira de Jesus K, Boiteux S, Zelwer C,
Castaing B |
(2002) "Crystal
structure of the Lactococcus lactis
formamidopyrimidine-DNA glycosylase bound to an abasic
site analogue-containing DNA." EMBO J.,
21, 2854-2865. doi: 10.1093/emboj/cdf304.
|
Crystal structure of lactococcus lactis
formamido-pyrimidine DNA glycosylase (alias fpg or
mutm) non covalently bound to an ap site containing
DNA. . SNAP output
|
|
1kix
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Peersen OB, Ruggles JA, Schultz SC |
(2002) "Dimeric
structure of the Oxytricha nova telomere end-binding
protein alpha-subunit bound to ssDNA."
Nat.Struct.Biol., 9, 182-187.
|
Dimeric structure of the o. nova telomere end binding
protein alpha subunit with bound ssDNA . SNAP output
|
|
1kln
|
transferase-DNA |
X-ray (3.2 Å) |
Beese LS, Derbyshire V, Steitz TA |
(1993) "Structure
of DNA polymerase I Klenow fragment bound to duplex
DNA." Science, 260,
352-355.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
|
1kqq
|
transcription-DNA |
NMR |
Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb
RT |
(2002) "The
structure of the Dead ringer-DNA complex reveals how
AT-rich interaction domains (ARIDs) recognize DNA."
EMBO J., 21, 1197-1209. doi:
10.1093/emboj/21.5.1197.
|
Solution structure of the dead ringer arid-DNA complex
. SNAP output
|
|
1krp
|
transferase-DNA |
X-ray (2.2 Å) |
Brautigam CA, Steitz TA |
(1998) "Structural
principles for the inhibition of the 3'-5' exonuclease
activity of Escherichia coli DNA polymerase I by
phosphorothioates." J.Mol.Biol.,
277, 363-377. doi: 10.1006/jmbi.1997.1586.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
|
1ksp
|
transferase-DNA |
X-ray (2.3 Å) |
Brautigam CA, Steitz TA |
(1998) "Structural
principles for the inhibition of the 3'-5' exonuclease
activity of Escherichia coli DNA polymerase I by
phosphorothioates." J.Mol.Biol.,
277, 363-377. doi: 10.1006/jmbi.1997.1586.
|
DNA polymerase i klenow fragment (e.c.2.7.7.7)
mutant-DNA complex . SNAP output
|
|
1ksx
|
replication-DNA |
X-ray (3.2 Å) |
Enemark EJ, Stenlund A, Joshua-Tor L |
(2002) "Crystal
structures of two intermediates in the assembly of the
papillomavirus replication initiation complex."
EMBO J., 21, 1487-1496. doi:
10.1093/emboj/21.6.1487.
|
Crystal structures of two intermediates in the assembly
of the papillomavirus replication initiation complex .
SNAP output
|
|
1ksy
|
replication-DNA |
X-ray (3.05 Å) |
Enemark EJ, Stenlund A, Joshua-Tor L |
(2002) "Crystal
structures of two intermediates in the assembly of the
papillomavirus replication initiation complex."
EMBO J., 21, 1487-1496. doi:
10.1093/emboj/21.6.1487.
|
Crystal structures of two intermediates in the assembly
of the papillomavirus replication initiation complex .
SNAP output
|
|
1ku7
|
transcription-DNA |
X-ray (2.4 Å) |
Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA,
Weinman O, Trester-Zedlitz ML, Darst SA |
(2002) "Structure
of the bacterial RNA polymerase promoter specificity
sigma subunit." Mol.Cell,
9, 527-539. doi: 10.1016/S1097-2765(02)00470-7.
|
Crystal structure of thermus aquatics RNA polymerase
sigmaa subunit region 4 bound to-35 element DNA .
SNAP output
|
|
1kx3
|
structural protein-DNA |
X-ray (2.0 Å) |
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond
TJ |
(2002) "Solvent
Mediated Interactions in the Structure of the
Nucleosome Core Particle at 1.9 A Resolution."
J.Mol.Biol., 319, 1097-1113.
doi: 10.1016/S0022-2836(02)00386-8.
|
X-ray structure of the nucleosome core particle,
ncp146, at 2.0 Å resolution . SNAP output
|
|
1kx4
|
structural protein-DNA |
X-ray (2.6 Å) |
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond
TJ |
(2002) "Solvent
Mediated Interactions in the Structure of the
Nucleosome Core Particle at 1.9 A Resolution."
J.Mol.Biol., 319, 1097-1113.
doi: 10.1016/S0022-2836(02)00386-8.
|
X-ray structure of the nucleosome core particle,
ncp146b, at 2.6 Å resolution . SNAP output
|
|
1kx5
|
structural protein-DNA |
X-ray (1.94 Å) |
Davey CA, Sargent DF, Luger K, Maeder AW, Richmond
TJ |
(2002) "Solvent
Mediated Interactions in the Structure of the
Nucleosome Core Particle at 1.9 A Resolution."
J.Mol.Biol., 319, 1097-1113.
doi: 10.1016/S0022-2836(02)00386-8.
|
X-ray structure of the nucleosome core particle,
ncp147, at 1.9 Å resolution . SNAP output
|
|
1l1m
|
transcription regulator-DNA |
NMR |
Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R,
Boelens R, Kaptein R |
(2002) "Plasticity
in protein-DNA recognition: lac repressor interacts
with its natural operator 01 through alternative
conformations of its DNA-binding domain." EMBO
J., 21, 2866-2876. doi: 10.1093/emboj/cdf318.
|
Solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o1
. SNAP output
|
|
1l1t
|
hydrolase-DNA |
X-ray (1.8 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg) bound to abasic-site containing DNA .
SNAP output
|
|
1l1v
|
DNA-antibiotic |
NMR |
Chou SH, Chin KH, Chen FM |
(2002) "Looped
Out and Perpendicular: Deformation of Watson-Crick Base
Pair Associated with Actinomycin D Binding."
Proc.Natl.Acad.Sci.USA, 99,
6625. doi: 10.1073/PNAS.102580399.
|
Unusual actd-dna_ta complex structure . SNAP output
|
|
1l1z
|
hydrolase-DNA |
X-ray (1.7 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg) covalent-DNA intermediate . SNAP output
|
|
1l2b
|
hydrolase-DNA |
X-ray (2.4 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg) DNA end-product structure . SNAP output
|
|
1l2c
|
hydrolase-DNA |
X-ray (2.2 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg)-DNA estranged thymine mismatch recognition
complex . SNAP
output
|
|
1l2d
|
hydrolase-DNA |
X-ray (2.0 Å) |
Fromme JC, Verdine GL |
(2002) "Structural
insights into lesion recognition and repair by the
bacterial 8-oxoguanine DNA glycosylase MutM."
Nat.Struct.Biol., 9, 544-552.
|
Mutm (fpg)-DNA estranged guanine mismatch recognition
complex . SNAP
output
|
|
1l3l
|
transcription-DNA |
X-ray (1.66 Å) |
Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T,
Molyneaux JM, Anderson JC, Bashkin JK, Winans SC,
Joachimiak A |
(2002) "Structure
of a bacterial quorum-sensing transcription factor
complexed with pheromone and DNA." Nature,
417, 971-974. doi: 10.1038/nature00833.
|
Crystal structure of a bacterial quorum-sensing
transcription factor complexed with pheromone and DNA .
SNAP output
|
|
1l3s
|
transferase-DNA |
X-ray (1.7 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
complexed to 9 base pairs of duplex DNA. . SNAP output
|
|
1l3t
|
transferase-DNA |
X-ray (1.7 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 10 base pairs of duplex DNA
following addition of a single dttp residue . SNAP output
|
|
1l3u
|
transferase-DNA |
X-ray (1.8 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 11 base pairs of duplex DNA
following addition of a dttp and a datp residue. .
SNAP output
|
|
1l3v
|
transferase-DNA |
X-ray (1.71 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 15 base pairs of duplex DNA
following addition of dttp, datp, dctp, and dgtp
residues. . SNAP
output
|
|
1l5u
|
transferase-DNA |
X-ray (1.95 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of bacillus DNA polymerase i fragment
product complex with 12 base pairs of duplex DNA
following addition of a dttp, a datp, and a dctp
residue. . SNAP
output
|
|
1lat
|
transcription-DNA |
X-ray (1.9 Å) |
Gewirth DT, Sigler PB |
(1995) "The basis
for half-site specificity explored through a
non-cognate steroid receptor-DNA complex."
Nat.Struct.Biol., 2, 386-394.
doi: 10.1038/nsb0595-386.
|
Glucocorticoid receptor mutant-DNA complex . SNAP output
|
|
1lau
|
hydrolase-DNA |
X-ray (1.8 Å) |
Savva R, McAuley-Hecht K, Brown T, Pearl L |
(1995) "The
structural basis of specific base-excision repair by
uracil-DNA glycosylase." Nature,
373, 487-493. doi: 10.1038/373487a0.
|
Uracil-DNA glycosylase . SNAP output
|
|
1lb2
|
gene regulation-DNA |
X-ray (3.1 Å) |
Benoff B, Yang H, Lawson CL, Parkinson G, Liu J,
Blatter E, Ebright YW, Berman HM, Ebright RH |
(2002) "Structural
basis of transcription activation: the CAP-alpha
CTD-DNA complex." Science,
297, 1562-1566. doi: 10.1126/science.1076376.
|
Structure of the e. coli alpha c-terminal domain of RNA
polymerase in complex with cap and DNA . SNAP output
|
|
1lcc
|
gene regulation-DNA |
NMR |
Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH,
Boelens R, Kaptein R |
(1993) "Structure
of the complex of lac repressor headpiece and an 11
base-pair half-operator determined by nuclear magnetic
resonance spectroscopy and restrained molecular
dynamics." J.Mol.Biol.,
234, 446-462. doi: 10.1006/jmbi.1993.1598.
|
Structure of the complex of lac repressor headpiece and
an 11 base-pair half-operator determined by nuclear
magnetic resonance spectroscopy and restrained
molecular dynamics . SNAP output
|
|
1lcd
|
gene regulation-DNA |
NMR |
Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH,
Boelens R, Kaptein R |
(1993) "Structure
of the complex of lac repressor headpiece and an 11
base-pair half-operator determined by nuclear magnetic
resonance spectroscopy and restrained molecular
dynamics." J.Mol.Biol.,
234, 446-462. doi: 10.1006/jmbi.1993.1598.
|
Structure of the complex of lac repressor headpiece and
an 11 base-pair half-operator determined by nuclear
magnetic resonance spectroscopy and restrained
molecular dynamics . SNAP output
|
|
1le5
|
transcription-DNA |
X-ray (2.75 Å) |
Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh
G |
(2002) "The
X-ray crystal structure of the NF-kB p50/p65
heterodimer bound to the Interferon beta-kB site."
J.Biol.Chem., 277,
24694-24700. doi: 10.1074/jbc.M200006200.
|
Crystal structure of a nf-kb heterodimer bound to an
ifnb-kb . SNAP
output
|
|
1le8
|
transcription-DNA |
X-ray (2.3 Å) |
Ke A, Mathias JR, Vershon AK, Wolberger C |
(2002) "Structural
and Thermodynamic Characterization of the DNA Binding
Properties of a Triple Alanine Mutant of
MATalpha2." Structure,
10, 961-971. doi: 10.1016/S0969-2126(02)00790-6.
|
Crystal structure of the mata1-matalpha2-3a heterodimer
bound to DNA complex . SNAP output
|
|
1le9
|
transcription-DNA |
X-ray (3.0 Å) |
Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh
G |
(2002) "The
x-ray crystal structure of the NF-kappa B p50.p65
heterodimer bound to the interferon beta -kappa B
site." J.Biol.Chem., 277,
24694-24700. doi: 10.1074/jbc.M200006200.
|
Crystal structure of a nf-kb heterodimer bound to the
ig-hiv-kb siti . SNAP
output
|
|
1lei
|
transcription-DNA |
X-ray (2.7 Å) |
Chen-Park FE, Huang DB, Noro B, Thanos D, Ghosh
G |
(2002) "The kB
DNA sequence from the HIV Long Terminal Repeat
functions as an allosteric regulator of HIV
transcription." J.Biol.Chem.,
277, 24701-24708. doi: 10.1074/jbc.M200007200.
|
The kb DNA sequence from the hlv-ltr functions as an
allosteric regulator of hiv transcription . SNAP output
|
|
1lfu
|
transcription |
NMR |
Sprules T, Green N, Featherstone M, Gehring K |
(2003) "Lock and
Key Binding of the HOX YPWM Peptide to the PBX
Homeodomain." J.Biol.Chem.,
278, 1053-1058. doi: 10.1074/jbc.M207504200.
|
NMR solution structure of the extended pbx homeodomain
bound to DNA . SNAP
output
|
|
1lli
|
transcription-DNA |
X-ray (2.1 Å) |
Lim WA, Hodel A, Sauer RT, Richards FM |
(1994) "The
crystal structure of a mutant protein with altered but
improved hydrophobic core packing."
Proc.Natl.Acad.Sci.USA, 91,
423-427. doi: 10.1073/pnas.91.1.423.
|
The crystal structure of a mutant protein with altered
but improved hydrophobic core packing . SNAP output
|
|
1llm
|
transcription-DNA |
X-ray (1.5 Å) |
Wolfe SA, Grant RA, Pabo CO |
(2003) "Structure
of a designed dimeric zinc finger protein bound to
DNA." Biochemistry, 42,
13401-13409. doi: 10.1021/bi034830b.
|
Crystal structure of a zif23-gcn4 chimera bound to DNA
. SNAP output
|
|
1lmb
|
transcription-DNA |
X-ray (1.8 Å) |
Beamer LJ, Pabo CO |
(1992) "Refined
1.8 A crystal structure of the lambda
repressor-operator complex." J.Mol.Biol.,
227, 177-196. doi: 10.1016/0022-2836(92)90690-L.
|
Refined 1.8 angstrom crystal structure of the lambda
repressor-operator complex . SNAP output
|
|
1lo1
|
hormone-growth factor receptor-DNA |
NMR |
Gearhart MD, Holmbeck SMA, Evans RM, Dyson HJ, Wright
PE |
(2003) "Monomeric
Complex of Human Orphan Estrogen Related Receptor-2
with DNA: A Pseudo-dimer Interface Mediates Extended
Half-site Recognition." J.Mol.Biol.,
327, 819-832. doi: 10.1016/S0022-2836(03)00183-9.
|
Estrogen related receptor 2 DNA binding domain in
complex with DNA . SNAP
output
|
|
1lpq
|
isomerase-DNA |
X-ray (3.14 Å) |
Lesher DT, Pommier Y, Stewart L, Redinbo MR |
(2002) "8-Oxoguanine
rearranges the active site of human topoisomerase
I." Proc.Natl.Acad.Sci.USA,
99, 12102-12107. doi: 10.1073/pnas.192282699.
|
Human DNA topoisomerase i (70 kda) in non-covalent
complex with a 22 base pair DNA duplex containing an
8-oxog lesion . SNAP
output
|
|
1lq1
|
transcription-DNA |
X-ray (2.3 Å) |
Zhao H, Msadek T, Zapf J, Madhusudan, Hoch JA,
Varughese KI |
(2002) "DNA
complexed structure of the key transcription factor
initiating development in sporulating bacteria."
Structure, 10, 1041-1050.
doi: 10.1016/S0969-2126(02)00803-1.
|
DNA complexed structure of the key transcription factor
initiating development in sporulation bacteria .
SNAP output
|
|
1lrr
|
replication inhibitor-DNA |
X-ray (2.65 Å) |
Guarne A, Zhao Q, Guirlando R, Yang W |
(2002) "Insights
into negative modulation of E. coli replication
initiation from the structure of SeqA-hemimethylated
DNA complex." NAT.STRUCT.BIOL.,
9, 839-843.
|
Crystal structure of e. coli seqa complexed with
hemimethylated DNA . SNAP output
|
|
1lv5
|
transferase-DNA |
X-ray (1.95 Å) |
Johnson SJ, Taylor JS, Beese LS |
(2003) "Processive
DNA synthesis observed in a polymerase crystal suggests
a mechanism for the prevention of frameshift
mutations." Proc.Natl.Acad.Sci.USA,
100, 3895-3900. doi: 10.1073/pnas.0630532100.
|
Crystal structure of the closed conformation of
bacillus DNA polymerase i fragment bound to DNA and
dctp . SNAP output
|
|
1lws
|
hydrolase-DNA |
X-ray (3.5 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2002) "Crystal
structure of the intein homing endonuclease PI-SceI
bound to its recognition sequence."
Nat.Struct.Biol., 9, 764-770.
doi: 10.1038/nsb840.
|
Crystal structure of the intein homing endonuclease
pi-scei bound to its recognition sequence . SNAP output
|
|
1lwt
|
hydrolase-DNA |
X-ray (3.2 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2002) "Crystal
structure of the intein homing endonuclease PI-SceI
bound to its recognition sequence."
Nat.Struct.Biol., 9, 764-770.
doi: 10.1038/nsb840.
|
Crystal structure of the intein homing endonuclease
pi-scei bound to its substrate DNA (ca2+ free) .
SNAP output
|
|
1lwv
|
hydrolase-DNA |
X-ray (2.3 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in Base Excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Borohydride-trapped hogg1 intermediate structure
co-crystallized with 8-aminoguanine . SNAP output
|
|
1lww
|
hydrolase-DNA |
X-ray (2.1 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in Base Excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Borohydride-trapped hogg1 intermediate structure
co-crystallized with 8-bromoguanine . SNAP output
|
|
1lwy
|
hydrolase-DNA |
X-ray (2.01 Å) |
Fromme JC, Bruner SD, Yang W, Karplus M, Verdine
GL |
(2003) "Product-Assisted
Catalysis in Base Excision DNA Repair."
Nat.Struct.Biol., 10,
204-211. doi: 10.1038/nsb902.
|
Hogg1 borohydride-trapped intermediate without
8-oxoguanine . SNAP
output
|
|
1m07
|
hydrolase-DNA |
X-ray (1.8 Å) |
Leu Y-J, Chern S-S, Wang S-C, Hsiao Y-Y, Amiraslanov
I, Liaw Y-C, Liao Y-D |
(2003) "Residues
involved in the catalysis, base specificity, and
cytotoxicity of ribonuclease from Rana catesbeiana
based upon mutagenesis and X-ray crystallography."
J.Biol.Chem., 278, 7300-7309.
doi: 10.1074/jbc.M206701200.
|
Residues involved in the catalysis and base specificity
of cytotoxic ribonuclease from bullfrog (rana
catesbeiana) . SNAP
output
|
|
1m0e
|
transferase-DNA |
X-ray (2.5 Å) |
Zhou L, Cheng X, Connolly BA, Dickman MJ, Hurd PJ,
Hornby DP |
(2002) "ZEBULARINE:
A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT
COMPLEX WITH DNA METHYLTRANSFERASES."
J.MOL.BIOL., 321, 591-599.
doi: 10.1016/S0022-2836(02)00676-9.
|
Zebularine: a novel DNA methylation inhibitor that
forms a covalent complex with DNA methyltransferase .
SNAP output
|
|
1m18
|
structural protein-DNA |
X-ray (2.45 Å) |
Suto RK, Edayathumangalam RS, White CL, Melander C,
Gottesfeld JM, Dervan PB, Luger K |
(2003) "Crystal
Structures of Nucleosome Core Particles in Complex with
Minor Groove DNA-binding Ligands."
J.Mol.Biol., 326, 371-380.
doi: 10.1016/S0022-2836(02)01407-9.
|
Ligand binding alters the structure and dynamics of
nucleosomal DNA . SNAP
output
|
|
1m19
|
structural protein-DNA |
X-ray (2.3 Å) |
Suto RK, Edayathumangalam RS, White CL, Melander C,
Gottesfeld JM, Dervan PB, Luger K |
(2003) "Crystal
Structures of Nucleosome Core Particles in Complex with
Minor Groove DNA-binding Ligands."
J.Mol.Biol., 326, 371-380.
doi: 10.1016/S0022-2836(02)01407-9.
|
Ligand binding alters the structure and dynamics of
nucleosomal DNA . SNAP
output
|
|
1m1a
|
structural protein-DNA |
X-ray (2.65 Å) |
Suto RK, Edayathumangalam RS, White CL, Melander C,
Gottesfeld JM, Dervan PB, Luger K |
(2003) "Crystal
Structures of Nucleosome Core Particles in Complex with
Minor Groove DNA-binding Ligands."
J.MOL.BIOL., 326, 371-380.
doi: 10.1016/S0022-2836(02)01407-9.
|
Ligand binding alters the structure and dynamics of
nucleosomal DNA . SNAP
output
|
|
1m3h
|
hydrolase-DNA |
X-ray (2.05 Å) |
Chung SJ, Verdine GL |
(2004) "Structures
of End Products Resulting from Lesion Processing by a
DNA Glycosylase/Lyase." Chem.Biol.,
11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014.
|
Crystal structure of hogg1 d268e mutant with product
oligonucleotide . SNAP
output
|
|
1m3q
|
hydrolase-DNA |
X-ray (1.9 Å) |
Chung SJ, Verdine GL |
(2004) "Structures
of End Products Resulting from Lesion Processing by a
DNA Glycosylase/Lyase." Chem.Biol.,
11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014.
|
Crystal structure of hogg1 d268e mutant with
base-excised DNA and 8-aminoguanine . SNAP output
|
|
1m5r
|
transferase-DNA |
X-ray (1.8 Å) |
Lariviere L, Morera S |
(2002) "A
Base-flipping mechanism for the T4 phage
beta-glucosyltransferase and identification of a
transition state analog." J.Mol.Biol.,
324, 483-489. doi: 10.1016/S0022-2836(02)01091-4.
|
Ternary complex of t4 phage bgt with udp and a 13 mer
DNA duplex . SNAP
output
|
|
1m5x
|
hydrolase-DNA |
X-ray (2.25 Å) |
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard
BL |
(2003) "Flexible
DNA Target Site Recognition by Divergent Homing
Endonuclease Isoschizomers I-CreI and I-MsoI."
J.Mol.Biol., 329, 253-269.
doi: 10.1016/S0022-2836(03)00447-9.
|
Crystal structure of the homing endonuclease i-msoi
bound to its DNA substrate . SNAP output
|
|
1m6x
|
ligase, lyase-DNA |
X-ray (2.8 Å) |
Conway AB, Chen Y, Rice PA |
(2003) "Structural
Plasticity of the Flp-Holliday Junction Complex."
J.Mol.Biol., 326, 425-434.
doi: 10.1016/S0022-2836(02)01370-0.
|
Flpe-holliday junction complex . SNAP output
|
|
1ma7
|
hydrolase, ligase-DNA |
X-ray (2.3 Å) |
Martin SS, Chu VC, Baldwin EP |
(2003) "Modulation
of the active complex assembly and turnover rate by
protein-DNA interactions in Cre-LoxP
recombination." Biochemistry,
42, 6814-6826. doi: 10.1021/bi0272306.
|
Crystal structure of cre site-specific recombinase
complexed with a mutant DNA substrate, loxp-a8-t27 .
SNAP output
|
|
1mdm
|
transcription-DNA |
X-ray (2.8 Å) |
Garvie CW, Pufall MA, Graves BJ, Wolberger C |
(2002) "STRUCTURAL
ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN
PROTEIN PARTNERSHIPS." J.Biol.Chem.,
277, 45529-45536. doi: 10.1074/jbc.M206327200.
|
Inhibited fragment of ets-1 and paired domain of pax5
bound to DNA . SNAP
output
|
|
1mdy
|
transcription-DNA |
X-ray (2.8 Å) |
Ma PC, Rould MA, Weintraub H, Pabo CO |
(1994) "Crystal
structure of MyoD bHLH domain-DNA complex: perspectives
on DNA recognition and implications for transcriptional
activation." Cell(Cambridge,Mass.),
77, 451-459. doi: 10.1016/0092-8674(94)90159-7.
|
Crystal structure of myod bhlh domain bound to DNA:
perspectives on DNA recognition and implications for
transcriptional activation . SNAP output
|
|
1mey
|
transferase-DNA |
X-ray (2.2 Å) |
Kim CA, Berg JM |
(1996) "A 2.2 A
Resolution Crystal Structure of a Designed Zinc Finger
Protein Bound to DNA." Nat.Struct.Biol.,
3, 940-945. doi: 10.1038/nsb1196-940.
|
Crystal structure of a designed zinc finger protein
bound to DNA . SNAP
output
|
|
1mhd
|
complex (transcription activator-DNA) |
X-ray (2.8 Å) |
Shi Y, Wang YF, Jayaraman L, Yang H, Massague J,
Pavletich NP |
(1998) "Crystal
structure of a Smad MH1 domain bound to DNA: insights
on DNA binding in TGF-beta signaling."
Cell(Cambridge,Mass.), 94,
585-594. doi: 10.1016/S0092-8674(00)81600-1.
|
Crystal structure of a smad mh1 domain bound to DNA .
SNAP output
|
|
1mht
|
transferase-DNA |
X-ray (2.6 Å) |
Klimasauskas S, Kumar S, Roberts RJ, Cheng X |
(1994) "HhaI
methyltransferase flips its target base out of the DNA
helix." Cell(Cambridge,Mass.),
76, 357-369. doi: 10.1016/0092-8674(94)90342-5.
|
Covalent ternary structure of hhai methyltransferase,
DNA and s-adenosyl-l-homocysteine . SNAP output
|
|
1mj1
|
ribosome |
cryo-EM (13.0 Å) |
Stark H, Rodnina MV, Wieden H-J, Zemlin F,
Wintermeyer W, van Heel M |
(2002) "Ribosome
Interactions of Aminoacyl-tRNA and Elongation Factor TU
in the Codon Recognition Complex."
Nat.Struct.Biol., 9, 849-854.
|
Fitting the ternary complex of ef-tu-trna-gtp and
ribosomal proteins into a 13 a cryo-EM map of the coli
70s ribosome . SNAP
output
|
|
1mj2
|
transcription-DNA |
X-ray (2.4 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine repressor mutant (q44k) plus corepressor
(s-adenosyl methionine) complexed to a consensus
operator sequence . SNAP
output
|
|
1mje
|
gene regulation-antitumor protein-DNA |
X-ray (3.5 Å) |
Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y,
Thoma NH, Zheng N, Chen PL, Lee WH, Pavletich NP |
(2002) "BRCA2
function in DNA binding and recombination from a
BRCA2-DSS1-ssDNA structure." Science,
297, 1837-1848. doi: 10.1126/science.297.5588.1837.
|
Structure of a brca2-dss1-ssDNA complex . SNAP output
|
|
1mjm
|
transcription-DNA |
X-ray (2.2 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine aporepressor mutant (q44k) complexed to half
of the consensus operator sequence . SNAP output
|
|
1mjo
|
transcription-DNA |
X-ray (2.1 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine holorepressor mutant (q44k) plus corepressor
(s-adenosyl methionine) complexed to the minimal met
consensus operator with the central ta step mutated to
at . SNAP output
|
|
1mjp
|
transcription-DNA |
X-ray (3.4 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine aporepressor mutant (q44k) complexed to the
minimal met consensus operator . SNAP output
|
|
1mjq
|
transcription-DNA |
X-ray (2.4 Å) |
Garvie CW, Phillips SE |
(2000) "Direct
and indirect readout in mutant Met repressor-operator
complexes." Structure Fold.Des.,
8, 905-914. doi: 10.1016/S0969-2126(00)00182-9.
|
Methionine repressor mutant (q44k) plus corepressor
(s-adenosyl methionine) complexed to an altered met
consensus operator sequence . SNAP output
|
|
1mm8
|
transcription-DNA |
X-ray (2.8 Å) |
Steiniger-White M, Bhasin A, Lovell S, Rayment I,
Reznikoff WS |
(2002) "Evidence
for "unseen" Transposase--DNA contacts."
J.Mol.Biol., 322, 971-982.
doi: 10.1016/S0022-2836(02)00877-X.
|
Crystal structure of tn5 transposase complexed with me
DNA . SNAP output
|
|
1mnm
|
transcription-DNA |
X-ray (2.25 Å) |
Tan S, Richmond TJ |
(1998) "Crystal
structure of the yeast MATalpha2/MCM1/DNA ternary
complex." Nature, 391,
660-666. doi: 10.1038/35563.
|
Yeast matalpha2-mcm1-DNA ternary transcription complex
crystal structure . SNAP
output
|
|
1mnn
|
transcription-DNA |
X-ray (1.4 Å) |
Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN |
(2002) "Structure
of the sporulation-specific transcription factor Ndt80
bound to DNA." Embo J.,
21, 5721-5732. doi: 10.1093/emboj/cdf572.
|
Structure of the sporulation specific transcription
factor ndt80 bound to DNA . SNAP output
|
|
1mnv
|
DNA-antibiotic |
X-ray (2.6 Å) |
Hou M-H, Robinson H, Gao Y-G, Wang AH-J |
(2002) "Crystal
Structure of Actinomycin D Bound to the Ctg Triplet
Repeat Sequences Linked to Neurological Diseases."
Nucleic Acids Res., 30, 4910.
doi: 10.1093/NAR/GKF619.
|
Actinomycin d binding to atgctgcat . SNAP output
|
|
1mow
|
hydrolase-DNA |
X-ray (2.4 Å) |
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat
Jr RJ, Stoddard BL |
(2002) "Design,
Activity and Structure of a Highly Specific Artificial
Endonuclease." Mol.Cell,
10, 895-905. doi: 10.1016/S1097-2765(02)00690-1.
|
E-drei . SNAP output
|
|
1mq2
|
transferase-DNA |
X-ray (3.1 Å) |
Krahn JM, Beard WA, Miller H, Grollman AP, Wilson
SH |
(2003) "Structure
of DNA Polymerase beta with the Mutagenic DNA Lesion
8-oxodeoxyguanine Reveals Structural Insights into its
Coding Potential." Structure,
11, 121-127. doi: 10.1016/S0969-2126(02)00930-9.
|
Human DNA polymerase beta complexed with gapped DNA
containing an 8-oxo-7,8-dihydro-guanine and damp .
SNAP output
|
|
1mq3
|
transferase-DNA |
X-ray (2.8 Å) |
Krahn JM, Beard WA, Miller H, Grollman AP, Wilson
SH |
(2003) "Structure
of DNA Polymerase beta with the Mutagenic DNA Lesion
8-oxodeoxyguanine Reveals Structural Insights into its
Coding Potential." Structure,
11, 121-127. doi: 10.1016/S0969-2126(02)00930-9.
|
Human DNA polymerase beta complexed with gapped DNA
containing an 8-oxo-7,8-dihydro-guanine template paired
with dctp . SNAP
output
|
|
1mse
|
DNA binding protein-DNA |
NMR |
Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T,
Kanai H, Sarai A, Ishii S, Nishimura Y |
(1994) "Solution
structure of a specific DNA complex of the Myb
DNA-binding domain with cooperative recognition
helices." Cell(Cambridge,Mass.),
79, 639-648. doi: 10.1016/0092-8674(94)90549-5.
|
Solution structure of a specific DNA complex of the myb
DNA-binding domain with cooperative recognition helices
. SNAP output
|
|
1msf
|
DNA binding protein-DNA |
NMR |
Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T,
Kanai H, Sarai A, Ishii S, Nishimura Y |
(1994) "Solution
structure of a specific DNA complex of the Myb
DNA-binding domain with cooperative recognition
helices." Cell(Cambridge,Mass.),
79, 639-648. doi: 10.1016/0092-8674(94)90549-5.
|
Solution structure of a specific DNA complex of the myb
DNA-binding domain with cooperative recognition helices
. SNAP output
|
|
1msw
|
transcription-DNA-RNA |
X-ray (2.1 Å) |
Yin YW, Steitz TA |
(2002) "Structural
Basis for the Transition from Initiation to Elongation
Transcription in T7 RNA Polymerase."
Science, 298, 1387-1395. doi:
10.1126/science.1077464.
|
Structural basis for the transition from initiation to
elongation transcription in t7 RNA polymerase .
SNAP output
|
|
1mtl
|
hydrolase-DNA |
X-ray (2.8 Å) |
Barrett TE, Savva R, Barlow T, Brown T, Jiricny J,
Pearl LH |
(1998) "Structure
of a DNA base-excision product resembling a cisplatin
inter-strand adduct." Nat.Struct.Biol.,
5, 697-701. doi: 10.1038/1394.
|
Non-productive mug-DNA complex . SNAP output
|
|
1muh
|
transcription-DNA |
X-ray (2.3 Å) |
Davies DR, Goryshin IY, Reznikoff WS, Rayment I |
(2000) "Three-dimensional
structure of the Tn5 synaptic complex transposition
intermediate." Science,
289, 77-85. doi: 10.1126/science.289.5476.77.
|
Crystal structure of tn5 transposase complexed with
transposon end DNA . SNAP output
|
|
1mus
|
transcription-DNA |
X-ray (1.9 Å) |
Steiniger-White M, Rayment I, Reznikoff WS |
(2004) "Structure/function
insights into Tn5 transposition."
Curr.Opin.Struct.Biol., 14,
50-57. doi: 10.1016/j.sbi.2004.01.008.
|
Crystal structure of tn5 transposase complexed with
resolved outside end DNA . SNAP output
|
|
1mvm
|
virus-DNA |
X-ray (3.5 Å) |
Llamas-Saiz AL, Agbandje-McKenna M, Wikoff WR,
Bratton J, Tattersall P, Rossmann MG |
(1997) "Structure
determination of minute virus of mice." Acta
Crystallogr.,Sect.D, 53, 93-102.
doi: 10.1107/S0907444996010566.
|
Mvm(strain i), complex(viral coat-DNA), vp2, ph=7.5,
t=4 degrees c . SNAP
output
|
|
1mw8
|
isomerase |
X-ray (1.9 Å) |
Perry K, Mondragon A |
(2003) "Structure
of a Complex between E. coli DNA Topoisomerase I and
Single-Stranded DNA." Structure,
11, 1349-1358. doi: 10.1016/j.str.2003.09.013.
|
Crystal structure of a complex between h365r mutant of
67 kda n-terminal fragment of e. coli DNA topoisomerase
i and 5'-acttcgggatg-3' . SNAP output
|
|
1mwi
|
hydrolase-DNA |
X-ray (2.35 Å) |
Barrett TE, Savva R, Panayotou G, Barlow T, Brown T,
Jiricny J, Pearl LH |
(1998) "Crystal
structure of a G:T/U mismatch-specific DNA glycosylase:
mismatch recognition by complementary-strand
interactions." Cell(Cambridge,Mass.),
92, 117-129. doi: 10.1016/S0092-8674(00)80904-6.
|
Crystal structure of a mug-DNA product complex .
SNAP output
|
|
1mwj
|
hydrolase-DNA |
X-ray (2.85 Å) |
Barrett TE, Scharer O, Savva R, Brown T, Jiricny J,
Verdine GL, Pearl LH |
(1999) "Crystal
Structure of a thwarted mismatch glycosylase DNA repair
complex." Embo J., 18,
6599-6609. doi: 10.1093/emboj/18.23.6599.
|
Crystal structure of a mug-DNA pseudo substrate complex
. SNAP output
|
|
1n39
|
hydrolase, lyase-DNA |
X-ray (2.2 Å) |
Norman DP, Chung SJ, Verdine GL |
(2003) "Structural
and biochemical exploration of a critical amino acid in
human 8-oxoguanine glycosylase."
Biochemistry, 42, 1564-1572.
doi: 10.1021/bi026823d.
|
Structural and biochemical exploration of a critical
amino acid in human 8-oxoguanine glycosylase . SNAP output
|
|
1n3a
|
hydrolase, lyase-DNA |
X-ray (2.2 Å) |
Norman DP, Chung SJ, Verdine GL |
(2003) "Structural
and biochemical exploration of a critical amino acid in
human 8-oxoguanine glycosylase."
Biochemistry, 42, 1564-1572.
doi: 10.1021/bi026823d.
|
Structural and biochemical exploration of a critical
amino acid in human 8-oxoguanine glycosylase . SNAP output
|
|
1n3c
|
hydrolase, lyase-DNA |
X-ray (2.7 Å) |
Norman DP, Chung SJ, Verdine GL |
(2003) "Structural
and biochemical exploration of a critical amino acid in
human 8-oxoguanine glycosylase."
Biochemistry, 42, 1564-1572.
doi: 10.1021/bi026823d.
|
Structural and biochemical exploration of a critical
amino acid in human 8-oxoguanine glycosylase . SNAP output
|
|
1n3e
|
hydrolase-DNA |
X-ray (2.5 Å) |
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard
BL |
(2003) "Flexible
DNA Target Site Recognition by Divergent Homing
Endonuclease Isoschizomers I-CreI and I-MsoI."
J.Mol.Biol., 329, 253-269.
doi: 10.1016/S0022-2836(03)00447-9.
|
Crystal structure of i-crei bound to a palindromic DNA
sequence i (palindrome of left side of wildtype DNA
target sequence) . SNAP
output
|
|
1n3f
|
hydrolase-DNA |
X-ray (2.0 Å) |
Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard
BL |
(2003) "Flexible
DNA Target Site Recognition by Divergent Homing
Endonuclease Isoschizomers I-CreI and I-MsoI."
J.Mol.Biol., 329, 253-269.
doi: 10.1016/S0022-2836(03)00447-9.
|
Crystal structure of i-crei bound to a palindromic DNA
sequence ii (palindrome of right side of wildtype DNA
target sequence) . SNAP
output
|
|
1n48
|
transferase-DNA |
X-ray (2.2 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
"A Y-family polymerase complexed with abasic lesions:
catching DNA with a loaded nucleoside triphosphate." |
Y-family DNA polymerase dpo4 in complex with DNA
containing abasic lesion . SNAP output
|
|
1n56
|
transferase-DNA |
X-ray (2.4 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of replication through an abasic lesion; structural
basis for base substitutions and frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/s1097-2765(04)00101-7.
|
Y-family DNA polymerase dpo4 in complex with DNA
containing abasic lesion . SNAP output
|
|
1n5y
|
transferase-immune system-DNA |
X-ray (3.1 Å) |
Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft
JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer
PL, Hughes SH, Arnold E |
(2002) "Structure
of HIV-1 Reverse Transcriptase with Pre-Translocation
and Post-Translocation AZTMP-Terminated DNA."
Embo J., 21, 6614-6624. doi:
10.1093/emboj/cdf637.
|
Hiv-1 reverse transcriptase crosslinked to
post-translocation aztmp-terminated DNA (complex p) .
SNAP output
|
|
1n6j
|
transcription-DNA |
X-ray (2.2 Å) |
Han A, Pan F, Stroud JC, Youn HD, Liu JO, Chen L |
(2003) "Sequence-specific
recruitment of transcriptional co-repressor Cabin1 by
myocyte enhancer factor-2." Nature,
422, 730-734. doi: 10.1038/nature01555.
|
Structural basis of sequence-specific recruitment of
histone deacetylases by myocyte enhancer factor-2 .
SNAP output
|
|
1n6q
|
transferase-immune system-DNA |
X-ray (3.0 Å) |
Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft
JJ, Ilankumaran I, Ramesha AR, Sayer JM, Jerina DM, Boyer
PL, Hughes SH, Arnold E |
(2002) "Structures
of HIV-1 Reverse Transcriptase with Pre- and
Post-translocation AZTMP-terminated DNA." Embo
J., 21, 6614-6624. doi: 10.1093/emboj/cdf637.
|
Hiv-1 reverse transcriptase crosslinked to
pre-translocation aztmp-terminated DNA (complex n) .
SNAP output
|
|
1nfk
|
transcription-DNA |
X-ray (2.3 Å) |
Ghosh G, van Duyne G, Ghosh S, Sigler PB |
(1995) "Structure
of NF-kappa B p50 homodimer bound to a kappa B
site." Nature, 373,
303-310. doi: 10.1038/373303a0.
|
Structure of the nuclear factor kappa-b (nf-kb) p50
homodimer . SNAP
output
|
|
1ng9
|
DNA binding protein |
X-ray (2.6 Å) |
Lamers MH, Winterwerp HHK, Sixma TK |
(2003) "The
alternating ATPase domains of MutS control DNA mismatch
repair." Embo J., 22,
746-756. doi: 10.1093/emboj/cdg064.
|
E.coli muts r697a: an atpase-asymmetry mutant .
SNAP output
|
|
1ngm
|
transcription-DNA |
X-ray (2.95 Å) |
Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler
PB |
(2003) "Crystal
structure of a transcription factor IIIB core interface
ternary complex." Nature,
422, 534-539. doi: 10.1038/nature01534.
|
Crystal structure of a yeast brf1-tbp-DNA ternary
complex . SNAP
output
|
|
1nh2
|
transcription-DNA |
X-ray (1.9 Å) |
Bleichenbacher M, Tan S, Richmond TJ |
(2003) "Novel
interactions between the components of human and yeast
TFIIA/TBP/DNA complexes." J.Mol.Biol.,
332, 783-793. doi: 10.1016/S0022-2836(03)00887-8.
|
Crystal structure of a yeast tfiia-tbp-DNA complex .
SNAP output
|
|
1nh3
|
isomerase-DNA |
X-ray (3.1 Å) |
Chrencik JE, Burgin AB, Pommier Y, Stewart L, Redinbo
MR |
(2003) "Structural
Impact of the Leukemia Drug
1-beta-D-Arabinofuranosylcytosine (Ara-C) on the
Covalent Human Topoisomerase I-DNA Complex."
J.Biol.Chem., 278,
12461-12466. doi: 10.1074/jbc.M212930200.
|
Human topoisomerase i ara-c complex . SNAP output
|
|
1njw
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Guanine-thymine mismatch at the polymerase active site
. SNAP output
|
|
1njx
|
transferase-DNA |
X-ray (1.65 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Thymine-guanine mismatch at the polymerase active site
. SNAP output
|
|
1njy
|
transferase-DNA |
X-ray (2.0 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Thymine-thymine mismatch at the polymerase active site
. SNAP output
|
|
1njz
|
transferase-DNA |
X-ray (2.0 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Cytosine-thymine mismatch at the polymerase active site
. SNAP output
|
|
1nk0
|
transferase-DNA |
X-ray (1.7 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Adenine-guanine mismatch at the polymerase active site
. SNAP output
|
|
1nk2
|
DNA binding protein-DNA |
NMR |
Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti
JA |
(1997) "Interactions
of the vnd/NK-2 homeodomain with DNA by nuclear
magnetic resonance spectroscopy: basis of binding
specificity." Biochemistry,
36, 5372-5380. doi: 10.1021/bi9620060.
|
Vnd-nk-2 homeodomain-DNA complex, NMR, 20 structures .
SNAP output
|
|
1nk3
|
DNA binding protein-DNA |
NMR |
Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti
JA |
(1997) "Interactions
of the vnd/NK-2 homeodomain with DNA by nuclear
magnetic resonance spectroscopy: basis of binding
specificity." Biochemistry,
36, 5372-5380. doi: 10.1021/bi9620060.
|
Vnd-nk-2 homeodomain-DNA complex, NMR, minimized
average structure . SNAP
output
|
|
1nk4
|
transferase-DNA |
X-ray (1.6 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Guanine-guanine mismatch at the polymerase active site
. SNAP output
|
|
1nk5
|
transferase-DNA |
X-ray (2.1 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Adenine-adenine mismatch at the polymerase active site
. SNAP output
|
|
1nk6
|
transferase-DNA |
X-ray (2.1 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Cytosine-cytosine mismatch at the polymerase active
site . SNAP output
|
|
1nk7
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
Guanine-adenine mismatch at the polymerase active site
. SNAP output
|
|
1nk8
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after a single round of primer
extension, following incorporation of dctp. . SNAP output
|
|
1nk9
|
transferase-DNA |
X-ray (1.9 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after two rounds of primer
extension, following incorporation of dctp and dgtp. .
SNAP output
|
|
1nkb
|
transferase-DNA |
X-ray (2.0 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after three rounds of primer
extension, following incorporation of dctp, dgtp, and
dttp. . SNAP output
|
|
1nkc
|
transferase-DNA |
X-ray (1.8 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
guanine-thymine mismatch after five rounds of primer
extension, following incorporation of dctp, dgtp, dttp,
and datp. . SNAP
output
|
|
1nke
|
transferase-DNA |
X-ray (1.8 Å) |
Johnson SJ, Beese LS |
(2004) "Structures
of mismatch replication errors observed in a DNA
polymerase." Cell(Cambridge,Mass.),
116, 803-816. doi: 10.1016/S0092-8674(04)00252-1.
|
A bacillus DNA polymerase i product complex bound to a
cytosine-thymine mismatch after a single round of
primer extension, following incorporation of dctp. .
SNAP output
|
|
1nkp
|
transcription-DNA |
X-ray (1.8 Å) |
Nair SK, Burley SK |
(2003) "X-ray
structures of Myc-Max and Mad-Max recognizing DNA:
Molecular bases of regulation by proto-oncogenic
transcription factors."
Cell(Cambridge,Mass.), 112,
193-205. doi: 10.1016/S0092-8674(02)01284-9.
|
Crystal structure of myc-max recognizing DNA . SNAP output
|
|
1nlw
|
transcription-DNA |
X-ray (2.0 Å) |
Nair SK, Burley SK |
(2003) "X-ray
structures of Myc-Max and Mad-Max recognizing DNA:
Molecular bases of regulation by proto-oncogenic
transcription factors."
Cell(Cambridge,Mass.), 112,
193-205. doi: 10.1016/S0092-8674(02)01284-9.
|
Crystal structure of mad-max recognizing DNA . SNAP output
|
|
1nne
|
DNA binding protein-DNA |
X-ray (3.11 Å) |
Alani E, Lee JY, Schofield MJ, Kijas AW, Hsieh P,
Yang W |
(2003) "Crystal
structure and biochemical analysis of the
MutS-ADP-Beryllium Fluoride complex suggests a
conserved mechanism for ATP interactions in mismatch
repair." J.Biol.Chem.,
278, 16088-16094. doi: 10.1074/jbc.M213193200.
|
Crystal structure of the muts-adpbef3-DNA complex .
SNAP output
|
|
1nnj
|
hydrolase |
X-ray (1.9 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Crystal structure complex between the lactococcus
lactis fpg and an abasic site containing DNA . SNAP output
|
|
1nop
|
hydrolase-DNA |
X-ray (2.3 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WGJ |
(2003) "Crystal
structure of a transition state mimic for Tdp1
assembled from vanadate, DNA, and a topoisomerase
I-derived peptide." Chem.Biol.,
10, 139-147. doi: 10.1016/S1074-5521(03)00021-8.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase (tdp1) in complex with vanadate, DNA
and a human topoisomerase i-derived peptide . SNAP output
|
|
1noy
|
transferase-DNA |
X-ray (2.2 Å) |
Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA |
(1996) "Crystal
structures of an NH2-terminal fragment of T4 DNA
polymerase and its complexes with single-stranded DNA
and with divalent metal ions."
Biochemistry, 35, 8110-8119.
doi: 10.1021/bi960178r.
|
DNA polymerase (e.c.2.7.7.7)-DNA complex . SNAP output
|
|
1nvp
|
transcription-DNA |
X-ray (2.1 Å) |
Bleichenbacher M, Tan S, Richmond TJ |
(2003) "Novel
interactions between the components of human and yeast
TFIIA/TBP/DNA complexes." J.Mol.Biol.,
332, 783-793. doi: 10.1016/S0022-2836(03)00887-8.
|
Human tfiia-tbp-DNA complex . SNAP output
|
|
1nwq
|
transcription-DNA |
X-ray (2.8 Å) |
Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson
PF |
(2003) "Structural
Basis for DNA Recognition by the Basic Region Leucine
Zipper Transcription Factor CCAAT/enhancer Binding
Protein Alpha." J.Biol.Chem.,
278, 15178-15184. doi: 10.1074/jbc.M300417200.
|
Crystal structure of c-ebpalpha-DNA complex . SNAP output
|
|
1nzb
|
replication-DNA |
X-ray (3.1 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of wild type cre recombinase-loxp
synapse . SNAP
output
|
|
1o3q
|
gene regulation-DNA |
X-ray (3.0 Å) |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: DNA Binding Specificity Based on
Energetics of DNA Kinking." J.Mol.Biol.,
314, 63-74. doi: 10.1006/jmbi.2001.5089.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
|
1o3r
|
gene regulation-DNA |
X-ray (3.0 Å) |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: DNA Binding Specificity Based on
Energetics of DNA Kinking." J.Mol.Biol.,
314, 63-74. doi: 10.1006/jmbi.2001.5089.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
|
1o3s
|
gene regulation-DNA |
X-ray (3.0 Å) |
Chen S, Gunasekera A, Zhang X, Kunkel TA, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: Alteration of DNA Binding Specificity
Through Alteration of DNA Kinking."
J.Mol.Biol., 314, 75-82. doi:
10.1006/jmbi.2001.5090.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
|
1o3t
|
gene regulation-DNA |
X-ray (2.8 Å) |
Chen S, Vojtechovsky J, Parkinson GN, Ebright RH,
Berman HM |
(2001) "Indirect
Readout of DNA Sequence at the Primary-kink Site in the
CAP-DNA Complex: DNA Binding Specificity Based on
Energetics of DNA Kinking." J.Mol.Biol.,
314, 63-74. doi: 10.1006/jmbi.2001.5089.
|
Protein-DNA recognition and DNA deformation revealed in
crystal structures of cap-DNA complexes . SNAP output
|
|
1o4x
|
transcription-DNA |
NMR |
Williams DC, Cai M, Clore GM |
(2004) "Molecular
basis for synergistic transcriptional activation by
Oct1 and Sox2 revealed from the solution structure of
the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription
factor complex." J.Biol.Chem.,
279, 1449-1457. doi: 10.1074/jbc.M309790200.
|
Ternary complex of the DNA binding domains of the oct1
and sox2 transcription factors with a 19mer
oligonucleotide from the hoxb1 regulatory element .
SNAP output
|
|
1oct
|
transcription-DNA |
X-ray (3.0 Å) |
Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO |
(1994) "Crystal
structure of the Oct-1 POU domain bound to an octamer
site: DNA recognition with tethered DNA-binding
modules." Cell(Cambridge,Mass.),
77, 21-32. doi: 10.1016/0092-8674(94)90231-3.
|
Crystal structure of the oct-1 pou domain bound to an
octamer site: DNA recognition with tethered DNA-binding
modules . SNAP
output
|
|
1odg
|
hydrolase |
X-ray (2.8 Å) |
Bunting KA, Roe SM, Headley A, Brown T, Savva R,
Pearl LH |
(2003) "Crystal
Structure of the Escherichia Coli Dcm Very-Short-Patch
DNA Repair Endonuclease Bound to its Reaction
Product-Site in a DNA Superhelix." Nucleic
Acids Res., 31, 1633. doi:
10.1093/NAR/GKG273.
|
Very-short-patch DNA repair endonuclease bound to its
reaction product site . SNAP output
|
|
1odh
|
transcription factor-DNA |
X-ray (2.85 Å) |
Cohen SX, Moulin M, Hashemolhosseini S, Kilian K,
Wegner M, Muller CW |
(2003) "Crystal
Structure of the Gcm Domain-DNA Complex: A DNA-Binding
Domain with a Novel Fold and Mode of Target Site
Recognition." Embo J.,
22, 1835. doi: 10.1093/EMBOJ/CDG182.
|
Structure of the gcm domain bound to DNA . SNAP output
|
|
1oe4
|
hydrolase-DNA |
X-ray (2.0 Å) |
Wibley JEA, Waters TR, Haushalter K, Verdine GL,
Pearl LH |
(2003) "Structure
and Specificity of the Vertebrate Anti-Mutator
Uracil-DNA Glycosylase Smug1." Mol.Cell,
11, 1647. doi: 10.1016/S1097-2765(03)00235-1.
|
Xenopus smug1, an anti-mutator uracil-DNA glycosylase .
SNAP output
|
|
1oe5
|
hydrolase-DNA |
X-ray (2.3 Å) |
Wibley JEA, Waters TR, Haushalter K, Verdine GL,
Pearl LH |
(2003) "Structure
and Specificity of the Vertebrate Anti-Mutator
Uracil-DNA Glycosylase Smug1." Mol.Cell,
11, 1647. doi: 10.1016/S1097-2765(03)00235-1.
|
Xenopus smug1, an anti-mutator uracil-DNA glycosylase .
SNAP output
|
|
1oe6
|
hydrolase-DNA |
X-ray (2.65 Å) |
Wibley JEA, Waters TR, Haushalter K, Verdine GL,
Pearl LH |
(2003) "Structure
and Specificity of the Vertebrate Anti-Mutator
Uracil-DNA Glycosylase Smug1." Mol.Cell,
11, 1647. doi: 10.1016/S1097-2765(03)00235-1.
|
Xenopus smug1, an anti-mutator uracil-DNA glycosylase .
SNAP output
|
|
1oh5
|
DNA binding |
X-ray (2.9 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with a c:a mismatch . SNAP output
|
|
1oh6
|
DNA binding |
X-ray (2.4 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with an a:a mismatch . SNAP output
|
|
1oh7
|
DNA binding |
X-ray (2.5 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with a g:g mismatch . SNAP output
|
|
1oh8
|
DNA binding |
X-ray (2.9 Å) |
Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK,
Perrakis A, Sixma TK |
(2003) "Structures
of E. Coli DNA Mismatch Repair Enzyme Muts in Complex
with Different Mismatches: A Common Recognition Mode
for Diverse Substrates." Nucleic Acids
Res., 31, 4814. doi: 10.1093/NAR/GKG677.
|
The crystal structure of e. coli muts binding to DNA
with an unpaired thymidine . SNAP output
|
|
1oj8
|
hydrolase |
X-ray (1.7 Å) |
Tsai C-J, Liu J-H, Liao Y-D, Chen L-Y, Cheng P-T, Sun
Y-J |
"Retro and Novel Binding Modes in Cytotoxic
Ribonucleases from Rana Catesbeiana of Two Crystal
Structures Complexed with (2',5'Cpg) and
D(Apcpgpa)." |
Novel and retro binding modes in cytotoxic
ribonucleases from rana catesbeiana of two crystal
structures complexed with d(apcpgpa) and (2',5'cpg) .
SNAP output
|
|
1omh
|
transferase-DNA |
X-ray (1.95 Å) |
Guasch A, Lucas M, Moncalian G, Cabezas M,
Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M |
(2003) "Recognition
and processing of the origin of transfer DNA by
conjugative relaxase TrwC."
Nat.Struct.Biol., 10,
1002-1010. doi: 10.1038/nsb1017.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-free structure. . SNAP output
|
|
1orn
|
hydrolase-DNA |
X-ray (1.7 Å) |
Fromme JC, Verdine GL |
(2003) "Structure
of a Trapped Endonuclease III-DNA Covalent
Intermediate." Embo J.,
22, 3461-3471. doi: 10.1093/emboj/cdg311.
|
Structure of a trapped endonuclease iii-DNA covalent
intermediate: estranged-guanine complex . SNAP output
|
|
1orp
|
hydrolase-DNA |
X-ray (2.2 Å) |
Fromme JC, Verdine GL |
(2003) "Structure
of a Trapped Endonuclease III-DNA Covalent
Intermediate." Embo J.,
22, 3461-3471. doi: 10.1093/emboj/cdg311.
|
Structure of a trapped endonuclease iii-DNA covalent
intermediate: estranged-adenine complex . SNAP output
|
|
1osb
|
transferase-DNA |
X-ray (2.65 Å) |
Guasch A, Lucas M, Moncalian G, Cabezas M,
Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M |
(2003) "Recognition
and processing of the origin of transfer DNA by
conjugative relaxase TrwC."
Nat.Struct.Biol., 10,
1002-1010. doi: 10.1038/nsb1017.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-free structure. . SNAP output
|
|
1osl
|
transcription-DNA |
NMR |
Kalodimos CG, Biris N, Bonvin AM, Levandoski MM,
Guennuegues M, Boelens R, Kaptein R |
(2004) "Structure
and flexibility adaptation in nonspecific and specific
protein-DNA complexes." Science,
305, 386-389. doi: 10.1126/science.1097064.
|
Solution structure of a dimeric lactose DNA-binding
domain complexed to a nonspecific DNA sequence .
SNAP output
|
|
1otc
|
protein-DNA |
X-ray (2.8 Å) |
Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA,
Schultz SC |
(1998) "Crystal
structure of the Oxytricha nova telomere end binding
protein complexed with single strand DNA."
Cell(Cambridge,Mass.), 95,
963-974. doi: 10.1016/S0092-8674(00)81720-1.
|
The o. nova telomere end binding protein complexed with
single strand DNA . SNAP
output
|
|
1oup
|
hydrolase-DNA |
X-ray (2.3 Å) |
Li C-L, Hor L-I, Chang Z-F, Tsai L-C, Yang W-Z, Yuan
HS |
(2003) "DNA
binding and cleavage by the periplasmic nuclease Vvn: a
novel structure with a known active site." Embo
J., 22, 4014-4025. doi: 10.1093/emboj/cdg377.
|
Crystal structure of the periplasmic endonuclease vvn
complexed with octamer double stranded DNA . SNAP output
|
|
1ouq
|
replication-DNA |
X-ray (3.2 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of wild-type cre recombinase-loxp
synapse . SNAP
output
|
|
1ouz
|
transcription-DNA |
X-ray (2.41 Å) |
Lynch TW, Read EK, Mattis AN, Gardner JF, Rice
PA |
(2003) "Integration
Host Factor: putting a twist on protein-DNA
recognition." J.Mol.Biol.,
330, 493-502. doi: 10.1016/S0022-2836(03)00529-1.
|
Crystal structure of a mutant ihf (betae44a) complexed
with a variant h' site (t44a) . SNAP output
|
|
1ovf
|
DNA-antibiotic |
NMR |
Chin K-H, Chen F-M, Chou S-H |
(2003) "Solution
Structure of the Actd-5'-Ccgtt(3)Gtgg-3' Complex: Drug
Interaction with Tandem G.T Mismatches and Hairpin Loop
Backbone." Nucleic Acids Res.,
31, 2622. doi: 10.1093/NAR/GKG353.
|
NMR structure of actd-5'-ccgttttgtgg-3' complex .
SNAP output
|
|
1owf
|
transcription-DNA |
X-ray (1.95 Å) |
Lynch TW, Read EK, Mattis AN, Gardner JF, Rice
PA |
(2003) "Integration
Host Factor: putting a twist on protein-DNA
recognition." J.Mol.Biol.,
330, 493-502. doi: 10.1016/S0022-2836(03)00529-1.
|
Crystal structure of a mutant ihf (betae44a) complexed
with the native h' site . SNAP output
|
|
1owg
|
transcription-DNA |
X-ray (2.1 Å) |
Lynch TW, Read EK, Mattis AN, Gardner JF, Rice
PA |
(2003) "Integration
Host Factor: putting a twist on protein-DNA
recognition." J.Mol.Biol.,
330, 493-502. doi: 10.1016/S0022-2836(03)00529-1.
|
Crystal structure of wt ihf complexed with an altered
h' site (t44a) . SNAP
output
|
|
1owr
|
transcription-DNA |
X-ray (3.0 Å) |
Stroud JC, Chen L |
(2003) "Structure
of NFAT Bound to DNA as a Monomer."
J.Mol.Biol., 334, 1009-1022.
doi: 10.1016/j.jmb.2003.09.065.
|
Crystal structure of human nfat1 bound monomerically to
DNA . SNAP output
|
|
1ozj
|
transcription-DNA |
X-ray (2.4 Å) |
Chai J, Wu J-W, Yan N, Massague J, Pavletich NP, Shi
Y |
(2003) "Features
of a Smad3 MH1-DNA complex. Roles of water and zinc in
DNA binding." J.Biol.Chem.,
278, 20327-20331. doi: 10.1074/jbc.C300134200.
|
Crystal structure of smad3-mh1 bound to DNA at 2.4 Å
resolution . SNAP
output
|
|
1p34
|
structural protein-DNA |
X-ray (2.7 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3a
|
structural protein-DNA |
X-ray (3.0 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3b
|
structural protein-DNA |
X-ray (3.0 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3f
|
structural protein-DNA |
X-ray (2.9 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3g
|
structural protein-DNA |
X-ray (2.7 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3i
|
structural protein-DNA |
X-ray (2.3 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3k
|
structural protein-DNA |
X-ray (2.9 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3l
|
structural protein-DNA |
X-ray (2.4 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3m
|
structural protein-DNA |
X-ray (2.9 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3o
|
structural protein-DNA |
X-ray (2.75 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p3p
|
structural protein-DNA |
X-ray (2.7 Å) |
Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam
RS, Dyer PN, White CL, Luger K |
(2004) "Crystal
structures of histone Sin mutant nucleosomes reveal
altered protein-DNA interactions." EMBO
J., 23, 260-271. doi: 10.1038/sj.emboj.7600046.
|
Crystallographic studies of nucleosome core particles
containing histone 'sin' mutants . SNAP output
|
|
1p47
|
transcription-DNA |
X-ray (2.2 Å) |
Peisach E, Pabo CO |
(2003) "Constraints
for Zinc Finger Linker Design as Inferred from X-ray
Crystal Structure of Tandem Zif268-DNA Complexes."
J.Mol.Biol., 330, 1-7. doi:
10.1016/S0022-2836(03)00572-2.
|
Crystal structure of tandem zif268 molecules complexed
to DNA . SNAP output
|
|
1p4e
|
DNA binding protein-recombination-DNA |
X-ray (2.7 Å) |
Rice PA, Chen Y |
(2003) "The role
of the conserved Trp330 in Flp-mediated recombination.
Functional and structural analysis."
J.Biol.Chem., 278,
24800-24807. doi: 10.1074/jbc.M300853200.
|
Flpe w330f mutant-DNA holliday junction complex .
SNAP output
|
|
1p51
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Swinger KK, Lemberg KM, Zhang Y, Rice PA |
(2003) "Flexible
DNA bending in HU-DNA cocrystal structures."
Embo J., 22, 3749-3760. doi:
10.1093/emboj/cdg351.
|
Anabaena hu-DNA cocrystal structure (ahu6) . SNAP output
|
|
1p59
|
hydrolase-DNA |
X-ray (2.5 Å) |
Fromme JC, Verdine GL |
(2003) "Structure
of a Trapped Endonuclease III-DNA Covalent
Intermediate." Embo J.,
22, 3461-3471. doi: 10.1093/emboj/cdg311.
|
Structure of a non-covalent endonuclease iii-DNA
complex . SNAP
output
|
|
1p5w
|
virus-DNA |
X-ray (3.3 Å) |
Govindasamy L, Hueffer K, Parrish CR,
Agbandje-McKenna M |
(2003) "Structures
of host range-controlling regions of the capsids of
canine and feline parvoviruses and mutants."
J.Virol., 77, 12211-12221.
doi: 10.1128/JVI.77.22.12211-12221.2003.
|
The structures of host range controlling regions of the
capsids of canine and feline parvoviruses and mutants .
SNAP output
|
|
1p71
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Swinger KS, Lemberg KM, Zhang Y, Rice PA |
(2003) "Flexible
DNA bending in HU-DNA cocrystal structures."
Embo J., 22, 3749-3760. doi:
10.1093/emboj/cdg351.
|
Anabaena hu-DNA corcrystal structure (tr3) . SNAP output
|
|
1p78
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Swinger KS, Lemberg KM, Zhang Y, Rice PA |
(2003) "Flexible
DNA bending in HU-DNA cocrystal structures."
Embo J., 22, 3749-3760. doi:
10.1093/emboj/cdg351.
|
Anabaena hu-DNA cocrystal structure (ahu2) . SNAP output
|
|
1p7d
|
DNA binding protein-DNA |
X-ray (2.95 Å) |
Aihara H, Kwon HJ, Nunes-Duby SE, Landy A,
Ellenberger T |
(2003) "A
Conformational Switch Controls the DNA Cleavage
Activity of Lambda Integrase." Mol.Cell,
12, 187-198. doi: 10.1016/S1097-2765(03)00268-5.
|
Crystal structure of the lambda integrase (residues
75-356) bound to DNA . SNAP output
|
|
1p7h
|
transcription-DNA |
X-ray (2.6 Å) |
Giffin MJ, Stroud JC, Bates DL, von Koenig KD, Hardin
J, Chen L |
(2003) "Structure
of NFAT1 bound as a dimer to the HIV-1 LTR kappa B
element." Nat.Struct.Biol.,
10, 800-806. doi: 10.1038/nsb981.
|
Structure of nfat1 bound as a dimer to the hiv-1 ltr kb
element . SNAP
output
|
|
1p8k
|
hydrolase-DNA |
X-ray (2.6 Å) |
Bolduc JM, Spiegel PC, Chatterjee P, Brady KL,
Downing ME, Caprara MG, Waring RB, Stoddard BL |
(2003) "Structural
and biochemical analyses of DNA and RNA binding by a
bifunctional homing endonuclease and group I intron
splicing factor." Genes Dev.,
17, 2875-2888. doi: 10.1101/gad.1109003.
|
The structure and DNA recognition of a bifunctional
homing endonuclease and group i intron splicing factor
. SNAP output
|
|
1pa6
|
DNA binding protein-DNA |
X-ray (2.45 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
shuffling and ssDNA recognition in Oxytricha nova
telomere end-binding protein complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgagg . SNAP
output
|
|
1par
|
transcription-DNA |
X-ray (2.6 Å) |
Raumann BE, Rould MA, Pabo CO, Sauer RT |
(1994) "DNA
recognition by beta-sheets in the Arc
repressor-operator crystal structure."
Nature, 367, 754-757. doi:
10.1038/367754a0.
|
DNA recognition by beta-sheets in the arc
repressor-operator crystal structure . SNAP output
|
|
1pdn
|
gene regulation-DNA |
X-ray (2.5 Å) |
Xu W, Rould MA, Jun S, Desplan C, Pabo CO |
(1995) "Crystal
structure of a paired domain-DNA complex at 2.5 A
resolution reveals structural basis for Pax
developmental mutations."
Cell(Cambridge,Mass.), 80,
639-650. doi: 10.1016/0092-8674(95)90518-9.
|
Crystal structure of a paired domain-DNA complex at 2.5
angstroms resolution reveals structural basis for pax
developmental mutations . SNAP output
|
|
1per
|
transcription-DNA |
X-ray (2.5 Å) |
Rodgers DW, Harrison SC |
(1993) "The
complex between phage 434 repressor DNA-binding domain
and operator site OR3: structural differences between
consensus and non-consensus half-sites."
Structure, 1, 227-240. doi:
10.1016/0969-2126(93)90012-6.
|
The complex between phage 434 repression DNA-binding
domain and operator site or3: structural differences
between consensus and non-consensus half-sites .
SNAP output
|
|
1pfe
|
DNA-antibiotic |
X-ray (1.1 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
Echinomycin-(gcgtacgc)2 complex . SNAP output
|
|
1pfi
|
virus |
fiber diffraction |
Liu DJ, Day LA |
(1994) "Pf1 virus
structure: helical coat protein and DNA with paraxial
phosphates." Science,
265, 671-674.
|
Pf1 virus structure: helical coat protein and DNA with
paraxial phosphates . SNAP output
|
|
1pgz
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Myers JC, Moore SA, Shamoo Y |
(2003) "Structure-based
incorporation of
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
into the human telomeric repeat DNA as a probe for UP1
binding and destabilization of G-tetrad
structures." J.Biol.Chem.,
278, 42300-42306. doi: 10.1074/jbc.M306147200.
|
Crystal structure of up1 complexed with
d(ttagggttag(6-mi)g); a human telomeric repeat
containing
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
(6-mi) . SNAP output
|
|
1ph1
|
DNA binding protein-DNA |
X-ray (2.51 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and Ssdna Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttggggt . SNAP
output
|
|
1ph2
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttg . SNAP
output
|
|
1ph3
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttggtg . SNAP
output
|
|
1ph4
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttggcg . SNAP
output
|
|
1ph5
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttg(3dr)gg . SNAP
output
|
|
1ph6
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgtgg . SNAP
output
|
|
1ph7
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgigg . SNAP
output
|
|
1ph8
|
DNA binding protein-DNA |
X-ray (2.36 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and Ssdna Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgcgg . SNAP
output
|
|
1ph9
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
ggggttttgagg . SNAP
output
|
|
1phj
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Theobald DL, Schultz SC |
(2003) "Nucleotide
Shuffling and ssDNA Recognition in Oxytricha Nova
Telomere End-Binding Protein Complexes." Embo
J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
|
Crystal structure of the oxytricha nova telomere
end-binding protein complexed with noncognate ssDNA
gg(3dr)gttttgggg . SNAP
output
|
|
1pji
|
hydrolase-DNA |
X-ray (1.9 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Crystal structure of wild type lactococcus lactis fpg
complexed to a 1,3 propanediol containing DNA .
SNAP output
|
|
1pjj
|
hydrolase-DNA |
X-ray (1.9 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Complex between the lactococcus lactis fpg and an
abasic site containing DNA. . SNAP output
|
|
1pm5
|
hydrolase-DNA |
X-ray (1.95 Å) |
Pereira de Jesus K, Serre L, Zelwer C, Castaing
B |
(2005) "Structural
insights into abasic site for Fpg specific binding and
catalysis: comparative high-resolution crystallographic
studies of Fpg bound to various models of abasic site
analogues-containing DNA." Nucleic Acids
Res., 33, 5936-5944. doi:
10.1093/nar/gki879.
|
Crystal structure of wild type lactococcus lactis fpg
complexed to a tetrahydrofuran containing DNA .
SNAP output
|
|
1pnr
|
transcription-DNA |
X-ray (2.7 Å) |
Schumacher MA, Choi KY, Zalkin H, Brennan RG |
(1994) "Crystal
structure of LacI member, PurR, bound to DNA: minor
groove binding by alpha helices." Science,
266, 763-770.
|
Purine repressor-hypoxanthine-purf-operator complex .
SNAP output
|
|
1po6
|
RNA binding protein-DNA |
X-ray (2.1 Å) |
Myers JC, Moore SA, Shamoo Y |
(2003) "Structure-based
incorporation of
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
into the human telomeric repeat DNA as a probe for UP1
binding and destabilization of G-tetrad
structures." J.BIOL.CHEM.,
278, 42300-42306. doi: 10.1074/jbc.M306147200.
|
Crystal structure of up1 complexed with
d(tagg(6mi)ttaggg): a human telomeric repeat containing
6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine
(6mi) . SNAP output
|
|
1pp7
|
transcription-DNA |
X-ray (2.45 Å) |
Schumacher MA, Lau AOT, Johnson PJ |
(2003) "Structural
Basis of Core Promoter Recognition in a Primitive
Eukaryote." Cell(Cambridge,Mass.),
115, 413-424. doi: 10.1016/S0092-8674(03)00887-0.
|
Crystal structure of the t. vaginalis initiator binding
protein bound to the ferredoxin inr . SNAP output
|
|
1pp8
|
transcription-DNA |
X-ray (3.05 Å) |
Schumacher MA, Lau AOT, Johnson PJ |
(2003) "Structural
Basis of Core Promoter Recognition in a Primitive
Eukaryote." Cell(Cambridge,Mass.),
115, 413-424. doi: 10.1016/S0092-8674(03)00887-0.
|
Crystal structure of the t. vaginalis ibp39 initiator
binding domain (ibd) bound to the alpha-scs inr element
. SNAP output
|
|
1pt3
|
hydrolase-DNA |
X-ray (2.5 Å) |
Hsia KC, Chak KF, Liang PH, Cheng YS, Ku WY, Yuan
HS |
(2004) "DNA
binding and degradation by the HNH protein ColE7."
STRUCTURE, 12, 205-214. doi:
10.1016/S0969-2126(04)00006-1.
|
Crystal structures of nuclease-cole7 complexed with
octamer DNA . SNAP
output
|
|
1pue
|
transcription-DNA |
X-ray (2.1 Å) |
Kodandapani R, Pio F, Ni CZ, Piccialli G, Klemsz M,
McKercher S, Maki RA, Ely KR |
(1996) "A new
pattern for helix-turn-helix recognition revealed by
the PU.1 ETS-domain-DNA complex." Nature,
380, 456-460. doi: 10.1038/380456a0.
|
Pu.1 ets domain-DNA complex . SNAP output
|
|
1puf
|
transcription-DNA |
X-ray (1.9 Å) |
LARONDE-LEBLANC NA, Wolberger C |
(2003) "STRUCTURE
OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA
RECOGNITION ANTERIOR TO POSTERIOR." Genes
Dev., 17, 2060-2072. doi:
10.1101/gad.1103303.
|
Crystal structure of hoxa9 and pbx1 homeodomains bound
to DNA . SNAP output
|
|
1pv4
|
transcription-DNA |
X-ray (3.0 Å) |
Skordalakes E, Berger JM |
(2003) "Structure
of the Rho transcription terminator: mechanism of mRNA
recognition and helicase loading."
Cell(Cambridge,Mass.), 114,
135-146. doi: 10.1016/S0092-8674(03)00512-9.
|
X-ray crystal structure of the rho transcription
termination factor in complex with single stranded DNA
. SNAP output
|
|
1pvi
|
hydrolase-DNA |
X-ray (2.6 Å) |
Cheng X, Balendiran K, Schildkraut I, Anderson
JE |
(1994) "Structure
of PvuII endonuclease with cognate DNA." EMBO
J., 13, 3927-3935.
|
Structure of pvuii endonuclease with cognate DNA .
SNAP output
|
|
1pvp
|
recombination-DNA |
X-ray (2.35 Å) |
Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H,
Schultz PG, Santoro SW |
(2003) "A
specificity switch in selected cre recombinase variants
is mediated by macromolecular plasticity and
water." Chem.Biol., 10,
1085-1094. doi: 10.1016/j.chembiol.2003.10.015.
|
Basis for a switch in substrate specificity: crystal
structure of selected variant of cre site-specific
recombinase, alshg bound to the engineered recognition
site loxm7 . SNAP
output
|
|
1pvq
|
recombination-DNA |
X-ray (2.75 Å) |
Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H,
Schultz PG, Santoro SW |
(2003) "A
specificity switch in selected cre recombinase variants
is mediated by macromolecular plasticity and
water." Chem.Biol., 10,
1085-1094. doi: 10.1016/j.chembiol.2003.10.015.
|
Basis for a switch in substrate specificity: crystal
structure of selected variant of cre site-specific
recombinase, lnsgg bound to the engineered recognition
site loxm7 . SNAP
output
|
|
1pvr
|
recombination-DNA |
X-ray (2.65 Å) |
Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H,
Schultz PG, Santoro SW |
(2003) "A
specificity switch in selected cre recombinase variants
is mediated by macromolecular plasticity and
water." Chem.Biol., 10,
1085-1094. doi: 10.1016/j.chembiol.2003.10.015.
|
Basis for a switch in substrate specificity: crystal
structure of selected variant of cre site-specific
recombinase, lnsgg bound to the loxp (wildtype)
recognition site . SNAP
output
|
|
1pyi
|
transcription-DNA |
X-ray (3.2 Å) |
Marmorstein R, Harrison SC |
(1994) "Crystal
structure of a PPR1-DNA complex: DNA recognition by
proteins containing a Zn2Cys6 binuclear cluster."
Genes Dev., 8, 2504-2512.
|
Crystal structure of a ppr1-DNA complex: DNA
recognition by proteins containing a zn2cys6 binuclear
cluster . SNAP
output
|
|
1pzu
|
transcription-DNA |
X-ray (3.1 Å) |
Jin L, Sliz P, Chen L, Macian F, Rao A, Hogan PG,
Harrison SC |
(2003) "An
asymmetric NFAT1 dimer on a pseudo-palindromic KB-like
DNA site." Nat.Struct.Biol.,
10, 807-811. doi: 10.1038/nsb975.
|
An asymmetric nfat1-rhr homodimer on a
pseudo-palindromic, kappa-b site . SNAP output
|
|
1q0t
|
transferase-DNA |
X-ray (3.1 Å) |
Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X,
Schlagman SL, Kossykh V, Hattman S, Cheng X |
(2003) "Structure
of the bacteriophage T4 DNA adenine
methyltransferase." Nat.Struct.Biol.,
10, 849-855. doi: 10.1038/nsb973.
|
Ternary structure of t4dam with adohcy and DNA .
SNAP output
|
|
1q3f
|
hydrolase-DNA |
X-ray (1.9 Å) |
Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel
LM, Stivers JT |
(2003) "Electrostatic
guidance of glycosyl cation migration along the
reaction coordinate of uracil DNA glycosylase."
Biochemistry, 42,
12455-12460. doi: 10.1021/bi035372+.
|
Uracil DNA glycosylase bound to a cationic
1-aza-2'-deoxyribose-containing DNA . SNAP output
|
|
1q3u
|
replication-DNA |
X-ray (2.9 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of a wild-type cre recombinase-loxp
synapse: pre-cleavage complex . SNAP output
|
|
1q3v
|
replication-DNA |
X-ray (2.91 Å) |
Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck
D |
(2003) "Crystal
structure of a wild-type Cre recombinase-loxP synapse
reveals a novel spacer conformation suggesting an
alternative mechanism for DNA cleavage activation."
Nucleic Acids Res., 31,
5449-5460. doi: 10.1093/nar/gkg732.
|
Crystal structure of a wild-type cre recombinase-loxp
synapse: phosphotyrosine covalent intermediate .
SNAP output
|
|
1q9x
|
transferase,replication-DNA |
X-ray (2.69 Å) |
Freisinger E, Grollman AP, Miller H, Kisker C |
(2004) "Lesion
(in)tolerance reveals insights into DNA replication
fidelity." Embo J., 23,
1494-1505. doi: 10.1038/sj.emboj.7600158.
|
Crystal structure of enterobacteria phage rb69 gp43 DNA
polymerase complexed with tetrahydrofuran containing
DNA . SNAP output
|
|
1q9y
|
transferase, replication-DNA |
X-ray (2.8 Å) |
Freisinger E, Grollman AP, Miller H, Kisker C |
(2004) "Lesion
(in)tolerance reveals insights into DNA replication
fidelity." Embo J., 23,
1494-1505. doi: 10.1038/sj.emboj.7600158.
|
Crystal structure of enterobacteria phage rb69 gp43 DNA
polymerase complexed with 8-oxoguanosine containing DNA
. SNAP output
|
|
1qai
|
transferase-DNA |
X-ray (2.3 Å) |
Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP,
Gu J, Georgiadis MM |
(2000) "Crystal
structures of an N-terminal fragment from Moloney
murine leukemia virus reverse transcriptase complexed
with nucleic acid: functional implications for
template-primer binding to the fingers domain."
J.Mol.Biol., 296, 613-622.
doi: 10.1006/jmbi.1999.3477.
|
Crystal structures of the n-terminal fragment from
moloney murine leukemia virus reverse transcriptase
complexed with nucleic acid: functional implications
for template-primer binding to the fingers domain .
SNAP output
|
|
1qaj
|
transferase-DNA |
X-ray (2.3 Å) |
Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP,
Gu J, Georgiadis MM |
(2000) "Crystal
structures of an N-terminal fragment from Moloney
murine leukemia virus reverse transcriptase complexed
with nucleic acid: functional implications for
template-primer binding to the fingers domain."
J.Mol.Biol., 296, 613-632.
doi: 10.1006/jmbi.1999.3477.
|
Crystal structures of the n-terminal fragment from
moloney murine leukemia virus reverse transcriptase
complexed with nucleic acid: functional implications
for template-primer binding to the fingers domain .
SNAP output
|
|
1qbj
|
hydrolase-DNA |
X-ray (2.1 Å) |
Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich
A |
(1999) "Crystal
structure of the Zalpha domain of the human editing
enzyme ADAR1 bound to left-handed Z-DNA."
Science, 284, 1841-1845. doi:
10.1126/science.284.5421.1841.
|
Crystal structure of the zalpha z-DNA complex .
SNAP output
|
|
1qln
|
nucleotidyltransferase |
X-ray (2.4 Å) |
Cheetham GMT, Steitz TA |
(1999) "Structure
of a Transcribing T7 RNA Polymerase Initiation
Complex." Science, 286,
2305. doi: 10.1126/SCIENCE.286.5448.2305.
|
Structure of a transcribing t7 RNA polymerase
initiation complex . SNAP output
|
|
1qn3
|
tata box-binding protein (tbp) |
X-ray (1.95 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the c(-25) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qn4
|
tata box-binding protein (tbp) |
X-ray (1.86 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-24) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qn5
|
tata box-binding protein (tbp) |
X-ray (1.93 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the g(-26) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qn6
|
tata box-binding protein (tbp) |
X-ray (2.1 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-26) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qn7
|
tata box-binding protein (tbp) |
X-ray (2.3 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-27) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qn8
|
tata box-binding protein (tbp) |
X-ray (2.1 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-28) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qn9
|
tata box-binding protein (tbp) |
X-ray (1.9 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the c(-29) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qna
|
tata box-binding protein (tbp) |
X-ray (1.8 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-30) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qnb
|
tata box-binding protein (tbp) |
X-ray (2.23 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the t(-25) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qnc
|
tata box-binding protein (tbp) |
X-ray (2.3 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the a(-31) adenovirus major late
promoter tata box variant bound to wild-type tbp
(arabidopsis thaliana tbp isoform 2). tata element
recognition by the tata box-binding protein has been
conserved throughout evolution. . SNAP output
|
|
1qne
|
tata box-binding protein (tbp) |
X-ray (1.9 Å) |
Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T,
Burley SK |
(1999) "TATA
Element Recognition by the TATA Box-Binding Protein Has
Been Conserved Throughout Evolution." Genes
Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217.
|
Crystal structure of the adenovirus major late promoter
tata box bound to wild-type tbp (arabidopsis thaliana
tbp isoform 2). . SNAP
output
|
|
1qp0
|
transcription-DNA |
X-ray (2.9 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor-hypoxanthine-palindromic operator
complex . SNAP
output
|
|
1qp4
|
transcription-DNA |
X-ray (3.0 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor-hypoxanthine-palindromic operator
complex . SNAP
output
|
|
1qp7
|
transcription-DNA |
X-ray (2.9 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
|
1qp9
|
transcription-DNA |
X-ray (2.8 Å) |
Lukens AK, King DA, Marmorstein R |
(2000) "Structure
of HAP1-PC7 bound to DNA: implications for DNA
recognition and allosteric effects of DNA-binding on
transcriptional activation." Nucleic Acids
Res., 28, 3853-3863. doi:
10.1093/nar/28.20.3853.
|
Structure of hap1-pc7 complexed to the uas of cyc7 .
SNAP output
|
|
1qpi
|
transcription-DNA |
X-ray (2.5 Å) |
Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs
W |
(2000) "Structural
basis of gene regulation by the tetracycline inducible
Tet repressor-operator system."
Nat.Struct.Biol., 7, 215-219.
doi: 10.1038/73324.
|
Crystal structure of tetracycline repressor-operator
complex . SNAP
output
|
|
1qps
|
hydrolase-DNA |
X-ray (2.5 Å) |
Horvath MM, Choi J, Kim Y, Wilkosz P, Rosenberg
JM |
"The Integration of Recognition and Cleavage: X-Ray
Structures of Pre- Transition State and Post-Reactive
DNA-Eco RI Endonuclease Complexes." |
The crystal structure of a post-reactive cognate
DNA-eco ri complex at 2.50 a in the presence of mn2+
ion . SNAP output
|
|
1qpz
|
transcription-DNA |
X-ray (2.5 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor-hypoxanthine-palindromic operator
complex . SNAP
output
|
|
1qqa
|
gene regulation-DNA |
X-ray (3.0 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
|
1qqb
|
gene regulation-DNA |
X-ray (2.7 Å) |
Glasfeld A, Koehler AN, Schumacher MA, Brennan
RG |
(1999) "The role
of lysine 55 in determining the specificity of the
purine repressor for its operators through minor groove
interactions." J.Mol.Biol.,
291, 347-361. doi: 10.1006/jmbi.1999.2946.
|
Purine repressor mutant-hypoxanthine-palindromic
operator complex . SNAP
output
|
|
1qrh
|
hydrolase-DNA |
X-ray (2.5 Å) |
Choi J, Kim Y, Greene P, Hager P, Rosenberg JM |
"X-Ray Structure of the DNA-Eco RI Endonuclease
Complexes with the ED144 and RK145 Mutations." |
X-ray structure of the DNA-eco ri endonuclease
complexes with an r145k mutation at 2.7 a . SNAP output
|
|
1qri
|
hydrolase-DNA |
X-ray (2.6 Å) |
Choi J, Kim Y, Greene P, Hager P, Rosenberg JM |
"X-Ray Structure of the DNA-Eco RI Endonuclease
Complexes with the ED144 and RK145 Mutations." |
X-ray structure of the DNA-eco ri endonuclease
complexes with an e144d mutation at 2.7 a . SNAP output
|
|
1qrv
|
gene regulation-DNA |
X-ray (2.2 Å) |
Murphy IV FV, Sweet RM, Churchill ME |
(1999) "The
structure of a chromosomal high mobility group
protein-DNA complex reveals sequence-neutral mechanisms
important for non-sequence-specific DNA
recognition." EMBO J.,
18, 6610-6618. doi: 10.1093/emboj/18.23.6610.
|
Crystal structure of the complex of hmg-d and DNA .
SNAP output
|
|
1qsl
|
transferase-DNA |
X-ray (2.2 Å) |
Brautigam CA, Aschheim K, Steitz TA |
(1999) "Structural
elucidation of the binding and inhibitory properties of
lanthanide (III) ions at the 3'-5' exonucleolytic
active site of the Klenow fragment."
Chem.Biol., 6, 901-908. doi:
10.1016/S1074-5521(00)80009-5.
|
Klenow fragment complexed with single-stranded
substrate and europium (iii) ion . SNAP output
|
|
1qss
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Mitaxov V, Waksman G |
(1999) "Structure-based
design of Taq DNA polymerases with improved properties
of dideoxynucleotide incorporation."
Proc.Natl.Acad.Sci.USA, 96,
9491-9496. doi: 10.1073/pnas.96.17.9491.
|
Ddgtp-trapped closed ternary complex of the large
fragment of DNA polymerase i from thermus aquaticus .
SNAP output
|
|
1qsy
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Mitaxov V, Waksman G |
(1999) "Structure-based
design of Taq DNA polymerases with improved properties
of dideoxynucleotide incorporation."
Proc.Natl.Acad.Sci.USA, 96,
9491-9496. doi: 10.1073/pnas.96.17.9491.
|
Ddatp-trapped closed ternary complex of the large
fragment of DNA polymerase i from thermus aquaticus .
SNAP output
|
|
1qtm
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Mitaxov V, Waksman G |
(1999) "Structure-based
design of Taq DNA polymerases with improved properties
of dideoxynucleotide incorporation."
Proc.Natl.Acad.Sci.USA, 96,
9491-9496. doi: 10.1073/pnas.96.17.9491.
|
Ddttp-trapped closed ternary complex of the large
fragment of DNA polymerase i from thermus aquaticus .
SNAP output
|
|
1qum
|
hydrolase-DNA |
X-ray (1.55 Å) |
Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer
JA |
(1999) "Structure
of the DNA repair enzyme endonuclease IV and its DNA
complex: double-nucleotide flipping at abasic sites and
three-metal-ion catalysis."
Cell(Cambridge,Mass.), 98,
397-408. doi: 10.1016/S0092-8674(00)81968-6.
|
Crystal structure of escherichia coli endonuclease iv
in complex with damaged DNA . SNAP output
|
|
1qx0
|
transferase-DNA |
X-ray (2.26 Å) |
Guasch A, Lucas M, Moncalian G, Cabezas M, Prez-Luque
R, Gomis-Rth FX, de la Cruz F, Coll M |
(2003) "RECOGNITION
AND PROCESSING OF THE ORIGIN OF TRANSFER DNA BY
CONJUGATIVE RELAXASE TRWC."
Nat.Struct.Biol., 10,
1002-1010. doi: 10.1038/nsb1017.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-bound structure . SNAP output
|
|
1qzg
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Lei M, Podell ER, Baumann P, Cech TR |
(2003) "DNA
self-recognition in the structure of Pot1 bound to
telomeric single-stranded DNA." Nature,
426, 198-203. doi: 10.1038/nature02092.
|
Crystal structure of pot1 (protection of telomere)-
ssDNA complex . SNAP
output
|
|
1qzh
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Lei M, Podell ER, Baumann P, Cech TR |
(2003) "DNA
self-recognition in the structure of Pot1 bound to
telomeric single-stranded DNA." Nature,
426, 198-203. doi: 10.1038/nature02092.
|
Crystal structure of pot1 (protection of telomere)-
ssDNA complex . SNAP
output
|
|
1r0a
|
transferase-immune system-DNA |
X-ray (2.8 Å) |
Peletskaya EN, Kogon AA, Tuske S, Arnold E, Hughes
SH |
(2004) "Nonnucleoside
inhibitor binding affects the interactions of the
fingers subdomain of human immunodeficiency virus type
1 reverse transcriptase with DNA."
J.Virol., 78, 3387-3397. doi:
10.1128/JVI.78.7.3387-3397.2004.
|
Crystal structure of hiv-1 reverse transcriptase
covalently tethered to DNA template-primer solved to
2.8 angstroms . SNAP
output
|
|
1r0n
|
transcription-DNA |
X-ray (2.6 Å) |
Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad
F |
(2003) "Structure
of the heterodimeric Ecdysone Receptor DNA-binding
complex." Embo J., 22,
5827-5840. doi: 10.1093/emboj/cdg569.
|
Crystal structure of heterodimeric ecdsyone receptor
DNA binding complex . SNAP output
|
|
1r0o
|
transcription-DNA |
X-ray (2.24 Å) |
Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad
F |
(2003) "Structure
of the Heterodimeric Ecdysone Receptor DNA-binding
Complex." Embo J., 22,
5827-5840. doi: 10.1093/emboj/cdg569.
|
Crystal structure of the heterodimeric ecdysone
receptor DNA-binding complex . SNAP output
|
|
1r2y
|
hydrolase-DNA |
X-ray (2.34 Å) |
Fromme JC, Verdine GL |
(2003) "DNA
Lesion Recognition by the Bacterial Repair Enzyme
MutM." J.Biol.Chem., 278,
51543-51548. doi: 10.1074/jbc.M307768200.
|
Mutm (fpg) bound to 8-oxoguanine (oxog) containing DNA
. SNAP output
|
|
1r2z
|
hydrolase-DNA |
X-ray (1.63 Å) |
Fromme JC, Verdine GL |
(2003) "DNA
Lesion Recognition by the Bacterial Repair Enzyme
MutM." J.Biol.Chem., 278,
51543-51548. doi: 10.1074/jbc.M307768200.
|
Mutm (fpg) bound to 5,6-dihydrouracil (dhu) containing
DNA . SNAP output
|
|
1r49
|
isomerase-DNA |
X-ray (3.13 Å) |
Interthal H, Quigley PM, Hol WG, Champoux JJ |
(2004) "The role
of lysine 532 in the catalytic mechanism of human
topoisomerase I." J.Biol.Chem.,
279, 2984-2992. doi: 10.1074/jbc.M309959200.
|
Human topoisomerase i (topo70) double mutant
k532r-y723f . SNAP
output
|
|
1r4i
|
transcription-DNA |
X-ray (3.1 Å) |
Shaffer PL, Jivan A, Dollins DE, Claessens F, Gewirth
DT |
(2004) "Structural
basis of androgen receptor binding to selective
androgen response elements."
Proc.Natl.Acad.Sci.USA, 101,
4758-4763. doi: 10.1073/pnas.0401123101.
|
Crystal structure of androgen receptor DNA-binding
domain bound to a direct repeat response element .
SNAP output
|
|
1r4o
|
transcription-DNA |
X-ray (2.5 Å) |
Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto
KR, Sigler PB |
(1991) "Crystallographic
Analysis of the Interaction of The Glucocorticoid
Receptor with DNA." Nature,
352, 497-505. doi: 10.1038/352497a0.
|
Crystallographic analysis of the interaction of the
glucocorticoid receptor with DNA . SNAP output
|
|
1r4r
|
transcription-DNA |
X-ray (3.0 Å) |
Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto
KR, Sigler PB |
(1991) "Crystallographic
Analysis of the Interaction of the Glucocorticoid
Receptor with DNA." Nature,
352, 497-505. doi: 10.1038/352497a0.
|
Crystallographic analysis of the interaction of the
glucocorticoid receptor with DNA . SNAP output
|
|
1r71
|
transcription-DNA |
X-ray (2.2 Å) |
Khare D, Ziegelin G, Lanka E, Heinemann U |
(2004) "Sequence-specific
DNA binding determined by contacts outside the
helix-turn-helix motif of the ParB homolog KorB."
Nat.Struct.Mol.Biol., 11,
656-663. doi: 10.1038/nsmb773.
|
Crystal structure of the DNA binding domain of korb in
complex with the operator DNA . SNAP output
|
|
1r7m
|
hydrolase-DNA |
X-ray (2.25 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2003) "The
crystal structure of the gene targeting homing
endonuclease I-SceI reveals the origins of its target
site specificity." J.Mol.Biol.,
334, 685-695. doi: 10.1016/j.jmb.2003.09.068.
|
The homing endonuclease i-scei bound to its DNA
recognition region . SNAP output
|
|
1r8d
|
transcription-DNA |
X-ray (2.7 Å) |
Newberry KJ, Brennan RG |
(2004) "The
structural mechanism for transcription activation by
MerR family member multidrug transporter activation, N
terminus." J.Biol.Chem.,
279, 20356-20362. doi: 10.1074/jbc.M400960200.
|
Crystal structure of mtan bound to DNA . SNAP output
|
|
1r8e
|
transcription-DNA |
X-ray (2.4 Å) |
Newberry KJ, Brennan RG |
(2004) "The
structural mechanism for transcription activation by
MerR family member multidrug transporter activation, N
terminus." J.Biol.Chem.,
279, 20356-20362. doi: 10.1074/jbc.M400960200.
|
Crystal structure of bmrr bound to DNA at 2.4a
resolution . SNAP
output
|
|
1r9s
|
transcription-DNA-RNA hybrid |
X-ray (4.25 Å) |
Westover KD, Bushnell DA, Kornberg RD |
(2004) "Structural
basis of transcription: nucleotide selection by
rotation in the RNA polymerase II active center."
Cell(Cambridge,Mass.), 119,
481-489. doi: 10.1016/j.cell.2004.10.016.
|
RNA polymerase ii strand separated elongation complex,
matched nucleotide . SNAP output
|
|
1r9t
|
transcription-DNA-RNA hybrid |
X-ray (3.5 Å) |
Westover KD, Bushnell DA, Kornberg RD |
(2004) "Structural
basis of transcription: nucleotide selection by
rotation in the RNA polymerase II active center."
Cell(Cambridge,Mass.), 119,
481-489. doi: 10.1016/j.cell.2004.10.016.
|
RNA polymerase ii strand separated elongation complex,
mismatched nucleotide . SNAP output
|
|
1ram
|
transcription-DNA |
X-ray (2.7 Å) |
Chen YQ, Ghosh S, Ghosh G |
(1998) "A novel
DNA recognition mode by the NF-kappa B p65
homodimer." Nat.Struct.Biol.,
5, 67-73. doi: 10.1038/nsb0198-67.
|
A novel DNA recognition mode by nf-kb p65 homodimer .
SNAP output
|
|
1rb8
|
virus-DNA |
X-ray (3.5 Å) |
Bernal RA, Hafenstein S, Esmeralda R, Fane BA,
Rossmann MG |
(2004) "The
phiX174 Protein J Mediates DNA Packaging and Viral
Attachment to Host Cells." J.Mol.Biol.,
337, 1109-1122. doi: 10.1016/j.jmb.2004.02.033.
|
The phix174 DNA binding protein j in two different
capsid environments. . SNAP output
|
|
1rbj
|
hydrolase-DNA |
X-ray (2.7 Å) |
Ko TP, Williams R, McPherson A |
(1996) "Structure
of a ribonuclease B+d(pA)4 complex." Acta
Crystallogr.,Sect.D, 52, 160-164.
doi: 10.1107/S0907444995009127.
|
Ribonuclease b complex with d(tetra-(deoxy-adenylate))
. SNAP output
|
|
1rc8
|
transferase-DNA |
X-ray (2.75 Å) |
Eastberg JH, Pelletier J, Stoddard BL |
(2004) "Recognition
of DNA substrates by T4 bacteriophage polynucleotide
kinase." Nucleic Acids Res.,
32, 653-660. doi: 10.1093/nar/gkh212.
|
T4 polynucleotide kinase bound to 5'-gtcac-3' ssDNA .
SNAP output
|
|
1rcn
|
hydrolase-DNA |
X-ray (2.32 Å) |
Fontecilla-Camps JC, de Llorens R, le Du MH, Cuchillo
CM |
(1994) "Crystal
structure of ribonuclease A.d(ApTpApApG) complex.
Direct evidence for extended substrate
recognition." J.Biol.Chem.,
269, 21526-21531.
|
Crystal structure of the ribonuclease a d(aptpapapg)
complex : direct evidence for extended substrate
recognition . SNAP
output
|
|
1rcs
|
transcription-DNA |
NMR |
Zhang H, Zhao D, Revington M, Lee W, Jia X,
Arrowsmith C, Jardetzky O |
(1994) "The
solution structures of the trp repressor-operator DNA
complex." J.Mol.Biol.,
238, 592-614. doi: 10.1006/jmbi.1994.1317.
|
NMR study of trp repressor-operator DNA complex .
SNAP output
|
|
1rep
|
replication-DNA |
X-ray (2.6 Å) |
Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C,
Miki K |
(1999) "Crystal
structure of a prokaryotic replication initiator
protein bound to DNA at 2.6 A resolution." EMBO
J., 18, 4597-4607. doi: 10.1093/emboj/18.17.4597.
|
Crystal structure of replication initiator protein
repe54 of mini-f plasmid complexed with an iteron DNA .
SNAP output
|
|
1rff
|
hydrolase-DNA |
X-ray (1.7 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octapeptide
klnyydpr, and tetranucleotide agtt. . SNAP output
|
|
1rfi
|
hydrolase-DNA |
X-ray (2.2 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, pentapeptide
klnyk, and tetranucleotide agtc . SNAP output
|
|
1rg1
|
hydrolase-DNA |
X-ray (2.1 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agtt . SNAP output
|
|
1rg2
|
hydrolase-DNA |
X-ray (2.1 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agta . SNAP output
|
|
1rgt
|
hydrolase-DNA |
X-ray (2.0 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agtc . SNAP output
|
|
1rgu
|
hydrolase-DNA |
X-ray (2.22 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
The crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine,
and tetranucleotide agtg . SNAP output
|
|
1rh0
|
hydrolase-DNA |
X-ray (2.3 Å) |
Davies DR, Interthal H, Champoux JJ, Hol WG |
(2004) "Explorations
of peptide and oligonucleotide binding sites of
tyrosyl-DNA phosphodiesterase using vanadate
complexes." J.Med.Chem.,
47, 829-837. doi: 10.1021/jm030487x.
|
Crystal structure of human tyrosyl-DNA
phosphodiesterase complexed with vanadate, octopamine
and trinucleotide gtt . SNAP output
|
|
1rh6
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Sam MD, Cascio D, Johnson RC, Clubb RT |
(2004) "Crystal
structure of the excisionase-DNA complex from
bacteriophage lambda." J.Mol.Biol.,
338, 229-240. doi: 10.1016/j.jmb.2004.02.053.
|
Bacteriophage lambda excisionase (xis)-DNA complex .
SNAP output
|
|
1rio
|
transcription-DNA |
X-ray (2.3 Å) |
Jain D, Nickels BE, Sun L, Hochschild A, Darst
SA |
(2004) "Structure
of a ternary transcription activation complex."
Mol.Cell, 13, 45-53. doi:
10.1016/S1097-2765(03)00483-0.
|
Structure of bacteriophage lambda ci-ntd in complex
with sigma-region4 of thermus aquaticus bound to DNA .
SNAP output
|
|
1rm1
|
transcription-DNA |
X-ray (2.5 Å) |
Jin X, Gewirth DT, Geiger JH |
"High Resolution Structure of a Yeast
TFIIA/TBP/TATA-box DNA Complex." |
Structure of a yeast tfiia-tbp-tata-box DNA complex .
SNAP output
|
|
1rnb
|
endonuclease |
X-ray (1.9 Å) |
Baudet S, Janin J |
(1991) "Crystal
structure of a barnase-d(GpC) complex at 1.9 A
resolution." J.Mol.Biol.,
219, 123-132. doi: 10.1016/0022-2836(91)90862-Z.
|
Crystal structure of a barnase-d(*gp*c) complex at 1.9
angstroms resolution . SNAP output
|
|
1rpe
|
gene regulation-DNA |
X-ray (2.5 Å) |
Shimon LJ, Harrison SC |
(1993) "The phage
434 OR2/R1-69 complex at 2.5 A resolution."
J.Mol.Biol., 232, 826-838.
doi: 10.1006/jmbi.1993.1434.
|
The phage 434 or2-r1-69 complex at 2.5 angstroms
resolution . SNAP
output
|
|
1rpz
|
transferase-DNA |
X-ray (2.9 Å) |
Eastberg JH, Pelletier J, Stoddard BL |
(2004) "Recognition
of DNA substrates by T4 bacteriophage polynucleotide
kinase." Nucleic Acids Res.,
32, 653-660. doi: 10.1093/nar/gkh212.
|
T4 polynucleotide kinase bound to 5'-tgcac-3' ssDNA .
SNAP output
|
|
1rr8
|
isomerase-DNA |
X-ray (2.6 Å) |
Chrencik JE, Staker BL, Burgin AB, Pourquier P,
Pommier Y, Stewart L, Redinbo MR |
(2004) "Mechanisms
of camptothecin resistance by human topoisomerase I
mutations." J.Mol.Biol.,
339, 773-784. doi: 10.1016/j.jmb.2004.03.077.
|
Structural mechanisms of camptothecin resistance by
mutations in human topoisomerase i . SNAP output
|
|
1rrc
|
transferase-DNA |
X-ray (2.46 Å) |
Eastberg JH, Pelletier J, Stoddard BL |
(2004) "Recognition
of DNA substrates by T4 bacteriophage polynucleotide
kinase." Nucleic Acids Res.,
32, 653-660. doi: 10.1093/nar/gkh212.
|
T4 polynucleotide kinase bound to 5'-gtc-3' ssDNA .
SNAP output
|
|
1rrj
|
isomerase-DNA |
X-ray (2.3 Å) |
Chrencik JE, Staker BL, Burgin AB, Pourquier P,
Pommier Y, Stewart L, Redinbo MR |
(2004) "Mechanisms
of camptothecin resistance by human topoisomerase I
mutations." J.Mol.Biol.,
339, 773-784. doi: 10.1016/j.jmb.2004.03.077.
|
Structural mechanisms of camptothecin resistance by
mutations in human topoisomerase i . SNAP output
|
|
1rrq
|
hydrolase-DNA |
X-ray (2.22 Å) |
Fromme JC, Banerjee A, Huang SJ, Verdine GL |
(2004) "Structural
basis for removal of adenine mispaired with
8-oxoguanine by MutY adenine DNA glycosylase."
Nature, 427, 652-656. doi:
10.1038/nature02306.
|
Muty adenine glycosylase in complex with DNA containing
an a:oxog pair . SNAP
output
|
|
1rrs
|
hydrolase-DNA |
X-ray (2.4 Å) |
Fromme JC, Banerjee A, Huang SJ, Verdine GL |
(2004) "Structural
basis for removal of adenine mispaired with
8-oxoguanine by MutY adenine DNA glycosylase."
Nature, 427, 652-656. doi:
10.1038/nature02306.
|
Muty adenine glycosylase in complex with DNA containing
an abasic site . SNAP
output
|
|
1rta
|
hydrolase-DNA |
X-ray (2.5 Å) |
Birdsall DL, McPherson A |
(1992) "Crystal
structure disposition of thymidylic acid tetramer in
complex with ribonuclease A."
J.Biol.Chem., 267,
22230-22236.
|
Crystal structure disposition of thymidylic acid
tetramer in complex with ribonuclease a . SNAP output
|
|
1rtd
|
transferase-DNA |
X-ray (3.2 Å) |
Huang H, Chopra R, Verdine GL, Harrison SC |
(1998) "Structure
of a covalently trapped catalytic complex of HIV-1
reverse transcriptase: implications for drug
resistance." Science,
282, 1669-1675. doi: 10.1126/science.282.5394.1669.
|
Structure of a catalytic complex of hiv-1 reverse
transcriptase: implications for nucleoside analog drug
resistance . SNAP
output
|
|
1run
|
transcription-DNA |
X-ray (2.7 Å) |
Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X,
Kunkel TA, Berman H, Ebright RH |
(1996) "Aromatic
hydrogen bond in sequence-specific protein DNA
recognition." Nat.Struct.Biol.,
3, 837-841. doi: 10.1038/nsb1096-837.
|
Catabolite gene activator protein (cap)-DNA complex +
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
|
1ruo
|
transcription-DNA |
X-ray (2.7 Å) |
Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X,
Kunkel TA, Berman H, Ebright RH |
(1996) "Aromatic
hydrogen bond in sequence-specific protein DNA
recognition." Nat.Struct.Biol.,
3, 837-841. doi: 10.1038/nsb1096-837.
|
Catabolite gene activator protein (cap) mutant-DNA
complex + adenosine-3',5'-cyclic-monophosphate .
SNAP output
|
|
1rv5
|
hydrolase-DNA |
X-ray (2.1 Å) |
Horton NC, Perona JJ |
(1998) "Role of
protein-induced bending in the specificity of DNA
recognition: crystal structure of EcoRV endonuclease
complexed with d(AAAGAT) + d(ATCTT)."
J.Mol.Biol., 277, 779-783.
doi: 10.1006/jmbi.1998.1655.
|
Complex of ecorv endonuclease with d(aaagat)-d(atctt) .
SNAP output
|
|
1rva
|
hydrolase-DNA |
X-ray (2.0 Å) |
Kostrewa D, Winkler FK |
(1995) "Mg2+
binding to the active site of EcoRV endonuclease: a
crystallographic study of complexes with substrate and
product DNA at 2 A resolution."
Biochemistry, 34, 683-696.
doi: 10.1021/bi00002a036.
|
Mg2+ binding to the active site of eco rv endonuclease:
a crystallographic study of complexes with substrate
and product DNA at 2 angstroms resolution . SNAP output
|
|
1rvb
|
hydrolase-DNA |
X-ray (2.1 Å) |
Kostrewa D, Winkler FK |
(1995) "Mg2+
binding to the active site of EcoRV endonuclease: a
crystallographic study of complexes with substrate and
product DNA at 2 A resolution."
Biochemistry, 34, 683-696.
doi: 10.1021/bi00002a036.
|
Mg2+ binding to the active site of eco rv endonuclease:
a crystallographic study of complexes with substrate
and product DNA at 2 angstroms resolution . SNAP output
|
|
1rvc
|
hydrolase-DNA |
X-ray (2.1 Å) |
Kostrewa D, Winkler FK |
(1995) "Mg2+
binding to the active site of EcoRV endonuclease: a
crystallographic study of complexes with substrate and
product DNA at 2 A resolution."
Biochemistry, 34, 683-696.
doi: 10.1021/bi00002a036.
|
Mg2+ binding to the active site of eco rv endonuclease:
a crystallographic study of complexes with substrate
and product DNA at 2 angstroms resolution . SNAP output
|
|
1rxv
|
hydrolase-DNA |
X-ray (2.5 Å) |
Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B,
Shen B, Tainer JA |
(2004) "Structural
Basis for FEN-1 Substrate Specificity and PCNA-Mediated
Activation in DNA Replication and Repair."
Cell(Cambridge,Mass.), 116,
39-50. doi: 10.1016/S0092-8674(03)01036-5.
|
Crystal structure of a. fulgidus fen-1 bound to DNA .
SNAP output
|
|
1rxw
|
hydrolase-DNA |
X-ray (2.0 Å) |
Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B,
Shen B, Tainer JA |
(2004) "Structural
Basis for FEN-1 Substrate Specificity and PCNA-Mediated
Activation in DNA Replication and Repair."
Cell(Cambridge,Mass.), 116,
39-50. doi: 10.1016/S0092-8674(03)01036-5.
|
Crystal structure of a. fulgidus fen-1 bound to DNA .
SNAP output
|
|
1ryr
|
transferase-DNA |
X-ray (2.28 Å) |
Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W |
(2003) "Replication
of a Cis-Syn Thymine Dimer at Atomic Resolution."
Nature, 424, 1083-1087. doi:
10.1038/nature01919.
|
Replication of a cis-syn thymine dimer at atomic
resolution . SNAP
output
|
|
1rys
|
transferase-DNA |
X-ray (2.03 Å) |
Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W |
(2003) "Replication
of a Cis-Syn Thymine Dimer at Atomic Resolution."
Nature, 424, 1083-1087. doi:
10.1038/nature01919.
|
Replication of a cis-syn thymine dimer at atomic
resolution . SNAP
output
|
|
1rz9
|
viral protein-DNA |
X-ray (3.1 Å) |
Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda
F |
(2004) "The
nuclease domain of adeno-associated virus rep
coordinates replication initiation using two distinct
DNA recognition interfaces." Mol.Cell,
13, 403-414. doi: 10.1016/S1097-2765(04)00023-1.
|
Crystal structure of aav rep complexed with the
rep-binding sequence . SNAP output
|
|
1rzr
|
transcription-transport protein-DNA |
X-ray (2.8 Å) |
Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W,
Brennan RG |
(2004) "Structural
basis for allosteric control of the transcription
regulator CcpA by the phosphoprotein HPr-Ser46-P."
Cell(Cambridge,Mass.), 118,
731-741. doi: 10.1016/j.cell.2004.08.027.
|
Crystal structure of transcriptional
regulator-phosphoprotein-DNA complex . SNAP output
|
|
1rzt
|
transferase-DNA |
X-ray (2.1 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel
TA, Pedersen LC |
(2004) "A
structural solution for the DNA polymerase
lambda-dependent repair of DNA gaps with minimal
homology." Mol.Cell, 13,
561-572. doi: 10.1016/S1097-2765(04)00061-9.
|
Crystal structure of DNA polymerase lambda complexed
with a two nucleotide gap DNA molecule . SNAP output
|
|
1s0m
|
transferase-DNA |
X-ray (2.7 Å) |
Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F,
Woodgate R, Jerina DM, Yang W |
(2004) "Crystal
structure of a benzo[a]pyrene diol epoxide adduct in a
ternary complex with a DNA polymerase."
Proc.Natl.Acad.Sci.USA, 101,
2265-2269. doi: 10.1073/pnas.0308332100.
|
Crystal structure of a benzo[a]pyrene diol epoxide
adduct in a ternary complex with a DNA polymerase .
SNAP output
|
|
1s0n
|
transferase-DNA |
X-ray (2.8 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of Replication through an Abasic Lesion; Structural
Basis for Base Substitutions and Frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/S1097-2765(04)00101-7.
|
Snapshots of replication through an abasic lesion:
structural basis for base substitution and frameshift .
SNAP output
|
|
1s0o
|
transferase-DNA |
X-ray (2.1 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of Replication through an Abasic Lesion; Structural
Basis for Base Substitutions and Frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/S1097-2765(04)00101-7.
|
Snapshots of replication through an abasic lesion:
structural basis for base substitution and frameshift .
SNAP output
|
|
1s0v
|
transferase-DNA-RNA hybrid |
X-ray (3.2 Å) |
Temiakov D, Patlan V, Anikin M, McAllister WT,
Yokoyama S, Vassylyev DG |
(2004) "Structural
basis for substrate selection by t7 RNA
polymerase." Cell(Cambridge,Mass.),
116, 381-391. doi: 10.1016/S0092-8674(04)00059-5.
|
Structural basis for substrate selection by t7 RNA
polymerase . SNAP
output
|
|
1s10
|
transferase-DNA |
X-ray (2.1 Å) |
Ling H, Boudsocq F, Woodgate R, Yang W |
(2004) "Snapshots
of Replication through an Abasic Lesion; Structural
Basis for Base Substitutions and Frameshifts."
Mol.Cell, 13, 751-762. doi:
10.1016/S1097-2765(04)00101-7.
|
Snapshots of replication through an abasic lesion:
structural basis for base substitution and frameshift .
SNAP output
|
|
1s32
|
structural protein-DNA |
X-ray (2.05 Å) |
Edayathumangalam RS, Weyermann P, Gottesfeld JM,
Dervan PB, Luger K |
(2004) "Molecular
Recognition of the Nucleosomal 'Supergroove'."
Proc.Natl.Acad.Sci.USA, 101,
6864-6869. doi: 10.1073/pnas.0401743101.
|
Molecular recognition of the nucleosomal 'supergroove'
. SNAP output
|
|
1s40
|
cell cycle-DNA |
NMR |
Mitton-Fry RM, Anderson EM, Theobald DL, Glustrom LW,
Wuttke DS |
(2004) "Structural
basis for telomeric single-stranded DNA recognition by
yeast Cdc13." J.Mol.Biol.,
338, 241-255. doi: 10.1016/j.jmb.2004.01.063.
|
Solution structure of the cdc13 DNA-binding domain
complexed with a single-stranded telomeric DNA 11-mer .
SNAP output
|
|
1s6m
|
DNA binding protein-DNA |
X-ray (2.28 Å) |
Boer R, Russi S, Guasch A, Lucas M, Blanco AG,
Perez-Luque R, Coll M, de la Cruz F |
(2006) "Unveiling
the molecular mechanism of a conjugative relaxase: The
structure of TrwC complexed with a 27-mer DNA
comprising the recognition hairpin and the cleavage
site." J.Mol.Biol., 358,
857-869. doi: 10.1016/j.jmb.2006.02.018.
|
Conjugative relaxase trwc in complex with orit DNA.
metal-bound structure . SNAP output
|
|
1s76
|
transferase |
X-ray (2.88 Å) |
Yin YW, Steitz TA |
(2004) "The
structural mechanism of translocation and helicase
activity in T7 RNA polymerase."
Cell(Cambridge,Mass.), 116,
393-404. doi: 10.1016/S0092-8674(04)00120-5.
|
T7 RNA polymerase alpha beta methylene atp elongation
complex . SNAP
output
|
|
1s77
|
transferase |
X-ray (2.69 Å) |
Yin YW, Steitz TA |
(2004) "The
structural mechanism of translocation and helicase
activity in T7 RNA polymerase."
Cell(Cambridge,Mass.), 116,
393-404. doi: 10.1016/S0092-8674(04)00120-5.
|
T7 rnap product pyrophosphate elongation complex .
SNAP output
|
|
1s97
|
transferase-DNA |
X-ray (2.4 Å) |
Trincao J, Johnson RE, Wolfle WT, Escalante CR,
Prakash S, Prakash L, Aggarwal AK |
(2004) "Dpo4 is
hindered in extending a G.T mismatch by a reverse
wobble." Nat.Struct.Mol.Biol.,
11, 457-462. doi: 10.1038/nsmb755.
|
Dpo4 with gt mismatch . SNAP output
|
|
1s9f
|
transferase-DNA |
X-ray (2.0 Å) |
Trincao J, Johnson RE, Wolfle WT, Escalante CR,
Prakash S, Prakash L, Aggarwal AK |
(2004) "Dpo4 is
hindered in extending a G.T mismatch by a reverse
wobble." Nat.Struct.Mol.Biol.,
11, 457-462. doi: 10.1038/nsmb755.
|
Dpo with at matched . SNAP output
|
|
1s9k
|
transcription-DNA |
X-ray (3.1 Å) |
Wang D, Stroud JC, Chen L |
"Crystal Structure of Human NFAT1 and Fos-Jun on the
IL-2 ARRE1 Site." |
Crystal structure of human nfat1 and fos-jun on the
il-2 arre1 site . SNAP
output
|
|
1sa3
|
hydrolase-DNA |
X-ray (1.95 Å) |
Xu QS, Kucera RB, Roberts RJ, Guo HC |
(2004) "An
Asymmetric Complex of Restriction Endonuclease MspI on
Its Palindromic DNA Recognition Site."
STRUCTURE, 12, 1741-1747.
doi: 10.1016/j.str.2004.07.014.
|
An asymmetric complex of restriction endonuclease mspi
on its palindromic DNA recognition site . SNAP output
|
|
1sax
|
transcription-DNA |
X-ray (2.8 Å) |
Garcia-Castellanos R, Mallorqui-Fernandez G, Marrero
A, Potempa J, Coll M, Gomis-Ruth FX |
(2004) "On the
transcriptional regulation of methicillin resistance:
MecI repressor in complex with its operator."
J.Biol.Chem., 279,
17888-17896. doi: 10.1074/jbc.M313123200.
|
Three-dimensional structure of s.aureus
methicillin-resistance regulating transcriptional
repressor meci in complex with 25-bp ds-DNA . SNAP output
|
|
1sc7
|
isomerase-DNA |
X-ray (3.0 Å) |
Staker BL, Feese MD, Cushman M, Pommier Y, Zembower
D, Stewart L, Burgin AB |
(2005) "Structures
of three classes of anticancer agents bound to the
human topoisomerase I-DNA covalent complex."
J.Med.Chem., 48, 2336-2345.
doi: 10.1021/jm049146p.
|
Human DNA topoisomerase i (70 kda) in complex with the
indenoisoquinoline mj-ii-38 and covalent complex with a
22 base pair DNA duplex . SNAP output
|
|
1seu
|
isomerase-DNA |
X-ray (3.0 Å) |
Staker BL, Feese MD, Cushman M, Pommier Y, Zembower
D, Stewart L, Burgin AB |
(2005) "Structures
of three classes of anticancer agents bound to the
human topoisomerase I-DNA covalent complex."
J.Med.Chem., 48, 2336-2345.
doi: 10.1021/jm049146p.
|
Human DNA topoisomerase i (70 kda) in complex with the
indolocarbazole sa315f and covalent complex with a 22
base pair DNA duplex . SNAP output
|
|
1sfo
|
transcription-DNA-RNA hybrid |
X-ray (3.61 Å) |
Westover KD, Bushnell DA, Kornberg RD |
(2004) "Structural
Basis of Transcription: Separation of RNA from DNA by
RNA Polymerase II." Science,
303, 1014-1016. doi: 10.1126/science.1090839.
|
RNA polymerase ii strand separated elongation complex .
SNAP output
|
|
1sfu
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Ha SC, Lokanath NK, Van Quyen D, Wu CA, Lowenhaupt K,
Rich A, Kim YG, Kim KK |
(2004) "A
poxvirus protein forms a complex with left-handed
Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound
to DNA." Proc.Natl.Acad.Sci.USA,
101, 14367-14372. doi: 10.1073/pnas.0405586101.
|
Crystal structure of the viral zalpha domain bound to
left-handed z-DNA . SNAP
output
|
|
1si2
|
gene regulation-RNA-DNA |
X-ray (2.6 Å) |
Ma JB, Ye K, Patel DJ |
(2004) "Structural
basis for overhang-specific small interfering RNA
recognition by the PAZ domain." Nature,
429, 318-322. doi: 10.1038/nature02519.
|
Crystal structure of the paz domain of human eif2c1 in
complex with a 9-mer sirna-like duplex of
deoxynucleotide overhang . SNAP output
|
|
1skm
|
transferase-DNA |
X-ray (2.2 Å) |
Horton JR, Ratner G, Banavali NK, Huang N, Choi Y,
Maier MA, Marquez VE, MacKerell AD, Cheng X |
(2004) "Caught
in the act: visualization of an intermediate in the DNA
base-flipping pathway induced by HhaI
methyltransferase." Nucleic Acids Res.,
32, 3877-3886. doi: 10.1093/nar/gkh701.
|
Hhai methyltransferase in complex with DNA containing
an abasic south carbocyclic sugar at its target site .
SNAP output
|
|
1skn
|
transcription-DNA |
X-ray (2.5 Å) |
Rupert PB, Daughdrill GW, Bowerman B, Matthews
BW |
(1998) "A new
DNA-binding motif in the Skn-1 binding domain-DNA
complex." Nat.Struct.Biol.,
5, 484-491. doi: 10.1038/nsb0698-484.
|
The binding domain of skn-1 in complex with DNA: a new
DNA-binding motif . SNAP
output
|
|
1skr
|
transferase-electron transport-DNA |
X-ray (2.4 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
T7 DNA polymerase complexed to DNA primer-template and
ddatp . SNAP output
|
|
1sks
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Binary 3' complex of t7 DNA polymerase with a DNA
primer-template containing a cis-syn thymine dimer on
the template . SNAP
output
|
|
1skw
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Binary 3' complex of t7 DNA polymerase with a DNA
primer-template containing a disordered cis-syn thymine
dimer on the template . SNAP output
|
|
1sl0
|
transferase-electron transport-DNA |
X-ray (3.2 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Ternary 3' complex of t7 DNA polymerase with a DNA
primer-template containing a disordered cis-syn thymine
dimer on the template and an incoming nucleotide .
SNAP output
|
|
1sl1
|
transferase-electron transport-DNA |
X-ray (2.2 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Binary 5' complex of t7 DNA polymerase with a DNA
primer-template containing a cis-syn thymine dimer on
the template . SNAP
output
|
|
1sl2
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS,
Ellenberger T |
(2004) "Nucleotide
insertion opposite a cis-syn thymine dimer by a
replicative DNA polymerase from bacteriophage T7."
Nat.Struct.Mol.Biol., 11,
784-790. doi: 10.1038/nsmb792.
|
Ternary 5' complex of t7 DNA polymerase with a DNA
primer-template containing a cis-syn thymine dimer on
the template and an incoming nucleotide . SNAP output
|
|
1srs
|
transcription-DNA |
X-ray (3.2 Å) |
Pellegrini L, Tan S, Richmond TJ |
(1995) "Structure
of serum response factor core bound to DNA."
Nature, 376, 490-498. doi:
10.1038/376490a0.
|
Serum response factor (srf) core complexed with
specific sre DNA . SNAP
output
|
|
1ssp
|
hydrolase-DNA |
X-ray (1.9 Å) |
Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE,
Tainer JA |
(1998) "Base
excision repair initiation revealed by crystal
structures and binding kinetics of human uracil-DNA
glycosylase with DNA." EMBO J.,
17, 5214-5226. doi: 10.1093/emboj/17.17.5214.
|
Wild-type uracil-DNA glycosylase bound to
uracil-containing DNA . SNAP output
|
|
1stx
|
hydrolase-DNA |
X-ray (2.1 Å) |
Horton NC, Perona JJ |
(2004) "DNA
cleavage by EcoRV endonuclease: two metal ions in three
metal ion binding sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
Structure of the k38a mutant of ecorv bound to cognate
DNA and mn2+ . SNAP
output
|
|
1suz
|
hydrolase-DNA |
X-ray (1.8 Å) |
Horton NC, Perona JJ |
(2004) "DNA
Cleavage by EcoRV Endonuclease: Two Metal Ions in Three
Metal Ion Binding Sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
The structure of k92a ecorv bound to cognate DNA and
mg2+ . SNAP output
|
|
1svc
|
transcription-DNA |
X-ray (2.6 Å) |
Muller CW, Rey FA, Sodeoka M, Verdine GL, Harrison
SC |
(1995) "Structure
of the NF-kappa B p50 homodimer bound to DNA."
Nature, 373, 311-317. doi:
10.1038/373311a0.
|
Nfkb p50 homodimer bound to DNA . SNAP output
|
|
1sx5
|
hydrolase-DNA |
X-ray (1.5 Å) |
Horton NC, Perona JJ |
(2004) "DNA
cleavage by EcoRV endonuclease: Two metal ions in three
metal ion binding sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
K38a ecorv bound to cleaved DNA and mn2+: p1 crystal
form . SNAP output
|
|
1sx8
|
hydrolase-DNA |
X-ray (2.15 Å) |
Horton NC, Perona JJ |
(2004) "DNA
Cleavage by EcoRV Endonuclease: Two Metal Ions in Three
Metal Ion Binding Sites." Biochemistry,
43, 6841-6857. doi: 10.1021/bi0499056.
|
Ecorv bound to cognate DNA and mn2+ . SNAP output
|
|
1sxp
|
transferase-DNA |
X-ray (2.5 Å) |
Lariviere L, Morera S |
(2004) "Structural
evidence of a passive base flipping mechanism for
{beta}-Glucosyltransferase." J.Biol.Chem.,
279, 34715-34720. doi: 10.1074/jbc.M404394200.
|
Bgt in complex with a 13mer DNA containing a central
a:g mismatch . SNAP
output
|
|
1sxq
|
transferase-DNA |
X-ray (1.8 Å) |
Lariviere L, Morera S |
(2004) "Structural
evidence of a passive base flipping mechanism for
{beta}-Glucosyltransferase." J.Biol.Chem.,
279, 34715-34720. doi: 10.1074/jbc.M404394200.
|
Bgt in complex with a 13mer DNA containing a central
c:g base pair and udp . SNAP output
|
|
1t03
|
transferase-antibody-DNA |
X-ray (3.1 Å) |
Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger
LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P,
Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH,
Arnold E |
(2004) "Structure
of HIV-1 RT-DNA complexes before and after
incorporation of the anti-AIDS drug tenofovir."
Nat.Struct.Mol.Biol., 11,
469-474. doi: 10.1038/nsmb760.
|
Hiv-1 reverse transcriptase crosslinked to tenofovir
terminated template-primer (complex p) . SNAP output
|
|
1t05
|
transferase-DNA |
X-ray (3.0 Å) |
Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger
LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P,
Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH,
Arnold E |
(2004) "Structures
of HIV-1 RT-DNA complexes before and after
incorporation of the anti-AIDS drug tenofovir."
Nat.Struct.Mol.Biol., 11,
469-474. doi: 10.1038/nsmb760.
|
Hiv-1 reverse transcriptase crosslinked to
template-primer with tenofovir-diphosphate bound as the
incoming nucleotide substrate . SNAP output
|
|
1t2k
|
transcription-DNA |
X-ray (3.0 Å) |
Panne D, Maniatis T, Harrison SC |
(2004) "Crystal
structure of ATF-2/c-Jun and IRF-3 bound to the
interferon-beta enhancer." Embo J.,
23, 4384-4393. doi: 10.1038/sj.emboj.7600453.
|
Structure of the DNA binding domains of irf3, atf-2 and
jun bound to DNA . SNAP
output
|
|
1t2s
|
nucleic acid binding protein-DNA |
NMR |
Lingel A, Simon B, Izaurralde E, Sattler M |
(2004) "Nucleic
acid 3'-end recognition by the Argonaute2 PAZ
domain." Nat.Struct.Mol.Biol.,
11, 576-577. doi: 10.1038/nsmb777.
|
Structural basis for 3' end recognition of nucleic
acids by the drosophila argonaute 2 paz domain .
SNAP output
|
|
1t2t
|
hydrolase-DNA |
X-ray (2.5 Å) |
Edgell DR, Derbyshire V, Van Roey P, LaBonne S,
Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M |
(2004) "Intron-encoded
homing endonuclease I-TevI also functions as a
transcriptional autorepressor."
Nat.Struct.Mol.Biol., 11,
936-944. doi: 10.1038/nsmb823.
|
Crystal structure of the DNA-binding domain of intron
endonuclease i-tevi with operator site . SNAP output
|
|
1t38
|
transferase-DNA |
X-ray (3.2 Å) |
Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg
AE, Tainer JA |
(2004) "DNA
binding and nucleotide flipping by the human DNA repair
protein AGT." Nat.Struct.Mol.Biol.,
11, 714-720. doi: 10.1038/nsmb791.
|
Human o6-alkylguanine-DNA alkyltransferase bound to DNA
containing o6-methylguanine . SNAP output
|
|
1t39
|
transferase-DNA |
X-ray (3.3 Å) |
Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg
AE, Tainer JA |
(2004) "DNA
binding and nucleotide flipping by the human DNA repair
protein AGT." Nat.Struct.Mol.Biol.,
11, 714-720. doi: 10.1038/nsmb791.
|
Human o6-alkylguanine-DNA alkyltransferase covalently
crosslinked to DNA . SNAP output
|
|
1t3n
|
replication-DNA |
X-ray (2.3 Å) |
Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal
AK |
(2004) "Replication
by human DNA polymerase-iota occurs by Hoogsteen
base-pairing." Nature,
430, 377-380. doi: 10.1038/nature02692.
|
Structure of the catalytic core of DNA polymerase iota
in complex with DNA and dttp . SNAP output
|
|
1t7p
|
transferase-DNA |
X-ray (2.2 Å) |
Doublie S, Tabor S, Long AM, Richardson CC,
Ellenberger T |
(1998) "Crystal
structure of a bacteriophage T7 DNA replication complex
at 2.2 A resolution." Nature,
391, 251-258. doi: 10.1038/34593.
|
T7 DNA polymerase complexed to DNA primer-template,a
nucleoside triphosphate, and its processivity factor
thioredoxin . SNAP
output
|
|
1t8e
|
transferase-electron transport-DNA |
X-ray (2.54 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with dctp at the
insertion site. . SNAP
output
|
|
1t8i
|
isomerase-DNA |
X-ray (3.0 Å) |
Staker BL, Feese MD, Cushman M, Pommier Y, Zembower
D, Stewart L, Burgin AB |
(2005) "Structures
of three classes of anticancer agents bound to the
human topoisomerase I-DNA covalent complex."
J.Med.Chem., 48, 2336-2345.
doi: 10.1021/jm049146p.
|
Human DNA topoisomerase i (70 kda) in complex with the
poison camptothecin and covalent complex with a 22 base
pair DNA duplex . SNAP
output
|
|
1t9i
|
hydrolase-DNA |
X-ray (1.6 Å) |
Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M,
Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL |
(2004) "Metal-Dependent
DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing
Endonuclease." Biochemistry,
43, 14015-14026. doi: 10.1021/bi048970c.
|
I-crei(d20n)-DNA complex . SNAP output
|
|
1t9j
|
hydrolase-DNA |
X-ray (2.0 Å) |
Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M,
Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL |
(2004) "Metal-Dependent
DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing
Endonuclease." Biochemistry,
43, 14015-14026. doi: 10.1021/bi048970c.
|
I-crei(q47e)-DNA complex . SNAP output
|
|
1tau
|
transferase-DNA |
X-ray (3.0 Å) |
Eom SH, Wang J, Steitz TA |
(1996) "Structure
of Taq ploymerase with DNA at the polymerase active
site." Nature, 382,
278-281. doi: 10.1038/382278a0.
|
Taq polymerase (e.c.2.7.7.7)-DNA-b-octylglucoside
complex . SNAP
output
|
|
1tc3
|
DNA binding protein-DNA |
X-ray (2.45 Å) |
van Pouderoyen G, Ketting RF, Perrakis A, Plasterk
RH, Sixma TK |
(1997) "Crystal
structure of the specific DNA-binding domain of Tc3
transposase of C.elegans in complex with transposon
DNA." EMBO J., 16,
6044-6054. doi: 10.1093/emboj/16.19.6044.
|
Transposase tc3a1-65 from caenorhabditis elegans .
SNAP output
|
|
1tdz
|
hydrolase-DNA |
X-ray (1.8 Å) |
Coste F, Ober M, Carell T, Boiteux S, Zelwer C,
Castaing B |
(2004) "Structural
basis for the recognition of the FapydG lesion
(2,6-diamino-4-hydroxy-5-formamidopyrimidine) by
formamidopyrimidine-DNA glycosylase."
J.Biol.Chem., 279,
44074-44083. doi: 10.1074/jbc.M405928200.
|
Crystal structure complex between the lactococcus
lactis fpg (mutm) and a fapy-dg containing DNA .
SNAP output
|
|
1tez
|
lyase-DNA |
X-ray (1.8 Å) |
Mees A, Klar T, Gnau P, Hennecke U, Eker APM, Carell
T, Essen L-O |
(2004) "Crystal
structure of a photolyase bound to a CPD-like DNA
lesion after in situ repair." Science,
306, 1789-1793. doi: 10.1126/science.1101598.
|
Complex between DNA and the DNA photolyase from
anacystis nidulans . SNAP output
|
|
1tf3
|
transcription-DNA |
NMR |
Foster MP, Wuttke DS, Radhakrishnan I, Case DA,
Gottesfeld JM, Wright PE |
(1997) "Domain
packing and dynamics in the DNA complex of the
N-terminal zinc fingers of TFIIIA."
Nat.Struct.Biol., 4, 605-608.
doi: 10.1038/nsb0897-605.
|
Tfiiia finger 1-3 bound to DNA, NMR, 22 structures .
SNAP output
|
|
1tf6
|
transcription-DNA |
X-ray (3.1 Å) |
Nolte RT, Conlin RM, Harrison SC, Brown RS |
(1998) "Differing
roles for zinc fingers in DNA recognition: structure of
a six-finger transcription factor IIIA complex."
Proc.Natl.Acad.Sci.USA, 95,
2938-2943. doi: 10.1073/pnas.95.6.2938.
|
Co-crystal structure of xenopus tfiiia zinc finger
domain bound to the 5s ribosomal RNA gene internal
control region . SNAP
output
|
|
1tgh
|
transcription-DNA |
X-ray (2.9 Å) |
Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ,
Dickerson RE |
(1996) "How
proteins recognize the TATA box."
J.Mol.Biol., 261, 239-254.
doi: 10.1006/jmbi.1996.0456.
|
Tata binding protein (tbp)-DNA complex . SNAP output
|
|
1tk0
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with 8 oxo guanosine
and ddctp at the insertion site . SNAP output
|
|
1tk5
|
transferase-electron transport-DNA |
X-ray (2.2 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase binary complex with 8 oxo guanosine
in the templating strand . SNAP output
|
|
1tk8
|
transferase-electron transport-DNA |
X-ray (2.5 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with 8 oxo guanosine
and damp at the elongation site . SNAP output
|
|
1tkd
|
transferase-electron transport-DNA |
X-ray (2.49 Å) |
Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel
TA, Ellenberger T |
(2004) "Structural
basis for the dual coding potential of 8-oxoguanosine
by a high-fidelity DNA polymerase." Embo
J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354.
|
T7 DNA polymerase ternary complex with 8 oxo guanosine
and dcmp at the elongation site . SNAP output
|
|
1tl8
|
isomerase-DNA |
X-ray (3.1 Å) |
Ioanoviciu A, Antony S, Pommier Y, Staker BL, Stewart
L, Cushman M |
(2005) "Synthesis
and Mechanism of Action Studies of a Series of
Norindenoisoquinoline Topoisomerase I Poisons Reveal an
Inhibitor with a Flipped Orientation in the Ternary
DNA-Enzyme-Inhibitor Complex As Determined by X-ray
Crystallographic Analysis." J.Med.Chem.,
48, 4803-4814. doi: 10.1021/jm050076b.
|
Human DNA topoisomerase i (70 kda) in complex with the
indenoisoquinoline ai-iii-52 and covalent complex with
a 22 base pair DNA duplex . SNAP output
|
|
1tn9
|
integrase-DNA |
NMR |
Wojciak JM, Connolly KM, Clubb RT |
(1999) "NMR
structure of the Tn916 integrase-DNA complex."
Nat.Struct.Biol., 6, 366-373.
doi: 10.1038/7603.
|
The solution structure of tn916 integrase n-terminal
domain-DNA complex . SNAP output
|
|
1tqe
|
transcription-protein binding-DNA |
X-ray (2.7 Å) |
Han A, He J, Wu Y, Liu JO, Chen L |
(2005) "Mechanism
of Recruitment of Class II Histone Deacetylases by
Myocyte Enhancer Factor-2." J.Mol.Biol.,
345, 91-102. doi: 10.1016/j.jmb.2004.10.033.
|
Mechanism of recruitment of class ii histone
deacetylases by myocyte enhancer factor-2 . SNAP output
|
|
1tro
|
transcription-DNA |
X-ray (1.9 Å) |
Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL,
Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB |
(1988) "Crystal
structure of trp repressor/operator complex at atomic
resolution." Nature, 335,
321-329. doi: 10.1038/335321a0.
|
Crystal structure of trp repressor operator complex at
atomic resolution . SNAP
output
|
|
1trr
|
transcription-DNA |
X-ray (2.4 Å) |
Lawson CL, Carey J |
(1993) "Tandem
binding in crystals of a trp repressor/operator
half-site complex." Nature,
366, 178-182. doi: 10.1038/366178a0.
|
Tandem binding in crystals of a trp repressor-operator
half-site complex . SNAP
output
|
|
1tsr
|
antitumor protein-DNA |
X-ray (2.2 Å) |
Cho Y, Gorina S, Jeffrey PD, Pavletich NP |
(1994) "Crystal
structure of a p53 tumor suppressor-DNA complex:
understanding tumorigenic mutations."
Science, 265, 346-355.
|
P53 core domain in complex with DNA . SNAP output
|
|
1ttu
|
transcription |
X-ray (2.85 Å) |
Kovall RA, Hendrickson WA |
(2004) "Crystal
structure of the nuclear effector of Notch signaling,
CSL, bound to DNA." Embo J.,
23, 3441-3451. doi: 10.1038/sj.emboj.7600349.
|
Crystal structure of csl bound to DNA . SNAP output
|
|
1tup
|
antitumor protein-DNA |
X-ray (2.2 Å) |
Cho Y, Gorina S, Jeffrey PD, Pavletich NP |
(1994) "Crystal
structure of a p53 tumor suppressor-DNA complex:
understanding tumorigenic mutations."
Science, 265, 346-355.
|
Tumor suppressor p53 complexed with DNA . SNAP output
|
|
1tv9
|
transferase-DNA |
X-ray (2.0 Å) |
Krahn JM, Beard WM, Wilson SH |
(2004) "STRUCTURAL
INSIGHTS INTO DNA POLYMERASE BETA DETERRENTS FOR
MISINCORPORATION SUPPORT OF AN INDUCED-FIT MECHANISM
FOR FIDELITY." Structure,
12, 1823-1832. doi: 10.1016/j.str.2004.08.001.
|
Human DNA polymerase beta complexed with nicked DNA
containing a mismatched template adenine and incoming
cytidine . SNAP
output
|
|
1tva
|
transferase-DNA |
X-ray (2.6 Å) |
Krahn JM, Beard WA, Wilson SH |
(2004) "Structural
insights into DNA polymerase Beta deterrents for
misincorporation support an induced-fit mechanism for
fidelity." Structure, 12,
1823-1832. doi: 10.1016/j.str.2004.08.001.
|
Human DNA polymerase beta complexed with nicked DNA
containing a mismatched template thymidine and incoming
cytidine . SNAP
output
|
|
1tw8
|
hydrolase-DNA |
X-ray (2.8 Å) |
Etzkorn C, Horton NC |
(2004) "Ca2+
binding in the active site of HincII: implications for
the catalytic mechanism." Biochemistry,
43, 13256-13270.
|
Hincii bound to ca2+ and cognate DNA gtcgac . SNAP output
|
|
1tx3
|
hydrolase-DNA |
X-ray (2.5 Å) |
Etzkorn C, Horton NC |
(2004) "Ca2+
binding in the active site of HincII: implications for
the catalytic mechanism." Biochemistry,
43, 13256-13270. doi: 10.1021/bi0490082.
|
Hincii bound to cognate DNA . SNAP output
|
|
1u0c
|
hydrolase-DNA |
X-ray (2.5 Å) |
Sussman D, Chadsey M, Fauce S, Engel A, Bruett A,
Monnat R, Stoddard BL, Seligman LM |
(2004) "Isolation
and characterization of new homing endonuclease
specificities at individual target site positions."
J.Mol.Biol., 342, 31-41. doi:
10.1016/j.jmb.2004.07.031.
|
Y33c mutant of homing endonuclease i-crei . SNAP output
|
|
1u0d
|
hydrolase-DNA |
X-ray (2.9 Å) |
Sussman D, Chadsey M, Fauce S, Engel A, Bruett A,
Monnat R, Stoddard BL, Seligman LM |
(2004) "Isolation
and characterization of new homing endonuclease
specificities at individual target site positions."
J.Mol.Biol., 342, 31-41. doi:
10.1016/j.jmb.2004.07.031.
|
Y33h mutant of homing endonuclease i-crei . SNAP output
|
|
1u1k
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtt 7da
ggg); a human telomeric repeat containing
7-deaza-adenine . SNAP
output
|
|
1u1l
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtt prn
ggg); a human telomeric repeat containing nebularine .
SNAP output
|
|
1u1m
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtta 7gu
gg); a human telomeric repeat containing
7-deaza-guanine . SNAP
output
|
|
1u1n
|
transport protein-DNA |
X-ray (2.1 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtta
(prn)gg); a human telomeric repeat containing
nebularine . SNAP
output
|
|
1u1o
|
transport protein-DNA |
X-ray (2.0 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with
d(ttagggttag(di)g); a human telomeric repeat containing
inosine . SNAP
output
|
|
1u1p
|
transport protein-DNA |
X-ray (1.9 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with d(ttagggtta 2pr
gg); a human telomeric repeat containing 2-aminopurine
. SNAP output
|
|
1u1q
|
transport protein-DNA |
X-ray (1.8 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with
d(ttagggtta(di)gg); a human telomeric repeat containing
inosine . SNAP
output
|
|
1u1r
|
transport protein-DNA |
X-ray (1.8 Å) |
Myers JC, Shamoo Y |
(2004) "Human
UP1 as a Model for Understanding Purine Recognition in
the Family of Proteins Containing the RNA Recognition
Motif (RRM)." J.Mol.Biol.,
342, 743-756. doi: 10.1016/j.jmb.2004.07.029.
|
Crystal structure of up1 complexed with
d(ttagggttag(2pr)g); a human telomeric repeat
containing 2-aminopurine . SNAP output
|
|
1u1y
|
virus-RNA |
X-ray (2.85 Å) |
Horn WT, Convery MA, Stonehouse NJ, Adams CJ, Liljas
L, Phillips SE, Stockley PG |
(2004) "The
crystal structure of a high affinity RNA stem-loop
complexed with the bacteriophage MS2 capsid: further
challenges in the modeling of ligand-RNA
interactions." Rna, 10,
1776-1782. doi: 10.1261/rna.7710304.
|
Crystal structure of a complex between wt bacteriophage
ms2 coat protein and an f5 aptamer RNA stemloop with
2aminopurine substituted at the-10 position . SNAP output
|
|
1u35
|
structural protein-DNA |
X-ray (3.0 Å) |
Chakravarthy S, Gundimella SK, Caron C, Perche PY,
Pehrson JR, Khochbin S, Luger K |
(2005) "Structural
characterization of the histone variant macroH2A."
Mol.Cell.Biol., 25,
7616-7624. doi: 10.1128/MCB.25.17.7616-7624.2005.
|
Crystal structure of the nucleosome core particle
containing the histone domain of macroh2a . SNAP output
|
|
1u3e
|
DNA binding protein-DNA |
X-ray (2.92 Å) |
Shen BW, Landthaler M, Shub DA, Stoddard BL |
(2004) "DNA
Binding and Cleavage by the HNH Homing Endonuclease
I-HmuI." J.Mol.Biol.,
342, 43-56. doi: 10.1016/j.jmb.2004.07.032.
|
DNA binding and cleavage by the hnh homing endonuclease
i-hmui . SNAP output
|
|
1u45
|
transferase-DNA |
X-ray (2.01 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
8oxoguanine at the pre-insertion site of the polymerase
active site . SNAP
output
|
|
1u47
|
transferase-DNA |
X-ray (2.0 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Cytosine-8-oxoguanine base pair at the polymerase
active site . SNAP
output
|
|
1u48
|
transferase-DNA |
X-ray (2.1 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Extension of a cytosine-8-oxoguanine base pair .
SNAP output
|
|
1u49
|
transferase-DNA |
X-ray (2.15 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Adenine-8oxoguanine mismatch at the polymerase active
site . SNAP output
|
|
1u4b
|
transferase-DNA |
X-ray (1.6 Å) |
Hsu GW, Ober M, Carell T, Beese LS |
(2004) "Error-prone
replication of oxidatively damaged DNA by a
high-fidelity DNA polymerase." Nature,
431, 217-221. doi: 10.1038/nature02908.
|
Extension of an adenine-8oxoguanine mismatch . SNAP output
|
|
1u78
|
DNA binding protein-DNA |
X-ray (2.69 Å) |
Watkins S, van Pouderoyen G, Sixma TK |
(2004) "Structural
analysis of the bipartite DNA-binding domain of Tc3
transposase bound to transposon DNA." Nucleic
Acids Res., 32, 4306-4312. doi:
10.1093/nar/gkh770.
|
Structure of the bipartite DNA-binding domain of tc3
transposase bound to transposon DNA . SNAP output
|
|
1u8b
|
metal binding protein-DNA |
X-ray (2.1 Å) |
He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dotsch V,
Wei H, Gross JD, Lane WS, Wagner G, Verdine GL |
(2005) "A
methylation-dependent electrostatic switch controls DNA
repair and transcriptional activation by E. coli
ada." Mol.Cell, 20,
117-129. doi: 10.1016/j.molcel.2005.08.013.
|
Crystal structure of the methylated n-ada-DNA complex .
SNAP output
|
|
1u8r
|
metal-binding protein,transcription-DNA |
X-ray (2.75 Å) |
Wisedchaisri G, Holmes RK, Hol WGJ |
(2004) "Crystal
Structure of an IdeR-DNA Complex Reveals a
Conformational Change in Activated IdeR for
Base-specific Interactions." J.Mol.Biol.,
342, 1155-1169. doi: 10.1016/j.jmb.2004.07.083.
|
Crystal structure of an ider-DNA complex reveals a
conformational change in activated ider for
base-specific interactions . SNAP output
|
|
1ua0
|
transferase-DNA |
X-ray (2.1 Å) |
Hsu GW, Kiefer JR, Burnouf D, Becherel OJ, Fuchs RPP,
Beese LS |
(2004) "Observing
translesion synthesis of an aromatic amine DNA adduct
by a high-fidelity DNA polymerase."
J.Biol.Chem., 279,
50280-50285. doi: 10.1074/jbc.M409224200.
|
Aminofluorene DNA adduct at the pre-insertion site of a
DNA polymerase . SNAP
output
|
|
1ua1
|
transferase-DNA |
X-ray (2.0 Å) |
Hsu GW, Kiefer JR, Becherel OJ, Fuchs RPP, Beese
LS |
(2004) "Observing
translesion synthesis of an aromatic amine DNA adduct
by a high-fidelity DNA polymerase."
J.Biol.Chem., 279,
50280-50285. doi: 10.1074/jbc.M409224200.
|
Structure of aminofluorene adduct paired opposite
cytosine at the polymerase active site. . SNAP output
|
|
1uaa
|
hydrolase-DNA |
X-ray (3.0 Å) |
Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman
G |
(1997) "Major
domain swiveling revealed by the crystal structures of
complexes of E. coli Rep helicase bound to
single-stranded DNA and ADP."
Cell(Cambridge,Mass.), 90,
635-647. doi: 10.1016/S0092-8674(00)80525-5.
|
E. coli rep helicase-DNA complex . SNAP output
|
|
1ubd
|
transcription-DNA |
X-ray (2.5 Å) |
Houbaviy HB, Usheva A, Shenk T, Burley SK |
(1996) "Cocrystal
structure of YY1 bound to the adeno-associated virus P5
initiator." Proc.Natl.Acad.Sci.USA,
93, 13577-13582. doi: 10.1073/pnas.93.24.13577.
|
Co-crystal structure of human yy1 zinc finger domain
bound to the adeno-associated virus p5 initiator
element . SNAP
output
|
|
1unj
|
DNA-antibiotic |
X-ray (2.5 Å) |
Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement
R, Machinek R, Sheldrick GM, Uson I |
(2005) "Crystal
and Solution Structures of 7-Amino-Actinomycin D
Complexes with D(Ttagbrut), D(Ttagtt) and
D(Tttagttt)." Acta Crystallogr.,Sect.D,
61, 407. doi: 10.1107/S090744490500082X.
|
Crystal structure of a 7-aminoactinomycin d complex
with non-complementary DNA . SNAP output
|
|
1unm
|
DNA-antibiotic |
X-ray (2.0 Å) |
Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement
R, Machinek R, Sheldrick GM, Uson I |
(2005) "Crystal
and Solution Structures of 7-Amino-Actinomycin D
Complexes with D(Ttagbrut), D(Ttagtt) and
D(Tttagttt)." Acta Crystallogr.,Sect.D,
61, 407. doi: 10.1107/S090744490500082X.
|
Crystal structure of 7-aminoactinomycin d with
non-complementary DNA . SNAP output
|
|
1urn
|
transcription-RNA |
X-ray (1.92 Å) |
Oubridge C, Ito N, Evans PR, Teo CH, Nagai K |
(1994) "Crystal
structure at 1.92 A resolution of the RNA-binding
domain of the U1A spliceosomal protein complexed with
an RNA hairpin." Nature,
372, 432-438. doi: 10.1038/372432a0.
|
U1a mutant-RNA complex + glycerol . SNAP output
|
|
1uut
|
hydrolase-DNA |
X-ray (2.0 Å) |
Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda
F |
(2004) "The
Nuclease Domain of Adeno-Associated Virus Rep
Coordinates Replication Initiation Using Two Distinct
DNA Recognition Interfaces." Mol.Cell,
13, 403. doi: 10.1016/S1097-2765(04)00023-1.
|
The nuclease domain of adeno-associated virus rep
complexed with the rbe' stemloop of the viral inverted
terminal repeat . SNAP
output
|
|
1v14
|
hydrolase |
X-ray (2.9 Å) |
Mate MJ, Kleanthous C |
(2004) "Structure-Based
Analysis of the Metal-Dependent Mechanism of H-N-H
Endonucleases." J.Biol.Chem.,
279, 34763. doi: 10.1074/JBC.M403719200.
|
Crystal structure of the colicin e9, mutant his103ala,
in complex with mg+2 and dsDNA (resolution 2.9a) .
SNAP output
|
|
1v15
|
hydrolase |
X-ray (2.4 Å) |
Mate MJ, Kleanthous C |
(2004) "Structure-Based
Analysis of the Metal-Dependent Mechanism of H-N-H
Endonucleases." J.Biol.Chem.,
279, 34763. doi: 10.1074/JBC.M403719200.
|
Crystal structure of the colicin e9, mutant his103ala,
in complex with zn+2 and dsDNA (resolution 2.4a) .
SNAP output
|
|
1vas
|
hydrolase-DNA |
X-ray (2.75 Å) |
Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai
S, Ohtsuka E, Morikawa K |
(1995) "Atomic
model of a pyrimidine dimer excision repair enzyme
complexed with a DNA substrate: structural basis for
damaged DNA recognition."
Cell(Cambridge,Mass.), 83,
773-782. doi: 10.1016/0092-8674(95)90190-6.
|
Atomic model of a pyrimidine dimer specific excision
repair enzyme complexed with a DNA substrate:
structural basis for damaged DNA recognition . SNAP output
|
|
1vfc
|
structural protein-DNA |
NMR |
Hanaoka S, Nagadoi A, Nishimura Y |
(2005) "Comparison
between TRF2 and TRF1 of their telomeric DNA-bound
structures and DNA-binding activities." Protein
Sci., 14, 119-130. doi: 10.1110/ps.04983705.
|
Solution structure of the DNA complex of human trf2 .
SNAP output
|
|
1vkx
|
transcription-DNA |
X-ray (2.9 Å) |
Chen FE, Huang DB, Chen YQ, Ghosh G |
(1998) "Crystal
structure of p50/p65 heterodimer of transcription
factor NF-kappaB bound to DNA." Nature,
391, 410-413. doi: 10.1038/34956.
|
Crystal structure of the nfkb p50-p65 heterodimer
complexed to the immunoglobulin kb DNA . SNAP output
|
|
1vol
|
transcription-DNA |
X-ray (2.7 Å) |
Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake K,
Lee DK, Roeder RG, Burley SK |
(1995) "Crystal
structure of a TFIIB-TBP-TATA-element ternary
complex." Nature, 377,
119-128. doi: 10.1038/377119a0.
|
Tfiib (human core domain)-tbp (a.thaliana)-tata element
ternary complex . SNAP
output
|
|
1vpw
|
transcription-DNA |
X-ray (2.7 Å) |
Arvidson DN, Lu F, Faber C, Zalkin H, Brennan RG |
(1998) "The
structure of PurR mutant L54M shows an alternative
route to DNA kinking." Nat.Struct.Biol.,
5, 436-441. doi: 10.1038/nsb0698-436.
|
Structure of the purr mutant, l54m, bound to
hypoxanthine and purf operator DNA . SNAP output
|
|
1vq5
|
ribosome |
X-ray (2.6 Å) |
Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz
TA |
(2005) "Structural
Insights into the Roles of Water and the 2' Hydroxyl of
the P Site tRNA in the Peptidyl Transferase
Reaction." Mol.Cell, 20,
437-448. doi: 10.1016/j.molcel.2005.09.006.
|
The structure of the transition state analogue "raa"
bound to the large ribosomal subunit of haloarcula
marismortui . SNAP
output
|
|
1vqp
|
ribosome |
X-ray (2.25 Å) |
Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz
TA |
(2005) "Structural
Insights into the Roles of Water and the 2' Hydroxyl of
the P Site tRNA in the Peptidyl Transferase
Reaction." Mol.Cell, 20,
437-448. doi: 10.1016/j.molcel.2005.09.006.
|
The structure of the transition state analogue "rap"
bound to the large ribosomal subunit of haloarcula
marismortui . SNAP
output
|
|
1vrl
|
hydrolase-DNA |
X-ray (2.5 Å) |
Fromme JC, Banerjee A, Huang SJ, Verdine GL |
(2004) "Structural
basis for removal of adenine mispaired with
8-oxoguanine by MutY adenine DNA glycosylase."
Nature, 427, 652-656. doi:
10.1038/nature02306.
|
Muty adenine glycosylase in complex with DNA and soaked
adenine free base . SNAP
output
|
|
1vrr
|
hydrolase-DNA |
X-ray (2.7 Å) |
Townson SA, Samuelson JC, Xu SY, Aggarwal AK |
(2005) "Implications
for Switching Restriction Enzyme Specificities from the
Structure of BstYI Bound to a BglII DNA Sequence."
Structure, 13, 791-801. doi:
10.1016/j.str.2005.02.018.
|
Crystal structure of the restriction endonuclease bstyi
complex with DNA . SNAP
output
|
|
1vs2
|
DNA-antibiotic |
X-ray (2.0 Å) |
Wang AH, Ughetto G, Quigley GJ, Rich A |
(1986) "Interactions
of Quinoxaline Antibiotic and DNA: The Molecular
Structure of a Triostin A-D(Gcgtacgc) Complex."
J.Biomol.Struct.Dyn., 4, 319.
|
Interactions of quinoxaline antibiotic and DNA: the
molecular structure of a triostin a-d(gcgtacgc) complex
. SNAP output
|
|
1vtg
|
DNA-antibiotic |
X-ray (1.67 Å) |
Wang AH, Ughetto G, Quigley GJ, Hakoshima T, van der
Marel GA, van Boom JH, Rich A |
(1984) "The
molecular structure of a DNA-triostin A complex."
Science, 225, 1115-1121.
|
The molecular structure of a DNA-triostin a complex .
SNAP output
|
|
1vtl
|
transcription-DNA |
X-ray (2.25 Å) |
Kim JL, Nikolov DB, Burley SK |
(1993) "Co-Crystal
Structure of TBP Recognizing the Minor Groove of a TATA
Element." Nature, 365,
520-527. doi: 10.1038/365520a0.
|
Co-crystal structure of tbp recognizing the minor
groove of a tata element . SNAP output
|
|
1vtn
|
transcription-DNA |
X-ray (2.5 Å) |
Clark KL, Halay ED, Lai E, Burley SK |
(1993) "Co-Crystal
Structure of the HNF-3/Fork Head DNA-Recognition Motif
Resembles Histone H5." Nature,
364, 412-420. doi: 10.1038/364412a0.
|
Co-crystal structure of the hnf-3-fork head
DNA-recognition motif resembles histone h5 . SNAP output
|
|
1vto
|
transcription-DNA |
X-ray (1.9 Å) |
Kim JL, Burley SK |
(1994) "1.9 A
Resolution Refined Structure of TBP Recognizing the
Minor Groove of TATAAAAG."
Nat.Struct.Biol., 1, 638-653.
|
1.9 Å resolution refined structure of tbp recognizing
the minor groove of tataaaag . SNAP output
|
|
1w0t
|
DNA binding protein |
X-ray (2.0 Å) |
Court RI, Chapman LM, Fairall L, Rhodes D |
(2005) "How the
Human Telomeric Proteins Trf1 and Trf2 Recognize
Telomeric DNA: A View from High-Resolution Crystal
Structures." Embo Rep.,
6, 39. doi: 10.1038/SJ.EMBOR.7400314.
|
Htrf1 DNA-binding domain in complex with telomeric DNA.
. SNAP output
|
|
1w0u
|
DNA binding protein |
X-ray (1.8 Å) |
Court RI, Chapman LM, Fairall L, Rhodes D |
(2005) "How the
Human Telomeric Proteins Trf1 and Trf2 Recognize
Telomeric DNA: A View from High-Resolution Crystal
Structures." Embo Rep.,
6, 39. doi: 10.1038/SJ.EMBOR.7400314.
|
Htrf2 DNA-binding domain in complex with telomeric DNA.
. SNAP output
|
|
1w36
|
recombination |
X-ray (3.1 Å) |
Singleton MR, Dillingham MS, Gaudier M,
Kowalczykowski SC, Wigley DB |
(2004) "Crystal
Structure of Recbcd Enzyme Reveals a Machine for
Processing DNA Breaks." Nature,
432, 187. doi: 10.1038/NATURE02988.
|
Recbcd:DNA complex . SNAP output
|
|
1w7a
|
DNA binding |
X-ray (2.27 Å) |
Lamers MH, Georgijevic D, Lebbink J, Winterwerp HHK,
Agianian B, De Wind N, Sixma TK |
(2004) "ATP
Increases the Affinity between Muts ATPase Domains:
Implications for ATP Hydrolysis and Conformational
Changes." J.Biol.Chem.,
279, 43879. doi: 10.1074/JBC.M406380200.
|
Atp bound muts . SNAP
output
|
|
1wb9
|
DNA-binding |
X-ray (2.1 Å) |
Lebbink JHG, Georgijevic D, Natrajan G, Fish A,
Winterwerp HHK, Sixma TK, De Wind N |
(2006) "Dual
Role of Muts Glutamate 38 in DNA Mismatch
Discrimination and in the Authorization of Repair."
Embo J., 25, 409. doi:
10.1038/SJ.EMBOJ.7600936.
|
Crystal structure of e. coli DNA mismatch repair enzyme
muts, e38t mutant, in complex with a g.t mismatch .
SNAP output
|
|
1wbb
|
DNA-binding |
X-ray (2.5 Å) |
Lebbink JHG, Georgijevic D, Natrajan G, Fish A,
Winterwerp HHK, Sixma TK, De Wind N |
(2006) "Dual
Role of Muts Glutamate 38 in DNA Mismatch
Discrimination and in the Authorization of Repair."
Embo J., 25, 409. doi:
10.1038/SJ.EMBOJ.7600936.
|
Crystal structure of e. coli DNA mismatch repair enzyme
muts, e38a mutant, in complex with a g.t mismatch .
SNAP output
|
|
1wbd
|
DNA-binding |
X-ray (2.4 Å) |
Lebbink JHG, Georgijevic D, Natrajan G, Fish A,
Winterwerp HHK, Sixma TK, De Wind N |
(2006) "Dual
Role of Muts Glutamate 38 in DNA Mismatch
Discrimination and in the Authorization of Repair."
Embo J., 25, 409. doi:
10.1038/SJ.EMBOJ.7600936.
|
Crystal structure of e. coli DNA mismatch repair enzyme
muts, e38q mutant, in complex with a g.t mismatch .
SNAP output
|
|
1wd0
|
structural protein-DNA |
X-ray (1.9 Å) |
Ko TP, Chu HM, Chen CY, Chou CC, Wang AH |
(2004) "Structures
of the hyperthermophilic chromosomal protein Sac7d in
complex with DNA decamers." Acta
Crystallogr.,Sect.D, 60,
1381-1387. doi: 10.1107/S0907444904012065.
|
Crystal structures of the hyperthermophilic chromosomal
protein sac7d in complex with DNA decamers . SNAP output
|
|
1wd1
|
structural protein-DNA |
X-ray (2.2 Å) |
Ko TP, Chu HM, Chen CY, Chou CC, Wang AH |
(2004) "Structures
of the hyperthermophilic chromosomal protein Sac7d in
complex with DNA decamers." Acta
Crystallogr.,Sect.D, 60,
1381-1387. doi: 10.1107/S0907444904012065.
|
Crystal structures of the hyperthermophilic chromosomal
protein sac7d in complex with DNA decamers . SNAP output
|
|
1wet
|
transcription-DNA |
X-ray (2.6 Å) |
Schumacher MA, Glasfeld A, Zalkin H, Brennan RG |
(1997) "The X-ray
structure of the PurR-guanine-purF operator complex
reveals the contributions of complementary
electrostatic surfaces and a water-mediated hydrogen
bond to corepressor specificity and binding
affinity." J.Biol.Chem.,
272, 22648-22653. doi: 10.1074/jbc.272.36.22648.
|
Structure of the purr-guanine-purf operator complex .
SNAP output
|
|
1wtb
|
transcription-DNA |
NMR |
Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi
S, Ishikawa F, Katahira M |
(2005) "Structure
of hnRNP D complexed with single-stranded telomere DNA
and unfolding of the quadruplex by heterogeneous
nuclear ribonucleoprotein D."
J.Biol.Chem., 280,
18862-18870. doi: 10.1074/jbc.M411822200.
|
Complex structure of the c-terminal RNA-binding domain
of hnrnp d (auf1) with telomere DNA . SNAP output
|
|
1wte
|
hydrolase-DNA |
X-ray (1.9 Å) |
Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo
N, Kita K, Sato M |
(2005) "Crystal
structures of type II restriction endonuclease EcoO109I
and its complex with cognate DNA."
J.Biol.Chem., 280, 5605-5610.
doi: 10.1074/jbc.M411684200.
|
Crystal structure of type ii restrcition endonuclease,
ecoo109i complexed with cognate DNA . SNAP output
|
|
1wto
|
DNA binding protein-DNA |
X-ray (1.5 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d double
mutant v26f-m29f in complex with DNA gcgatcgc .
SNAP output
|
|
1wtp
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29f in complex with DNA gcga(ubr)cgc . SNAP output
|
|
1wtq
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29f in complex with DNA gtaattac . SNAP output
|
|
1wtr
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29a in complex with DNA gcgatcgc . SNAP output
|
|
1wtv
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant m29a in complex with DNA gtaattac . SNAP output
|
|
1wtw
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant v26a in complex with DNA gcgatcgc . SNAP output
|
|
1wtx
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." NUCLEIC ACIDS
RES., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d single
mutant v26a in complex with DNA gtaattac . SNAP output
|
|
1wvl
|
structural protein-DNA |
X-ray (2.6 Å) |
Wu SW, Ko TP, Chou CC, Wang AH |
(2005) "Design
and characterization of a multimeric DNA binding
protein using Sac7d and GCN4 as templates."
Proteins, 60, 617-628. doi:
10.1002/prot.20524.
|
Crystal structure of multimeric DNA-binding protein
sac7d-gcn4 with DNA decamer . SNAP output
|
|
1x0f
|
transcription-DNA |
NMR |
Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi
S, Ishikawa F, Katahira M |
(2005) "Structure
of hnRNP D complexed with single-stranded telomere DNA
and unfolding of the quadruplex by heterogeneous
nuclear ribonucleoprotein D."
J.Biol.Chem., 280,
18862-18870. doi: 10.1074/jbc.M411822200.
|
Complex structure of the c-terminal RNA-binding domain
of hnrnp d(auf1) with telomeric DNA . SNAP output
|
|
1x9m
|
transferase-electron transport-DNA |
X-ray (2.1 Å) |
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC,
Romano LJ, Ellenberger T |
(2004) "Crystal
structures of 2-acetylaminofluorene and 2-aminofluorene
in complex with T7 DNA polymerase reveal mechanisms of
mutagenesis." Proc.Natl.Acad.Sci.USA,
101, 16186-16191. doi: 10.1073/pnas.0406516101.
|
T7 DNA polymerase in complex with an
n-2-acetylaminofluorene-adducted DNA . SNAP output
|
|
1x9n
|
ligase-DNA |
X-ray (3.0 Å) |
Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger
T |
(2004) "Human
DNA ligase I completely encircles and partially unwinds
nicked DNA." Nature, 432,
473-478. doi: 10.1038/nature03082.
|
Crystal structure of human DNA ligase i bound to
5'-adenylated, nicked DNA . SNAP output
|
|
1x9s
|
transferase-electron transport-DNA |
X-ray (2.7 Å) |
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC,
Romano LJ, Ellenberger T |
(2004) "Crystal
structures of 2-acetylaminofluorene and 2-aminofluorene
in complex with T7 DNA polymerase reveal mechanisms of
mutagenesis." Proc.Natl.Acad.Sci.Usa,
101, 16186-16191. doi: 10.1073/pnas.0406516101.
|
T7 DNA polymerase in complex with a primer-template DNA
containing a disordered n-2 aminofluorene on the
template, crystallized with dideoxy-ctp as the incoming
nucleotide. . SNAP
output
|
|
1x9w
|
transferase-electron transport-DNA |
X-ray (2.3 Å) |
Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC,
Romano LJ, Ellenberger T |
(2004) "Crystal
structures of 2-acetylaminofluorene and 2-aminofluorene
in complex with T7 DNA polymerase reveal mechanisms of
mutagenesis." Proc.Natl.Acad.Sci.Usa,
101, 16186-16191. doi: 10.1073/pnas.0406516101.
|
T7 DNA polymerase in complex with a primer-template DNA
containing a disordered n-2 aminofluorene on the
template, crystallized with dideoxy-atp as the incoming
nucleotide. . SNAP
output
|
|
1xbr
|
transcription-DNA |
X-ray (2.5 Å) |
Muller CW, Herrmann BG |
(1997) "Crystallographic
structure of the T domain-DNA complex of the Brachyury
transcription factor." Nature,
389, 884-888. doi: 10.1038/39929.
|
T domain from xenopus laevis bound to DNA . SNAP output
|
|
1xc8
|
hydrolase-DNA |
X-ray (1.95 Å) |
Coste F, Ober M, Carell T, Boiteux S, Zelwer C,
Castaing B |
(2004) "Structural
basis for the recognition of the FapydG lesion
(2,6-diamino-4-hydroxy-5-formamidopyrimidine) by
formamidopyrimidine-DNA glycosylase."
J.Biol.Chem., 279,
44074-44083. doi: 10.1074/jbc.M405928200.
|
Crystal structure complex between the wild-type
lactococcus lactis fpg (mutm) and a fapy-dg containing
DNA . SNAP output
|
|
1xc9
|
transferase-DNA |
X-ray (1.9 Å) |
Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese
LS |
(2005) "Structure
of a High Fidelity DNA Polymerase Bound to a
Benzo[a]pyrene Adduct That Blocks Replication."
J.Biol.Chem., 280, 3764-3770.
doi: 10.1074/jbc.M411276200.
|
Structure of a high-fidelity polymerase bound to a
benzo[a]pyrene adduct that blocks replication .
SNAP output
|
|
1xf2
|
immune system-DNA |
X-ray (2.3 Å) |
Schuermann JP, Prewitt SP, Davies C, Deutscher SL,
Tanner JJ |
(2005) "Evidence
for Structural Plasticity of Heavy Chain
Complementarity-determining Region 3 in Antibody-ssDNA
Recognition." J.Mol.Biol.,
347, 965-978. doi: 10.1016/j.jmb.2005.02.008.
|
Structure of fab DNA-1 complexed with dt3 . SNAP output
|
|
1xhu
|
hydrolase-DNA |
X-ray (2.95 Å) |
Etzkorn C, Horton NC |
(2004) "Mechanistic
Insights from the Structures of HincII Bound to Cognate
DNA Cleaved from Addition of Mg(2+) and Mn(2+)."
J.Mol.Biol., 343, 833-849.
doi: 10.1016/j.jmb.2004.08.082.
|
Hincii bound to cleaved, cognate DNA containing gtcgac
. SNAP output
|
|
1xhv
|
hydrolase-DNA |
X-ray (2.5 Å) |
Etzkorn C, Horton NC |
(2004) "Mechanistic
Insights from the Structures of HincII Bound to Cognate
DNA Cleaved from Addition of Mg(2+) and Mn(2+)."
J.Mol.Biol., 343, 833-849.
doi: 10.1016/j.jmb.2004.08.082.
|
Hincii bound to cleaved cognate DNA gtcgac and mn2+ .
SNAP output
|
|
1xhz
|
transferase-DNA |
X-ray (2.7 Å) |
Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M,
Blanco L, Salas M, Steitz TA |
(2004) "Insights
into Strand Displacement and Processivity from the
Crystal Structure of the Protein-Primed DNA Polymerase
of Bacteriophage phi29." Mol.Cell,
16, 609-618. doi: 10.1016/j.molcel.2004.10.019.
|
Phi29 DNA polymerase, orthorhombic crystal form, ssDNA
complex . SNAP
output
|
|
1xi1
|
transferase-DNA |
X-ray (2.2 Å) |
Wang J, Kamtekar S, Berman AJ, Steitz TA |
(2005) "Correction
of X-ray intensities from single crystals containing
lattice-translocation defects." Acta
Crystallogr.,Sect.D, 61, 67-74.
doi: 10.1107/S0907444904026721.
|
Phi29 DNA polymerase ssDNA complex, monoclinic crystal
form . SNAP output
|
|
1xjv
|
transcription-DNA |
X-ray (1.73 Å) |
Lei M, Podell ER, Cech TR |
(2004) "Structure
of human POT1 bound to telomeric single-stranded DNA
provides a model for chromosome end-protection."
Nat.Struct.Mol.Biol., 11,
1223-1229. doi: 10.1038/nsmb867.
|
Crystal structure of human pot1 bound to telomeric
single-stranded DNA (ttagggttag) . SNAP output
|
|
1xns
|
hydrolase, ligase-DNA |
X-ray (2.8 Å) |
Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD |
(2005) "Peptide
trapping of the Holliday junction intermediate in
Cre-loxP site-specific recombination."
J.Biol.Chem., 280, 8290-8299.
doi: 10.1074/jbc.M411668200.
|
Peptide trapped holliday junction intermediate in
cre-loxp recombination . SNAP output
|
|
1xo0
|
hydrolase, ligase-DNA |
X-ray (2.0 Å) |
Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD |
(2005) "Peptide
trapping of the Holliday junction intermediate in
Cre-loxP site-specific recombination."
J.Biol.Chem., 280, 8290-8299.
doi: 10.1074/jbc.M411668200.
|
High resolution structure of the holliday junction
intermediate in cre-loxp site-specific recombination .
SNAP output
|
|
1xpx
|
transcription regulation-DNA |
X-ray (2.8 Å) |
Yousef MS, Matthews BW |
(2005) "Structural
Basis of Prospero-DNA Interaction: Implications for
Transcription Regulationin Developing Cells."
STRUCTURE, 13, 601-607. doi:
10.1016/j.str.2005.01.023.
|
Structural basis of prospero-DNA interaction;
implications for transcription regulation in developing
cells . SNAP output
|
|
1xs9
|
transcription-DNA |
NMR |
Dangi B, Gronenborn AM, Rosner JL, Martin RG |
(2004) "Versatility
of the carboxy-terminal domain of the alpha subunit of
RNA polymerase in transcriptional activation: use of
the DNA contact site as a protein contact site for
MarA." Mol.Microbiol.,
54, 45-59. doi: 10.1111/j.1365-2958.2004.04250.x.
|
A model of the ternary complex formed between mara, the
alpha-ctd of RNA polymerase and DNA . SNAP output
|
|
1xsd
|
transcription-DNA |
X-ray (2.7 Å) |
Safo MK, Zhao Q, Ko T-P, Musayev FN, Robinson H,
Scarsdale N, Wang AH-J, Archer GL |
(2005) "Crystal
structures of the BlaI repressor from Staphylococcus
aureus and its complex with DNA: insights into
transcriptional regulation of the bla and mec
operons." J.Bacteriol.,
187, 1833-1844. doi: 10.1128/JB.187.5.1833-1844.2005.
|
Crystal structure of the blai repressor in complex with
DNA . SNAP output
|
|
1xsl
|
transferase-DNA |
X-ray (2.3 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA,
Pedersen LC |
(2005) "A closed
conformation for the Pol lambda catalytic cycle."
Nat.Struct.Mol.Biol., 12,
97-98. doi: 10.1038/nsmb876.
|
Crystal structure of human DNA polymerase lambda in
complex with a one nucleotide DNA gap . SNAP output
|
|
1xsn
|
transferase-DNA |
X-ray (1.95 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA,
Pedersen LC |
(2005) "A closed
conformation for the Pol lambda catalytic cycle."
Nat.Struct.Mol.Biol., 12,
97-98. doi: 10.1038/nsmb876.
|
Crystal structure of human DNA polymerase lambda in
complex with a one nucleotide DNA gap and ddttp .
SNAP output
|
|
1xsp
|
transferase-DNA |
X-ray (2.2 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA,
Pedersen LC |
(2005) "A closed
conformation for the Pol lambda catalytic cycle."
Nat.Struct.Mol.Biol., 12,
97-98. doi: 10.1038/nsmb876.
|
Crystal structure of human DNA polymerase lambda in
complex with nicked DNA and pyrophosphate . SNAP output
|
|
1xvk
|
DNA-antibiotic |
X-ray (1.26 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
X-ray structure of an echinomycin-(gcgtacgc)2 complex .
SNAP output
|
|
1xvn
|
DNA-antibiotic |
X-ray (1.5 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
Echinomycin (acgtacgt)2 complex . SNAP output
|
|
1xvr
|
DNA-antibiotic |
X-ray (1.4 Å) |
Cuesta-Seijo JA, Sheldrick GM |
(2005) "Structures
of Complexes between Echinomycin and Duplex DNA."
Acta Crystallogr.,Sect.D, 61,
442. doi: 10.1107/S090744490500137X.
|
Echinomycin (cgtacg)2 complex . SNAP output
|
|
1xyi
|
structural protein-DNA |
X-ray (1.45 Å) |
Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang
AH-J |
(2005) "Probing
the DNA kink structure induced by the hyperthermophilic
chromosomal protein Sac7d." Nucleic Acids
Res., 33, 430-438. doi: 10.1093/nar/gki191.
|
Hyperthermophile chromosomal protein sac7d double
mutant val26ala-met29ala in complex with DNA gcgatcgc .
SNAP output
|
|
1y1w
|
transcription,transferase-DNA-RNA hybrid |
X-ray (4.0 Å) |
Kettenberger H, Armache K-J, Cramer P |
(2004) "Complete
RNA Polymerase II Elongation Complex Structure and Its
Interactions with NTP and TFIIS."
Mol.Cell, 16, 955-965. doi:
10.1016/j.molcel.2004.11.040.
|
Complete RNA polymerase ii elongation complex .
SNAP output
|
|
1y6f
|
transferase-DNA |
X-ray (2.4 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp-glucose
and DNA containing an abasic site . SNAP output
|
|
1y6g
|
transferase-DNA |
X-ray (2.8 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp and a
13_mer DNA containing a hmu base at 2.8 Å resolution .
SNAP output
|
|
1y77
|
transcription,transferase-DNA-RNA hybrid |
X-ray (4.5 Å) |
Kettenberger H, Armache K-J, Cramer P |
(2004) "Complete
RNA Polymerase II Elongation Complex Structure and Its
Interactions with NTP and TFIIS."
Mol.Cell, 16, 955-965. doi:
10.1016/j.molcel.2004.11.040.
|
Complete RNA polymerase ii elongation complex with
substrate analogue gmpcpp . SNAP output
|
|
1y8z
|
transferase-DNA |
X-ray (1.9 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp and a
13-mer DNA containing a hmu base at 1.9 Å resolution .
SNAP output
|
|
1ya6
|
transferase-DNA |
X-ray (2.4 Å) |
Lariviere L, Sommer N, Morera S |
(2005) "Structural
evidence of a passive base-flipping mechanism for AGT,
an unusual GT-B glycosyltransferase."
J.Mol.Biol., 352, 139-150.
doi: 10.1016/j.jmb.2005.07.007.
|
Alpha-glucosyltransferase in complex with udp and a
13-mer DNA containing a central a:g mismatch . SNAP output
|
|
1yf3
|
transferase-DNA |
X-ray (2.29 Å) |
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng
X |
(2005) "Transition
from Nonspecific to Specific DNA Interactions along the
Substrate-Recognition Pathway of Dam
Methyltransferase." Cell(Cambridge,Mass.),
121, 349-361. doi: 10.1016/j.cell.2005.02.021.
|
T4dam in complex with adohcy and 13-mer oligonucleotide
making non- and semi-specific (~1-4) contact . SNAP output
|
|
1yfh
|
transferase-DNA |
X-ray (3.01 Å) |
Duguid EM, Rice PA, He C |
(2005) "The
structure of the human AGT protein bound to DNA and its
implications for damage detection."
J.Mol.Biol., 350, 657-666.
doi: 10.1016/j.jmb.2005.05.028.
|
Wt human o6-alkylguanine-DNA alkyltransferase bound to
DNA containing an alkylated cytosine . SNAP output
|
|
1yfi
|
hydrolase-DNA |
X-ray (2.7 Å) |
Xu QS, Roberts RJ, Guo H-C |
(2005) "Two
crystal forms of the restriction enzyme MspI-DNA
complex show the same novel structure." Protein
Sci., 14, 2590-2600. doi:
10.1110/ps.051565105.
|
Crystal structure of restriction endonuclease mspi in
complex with its cognate DNA in p212121 space group .
SNAP output
|
|
1yfj
|
transferase-DNA |
X-ray (2.69 Å) |
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng
X |
(2005) "Transition
from Nonspecific to Specific DNA Interactions along the
Substrate-Recognition Pathway of Dam
Methyltransferase." Cell(Cambridge,Mass.),
121, 349-361. doi: 10.1016/j.cell.2005.02.021.
|
T4dam in complex with adohcy and 15-mer oligonucleotide
showing semi-specific and specific contact . SNAP output
|
|
1yfl
|
transferase-DNA |
X-ray (3.09 Å) |
Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng
X |
(2005) "Transition
from Nonspecific to Specific DNA Interactions along the
Substrate-Recognition Pathway of Dam
Methyltransferase." Cell(Cambridge,Mass.),
121, 349-361. doi: 10.1016/j.cell.2005.02.021.
|
T4dam in complex with sinefungin and 16-mer
oligonucleotide showing semi-specific and specific
contact and flipped base . SNAP output
|
|
1ynw
|
transcription-DNA |
X-ray (3.0 Å) |
Shaffer PL, Gewirth DT |
(2004) "Structural
analysis of RXR-VDR interactions on DR3 DNA."
J.Steroid Biochem.Mol.Biol.,
89-90, 215-219. doi: 10.1016/j.jsbmb.2004.03.084.
|
Crystal structure of vitamin d receptor and 9-cis
retinoic acid receptor DNA-binding domains bound to a
dr3 response element . SNAP output
|
|
1yo5
|
transcription-DNA |
X-ray (2.0 Å) |
Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y,
Ghosh D, Gulick AM |
(2005) "Analysis
of the 2.0 A Crystal Structure of the Protein-DNA
Complex of the Human PDEF Ets Domain Bound to the
Prostate Specific Antigen Regulatory Site."
Biochemistry, 44, 7095-7106.
doi: 10.1021/bi047352t.
|
Analysis of the 2.0a crystal structure of the
protein-DNA complex of human pdef ets domain bound to
the prostate specific antigen regulatory site .
SNAP output
|
|
1yqk
|
hydrolase-DNA |
X-ray (2.5 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Human 8-oxoguanine glycosylase crosslinked with guanine
containing DNA . SNAP
output
|
|
1yql
|
hydrolase-DNA |
X-ray (2.6 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Catalytically inactive hogg1 crosslinked with
7-deaza-8-azaguanine containing DNA . SNAP output
|
|
1yqm
|
hydrolase-DNA |
X-ray (2.5 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Catalytically inactive human 8-oxoguanine glycosylase
crosslinked to 7-deazaguanine containing DNA . SNAP output
|
|
1yqr
|
hydrolase-DNA |
X-ray (2.43 Å) |
Banerjee A, Yang W, Karplus M, Verdine GL |
(2005) "Structure
of a repair enzyme interrogating undamaged DNA
elucidates recognition of damaged DNA."
Nature, 434, 612-618. doi:
10.1038/nature03458.
|
Catalytically inactive human 8-oxoguanine glycosylase
crosslinked to oxog containing DNA . SNAP output
|
|
1yrn
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Li T, Stark MR, Johnson AD, Wolberger C |
(1995) "Crystal
structure of the MATa1/MAT alpha 2 homeodomain
heterodimer bound to DNA." Science,
270, 262-269.
|
Crystal structure of the mata1-matalpha2 homeodomain
heterodimer bound to DNA . SNAP output
|
|
1ysa
|
transcription-DNA |
X-ray (2.9 Å) |
Ellenberger TE, Brandl CJ, Struhl K, Harrison SC |
(1992) "The GCN4
basic region leucine zipper binds DNA as a dimer of
uninterrupted alpha helices: crystal structure of the
protein-DNA complex."
Cell(Cambridge,Mass.), 71,
1223-1237. doi: 10.1016/S0092-8674(05)80070-4.
|
The gcn4 basic region leucine zipper binds DNA as a
dimer of uninterrupted alpha helices: crystal structure
of the protein-DNA complex . SNAP output
|
|
1ytb
|
transcription-DNA |
X-ray (1.8 Å) |
Kim Y, Geiger JH, Hahn S, Sigler PB |
(1993) "Crystal
structure of a yeast TBP/TATA-box complex."
Nature, 365, 512-520. doi:
10.1038/365512a0.
|
Crystal structure of a yeast tbp-tata-box complex .
SNAP output
|
|
1ytf
|
transcription-DNA |
X-ray (2.5 Å) |
Tan S, Hunziker Y, Sargent DF, Richmond TJ |
(1996) "Crystal
structure of a yeast TFIIA/TBP/DNA complex."
Nature, 381, 127-134. doi:
10.1038/381127a0.
|
Yeast tfiia-tbp-DNA complex . SNAP output
|
|
1yui
|
DNA binding protein-DNA |
NMR |
Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn
AM, Clore GM |
(1997) "The
solution structure of a specific GAGA factor-DNA
complex reveals a modular binding mode."
Nat.Struct.Biol., 4, 122-132.
doi: 10.1038/nsb0297-122.
|
Solution NMR structure of the gaga factor-DNA complex,
regularized mean structure . SNAP output
|
|
1yuj
|
DNA binding protein-DNA |
NMR |
Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn
AM, Clore GM |
(1997) "The
solution structure of a specific GAGA factor-DNA
complex reveals a modular binding mode."
Nat.Struct.Biol., 4, 122-132.
doi: 10.1038/nsb0297-122.
|
Solution NMR structure of the gaga factor-DNA complex,
50 structures . SNAP
output
|
|
1z19
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy
A, Ellenberger T |
(2005) "A
structural basis for allosteric control of DNA
recombination by lambda integrase."
Nature, 435, 1059-1066. doi:
10.1038/nature03657.
|
Crystal structure of a lambda integrase(75-356) dimer
bound to a coc' core site . SNAP output
|
|
1z1b
|
DNA binding protein-DNA |
X-ray (3.8 Å) |
Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy
A, Ellenberger T |
(2005) "A
structural basis for allosteric control of DNA
recombination by lambda integrase."
Nature, 435, 1059-1066. doi:
10.1038/nature03657.
|
Crystal structure of a lambda integrase dimer bound to
a coc' core site . SNAP
output
|
|
1z1c
|
virus-DNA |
X-ray (3.5 Å) |
Kontou M, Govindasamy L, Nam HJ, Bryant N,
Llamas-Saiz AL, Foces-Foces C, Hernando E, Rubio MP,
McKenna R, Almendral JM, Agbandje-McKenna M |
(2005) "Structural
determinants of tissue tropism and in vivo
pathogenicity for the parvovirus minute virus of
mice." J.Virol., 79,
10931-10943. doi: 10.1128/JVI.79.17.10931-10943.2005.
|
Structural determinants of tissue tropism and in vivo
pathogenicity for the parvovirus minute virus of mice .
SNAP output
|
|
1z1g
|
DNA binding protein-DNA |
X-ray (4.4 Å) |
Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy
A, Ellenberger T |
(2005) "A
structural basis for allosteric control of DNA
recombination by lambda integrase."
Nature, 435, 1059-1066. doi:
10.1038/nature03657.
|
Crystal structure of a lambda integrase tetramer bound
to a holliday junction . SNAP output
|
|
1z63
|
hydrolase-DNA complex |
X-ray (3.0 Å) |
Durr H, Korner C, Muller M, Hickmann V, Hopfner
KP |
(2005) "X-ray
structures of the Sulfolobus solfataricus SWI2/SNF2
ATPase core and its complex with DNA."
Cell(Cambridge,Mass.), 121,
363-373. doi: 10.1016/j.cell.2005.03.026.
|
Sulfolobus solfataricus swi2-snf2 atpase core in
complex with dsDNA . SNAP output
|
|
1z9c
|
transcription-DNA |
X-ray (2.64 Å) |
Hong M, Fuangthong M, Helmann JD, Brennan RG |
(2005) "Structure
of an OhrR-ohrA Operator Complex Reveals the DNA
Binding Mechanism of the MarR Family."
Mol.Cell, 20, 131-141. doi:
10.1016/j.molcel.2005.09.013.
|
Crystal structure of ohrr bound to the ohra promoter:
structure of marr family protein with operator DNA .
SNAP output
|
|
1zaa
|
transcription-DNA |
X-ray (2.1 Å) |
Pavletich NP, Pabo CO |
(1991) "Zinc
finger-DNA recognition: crystal structure of a
Zif268-DNA complex at 2.1 A." Science,
252, 809-817.
|
Zinc finger-DNA recognition: crystal structure of a
zif268-DNA complex at 2.1 angstroms . SNAP output
|
|
1zay
|
transcription-DNA |
X-ray (2.7 Å) |
Zheleznova EE, Brennan RG |
"The Roles of Exocyclic Groups in the Central
Base-Pair Step in Modulating the Affinity of PurR for its
Operator." |
Purine repressor-hypoxanthine-modified-purf-operator
complex . SNAP
output
|
|
1zbb
|
structural protein-DNA |
X-ray (9.0 Å) |
Schalch T, Duda S, Sargent DF, Richmond TJ |
(2005) "X-ray
structure of a tetranucleosome and its implications for
the chromatin fibre." Nature,
436, 138-141. doi: 10.1038/nature03686.
|
Structure of the 4_601_167 tetranucleosome . SNAP output
|
|
1zbi
|
hydrolase-RNA-DNA |
X-ray (1.85 Å) |
Nowotny M, Gaidamakov SA, Crouch RJ, Yang W |
(2005) "Crystal
Structures of RNase H Bound to an RNA/DNA Hybrid:
Substrate Specificity and Metal-Dependent
Catalysis." Cell(Cambridge,Mass.),
121, 1005-1016. doi: 10.1016/j.cell.2005.04.024.
|
Bacillus halodurans rnase h catalytic domain mutant
d132n in complex with 12-mer RNA-DNA hybrid . SNAP output
|
|
1zbl
|
hydrolase-RNA-DNA |
X-ray (2.2 Å) |
Nowotny M, Gaidamakov SA, Crouch RJ, Yang W |
(2005) "Crystal
Structures of RNase H Bound to an RNA/DNA Hybrid:
Substrate Specificity and Metal-Dependent
Catalysis." Cell(Cambridge,Mass.),
121, 1005-1016. doi: 10.1016/j.cell.2005.04.024.
|
Bacillus halodurans rnase h catalytic domain mutant
d192n in complex with 12-mer RNA-DNA hybrid . SNAP output
|
|
1zet
|
replication-DNA |
X-ray (2.3 Å) |
Wang J |
(2005) "DNA
polymerases: Hoogsteen base-pairing in DNA
replication?." Nature,
437, E6-7; discussion E7. doi:
10.1038/nature04199.
|
X-ray data do not support hoogsteen base-pairing during
replication by human polymerase iota . SNAP output
|
|
1zg1
|
transcription-DNA |
X-ray (2.3 Å) |
Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML,
Gunsalus RP, Dickerson RE |
(2005) "Primary
and Secondary Modes of DNA Recognition by the NarL
Two-Component Response Regulator."
Biochemistry, 44,
14538-14552. doi: 10.1021/bi050734u.
|
Narl complexed to nirb promoter non-palindromic
tail-to-tail DNA site . SNAP output
|
|
1zg5
|
transcription-DNA |
X-ray (2.3 Å) |
Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML,
Gunsalus RP, Dickerson RE |
(2005) "Primary
and Secondary Modes of DNA Recognition by the NarL
Two-Component Response Regulator."
Biochemistry, 44,
14538-14552. doi: 10.1021/bi050734u.
|
Narl complexed to narg-89 promoter palindromic
tail-to-tail DNA site . SNAP output
|
|
1zgw
|
transcription regulator-DNA |
NMR |
He C, Hus JC, Sun LJ, Zhou P, Norman DP, Doetsch V,
Wei H, Gross JD, Lane WS, Wagner G, Verdine GL |
(2005) "A
Methylation-Dependent Electrostatic Switch Controls DNA
Repair and Transcriptional Activation by E. coli
Ada." Mol.Cell, 20,
117-129. doi: 10.1016/j.molcel.2005.08.013.
|
NMR structure of e. coli ada protein in complex with
DNA . SNAP output
|
|
1zjm
|
DNA-lyase-transferase |
X-ray (2.1 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2005) "Nucleotide-induced
DNA polymerase active site motions accommodating a
mutagenic DNA intermediate." STRUCTURE,
13, 1225-1233. doi: 10.1016/j.str.2005.05.010.
|
Human DNA polymerase beta complexed with DNA containing
an a-a mismatched primer terminus . SNAP output
|
|
1zjn
|
DNA-lyase-transferase |
X-ray (2.61 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2005) "Nucleotide-induced
DNA polymerase active site motions accommodating a
mutagenic DNA intermediate." STRUCTURE,
13, 1225-1233. doi: 10.1016/j.str.2005.05.010.
|
Human DNA polymerase beta complexed with DNA containing
an a-a mismatched primer terminus with dgtp . SNAP output
|
|
1zla
|
structural protein-DNA |
X-ray (2.9 Å) |
Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov
V, Walter JC, Luger K, Kaye KM |
(2006) "The
nucleosomal surface as a docking station for Kaposi's
sarcoma herpesvirus LANA." Science,
311, 856-861. doi: 10.1126/science.1120541.
|
X-ray structure of a kaposi's sarcoma herpesvirus lana
peptide bound to the nucleosomal core . SNAP output
|
|
1zlk
|
transcription-DNA |
X-ray (3.1 Å) |
Wisedchaisri G, Wu M, Rice AE, Roberts DM, Sherman
DR, Hol WGJ |
(2005) "Structures
of Mycobacterium tuberculosis DosR and DosR-DNA complex
involved in gene activation during adaptation to
hypoxic latency." J.Mol.Biol.,
354, 630-641. doi: 10.1016/j.jmb.2005.09.048.
|
Crystal structure of the mycobacterium tuberculosis
hypoxic response regulator dosr c-terminal domain-DNA
complex . SNAP
output
|
|
1zm5
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Boer R, Russi S, Guasch A, Lucas M, Blanco AG,
Perez-Luque R, Coll M, de la Cruz F |
(2006) "Unveiling
the Molecular Mechanism of a Conjugative Relaxase: The
Structure of TrwC Complexed with a 27-mer DNA
Comprising the Recognition Hairpin and the Cleavage
Site." J.Mol.Biol., 358,
857-869. doi: 10.1016/j.jmb.2006.02.018.
|
Conjugative relaxase trwc in complex with orit DNA,
cooper-bound structure . SNAP output
|
|
1zme
|
transcription-DNA |
X-ray (2.5 Å) |
Swaminathan K, Flynn P, Reece RJ, Marmorstein R |
(1997) "Crystal
structure of a PUT3-DNA complex reveals a novel
mechanism for DNA recognition by a protein containing a
Zn2Cys6 binuclear cluster."
Nat.Struct.Biol., 4, 751-759.
doi: 10.1038/nsb0997-751.
|
Crystal structure of put3-DNA complex . SNAP output
|
|
1zns
|
hydrolase-DNA |
X-ray (2.5 Å) |
Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y,
Cheng YS, Yuan HS |
(2006) "Crystal
structural analysis and metal-dependent stability and
activity studies of the ColE7 endonuclease domain in
complex with DNA/Zn2+ or inhibitor/Ni2+."
Protein Sci., 15, 269-280.
doi: 10.1110/ps.051903406.
|
Crystal structure of n-cole7-12-bp DNA-zn complex .
SNAP output
|
|
1zq3
|
transcription-DNA |
NMR |
Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli
CA, Ma J, Rance M |
(2006) "The
solution structure of the native K50 Bicoid homeodomain
bound to the consensus TAATCC DNA-binding site."
J.Mol.Biol., 356, 1137-1151.
doi: 10.1016/j.jmb.2005.12.007.
|
NMR solution structure of the bicoid homeodomain bound
to the consensus DNA binding site taatcc . SNAP output
|
|
1zqa
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (150 millimolar) at ph 7.5 . SNAP output
|
|
1zqb
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
bacl2 (150 millimolar) . SNAP output
|
|
1zqc
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (15 millimolar) . SNAP output
|
|
1zqd
|
transferase-DNA |
X-ray (3.5 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (150 millimolar) . SNAP output
|
|
1zqe
|
transferase-DNA |
X-ray (3.7 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
crcl3 (saturated solution) . SNAP output
|
|
1zqf
|
transferase-DNA |
X-ray (2.9 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cscl (150 millimolar) . SNAP output
|
|
1zqg
|
transferase-DNA |
X-ray (3.1 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
a sodium-free artificial mother liquor at ph 6.5 .
SNAP output
|
|
1zqh
|
transferase-DNA |
X-ray (3.1 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
a sodium-free artificial mother liquor at ph 7.5 .
SNAP output
|
|
1zqi
|
transferase-DNA |
X-ray (2.7 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (150 millimolar) . SNAP output
|
|
1zqj
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (15 millimolar) and mgcl2 (15 millimolar) .
SNAP output
|
|
1zqk
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (75 millimolar) and mgcl2 (75 millimolar) .
SNAP output
|
|
1zql
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
mncl2 (15 millimolar) and mgcl2 (15 millimolar) .
SNAP output
|
|
1zqm
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
mncl2 (15 millimolar) . SNAP output
|
|
1zqn
|
transferase-DNA |
X-ray (3.0 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
bacl2 (15 millimolar) and nacl (15 millimolar) .
SNAP output
|
|
1zqo
|
transferase-DNA |
X-ray (3.2 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
cacl2 (15 millimolar) and nacl (15 millimolar) .
SNAP output
|
|
1zqp
|
transferase-DNA |
X-ray (2.8 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
kcl (75 millimolar) and nacl (75 millimolar) . SNAP output
|
|
1zqq
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
mncl2 (15 millimolar) and nacl (15 millimolar) .
SNAP output
|
|
1zqr
|
transferase-DNA |
X-ray (3.7 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked
in the presence of nicl2 . SNAP output
|
|
1zqs
|
transferase-DNA |
X-ray (3.3 Å) |
Pelletier H, Sawaya MR |
(1996) "Characterization
of the metal ion binding helix-hairpin-helix motifs in
human DNA polymerase beta by X-ray structural
analysis." Biochemistry,
35, 12778-12787. doi: 10.1021/bi960790i.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
tlcl (0.5 millimolar) . SNAP output
|
|
1zqt
|
transferase-DNA |
X-ray (3.4 Å) |
Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut
J |
(1996) "A
structural basis for metal ion mutagenicity and
nucleotide selectivity in human DNA polymerase
beta." Biochemistry, 35,
12762-12777. doi: 10.1021/bi9529566.
|
DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed
with seven base pairs of DNA; soaked in the presence of
datp (0.01 millimolar) and zncl2 (0.02 millimolar) .
SNAP output
|
|
1zr2
|
recombination-DNA |
X-ray (3.9 Å) |
Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND,
Steitz TA |
(2005) "Structure
of a synaptic gamma delta resolvase tetramer covalently
linked to two cleaved DNAs." Science,
309, 1210-1215. doi: 10.1126/science.1112064.
|
Structure of a synaptic gamma-delta resolvase tetramer
covalently linked to two cleaved dnas . SNAP output
|
|
1zr4
|
recombination-DNA |
X-ray (3.4 Å) |
Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND,
Steitz TA |
(2005) "Structure
of a synaptic gamma delta resolvase tetramer covalently
linked to two cleaved DNAs." Science,
309, 1210-1215. doi: 10.1126/science.1112064.
|
Structure of a synaptic gamma-delta resolvase tetramer
covalently linked to two cleaved dnas . SNAP output
|
|
1zrc
|
gene regulation-DNA |
X-ray (2.8 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-icap38 DNA . SNAP output
|
|
1zrd
|
gene regulation-DNA |
X-ray (2.8 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-[6a;17t]icap38 DNA .
SNAP output
|
|
1zre
|
gene regulation-DNA |
X-ray (2.8 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-[6g;17c]icap38 DNA .
SNAP output
|
|
1zrf
|
gene regulation-DNA |
X-ray (2.1 Å) |
Napoli AA, Lawson CL, Ebright RH, Berman HM |
(2006) "Indirect
readout of DNA sequence at the primary-kink site in the
CAP-DNA complex: recognition of pyrimidine-purine and
purine-purine steps." J.Mol.Biol.,
357, 173-183. doi: 10.1016/j.jmb.2005.12.051.
|
4 crystal structures of cap-DNA with all base-pair
substitutions at position 6, cap-[6c;17g]icap38 DNA .
SNAP output
|
|
1zs4
|
transcription-DNA |
X-ray (1.7 Å) |
Jain D, Kim Y, Maxwell KL, Beasley S, Zhang R, Gussin
GN, Edwards AM, Darst SA |
(2005) "Crystal
Structure of Bacteriophage lambdacII and Its DNA
Complex." Mol.Cell, 19,
259-269. doi: 10.1016/j.molcel.2005.06.006.
|
Structure of bacteriophage lambda cii protein in
complex with DNA . SNAP
output
|
|
1ztg
|
DNA, RNA binding protein-DNA |
X-ray (3.0 Å) |
Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR,
Barker A, Leedman PJ, Wilce JA, Wilce MCJ |
(2012) "Contribution
of the first K-homology domain of poly(C)-binding
protein 1 to its affinity and specificity for C-rich
oligonucleotides." Nucleic Acids Res.,
40, 5101-5114. doi: 10.1093/nar/gks058.
|
Human alpha polyc binding protein kh1 . SNAP output
|
|
1ztt
|
transferase-DNA |
X-ray (1.85 Å) |
Goodwin KD, Long EC, Georgiadis MM |
(2005) "A
host-guest approach for determining drug-DNA
interactions: an example using netropsin."
Nucleic Acids Res., 33,
4106-4116. doi: 10.1093/nar/gki717.
|
Netropsin bound to d(cttaattcgaattaag) in complex with
mmlv rt catalytic fragment . SNAP output
|
|
1ztw
|
transferase-DNA |
X-ray (1.8 Å) |
Goodwin KD, Long EC, Georgiadis MM |
(2005) "A
host-guest approach for determining drug-DNA
interactions: an example using netropsin."
Nucleic Acids Res., 33,
4106-4116. doi: 10.1093/nar/gki717.
|
D(cttaattcgaattaag) complexed with moloney murine
leukemia virus reverse transcriptase catalytic fragment
. SNAP output
|
|
1zvv
|
transcription-DNA |
X-ray (2.98 Å) |
Schumacher MA, Seidel G, Hillen W, Brennan RG |
(2006) "Phosphoprotein
Crh-Ser46-P displays altered binding to CcpA to effect
carbon catabolite regulation."
J.Biol.Chem., 281, 6793-6800.
doi: 10.1074/jbc.M509977200.
|
Crystal structure of a ccpa-crh-DNA complex . SNAP output
|
|
1zx4
|
cell cycle |
X-ray (2.98 Å) |
Schumacher MA, Funnell BE |
(2005) "Structures
of ParB bound to DNA reveal mechanism of partition
complex formation." Nature,
438, 516-519. doi: 10.1038/nature04149.
|
Structure of parb bound to DNA . SNAP output
|
|
1zyq
|
transferase-electron transport-DNA |
X-ray (2.7 Å) |
Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA,
Ellenberger T |
(2005) "A lysine
residue in the fingers subdomain of t7 DNA polymerase
modulates the miscoding potential of
8-oxo-7,8-dihydroguanosine." Structure,
13, 1653-1659. doi: 10.1016/j.str.2005.07.020.
|
T7 DNA polymerase in complex with 8og and incoming
ddatp . SNAP output
|
|
1zzi
|
structural protein-DNA |
X-ray (1.8 Å) |
Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack
S |
(2005) "X-Ray
Crystallographic and NMR Studies of the Third KH Domain
of hnRNP K in Complex with Single-Stranded Nucleic
Acids." STRUCTURE, 13,
1055-1067. doi: 10.1016/j.str.2005.04.008.
|
Crystal structure analysis of the third kh domain of
hnrnp k in complex with ssDNA . SNAP output
|
|
1zzj
|
structural protein-DNA |
X-ray (2.3 Å) |
Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack
S |
(2005) "X-Ray
Crystallographic and NMR Studies of the Third KH Domain
of hnRNP K in Complex with Single-Stranded Nucleic
Acids." STRUCTURE, 13,
1055-1067. doi: 10.1016/j.str.2005.04.008.
|
Structure of the third kh domain of hnrnp k in complex
with 15-mer ssDNA . SNAP
output
|
|
209d
|
DNA-antibiotic |
X-ray (3.0 Å) |
Shinomiya M, Chu W, Carlson RG, Weaver RF, Takusagawa
F |
(1995) "Structural,
Physical, and Biological Characteristics of RNA.DNA
Binding Agent N8-Actinomycin D."
Biochemistry, 34, 8481. doi:
10.1021/BI00026A032.
|
Structural, physical and biological characteristics of
RNA:DNA binding agent n8-actinomycin d . SNAP output
|
|
2a07
|
transcription-DNA |
X-ray (1.9 Å) |
Stroud JC, Wu Y, Bates DL, Han A, Nowick K, Paabo S,
Tong H, Chen L |
(2006) "Structure
of the Forkhead Domain of FOXP2 Bound to DNA."
Structure, 14, 159-166. doi:
10.1016/j.str.2005.10.005.
|
Crystal structure of foxp2 bound specifically to DNA. .
SNAP output
|
|
2a0i
|
hydrolase-DNA |
X-ray (2.72 Å) |
Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A,
Hargreaves V, Schildbach JF |
(2005) "Inter-
and intramolecular determinants of the specificity of
single-stranded DNA binding and cleavage by the f
factor relaxase." Structure,
13, 1533-1544. doi: 10.1016/j.str.2005.06.013.
|
F factor trai relaxase domain bound to f orit
single-stranded DNA . SNAP output
|
|
2a3v
|
recombination |
X-ray (2.8 Å) |
MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul
DN |
(2006) "Structural
basis for broad DNA-specificity in integron
recombination." Nature,
440, 1157-1162. doi: 10.1038/nature04643.
|
Structural basis for broad DNA-specificity in integron
recombination . SNAP
output
|
|
2a66
|
transcription-DNA |
X-ray (2.2 Å) |
Solomon IH, Hager JM, Safi R, McDonnell DP, Redinbo
MR, Ortlund EA |
(2005) "Crystal
Structure of the Human LRH-1 DBD-DNA Complex Reveals
Ftz-F1 Domain Positioning is Required for Receptor
Activity." J.Mol.Biol.,
354, 1091-1102. doi: 10.1016/j.jmb.2005.10.009.
|
Human liver receptor homologue DNA-binding domain
(hlrh-1 dbd) in complex with dsDNA from the hcyp7a1
promoter . SNAP
output
|
|
2a6o
|
transcription-DNA |
X-ray (2.6 Å) |
Ronning DR, Guynet C, Ton-Hoang B, Perez ZN,
Ghirlando R, Chandler M, Dyda F |
(2005) "Active
site sharing and subterminal hairpin recognition in a
new class of DNA transposases." Mol.Cell,
20, 143-154. doi: 10.1016/j.molcel.2005.07.026.
|
Crystal structure of the ishp608 transposase in complex
with stem-loop DNA . SNAP output
|
|
2ac0
|
apoptosis-DNA |
X-ray (1.8 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex i) . SNAP
output
|
|
2acj
|
hydrolase-DNA |
X-ray (2.6 Å) |
Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK |
(2005) "Crystal
structure of a junction between B-DNA and Z-DNA reveals
two extruded bases." Nature,
437, 1183-1186. doi: 10.1038/nature04088.
|
Crystal structure of the b-z junction containing DNA
bound to z-DNA binding proteins . SNAP output
|
|
2adw
|
DNA-antibiotic |
X-ray (1.6 Å) |
Cuesta-Seijo JA, Weiss MS, Sheldrick GM |
(2006) "Serendipitous
Sad Phasing of an Echinomycin-(Acgtacgt)2
Bisintercalation Complex." Acta
Crystallogr.,Sect.D, 62, 417.
doi: 10.1107/S0907444906003763.
|
Crystal structure of echinomycin-(acgtacgt)2 solved by
sad . SNAP output
|
|
2ady
|
apoptosis-DNA |
X-ray (2.5 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex iv) . SNAP
output
|
|
2ago
|
transferase-DNA |
X-ray (2.85 Å) |
Vaisman A, Ling H, Woodgate R, Yang W |
(2005) "Fidelity
of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis." Embo J.,
24, 2957-2967. doi: 10.1038/sj.emboj.7600786.
|
Fidelity of dpo4: effect of metal ions, nucleotide
selection and pyrophosphorolysis . SNAP output
|
|
2agp
|
transferase-DNA |
X-ray (2.9 Å) |
Vaisman A, Ling H, Woodgate R, Yang W |
(2005) "Fidelity
of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis." Embo J.,
24, 2957-2967. doi: 10.1038/sj.emboj.7600786.
|
Fidelity of dpo4: effect of metal ions, nucleotide
selection and pyrophosphorolysis . SNAP output
|
|
2agq
|
transferase-DNA |
X-ray (2.1 Å) |
Vaisman A, Ling H, Woodgate R, Yang W |
(2005) "Fidelity
of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis." Embo J.,
24, 2957-2967. doi: 10.1038/sj.emboj.7600786.
|
Fidelity of dpo4: effect of metal ions, nucleotide
selection and pyrophosphorolysis . SNAP output
|
|
2ahi
|
apoptosis-DNA |
X-ray (1.85 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex iii) . SNAP
output
|
|
2ajq
|
transferase,transcription-DNA |
X-ray (2.6 Å) |
Brieba L, Ellenberger T |
"Structure of replicative DNA polymerase provides
insigts into the mechanisms for processivity,
frameshifting and editing." |
Structure of replicative DNA polymerase provides
insigts into the mechanisms for processivity,
frameshifting and editing . SNAP output
|
|
2alz
|
transferase-DNA |
X-ray (2.5 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2005) "Human
DNA Polymerase iota Incorporates dCTP Opposite Template
G via a G.C+ Hoogsteen Base Pair."
Structure, 13, 1569-1577.
doi: 10.1016/j.str.2005.08.010.
|
Ternary complex of hpoli with DNA and dctp . SNAP output
|
|
2aoq
|
hydrolase-DNA |
X-ray (2.2 Å) |
Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang
W |
(2005) "MutH
complexed with hemi- and unmethylated DNAs: coupling
base recognition and DNA cleavage."
Mol.Cell, 20, 155-166. doi:
10.1016/j.molcel.2005.08.019.
|
Crystal structure of muth-unmethylated DNA complex .
SNAP output
|
|
2aor
|
hydrolase-DNA |
X-ray (2.0 Å) |
Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang
W |
(2005) "MutH
complexed with hemi- and unmethylated DNAs: coupling
base recognition and DNA cleavage."
Mol.Cell, 20, 155-166. doi:
10.1016/j.molcel.2005.08.019.
|
Crystal structure of muth-hemimethylated DNA complex .
SNAP output
|
|
2aq4
|
transferase |
X-ray (2.32 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2005) "Rev1
employs a novel mechanism of DNA synthesis using a
protein template." Science,
309, 2219-2222. doi: 10.1126/science.1116336.
|
Ternary complex of the catalytic core of rev1 with DNA
and dctp. . SNAP
output
|
|
2as5
|
transcription-DNA |
X-ray (2.7 Å) |
Wu Y, Borde M, Heissmeyer V, Feuerer M, Lapan AD,
Stroud JC, Bates DL, Guo L, Han A, Ziegler SF, Mathis D,
Benoist C, Chen L, Rao A |
(2006) "FOXP3
Controls Regulatory T Cell Function through Cooperation
with NFAT." Cell(Cambridge,Mass.),
126, 375-387. doi: 10.1016/j.cell.2006.05.042.
|
Structure of the DNA binding domains of nfat and foxp2
bound specifically to DNA. . SNAP output
|
|
2asd
|
transferase-DNA |
X-ray (1.95 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Oxog-modified insertion ternary complex . SNAP output
|
|
2asj
|
transferase-DNA |
X-ray (2.35 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Oxog-modified preinsertion binary complex . SNAP output
|
|
2asl
|
transferase-DNA |
X-ray (2.65 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Oxog-modified postinsertion binary complex . SNAP output
|
|
2ata
|
apoptosis-DNA |
X-ray (2.2 Å) |
Kitayner M, Rozenberg H, Kessler N, Rabinovich D,
Shaulov L, Haran TE, Shakked Z |
(2006) "Structural
Basis of DNA Recognition by p53 Tetramers."
Mol.Cell, 22, 741-753. doi:
10.1016/j.molcel.2006.05.015.
|
Structural basis of DNA recognition by p53 tetramers
(complex ii) . SNAP
output
|
|
2atl
|
transferase-DNA |
X-ray (2.8 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Unmodified insertion ternary complex . SNAP output
|
|
2au0
|
transferase-DNA |
X-ray (2.7 Å) |
Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde
S, Geacintov NE, Patel DJ |
(2006) "Stepwise
Translocation of Dpo4 Polymerase during Error-Free
Bypass of an oxoG Lesion." Plos Biol.,
4, 1-18. doi: 10.1371/journal.pbio.0040011.
|
Unmodified preinsertion binary complex . SNAP output
|
|
2axy
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James
TL |
(2005) "Crystal
Structure of the First KH Domain of Human
Poly(C)-binding Protein-2 in Complex with a C-rich
Strand of Human Telomeric DNA at 1.7 A."
J.Biol.Chem., 280,
38823-38830. doi: 10.1074/jbc.M508183200.
|
Crystal structure of kh1 domain of human
poly(c)-binding protein-2 with c-rich strand of human
telomeric DNA . SNAP
output
|
|
2ayb
|
transcription-DNA |
X-ray (3.2 Å) |
Hooley E, Fairweather V, Clarke AR, Gaston K, Brady
RL |
(2006) "The
recognition of local DNA conformation by the human
papillomavirus type 6 E2 protein." Nucleic
Acids Res., 34, 3897-3908. doi:
10.1093/nar/gkl466.
|
Crystal structure of hpv6a e2 DNA binding domain bound
to a 16 base pair DNA target . SNAP output
|
|
2ayg
|
transcription-DNA |
X-ray (3.1 Å) |
Hooley E, Fairweather V, Clarke AR, Gaston K, Brady
RL |
(2006) "The
recognition of local DNA conformation by the human
papillomavirus type 6 E2 protein." Nucleic
Acids Res., 34, 3897-3908. doi:
10.1093/nar/gkl466.
|
Crystal structure of hpv6a e2 DNA binding domain bound
to an 18 base pair DNA target . SNAP output
|
|
2b0d
|
hydrolase-DNA |
X-ray (2.0 Å) |
Hiller DA, Rodriguez AM, Perona JJ |
(2005) "Non-cognate
Enzyme-DNA Complex: Structural and Kinetic Analysis of
EcoRV Endonuclease Bound to the EcoRI Recognition Site
GAATTC." J.Mol.Biol.,
354, 121-136. doi: 10.1016/j.jmb.2005.09.046.
|
Ecorv restriction endonuclease-gaattc-ca2+ . SNAP output
|
|
2b0e
|
hydrolase-DNA |
X-ray (1.9 Å) |
Hiller DA, Rodriguez AM, Perona JJ |
(2005) "Non-cognate
Enzyme-DNA Complex: Structural and Kinetic Analysis of
EcoRV Endonuclease Bound to the EcoRI Recognition Site
GAATTC." J.Mol.Biol.,
354, 121-136. doi: 10.1016/j.jmb.2005.09.046.
|
Ecorv restriction endonuclease-gaautc-ca2+ . SNAP output
|
|
2b9s
|
isomerase-DNA |
X-ray (2.27 Å) |
Davies DR, Mushtaq A, Interthal H, Champoux JJ, Hol
WG |
(2006) "The
Structure of the Transition State of the Heterodimeric
Topoisomerase I of Leishmania donovani as a Vanadate
Complex with Nicked DNA." J.Mol.Biol.,
357, 1202-1210. doi: 10.1016/j.jmb.2006.01.022.
|
Crystal structure of heterodimeric l. donovani
topoisomerase i-vanadate-DNA complex . SNAP output
|
|
2bam
|
hydrolase-DNA |
X-ray (2.0 Å) |
Viadiu H, Aggarwal AK |
(1998) "The role
of metals in catalysis by the restriction endonuclease
BamHI." Nat.Struct.Biol.,
5, 910-916. doi: 10.1038/2352.
|
Restriction endonuclease bamhi complex with DNA and
calcium ions (pre-reactive complex). . SNAP output
|
|
2bcq
|
transferase, lyase-DNA |
X-ray (1.65 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired dtmp . SNAP output
|
|
2bcr
|
transferase, lyase-DNA |
X-ray (1.75 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired damp . SNAP output
|
|
2bcs
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired dcmp . SNAP output
|
|
2bcu
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with a DNA duplex
containing an unpaired damp and a t:t mismatch .
SNAP output
|
|
2bcv
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2006) "Structural
analysis of strand misalignment during DNA synthesis by
a human DNA polymerase."
Cell(Cambridge,Mass.), 124,
331-342. doi: 10.1016/j.cell.2005.10.039.
|
DNA polymerase lambda in complex with dttp and a DNA
duplex containing an unpaired dtmp . SNAP output
|
|
2bdp
|
transferase-DNA |
X-ray (1.8 Å) |
Kiefer JR, Mao C, Braman JC, Beese LS |
(1998) "Visualizing
DNA replication in a catalytically active Bacillus DNA
polymerase crystal." Nature,
391, 304-307. doi: 10.1038/34693.
|
Crystal structure of bacillus DNA polymerase i fragment
complexed to 9 base pairs of duplex DNA . SNAP output
|
|
2bgw
|
hydrolase |
X-ray (2.8 Å) |
Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A,
Knowles PP, White MF, McDonald NQ |
(2005) "Structure
of an XPF endonuclease with and without DNA suggests a
model for substrate recognition." EMBO J.,
24, 895-905. doi: 10.1038/sj.emboj.7600581.
|
Xpf from aeropyrum pernix, complex with DNA . SNAP output
|
|
2bjc
|
transcription regulator |
NMR |
Salinas RK, Folkers GE, Bonvin AMJJ, Das D, Boelens
R, Kaptein R |
(2005) "Altered
Specificity in DNA Binding by the Lac Repressor: A
Mutant Lac Headpiece that Mimics the Gal
Repressor." Chembiochem,
6, 1628. doi: 10.1002/CBIC.200500049.
|
NMR structure of a protein-DNA complex of an altered
specificity mutant of the lac repressor headpiece that
mimics the gal repressor . SNAP output
|
|
2bnw
|
DNA-binding-regulatory protein |
X-ray (2.45 Å) |
Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger
W |
(2006) "Structures
of Omega Repressors Bound to Direct and Inverted DNA
Repeats Explain Modulation of Transcription."
Nucleic Acids Res., 34, 1450.
doi: 10.1093/NAR/GKL015.
|
Structural basis for cooperative binding of
ribbon-helix-helix omega repressor to direct DNA heptad
repeats . SNAP
output
|
|
2bnz
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger
W |
(2006) "Structures
of Omega Repressors Bound to Direct and Inverted DNA
Repeats Explain Modulation of Transcription."
Nucleic Acids Res., 34, 1450.
doi: 10.1093/NAR/GKL015.
|
Structural basis for cooperative binding of
ribbon-helix-helix omega repressor to inverted DNA
heptad repeats . SNAP
output
|
|
2bop
|
transcription-DNA |
X-ray (1.7 Å) |
Hegde RS, Grossman SR, Laimins LA, Sigler PB |
(1992) "Crystal
structure at 1.7 A of the bovine papillomavirus-1 E2
DNA-binding domain bound to its DNA target."
Nature, 359, 505-512. doi:
10.1038/359505a0.
|
Crystal structure at 1.7 angstroms of the bovine
papillomavirus-1 e2 DNA-binding domain bound to its DNA
target . SNAP output
|
|
2bpa
|
virus-DNA |
X-ray (3.0 Å) |
McKenna R, Xia D, Willingmann P, Ilag LL,
Krishnaswamy S, Rossmann MG, Olson NH, Baker TS,
Incardona NL |
(1992) "Atomic
structure of single-stranded DNA bacteriophage phi X174
and its functional implications." Nature,
355, 137-143. doi: 10.1038/355137a0.
|
Atomic structure of single-stranded DNA bacteriophage
phix174 and its functional implications . SNAP output
|
|
2bpf
|
transferase-DNA |
X-ray (2.9 Å) |
Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut
J |
(1994) "Structures
of ternary complexes of rat DNA polymerase beta, a DNA
template-primer, and ddCTP." Science,
264, 1891-1903.
|
Structures of ternary complexes of rat DNA polymerase
beta, a DNA template-primer, and ddctp . SNAP output
|
|
2bpg
|
transferase-DNA |
X-ray (3.6 Å) |
Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut
J |
(1994) "Structures
of ternary complexes of rat DNA polymerase beta, a DNA
template-primer, and ddCTP." Science,
264, 1891-1903.
|
Structures of ternary complexes of rat DNA polymerase
beta, a DNA template-primer, and ddctp . SNAP output
|
|
2bq3
|
transferase |
X-ray (2.0 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
|
2bqr
|
transferase |
X-ray (2.37 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
|
2bqu
|
transferase |
X-ray (2.5 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
|
2br0
|
transferase |
X-ray (2.17 Å) |
Zang H, Goodenough AK, Choi JY, Irimia A,
Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M,
Guengerich FP |
(2005) "DNA
Adduct Bypass Polymerization by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Analysis and Crystal Structures of
Multiple Base Pair Substitution and Frameshift Products
with the Adduct 1,N2-Ethenoguanine."
J.Biol.Chem., 280, 29750.
doi: 10.1074/JBC.M504756200.
|
DNA adduct bypass polymerization by sulfolobus
solfataricus dpo4. analysis and crystal structures of
multiple base-pair substitution and frameshift products
with the adduct 1,n2-ethenoguanine . SNAP output
|
|
2bsq
|
transcription |
X-ray (3.0 Å) |
Mattison K, Wilbur JS, So M, Brennan RG |
(2006) "Structure
of Fitab from Neisseria Gonorrhoeae Bound to DNA
Reveals a Tetramer of Toxin-Antitoxin Heterodimers
Containing Pin Domains and Ribbon-Helix-Helix
Motifs." J.Biol.Chem.,
281, 37942. doi: 10.1074/JBC.M605198200.
|
Fitab bound to DNA . SNAP output
|
|
2bzf
|
DNA binding protein |
X-ray (2.87 Å) |
Bradley CM, Ronning DR, Ghirlando R, Craigie R, Dyda
F |
(2005) "Structural
Basis for DNA Bridging by Barrier-to-Autointegration
Factor." Nat.Struct.Mol.Biol.,
12, 935. doi: 10.1038/NSMB989.
|
Structural basis for DNA bridging by
barrier-to-autointegration factor (baf) . SNAP output
|
|
2c22
|
polymerase |
X-ray (2.56 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, Guengerich FP |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
|
2c28
|
polymerase |
X-ray (2.27 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, P Guengerich F |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
|
2c2d
|
polymerase |
X-ray (2.57 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, P Guengerich F |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
|
2c2e
|
polymerase |
X-ray (2.61 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, P Guengerich F |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
|
2c2r
|
polymerase |
X-ray (2.55 Å) |
Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch
LV, Egli M, Guengerich FP |
(2006) "Efficient
and High Fidelity Incorporation of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus
Solfataricus DNA Polymerase Dpo4."
J.Biol.Chem., 281, 2358. doi:
10.1074/JBC.M510889200.
|
Efficient and high fidelity incorporation of dctp
opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus
solfataricus DNA polymerase dpo4 . SNAP output
|
|
2c5r
|
DNA-binding protein-DNA |
X-ray (2.9 Å) |
Albert A, Munoz-Espin D, Jimenez M, Asensio JL,
Hermoso JA, Salas M, Meijer WJJ |
(2005) "Structural
Basis for Membrane Anchorage of Viral Phi 29 DNA During
Replication." J.Biol.Chem.,
280, 42486. doi: 10.1074/JBC.C500429200.
|
The structure of phage phi29 replication organizer
protein p16.7 in complex with double stranded DNA .
SNAP output
|
|
2c62
|
transcription |
X-ray (1.74 Å) |
Werten S, Moras D |
(2006) "A Global
Transcription Cofactor Bound to Juxtaposed Strands of
Unwound DNA." Nat.Struct.Mol.Biol.,
13, 181. doi: 10.1038/NSMB1044.
|
Crystal structure of the human transcription cofactor
pc4 in complex with single-stranded DNA . SNAP output
|
|
2c6y
|
transcription regulation |
X-ray (2.4 Å) |
Tsai K-L, Huang C-Y, Chang C-H, Sun Y-J, Chuang W-J,
Hsiao C-D |
(2006) "Crystal
Structure of the Human Foxk1A-DNA Complex and its
Implications on the Diverse Binding Specificity of
Winged Helix/Forkhead Proteins."
J.Biol.Chem., 281, 17400.
doi: 10.1074/JBC.M600478200.
|
Crystal structure of interleukin enhancer-binding
factor 1 bound to DNA . SNAP output
|
|
2c7a
|
receptor-DNA |
X-ray (2.5 Å) |
Roemer SC, Donham DC, Sherman L, Pon VH, Edwards DP,
Churchill MEA |
(2006) "Structure
of the Progesterone Receptor-Deoxyribonucleic Acid
Complex: Novel Interactions Required for Binding to
Half-Site Response Elements."
Mol.Endocrinol., 20, 3042.
doi: 10.1210/ME.2005-0511.
|
Structure of the progesterone receptor-DNA complex .
SNAP output
|
|
2c7o
|
transferase-DNA |
X-ray (1.9 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with 13mer
oligonucleotide containing 2-aminopurine adjacent to
the target base (pcgc:gmgc) and sah . SNAP output
|
|
2c7p
|
transferase-DNA |
X-ray (1.7 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with oligonucleotide
containing 2- aminopurine opposite to the target base
(gcgc:gmpc) and sah . SNAP output
|
|
2c7q
|
transferase-DNA |
X-ray (1.85 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase complex with oligonucleotide
containing 2- aminopurine outside the recognition
sequence (paired with g) and sah . SNAP output
|
|
2c7r
|
transferase-DNA |
X-ray (1.9 Å) |
Neely RK, Daujotyte D, Grazulis S, Magennis SW,
Dryden DTF, Klimasauskas S, Jones AC |
(2005) "Time-Resolved
Fluorescence of 2-Aminopurine as a Probe of Base
Flipping in M.HhaI-DNA Complexes." Nucleic
Acids Res., 33, 6953. doi:
10.1093/NAR/GKI995.
|
Hhai DNA methyltransferase (t250g mutant) complex with
oligonucleotide containing 2-aminopurine as a target
base (gpgc:gmgc) and sah . SNAP output
|
|
2c9l
|
viral protein |
X-ray (2.25 Å) |
Petosa C, Morand P, Baudin F, Moulin M, Artero JB,
Muller CW |
(2006) "Structural
Basis of Lytic Cycle Activation by the Epstein-Barr
Virus Zebra Protein." Mol.Cell,
21, 565. doi: 10.1016/J.MOLCEL.2006.01.006.
|
Structure of the epstein-barr virus zebra protein .
SNAP output
|
|
2c9n
|
viral protein |
X-ray (3.3 Å) |
Petosa C, Morand P, Baudin F, Moulin M, Artero JB,
Muller CW |
(2006) "Structural
Basis of Lytic Cycle Activation by the Epstein-Barr
Virus Zebra Protein." Mol.Cell,
21, 565. doi: 10.1016/J.MOLCEL.2006.01.006.
|
Structure of the epstein-barr virus zebra protein at
approximately 3. 5 angstrom resolution . SNAP output
|
|
2cax
|
transcriptional repressor |
X-ray (2.9 Å) |
Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger
W |
(2006) "Structures
of Omega Repressors Bound to Direct and Inverted DNA
Repeats Explain Modulation of Transcription."
Nucleic Acids Res., 34, 1450.
doi: 10.1093/NAR/GKL015.
|
Structural basis for cooperative binding of
ribbon-helix-helix repressor omega to mutated direct
DNA heptad repeats . SNAP output
|
|
2ccz
|
DNA-replication |
X-ray (2.7 Å) |
Huang C-Y, Hsu C-H, Sun Y-J, Wu H-N, Hsiao C-D |
(2006) "Complexed
Crystal Structure of Replication Restart Primsome
Protein Prib Reveals a Novel Single-Stranded
DNA-Binding Mode." Nucleic Acids Res.,
34, 3878. doi: 10.1093/NAR/GKL536.
|
Crystal structure of e. coli primosomol protein prib
bound to ssDNA . SNAP
output
|
|
2cdm
|
DNA-DNA-binding protein |
X-ray (2.7 Å) |
Boer R, Russi S, Guasch A, Lucas M, Blanco AG,
Perez-Luque R, Coll M, De La Cruz F |
(2006) "Unveiling
the Molecular Mechanism of a Conjugative Relaxase: The
Structure of Trwc Complexed with a 27-mer DNA
Comprising the Recognition Hairpin and the Cleavage
Site." J.Mol.Biol., 358,
857. doi: 10.1016/J.JMB.2006.02.018.
|
The structure of trwc complexed with a 27-mer DNA
comprising the recognition hairpin and the cleavage
site . SNAP output
|
|
2cgp
|
transcription-DNA |
X-ray (2.2 Å) |
Passner JM, Steitz TA |
(1997) "The
structure of a CAP-DNA complex having two cAMP
molecules bound to each monomer."
Proc.Natl.Acad.Sci.USA, 94,
2843-2847. doi: 10.1073/pnas.94.7.2843.
|
Catabolite gene activator protein-DNA complex,
adenosine-3',5'-cyclic-monophosphate . SNAP output
|
|
2crx
|
hydrolase, ligase-DNA |
X-ray (2.5 Å) |
Gopaul DN, Guo F, Van Duyne GD |
(1998) "Structure
of the Holliday junction intermediate in Cre-loxP
site-specific recombination." EMBO J.,
17, 4175-4187. doi: 10.1093/emboj/17.14.4175.
|
Structure of the holliday junction intermediate in
cre-loxp site-specific recombination . SNAP output
|
|
2cv5
|
structural protein-DNA |
X-ray (2.5 Å) |
Tsunaka Y, Kajimura N, Tate S, Morikawa K |
(2005) "Alteration
of the nucleosomal DNA path in the crystal structure of
a human nucleosome core particle." Nucleic
Acids Res., 33, 3424-3434. doi:
10.1093/nar/gki663.
|
Crystal structure of human nucleosome core particle .
SNAP output
|
|
2d45
|
transcription-DNA |
X-ray (3.8 Å) |
Safo MK, Ko TP, Musayev FN, Zhao Q, Wang AH, Archer
GL |
(2006) "Structure
of the MecI repressor from Staphylococcus aureus in
complex with the cognate DNA operator of mec."
Acta Crystallogr.,Sect.F, 62,
320-324. doi: 10.1107/S1744309106009742.
|
Crystal structure of the meci-meca repressor-operator
complex . SNAP
output
|
|
2d55
|
DNA-antibiotic |
X-ray (3.0 Å) |
Kamitori S, Takusagawa F |
(1992) "Crystal
Structure of the 2:1 Complex between D(Gaagcttc) and
the Anticancer Drug Actinomycin D."
J.Mol.Biol., 225, 445. doi:
10.1016/0022-2836(92)90931-9.
|
Structural, physical and biological characteristics of
RNA.DNA binding agent n8-actinomycin d . SNAP output
|
|
2d5v
|
transcription-DNA |
X-ray (2.0 Å) |
Iyaguchi D, Yao M, Watanabe N, Nishihira J, Tanaka
I |
(2007) "DNA
recognition mechanism of the ONECUT homeodomain of
transcription factor HNF-6." Structure,
15, 75-83. doi: 10.1016/j.str.2006.11.004.
|
Crystal structure of hnf-6alpha DNA-binding domain in
complex with the ttr promoter . SNAP output
|
|
2d7d
|
hydrolase-DNA |
X-ray (2.1 Å) |
Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR,
Barrett TE |
(2006) "Structural
insights into the cryptic DNA-dependent ATPase activity
of UvrB." J.Mol.Biol.,
357, 62-72. doi: 10.1016/j.jmb.2005.12.059.
|
Structural insights into the cryptic DNA dependent
atp-ase activity of uvrb . SNAP output
|
|
2d7g
|
hydrolase |
X-ray (3.3 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the aa complex of the n-terminal
domain of pria . SNAP
output
|
|
2d7h
|
hydrolase |
X-ray (3.0 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the ccc complex of the n-terminal
domain of pria . SNAP
output
|
|
2da8
|
DNA-antibiotic |
NMR |
Addess KJ, Sinsheimer JS, Feigon J |
(1993) "Solution
Structure of a Complex between
[N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2."
Biochemistry, 32, 2498. doi:
10.1021/BI00061A006.
|
Solution structure of a complex between
(n-mecys3,n-mecys7)tandem and (d(gatatc))2 . SNAP output
|
|
2db3
|
hydrolase-RNA |
X-ray (2.2 Å) |
Sengoku T, Nureki O, Nakamura A, Kobayashi S,
Yokoyama S |
(2006) "Structural
basis for RNA unwinding by the DEAD-box protein
Drosophila Vasa." Cell(Cambridge,Mass.),
125, 287-300. doi: 10.1016/j.cell.2006.01.054.
|
Structural basis for RNA unwinding by the dead-box
protein drosophila vasa . SNAP output
|
|
2ddg
|
hydrolase-DNA |
X-ray (2.1 Å) |
Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui
R |
(2007) "Crystal
structure of family 5 uracil-DNA glycosylase bound to
DNA." J.Mol.Biol., 373,
839-850. doi: 10.1016/j.jmb.2007.08.022.
|
Crystal structure of uracil-DNA glycosylase in complex
with ap:g containing DNA . SNAP output
|
|
2dem
|
hydrolase-DNA |
X-ray (1.95 Å) |
Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui
R |
(2007) "Crystal
structure of family 5 uracil-DNA glycosylase bound to
DNA." J.Mol.Biol., 373,
839-850. doi: 10.1016/j.jmb.2007.08.022.
|
Crystal structure of uracil-DNA glycosylase in complex
with ap:a containing DNA . SNAP output
|
|
2dgc
|
transcription-DNA |
X-ray (2.2 Å) |
Keller W, Konig P, Richmond TJ |
(1995) "Crystal
structure of a bZIP/DNA complex at 2.2 A: determinants
of DNA specific recognition." J.Mol.Biol.,
254, 657-667. doi: 10.1006/jmbi.1995.0645.
|
Gcn4 basic domain, leucine zipper complexed with
atf-creb site DNA . SNAP
output
|
|
2dlc
|
ligase-trna |
X-ray (2.4 Å) |
Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M,
Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T,
Nishikawa K, Nakamura KT |
(2007) "Structural
basis for recognition of cognate tRNA by tyrosyl-tRNA
synthetase from three kingdoms." Nucleic Acids
Res., 35, 4289-4300. doi:
10.1093/nar/gkm417.
|
Crystal structure of the ternary complex of yeast
tyrosyl-trna synthetase . SNAP output
|
|
2dnj
|
hydrolase-DNA |
X-ray (2.0 Å) |
Lahm A, Suck D |
(1991) "DNase
I-induced DNA conformation. 2 A structure of a DNase
I-octamer complex." J.Mol.Biol.,
222, 645-667. doi: 10.1016/0022-2836(91)90502-W.
|
Dnase i-induced DNA conformation. 2 angstroms structure
of a dnase i-octamer complex . SNAP output
|
|
2dp6
|
hydrolase-DNA |
X-ray (1.8 Å) |
Kosaka H, Nakagawa N, Masui R, Kuramitsu S |
"Structure of Family 5 Uracil-DNA Glycosylase Bound
to DNA Reveals Insights into the Mechanism for Substrate
Recognition and Catalysis." |
Crystal structure of uracil-DNA glycosylase in complex
with ap:c containing DNA . SNAP output
|
|
2dpd
|
DNA binding protein-DNA |
X-ray (3.17 Å) |
Vivian JP, Wilce J, Wilce MCJ |
"Crystal structure of the Replication Termination
Protein in complex with a pseudosymmetric B-site." |
Crystal structure of the replication termination
protein in complex with a pseudosymmetric b-site .
SNAP output
|
|
2dpi
|
transferase-DNA |
X-ray (2.3 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "Hoogsteen
base pair formation promotes synthesis opposite the
1,N(6)-ethenodeoxyadenosine lesion by human DNA
polymerase iota." Nat.Struct.Mol.Biol.,
13, 619-625. doi: 10.1038/nsmb1118.
|
Ternary complex of hpoli with DNA and dctp . SNAP output
|
|
2dpj
|
transferase-DNA |
X-ray (2.3 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "Hoogsteen
base pair formation promotes synthesis opposite the
1,N(6)-ethenodeoxyadenosine lesion by human DNA
polymerase iota." Nat.Struct.Mol.Biol.,
13, 619-625. doi: 10.1038/nsmb1118.
|
Structure of hpoli with DNA and dttp . SNAP output
|
|
2dpu
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Vivian JP, Wilce J, Wilce MCJ |
"Crystal structure of the replication termination
protein in complex with a pseudosymmetric 21mer B-site
DNA." |
Crystal structure of the replication termination
protein in complex with a pseudosymmetric 21mer b-site
DNA . SNAP output
|
|
2drp
|
transcription-DNA |
X-ray (2.8 Å) |
Fairall L, Schwabe JW, Chapman L, Finch JT, Rhodes
D |
(1993) "The
crystal structure of a two zinc-finger peptide reveals
an extension to the rules for zinc-finger/DNA
recognition." Nature,
366, 483-487. doi: 10.1038/366483a0.
|
The crystal structure of a two zinc-finger peptide
reveals an extension to the rules for zinc-finger-DNA
recognition . SNAP
output
|
|
2dtu
|
transferase-DNA |
X-ray (2.37 Å) |
Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie
S |
(2007) "Structural
and biochemical investigation of the role in
proofreading of a beta hairpin loop found in the
exonuclease domain of a replicative DNA polymerase of
the B family." J.Biol.Chem.,
282, 1432-1444. doi: 10.1074/jbc.M605675200.
|
Crystal structure of the beta hairpin loop deletion
variant of rb69 gp43 in complex with DNA containing an
abasic site analog . SNAP output
|
|
2dwl
|
hydrolase-DNA |
X-ray (3.2 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the pria protein complexed with
oligonucleotides . SNAP
output
|
|
2dwm
|
hydrolase-DNA |
X-ray (3.15 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the pria protein complexed with
oligonucleotides . SNAP
output
|
|
2dwn
|
hydrolase-DNA |
X-ray (3.35 Å) |
Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T,
Masai H, Saito M, Shirai T, Kohda D |
(2007) "Structural
basis of the 3'-end recognition of a leading strand in
stalled replication forks by PriA." EMBO
J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697.
|
Crystal structure of the pria protein complexed with
oligonucleotides . SNAP
output
|
|
2dy4
|
transferase-DNA |
X-ray (2.65 Å) |
Aller P, Rould MA, Hogg M, Wallace SS, Doublie S |
(2007) "A
structural rationale for stalling of a replicative DNA
polymerase at the most common oxidative thymine lesion,
thymine glycol." Proc.Natl.Acad.Sci.USA,
104, 814-818. doi: 10.1073/pnas.0606648104.
|
Crystal structure of rb69 gp43 in complex with DNA
containing thymine glycol . SNAP output
|
|
2e1c
|
transcription-DNA |
X-ray (2.1 Å) |
Yokoyama K, Ishijima SA, Koike H, Kurihara C,
Shimowasa A, Kabasawa M, Kawashima T, Suzuki M |
(2007) "Feast/Famine
Regulation by Transcription Factor FL11 for the
Survival of the Hyperthermophilic Archaeon Pyrococcus
OT3." Structure, 15,
1542-1554. doi: 10.1016/j.str.2007.10.015.
|
Structure of putative hth-type transcriptional
regulator ph1519-DNA complex . SNAP output
|
|
2e2h
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.95 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex at 5 mm mg2+ with
gtp . SNAP output
|
|
2e2i
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.41 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 5 mm mg+2 with
2'-dgtp . SNAP
output
|
|
2e2j
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.5 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 5 mm mg+2 with
gmpcpp . SNAP output
|
|
2e42
|
transcription-DNA |
X-ray (1.8 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada
K, Ogata K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer v285a
mutant bound to a high affinity DNA fragment . SNAP output
|
|
2e43
|
transcription-DNA |
X-ray (2.1 Å) |
Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada
K, Ogata K |
"Structural Basis for Flexible Base Recognition by
C/Ebpbeta." |
Crystal structure of c-ebpbeta bzip homodimer k269a
mutant bound to a high affinity DNA fragment . SNAP output
|
|
2e52
|
hydrolase-DNA |
X-ray (2.0 Å) |
Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I |
(2009) "Structures
of restriction endonuclease HindIII in complex with its
cognate DNA and divalent cations." Acta
Crystallogr.,Sect.D, 65,
1326-1333. doi: 10.1107/S0907444909041134.
|
Crystal structural analysis of hindiii restriction
endonuclease in complex with cognate DNA at 2.0
angstrom resolution . SNAP output
|
|
2ea0
|
hydrolase-DNA |
X-ray (1.4 Å) |
Golan G, Zharkov DO, Grollman AP, Shoham G |
"Active site plasticity of endonuclease VIII:
Conformational changes compensating for different
substrate and mutations of critical residues." |
Crystal structure of the DNA repair enzyme
endonuclease-viii (nei) from e. coli in complex with
ap-site containing DNA substrate . SNAP output
|
|
2efw
|
replication-DNA |
X-ray (2.5 Å) |
Vivian JP, Porter CJ, Wilce JA, Wilce MCJ |
(2007) "An
asymmetric structure of the Bacillus subtilis
replication terminator protein in complex with
DNA." J.Mol.Biol., 370,
481-491. doi: 10.1016/j.jmb.2007.02.067.
|
Crystal structure of the rtp:nrb complex from bacillus
subtilis . SNAP
output
|
|
2er8
|
transcription activator-DNA |
X-ray (2.85 Å) |
Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB,
Marmorstein R |
(2006) "Structure
of a Leu3-DNA complex: recognition of everted CGG
half-sites by a Zn2Cys6 binuclear cluster protein."
Structure, 14, 725-735. doi:
10.1016/j.str.2005.11.025.
|
Crystal structure of leu3 DNA-binding domain complexed
with a 12mer DNA duplex . SNAP output
|
|
2ere
|
transcription activator-DNA |
X-ray (3.0 Å) |
Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB,
Marmorstein R |
(2006) "Structure
of a Leu3-DNA complex: recognition of everted CGG
half-sites by a Zn2Cys6 binuclear cluster protein."
Structure, 14, 725-735. doi:
10.1016/j.str.2005.11.025.
|
Crystal structure of a leu3 DNA-binding domain
complexed with a 15mer DNA duplex . SNAP output
|
|
2erg
|
transcription activator-DNA |
X-ray (3.15 Å) |
Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB,
Marmorstein R |
(2006) "Structure
of a Leu3-DNA complex: recognition of everted CGG
half-sites by a Zn2Cys6 binuclear cluster protein."
Structure, 14, 725-735. doi:
10.1016/j.str.2005.11.025.
|
Crystal structure of leu3 DNA-binding domain with a
single h50c mutation complexed with a 15mer DNA duplex
. SNAP output
|
|
2es2
|
gene regulation |
X-ray (1.78 Å) |
Max KE, Zeeb M, Bienert R, Balbach J, Heinemann
U |
(2006) "T-rich
DNA single strands bind to a preformed site on the
bacterial cold shock protein Bs-CspB."
J.Mol.Biol., 360, 702-714.
doi: 10.1016/j.jmb.2006.05.044.
|
Crystal structure analysis of the bacillus subtilis
cold shock protein bs-cspb in complex with
hexathymidine . SNAP
output
|
|
2etw
|
cell cycle-DNA |
X-ray (1.67 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Principles of protein-DNA recognition revealed in the
structural analysis of ndt80-mse DNA complexes .
SNAP output
|
|
2euv
|
cell cycle-DNA |
X-ray (1.94 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Principles of protein-DNA recognition revealed in the
structural analysis of ndt80-mse DNA complexes .
SNAP output
|
|
2euw
|
cell cycle-DNA |
X-ray (1.68 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma4t) .
SNAP output
|
|
2eux
|
cell cycle-DNA |
X-ray (1.57 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse variant va4g) .
SNAP output
|
|
2euz
|
cell cycle-DNA |
X-ray (1.56 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant mc5t) .
SNAP output
|
|
2evf
|
cell cycle-DNA |
X-ray (1.56 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma6t) .
SNAP output
|
|
2evg
|
cell cycle-DNA |
X-ray (1.55 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma7t) .
SNAP output
|
|
2evh
|
cell cycle-DNA |
X-ray (1.989 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma7g) .
SNAP output
|
|
2evi
|
cell cycle-DNA |
X-ray (1.8 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of a ndt80-DNA complex (mse mutant ma8t) .
SNAP output
|
|
2evj
|
cell cycle-DNA |
X-ray (1.89 Å) |
Lamoureux JS, Glover JN |
(2006) "Principles
of Protein-DNA Recognition Revealed in the Structural
Analysis of Ndt80-MSE DNA Complexes."
Structure, 14, 555-565. doi:
10.1016/j.str.2005.11.017.
|
Structure of an ndt80-DNA complex (mse mutant ma9c) .
SNAP output
|
|
2ewj
|
replication-DNA |
X-ray (2.7 Å) |
Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon
C, Hill TM, Dixon NE |
(2006) "A
molecular mousetrap determines polarity of termination
of DNA replication in E. coli."
Cell(Cambridge,Mass.), 125,
1309-1319. doi: 10.1016/j.cell.2006.04.040.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA- locked form . SNAP output
|
|
2ex5
|
hydrolase-DNA |
X-ray (2.2 Å) |
Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux
C, Stoddard BL |
(2006) "The
structure of I-CeuI homing endonuclease: Evolving
asymmetric DNA recognition from a symmetric protein
scaffold." Structure, 14,
869-880. doi: 10.1016/j.str.2006.03.009.
|
Group i intron-encoded homing endonuclease i-ceui
complexed with DNA . SNAP output
|
|
2exf
|
viral protein-DNA |
NMR |
Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF,
Roques BP, Mely Y, Bouaziz S, Morellet N |
(2008) "How the
HIV-1 nucleocapsid protein binds and destabilises the
(-)primer binding site during reverse
transcription." J.Mol.Biol.,
383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046.
|
Solution structure of the hiv-1 nucleocapsid
(ncp7(12-55)) complexed with the DNA (-) primer binding
site . SNAP output
|
|
2ezd
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the second DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, minimized average structure . SNAP output
|
|
2eze
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the second DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, 35 structures . SNAP output
|
|
2ezf
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the third DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, minimized average structure . SNAP output
|
|
2ezg
|
DNA binding protein-DNA |
NMR |
Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R,
Gronenborn AM, Clore GM |
(1997) "The
solution structure of an HMG-I(Y)-DNA complex defines a
new architectural minor groove binding motif."
Nat.Struct.Biol., 4, 657-665.
doi: 10.1038/nsb0897-657.
|
Solution structure of a complex of the third DNA
binding domain of human hmg-i(y) bound to DNA dodecamer
containing the prdii site of the interferon-beta
promoter, NMR, 35 structures . SNAP output
|
|
2ezv
|
hydrolase-DNA |
X-ray (2.4 Å) |
Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S,
Schildkraut I, Aggarwal AK |
(2005) "A view
of consecutive binding events from structures of
tetrameric endonuclease SfiI bound to DNA."
Embo J., 24, 4198-4208. doi:
10.1038/sj.emboj.7600880.
|
Crystal structure of tetrameric restriction
endonuclease sfii bound to cognate DNA. . SNAP output
|
|
2f03
|
hydrolase-DNA |
X-ray (3.05 Å) |
Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S,
Schildkraut I, Aggarwal AK |
(2005) "A view
of consecutive binding events from structures of
tetrameric endonuclease SfiI bound to DNA."
Embo J., 24, 4198-4208. doi:
10.1038/sj.emboj.7600880.
|
Crystal structure of tetrameric restriction
endonuclease sfii in complex with cognate DNA (partial
bound form) . SNAP
output
|
|
2f55
|
hydrolase-DNA |
X-ray (3.3 Å) |
Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora
B, Sharma SD, Cameron CE, Raney KD, Sakon J |
(2006) "Structural
and biological identification of residues on the
surface of NS3 helicase required for optimal
replication of the hepatitis C virus."
J.Biol.Chem., 281, 3528-3535.
doi: 10.1074/jbc.M512100200.
|
Two hepatitis c virus ns3 helicase domains complexed
with the same strand of DNA . SNAP output
|
|
2f5n
|
hydrolase-DNA |
X-ray (2.0 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Mutm crosslinked to undamaged DNA sampling a:t base
pair ic1 . SNAP
output
|
|
2f5o
|
hydrolase-DNA |
X-ray (2.05 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Mutm crosslinked to undamaged DNA sampling g:c base
pair ic3 . SNAP
output
|
|
2f5p
|
hydrolase-DNA |
X-ray (2.0 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Mutm crosslinked to undamaged DNA sampling a:t base
pair ic2 . SNAP
output
|
|
2f5q
|
hydrolase-DNA |
X-ray (2.35 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Catalytically inactive (e3q) mutm crosslinked to oxog:c
containing DNA cc2 . SNAP output
|
|
2f5s
|
hydrolase-DNA |
X-ray (2.35 Å) |
Banerjee A, Santos WL, Verdine GL |
(2006) "Structure
of a DNA glycosylase searching for lesions."
Science, 311, 1153-1157. doi:
10.1126/science.1120288.
|
Catalytically inactive (e3q) mutm crosslinked to oxog:c
containing DNA cc1 . SNAP output
|
|
2f8n
|
structural protein-DNA |
X-ray (2.9 Å) |
Chakravarthy S, Luger K |
"Nucleosomes containing the histone domain of
macroH2A: In vitro possibilities." |
2.9 angstrom x-ray structure of hybrid macroh2a
nucleosomes . SNAP
output
|
|
2f8x
|
transcription-DNA |
X-ray (3.25 Å) |
Nam Y, Sliz P, Song L, Aster JC, Blacklow SC |
(2006) "Structural
basis for cooperativity in recruitment of MAML
coactivators to Notch transcription complexes."
Cell(Cambridge,Mass.), 124,
973-983. doi: 10.1016/j.cell.2005.12.037.
|
Crystal structure of activated notch, csl and maml on
hes-1 promoter DNA sequence . SNAP output
|
|
2fcc
|
hydrolase |
X-ray (2.3 Å) |
Golan G, Zharkov DO, Grollman AP, Dodson ML,
McCullough AK, Lloyd RS, Shoham G |
(2006) "Structure
of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine
Covalent Complex with Abasic Site-containing DNA."
J.Mol.Biol., 362, 241-258.
doi: 10.1016/j.jmb.2006.06.059.
|
Crystal structure of t4 pyrimidine dimer glycosylase
(t4-pdg) covalently complexed with a DNA substrate
containing abasic site . SNAP output
|
|
2fd8
|
oxidoreductase-DNA |
X-ray (2.3 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t .
SNAP output
|
|
2fdc
|
DNA binding protein-DNA |
X-ray (3.3 Å) |
Truglio JJ, Karakas E, Rhau B, Wang H, DellaVecchia
MJ, Van Houten B, Kisker C |
(2006) "Structural
basis for DNA recognition and processing by UvrB."
Nat.Struct.Mol.Biol., 13,
360-364. doi: 10.1038/nsmb1072.
|
Structural basis of DNA damage recognition and
processing by uvrb: crystal structure of a uvrb-DNA
complex . SNAP
output
|
|
2fdf
|
oxidoreductase-DNA |
X-ray (2.1 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with co(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t .
SNAP output
|
|
2fdg
|
oxidoreductase-DNA |
X-ray (2.2 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
succinate, and methylated trinucleotide t-mea-t .
SNAP output
|
|
2fdh
|
oxidoreductase-DNA |
X-ray (2.1 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with mn(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t .
SNAP output
|
|
2fdi
|
oxidoreductase-DNA |
X-ray (1.8 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t
(air 3 hours) . SNAP
output
|
|
2fdk
|
oxidoreductase-DNA |
X-ray (2.3 Å) |
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC,
Gibney BR, Hunt JF |
(2006) "Crystal
structures of catalytic complexes of the oxidative
DNA/RNA repair enzyme AlkB." Nature,
439, 879-884. doi: 10.1038/nature04561.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate, and methylated trinucleotide t-mea-t
(air 9 days) . SNAP
output
|
|
2ff0
|
hormone-growth factor-DNA |
NMR |
Little TH, Zhang Y, Matulis CK, Weck J, Zhang Z,
Ramachandran A, Mayo KE, Radhakrishnan I |
(2006) "Sequence-specific
deoxyribonucleic Acid (DNA) recognition by
steroidogenic factor 1: a helix at the carboxy terminus
of the DNA binding domain is necessary for complex
stability." Mol.Endocrinol.,
20, 831-843. doi: 10.1210/me.2005-0384.
|
Solution structure of steroidogenic factor 1 DNA
binding domain bound to its target sequence in the
inhibin alpha-subunit promoter . SNAP output
|
|
2fio
|
transcription-DNA |
X-ray (2.7 Å) |
Badia D, Camacho A, Perez-Lago L, Escandon C, Salas
M, Coll M |
(2006) "The
structure of phage phi29 transcription regulator p4-DNA
complex reveals an N-hook motif for DNA."
Mol.Cell, 22, 73-81. doi:
10.1016/j.molcel.2006.02.019.
|
Phage phi29 transcription regulator p4-DNA complex .
SNAP output
|
|
2fj7
|
structural protein-DNA |
X-ray (3.2 Å) |
Bao Y, White CL, Luger K |
(2006) "Nucleosome
Core Particles Containing a Poly(dA.dT) Sequence
Element Exhibit a Locally Distorted DNA Structure."
J.Mol.Biol., 361, 617-624.
doi: 10.1016/j.jmb.2006.06.051.
|
Crystal structure of nucleosome core particle
containing a poly (da.dt) sequence element . SNAP output
|
|
2fjv
|
transferase-DNA |
X-ray (2.05 Å) |
Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson
WD, Georgiadis MM, Long EC |
(2006) "A
High-Throughput, High-Resolution Strategy for the Study
of Site-Selective DNA Binding Agents: Analysis of a
"Highly Twisted" Benzimidazole-Diamidine."
J.Am.Chem.Soc., 128,
7846-7854. doi: 10.1021/ja0600936.
|
Rt29 bound to d(cttaattcgaattaag) in complex with mmlv
rt catalytic fragment . SNAP output
|
|
2fjw
|
transferase-DNA |
X-ray (1.95 Å) |
Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson
WD, Georgiadis MM, Long EC |
(2006) "A
High-Throughput, High-Resolution Strategy for the Study
of Site-Selective DNA Binding Agents: Analysis of a
"Highly Twisted" Benzimidazole-Diamidine."
J.Am.Chem.Soc., 128,
7846-7854. doi: 10.1021/ja0600936.
|
D(cttgaatgcattcaag) in complex with mmlv rt catalytic
fragment . SNAP
output
|
|
2fjx
|
transferase-DNA |
X-ray (1.8 Å) |
Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson
WD, Georgiadis MM, Long EC |
(2006) "A
High-Throughput, High-Resolution Strategy for the Study
of Site-Selective DNA Binding Agents: Analysis of a
"Highly Twisted" Benzimidazole-Diamidine."
J.Am.Chem.Soc., 128,
7846-7854. doi: 10.1021/ja0600936.
|
Rt29 bound to d(cttgaatgcattcaag) in complex with mmlv
rt catalytic fragment . SNAP output
|
|
2fkc
|
hydrolase-DNA |
X-ray (2.39 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Crystal form i of pre-reactive complex of restriction
endonuclease hinp1i with cognate DNA and calcium ion .
SNAP output
|
|
2fkh
|
hydrolase-DNA |
X-ray (3.09 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Crystal form ii of pre-reactive complex of restriction
endonuclease hinp1i with cognate DNA and calcium ions .
SNAP output
|
|
2fl3
|
hydrolase-DNA |
X-ray (2.39 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Binary complex of restriction endonuclease hinp1i with
cognate DNA . SNAP
output
|
|
2flc
|
hydrolase-DNA |
X-ray (2.59 Å) |
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG,
Roberts RJ, Cheng X |
(2006) "DNA
nicking by HinP1I endonuclease: bending, base flipping
and minor groove expansion." Nucleic Acids
Res., 34, 939-948. doi: 10.1093/nar/gkj484.
|
Post-reactive complex of restriction endonuclease
hinp1i with nicked cognate DNA and magnesium ions .
SNAP output
|
|
2fld
|
hydrolase-DNA |
X-ray (2.0 Å) |
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat
RJ, Stoddard BL, Baker D |
(2006) "Computational
redesign of endonuclease DNA binding and cleavage
specificity." Nature,
441, 656-659. doi: 10.1038/nature04818.
|
I-msoi re-designed for altered DNA cleavage specificity
. SNAP output
|
|
2fll
|
replication-DNA |
X-ray (2.6 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "An
incoming nucleotide imposes an anti to syn
conformational change on the templating purine in the
human DNA polymerase-iota active site."
Structure, 14, 749-755. doi:
10.1016/j.str.2006.01.010.
|
Ternary complex of human DNA polymerase iota with DNA
and dttp . SNAP
output
|
|
2fln
|
replication-DNA |
X-ray (2.5 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "An
incoming nucleotide imposes an anti to syn
conformational change on the templating purine in the
human DNA polymerase-iota active site."
Structure, 14, 749-755. doi:
10.1016/j.str.2006.01.010.
|
Binary complex of catalytic core of human DNA
polymerase iota with DNA (template a) . SNAP output
|
|
2flp
|
replication-DNA |
X-ray (2.4 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2006) "An
incoming nucleotide imposes an anti to syn
conformational change on the templating purine in the
human DNA polymerase-iota active site."
Structure, 14, 749-755. doi:
10.1016/j.str.2006.01.010.
|
Binary complex of the catalytic core of human DNA
polymerase iota with DNA (template g) . SNAP output
|
|
2fmp
|
transferase-DNA |
X-ray (1.65 Å) |
Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC,
Wilson SH |
(2006) "Magnesium-induced
assembly of a complete DNA polymerase catalytic
complex." Structure, 14,
757-766. doi: 10.1016/j.str.2006.01.011.
|
DNA polymerase beta with a terminated gapped DNA
substrate and ddctp with sodium in the catalytic site .
SNAP output
|
|
2fmq
|
transferase-DNA |
X-ray (2.2 Å) |
Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC,
Wilson SH |
(2006) "Magnesium-induced
assembly of a complete DNA polymerase catalytic
complex." Structure, 14,
757-766. doi: 10.1016/j.str.2006.01.011.
|
Sodium in active site of DNA polymerase beta . SNAP output
|
|
2fms
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC,
Wilson SH |
(2006) "Magnesium-induced
assembly of a complete DNA polymerase catalytic
complex." Structure, 14,
757-766. doi: 10.1016/j.str.2006.01.011.
|
DNA polymerase beta with a gapped DNA substrate and
dumpnpp with magnesium in the catalytic site . SNAP output
|
|
2fo1
|
gene regulation-signalling protein-DNA |
X-ray (3.12 Å) |
Wilson JJ, Kovall RA |
(2006) "Crystal
structure of the CSL-Notch-Mastermind ternary complex
bound to DNA." Cell(Cambridge,Mass.),
124, 985-996. doi: 10.1016/j.cell.2006.01.035.
|
Crystal structure of the csl-notch-mastermind ternary
complex bound to DNA . SNAP output
|
|
2fqz
|
hydrolase-DNA |
X-ray (2.0 Å) |
Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis
S, Czapinska H, Manakova E, Siksnys V |
(2006) "Nucleotide
flips determine the specificity of the Ecl18kI
restriction endonuclease." Embo J.,
25, 2219-2229. doi: 10.1038/sj.emboj.7601096.
|
Metal-depleted ecl18ki in complex with uncleaved DNA .
SNAP output
|
|
2fr4
|
immune system-DNA |
X-ray (1.95 Å) |
Ou Z, Bottoms CA, Henzl MT, Tanner JJ |
(2007) "Impact
of DNA hairpin folding energetics on antibody-ssDNA
association." J.Mol.Biol.,
374, 1029-1040. doi: 10.1016/j.jmb.2007.09.084.
|
Structure of fab DNA-1 complexed with a stem-loop DNA
ligand . SNAP output
|
|
2fvp
|
transferase-DNA |
X-ray (2.25 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
|
2fvq
|
transferase-DNA |
X-ray (2.3 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
|
2fvr
|
transferase-DNA |
X-ray (2.2 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
|
2fvs
|
transferase-DNA |
X-ray (2.35 Å) |
Montano SP, Cote ML, Roth MJ, Georgiadis MM |
(2006) "Crystal
structures of oligonucleotides including the integrase
processing site of the Moloney murine leukemia
virus." Nucleic Acids Res.,
34, 5353-5360. doi: 10.1093/nar/gkl693.
|
A structural study of the ca dinucleotide step in the
integrase processing site of moloney murine leukemia
virus . SNAP output
|
|
2g1p
|
transferase-DNA |
X-ray (1.89 Å) |
Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng
X |
(2006) "Structure
and substrate recognition of the Escherichia coli DNA
adenine methyltransferase." J.Mol.Biol.,
358, 559-570. doi: 10.1016/j.jmb.2006.02.028.
|
Structure of e. coli DNA adenine methyltransferase
(dam) . SNAP output
|
|
2g8f
|
hydrolase-RNA-DNA |
X-ray (1.65 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain e188a mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
|
2g8h
|
hydrolase-RNA-DNA |
X-ray (1.85 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d192n mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
|
2g8i
|
hydrolase-RNA-DNA |
X-ray (1.65 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d192n mutant in
complex with mn2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
|
2g8k
|
hydrolase-RNA-DNA |
X-ray (1.65 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d192n mutant in
complex with ca2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
|
2g8u
|
hydrolase-RNA-DNA |
X-ray (2.7 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain d132n mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site) . SNAP
output
|
|
2g8v
|
hydrolase-RNA-DNA |
X-ray (1.85 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain e188a mutant in
complex with mg2+ and RNA-DNA hybrid (reaction product)
. SNAP output
|
|
2g8w
|
hydrolase-RNA-DNA |
X-ray (2.05 Å) |
Nowotny M, Yang W |
(2006) "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
|
B. halodurans rnase h catalytic domain e188a mutant in
complex with ca2+ and RNA-DNA hybrid . SNAP output
|
|
2gat
|
transcription-DNA |
NMR |
Tjandra N, Omichinski JG, Gronenborn AM, Clore GM,
Bax A |
(1997) "Use of
dipolar 1H-15N and 1H-13C couplings in the structure
determination of magnetically oriented macromolecules
in solution." Nat.Struct.Biol.,
4, 732-738. doi: 10.1038/nsb0997-732.
|
Solution structure of the c-terminal domain of chicken
gata-1 bound to DNA, NMR, regularized mean structure .
SNAP output
|
|
2gb7
|
hydrolase-DNA |
X-ray (1.7 Å) |
Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis
S, Czapinska H, Manakova E, Siksnys V |
(2006) "Nucleotide
flips determine the specificity of the Ecl18kI
restriction endonuclease." Embo J.,
25, 2219-2229. doi: 10.1038/sj.emboj.7601096.
|
Metal-depleted ecl18ki in complex with uncleaved,
modified DNA . SNAP
output
|
|
2ge5
|
hydrolase-DNA |
X-ray (2.4 Å) |
Hiller DA, Perona JJ |
(2006) "Positively
Charged C-Terminal Subdomains of EcoRV Endonuclease:
Contributions to DNA Binding, Bending, and
Cleavage." Biochemistry,
45, 11453-11463. doi: 10.1021/bi0606400.
|
Ecorv restriction endonuclease c-terminal deletion
mutant-gatatc-ca2+ . SNAP output
|
|
2geq
|
transcription-DNA |
X-ray (2.3 Å) |
Ho WC, Fitzgerald MX, Marmorstein R |
(2006) "Structure
of the p53 Core Domain Dimer Bound to DNA."
J.Biol.Chem., 281,
20494-20502. doi: 10.1074/jbc.M603634200.
|
Crystal structure of a p53 core dimer bound to DNA .
SNAP output
|
|
2gie
|
hydrolase-DNA |
X-ray (2.6 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Hincii bound to cognate DNA gttaac . SNAP output
|
|
2gig
|
hydrolase-DNA |
X-ray (1.83 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Alteration of sequence specificity of the type ii
restriction endonuclease hincii through an indirect
readout mechanism . SNAP
output
|
|
2gih
|
hydrolase-DNA |
X-ray (2.5 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Q138f hincii bound to cognate DNA gtcgac and ca2+ .
SNAP output
|
|
2gii
|
hydrolase-DNA |
X-ray (2.3 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Q138f hincii bound to cognate DNA gttaac . SNAP output
|
|
2gij
|
hydrolase-DNA |
X-ray (1.93 Å) |
Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton
NC |
(2006) "Alteration
of Sequence Specificity of the Type II Restriction
Endonuclease HincII through an Indirect Readout
Mechanism." J.Biol.Chem.,
281, 23852-23869. doi: 10.1074/jbc.M512339200.
|
Q138f hincii bound to cognate DNA gttaac and ca2+ .
SNAP output
|
|
2gkd
|
toxin-DNA |
NMR |
Singh S, Hager MH, Zhang C, Griffith BR, Lee MS,
Hallenga K, Markley JL, Thorson JS |
(2006) "Structural
insight into the self-sacrifice mechanism of enediyne
resistance." Acs Chem.Biol.,
1, 451-460. doi: 10.1021/cb6002898.
|
Structural insight into self-sacrifice mechanism of
enediyne resistance . SNAP output
|
|
2gli
|
transcription-DNA |
X-ray (2.6 Å) |
Pavletich NP, Pabo CO |
(1993) "Crystal
structure of a five-finger GLI-DNA complex: new
perspectives on zinc fingers." Science,
261, 1701-1707.
|
Five-finger gli-DNA complex . SNAP output
|
|
2glo
|
transcription-DNA |
NMR |
Cordier F, Hartmann B, Rogowski M, Affolter M,
Grzesiek S |
(2006) "DNA
recognition by the brinker repressor - an extreme case
of coupling between binding and folding."
J.Mol.Biol., 361, 659-672.
doi: 10.1016/j.jmb.2006.06.045.
|
Solution structure of the brinker DNA binding domain in
complex with the omb enhancer . SNAP output
|
|
2gm4
|
recombination, DNA |
X-ray (3.5 Å) |
Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV,
Boocock MR, Grindley ND, Steitz TA |
(2006) "Implications
of structures of synaptic tetramers of gamma delta
resolvase for the mechanism of recombination."
Proc.Natl.Acad.Sci.Usa, 103,
10642-10647. doi: 10.1073/pnas.0604062103.
|
An activated, tetrameric gamma-delta resolvase: hin
chimaera bound to cleaved DNA . SNAP output
|
|
2gws
|
transferase-DNA |
X-ray (2.4 Å) |
Picher AJ, Garcia-Diaz M, Bebenek K, Pedersen LC,
Kunkel TA, Blanco L |
(2006) "Promiscuous
mismatch extension by human DNA polymerase lambda."
Nucleic Acids Res., 34,
3259-3266. doi: 10.1093/nar/gkl377.
|
Crystal structure of human DNA polymerase lambda with a
g-g mismatch in the primer terminus . SNAP output
|
|
2gxa
|
replication-DNA |
X-ray (3.15 Å) |
Enemark EJ, Joshua-Tor L |
(2006) "Mechanism
of DNA translocation in a replicative hexameric
helicase." Nature, 442,
270-275. doi: 10.1038/nature04943.
|
Crystal structure of papillomavirus e1 hexameric
helicase with ssDNA and mgadp . SNAP output
|
|
2gzk
|
DNA-structural protein |
NMR |
Stott K, Tang GS, Lee KB, Thomas JO |
(2006) "Structure
of a Complex of Tandem HMG Boxes and DNA."
J.Mol.Biol., 360, 90-104.
doi: 10.1016/j.jmb.2006.04.059.
|
Structure of a complex of tandem hmg boxes and DNA .
SNAP output
|
|
2h1k
|
transcription-DNA |
X-ray (2.42 Å) |
Longo A, Guanga GP, Rose RB |
(2007) "Structural
basis for induced fit mechanisms in DNA recognition by
the pdx1 homeodomain." Biochemistry,
46, 2948-2957. doi: 10.1021/bi060969l.
|
Crystal structure of the pdx1 homeodomain in complex
with DNA . SNAP
output
|
|
2h1o
|
gene regulation-DNA complex |
X-ray (3.0 Å) |
Mattison K, Wilbur JS, So M, Brennan RG |
(2006) "Structure
of FitAB from Neisseria gonorrhoeae bound to DNA
reveals a tetramer of toxin-antitoxin heterodimers
containing pin domains and ribbon-helix-helix
motifs." J.Biol.Chem.,
281, 37942-37951. doi: 10.1074/jbc.M605198200.
|
Structure of fitab bound to ir36 DNA fragment .
SNAP output
|
|
2h27
|
transferase-DNA |
X-ray (2.3 Å) |
Lane WJ, Darst SA |
(2006) "The
structural basis for promoter -35 element recognition
by the group IV sigma factors." Plos
Biol., 4, e269. doi: 10.1371/journal.pbio.0040269.
|
Crystal structure of escherichia coli sigmae region 4
bound to its-35 element DNA . SNAP output
|
|
2h3a
|
immune system-DNA |
NMR |
Madl T, Van Melderen L, Mine N, Respondek M, Oberer
M, Keller W, Khatai L, Zangger K |
(2006) "Structural
Basis for Nucleic Acid and Toxin Recognition of the
Bacterial Antitoxin CcdA." J.Mol.Biol.,
364, 170-185. doi: 10.1016/j.jmb.2006.08.082.
|
Structural basis for nucleic acid and toxin recognition
of the bacterial antitoxin ccda . SNAP output
|
|
2h3c
|
immune system-DNA |
NMR |
Madl T, Van Melderen L, Mine N, Respondek M, Oberer
M, Keller W, Khatai L, Zangger K |
(2006) "Structural
Basis for Nucleic Acid and Toxin Recognition of the
Bacterial Antitoxin CcdA." J.Mol.Biol.,
364, 170-185. doi: 10.1016/j.jmb.2006.08.082.
|
Structural basis for nucleic acid and toxin recognition
of the bacterial antitoxin ccda . SNAP output
|
|
2h7f
|
isomerase-DNA |
X-ray (2.7 Å) |
Perry K, Hwang Y, Bushman FD, Van Duyne GD |
(2006) "Structural
basis for specificity in the poxvirus
topoisomerase." Mol.Cell,
23, 343-354. doi: 10.1016/j.molcel.2006.06.015.
|
Structure of variola topoisomerase covalently bound to
DNA . SNAP output
|
|
2h7g
|
isomerase-DNA |
X-ray (1.9 Å) |
Perry K, Hwang Y, Bushman FD, Van Duyne GD |
(2006) "Structural
basis for specificity in the poxvirus
topoisomerase." Mol.Cell,
23, 343-354. doi: 10.1016/j.molcel.2006.06.015.
|
Structure of variola topoisomerase non-covalently bound
to DNA . SNAP output
|
|
2h7h
|
viral protein-DNA |
X-ray (2.3 Å) |
Kim Y, Borovilos M |
"Crystal structure of the JUN BZIP homodimer
complexed with AP-1 DNA." |
Crystal structure of the jun bzip homodimer complexed
with ap-1 DNA . SNAP
output
|
|
2h8c
|
hydrolase-DNA |
X-ray (3.1 Å) |
Macmaster R, Sedelnikova S, Baker PJ, Bolt EL, Lloyd
RG, Rafferty JB |
(2006) "RusA
Holliday junction resolvase: DNA complex
structure--insights into selectivity and
specificity." Nucleic Acids Res.,
34, 5577-5584. doi: 10.1093/nar/gkl447.
|
Structure of rusa d70n in complex with DNA . SNAP output
|
|
2h8r
|
transcription activator-DNA |
X-ray (3.2 Å) |
Lu P, Rha GB, Chi YI |
(2007) "Structural
basis of disease-causing mutations in hepatocyte
nuclear factor 1beta." Biochemistry,
46, 12071-12080. doi: 10.1021/bi7010527.
|
Hepatocyte nuclear factor 1b bound to DNA: mody5 gene
product . SNAP
output
|
|
2han
|
transcription-DNA |
X-ray (1.95 Å) |
Jakob M, Kolodziejczyk R, Orlowski M, Krzywda S,
Kowalska A, Dutko-Gwozdz J, Gwozdz T, Kochman M,
Jaskolski M, Ozyhar A |
(2007) "Novel
DNA-binding element within the C-terminal extension of
the nuclear receptor DNA-binding domain."
Nucleic Acids Res., 35,
2705-2718. doi: 10.1093/nar/gkm162.
|
Structural basis of heterodimeric ecdysteroid receptor
interaction with natural response element hsp27 gene
promoter . SNAP
output
|
|
2hap
|
gene regulation-DNA |
X-ray (2.5 Å) |
King DA, Zhang L, Guarente L, Marmorstein R |
(1999) "Structure
of HAP1-18-DNA implicates direct allosteric effect of
protein-DNA interactions on transcriptional
activation." Nat.Struct.Biol.,
6, 22-27. doi: 10.1038/4893.
|
Structure of a hap1-18-DNA complex reveals that
protein-DNA interactions can have direct allosteric
effects on transcriptional activation . SNAP output
|
|
2hax
|
gene regulation-DNA |
X-ray (1.29 Å) |
Max KE, Zeeb M, Bienert R, Balbach J, Heinemann
U |
(2007) "Common
mode of DNA binding to cold shock domains. Crystal
structure of hexathymidine bound to the domain-swapped
form of a major cold shock protein from Bacillus
caldolyticus." Febs J.,
274, 1265-1279. doi: 10.1111/j.1742-4658.2007.05672.x.
|
Crystal structure of bacillus caldolyticus cold shock
protein in complex with hexathymidine . SNAP output
|
|
2hdc
|
protein-DNA |
NMR |
Jin C, Marsden I, Chen X, Liao X |
(1999) "Dynamic
DNA contacts observed in the NMR structure of winged
helix protein-DNA complex." J.Mol.Biol.,
289, 683-690. doi: 10.1006/jmbi.1999.2819.
|
Structure of transcription factor genesis-DNA complex .
SNAP output
|
|
2hdd
|
transcription-DNA |
X-ray (1.9 Å) |
Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE,
Sauer RT, Pabo CO |
(1997) "Engrailed
(Gln50-->Lys) homeodomain-DNA complex at 1.9 A
resolution: structural basis for enhanced affinity and
altered specificity." Structure,
5, 1047-1054. doi: 10.1016/S0969-2126(97)00256-6.
|
Engrailed homeodomain q50k variant DNA complex .
SNAP output
|
|
2heo
|
immune system-DNA |
X-ray (1.7 Å) |
Magis C, Gasparini D, Lecoq A, Le Du MH, Stura E,
Charbonnier JB, Mourier G, Boulain JC, Pardo L, Caruana
A, Joly A, Lefranc M, Masella M, Menez A, Cuniasse P |
(2006) "Structure-based
secondary structure-independent approach to design
protein ligands: Application to the design of Kv1.2
potassium channel blockers."
J.Am.Chem.Soc., 128,
16190-16205. doi: 10.1021/ja0646491.
|
General structure-based approach to the design of
protein ligands: application to the design of kv1.2
potassium channel blockers. . SNAP output
|
|
2hhq
|
transferase-DNA |
X-ray (1.8 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
O6-methyl-guanine:t pair in the polymerase-10 basepair
position . SNAP
output
|
|
2hhs
|
transferase-DNA |
X-ray (1.8 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
O6-methyl:c pair in the polymerase-10 basepair position
. SNAP output
|
|
2hht
|
transferase-DNA |
X-ray (2.05 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
C:o6-methyl-guanine pair in the polymerase-2 basepair
position . SNAP
output
|
|
2hhu
|
transferase-DNA |
X-ray (1.8 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
C:o6-methyl-guanine in the polymerase postinsertion
site (-1 basepair position) . SNAP output
|
|
2hhv
|
transferase-DNA |
X-ray (1.55 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
T:o6-methyl-guanine in the polymerase-2 basepair
position . SNAP
output
|
|
2hhw
|
transferase-DNA |
X-ray (1.88 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
Ddttp:o6-methyl-guanine pair in the polymerase active
site, in the closed conformation . SNAP output
|
|
2hhx
|
transferase-DNA |
X-ray (2.26 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
O6-methyl-guanine in the polymerase template
preinsertion site . SNAP
output
|
|
2hmi
|
immune system-DNA |
X-ray (2.8 Å) |
Ding J, Das K, Hsiou Y, Sarafianos SG, Clark Jr AD,
Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E |
(1998) "Structure
and functional implications of the polymerase active
site region in a complex of HIV-1 RT with a
double-stranded DNA template-primer and an antibody Fab
fragment at 2.8 A resolution."
J.Mol.Biol., 284, 1095-1111.
doi: 10.1006/jmbi.1998.2208.
|
Hiv-1 reverse transcriptase-fragment of fab 28-DNA
complex . SNAP
output
|
|
2hof
|
recombination-DNA |
X-ray (2.4 Å) |
Ghosh K, Guo F, Van Duyne GD |
(2007) "Synapsis
of loxP sites by Cre recombinase."
J.Biol.Chem., 282,
24004-24016. doi: 10.1074/jbc.M703283200.
|
Crystal structure of the pre-cleavage synaptic complex
in the cre-loxp site-specific recombination . SNAP output
|
|
2hoi
|
recombination-DNA |
X-ray (2.601 Å) |
Ghosh K, Guo F, Van Duyne GD |
(2007) "Synapsis
of loxP sites by Cre recombinase."
J.Biol.Chem., 282,
24004-24016. doi: 10.1074/jbc.M703283200.
|
Crystal structure of the tetrameric pre-cleavage
synaptic complex in the cre-loxp site-specific
recombination . SNAP
output
|
|
2hos
|
transcription-DNA |
X-ray (1.9 Å) |
Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE,
Shokat KM |
(2006) "Structure
and properties of a re-engineered homeodomain
protein-DNA interface." Acs Chem.Biol.,
1, 755-760. doi: 10.1021/cb6003756.
|
Phage-selected homeodomain bound to unmodified DNA .
SNAP output
|
|
2hot
|
transcription-DNA |
X-ray (2.19 Å) |
Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE,
Shokat KM |
(2006) "Structure
and properties of a re-engineered homeodomain
protein-DNA interface." Acs Chem.Biol.,
1, 755-760. doi: 10.1021/cb6003756.
|
Phage selected homeodomain bound to modified DNA .
SNAP output
|
|
2hr1
|
transferase-DNA |
X-ray (1.96 Å) |
Shieh FK, Youngblood B, Reich NO |
(2006) "The Role
of Arg165 Towards Base Flipping, Base Stabilization and
Catalysis in M.HhaI." J.Mol.Biol.,
362, 516-527. doi: 10.1016/j.jmb.2006.07.030.
|
Ternary structure of wt m.hhai c5-cytosine DNA
methyltransferase with unmodified DNA and adohcy .
SNAP output
|
|
2ht0
|
transcription-DNA |
X-ray (2.0 Å) |
Swinger KK, Rice PA |
(2007) "Structure-based
Analysis of HU-DNA Binding." J.Mol.Biol.,
365, 1005-1016. doi: 10.1016/j.jmb.2006.10.024.
|
Ihf bound to doubly nicked DNA . SNAP output
|
|
2hvh
|
transferase-DNA |
X-ray (2.492 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
Ddctp:o6meg pair in the polymerase active site (0
position) . SNAP
output
|
|
2hvi
|
transferase-DNA |
X-ray (1.98 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
Ddctp:g pair in the polymerase active site (0 position)
. SNAP output
|
|
2hvr
|
ligase-RNA-DNA |
X-ray (2.45 Å) |
Nandakumar J, Shuman S, Lima CD |
(2006) "RNA
Ligase Structures Reveal the Basis for RNA Specificity
and Conformational Changes that Drive Ligation
Forward." Cell(Cambridge,Mass.),
127, 71-84. doi: 10.1016/j.cell.2006.08.038.
|
Structure of t4 RNA ligase 2 with nicked 5'-adenylated
nucleic acid duplex containing a 3'-deoxyribonucleotide
at the nick . SNAP
output
|
|
2hvs
|
ligase-DNA-RNA |
X-ray (2.5 Å) |
Nandakumar J, Shuman S, Lima CD |
(2006) "RNA
Ligase Structures Reveal the Basis for RNA Specificity
and Conformational Changes that Drive Ligation
Forward." Cell(Cambridge,Mass.),
127, 71-84. doi: 10.1016/j.cell.2006.08.038.
|
Structure of t4 RNA ligase 2 with nicked 5'-adenylated
nucleic acid duplex containing a 2'-deoxyribonucleotide
at the nick . SNAP
output
|
|
2hvy
|
isomerase-biosynthetic protein-RNA |
X-ray (2.3 Å) |
Li L, Ye K |
(2006) "Crystal
structure of an H/ACA box ribonucleoprotein
particle." Nature, 443,
302-307. doi: 10.1038/nature05151.
|
Crystal structure of an h-aca box rnp from pyrococcus
furiosus . SNAP
output
|
|
2hw3
|
transferase-DNA |
X-ray (1.98 Å) |
Warren JJ, Forsberg LJ, Beese LS |
(2006) "The
structural basis for the mutagenicity of
O6-methyl-guanine lesions."
Proc.Natl.Acad.Sci.Usa, 103,
19701-19706. doi: 10.1073/pnas.0609580103.
|
T:o6-methyl-guanine pair in the polymerase
postinsertion site (-1 basepair position) . SNAP output
|
|
2hzv
|
metal binding protein-DNA |
X-ray (3.1 Å) |
Schreiter ER, Wang SC, Zamble DB, Drennan CL |
(2006) "NikR-operator
complex structure and the mechanism of repressor
activation by metal ions."
Proc.Natl.Acad.Sci.Usa, 103,
13676-13681. doi: 10.1073/pnas.0606247103.
|
Nikr-operator DNA complex . SNAP output
|
|
2i05
|
replication-DNA |
X-ray (2.6 Å) |
Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE |
"Polarity of Termination of DNA Replication in E.
coli." |
Escherichia coli replication terminator protein (tus)
complexed with tera DNA . SNAP output
|
|
2i06
|
replication-DNA |
X-ray (2.2 Å) |
Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE |
"Polarity of Termination of DNA Replication in E.
coli." |
Escherichia coli replication terminator protein (tus)
complexed with DNA- locked form . SNAP output
|
|
2i0q
|
structural protein-DNA |
X-ray (1.91 Å) |
Buczek P, Horvath MP |
(2006) "Structural
reorganization and the cooperative binding of
single-stranded telomere DNA in Sterkiella nova."
J.Biol.Chem., 281,
40124-40134. doi: 10.1074/jbc.M607749200.
|
Crystal structure of a telomere single-strand
DNA-protein complex from o. nova with full-length alpha
and beta telomere proteins . SNAP output
|
|
2i13
|
DNA binding protein-DNA |
X-ray (1.96 Å) |
Segal DJ, Crotty JW, Bhakta MS, Barbas CF, Horton
NC |
(2006) "Structure
of Aart, a Designed Six-finger Zinc Finger Peptide,
Bound to DNA." J.Mol.Biol.,
363, 405-421. doi: 10.1016/j.jmb.2006.08.016.
|
Aart, a six finger zinc finger designed to recognize
ann triplets . SNAP
output
|
|
2i3p
|
hydrolase-DNA |
X-ray (2.3 Å) |
Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb
B, Sussman D, Stoddard BL, Seligman LM |
(2006) "Homing
endonuclease I-CreI derivatives with novel DNA target
specificities." Nucleic Acids Res.,
34, 4791-4800. doi: 10.1093/nar/gkl645.
|
K28r mutant of homing endonuclease i-crei . SNAP output
|
|
2i3q
|
hydrolase-DNA |
X-ray (2.3 Å) |
Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb
B, Sussman D, Stoddard BL, Seligman LM |
(2006) "Homing
endonuclease I-CreI derivatives with novel DNA target
specificities." Nucleic Acids Res.,
34, 4791-4800. doi: 10.1093/nar/gkl645.
|
Q44v mutant of homing endonuclease i-crei . SNAP output
|
|
2i5s
|
hydrolase-DNA |
X-ray (1.9 Å) |
Lee JE, Bae E, Bingman CA, Phillips Jr GN, Raines
RT |
(2008) "Structural
basis for catalysis by onconase."
J.Mol.Biol., 375, 165-177.
doi: 10.1016/j.jmb.2007.09.089.
|
Crystal structure of onconase with bound nucleic acid .
SNAP output
|
|
2i5w
|
hydrolase, lyase-DNA |
X-ray (2.6 Å) |
Banerjee A, Verdine GL |
(2006) "A
nucleobase lesion remodels the interaction of its
normal neighbor in a DNA glycosylase complex."
Proc.Natl.Acad.Sci.Usa, 103,
15020-15025. doi: 10.1073/pnas.0603644103.
|
Structure of hogg1 crosslinked to DNA sampling a normal
g adjacent to an oxog . SNAP output
|
|
2i9g
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Shock DD, Prasad R, Beard WA, Hou EW,
Pedersen LC, Sayer JM, Yagi H, Kumar S, Jerina DM, Wilson
SH |
(2006) "Structure
of DNA polymerase beta with a benzo[c]phenanthrene diol
epoxide-adducted template exhibits mutagenic
features." Proc.Natl.Acad.Sci.Usa,
103, 17231-17236. doi: 10.1073/pnas.0605069103.
|
DNA polymerase beta with a benzo[c]phenanthrene diol
epoxide adducted guanine base . SNAP output
|
|
2i9k
|
transferase-DNA |
X-ray (2.65 Å) |
Youngblood B, Shieh FK, De Los Rios S, Perona JJ,
Reich NO |
(2006) "Engineered
Extrahelical Base Destabilization Enhances Sequence
Discrimination of DNA Methyltransferase M.HhaI."
J.Mol.Biol., 362, 334-346.
doi: 10.1016/j.jmb.2006.07.031.
|
Engineered extrahelical base destabilization enhances
sequence discrimination of DNA methyltransferase m.hhai
. SNAP output
|
|
2i9t
|
transcription-DNA |
X-ray (2.8 Å) |
Escalante CR, Shen L, Thanos D, Aggarwal AK |
(2002) "Structure
of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA
element from the interferon-beta promoter."
Structure, 10, 383-391. doi:
10.1016/S0969-2126(02)00723-2.
|
Structure of nf-kb p65-p50 heterodimer bound to prdii
element of b-interferon promoter . SNAP output
|
|
2ia6
|
transferase-DNA |
X-ray (2.5 Å) |
Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling
H |
(2007) "A
structural gap in Dpo4 supports mutagenic bypass of a
major benzo[a]pyrene dG adduct in DNA through template
misalignment." Proc.Natl.Acad.Sci.Usa,
104, 14905-14910. doi: 10.1073/pnas.0700717104.
|
Bypass of major benzopyrene-dg adduct by y-family DNA
polymerase with unique structural gap . SNAP output
|
|
2ibk
|
transferase-DNA |
X-ray (2.25 Å) |
Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling
H |
(2007) "A
structural gap in Dpo4 supports mutagenic bypass of a
major benzo[a]pyrene dG adduct in DNA through template
misalignment." Proc.Natl.Acad.Sci.Usa,
104, 14905-14910. doi: 10.1073/pnas.0700717104.
|
Bypass of major benzopyrene-dg adduct by y-family DNA
polymerase with unique structural gap . SNAP output
|
|
2ibs
|
transferase-DNA |
X-ray (2.4 Å) |
Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden
DTF, Scheidig AJ, Jones AC, Weinhold E |
(2007) "2-Aminopurine
Flipped into the Active Site of the Adenine-Specific
DNA Methyltransferase M.TaqI: Crystal Structures and
Time-Resolved Fluorescence."
J.Am.Chem.Soc., 129,
6240-6248. doi: 10.1021/ja069366n.
|
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing 2-aminopurine at
the target position . SNAP output
|
|
2ibt
|
transferase-DNA |
X-ray (1.7 Å) |
Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden
DTF, Scheidig AJ, Jones AC, Weinhold E |
(2007) "2-Aminopurine
Flipped into the Active Site of the Adenine-Specific
DNA Methyltransferase M.TaqI: Crystal Structures and
Time-Resolved Fluorescence."
J.Am.Chem.Soc., 129,
6240-6248. doi: 10.1021/ja069366n.
|
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing 2-aminopurine at
the target position and an abasic site analog at the
target base partner position . SNAP output
|
|
2ief
|
DNA binding protein-DNA |
X-ray (2.601 Å) |
Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson
RC, Clubb RT |
(2007) "Structure
of the cooperative Xis-DNA complex reveals a
micronucleoprotein filament that regulates phage lambda
intasome assembly."
Proc.Natl.Acad.Sci.Usa, 104,
2109-2114. doi: 10.1073/pnas.0607820104.
|
Structure of the cooperative excisionase (xis)-DNA
complex reveals a micronucleoprotein filament .
SNAP output
|
|
2ih2
|
transferase-DNA |
X-ray (1.61 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Influence of the target base partner on the
methylation rate of the adenine-specific DNA
methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing
5-methylpyrimidin-2(1h)-one at the target base partner
position . SNAP
output
|
|
2ih4
|
transferase-DNA |
X-ray (2.1 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Influence of the target base partner on the
methylation rate of the adenine-specific DNA
methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing pyrrolo-dc at
the target base partner position . SNAP output
|
|
2ih5
|
transferase-DNA |
X-ray (1.8 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Influence of the target base partner on the
methylation rate of the adenine-specific DNA
methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing an abasic site
analog at the target base partner position . SNAP output
|
|
2ihm
|
transferase-DNA |
X-ray (2.4 Å) |
Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X,
Ramsden DA, Kunkel TA, Pedersen LC |
(2007) "Structural
insight into the substrate specificity of DNA
Polymerase mu." Nat.Struct.Mol.Biol.,
14, 45-53. doi: 10.1038/nsmb1180.
|
Polymerase mu in ternary complex with gapped 11mer DNA
duplex and bound incoming nucleotide . SNAP output
|
|
2ihn
|
hydrolase-DNA |
X-ray (3.0 Å) |
Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser
TC |
(2007) "Crystal
structure of bacteriophage T4 5' nuclease in complex
with a branched DNA reveals how FEN-1 family nucleases
bind their substrates." J.Biol.Chem.,
282, 31713-31724. doi: 10.1074/jbc.M703209200.
|
Co-crystal of bacteriophage t4 rnase h with a fork DNA
substrate . SNAP
output
|
|
2iie
|
recombination-DNA |
X-ray (2.41 Å) |
Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA |
(2007) "A
Divalent Metal-mediated Switch Controlling
Protein-induced DNA Bending." J.Mol.Biol.,
367, 731-740. doi: 10.1016/j.jmb.2006.09.082.
|
Single chain integration host factor protein (scihf2)
in complex with DNA . SNAP output
|
|
2iif
|
recombination-DNA |
X-ray (2.72 Å) |
Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA |
(2007) "A
Divalent Metal-mediated Switch Controlling
Protein-induced DNA Bending." J.Mol.Biol.,
367, 731-740. doi: 10.1016/j.jmb.2006.09.082.
|
Single chain integration host factor mutant protein
(scihf2-k45ae) in complex with DNA . SNAP output
|
|
2imw
|
transferase-DNA |
X-ray (2.05 Å) |
Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J,
Taylor JS, Yang W, Suo Z |
(2007) "Mechanism
of Template-independent Nucleotide Incorporation
Catalyzed by a Template-dependent DNA Polymerase."
J.Mol.Biol., 365, 590-602.
doi: 10.1016/j.jmb.2006.10.008.
|
Mechanism of template-independent nucleotide
incorporation catalyzed by a template-dependent DNA
polymerase . SNAP
output
|
|
2irf
|
gene regulation-DNA |
X-ray (2.2 Å) |
Fujii Y, Shimizu T, Kusumoto M, Kyogoku Y, Taniguchi
T, Hakoshima T |
(1999) "Crystal
structure of an IRF-DNA complex reveals novel DNA
recognition and cooperative binding to a tandem repeat
of core sequences." EMBO J.,
18, 5028-5041. doi: 10.1093/emboj/18.18.5028.
|
Crystal structure of an irf-2-DNA complex. . SNAP output
|
|
2is1
|
hydrolase-DNA |
X-ray (2.9 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA-so4 complex . SNAP output
|
|
2is2
|
hydrolase-DNA |
X-ray (3.0 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA binary complex . SNAP output
|
|
2is4
|
hydrolase-DNA |
X-ray (2.6 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA-adpnp ternary complex .
SNAP output
|
|
2is6
|
hydrolase-DNA |
X-ray (2.2 Å) |
Lee JY, Yang W |
(2006) "UvrD
helicase unwinds DNA one base pair at a time by a
two-part power stroke."
Cell(Cambridge,Mass.), 127,
1349-1360. doi: 10.1016/j.cell.2006.10.049.
|
Crystal structure of uvrd-DNA-adpmgf3 ternary complex .
SNAP output
|
|
2iso
|
transferase-DNA |
X-ray (2.1 Å) |
Sucato CA, Upton TG, Kashemirov BA, Batra VK,
Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH,
McKenna CE, Florian J, Warshel A, Goodman MF |
(2007) "Modifying
the beta,gamma Leaving-Group Bridging Oxygen Alters
Nucleotide Incorporation Efficiency, Fidelity, and the
Catalytic Mechanism of DNA Polymerase beta."
Biochemistry, 46, 461-471.
doi: 10.1021/bi061517b.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-difluoromethylene triphosphate . SNAP output
|
|
2isp
|
transferase-DNA |
X-ray (2.2 Å) |
Sucato CA, Upton TG, Kashemirov BA, Batra VK,
Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH,
McKenna CE, Florian J, Warshel A, Goodman MF |
(2007) "Modifying
the beta,gamma Leaving-Group Bridging Oxygen Alters
Nucleotide Incorporation Efficiency, Fidelity, and the
Catalytic Mechanism of DNA Polymerase beta."
Biochemistry, 46, 461-471.
doi: 10.1021/bi061517b.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-methylene triphosphate . SNAP output
|
|
2isz
|
transcription-DNA |
X-ray (2.403 Å) |
Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE,
Holmes RK, Beeson C, Hol WG |
(2007) "Crystal
structures, metal activation, and DNA-binding
properties of two-domain IdeR from Mycobacterium
tuberculosis." Biochemistry,
46, 436-447. doi: 10.1021/bi0609826.
|
Crystal structure of a two-domain ider-DNA complex
crystal form i . SNAP
output
|
|
2it0
|
transcription-DNA |
X-ray (2.6 Å) |
Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE,
Holmes RK, Beeson C, Hol WG |
(2007) "Crystal
structures, metal activation, and DNA-binding
properties of two-domain IdeR from Mycobacterium
tuberculosis." Biochemistry,
46, 436-447. doi: 10.1021/bi0609826.
|
Crystal structure of a two-domain ider-DNA complex
crystal form ii . SNAP
output
|
|
2itl
|
DNA binding protein-DNA |
X-ray (1.65 Å) |
Bochkareva E, Martynowski D, Seitova A, Bochkarev
A |
(2006) "Structure
of the origin-binding domain of simian virus 40 large T
antigen bound to DNA." Embo J.,
25, 5961-5969. doi: 10.1038/sj.emboj.7601452.
|
The origin binding domain of the sv40 large t antigen
bound to the functional pen palindrome DNA (23 bp) .
SNAP output
|
|
2ivh
|
hydrolase |
X-ray (2.8 Å) |
Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS |
(2007) "Structural
Basis for Sequence-Dependent DNA Cleavage by
Nonspecific Endonucleases." Nucleic Acids
Res., 35, 584. doi: 10.1093/NAR/GKL621.
|
Crystal structure of the nuclease domain of cole7
(h545q mutant) in complex with an 18-bp duplex DNA .
SNAP output
|
|
2ivk
|
hydrolase |
X-ray (2.9 Å) |
Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS |
(2007) "Structural
Basis for Sequence-Dependent DNA Cleavage by
Nonspecific Endonucleases." Nucleic Acids
Res., 35, 584. doi: 10.1093/NAR/GKL621.
|
Crystal structure of the periplasmic endonuclease vvn
complexed with a 16-bp DNA . SNAP output
|
|
2j6s
|
transferase-DNA |
X-ray (2.5 Å) |
Eoff RL, Irimia A, Egli M, Guengerich FP |
(2007) "Sulfolobus
Solfataricus DNA Polymerase Dpo4 is Partially Inhibited
by "Wobble" Pairing between O6- Methylguanine and
Cytosine, But Accurate Bypass is Preferred."
J.Biol.Chem., 282, 1456. doi:
10.1074/JBC.M609661200.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, o6- methylguanine modified DNA, and datp. .
SNAP output
|
|
2j6t
|
transferase-DNA |
X-ray (2.6 Å) |
Eoff RL, Irimia A, Egli M, Guengerich FP |
(2007) "Sulfolobus
Solfataricus DNA Polymerase Dpo4 is Partially Inhibited
by "Wobble" Pairing between O6- Methylguanine and
Cytosine, But Accurate Bypass is Preferred."
J.Biol.Chem., 282, 1456. doi:
10.1074/JBC.M609661200.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, o6- methylguanine modified DNA, and datp. .
SNAP output
|
|
2j6u
|
transferase-DNA |
X-ray (2.5 Å) |
Eoff RL, Irimia A, Egli M, Guengerich FP |
(2007) "Sulfolobus
Solfataricus DNA Polymerase Dpo4 is Partially Inhibited
by "Wobble" Pairing between O6- Methylguanine and
Cytosine, But Accurate Bypass is Preferred."
J.Biol.Chem., 282, 1456. doi:
10.1074/JBC.M609661200.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, o6- methylguanine modified DNA, and dgtp. .
SNAP output
|
|
2ja5
|
transferase |
X-ray (3.8 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "Cpd
Damage Recognition by Transcribing RNA Polymerase
II." Science, 315, 859.
doi: 10.1126/SCIENCE.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex a . SNAP
output
|
|
2ja6
|
transferase |
X-ray (4.0 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "CPD
damage recognition by transcribing RNA polymerase
II." Science, 315,
859-862. doi: 10.1126/science.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex b . SNAP
output
|
|
2ja7
|
transferase |
X-ray (3.8 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "Cpd
Damage Recognition by Transcribing RNA Polymerase
II." Science, 315, 859.
doi: 10.1126/SCIENCE.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex c . SNAP
output
|
|
2ja8
|
transferase |
X-ray (3.8 Å) |
Brueckner F, Hennecke U, Carell T, Cramer P |
(2007) "Cpd
Damage Recognition by Transcribing RNA Polymerase
II." Science, 315, 859.
doi: 10.1126/SCIENCE.1135400.
|
Cpd lesion containing RNA polymerase ii elongation
complex d . SNAP
output
|
|
2jea
|
hydrolase-RNA |
X-ray (2.33 Å) |
Lorentzen E, Dziembowski A, Lindner D, Seraphin B,
Conti E |
(2007) "RNA
Channelling by the Archaeal Exosome." Embo
Rep., 8, 470. doi: 10.1038/SJ.EMBOR.7400945.
|
Structure of a 9-subunit archaeal exosome bound to RNA
. SNAP output
|
|
2jef
|
transferase-DNA |
X-ray (2.17 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleotide
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state and x-ray crystallography of
correct and incorrect pairing . SNAP output
|
|
2jeg
|
transferase |
X-ray (2.38 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleoside
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state kinetics and x- ray
crystallography of correct and incorrect pairing .
SNAP output
|
|
2jei
|
transferase |
X-ray (2.39 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleoside
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state kinetics and x- ray
crystallography of correct and incorrect pairing .
SNAP output
|
|
2jej
|
transferase |
X-ray (1.86 Å) |
Eoff RL, Angel KC, Egli M, Guengerich FP |
(2007) "Molecular
Basis of Selectivity of Nucleoside Triphosphate
Incorporation Opposite O6-Benzylguanine by Sulfolobus
Solfataricus DNA Polymerase Dpo4: Steady-State and
Pre-Steady-State Kinetics and X-Ray Crystallography of
Correct and Incorrect Pairing."
J.Biol.Chem., 282, 13573.
doi: 10.1074/JBC.M700656200.
|
The molecular basis of selectivity of nucleoside
triphosphate incorporation opposite o6-benzylguanine by
sulfolobus solfataricus DNA polymerase iv: steady-state
and pre-steady-state kinetics and x- ray
crystallography of correct and incorrect pairing .
SNAP output
|
|
2jg3
|
transferase-DNA |
X-ray (1.9 Å) |
Pljevaljcic G, Schmidt F, Scheidig AJ, Lurz R,
Weinhold E |
(2007) "Quantitative
Labeling of Long Plasmid DNA with Nanometer
Precision." Chembiochem,
8, 1516. doi: 10.1002/CBIC.200700294.
|
Mtaqi with baz . SNAP
output
|
|
2jlg
|
transferase |
X-ray (2.8 Å) |
Poranen MM, Salgado PS, Koivunen MRL, Wright S,
Bamford DH, Stuart DI, Grimes JM |
(2008) "Structural
Explanation for the Role of Mn2+ in the Activity of
{Phi}6 RNA-Dependent RNA Polymerase." Nucleic
Acids Res., 36, 6633. doi:
10.1093/NAR/GKN632.
|
Structural explanation for the role of mn in the
activity of phi6 RNA-dependent RNA polymerase .
SNAP output
|
|
2jp9
|
transcription-DNA |
NMR |
Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA,
Dyson HJ, Wright PE |
(2007) "Structure
of the wilms tumor suppressor protein zinc finger
domain bound to DNA." J.Mol.Biol.,
372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017.
|
Structure of the wilms tumor suppressor protein zinc
finger domain bound to DNA . SNAP output
|
|
2jpa
|
transcription-DNA |
NMR |
Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA,
Dyson HJ, Wright PE |
(2007) "Structure
of the wilms tumor suppressor protein zinc finger
domain bound to DNA." J.Mol.Biol.,
372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017.
|
Structure of the wilms tumor suppressor protein zinc
finger domain bound to DNA . SNAP output
|
|
2jx1
|
transcription-DNA |
NMR |
Gamsjaeger R, Swanton MK, Kobus FJ, Lehtomaki E,
Lowry JA, Kwan AH, Matthews JM, Mackay JP |
"Structure of the fifth zinc finger of Myelin
Transcription Factor 1 in complex with RARE DNA." |
Structure of the fifth zinc finger of myelin
transcription factor 1 in complex with rare DNA .
SNAP output
|
|
2jxi
|
DNA binding protein, DNA |
NMR |
Halouska S, Zhou Y, Becker DF, Powers R |
(2008) "Solution
structure of the Pseudomonas putida protein PpPutA45
and its DNA complex." Proteins,
75, 12-27. doi: 10.1002/prot.22217.
|
Solution structure of the DNA-binding domain of
pseudomonas putida proline utilization a (puta) bound
to gttgca DNA sequence . SNAP output
|
|
2jzw
|
viral protein-DNA |
NMR |
Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF,
Roques BP, Mely Y, Bouaziz S, Morellet N |
(2008) "How the
HIV-1 nucleocapsid protein binds and destabilises the
(-)primer binding site during reverse
transcription." J.Mol.Biol.,
383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046.
|
How the hiv-1 nucleocapsid protein binds and
destabilises the (-)primer binding site during reverse
transcription . SNAP
output
|
|
2k1n
|
transcription-DNA |
NMR |
Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance
M, Strauch MA, Cavanagh J |
(2008) "Insights
into the Nature of DNA Binding of AbrB-like
Transcription Factors." Structure,
16, 1702-1713. doi: 10.1016/j.str.2008.08.014.
|
DNA bound structure of the n-terminal domain of abrb .
SNAP output
|
|
2k7f
|
replication-DNA |
NMR |
Kobayashi M, Ab E, Bonvin AM, Siegal G |
(2010) "Structure
of the DNA-bound BRCA1 C-terminal region from human
replication factor C p140 and model of the protein-DNA
complex." J.Biol.Chem.,
285, 10087-10097. doi: 10.1074/jbc.M109.054106.
|
Haddock calculated model of the complex between the
brct region of rfc p140 and dsDNA . SNAP output
|
|
2kae
|
transcription-DNA |
NMR |
Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH,
Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP |
(2009) "Structural
Analysis of MED-1 Reveals Unexpected Diversity in the
Mechanism of DNA Recognition by GATA-type Zinc Finger
Domains." J.Biol.Chem.,
284, 5827-5835. doi: 10.1074/jbc.M808712200.
|
Data-driven model of med1:DNA complex . SNAP output
|
|
2kdz
|
transcription-DNA |
NMR |
Lou YC, Wei SY, Rajasekaran M, Chou CC, Hsu HM, Tai
JH, Chen C |
(2009) "NMR
structural analysis of DNA recognition by a novel Myb1
DNA-binding domain in the protozoan parasite
Trichomonas vaginalis." Nucleic Acids Res.
doi: 10.1093/nar/gkp097.
|
Structure of the r2r3 DNA binding domain of myb1
protein from protozoan parasite trichomonas vaginalis
in complex with mre-1-mre-2r DNA . SNAP output
|
|
2kei
|
transcription-DNA |
NMR |
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk
H, Bonvin AM, Kaptein R, Boelens R |
(2009) "Specificity
and affinity of Lac repressor for the auxiliary
operators O2 and O3 are explained by the structures of
their protein-DNA complexes." J.Mol.Biol.,
390, 478-489. doi: 10.1016/j.jmb.2009.05.022.
|
Refined solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o1
. SNAP output
|
|
2kej
|
transcription-DNA |
NMR |
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk
H, Bonvin AM, Kaptein R, Boelens R |
(2009) "Specificity
and affinity of Lac repressor for the auxiliary
operators O2 and O3 are explained by the structures of
their protein-DNA complexes." J.Mol.Biol.,
390, 478-489. doi: 10.1016/j.jmb.2009.05.022.
|
Solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o2
. SNAP output
|
|
2kek
|
transcription-DNA |
NMR |
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk
H, Bonvin AM, Kaptein R, Boelens R |
(2009) "Specificity
and affinity of Lac repressor for the auxiliary
operators O2 and O3 are explained by the structures of
their protein-DNA complexes." J.Mol.Biol.,
390, 478-489. doi: 10.1016/j.jmb.2009.05.022.
|
Solution structure of a dimer of lac repressor
DNA-binding domain complexed to its natural operator o3
. SNAP output
|
|
2kfn
|
transferase-DNA |
X-ray (2.03 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with bridging-sulfur substrate and
manganese . SNAP
output
|
|
2kfz
|
transferase-DNA |
X-ray (2.03 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with bridging-sulfur substrate and zinc
only . SNAP output
|
|
2kkf
|
DNA binding protein-DNA |
NMR |
Cierpicki T, Risner LE, Grembecka J, Lukasik SM,
Popovic R, Omonkowska M, Shultis DD, Zeleznik-Le NJ,
Bushweller JH |
(2010) "Structure
of the MLL CXXC domain-DNA complex and its functional
role in MLL-AF9 leukemia."
Nat.Struct.Mol.Biol., 17,
62-68. doi: 10.1038/nsmb.1714.
|
Solution structure of mll cxxc domain in complex with
palindromic cpg DNA . SNAP output
|
|
2kmk
|
DNA binding protein-DNA |
NMR |
Lee S, Doddapaneni K, Hogue A, McGhee L, Meyers S, Wu
Z |
(2010) "Solution
structure of Gfi-1 zinc domain bound to consensus
DNA." J.Mol.Biol., 397,
1055-1066. doi: 10.1016/j.jmb.2010.02.006.
|
Gfi-1 zinc fingers 3-5 complexed with DNA . SNAP output
|
|
2kn7
|
hydrolase-DNA |
NMR |
Das D, Folkers GE, van Dijk M, Jaspers NGJ,
Hoeijmakers JHJ, Kaptein R, Boelens R |
(2012) "The
structure of the XPF-ssDNA complex underscores the
distinct roles of the XPF and ERCC1 helix-
hairpin-helix domains in ss/ds DNA recognition."
Structure, 20, 667-675. doi:
10.1016/j.str.2012.02.009.
|
Structure of the xpf-single strand DNA complex .
SNAP output
|
|
2ko0
|
transcription-DNA |
NMR |
Campagne S, Saurel O, Gervais V, Milon A |
(2010) "Structural
determinants of specific DNA-recognition by the THAP
zinc finger." Nucleic Acids Res. doi:
10.1093/nar/gkq053.
|
Solution structure of the thap zinc finger of thap1 in
complex with its DNA target . SNAP output
|
|
2ktq
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Korolev S, Waksman G |
(1998) "Crystal
structures of open and closed forms of binary and
ternary complexes of the large fragment of Thermus
aquaticus DNA polymerase I: structural basis for
nucleotide incorporation." EMBO J.,
17, 7514-7525. doi: 10.1093/emboj/17.24.7514.
|
Open ternary complex of the large fragment of DNA
polymerase i from thermus aquaticus . SNAP output
|
|
2kv6
|
DNA binding protein-DNA |
NMR |
Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough
AK, Lloyd RS, Stone MP |
(2010) "Minor
Groove Orientation of the KWKK Peptide Tethered via the
N-Terminal Amine to the Acrolein-Derived
1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a
Trimethylene Linkage ." Biochemistry,
49, 6155-6164. doi: 10.1021/bi100364f.
|
Tetrapeptide kwkk conjugated to oligonucleotide duplex
by a trimethylene tether . SNAP output
|
|
2ky8
|
transcription-DNA |
NMR |
Scarsdale JN, Webb HD, Ginder GD, Williams DC |
(2011) "Solution
structure and dynamic analysis of chicken MBD2 methyl
binding domain bound to a target-methylated DNA
sequence." Nucleic Acids Res.,
39, 6741-6752. doi: 10.1093/nar/gkr262.
|
Solution structure and dynamic analysis of chicken mbd2
methyl binding domain bound to a target methylated DNA
sequence . SNAP
output
|
|
2kzm
|
transferase-DNA |
X-ray (2.6 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with normal substrate and zinc and
manganese . SNAP
output
|
|
2kzz
|
transferase-DNA |
X-ray (2.25 Å) |
Brautigam CA, Sun S, Piccirilli JA, Steitz TA |
(1999) "Structures
of normal single-stranded DNA and
deoxyribo-3'-S-phosphorothiolates bound to the 3'-5'
exonucleolytic active site of DNA polymerase I from
Escherichia coli." Biochemistry,
38, 696-704. doi: 10.1021/bi981537g.
|
Klenow fragment with normal substrate and zinc only .
SNAP output
|
|
2l1g
|
transcription-DNA |
NMR |
Campagne S, Gervais V, Saurel O, Milon A |
"RDC refined solution structure of the THAP zinc
finger of THAP1 in complex with its 16bp RRM1 DNA
target." |
Rdc refined solution structure of the thap zinc finger
of thap1 in complex with its 16bp rrm1 DNA target .
SNAP output
|
|
2l45
|
viral protein-DNA |
NMR |
Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell
NP |
(2012) "Platinated
DNA affects zinc finger conformation. Interaction of a
platinated single-stranded oligonucleotide and the
C-terminal zinc finger of nucleocapsid protein
HIVNCp7." Biochemistry,
51, 1752-1761. doi: 10.1021/bi201834g.
|
C-terminal zinc knuckle of the hivncp7 with DNA .
SNAP output
|
|
2l46
|
viral protein-DNA |
NMR |
Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell
NP |
(2012) "Platinated
DNA affects zinc finger conformation. Interaction of a
platinated single-stranded oligonucleotide and the
C-terminal zinc finger of nucleocapsid protein
HIVNCp7." Biochemistry,
51, 1752-1761. doi: 10.1021/bi201834g.
|
C-terminal zinc finger of the hivncp7 with platinated
DNA . SNAP output
|
|
2l4l
|
viral protein-DNA |
NMR |
Bazzi A, Zargarian L, Chaminade F, Boudier C, De
Rocquigny H, Rene B, Mely Y, Fosse P, Mauffret O |
(2011) "Structural
insights into the cTAR DNA recognition by the HIV-1
nucleocapsid protein: role of sugar deoxyriboses in the
binding polarity of NC." Nucleic Acids
Res., 39, 3903-3916. doi:
10.1093/nar/gkq1290.
|
Structural insights into the ctar DNA recognition by
the hiv-1 nucleocapsid protein: role of sugar
deoxyriboses in the binding polarity of nc . SNAP output
|
|
2ld5
|
transcription-DNA |
NMR |
Zhang Y, Larsen CA, Stadler HS, Ames JB |
(2011) "Structural
basis for sequence specific DNA binding and protein
dimerization of HOXA13." Plos One,
6, e23069. doi: 10.1371/journal.pone.0023069.
|
Solution NMR-derived complex structure of hoxa13 DNA
binding domain bound to DNA . SNAP output
|
|
2lef
|
gene regulation-DNA |
NMR |
Love JJ, Li X, Case DA, Giese K, Grosschedl R, Wright
PE |
(1995) "Structural
basis for DNA bending by the architectural
transcription factor LEF-1." Nature,
376, 791-795. doi: 10.1038/376791a0.
|
Lef1 hmg domain (from mouse), complexed with DNA
(15bp), NMR, 12 structures . SNAP output
|
|
2lev
|
transcription regulator-DNA |
multiple methods: solution nmr, solution
scattering |
Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado
P, Griesinger C, Garcia J, Pons M |
(2011) "Indirect
DNA Readout by an H-NS Related Protein: Structure of
the DNA Complex of the C-Terminal Domain of Ler."
Plos Pathog., 7, e1002380.
doi: 10.1371/journal.ppat.1002380.
|
Structure of the DNA complex of the c-terminal domain
of ler . SNAP output
|
|
2lex
|
transcription-DNA |
NMR |
Yamasaki K, Kigawa T, Watanabe S, Inoue M, Yamasaki
T, Seki M, Shinozaki K, Yokoyama S |
(2012) "Structural
basis for sequence-spscific DNA recognition by an
Arabidopsis WRKY transcription factor."
J.Biol.Chem. doi: 10.1074/jbc.M111.279844.
|
Complex of the c-terminal wrky domain of atwrky4 and a
w-box DNA . SNAP
output
|
|
2lkx
|
transcription-DNA |
NMR |
Chaney BA, Clark-Baldwin K, Dave V, Ma J, Rance
M |
(2005) "Solution
structure of the K50 class homeodomain PITX2 bound to
DNA and implications for mutations that cause Rieger
syndrome." Biochemistry,
44, 7497-7511. doi: 10.1021/bi0473253.
|
NMR structure of the homeodomain of pitx2 in complex
with a taatcc DNA binding site . SNAP output
|
|
2lt7
|
metal binding protein-DNA |
NMR |
Buck-Koehntop BA, Stanfield RL, Ekiert DC,
Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE |
(2012) "Molecular
basis for recognition of methylated and specific DNA
sequences by the zinc finger protein Kaiso."
Proc.Natl.Acad.Sci.USA, 109,
15229-15234. doi: 10.1073/pnas.1213726109.
|
Solution NMR structure of kaiso zinc finger DNA binding
domain in complex with kaiso binding site DNA .
SNAP output
|
|
2ltt
|
transcription, DNA binding protein-DNA |
NMR |
Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW,
Janjua H, Xiao R, Acton TB, Montelione GT |
(2013) "Structures
of apo- and ssDNA-bound YdbC from Lactococcus lactis
uncover the function of protein domain family DUF2128
and expand the single-stranded DNA-binding domain
proteome." Nucleic Acids Res.,
41, 2756-2768. doi: 10.1093/nar/gks1348.
|
Solution NMR structure of ydbc:dt19g1 complex.
northeast structural genomics consortium (nesg) target
kr150 . SNAP output
|
|
2m2w
|
transferase-DNA |
NMR |
Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW,
Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai
MD |
(2014) "How a
low-fidelity DNA polymerase chooses non-Watson-Crick
from Watson-Crick incorporation."
J.Am.Chem.Soc., 136,
4927-4937. doi: 10.1021/ja4102375.
|
Ternary complex of asfv pol x with DNA and mgdgtp .
SNAP output
|
|
2map
|
transcription-DNA |
NMR |
Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain
FH |
(2014) "Structural
basis for -10 promoter element melting by
environmentally induced sigma factors."
Nat.Struct.Mol.Biol., 21,
269-276. doi: 10.1038/nsmb.2777.
|
Solution structure of the complex formed by the region
2 of e. coli sigmae and its cognate -10 promoter
element non template strand tgtcaaa. . SNAP output
|
|
2me6
|
transcription-DNA |
NMR |
Proudfoot A, Wuthrich K, Serrano P, Geralt M |
"NMR Structure of the homeodomain transcription
factor Gbx1 from Homo sapiens in complex with the DNA
sequence CGACTAATTAGTCG." |
NMR structure of the homeodomain transcription factor
gbx1 from homo sapiens in complex with the DNA sequence
cgactaattagtcg . SNAP
output
|
|
2mf8
|
metal binding protein-DNA |
NMR |
Gamsjaeger R, O'Connell MR, Cubeddu L, Shepherd NE,
Lowry JA, Kwan AH, Vandevenne M, Swanton MK, Matthews JM,
Mackay JP |
(2013) "A
structural analysis of DNA binding by myelin
transcription factor 1 double zinc fingers."
J.Biol.Chem., 288,
35180-35191. doi: 10.1074/jbc.M113.482075.
|
Haddock model of myt1 f4f5 - DNA complex . SNAP output
|
|
2mna
|
DNA binding protein-DNA |
NMR |
Gamsjaeger R, Kariawasam R, Gimenez AX, Touma C,
McIlwain E, Bernardo RE, Shepherd NE, Ataide SF, Dong Q,
Richard DJ, White MF, Cubeddu L |
(2015) "The
structural basis of DNA binding by the single-stranded
DNA-binding protein from Sulfolobus solfataricus."
Biochem.J., 465, 337-346.
doi: 10.1042/BJ20141140.
|
The structural basis of DNA binding by the
single-stranded DNA-binding protein from sulfolobus
solfataricus . SNAP
output
|
|
2moe
|
hydrolase-DNA |
NMR |
Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN,
Williams DC |
(2015) "Solution
structure and intramolecular exchange of
methyl-cytosine binding domain protein 4 (MBD4) on DNA
suggests a mechanism to scan for mCpG/TpG
mismatches." Nucleic Acids Res.,
42, 11218-11232. doi: 10.1093/nar/gku782.
|
Solution structure of mbd4 methyl-cytosine binding
domain bound to methylated DNA . SNAP output
|
|
2mru
|
DNA binding protein-DNA |
NMR |
Zorzini V, Buts L, Schrank E, Sterckx YG, Respondek
M, Engelberg-Kulka H, Loris R, Zangger K, van Nuland
NA |
(2015) "Escherichia
coli antitoxin MazE as transcription factor: insights
into MazE-DNA binding." Nucleic Acids
Res., 43, 1241-1256. doi:
10.1093/nar/gku1352.
|
Structure of truncated ecmaze-DNA complex . SNAP output
|
|
2mxf
|
transcription regulator-DNA |
NMR |
Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A,
Hughes TR, Liu J, Dove SL, Navarre WW, Xia B |
(2015) "A Novel
AT-Rich DNA Recognition Mechanism for Bacterial
Xenogeneic Silencer MvaT." Plos Pathog.,
11, e1004967. doi: 10.1371/journal.ppat.1004967.
|
Structure of the DNA complex of the c-terminal domain
of mvat . SNAP
output
|
|
2n21
|
hydrolase-DNA |
NMR |
Heddi B, Cheong VV, Martadinata H, Phan AT |
(2015) "Insights
into G-quadruplex specific recognition by the DEAH-box
helicase RHAU: Solution structure of a
peptide-quadruplex complex."
Proc.Natl.Acad.Sci.USA, 112,
9608-9613. doi: 10.1073/pnas.1422605112.
|
Solution structure of complex between DNA g-quadruplex
and g-quadruplex recognition domain of rhau . SNAP output
|
|
2n8a
|
transferase |
NMR |
Eustermann S, Wu WF, Langelier MF, Yang JC, Easton
LE, Riccio AA, Pascal JM, Neuhaus D |
(2015) "Structural
Basis of Detection and Signaling of DNA Single-Strand
Breaks by Human PARP-1." Mol.Cell,
60, 742-754. doi: 10.1016/j.molcel.2015.10.032.
|
1h, 13c and 15n chemical shift assignments and solution
structure for parp-1 f1f2 domains in complex with a DNA
single-strand break . SNAP output
|
|
2nbj
|
DNA binding protein-DNA |
NMR |
Paquet F, Loth K, Landon C |
"First 3D structure of an atypical protein-DNA
complex." |
DNA-archeal mc1 protein complex structure by NMR .
SNAP output
|
|
2nl8
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Bochkareva E, Martynowski D, Seitova A, Bochkarev
A |
(2006) "Structure
of the origin-binding domain of simian virus 40 large T
antigen bound to DNA." Embo J.,
25, 5961-5969. doi: 10.1038/sj.emboj.7601452.
|
The origin binding domain of the sv40 large t antigen
bound non specifically to a 17 bp palindrome DNA (sites
1 and 3) . SNAP
output
|
|
2nll
|
transcription-DNA |
X-ray (1.9 Å) |
Rastinejad F, Perlmann T, Evans RM, Sigler PB |
(1995) "Structural
determinants of nuclear receptor assembly on DNA direct
repeats." Nature, 375,
203-211. doi: 10.1038/375203a0.
|
Retinoid x receptor-thyroid hormone receptor
DNA-binding domain heterodimer bound to thyroid
response element DNA . SNAP output
|
|
2nmv
|
hydrolase-DNA |
X-ray (2.95 Å) |
Waters TR, Eryilmaz J, Geddes S, Barrett TE |
(2006) "Damage
detection by the UvrABC pathway: crystal structure of
UvrB bound to fluorescein-adducted DNA." Febs
Lett., 580, 6423-6427. doi:
10.1016/j.febslet.2006.10.051.
|
Damage detection by the uvrabc pathway: crystal
structure of uvrb bound to fluorescein-adducted DNA .
SNAP output
|
|
2nny
|
transcription-DNA |
X-ray (2.58 Å) |
Lamber EP, Vanhille L, Textor LC, Kachalova GS,
Sieweke MH, Wilmanns M |
(2008) "Regulation
of the transcription factor Ets-1 by DNA-mediated
homo-dimerization." Embo J.,
27, 2006-2017. doi: 10.1038/emboj.2008.117.
|
Crystal structure of the ets1 dimer DNA complex. .
SNAP output
|
|
2nob
|
hydrolase, lyase-DNA |
X-ray (2.1 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of catalytically inactive h270a human
8-oxoguanine glycosylase crosslinked to 8-oxoguanine
DNA . SNAP output
|
|
2noe
|
hydrolase, lyase-DNA |
X-ray (2.2 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of catalytically inactive g42a human
8-oxoguanine glycosylase complexed to 8-oxoguanine DNA
. SNAP output
|
|
2nof
|
hydrolase, lyase-DNA |
X-ray (2.35 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of q315f human 8-oxoguanine glycosylase
proximal crosslink to 8-oxoguanine DNA . SNAP output
|
|
2noh
|
hydrolase, lyase-DNA |
X-ray (2.01 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of catalytically inactive q315a human
8-oxoguanine glycosylase complexed to 8-oxoguanine DNA
. SNAP output
|
|
2noi
|
hydrolase, lyase-DNA |
X-ray (2.35 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of g42a human 8-oxoguanine glycosylase
crosslinked to undamaged g-containing DNA . SNAP output
|
|
2nol
|
hydrolase, lyase-DNA |
X-ray (2.57 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of catalytically inactive human 8-oxoguanine
glycosylase distal crosslink to oxog DNA . SNAP output
|
|
2noz
|
hydrolase, lyase-DNA |
X-ray (2.43 Å) |
Radom CT, Banerjee A, Verdine GL |
(2007) "Structural
characterization of human 8-oxoguanine DNA glycosylase
variants bearing active site mutations."
J.Biol.Chem., 282, 9182-9194.
doi: 10.1074/jbc.M608989200.
|
Structure of q315f human 8-oxoguanine glycosylase
distal crosslink to 8-oxoguanine DNA . SNAP output
|
|
2np2
|
DNA binding protein-DNA |
X-ray (3.02 Å) |
Mouw KW, Rice PA |
(2007) "Shaping
the Borrelia burgdorferi genome: crystal structure and
binding properties of the DNA-bending protein Hbb."
Mol.Microbiol., 63,
1319-1330. doi: 10.1111/j.1365-2958.2007.05586.x.
|
Hbb-DNA complex . SNAP
output
|
|
2np6
|
transferase-DNA |
X-ray (2.1 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Caught in the act II: Visualization of an
intermediate in the DNA base-flipping pathway induced by
the adenine-specific DNA methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing an abasic site
analog at the target position . SNAP output
|
|
2np7
|
transferase-DNA |
X-ray (1.9 Å) |
Lenz T, Scheidig AJ, Weinhold E |
"Caught in the act II: Visualization of an
intermediate in the DNA base-flipping pathway induced by
the adenine-specific DNA methyltransferase M.TaqI." |
Crystal structure of the adenine-specific DNA
methyltransferase m.taqi complexed with the cofactor
analog aeta and a 10 bp DNA containing an abasic site
analog at the target position and pyrrolo-dc at the
target base partner position . SNAP output
|
|
2nq9
|
hydrolase-DNA |
X-ray (1.45 Å) |
Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M,
Cunningham RP, Tainer JA |
(2008) "DNA
apurinic-apyrimidinic site binding and excision by
endonuclease IV." Nat.Struct.Mol.Biol.,
15, 515-522. doi: 10.1038/nsmb.1414.
|
High resolution crystal structure of escherichia coli
endonuclease iv (endo iv) y72a mutant bound to damaged
DNA . SNAP output
|
|
2nqb
|
structural protein-DNA |
X-ray (2.3 Å) |
Chakravarthy S, Luger K |
"Comparative analysis of nucleosome structures from
different species." |
Drosophila nucleosome structure . SNAP output
|
|
2nqj
|
hydrolase |
X-ray (2.45 Å) |
Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M,
Cunningham RP, Tainer JA |
(2008) "DNA
apurinic-apyrimidinic site binding and excision by
endonuclease IV." Nat.Struct.Mol.Biol.,
15, 515-522. doi: 10.1038/nsmb.1414.
|
Crystal structure of escherichia coli endonuclease iv
(endo iv) e261q mutant bound to damaged DNA . SNAP output
|
|
2nqp
|
isomerase-RNA |
X-ray (3.5 Å) |
Hur S, Stroud RM |
(2007) "How U38,
39, and 40 of Many tRNAs Become the Targets for
Pseudouridylation by TruA." Mol.Cell,
26, 189-203. doi: 10.1016/j.molcel.2007.02.027.
|
Crystal structure of pseudoudirinde synthase trua in
complex with leucyl trna . SNAP output
|
|
2nr0
|
isomerase-RNA |
X-ray (3.9 Å) |
Hur S, Stroud RM |
(2007) "How U38,
39, and 40 of Many tRNAs Become the Targets for
Pseudouridylation by TruA." Mol.Cell,
26, 189-203. doi: 10.1016/j.molcel.2007.02.027.
|
Crystal structure of pseudoudirinde synthase trua in
complex with leucyl trna . SNAP output
|
|
2nra
|
replication-DNA |
X-ray (3.1 Å) |
Swan MK, Bastia D, Davies C |
(2006) "Crystal
structure of pi initiator protein-iteron complex of
plasmid R6K: implications for initiation of plasmid DNA
replication." Proc.Natl.Acad.Sci.Usa,
103, 18481-18486. doi: 10.1073/pnas.0609046103.
|
Crystal structure of pi initiator protein in complex
with iteron DNA . SNAP
output
|
|
2ntc
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Meinke G, Phelan P, Moine S, Bochkareva E, Bochkarev
A, Bullock PA, Bohm A |
(2007) "The
Crystal Structure of the SV40 T-Antigen Origin Binding
Domain in Complex with DNA." Plos Biol.,
5, e23. doi: 10.1371/journal.pbio.0050023.
|
Crystal structure of sv40 large t antigen origin
binding domain with DNA . SNAP output
|
|
2ntz
|
cell cycle-DNA |
X-ray (3.35 Å) |
Schumacher MA, Mansoor A, Funnell BE |
(2007) "Structure
of a four-way bridged ParB-DNA complex provides insight
into P1 segrosome assembly." J.Biol.Chem.,
282, 10456-10464. doi: 10.1074/jbc.M610603200.
|
Structure of a parb-DNA complex reveals a double b-box
interaction . SNAP
output
|
|
2nvq
|
transcription,transferase-DNA-RNA hybrid |
X-ray (2.9 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 150 mm mg+2
with 2'dutp . SNAP
output
|
|
2nvt
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.36 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 150 mm mg+2
with gmpcpp . SNAP
output
|
|
2nvx
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.6 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 5 mm mg+2 with
2'-dutp . SNAP
output
|
|
2nvz
|
transcription,transferase-DNA-RNA hybrid |
X-ray (4.3 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
basis of transcription: role of the trigger loop in
substrate specificity and catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex with utp, updated
11-2006 . SNAP
output
|
|
2nzd
|
structural protein-DNA |
X-ray (2.65 Å) |
Ong MS, Richmond TJ, Davey CA |
(2007) "DNA
stretching and extreme kinking in the nucleosome
core." J.Mol.Biol., 368,
1067-1074. doi: 10.1016/j.jmb.2007.02.062.
|
Nucleosome core particle containing 145 bp of DNA .
SNAP output
|
|
2o19
|
isomerase-DNA |
X-ray (2.45 Å) |
Changela A, Digate RJ, Mondragon A |
(2007) "Structural
Studies of E. coli Topoisomerase III-DNA Complexes
Reveal a Novel Type IA Topoisomerase-DNA Conformational
Intermediate." J.Mol.Biol.,
368, 105-118. doi: 10.1016/j.jmb.2007.01.065.
|
Structure of e. coli topoisomersae iii in complex with
an 8-base single stranded oligonucleotide. frozen in
glycerol at ph 5.5 . SNAP output
|
|
2o49
|
transcription-DNA |
X-ray (2.0 Å) |
Yamasaki K, Akiba T, Yamasaki T, Harata K |
(2007) "Structural
basis for recognition of the matrix attachment region
of DNA by transcription factor SATB1." Nucleic
Acids Res., 35, 5073-5084. doi:
10.1093/nar/gkm504.
|
Crystal structure of the n-terminal cut domain of satb1
bound to matrix attachment region DNA . SNAP output
|
|
2o4a
|
transcription-DNA |
X-ray (1.75 Å) |
Yamasaki K, Akiba T, Yamasaki T, Harata K |
(2007) "Structural
basis for recognition of the matrix attachment region
of DNA by transcription factor SATB1." Nucleic
Acids Res., 35, 5073-5084. doi:
10.1093/nar/gkm504.
|
Crystal structure of the n-terminal cut domain of satb1
bound to matrix attachment region DNA . SNAP output
|
|
2o4i
|
hydrolase-DNA |
X-ray (3.5 Å) |
Brucet M, Querol-Audi J, Serra M, Ramirez-Espain X,
Bertlik K, Ruiz L, Lloberas J, Macias MJ, Fita I, Celada
A |
(2007) "Structure
of the dimeric exonuclease TREX1 in complex with DNA
displays a proline-rich binding site for WW
Domains." J.Biol.Chem.,
282, 14547-14557. doi: 10.1074/jbc.M700236200.
|
Structure of trex1 in complex with DNA . SNAP output
|
|
2o54
|
isomerase-DNA |
X-ray (2.5 Å) |
Changela A, Digate RJ, Mondragon A |
(2007) "Structural
Studies of E. coli Topoisomerase III-DNA Complexes
Reveal a Novel Type IA Topoisomerase-DNA Conformational
Intermediate." J.Mol.Biol.,
368, 105-118. doi: 10.1016/j.jmb.2007.01.065.
|
Structure of e. coli topoisomerase iii in complex with
an 8-base single stranded oligonucleotide. frozen in
glycerol at ph 7.0 . SNAP output
|
|
2o59
|
isomerase-DNA |
X-ray (2.5 Å) |
Changela A, Digate RJ, Mondragon A |
(2007) "Structural
Studies of E. coli Topoisomerase III-DNA Complexes
Reveal a Novel Type IA Topoisomerase-DNA Conformational
Intermediate." J.Mol.Biol.,
368, 105-118. doi: 10.1016/j.jmb.2007.01.065.
|
Structure of e. coli topoisomerase iii in complex with
an 8-base single stranded oligonucleotide. frozen in
glycerol ph 8.0 . SNAP
output
|
|
2o5c
|
isomerase-DNA |
X-ray (2.35 Å) |
Changela A, Digate RJ, Mondragon A |
(2007) "Structural
Studies of E. coli Topoisomerase III-DNA Complexes
Reveal a Novel Type IA Topoisomerase-DNA Conformational
Intermediate." J.Mol.Biol.,
368, 105-118. doi: 10.1016/j.jmb.2007.01.065.
|
Structure of e. coli topoisomerase iii in complex with
an 8-base single stranded oligonucleotide. frozen in
glucose ph 5.5 . SNAP
output
|
|
2o5e
|
isomerase-DNA |
X-ray (2.5 Å) |
Changela A, Digate RJ, Mondragon A |
(2007) "Structural
Studies of E. coli Topoisomerase III-DNA Complexes
Reveal a Novel Type IA Topoisomerase-DNA Conformational
Intermediate." J.Mol.Biol.,
368, 105-118. doi: 10.1016/j.jmb.2007.01.065.
|
Structure of e. coli topoisomerase iii in complex with
an 8-base single stranded oligonucleotide. frozen in
glucose ph 7.0 . SNAP
output
|
|
2o5i
|
transferase-DNA-RNA hybrid |
X-ray (2.5 Å) |
Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov
TH, Artsimovitch I |
(2007) "Structural
basis for transcription elongation by bacterial RNA
polymerase." Nature, 448,
157-162. doi: 10.1038/nature05932.
|
Crystal structure of the t. thermophilus RNA polymerase
elongation complex . SNAP output
|
|
2o5j
|
transferase-DNA-RNA hybrid |
X-ray (3.0 Å) |
Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M,
Artsimovitch I, Landick R |
(2007) "Structural
basis for substrate loading in bacterial RNA
polymerase." Nature, 448,
163-168. doi: 10.1038/nature05931.
|
Crystal structure of the t. thermophilus rnap
polymerase elongation complex with the ntp substrate
analog . SNAP output
|
|
2o61
|
transcription-DNA |
X-ray (2.8 Å) |
Panne D, Maniatis T, Harrison SC |
(2007) "An
Atomic Model of the Interferon-beta Enhanceosome."
Cell(Cambridge,Mass.), 129,
1111-1123. doi: 10.1016/j.cell.2007.05.019.
|
Crystal structure of nfkb, irf7, irf3 bound to the
interferon-b enhancer . SNAP output
|
|
2o6g
|
transcription-DNA |
X-ray (3.1 Å) |
Panne D, Maniatis T, Harrison SC |
(2007) "An
Atomic Model of the Interferon-beta Enhanceosome."
Cell(Cambridge,Mass.), 129,
1111-1123. doi: 10.1016/j.cell.2007.05.019.
|
Crystal structure of irf-3 bound to the interferon-b
enhancer . SNAP
output
|
|
2o6m
|
hydrolase-DNA |
X-ray (2.3 Å) |
Eastberg JH, Eklund J, Monnat R, Stoddard BL |
(2007) "Mutability
of an HNH nuclease imidazole general base and exchange
of a deprotonation mechanism."
Biochemistry, 46, 7215-7225.
doi: 10.1021/bi700418d.
|
H98q mutant of the homing endonuclease i-ppoi complexed
with DNA . SNAP
output
|
|
2o8b
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich
PL, Beese LS |
(2007) "Structure
of the Human MutSalpha DNA Lesion Recognition
Complex." Mol.Cell, 26,
579-592. doi: 10.1016/j.molcel.2007.04.018.
|
Human mutsalpha (msh2-msh6) bound to adp and a g t
mispair . SNAP
output
|
|
2o8c
|
DNA binding protein-DNA |
X-ray (3.37 Å) |
Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich
PL, Beese LS |
(2007) "Structure
of the Human MutSalpha DNA Lesion Recognition
Complex." Mol.Cell, 26,
579-592. doi: 10.1016/j.molcel.2007.04.018.
|
Human mutsalpha (msh2-msh6) bound to adp and an
o6-methyl-guanine t mispair . SNAP output
|
|
2o8d
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich
PL, Beese LS |
(2007) "Structure
of the Human MutSalpha DNA Lesion Recognition
Complex." Mol.Cell, 26,
579-592. doi: 10.1016/j.molcel.2007.04.018.
|
Human mutsalpha (msh2-msh6) bound to adp and a g du
mispair . SNAP
output
|
|
2o8e
|
DNA binding protein-DNA |
X-ray (3.3 Å) |
Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich
PL, Beese LS |
(2007) "Structure
of the Human MutSalpha DNA Lesion Recognition
Complex." Mol.Cell, 26,
579-592. doi: 10.1016/j.molcel.2007.04.018.
|
Human mutsalpha (msh2-msh6) bound to a g t mispair,
with adp bound to msh2 only . SNAP output
|
|
2o8f
|
DNA binding protein-DNA |
X-ray (3.25 Å) |
Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich
PL, Beese LS |
(2007) "Structure
of the Human MutSalpha DNA Lesion Recognition
Complex." Mol.Cell, 26,
579-592. doi: 10.1016/j.molcel.2007.04.018.
|
Human mutsalpha (msh2-msh6) bound to DNA with a single
base t insert . SNAP
output
|
|
2o8k
|
transcription-DNA |
NMR |
Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer
DE |
(2007) "Structural
basis of DNA recognition by the alternative
sigma-factor, sigma54." J.Mol.Biol.,
369, 1070-1078. doi: 10.1016/j.jmb.2007.04.019.
|
NMR structure of the sigma-54 rpon domain bound to
the-24 promoter element . SNAP output
|
|
2o93
|
transcription-DNA |
X-ray (3.05 Å) |
Bates DL, Barthel KK, Wu Y, Kalhor R, Stroud JC,
Giffin MJ, Chen L |
(2008) "Crystal
structure of NFAT bound to the HIV-1 LTR tandem kappaB
enhancer element." Structure,
16, 684-694. doi: 10.1016/j.str.2008.01.020.
|
Crystal structure of nfat bound to the hiv-1 ltr tandem
kappab enhancer element . SNAP output
|
|
2o9l
|
RNA polymerase sigma factor rpon-DNA |
NMR |
Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer
DE |
(2007) "Structural
basis of DNA recognition by the alternative
sigma-factor, sigma54." J.Mol.Biol.,
369, 1070-1078. doi: 10.1016/j.jmb.2007.04.019.
|
Amber refined NMR structure of the sigma-54 rpon domain
bound to the-24 promoter element . SNAP output
|
|
2oa8
|
hydrolase-DNA |
X-ray (2.1 Å) |
de Silva U, Choudhury S, Bailey SL, Harvey S, Perrino
FW, Hollis T |
(2007) "The
Crystal Structure of TREX1 Explains the 3' Nucleotide
Specificity and Reveals a Polyproline II Helix for
Protein Partnering." J.Biol.Chem.,
282, 10537-10543. doi: 10.1074/jbc.M700039200.
|
Crystal structure of mtrex1 with ssDNA . SNAP output
|
|
2oaa
|
hydrolase-DNA |
X-ray (1.5 Å) |
Kaus-Drobek M, Czapinska H, Sokolowska M, Tamulaitis
G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler
M |
(2007) "Restriction
endonuclease MvaI is a monomer that recognizes its
target sequence asymmetrically." Nucleic Acids
Res., 35, 2035-2046. doi:
10.1093/nar/gkm064.
|
Restriction endonuclease mvai-cognate DNA substrate
complex . SNAP
output
|
|
2odi
|
hydrolase-DNA |
X-ray (1.45 Å) |
Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis
G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler
M |
(2007) "Monomeric
restriction endonuclease BcnI in the apo form and in an
asymmetric complex with target DNA."
J.Mol.Biol., 369, 722-734.
doi: 10.1016/j.jmb.2007.03.018.
|
Restriction endonuclease bcni-cognate DNA substrate
complex . SNAP
output
|
|
2oeh
|
transcription-DNA |
NMR |
Cai S, Zhu L, Zhang Z, Chen Y |
(2007) "Determination
of the three-dimensional structure of the Mrf2-DNA
complex using paramagnetic spin labeling."
Biochemistry, 46, 4943-4950.
doi: 10.1021/bi061738h.
|
Determination of the three-dimensional structure of the
mrf2-DNA complex using paramagnetic spin labeling .
SNAP output
|
|
2ofi
|
3-methyladenine DNA glycosylase i-DNA |
X-ray (1.85 Å) |
Metz AH, Hollis T, Eichman BF |
(2007) "DNA
damage recognition and repair by 3-methyladenine DNA
glycosylase I (TAG)." Embo J.,
26, 2411-2420. doi: 10.1038/sj.emboj.7601649.
|
Crystal structure of 3-methyladenine DNA glycosylase i
(tag) bound to DNA-3ma . SNAP output
|
|
2og0
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Papagiannis CV, Sam MD, Abbani MA, Yoo D, Cascio D,
Clubb RT, Johnson RC |
(2007) "Fis
targets assembly of the xis nucleoprotein filament to
promote excisive recombination by phage lambda."
J.Mol.Biol., 367, 328-343.
doi: 10.1016/j.jmb.2006.12.071.
|
Crystal structure of the lambda xis-DNA complex .
SNAP output
|
|
2oh2
|
transferase-DNA |
X-ray (3.05 Å) |
Lone S, Townson SA, Uljon SN, Johnson RE, Brahma A,
Nair DT, Prakash S, Prakash L, Aggarwal AK |
"Ternary complex of the catalytic core of human DNA
polymerase Kappa with DNA and dTT." |
Ternary complex of human DNA polymerase . SNAP output
|
|
2ok0
|
immune system-DNA |
X-ray (1.89 Å) |
Sanguineti S, Centeno Crowley JM, Lodeiro Merlo MF,
Cerutti ML, Wilson IA, Goldbaum FA, Stanfield RL, de
Prat-Gay G |
(2007) "Specific
recognition of a DNA immunogen by its elicited
antibody." J.Mol.Biol.,
370, 183-195. doi: 10.1016/j.jmb.2007.04.046.
|
Fab ed10-DNA complex . SNAP output
|
|
2opf
|
hydrolase-DNA |
X-ray (1.85 Å) |
Golan G, Zharkov DO, Grollman AP, Shoham G |
"Active site plasticity of endonuclease VIII:
Conformational changes compensating for different
substrates and mutations of critical residues." |
Crystal structure of the DNA repair enzyme
endonuclease-viii (nei) from e. coli (r252a) in complex
with ap-site containing DNA substrate . SNAP output
|
|
2oq4
|
hydrolase-DNA |
X-ray (2.6 Å) |
Golan G, Zharkov DO, Grollman AP, Shoham G |
"Active site plasticity of endonuclease VIII:
Conformational changes compensating for different
substrates and mutations of critical residues." |
Crystal structure of the DNA repair enzyme
endonuclease-viii (nei) from e. coli (e2q) in complex
with ap-site containing DNA substrate . SNAP output
|
|
2or1
|
gene regulation-DNA |
X-ray (2.5 Å) |
Aggarwal AK, Rodgers DW, Drottar M, Ptashne M,
Harrison SC |
(1988) "Recognition
of a DNA operator by the repressor of phage 434: a view
at high resolution." Science,
242, 899-907.
|
Recognition of a DNA operator by the repressor of phage
434. a view at high resolution . SNAP output
|
|
2ost
|
hydrolase-DNA |
X-ray (3.1 Å) |
Zhao L, Bonocora RP, Shub DA, Stoddard BL |
(2007) "The
restriction fold turns to the dark side: a bacterial
homing endonuclease with a PD-(D/E)-XK motif."
Embo J., 26, 2432-2442. doi:
10.1038/sj.emboj.7601672.
|
The structure of a bacterial homing endonuclease :
i-ssp6803i . SNAP
output
|
|
2owo
|
ligase-DNA |
X-ray (2.3 Å) |
Nandakumar J, Nair PA, Shuman S |
(2007) "Last
Stop on the Road to Repair: Structure of E. coli DNA
Ligase Bound to Nicked DNA-Adenylate."
Mol.Cell, 26, 257-271. doi:
10.1016/j.molcel.2007.02.026.
|
Last stop on the road to repair: structure of e.coli
DNA ligase bound to nicked DNA-adenylate . SNAP output
|
|
2oxm
|
hydrolase-DNA |
X-ray (2.5 Å) |
Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel
LM, Stivers JT |
(2007) "Enzymatic
capture of an extrahelical thymine in the search for
uracil in DNA." Nature,
449, 433-437. doi: 10.1038/nature06131.
|
Crystal structure of a ung2-modified DNA complex that
represent a stabilized short-lived extrahelical state
in ezymatic DNA base flipping . SNAP output
|
|
2oxv
|
hydrolase-DNA |
X-ray (1.95 Å) |
Sapienza PJ, Rosenberg JM, Jen-Jacobson L |
(2007) "Structural
and thermodynamic basis for enhanced DNA binding by a
promiscuous mutant EcoRI endonuclease."
Structure, 15, 1368-1382.
doi: 10.1016/j.str.2007.09.014.
|
Structure of the a138t promiscuous mutant of the ecori
restriction endonuclease bound to its cognate
recognition site. . SNAP
output
|
|
2oyq
|
transferase-DNA |
X-ray (2.86 Å) |
Zahn KE, Belrhali H, Wallace SS, Doublie S |
(2007) "Caught
bending the a-rule: crystal structures of translesion
DNA synthesis with a non-natural nucleotide."
Biochemistry, 46,
10551-10561. doi: 10.1021/bi7008807.
|
Crystal structure of rb69 gp43 in complex with DNA with
5-nimp opposite an abasic site analog . SNAP output
|
|
2oyt
|
hydrolase-DNA |
X-ray (2.0 Å) |
Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel
LM, Stivers JT |
(2007) "Enzymatic
capture of an extrahelical thymine in the search for
uracil in DNA." Nature,
449, 433-437. doi: 10.1038/nature06131.
|
Crystal structure of ung2-DNA(tm) . SNAP output
|
|
2ozm
|
transferase-DNA |
X-ray (2.86 Å) |
Zahn KE, Belrhail H, Wallace SS, Doublie S |
(2007) "Caught
Bending the A-Rule: crystal structures of translesion
DNA synthesis with a non-natural nucleotide."
Biochemistry, 46,
10551-10561. doi: 10.1021/bi7008807.
|
Crystal structure of rb69 gp43 in complex with DNA with
5-nitp opposite an abasic site analog . SNAP output
|
|
2ozs
|
transferase-DNA |
X-ray (2.75 Å) |
Zahn KE, Belrhali H, Wallace SS, Doublie S |
(2007) "Caught
bending the a-rule: crystal structures of translesion
DNA synthesis with a non-natural nucleotide."
Biochemistry, 46,
10551-10561. doi: 10.1021/bi7008807.
|
Crystal structure of rb69 gp43 in complex with DNA with
datp opposite dtmp . SNAP output
|
|
2p0j
|
hydrolase-DNA |
X-ray (2.1 Å) |
Townson SA, Samuelson JC, Bao Y, Xu SY, Aggarwal
AK |
(2007) "BstYI
Bound to Noncognate DNA Reveals a "Hemispecific"
Complex: Implications for DNA Scanning."
Structure, 15, 449-459. doi:
10.1016/j.str.2007.03.002.
|
Structure of restriction endonuclease bstyi bound to
non-cognate DNA . SNAP
output
|
|
2p2r
|
RNA and DNA binding protein-DNA |
X-ray (1.6 Å) |
Fenn S, Du Z, Lee JK, Tjhen R, Stroud RM, James
TL |
(2007) "Crystal
structure of the third KH domain of human
poly(C)-binding protein-2 in complex with a C-rich
strand of human telomeric DNA at 1.6 A resolution."
Nucleic Acids Res., 35,
2651-2660. doi: 10.1093/nar/gkm139.
|
Crystal structure of the third kh domain of human
poly(c)-binding protein-2 in complex with c-rich strand
of human telomeric DNA . SNAP output
|
|
2p5g
|
transferase-DNA |
X-ray (2.8 Å) |
Zahn KE, Belrhali H, Wallace SS, Doublie S |
(2007) "Caught
bending the a-rule: crystal structures of translesion
DNA synthesis with a non-natural nucleotide."
Biochemistry, 46,
10551-10561. doi: 10.1021/bi7008807.
|
Crystal structure of rb69 gp43 in complex with DNA with
damp opposite an abasic site analog in a 21mer template
. SNAP output
|
|
2p5l
|
transcription repressor |
X-ray (2.85 Å) |
Garnett JA, Marincs F, Baumberg S, Stockley PG,
Phillips SE |
(2008) "Structure
and function of the arginine repressor-operator complex
from Bacillus subtilis." J.Mol.Biol.,
379, 284-298. doi: 10.1016/j.jmb.2008.03.007.
|
Crystal structure of a dimer of n-terminal domains of
ahrc in complex with an 18bp DNA operator site .
SNAP output
|
|
2p5o
|
transferase-DNA |
X-ray (2.8 Å) |
Hogg M, Wallace SS, Doublie S |
(2004) "Crystallographic
snapshots of a replicative DNA polymerase encountering
an abasic site." Embo J.,
23, 1483-1493. doi: 10.1038/sj.emboj.760015.
|
Crystal structure of rb69 gp43 in complex with DNA
containing an abasic site analog . SNAP output
|
|
2p66
|
transferase, lyase-DNA |
X-ray (2.5 Å) |
Prasad R, Batra VK, Yang X-P, Krahn JM, Pedersen LC,
Beard WA, Wilson SH |
(2005) "Structural
insight into the DNA Polymerase beta deoxyribose
phosphate lyase mechanism." DNA REPAIR,
4, 1347-1357. doi: 10.1016/j.dnarep.2005.08.009.
|
Human DNA polymerase beta complexed with
tetrahydrofuran (abasic site) containing DNA . SNAP output
|
|
2p6r
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Buttner K, Nehring S, Hopfner KP |
(2007) "Structural
basis for DNA duplex separation by a superfamily-2
helicase." Nat.Struct.Mol.Biol.,
14, 647-652. doi: 10.1038/nsmb1246.
|
Crystal structure of superfamily 2 helicase hel308 in
complex with unwound DNA . SNAP output
|
|
2p7c
|
transcription regulator |
NMR |
Boudet J, Duval V, Van Melckebeke H, Blackledge M,
Amoroso A, Joris B, Simorre JP |
(2007) "Conformational
and thermodynamic changes of the repressor/DNA operator
complex upon monomerization shed new light on
regulation mechanisms of bacterial resistance against
beta-lactam antibiotics." Nucleic Acids
Res., 35, 4384-4395. doi:
10.1093/nar/gkm448.
|
Solution structure of the bacillus licheniformis blai
monomeric form in complex with the blap half-operator.
. SNAP output
|
|
2pe5
|
transcription-DNA |
X-ray (3.5 Å) |
Daber R, Stayrook S, Rosenberg A, Lewis M |
(2007) "Structural
analysis of lac repressor bound to allosteric
effectors." J.Mol.Biol.,
370, 609-619. doi: 10.1016/j.jmb.2007.04.028.
|
Crystal structure of the lac repressor bound to onpg in
repressed state . SNAP
output
|
|
2pfj
|
hydrolase-DNA |
X-ray (3.1 Å) |
Hadden JM, Declais AC, Carr SB, Lilley DM, Phillips
SE |
(2007) "The
structural basis of Holliday junction resolution by T7
endonuclease I." Nature,
449, 621-624. doi: 10.1038/nature06158.
|
Crystal structure of t7 endo i resolvase in complex
with a holliday junction . SNAP output
|
|
2pfn
|
transferase, lyase-DNA |
X-ray (1.9 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2007) "Role of
the catalytic metal during polymerization by DNA
polymerase lambda." DNA Repair,
6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005.
|
Na in the active site of DNA polymerase lambda .
SNAP output
|
|
2pfo
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2007) "Role of
the catalytic metal during polymerization by DNA
polymerase lambda." DNA Repair,
6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005.
|
DNA polymerase lambda in complex with DNA and dupnpp .
SNAP output
|
|
2pfp
|
transferase, lyase-DNA |
X-ray (2.1 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2007) "Role of
the catalytic metal during polymerization by DNA
polymerase lambda." DNA Repair,
6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005.
|
DNA polymerase lambda in complex with DNA and dctp .
SNAP output
|
|
2pfq
|
transferase, lyase-DNA |
X-ray (2.1 Å) |
Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC,
Kunkel TA |
(2007) "Role of
the catalytic metal during polymerization by DNA
polymerase lambda." DNA Repair,
6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005.
|
Manganese promotes catalysis in a DNA polymerase
lambda-DNA crystal . SNAP output
|
|
2pi0
|
transcription activator-DNA |
X-ray (2.31 Å) |
Escalante CR, Nistal-Villan E, Shen L, Garcia-Sastre
A, Aggarwal AK |
(2007) "Structure
of IRF-3 bound to the PRDIII-I regulatory element of
the human interferon-beta enhancer."
Mol.Cell, 26, 703-716. doi:
10.1016/j.molcel.2007.04.022.
|
Crystal structure of irf-3 bound to the prdiii-i
regulatory element of the human interferon-b enhancer .
SNAP output
|
|
2pi4
|
transferase-DNA |
X-ray (2.5 Å) |
Kennedy WP, Momand JR, Yin YW |
(2007) "Mechanism
for de novo RNA synthesis and initiating nucleotide
specificity by t7 RNA polymerase."
J.Mol.Biol., 370, 256-268.
doi: 10.1016/j.jmb.2007.03.041.
|
T7rnap complexed with a phi10 protein and initiating
gtps. . SNAP output
|
|
2pi5
|
transferase-DNA |
X-ray (2.9 Å) |
Kennedy WP, Momand JR, Yin YW |
(2007) "Mechanism
for de novo RNA synthesis and initiating nucleotide
specificity by t7 RNA polymerase."
J.Mol.Biol., 370, 256-268.
doi: 10.1016/j.jmb.2007.03.041.
|
T7 RNA polymerase complexed with a phi10 promoter .
SNAP output
|
|
2pjr
|
hydrolase-DNA |
X-ray (2.9 Å) |
Velankar SS, Soultanas P, Dillingham MS, Subramanya
HS, Wigley DB |
(1999) "Crystal
structures of complexes of PcrA DNA helicase with a DNA
substrate indicate an inchworm mechanism."
Cell(Cambridge,Mass.), 97,
75-98. doi: 10.1016/S0092-8674(00)80716-3.
|
Helicase product complex . SNAP output
|
|
2ppb
|
transferase-DNA-RNA |
X-ray (3.0 Å) |
Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M,
Artsimovitch I, Landick R |
(2007) "Structural
basis for substrate loading in bacterial RNA
polymerase." Nature, 448,
163-168. doi: 10.1038/nature05931.
|
Crystal structure of the t. thermophilus rnap
polymerase elongation complex with the ntp substrate
analog and antibiotic streptolydigin . SNAP output
|
|
2pqu
|
RNA and DNA binding protein-DNA |
X-ray (2.12 Å) |
Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James
TL |
(2007) "X-ray
crystallographic and NMR studies of protein-protein and
protein-nucleic acid interactions involving the KH
domains from human poly(C)-binding protein-2."
Rna, 13, 1043-1051. doi:
10.1261/rna.410107.
|
Crystal structure of kh1 domain of human pcbp2
complexed to single-stranded 12-mer telomeric DNA .
SNAP output
|
|
2prt
|
transcription-DNA |
X-ray (3.15 Å) |
Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA,
Dyson HJ, Wright PE |
(2007) "Structure
of the Wilms tumor suppressor protein zinc finger
domain bound to DNA." J.Mol.Biol.,
372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017.
|
Structure of the wilms tumor suppressor protein zinc
finger domain bound to DNA . SNAP output
|
|
2pua
|
transcription-DNA |
X-ray (2.9 Å) |
Schumacher MA, Choi KY, Zalkin H, Brennan RG |
(1994) "Crystal
structure of LacI member, PurR, bound to DNA: minor
groove binding by alpha helices." Science,
266, 763-770.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2pub
|
transcription-DNA |
X-ray (2.7 Å) |
Schumacher MA, Choi KY, Zalkin H, Brennan RG |
(1994) "Crystal
structure of LacI member, PurR, bound to DNA: minor
groove binding by alpha helices." Science,
266, 763-770.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2puc
|
transcription-DNA |
X-ray (2.6 Å) |
Schumacher MA, Choi KY, Zalkin H, Brennan RG |
(1994) "Crystal
structure of LacI member, PurR, bound to DNA: minor
groove binding by alpha helices." Science,
266, 763-770.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2pud
|
transcription-DNA |
X-ray (2.6 Å) |
Schumacher MA, Choi KY, Zalkin H, Brennan RG |
(1994) "Crystal
structure of LacI member, PurR, bound to DNA: minor
groove binding by alpha helices." Science,
266, 763-770.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2pue
|
transcription-DNA |
X-ray (2.7 Å) |
Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner
BL, Zalkin H, Brennan RG |
(1998) "Structure-based
redesign of corepressor specificity of the Escherichia
coli purine repressor by substitution of residue
190." Biochemistry, 37,
971-982. doi: 10.1021/bi971942s.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2puf
|
transcription-DNA |
X-ray (3.0 Å) |
Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner
BL, Zalkin H, Brennan RG |
(1998) "Structure-based
redesign of corepressor specificity of the Escherichia
coli purine repressor by substitution of residue
190." Biochemistry, 37,
971-982. doi: 10.1021/bi971942s.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2pug
|
transcription-DNA |
X-ray (2.7 Å) |
Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner
BL, Zalkin H, Brennan RG |
(1998) "Structure-based
redesign of corepressor specificity of the Escherichia
coli purine repressor by substitution of residue
190." Biochemistry, 37,
971-982. doi: 10.1021/bi971942s.
|
Crystal structure of the laci family member, purr,
bound to DNA: minor groove binding by alpha helices .
SNAP output
|
|
2pvi
|
hydrolase-DNA |
X-ray (1.76 Å) |
Horton JR, Bonventre J, Cheng X |
(1998) "How is
modification of the DNA substrate recognized by the
PvuII restriction endonuclease?."
J.Biol.Chem., 379, 451-458.
|
Pvuii endonuclease complexed to an iodinated cognate
DNA . SNAP output
|
|
2pxi
|
lyase, transferase-DNA |
X-ray (2.1 Å) |
McKenna CE, Kashemirov BA, Upton TG, Batra VK,
Goodman MF, Pedersen LC, Beard WA, Wilson SH |
(2007) "(R)-beta,gamma-fluoromethylene-dGTP-DNA
ternary complex with DNA polymerase beta."
J.Am.Chem.Soc., 129,
15412-15413. doi: 10.1021/ja072127v.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monofluoromethylene triphosphate . SNAP output
|
|
2py5
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega
M, Blanco L, Salas M, Steitz TA |
(2007) "Structures
of phi29 DNA polymerase complexed with substrate: the
mechanism of translocation in B-family
polymerases." Embo J.,
26, 3494-3505. doi: 10.1038/sj.emboj.7601780.
|
Phi29 DNA polymerase complexed with single-stranded DNA
. SNAP output
|
|
2pyj
|
replication, transferase-DNA |
X-ray (2.03 Å) |
Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega
M, Blanco L, Salas M, Steitz TA |
(2007) "Structures
of phi29 DNA polymerase complexed with substrate: the
mechanism of translocation in B-family
polymerases." Embo J.,
26, 3494-3505. doi: 10.1038/sj.emboj.7601780.
|
Phi29 DNA polymerase complexed with primer-template DNA
and incoming nucleotide substrates (ternary complex) .
SNAP output
|
|
2pyl
|
replication, transferase-DNA |
X-ray (2.2 Å) |
Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega
M, Blanco L, Salas M, Steitz TA |
(2007) "Structures
of phi29 DNA polymerase complexed with substrate: the
mechanism of translocation in B-family
polymerases." Embo J.,
26, 3494-3505. doi: 10.1038/sj.emboj.7601780.
|
Phi29 DNA polymerase complexed with primer-template DNA
and incoming nucleotide substrates (ternary complex) .
SNAP output
|
|
2pyo
|
structural protein-DNA |
X-ray (2.43 Å) |
Clapier CR, Chakravarthy S, Petosa C,
Fernandez-Tornero C, Luger K, Muller CW |
(2007) "Structure
of the Drosophila nucleosome core particle highlights
evolutionary constraints on the H2A-H2B histone
dimer." Proteins, 71,
1-7. doi: 10.1002/prot.21720.
|
Drosophila nucleosome core . SNAP output
|
|
2pzs
|
replication, transferase-DNA |
X-ray (2.6 Å) |
Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega
M, Blanco L, Salas M, Steitz TA |
(2007) "Structures
of phi29 DNA polymerase complexed with substrate: the
mechanism of translocation in B-family
polymerases." Embo J.,
26, 3494-3505. doi: 10.1038/sj.emboj.7601780.
|
Phi29 DNA polymerase complexed with primer-template DNA
(post-translocation binary complex) . SNAP output
|
|
2q10
|
hydrolase-DNA |
X-ray (1.75 Å) |
Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis
G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler
M |
(2007) "Monomeric
Restriction Endonuclease BcnI in the Apo Form and in an
Asymmetric Complex with Target DNA."
J.Mol.Biol., 369, 722-734.
doi: 10.1016/j.jmb.2007.03.018.
|
Restriction endonuclease bcni (wild type)-cognate DNA
substrate complex . SNAP
output
|
|
2q2k
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Schumacher MA, Glover TC, Brzoska AJ, Jensen SO,
Dunham TD, Skurray RA, Firth N |
(2007) "Segrosome
structure revealed by a complex of ParR with centromere
DNA." Nature, 450,
1268-1271. doi: 10.1038/nature06392.
|
Structure of nucleic-acid binding protein . SNAP output
|
|
2q2t
|
ligase-DNA |
X-ray (2.3 Å) |
Nair PA, Nandakumar J, Smith P, Odell M, Lima CD,
Shuman S |
(2007) "Structural
basis for nick recognition by a minimal pluripotent DNA
ligase." Nat.Struct.Mol.Biol.,
14, 770-778. doi: 10.1038/nsmb1266.
|
Structure of chlorella virus DNA ligase-adenylate bound
to a 5' phosphorylated nick . SNAP output
|
|
2q2u
|
ligase-DNA |
X-ray (3.0 Å) |
Nair PA, Nandakumar J, Smith P, Odell M, Lima CD,
Shuman S |
(2007) "Structural
basis for nick recognition by a minimal pluripotent DNA
ligase." Nat.Struct.Mol.Biol.,
14, 770-778. doi: 10.1038/nsmb1266.
|
Structure of chlorella virus DNA ligase-product DNA
complex . SNAP
output
|
|
2qby
|
replication-DNA |
X-ray (3.35 Å) |
Dueber EL, Corn JE, Bell SD, Berger JM |
(2007) "Replication
origin recognition and deformation by a heterodimeric
archaeal Orc1 complex." Science,
317, 1210-1213. doi: 10.1126/science.1143690.
|
Crystal structure of a heterodimer of cdc6-orc1
initiators bound to origin DNA (from s. solfataricus) .
SNAP output
|
|
2qfj
|
transcription repressor-DNA |
X-ray (2.1 Å) |
Crichlow GV, Zhou H, Hsiao H-H, Frederick KB,
Debrosse M, Yang Y, Folta-Stogniew EJ, Chung H-J, Fan C,
De La Cruz EM, Levens D, Lolis E, Braddock D |
(2007) "Dimerization
of FIR upon FUSE DNA binding suggests a mechanism of
c-myc inhibition." EMBO J.,
27, 277-289. doi: 10.1038/sj.emboj.7601936.
|
Crystal structure of first two rrm domains of fir bound
to ssDNA from a portion of fuse . SNAP output
|
|
2qhb
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Cho H-S, Byun J-S, Jun S-H, Han W, Lee W |
"Complex structure of plant telomere bindig protein,
NgTRF and telomere DNA." |
Crystal structure of ngtrf complexed with telomeric DNA
. SNAP output
|
|
2qk9
|
hydrolase-DNA-RNA |
X-ray (2.55 Å) |
Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM,
Crouch RJ, Yang W |
(2007) "Structure
of Human RNase H1 Complexed with an RNA/DNA Hybrid:
Insight into HIV Reverse Transcription."
Mol.Cell, 28, 264-276. doi:
10.1016/j.molcel.2007.08.015.
|
Human rnase h catalytic domain mutant d210n in complex
with 18-mer RNA-DNA hybrid . SNAP output
|
|
2qkb
|
hydrolase-DNA-RNA |
X-ray (2.4 Å) |
Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM,
Crouch RJ, Yang W |
(2007) "Structure
of Human RNase H1 Complexed with an RNA/DNA Hybrid:
Insight into HIV Reverse Transcription."
Mol.Cell, 28, 264-276. doi:
10.1016/j.molcel.2007.08.015.
|
Human rnase h catalytic domain mutant d210n in complex
with 20-mer RNA-DNA hybrid . SNAP output
|
|
2qkk
|
hydrolase-DNA-RNA |
X-ray (3.2 Å) |
Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM,
Crouch RJ, Yang W |
(2007) "Structure
of Human RNase H1 Complexed with an RNA/DNA Hybrid:
Insight into HIV Reverse Transcription."
Mol.Cell, 28, 264-276. doi:
10.1016/j.molcel.2007.08.015.
|
Human rnase h catalytic domain mutant d210n in complex
with 14-mer RNA-DNA hybrid . SNAP output
|
|
2ql2
|
transcription-DNA |
X-ray (2.5 Å) |
Longo A, Guanga GP, Rose RB |
(2008) "Crystal
structure of E47-NeuroD1/beta2 bHLH domain-DNA complex:
heterodimer selectivity and DNA recognition."
Biochemistry, 47, 218-229.
doi: 10.1021/bi701527r.
|
Crystal structure of the basic-helix-loop-helix domains
of the heterodimer e47-neurod1 bound to DNA . SNAP output
|
|
2qnc
|
hydrolase-DNA |
X-ray (3.1 Å) |
Biertumpfel C, Yang W, Suck D |
(2007) "Crystal
structure of T4 endonuclease VII resolving a Holliday
junction." Nature, 449,
616-620. doi: 10.1038/nature06152.
|
Crystal structure of t4 endonuclease vii n62d mutant in
complex with a DNA holliday junction . SNAP output
|
|
2qnf
|
hydrolase-DNA |
X-ray (3.0 Å) |
Biertumpfel C, Yang W, Suck D |
(2007) "Crystal
structure of T4 endonuclease VII resolving a Holliday
junction." Nature, 449,
616-620. doi: 10.1038/nature06152.
|
Crystal structure of t4 endonuclease vii h43n mutant in
complex with heteroduplex DNA containing base
mismatches . SNAP
output
|
|
2qoj
|
hydrolase-DNA |
X-ray (2.4 Å) |
Scalley-Kim M, McConnell-Smith A, Stoddard BL |
(2007) "Coevolution
of a homing endonuclease and its host target
sequence." J.Mol.Biol.,
372, 1305-1319. doi: 10.1016/j.jmb.2007.07.052.
|
Coevolution of a homing endonuclease and its host
target sequence . SNAP
output
|
|
2qsg
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Min J-H, Pavletich NP |
(2007) "Recognition
of DNA damage by the Rad4 nucleotide excision repair
protein." Nature, 449,
570-575. doi: 10.1038/nature06155.
|
Crystal structure of rad4-rad23 bound to a uv-damaged
DNA . SNAP output
|
|
2qsh
|
DNA binding protein-DNA |
X-ray (2.805 Å) |
Min J-H, Pavletich NP |
(2007) "Recognition
of DNA damage by the Rad4 nucleotide excision repair
protein." Nature, 449,
570-575. doi: 10.1038/nature06155.
|
Crystal structure of rad4-rad23 bound to a mismatch DNA
. SNAP output
|
|
2r0q
|
recombination-DNA |
X-ray (3.2 Å) |
Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM,
Rice PA |
(2008) "Architecture
of a serine recombinase-DNA regulatory complex."
Mol.Cell, 30, 145-155. doi:
10.1016/j.molcel.2008.02.023.
|
Crystal structure of a serine recombinase- DNA
regulatory complex . SNAP output
|
|
2r1j
|
transcription-DNA |
X-ray (1.53 Å) |
Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams
LD |
(2008) "P22 c2
repressor-operator complex: mechanisms of direct and
indirect readout." Biochemistry,
47, 2325-2338. doi: 10.1021/bi701826f.
|
Crystal structure of the p22 c2 repressor protein in
complex with the synthetic operator 9t . SNAP output
|
|
2r2r
|
transferase-DNA |
X-ray (2.1 Å) |
Goodwin KD, Lewis MA, Long EC, Georgiadis MM |
(2008) "Crystal
structure of DNA-bound Co(III) bleomycin B2: Insights
on intercalation and minor groove binding."
Proc.Natl.Acad.Sci.Usa, 105,
5052-5056. doi: 10.1073/pnas.0708143105.
|
D(attagttataactaat) complexed with mmlv rt catalytic
fragment . SNAP
output
|
|
2r2s
|
transferase-DNA |
X-ray (2.8 Å) |
Goodwin KD, Lewis MA, Long EC, Georgiadis MM |
(2008) "Crystal
structure of DNA-bound Co(III) bleomycin B2: Insights
on intercalation and minor groove binding."
Proc.Natl.Acad.Sci.Usa, 105,
5052-5056. doi: 10.1073/pnas.0708143105.
|
Co(iii)bleomycinb2 bound to d(attagttataactaat)
complexed with mmlv rt catalytic fragment . SNAP output
|
|
2r2t
|
transferase-DNA |
X-ray (2.0 Å) |
Goodwin KD, Lewis MA, Long EC, Georgiadis MM |
(2008) "Crystal
structure of DNA-bound Co(III) bleomycin B2: Insights
on intercalation and minor groove binding."
Proc.Natl.Acad.Sci.Usa, 105,
5052-5056. doi: 10.1073/pnas.0708143105.
|
D(atttagttaactaaat) complexed with mmlv rt catalytic
fragment . SNAP
output
|
|
2r2u
|
transferase-DNA |
X-ray (2.3 Å) |
Goodwin KD, Lewis MA, Long EC, Georgiadis MM |
(2008) "Crystal
structure of DNA-bound Co(III) bleomycin B2: Insights
on intercalation and minor groove binding."
Proc.Natl.Acad.Sci.Usa, 105,
5052-5056. doi: 10.1073/pnas.0708143105.
|
Co(iii)bleomycinb2 bithiazole-c-terminal tail domain
bound to d(atttagttaactaaat) complexed with mmlv rt
catalytic fragment . SNAP output
|
|
2r5y
|
transcription-DNA |
X-ray (2.6 Å) |
Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A,
Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS |
(2007) "Functional
specificity of a Hox protein mediated by the
recognition of minor groove structure."
Cell(Cambridge,Mass.), 131,
530-543. doi: 10.1016/j.cell.2007.09.024.
|
Structure of scr-exd complex bound to a consensus
hox-exd site . SNAP
output
|
|
2r5z
|
transcription-DNA |
X-ray (2.6 Å) |
Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A,
Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS |
(2007) "Functional
specificity of a Hox protein mediated by the
recognition of minor groove structure."
Cell(Cambridge,Mass.), 131,
530-543. doi: 10.1016/j.cell.2007.09.024.
|
Structure of scr-exd complex bound to a DNA sequence
derived from the fkh gene . SNAP output
|
|
2r7y
|
hydrolase-RNA-DNA |
X-ray (1.8 Å) |
Jiang J-S, Gerlits O, Huang Z |
"Selenium Derivatized RNA/DNA Hybrid in complex with
RNase H CATALYTIC DOMAIN MUTANT D132N." |
Selenium derivatized RNA-DNA hybrid in complex with
rnase h catalytic domain mutant d132n . SNAP output
|
|
2r7z
|
transcription-DNA-RNA hybrid |
X-ray (3.8 Å) |
Damsma GE, Alt A, Brueckner F, Carell T, Cramer
P |
(2007) "Mechanism
of transcriptional stalling at cisplatin-damaged
DNA." Nat.Struct.Mol.Biol.,
14, 1127-1133. doi: 10.1038/nsmb1314.
|
Cisplatin lesion containing RNA polymerase ii
elongation complex . SNAP output
|
|
2r8g
|
replication, transferase-DNA |
X-ray (2.7 Å) |
Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone
MP |
(2008) "Insertion
of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct
by Sulfolobus solfataricus P2 DNA polymerase IV."
Biochemistry, 47, 7322-7334.
doi: 10.1021/bi800152j.
|
Selectivity of nucleoside triphosphate incorporation
opposite 1,n2-propanodeoxyguanosine (pdg) by the
sulfolobus solfataricus DNA polymerase dpo4 polymerase
. SNAP output
|
|
2r8h
|
replication, transferase-DNA |
X-ray (2.48 Å) |
Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone
MP |
(2008) "Insertion
of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct
by Sulfolobus solfataricus P2 DNA polymerase IV."
Biochemistry, 47, 7322-7334.
doi: 10.1021/bi800152j.
|
Selectivity of nucleoside triphosphate incorporation
opposite 1,n2-propanodeoxyguanosine (pdg) by the
sulfolobus solfataricus DNA polymerase dpo4 polymerase
. SNAP output
|
|
2r8i
|
replication, transferase-DNA |
X-ray (2.38 Å) |
Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone
MP |
(2008) "Insertion
of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct
by Sulfolobus solfataricus P2 DNA polymerase IV."
Biochemistry, 47, 7322-7334.
doi: 10.1021/bi800152j.
|
Selectivity of nucleoside triphosphate incorporation
opposite 1,n2-propanodeoxyguanosine (pdg) by the
sulfolobus solfataricus DNA polymerase dpo4 polymerase
. SNAP output
|
|
2r8j
|
replication, transferase-DNA |
X-ray (3.1 Å) |
Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC,
Kuch D, Hopfner KP, Carell T |
(2007) "Bypass
of DNA lesions generated during anticancer treatment
with cisplatin by DNA polymerase eta."
Science, 318, 967-970. doi:
10.1126/science.1148242.
|
Structure of the eukaryotic DNA polymerase eta in
complex with 1,2-d(gpg)-cisplatin containing DNA .
SNAP output
|
|
2r8k
|
replication, transferase-DNA |
X-ray (3.3 Å) |
Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC,
Kuch D, Hopfner KP, Carell T |
(2007) "Bypass
of DNA lesions generated during anticancer treatment
with cisplatin by DNA polymerase eta."
Science, 318, 967-970. doi:
10.1126/science.1148242.
|
Structure of the eukaryotic DNA polymerase eta in
complex with 1,2-d(gpg)-cisplatin containing DNA .
SNAP output
|
|
2r9l
|
transferase-DNA |
X-ray (2.4 Å) |
Brissett NC, Pitcher RS, Juarez R, Picher AJ, Green
AJ, Dafforn TR, Fox GC, Blanco L, Doherty AJ |
(2007) "Structure
of a NHEJ polymerase-mediated DNA synaptic
complex." Science, 318,
456-459. doi: 10.1126/science.1145112.
|
Polymerase domain from mycobacterium tuberculosis
ligase d in complex with DNA . SNAP output
|
|
2ram
|
transcription-DNA |
X-ray (2.4 Å) |
Chen YQ, Ghosh S, Ghosh G |
(1998) "A novel
DNA recognition mode by the NF-kappa B p65
homodimer." Nat.Struct.Biol.,
5, 67-73. doi: 10.1038/nsb0198-67.
|
A novel DNA recognition mode by nf-kb p65 homodimer .
SNAP output
|
|
2rba
|
hydrolase-DNA |
X-ray (2.79 Å) |
Maiti A, Morgan MT, Pozharski E, Drohat AC |
(2008) "Crystal
structure of human thymine DNA glycosylase bound to DNA
elucidates sequence-specific mismatch recognition."
Proc.Natl.Acad.Sci.Usa, 105,
8890-8895. doi: 10.1073/pnas.0711061105.
|
Structure of human thymine DNA glycosylase bound to
abasic and undamaged DNA . SNAP output
|
|
2rbf
|
oxidoreductase-DNA |
X-ray (2.25 Å) |
Zhou Y, Larson JD, Bottoms CA, Arturo EC, Henzl MT,
Jenkins JL, Nix JC, Becker DF, Tanner JJ |
(2008) "Structural
basis of the transcriptional regulation of the proline
utilization regulon by multifunctional PutA."
J.Mol.Biol., 381, 174-188.
doi: 10.1016/j.jmb.2008.05.084.
|
Structure of the ribbon-helix-helix domain of
escherichia coli puta (puta52) complexed with operator
DNA (o2) . SNAP
output
|
|
2rdj
|
transferase-DNA |
X-ray (2.2 Å) |
Wong JH, Fiala KA, Suo Z, Ling H |
(2008) "Snapshots
of a Y-family DNA polymerase in replication:
substrate-induced conformational transitions and
implications for fidelity of Dpo4."
J.Mol.Biol., 379, 317-330.
doi: 10.1016/j.jmb.2008.03.038.
|
Snapshots of a y-family DNA polymerase in replication:
dpo4 in apo and binary-ternary complex forms . SNAP output
|
|
2rgr
|
isomerase-DNA |
X-ray (3.0 Å) |
Dong KC, Berger JM |
(2007) "Structural
basis for gate-DNA recognition and bending by type IIA
topoisomerases." Nature,
450, 1201-1205. doi: 10.1038/nature06396.
|
Topoisomerase iia bound to g-segment DNA . SNAP output
|
|
2rve
|
hydrolase-DNA |
X-ray (3.0 Å) |
Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown
RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson
KS |
(1993) "The
crystal structure of EcoRV endonuclease and of its
complexes with cognate and non-cognate DNA
fragments." EMBO J., 12,
1781-1795.
|
The crystal structure of ecorv endonuclease and of its
complexes with cognate and non-cognate DNA segments .
SNAP output
|
|
2ssp
|
protein-DNA |
X-ray (2.25 Å) |
Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE,
Tainer JA |
(1998) "Base
excision repair initiation revealed by crystal
structures and binding kinetics of human uracil-DNA
glycosylase with DNA." EMBO J.,
17, 5214-5226. doi: 10.1093/emboj/17.17.5214.
|
Leucine-272-alanine uracil-DNA glycosylase bound to
abasic site-containing DNA . SNAP output
|
|
2stt
|
DNA binding protein-DNA |
NMR |
Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L,
Shiloach J, Gronenborn AM |
(1997) "Correction
of the NMR structure of the ETS1/DNA complex."
J.Biomol.NMR, 10, 317-328.
doi: 10.1023/A:1018399711996.
|
Solution NMR structure of the human ets1-DNA complex,
25 structures . SNAP
output
|
|
2stw
|
DNA binding protein-DNA |
NMR |
Werner MH, Clore GM, Fisher CL, Fisher RJ, Trinh L,
Shiloach J, Gronenborn AM |
(1997) "Correction
of the NMR structure of the ETS1/DNA complex."
J.Biomol.NMR, 10, 317-328.
doi: 10.1023/A:1018399711996.
|
Solution NMR structure of the human ets1-DNA complex,
restrained regularized mean structure . SNAP output
|
|
2up1
|
gene regulation-DNA |
X-ray (2.1 Å) |
Ding J, Hayashi MK, Zhang Y, Manche L, Krainer AR, Xu
RM |
(1999) "Crystal
structure of the two-RRM domain of hnRNP A1 (UP1)
complexed with single-stranded telomeric DNA."
Genes Dev., 13, 1102-1115.
|
Structure of up1-telomeric DNA complex . SNAP output
|
|
2uvr
|
transferase |
X-ray (2.9 Å) |
Eoff RL, Irimia A, Angel KC, Egli M, Guengerich
FP |
(2007) "Hydrogen
Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a
Charged Residue in the Little Finger Domain Determines
Miscoding Events in Sulfolobus Solfataricus DNA
Polymerase Dpo4." J.Biol.Chem.,
282, 19831. doi: 10.1074/JBC.M702290200.
|
Crystal structures of mutant dpo4 DNA polymerases with
8-oxog containing DNA template-primer constructs .
SNAP output
|
|
2uvu
|
transferase |
X-ray (2.7 Å) |
Eoff RL, Irimia A, Angel KC, Egli M, Guengerich
FP |
(2007) "Hydrogen
Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a
Charged Residue in the Little Finger Domain Determines
Miscoding Events in Sulfolobus Solfataricus DNA
Polymerase Dpo4." J.Biol.Chem.,
282, 19831. doi: 10.1074/JBC.M702290200.
|
Crystal structures of mutant dpo4 DNA polymerases with
8-oxog containing DNA template-primer constructs .
SNAP output
|
|
2uvv
|
transferase |
X-ray (2.2 Å) |
Eoff RL, Irimia A, Angel KC, Egli M, Guengerich
FP |
(2007) "Hydrogen
Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a
Charged Residue in the Little Finger Domain Determines
Miscoding Events in Sulfolobus Solfataricus DNA
Polymerase Dpo4." J.Biol.Chem.,
282, 19831. doi: 10.1074/JBC.M702290200.
|
Crystal structures of mutant dpo4 DNA polymerases with
8-oxog containing DNA template-primer constructs .
SNAP output
|
|
2uvw
|
transferase |
X-ray (2.09 Å) |
Eoff RL, Irimia A, Angel KC, Egli M, Guengerich
FP |
(2007) "Hydrogen
Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a
Charged Residue in the Little Finger Domain Determines
Miscoding Events in Sulfolobus Solfataricus DNA
Polymerase Dpo4." J.Biol.Chem.,
282, 19831. doi: 10.1074/JBC.M702290200.
|
Crystal structures of mutant dpo4 DNA polymerases with
8-oxog containing DNA template-primer constructs .
SNAP output
|
|
2uyc
|
transferase |
X-ray (2.0 Å) |
Daujotyte D, Grazulis S |
"HhaI DNA Methyltransferase R163N Mutant Complex with
13mer Gcgc-Gmgc Oligonucleotide and Sah." |
Hhai DNA methyltransferase r163n mutant complex with
13mer gcgc-gmgc oligonucleotide and sah . SNAP output
|
|
2uyh
|
transferase |
X-ray (2.63 Å) |
Daujotyte D, Grazulis S |
"HhaI DNA Methyltransferase S87Q-Q237S Mutant Complex
with 13mer Gcgc-Gmgc Oligonucleotide and Sah." |
Hhai DNA methyltransferase s87q-q237s mutant complex
with 13mer gcgc- gmgc oligonucleotide and sah .
SNAP output
|
|
2uz4
|
transferase |
X-ray (2.1 Å) |
Daujotyte D, Leinartaite L, Grazulis S |
"DNA Methyltransferase R165N Mutant." |
Hhai DNA methyltransferase r165n mutant complex with
13mer gcgc-gmgc oligonucleotide and sah . SNAP output
|
|
2uzk
|
transcription |
X-ray (2.7 Å) |
Tsai K-L, Sun Y-J, Huang C-Y, Yang J-Y, Hung M-C,
Hsiao C-D |
(2007) "Crystal
Structure of the Human Foxo3A-Dbd/DNA Complex Suggests
the Effects of Post-Translational Modification."
Nucleic Acids Res., 35, 6984.
doi: 10.1093/NAR/GKM703.
|
Crystal structure of the human foxo3a-dbd bound to DNA
. SNAP output
|
|
2v1u
|
replication |
X-ray (3.1 Å) |
Gaudier M, Schuwirth BS, Westcott SL, Wigley DB |
(2007) "Structural
Basis of DNA Replication Origin Recognition by an Orc
Protein." Science, 317,
1213. doi: 10.1126/SCIENCE.1143664.
|
Structure of the aeropyrum pernix orc1 protein in
complex with DNA . SNAP
output
|
|
2v2t
|
transcription |
X-ray (3.05 Å) |
Moorthy AK, Huang DB, Wang VY, Vu D, Ghosh G |
(2007) "X-Ray
Structure of a NF-kappaB p50/Relb/DNA Complex Reveals
Assembly of Multiple Dimers on Tandem kappaB
Sites." J.Mol.Biol., 373,
723. doi: 10.1016/J.JMB.2007.08.039.
|
X-ray structure of a nf-kb p50-relb-DNA complex .
SNAP output
|
|
2v4q
|
transferase |
X-ray (2.6 Å) |
Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M,
Guengerich FP, Marnett LJ |
(2009) "Structural
and Functional Analysis of Sulfolobus Solfataricus
Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the
Malondialdehyde-Deoxyguanosine Adduct."
Biochemistry, 48, 7079. doi:
10.1021/BI9003588.
|
Post-insertion complex of the y-family DNA polymerase
dpo4 with m1dg containing template DNA . SNAP output
|
|
2v4r
|
transferase |
X-ray (2.5 Å) |
Eoff RL, Stafford JB, Szekely J, Rizzo CJ, Egli M,
Guengerich FP, Marnett LJ |
(2009) "Structural
and Functional Analysis of Sulfolobus Solfataricus
Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the
Malondialdehyde-Deoxyguanosine Adduct."
Biochemistry, 48, 7079. doi:
10.1021/BI9003588.
|
Non-productive complex of the y-family DNA polymerase
dpo4 with dgtp skipping the m1dg adduct to pair with
the next template cytosine . SNAP output
|
|
2v6e
|
hydrolase |
X-ray (3.2 Å) |
Aihara H, Huang WM, Ellenberger T |
(2007) "An
Interlocked Dimer of the Protelomerase Telk Distorts
DNA Structure for the Formation of Hairpin
Telomeres." Mol.Cell, 27,
901. doi: 10.1016/J.MOLCEL.2007.07.026.
|
Protelomerase telk complexed with substrate DNA .
SNAP output
|
|
2v9w
|
transferase |
X-ray (3.0 Å) |
Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli
M |
(2007) "Structure
and Activity of Y-Class DNA Polymerase Dpo4 from
Sulfolobus Solfataricus with Templates Containing the
Hydrophobic Thymine Analog 2,4-Difluorotoluene."
J.Biol.Chem., 282, 36421.
doi: 10.1074/JBC.M707267200.
|
Complex structure of sulfolobus solfataricus dpo4 and
DNA duplex containing a hydrophobic thymine isostere
2,4-difluorotoluene nucleotide in the template strand .
SNAP output
|
|
2va2
|
transferase-DNA |
X-ray (2.8 Å) |
Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli
M |
(2007) "Structure
and Activity of Y-Class DNA Polymerase Dpo4 from
Sulfolobus Solfataricus with Templates Containing the
Hydrophobic Thymine Analog 2,4- Difluorotoluene."
J.Biol.Chem., 282, 36421.
doi: 10.1074/JBC.M707267200.
|
Complex structure of sulfolobus solfataricus dpo4 and
DNA duplex containing a hydrophobic thymine isostere
2,4-difluorotoluene nucleotide in the template strand .
SNAP output
|
|
2va3
|
transferase |
X-ray (2.98 Å) |
Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli
M |
(2007) "Structure
and Activity of Y-Class DNA Polymerase Dpo4 from
Sulfolobus Solfataricus with Templates Containing the
Hydrophobic Thymine Analog 2,4-Difluorotoluene."
J.Biol.Chem., 282, 36421.
doi: 10.1074/JBC.M707267200.
|
Complex structure of sulfolobus solfataricus dpo4 and
DNA duplex containing a hydrophobic thymine isostere
2,4-difluorotoluene nucleotide in the template strand .
SNAP output
|
|
2vbj
|
hydrolase-DNA |
X-ray (1.95 Å) |
Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F,
Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C,
Duchateau P, Paques F, Blanco FJ, Montoya G |
(2008) "Molecular
Basis of Xeroderma Pigmentosum Group C DNA Recognition
by Engineered Meganucleases." Nature,
456, 107. doi: 10.1038/NATURE07343.
|
Molecular basis of human xpc gene recognition and
cleavage by engineered homing endonuclease heterodimers
. SNAP output
|
|
2vbl
|
hydrolase |
X-ray (1.8 Å) |
Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F,
Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C,
Duchateau P, Paques F, Blanco FJ, Montoya G |
(2008) "Molecular
Basis of Xeroderma Pigmentosum Group C DNA Recognition
by Engineered Meganucleases." Nature,
456, 107. doi: 10.1038/NATURE07343.
|
Molecular basis of human xpc gene recognition and
cleavage by engineered homing endonuclease heterodimers
. SNAP output
|
|
2vbn
|
hydrolase |
X-ray (1.9 Å) |
Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F,
Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C,
Duchateau P, Paques F, Blanco FJ, Montoya G |
(2008) "Molecular
Basis of Xeroderma Pigmentosum Group C DNA Recognition
by Engineered Meganucleases." Nature,
456, 107. doi: 10.1038/NATURE07343.
|
Molecular basis of human xpc gene recognition and
cleavage by engineered homing endonuclease heterodimers
. SNAP output
|
|
2vbo
|
hydrolase |
X-ray (1.8 Å) |
Redondo P, Prieto J, Munoz IG, Alibes A, Stricher F,
Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C,
Duchateau P, Paques F, Blanco FJ, Montoya G |
(2008) "Molecular
Basis of Xeroderma Pigmentosum Group C DNA Recognition
by Engineered Meganucleases." Nature,
456, 107. doi: 10.1038/NATURE07343.
|
Molecular basis of human xpc gene recognition and
cleavage by engineered homing endonuclease heterodimers
. SNAP output
|
|
2ve9
|
transport protein |
X-ray (1.9 Å) |
Lowe J, Ellonen A, Allen MD, Atkinson C, Sherratt DJ,
Grainge I |
(2008) "Molecular
Mechanism of Sequence-Directed DNA Loading and
Translocation by Ftsk." Mol.Cell,
31, 498. doi: 10.1016/J.MOLCEL.2008.05.027.
|
Xray structure of kops bound gamma domain of ftsk (p.
aeruginosa) . SNAP
output
|
|
2vhg
|
DNA binding protein |
X-ray (2.9 Å) |
Barabas O, Ronning DR, Guynet C, Hickman AB,
Ton-Hoang B, Chandler M, Dyda F |
(2008) "Mechanism
of is200/is605 Family DNA Transposases: Activation and
Transposon-Directed Target Site Selection."
Cell(Cambridge,Mass.), 132,
208. doi: 10.1016/J.CELL.2007.12.029.
|
Crystal structure of the ishp608 transposase in complex
with right end 31-mer DNA . SNAP output
|
|
2vic
|
DNA binding protein |
X-ray (2.35 Å) |
Barabas O, Ronning DR, Guynet C, Hickman AB,
Ton-Hoang B, Chandler M, Dyda F |
(2008) "Mechanism
of is200/is605 Family DNA Transposases: Activation and
Transposon-Directed Target Site Selection."
Cell(Cambridge,Mass.), 132,
208. doi: 10.1016/J.CELL.2007.12.029.
|
Crystal structure of the ishp608 transposase in complex
with left end 26- mer DNA and manganese . SNAP output
|
|
2vih
|
DNA binding protein |
X-ray (2.1 Å) |
Barabas O, Ronning DR, Guynet C, Hickman AB,
Ton-Hoang B, Chandler M, Dyda F |
(2008) "Mechanism
of is200/is605 Family DNA Transposases: Activation and
Transposon-Directed Target Site Selection."
Cell(Cambridge,Mass.), 132,
208. doi: 10.1016/J.CELL.2007.12.029.
|
Crystal structure of the is608 transposase in complex
with left end 26-mer DNA . SNAP output
|
|
2vju
|
DNA binding protein |
X-ray (2.4 Å) |
Barabas O, Ronning DR, Guynet C, Hickman AB,
Ton-Hoang B, Chandler M, Dyda F |
(2008) "Mechanism
of is200/is605 Family DNA Transposases: Activation and
Transposon-Directed Target Site Selection."
Cell(Cambridge,Mass.), 132,
208. doi: 10.1016/J.CELL.2007.12.029.
|
Crystal structure of the is608 transposase in complex
with the complete right end 35-mer DNA and manganese .
SNAP output
|
|
2vjv
|
DNA binding protein |
X-ray (1.9 Å) |
Barabas O, Ronning DR, Guynet C, Hickman AB,
Ton-Hoang B, Chandler M, Dyda F |
(2008) "Mechanism
of is200/is605 Family DNA Transposases: Activation and
Transposon-Directed Target Site Selection."
Cell(Cambridge,Mass.), 132,
208. doi: 10.1016/J.CELL.2007.12.029.
|
Crystal structure of the is608 transposase in complex
with left end 26-mer DNA hairpin and a 6-mer DNA
representing the left end cleavage site . SNAP output
|
|
2vla
|
hydrolase |
X-ray (1.3 Å) |
Sukackaite R, Grazulis S, Bochtler M, Siksnys V |
(2008) "The
Recognition Domain of the Bpuji Restriction
Endonuclease in Complex with Cognate DNA at 1.3-A
Resolution." J.Mol.Biol.,
378, 1084. doi: 10.1016/J.JMB.2008.03.041.
|
Crystal structure of restriction endonuclease bpuji
recognition domain in complex with cognate DNA .
SNAP output
|
|
2voa
|
lyase |
X-ray (1.7 Å) |
Schmiedel R, Kuettner EB, Keim A, Strater N,
Greiner-Stoffele T |
(2009) "Structure
and Function of the Abasic Site Specificity Pocket of
an Ap Endonuclease from Archaeoglobus Fulgidus."
DNA Repair, 8, 219. doi:
10.1016/J.DNAREP.2008.10.009.
|
Structure of an ap endonuclease from archaeoglobus
fulgidus . SNAP
output
|
|
2vs7
|
DNA binding protein |
X-ray (2.05 Å) |
Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A,
Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ,
Montoya G |
(2008) "Crystal
Structure of I-Dmoi in Complex with its Target DNA
Provides New Insights Into Meganuclease
Engineering." Proc.Natl.Acad.Sci.USA,
105, 16888. doi: 10.1073/PNAS.0804795105.
|
The crystal structure of i-dmoi in complex with DNA and
ca . SNAP output
|
|
2vs8
|
DNA binding protein |
X-ray (2.1 Å) |
Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibes A,
Serrano L, Grizot S, Duchateau P, Paques F, Blanco FJ,
Montoya G |
(2008) "Crystal
Structure of I-Dmoi in Complex with its Target DNA
Provides New Insights Into Meganuclease
Engineering." Proc.Natl.Acad.Sci.USA,
105, 16888. doi: 10.1073/PNAS.0804795105.
|
The crystal structure of i-dmoi in complex with DNA and
mn . SNAP output
|
|
2vtb
|
lyase-DNA |
X-ray (2.01 Å) |
Pokorny R, Klar T, Hennecke U, Carell T, Batschauer
A, Essen L-O |
(2008) "Recognition
and Repair of Uv Lesions in Loop Structures of Duplex
DNA by Dash-Type Cryptochrome."
Proc.Natl.Acad.Sci.USA, 105,
21023. doi: 10.1073/PNAS.0805830106.
|
Structure of cryptochrome 3 - DNA complex . SNAP output
|
|
2vum
|
transferase |
X-ray (3.4 Å) |
Brueckner F, Cramer P |
(2008) "Structural
Basis of Transcription Inhibition by Alpha-Amanitin and
Implications for RNA Polymerase II Translocation."
Nat.Struct.Mol.Biol., 15,
811. doi: 10.1038/NSMB.1458.
|
Alpha-amanitin inhibited complete RNA polymerase ii
elongation complex . SNAP output
|
|
2vw9
|
DNA binding protein |
X-ray (2.3 Å) |
Chan K-W, Lee Y-J, Wang C-H, Huang H, Sun Y-J |
(2009) "Single-Stranded
DNA-Binding Protein Complex from Helicobacter Pylori
Suggests an Ssdna-Binding Surface."
J.Mol.Biol., 388, 508. doi:
10.1016/J.JMB.2009.03.022.
|
Single stranded DNA binding protein complex from
helicobacter pylori . SNAP output
|
|
2vwj
|
DNA replication |
X-ray (2.78 Å) |
Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly
BA |
(2008) "Uracil
Recognition in Archaeal DNA Polymerases Captured by
X-Ray Crystallography." J.Mol.Biol.,
381, 529. doi: 10.1016/J.JMB.2008.06.004.
|
Uracil recognition in archaeal DNA polymerases captured
by x-ray crystallography. . SNAP output
|
|
2vy1
|
transcription |
X-ray (2.104 Å) |
Hames C, Ptchelkine D, Grimm C, Thevenon E, Moyroud
E, Gerard F, Martiel JL, Benlloch R, Parcy F, Muller
CW |
(2008) "Structural
Basis for Leafy Floral Switch Function and Similarity
with Helix-Turn-Helix Proteins." Embo J.,
27, 2628. doi: 10.1038/EMBOJ.2008.184.
|
Structure of leafy transcription factor from
arabidopsis thaliana in complex with DNA from ap1
promoter . SNAP
output
|
|
2vy2
|
transcription |
X-ray (2.3 Å) |
Hames C, Ptchelkine D, Grimm C, Thevenon E, Moyroud
E, Gerard F, Martiel JL, Benlloch R, Parcy F, Muller
CW |
(2008) "Structural
Basis for Leafy Floral Switch Function and Similarity
with Helix-Turn-Helix Proteins." Embo J.,
27, 2628. doi: 10.1038/EMBOJ.2008.184.
|
Structure of leafy transcription factor from
arabidopsis thaliana in complex with DNA from ag-i
promoter . SNAP
output
|
|
2vye
|
hydrolase-DNA |
X-ray (4.1 Å) |
Lo YH, Tsai KL, Sun YJ, Chen WT, Huang CY, Hsiao
CD |
(2009) "The
Crystal Structure of a Replicative Hexameric Helicase
Dnac and its Complex with Single-Stranded DNA."
Nucleic Acids Res., 37, 804.
doi: 10.1093/NAR/GKN999.
|
Crystal structure of the dnac-ssDNA complex . SNAP output
|
|
2vz4
|
transcription |
X-ray (2.9 Å) |
Allan MG, Newberry KJ, Schuman J, Brennan RG,
Stetefeld J, Grzesiek S, Schirmer T |
"Structure of the Transcriptionally Inactive Merr
Domain Tipan in Complex with DNA." |
The n-terminal domain of merr-like protein tipal bound
to promoter DNA . SNAP
output
|
|
2w35
|
hydrolase |
X-ray (2.15 Å) |
Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH,
Alseth I, Gao H, Cao W, Tainer JA, Bjoras M |
(2009) "Structures
of Endonuclease V with DNA Reveal Initiation of
Deaminated Adenine Repair."
Nat.Struct.Mol.Biol., 16,
138. doi: 10.1038/NSMB.1538.
|
Structures of endonuclease v with DNA reveal initiation
of deaminated adenine repair . SNAP output
|
|
2w36
|
hydrolase |
X-ray (2.1 Å) |
Dalhus B, Arvai AS, Rosnes I, Olsen OE, Backe PH,
Alseth I, Gao H, Cao W, Tainer JA, Bjoras M |
(2009) "Structures
of Endonuclease V with DNA Reveal Initiation of
Deaminated Adenine Repair."
Nat.Struct.Mol.Biol., 16,
138. doi: 10.1038/NSMB.1538.
|
Structures of endonuclease v with DNA reveal initiation
of deaminated adenine repair . SNAP output
|
|
2w42
|
protein-DNA complex |
X-ray (1.9 Å) |
Parker JS, Parizotto EA, Wang M, Roe SM, Barford
D |
(2009) "Enhancement
of the Seed-Target Recognition Step in RNA Silencing by
a Piwi-Mid Domain Protein." Mol.Cell,
33, 204. doi: 10.1016/J.MOLCEL.2008.12.012.
|
The structure of a piwi protein from archaeoglobus
fulgidus complexed with a 16nt DNA duplex. . SNAP output
|
|
2w7n
|
transcription-DNA |
X-ray (1.85 Å) |
Koenig B, Mueller JJ, Lanka E, Heinemann U |
(2009) "Crystal
Structure of Kora Bound to Operator DNA: Insight Into
Repressor Cooperation in Rp4 Gene Regulation."
Nucleic Acids Res., 37, 1915.
doi: 10.1093/NAR/GKP044.
|
Crystal structure of kora bound to operator DNA:
insight into repressor cooperation in rp4 gene
regulation . SNAP
output
|
|
2w7o
|
DNA binding protein |
X-ray (3.16 Å) |
Irimia A, Eoff RL, Guengerich FP, Egli M |
(2009) "Structural
and Functional Elucidation of the Mechanism Promoting
Error-Prone Synthesis by Human DNA Polymerase Kappa
Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine
Adduct." J.Biol.Chem.,
284, 22467. doi: 10.1074/JBC.M109.003905.
|
Structure and activity of bypass synthesis by human DNA
polymerase kappa opposite the
7,8-dihydro-8-oxodeoxyguanosine adduct . SNAP output
|
|
2w7p
|
DNA binding protein |
X-ray (3.71 Å) |
Irimia A, Eoff RL, Guengerich FP, Egli M |
(2009) "Structural
and Functional Elucidation of the Mechanism Promoting
Error-Prone Synthesis by Human DNA Polymerase Kappa
Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine
Adduct." J.Biol.Chem.,
284, 22467. doi: 10.1074/JBC.M109.003905.
|
Structure and activity of bypass synthesis by human DNA
polymerase kappa opposite the
7,8-dihydro-8-oxodeoxyguanosine adduct . SNAP output
|
|
2w8k
|
transferase-DNA |
X-ray (3.1 Å) |
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M,
Guengerich FP |
(2009) "Versatility
of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4
in Translesion Synthesis Past Bulky N2-Alkylguanine
Adducts." J.Biol.Chem.,
284, 3563. doi: 10.1074/JBC.M807778200.
|
Y-family DNA polymerase dpo4 bypassing
n2-naphthyl-guanine adduct in syn orientation .
SNAP output
|
|
2w8l
|
transferase-DNA |
X-ray (3.0 Å) |
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M,
Guengerich FP |
(2009) "Versatility
of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4
in Translesion Synthesis Past Bulky N2-Alkylguanine
Adducts." J.Biol.Chem.,
284, 3563. doi: 10.1074/JBC.M807778200.
|
Y-family DNA polymerase dpo4 bypassing
n2-naphthyl-guanine adduct in anti orientation .
SNAP output
|
|
2w9a
|
transferase-DNA |
X-ray (2.6 Å) |
Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M,
Guengerich FP |
(2009) "Structure-Function
Relationships in Miscoding by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl
Substitution Produces Inactive and Miscoding Polymerase
Complexes." J.Biol.Chem.,
284, 17687. doi: 10.1074/JBC.M109014274.
|
Ternary complex of dpo4 bound to
n2,n2-dimethyl-deoxyguanosine modified DNA with
incoming dgtp . SNAP
output
|
|
2w9b
|
transferase-DNA |
X-ray (2.28 Å) |
Zhang H, Eoff RL, Kosekov ID, Rizzo CJ, Egli M,
Guengerich FP |
(2009) "Structure-Function
Relationships in Miscoding by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl
Substitution Produces Inactive and Miscoding Polymerase
Complexes." J.Biol.Chem.,
284, 17687. doi: 10.1074/JBC.M109014274.
|
Binary complex of dpo4 bound to
n2,n2-dimethyl-deoxyguanosine modified DNA . SNAP output
|
|
2w9c
|
transferase-DNA |
X-ray (2.9 Å) |
Zhang H, Eoff RL, Kosekov ID, Rizzo CJ, Egli M,
Guengerich FP |
(2009) "Structure-Function
Relationships in Miscoding by Sulfolobus Solfataricus
DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl
Substitution Produces Inactive and Miscoding Polymerase
Complexes." J.Biol.Chem.,
284, 17687. doi: 10.1074/JBC.M109014274.
|
Ternary complex of dpo4 bound to
n2,n2-dimethyl-deoxyguanosine modified DNA with
incoming dttp . SNAP
output
|
|
2wb2
|
lyase-DNA |
X-ray (2.95 Å) |
Glas AF, Schneider S, Maul MJ, Hennecke U, Carell
T |
(2009) "Crystal
Structure of the T(6-4)C Lesion in Complex with a (6-4)
DNA Photolyase and Repair of Uv- Induced (6-4) and
Dewar Photolesions." Chemistry,
15, 10387. doi: 10.1002/CHEM.200901004.
|
Drosophila melanogaster (6-4) photolyase bound to
double stranded DNA containing a t(6-4)c photolesion .
SNAP output
|
|
2wbs
|
transcription-DNA |
X-ray (1.7 Å) |
Schuetz A, Nana D, Rose C, Zocher G, Milanovic M,
Koenigsmann J, Blasig R, Heinemann U, Carstanjen D |
(2011) "The
Structure of the Klf4 DNA-Binding Domain Links to
Self-Renewal and Macrophage Differentiation."
Cell.Mol.Life Sci., 68, 3121.
doi: 10.1007/S00018-010-0618-X.
|
Crystal structure of the zinc finger domain of klf4
bound to its target DNA . SNAP output
|
|
2wbu
|
transcription-DNA |
X-ray (2.5 Å) |
Schuetz A, Nana D, Rose C, Zocher G, Milanovic M,
Koenigsmann J, Blasig R, Heinemann U, Carstanjen D |
(2011) "The
Structure of the Klf4 DNA-Binding Domain Links to
Self-Renewal and Macrophage Differentiation."
Cell.Mol.Life Sci., 68, 3121.
doi: 10.1007/S00018-010-0618-X.
|
Crystal structure of the zinc finger domain of klf4
bound to its target DNA . SNAP output
|
|
2wcc
|
protein-DNA |
NMR |
Fadeev EA, Sam MD, Clubb RT |
(2009) "NMR
Structure of the Amino-Terminal Domain of the Lambda
Integrase Protein in Complex with DNA: Immobilization
of a Flexible Tail Facilitates Beta- Sheet Recognition
of the Major Groove." J.Mol.Biol.,
388, 682. doi: 10.1016/J.JMB.2009.03.041.
|
Phage lambda intdbd1-64 complex with p prime 2 DNA .
SNAP output
|
|
2wiw
|
hydrolase-DNA |
X-ray (1.8 Å) |
Carolis C, Koehler C, Sauter C, Basquin J, Suck D,
Toeroe I |
"Crystal Structures of Holliday Junction Resolvases
from Archaeoglobus Fulgidus Bound to DNA Substrate." |
Crystal structures of holliday junction resolvases from
archaeoglobus fulgidus bound to DNA substrate .
SNAP output
|
|
2wiz
|
hydrolase-DNA |
X-ray (3.3 Å) |
Carolis C, Koehler C, Sauter C, Basquin J, Suck D,
Toeroe I |
"Crystal Structures of Holliday Junction Resolvases
from Archaeoglobus Fulgidus Bound to DNA Substrate." |
Crystal structures of holliday junction resolvases from
archaeoglobus fulgidus bound to DNA substrate .
SNAP output
|
|
2wj0
|
hydrolase-DNA |
X-ray (3.1 Å) |
Carolis C, Koehler C, Sauter C, Basquin J, Suck D,
Toeroe I |
"Crystal Structures of Holliday Junction Resolvases
from Archaeoglobus Fulgidus Bound to DNA Substrate." |
Crystal structures of holliday junction resolvases from
archaeoglobus fulgidus bound to DNA substrate .
SNAP output
|
|
2wq6
|
lyase-DNA |
X-ray (2.3 Å) |
Glas AF, Kaya E, Schneider S, Heil K, Fazio D, Maul
MJ, Carell T |
(2010) "DNA
(6-4) Photolyases Reduce Dewar Isomers for
Isomerization Into (6-4) Lesions."
J.Am.Chem.Soc., 132, 3254.
doi: 10.1021/JA910917F.
|
Structure of the 6-4 photolyase of d. melanogaster in
complex with the non-natural n4-methyl t(dewar)c lesion
. SNAP output
|
|
2wq7
|
lyase-DNA |
X-ray (2.0 Å) |
Glas AF, Kaya E, Schneider S, Heil K, Fazio D, Maul
MJ, Carell T |
(2010) "DNA
(6-4) Photolyases Reduce Dewar Isomers for
Isomerization Into (6-4) Lesions."
J.Am.Chem.Soc., 132, 3254.
doi: 10.1021/JA910917F.
|
Structure of the 6-4 photolyase of d. melanogaster in
complex with the non-natural n4-methyl t(6-4)c lesion .
SNAP output
|
|
2wt7
|
transcription |
X-ray (2.3 Å) |
Pogenberg V, Consani Textor L, Vanhille L, Holton SJ,
Sieweke MH, Wilmanns M |
(2014) "Design
of a bZIP Transcription Factor with
Homo/Heterodimer-Induced DNA-Binding Preference."
Structure, 22, 466. doi:
10.1016/J.STR.2013.12.017.
|
Crystal structure of the bzip heterodimeric complex
mafb:cfos bound to DNA . SNAP output
|
|
2wtf
|
transferase-DNA |
X-ray (2.5 Å) |
Reissner T, Schneider S, Schorr S, Carell T |
(2010) "Crystal
Structure of a Cisplatin-(1,3-Gtg) Cross-Link within
DNA Polymerase Eta."
Angew.Chem.Int.Ed.Engl., 49,
3077. doi: 10.1002/ANIE.201000414.
|
DNA polymerase eta in complex with the
cis-diammineplatinum (ii) 1,3- gtg intrastrand
cross-link . SNAP
output
|
|
2wtu
|
DNA binding protein-DNA |
X-ray (3.4 Å) |
Lebbink JH, Fish A, Reumer A, Natrajan G, Winterwerp
HH, Sixma TK |
(2010) "Magnesium
coordination controls the molecular switch function of
DNA mismatch repair protein MutS." J. Biol.
Chem., 285, 13131-13141. doi:
10.1074/jbc.M109.066001.
|
Crystal structure of escherichia coli muts in complex
with a 16 basepair oligo containing an a.a mismatch. .
SNAP output
|
|
2wty
|
transcription |
X-ray (2.9 Å) |
Pogenberg V, Consani Textor L, Vanhille L, Holton SJ,
Sieweke MH, Wilmanns M |
(2014) "Design
of a bZIP Transcription Factor with
Homo/Heterodimer-Induced DNA-Binding Preference."
Structure, 22, 466. doi:
10.1016/J.STR.2013.12.017.
|
Crystal structure of the homodimeric mafb in complex
with the t-mare binding site . SNAP output
|
|
2wwy
|
hydrolase-DNA |
X-ray (2.9 Å) |
Pike ACW, Zhang Y, Schnecke C, Chaikuad A, Krojer T,
Cooper CDO, von Delft F, Arrowsmith CH, Weigelt J,
Edwards A, Bountra C, Gileadi O |
(2015) "Recq1
Helicase-Driven DNA Unwinding, Annealing, and Branch
Migration: Insights from DNA Complex Structures."
Proc.Natl.Acad.Sci.USA, 112,
4286. doi: 10.1073/PNAS.1417594112.
|
Structure of human recq-like helicase in complex with a
DNA substrate . SNAP
output
|
|
2x1a
|
transcription-RNA |
X-ray (2.05 Å) |
Pancevac C, Goldstone DC, Ramos A, Taylor IA |
(2010) "Structure
of the RNA15 Rrm-RNA Complex Reveals the Molecular
Basis of Gu Specificity in Transcriptional 3-End
Processing Factors." Nucleic Acids Res.,
38, 3119. doi: 10.1093/NAR/GKQ002.
|
Structure of rna15 rrm with RNA bound (g) . SNAP output
|
|
2x6v
|
transcription-DNA |
X-ray (2.2 Å) |
Stirnimann CU, Ptchelkine D, Grimm C, Muller CW |
(2010) "Structural
Basis of Tbx5-DNA Recognition: The T-Box Domain in its
DNA-Bound and -Unbound Form." J.Mol.Biol.,
400, 71. doi: 10.1016/J.JMB.2010.04.052.
|
Crystal structure of human tbx5 in the DNA-bound and
DNA-free form . SNAP
output
|
|
2xc9
|
transferase-DNA |
X-ray (2.2 Å) |
Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP,
Egli M |
(2010) "Metal
Ion Dependence of the Active Site Conformation of the
Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus
Solfataricus." Acta Crystallogr.,Sect.F,
66, 1013. doi: 10.1107/S1744309110029374.
|
Binary complex of sulfolobus solfataricus dpo4 DNA
polymerase and 1, n2-ethenoguanine modified DNA,
magnesium form . SNAP
output
|
|
2xca
|
transferase-DNA |
X-ray (2.5 Å) |
Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP,
Egli M |
(2010) "Metal
Ion Dependence of the Active Site Conformation of the
Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus
Solfataricus." Acta Crystallogr.,Sect.F,
66, 1013. doi: 10.1107/S1744309110029374.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, 7,8- dihydro-8-oxodeoxyguanine modified DNA
and dgtp - magnesium form . SNAP output
|
|
2xcp
|
DNA-transferase |
X-ray (2.6 Å) |
Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP,
Egli M |
(2010) "Metal
Ion Dependence of the Active Site Conformation of the
Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus
Solfataricus." Acta Crystallogr.,Sect.F,
66, 1013. doi: 10.1107/S1744309110029374.
|
Ternary complex of sulfolobus solfataricus dpo4 DNA
polymerase, 7,8- dihydro-8-oxodeoxyguanine modified DNA
and dctp - magnesium form . SNAP output
|
|
2xcr
|
isomerase |
X-ray (3.5 Å) |
Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR,
Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang
J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders
MR, Singh O, Spitzfaden C, Shen C, Shillings A, Theobald
AF, Wohlkonig A, Pearson ND, Gwynn MN |
(2010) "Type Iia
Topoisomerase Inhibition by a New Class of
Antibacterial Agents." Nature,
466, 935. doi: 10.1038/NATURE09197.
|
The 3.5a crystal structure of the catalytic core (b'a'
region) of staphylococcus aureus DNA gyrase complexed
with gsk299423 and DNA . SNAP output
|
|
2xcs
|
isomerase |
X-ray (2.1 Å) |
Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR,
Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang
J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders
MR, Singh O, Spitzfaden C, Shen C, Shillings A, Theobald
AF, Wohlkonig A, Pearson ND, Gwynn MN |
(2010) "Type Iia
Topoisomerase Inhibition by a New Class of
Antibacterial Agents." Nature,
466, 935. doi: 10.1038/NATURE09197.
|
The 2.1a crystal structure of s. aureus gyrase complex
with gsk299423 and DNA . SNAP output
|
|
2xct
|
isomerase-DNA-antibiotic |
X-ray (3.35 Å) |
Bax BD, Chan PF, Eggleston DS, Fosberry A, Gentry DR,
Gorrec F, Giordano I, Hann MM, Hennessy A, Hibbs M, Huang
J, Jones E, Jones J, Brown KK, Lewis CJ, May EW, Saunders
MR, Singh O, Spitzfaden C, Shen C, Shillings A, Theobald
AF, Wohlkonig A, Pearson ND, Gwynn MN |
(2010) "Type Iia
Topoisomerase Inhibition by a New Class of
Antibacterial Agents." Nature,
466, 935. doi: 10.1038/NATURE09197.
|
The twinned 3.35a structure of s. aureus gyrase complex
with ciprofloxacin and DNA . SNAP output
|
|
2xe0
|
DNA binding protein-DNA |
X-ray (2.31 Å) |
Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo
P, Villate M, Merino N, Marenchino M, D'Abramo M,
Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotine
I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano
L, Blanco FJ, Montoya G |
(2011) "Molecular
Basis of Engineered Meganuclease Targeting of the
Endogenous Human Rag1 Locus." Nucleic Acids
Res., 39, 729-743. doi: 10.1093/NAR/GKQ801.
|
Molecular basis of engineered meganuclease targeting of
the endogenous human rag1 locus . SNAP output
|
|
2xgp
|
transferase-DNA |
X-ray (2.7 Å) |
Schorr S, Schneider S, Lammens K, Hopfner KP, Carell
T |
(2010) "Mechanism
of Replication Blocking and Bypass of Y-Family
Polymerase Eta by Bulky Acetylaminofluorene DNA
Adducts." Proc.Natl.Acad.Sci.USA,
107, 20720. doi: 10.1073/PNAS.1008894107.
|
Yeast DNA polymerase eta in complex with
c8-2-acetylaminofluorene containing DNA . SNAP output
|
|
2xgq
|
transferase-DNA |
X-ray (2.7 Å) |
Schorr S, Schneider S, Lammens K, Hopfner KP, Carell
T |
(2010) "Mechanism
of Replication Blocking and Bypass of Y-Family
Polymerase Eta by Bulky Acetylaminofluorene DNA
Adducts." Proc.Natl.Acad.Sci.USA,
107, 20720. doi: 10.1073/PNAS.1008894107.
|
Structure of yeast DNA polymerase eta in complex with
c8-n-acetyl-2- aminoanthracene containing DNA .
SNAP output
|
|
2xhb
|
transferase-DNA |
X-ray (2.72 Å) |
Killelea T, Ghosh S, Tan SS, Heslop P, Firbank SJ,
Kool ET, Connolly BA |
(2010) "Probing
the Interaction of Archaeal DNA Polymerases with
Deaminated Bases Using X-Ray Crystallography and
Non-Hydrogen Bonding Isosteric Base Analogues."
Biochemistry, 49, 5772. doi:
10.1021/BI100421R.
|
Crystal structure of DNA polymerase from thermococcus
gorgonarius in complex with hypoxanthine-containing DNA
. SNAP output
|
|
2xhi
|
lyase-DNA |
X-ray (1.55 Å) |
Dalhus B, Forsbring M, Helle IH, Vik ES, Forstrom RJ,
Backe PH, Alseth I, Bjoras M |
(2011) "Separation-of-Function
Mutants Unravel the Dual- Reaction Mode of Human
8-Oxoguanine DNA Glycosylase." Structure,
19, 117. doi: 10.1016/J.STR.2010.09.023.
|
Separation-of-function mutants unravel the dual
reaction mode of human 8-oxoguanine DNA glycosylase .
SNAP output
|
|
2xkk
|
isomerase-DNA-antibiotic |
X-ray (3.25 Å) |
Wohlkonig A, Chan PF, Fosberry AP, Homes P, Huang J,
Kranz M, Leydon VR, Miles TJ, Pearson ND, Perera RL,
Shillings AJ, Gwynn MN, Bax BD |
(2010) "Structural
Basis of Quinolone Inhibition of Type Iia
Topoisomerases and Target-Mediated Resistance."
Nat.Struct.Mol.Biol., 17,
1152. doi: 10.1038/NSMB.1892.
|
Crystal structure of moxifloxacin, DNA, and a.
baumannii topo iv (pare-parc fusion truncate) .
SNAP output
|
|
2xli
|
hydrolase-RNA |
X-ray (2.33 Å) |
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna
JA |
(2010) "Sequence-
and Structure-Specific RNA Processing by a Crispr
Endonuclease." Science,
329, 1355. doi: 10.1126/SCIENCE.1192272.
|
Crystal structure of the csy4-crrna complex, monoclinic
form . SNAP output
|
|
2xlj
|
hydrolase-RNA |
X-ray (2.6 Å) |
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna
JA |
(2010) "Sequence-
and Structure-Specific RNA Processing by a Crispr
Endonuclease." Science,
329, 1355. doi: 10.1126/SCIENCE.1192272.
|
Crystal structure of the csy4-crrna complex, hexagonal
form . SNAP output
|
|
2xlk
|
hydrolase-RNA |
X-ray (1.805 Å) |
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna
JA |
(2010) "Sequence-
and Structure-Specific RNA Processing by a Crispr
Endonuclease." Science,
329, 1355. doi: 10.1126/SCIENCE.1192272.
|
Crystal structure of the csy4-crrna complex,
orthorhombic form . SNAP
output
|
|
2xm3
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Hickman AB, James JA, Barabas O, Pasternak C,
Ton-Hoang B, Chandler M, Sommer S, Dyda F |
(2010) "DNA
Recognition and the Precleavage State During
Single-Stranded DNA Transposition in D.
Radiodurans." Embo J.,
29, 3840. doi: 10.1038/EMBOJ.2010.241.
|
Deinococcus radiodurans isdra2 transposase left end DNA
complex . SNAP
output
|
|
2xma
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Hickman AB, James JA, Barabas O, Pasternak C,
Ton-Hoang B, Chandler M, Sommer S, Dyda F |
(2010) "DNA
Recognition and the Precleavage State During
Single-Stranded DNA Transposition in D.
Radiodurans." Embo J.,
29, 3840. doi: 10.1038/EMBOJ.2010.241.
|
Deinococcus radiodurans isdra2 transposase right end
DNA complex . SNAP
output
|
|
2xnr
|
RNA binding protein-RNA |
X-ray (1.6 Å) |
Lunde BM, Horner M, Meinhart A |
(2011) "Structural
Insights Into Cis Element Recognition of
Non-Polyadenylated Rnas by the Nab3-Rrm."
Nucleic Acids Res., 39, 337.
doi: 10.1093/NAR/GKQ751.
|
Structural insights into cis element recognition of
non- polyadenylated rnas by the nab3-rrm . SNAP output
|
|
2xo6
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Hickman AB, James JA, Barabas O, Pasternak C,
Ton-Hoang B, Chandler M, Sommer S, Dyda F |
(2010) "DNA
Recognition and the Precleavage State During
Single-Stranded DNA Transposition in D.
Radiodurans." Embo J.,
29, 3840. doi: 10.1038/EMBOJ.2010.241.
|
Deinococcus radiodurans isdra2 transposase y132f mutant
complexed with left end recognition and cleavage site .
SNAP output
|
|
2xo7
|
transferase-DNA |
X-ray (2.85 Å) |
Muenzel M, Lercher L, Mueller M, Carell T |
(2010) "Chemical
Discrimination between Dc and 5Medc Via Their
Hydroxylamine Adducts." Nucleic Acids
Res., 38, E192. doi: 10.1093/NAR/GKQ724.
|
Crystal structure of a da:o-allylhydroxylamine-dc
basepair in complex with fragment DNA polymerase i from
bacillus stearothermophilus . SNAP output
|
|
2xqc
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Hickman AB, James JA, Barabas O, Pasternak C,
Ton-Hoang B, Chandler M, Sommer S, Dyda F |
(2010) "DNA
Recognition and the Precleavage State During
Single-Stranded DNA Transposition in D.
Radiodurans." Embo J.,
29, 3840. doi: 10.1038/EMBOJ.2010.241.
|
Deinococcus radiodurans isdra2 transposase complexed
with left end recognition and cleavage site and zn .
SNAP output
|
|
2xro
|
DNA-binding protein-DNA |
X-ray (3.4 Å) |
Lu D, Fillet S, Meng C, Alguel Y, Kloppsteck P,
Bergeron J, Krell T, Gallegos MT, Ramos J, Zhang X |
(2010) "Crystal
Structure of Ttgv in Complex with its DNA Operator
Reveals a General Model for Cooperative DNA Binding of
Tetrameric Gene Regulators." Genes Dev.,
24, 2556. doi: 10.1101/GAD.603510.
|
Crystal structure of ttgv in complex with its DNA
operator . SNAP
output
|
|
2xrz
|
lyase-DNA |
X-ray (2.2 Å) |
Kiontke S, Geisselbrecht Y, Pokorny R, Carell T,
Batschauer A, Essen LO |
(2011) "Crystal
Structures of an Archaeal Class II DNA Photolyase and
its Complex with Uv-Damaged Duplex DNA." Embo
J., 30, 4437. doi: 10.1038/EMBOJ.2011.313.
|
X-ray structure of archaeal class ii cpd photolyase
from methanosarcina mazei in complex with intact
cpd-lesion . SNAP
output
|
|
2xsd
|
transcription-DNA |
X-ray (2.049 Å) |
Jauch R, Choo SH, Ng CKL, Kolatkar PR |
(2011) "Crystal
Structure of the Dimeric Oct6 (POU3F1) POU Domain Bound
to Palindromic More DNA." Proteins,
79, 674. doi: 10.1002/PROT.22916.
|
Crystal structure of the dimeric oct-6 (pou3f1) pou
domain bound to palindromic more DNA . SNAP output
|
|
2xy5
|
transferase-DNA |
X-ray (2.22 Å) |
Kaul C, Mueller M, Wagner M, Schneider S, Carell
T |
(2011) "Reversible
Bond Formation Enables the Replication and
Amplification of a Crosslinking Salen Complex as an
Orthogonal Base Pair." Nature Chem.,
3, 794. doi: 10.1038/NCHEM.1117.
|
Crystal structure of an artificial salen-copper
basepair in complex with fragment DNA polymerase i from
bacillus stearothermophilus . SNAP output
|
|
2xy6
|
transferase-DNA |
X-ray (2.3 Å) |
Kaul C, Mueller M, Wagner M, Schneider S, Carell
T |
(2011) "Reversible
Bond Formation Enables the Replication and
Amplification of a Crosslinking Salen Complex as an
Orthogonal Base Pair." Nature Chem.,
3, 794. doi: 10.1038/NCHEM.1117.
|
Crystal structure of a salicylic aldehyde basepair in
complex with fragment DNA polymerase i from bacillus
stearothermophilus . SNAP output
|
|
2xy7
|
transferase-DNA |
X-ray (3.05 Å) |
Kaul C, Mueller M, Wagner M, Schneider S, Carell
T |
(2011) "Reversible
Bond Formation Enables the Replication and
Amplification of a Crosslinking Salen Complex as an
Orthogonal Base Pair." Nature Chem.,
3, 794. doi: 10.1038/NCHEM.1117.
|
Crystal structure of a salicylic aldehyde base in the
pre-insertion site of fragment DNA polymerase i from
bacillus stearothermophilus . SNAP output
|
|
2xzf
|
hydrolase-DNA |
X-ray (1.799 Å) |
Le Bihan YV, Izquierdo MA, Coste F, Aller P, Culard
F, Gehrke TH, Essalhi K, Carrel T, Castaing B |
(2011) "5-Hydroxy-5-Methylhydantoin
DNA Lesion, a Molecular Trap for DNA Glycosylases."
Nucleic Acids Res., 39, 6277.
doi: 10.1093/NAR/GKR215.
|
Crystal structure of a complex between the wild-type
lactococcus lactis fpg (mutm) and an oxidized
pyrimidine containing DNA at 293k . SNAP output
|
|
2xzu
|
hydrolase-DNA |
X-ray (1.82 Å) |
Le Bihan YV, Izquierdo MA, Coste F, Aller P, Culard
F, Gehrke TH, Essalhi K, Carrel T, Castaing B |
(2011) "5-Hydroxy-5-Methylhydantoin
DNA Lesion, a Molecular Trap for DNA Glycosylases."
Nucleic Acids Res., 39, 6277.
doi: 10.1093/NAR/GKR215.
|
Crystal structure of a complex between the wild-type
lactococcus lactis fpg (mutm) and an oxidized
pyrimidine containing DNA at 310k . SNAP output
|
|
2y1i
|
transferase-DNA |
X-ray (2.78 Å) |
Heil K, Kneuttinger AC, Schneider S, Lischke U,
Carell T |
(2011) "Crystal
Structures and Repair Studies Reveal the Identity and
the Base-Pairing Properties of the Uv-Induced Spore
Photoproduct DNA Lesion." Chemistry,
17, 9651. doi: 10.1002/CHEM.201100177.
|
Crystal structure of a s-diastereomer analogue of the
spore photoproduct in complex with fragment DNA
polymerase i from bacillus stearothermophilus .
SNAP output
|
|
2y1j
|
transferase-DNA |
X-ray (2.15 Å) |
Heil K, Kneuttinger AC, Schneider S, Lischke U,
Carell T |
(2011) "Crystal
Structures and Repair Studies Reveal the Identity and
the Base-Pairing Properties of the Uv-Induced Spore
Photoproduct DNA Lesion." Chemistry,
17, 9651. doi: 10.1002/CHEM.201100177.
|
Crystal structure of a r-diastereomer analogue of the
spore photoproduct in complex with fragment DNA
polymerase i from bacillus stearothermophilus .
SNAP output
|
|
2y35
|
hydrolase-DNA |
X-ray (3.2 Å) |
Jinek M, Coyle SM, Doudna JA |
(2011) "Coupled
5' Nucleotide Recognition and Processivity in
Xrn1-Mediated Mrna Decay." Mol.Cell,
41, 600. doi: 10.1016/J.MOLCEL.2011.02.004.
|
Crystal structure of xrn1-substrate complex . SNAP output
|
|
2y7h
|
transferase-DNA |
cryo-EM (18.0 Å) |
Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska
I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF |
(2009) "The
Structure of M.Ecoki Type I DNA Methyltransferase with
a DNA Mimic Antirestriction Protein." Nucleic
Acids Res., 37, 762. doi:
10.1093/NAR/GKN988.
|
Atomic model of the DNA-bound methylase complex from
the type i restriction-modification enzyme ecoki
(m2s1). based on fitting into em map 1534. . SNAP output
|
|
2y9h
|
hydrolase-RNA |
X-ray (2.5 Å) |
Sashital DG, Jinek M, Doudna JA |
(2011) "An
RNA-Induced Conformational Change Required for Crispr
RNA Cleavage by the Endoribonuclease Cse3."
Nat.Struct.Mol.Biol., 18,
680. doi: 10.1038/NSMB.2043.
|
Structure a of crispr endoribonuclease cse3 bound to 19
nt RNA . SNAP output
|
|
2y9z
|
transcription |
X-ray (3.601 Å) |
Yamada K, Frouws TD, Angst B, Fitzgerald DJ, Deluca
C, Schimmele K, Sargent DF, Richmond TJ |
(2011) "Structure
and Mechanism of the Chromatin Remodelling Factor
Isw1A." Nature, 472, 448.
doi: 10.1038/NATURE09947.
|
Chromatin remodeling factor isw1a(del_atpase) in DNA
complex . SNAP
output
|
|
2ypa
|
immune system |
X-ray (2.8 Å) |
El Omari K, Hoosdally SJ, Tuladhar K, Karia D,
Hall-Ponsele E, Platonova O, Vyas P, Patient R, Porcher
C, Mancini EJ |
(2013) "Structural
Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH
Heterodimer to Hematopoietic-Specific Transcriptional
Targets." Cell Rep., 4,
135. doi: 10.1016/J.CELREP.2013.06.008.
|
Structure of the scl:e47:lmo2:ldb1 complex bound to DNA
. SNAP output
|
|
2ypb
|
immune system |
X-ray (2.87 Å) |
El Omari K, Hoosdally SJ, Tuladhar K, Karia D,
Hall-Ponsele E, Platonova O, Vyas P, Patient R, Porcher
C, Mancini EJ |
(2013) "Structural
Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH
Heterodimer to Hematopoietic-Specific Transcriptional
Targets." Cell Rep., 4,
135. doi: 10.1016/J.CELREP.2013.06.008.
|
Structure of the scl:e47 complex bound to DNA .
SNAP output
|
|
2ypf
|
DNA binding protein-DNA |
X-ray (2.55 Å) |
Stella S, Molina R, Yefimenko I, Prieto J, Silva GH,
Bertonati C, Juillerat A, Duchateau P, Montoya G |
(2013) "Structure
of the Avrbs3-DNA Complex Provides New Insights Into
the Initial Thymine-Recognition Mechanism."
Acta Crystallogr.,Sect.D, 69,
1707. doi: 10.1107/S0907444913016429.
|
Structure of the avrbs3-DNA complex provides new
insights into the initial thymine-recognition mechanism
. SNAP output
|
|
2yu9
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.4 Å) |
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg
RD |
(2006) "Structural
Basis of Transcription: Role of the Trigger Loop in
Substrate Specificity and Catalysis."
Cell(Cambridge,Mass.), 127,
941-954. doi: 10.1016/j.cell.2006.11.023.
|
RNA polymerase ii elongation complex in 150 mm mg+2
with utp . SNAP
output
|
|
2yvh
|
transcription-DNA |
X-ray (2.5 Å) |
Itou H, Watanabe N, Yao M, Shirakihara Y, Tanaka
I |
(2010) "Crystal
Structures of the Multidrug Binding Repressor
Corynebacteriumglutamicum CgmR in Complex with Inducers
and with an Operator." J.Mol.Biol.,
403, 174-184. doi: 10.1016/j.jmb.2010.07.042.
|
Crystal structure of the operator-binding form of the
multi-drug binding transcriptional repressor cgmr .
SNAP output
|
|
2z33
|
transcription-DNA |
NMR |
Yamane T, Okamura H, Ikeguchi M, Nishimura Y, Kidera
A |
(2008) "Water-mediated
interactions between DNA and PhoB
DNA-binding/transactivation domain: NMR-restrained
molecular dynamics in explicit water environment."
Proteins, 71, 1970-1983. doi:
10.1002/prot.21874.
|
Solution structure of the DNA complex of phob
DNA-binding-transactivation domain . SNAP output
|
|
2z3x
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Lee KS, Bumbaca D, Kosman J, Setlow P, Jedrzejas
MJ |
(2008) "Structure
of a protein-DNA complex essential for DNA protection
in spores of Bacillus species." Proc. Natl.
Acad. Sci. U.S.A., 105,
2806-2811. doi: 10.1073/pnas.0708244105.
|
Structure of a protein-DNA complex essential for DNA
protection in spore of bacillus species . SNAP output
|
|
2z6a
|
transferase-DNA |
X-ray (2.88 Å) |
Youngblood B, Shieh FK, Buller F, Bullock T, Reich
NO |
(2007) "S-Adenosyl-l-methionine-Dependent
Methyl Transfer: Observable Precatalytic Intermediates
during DNA Cytosine Methylation."
Biochemistry, 46, 8766-8775.
doi: 10.1021/bi7005948.
|
S-adenosyl-l-methionine-dependent methyl transfer:
observable precatalytic intermediates during DNA
cytosine methylation . SNAP output
|
|
2z6q
|
transferase-DNA |
X-ray (2.79 Å) |
Shieh FK, Youngblood B, Reich NO |
(2006) "The role
of Arg165 towards base flipping, base stabilization and
catalysis in M.HhaI." J.Mol.Biol.,
362, 516-527. doi: 10.1016/j.jmb.2006.07.030.
|
Ternary structure of arg165ala m.hhai c5-cytosine DNA
methyltransferase with unmodified DNA and adohcy .
SNAP output
|
|
2z6u
|
transferase-DNA |
X-ray (2.72 Å) |
Shieh FK, Reich NO |
(2007) "AdoMet-dependent
Methyl-transfer: Glu(119) Is Essential for DNA
C5-Cytosine Methyltransferase M.HhaI."
J.Mol.Biol., 373, 1157-1168.
doi: 10.1016/j.jmb.2007.08.009.
|
Ternary structure of the glu119ala m.hhai, c5-cytosine
DNA methyltransferase, with unmodified DNA and adohcy .
SNAP output
|
|
2z70
|
hydrolase |
X-ray (1.7 Å) |
Rodriguez SM, Panjikar S, Van Belle K, Wyns L,
Messens J, Loris R |
(2008) "Nonspecific
base recognition mediated by water bridges and
hydrophobic stacking in ribonuclease I from Escherichia
coli." Protein Sci., 17,
681-690. doi: 10.1110/ps.073420708.
|
E.coli rnase 1 in complex with d(cgcgatcgcg) . SNAP output
|
|
2z9o
|
replication-DNA |
X-ray (3.14 Å) |
Nakamura A, Wada C, Miki K |
(2007) "Structural
basis for regulation of bifunctional roles in
replication initiator protein."
Proc.Natl.Acad.Sci.Usa, 104,
18484-18489. doi: 10.1073/pnas.0705623104.
|
Crystal structure of the dimeric form of repe in
complex with the repe operator DNA . SNAP output
|
|
2zcj
|
transferase-DNA |
X-ray (2.75 Å) |
Shieh FK, Reich NO |
(2007) "AdoMet-dependent
Methyl-transfer: Glu(119) Is Essential for DNA
C5-Cytosine Methyltransferase M.HhaI."
J.Mol.Biol., 373, 1157-1168.
doi: 10.1016/j.jmb.2007.08.009.
|
Ternary structure of the glu119gln m.hhai, c5-cytosine
DNA methyltransferase, with unmodified DNA and adohcy .
SNAP output
|
|
2zhg
|
transcription-DNA |
X-ray (2.8 Å) |
Watanabe S, Kita A, Kobayashi K, Miki K |
(2008) "Crystal
structure of the [2Fe-2S] oxidative-stress sensor SoxR
bound to DNA." Proc.Natl.Acad.Sci.Usa,
105, 4121-4126. doi: 10.1073/pnas.0709188105.
|
Crystal structure of soxr in complex with DNA .
SNAP output
|
|
2zkd
|
ligase |
X-ray (1.6 Å) |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa
M |
(2008) "Recognition
of hemi-methylated DNA by the SRA protein UHRF1 by a
base-flipping mechanism." Nature,
455, 818-821. doi: 10.1038/nature07249.
|
Crystal structure of the sra domain of mouse np95 in
complex with hemi-methylated cpg DNA . SNAP output
|
|
2zke
|
ligase |
X-ray (2.6 Å) |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa
M |
(2008) "Recognition
of hemi-methylated DNA by the SRA protein UHRF1 by a
base-flipping mechanism." Nature,
455, 818-821. doi: 10.1038/nature07249.
|
Crystal structure of the sra domain of mouse np95 in
complex with hemi-methylated cpg DNA . SNAP output
|
|
2zkf
|
ligase |
X-ray (2.55 Å) |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa
M |
(2008) "Recognition
of hemi-methylated DNA by the SRA protein UHRF1 by a
base-flipping mechanism." Nature,
455, 818-821. doi: 10.1038/nature07249.
|
Crystal structure of the sra domain of mouse np95 in
complex with hemi-methylated cpg DNA . SNAP output
|
|
2zo0
|
ligase-DNA |
X-ray (2.19 Å) |
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen
SE, Cheng X |
(2008) "The SRA
domain of UHRF1 flips 5-methylcytosine out of the DNA
helix." Nature, 455,
826-829. doi: 10.1038/nature07280.
|
Mouse np95 sra domain DNA specific complex 1 . SNAP output
|
|
2zo1
|
ligase-DNA |
X-ray (1.96 Å) |
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen
SE, Cheng X |
(2008) "The SRA
domain of UHRF1 flips 5-methylcytosine out of the DNA
helix." Nature, 455,
826-829. doi: 10.1038/nature07280.
|
Mouse np95 sra domain DNA specific complex 2 . SNAP output
|
|
2zo2
|
ligase-DNA |
X-ray (3.09 Å) |
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen
SE, Cheng X |
(2008) "The SRA
domain of UHRF1 flips 5-methylcytosine out of the DNA
helix." Nature, 455,
826-829. doi: 10.1038/nature07280.
|
Mouse np95 sra domain non-specific DNA complex .
SNAP output
|
|
316d
|
DNA-antibiotic |
X-ray (3.0 Å) |
Takusagawa F, Takusagawa KT, Carlson RG, Weaver
RF |
(1997) "Selectivity
of F8-Actinomycin D for RNA:DNA Hybrids and its
Anti-Leukemia Activity." Bioorg.Med.Chem.,
5, 1197. doi: 10.1016/S0968-0896(97)00062-X.
|
Selectivity of f8-actinomycin d for RNA:DNA hybrids and
its anti-leukemia activity . SNAP output
|
|
3a01
|
gene regulation-DNA |
X-ray (2.7 Å) |
Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K,
Kojima T, Tanokura M |
(2010) "Cooperative
DNA-binding and sequence-recognition mechanism of
aristaless and clawless." Embo J.,
29, 1613-1623. doi: 10.1038/emboj.2010.53.
|
Crystal structure of aristaless and clawless
homeodomains bound to DNA . SNAP output
|
|
3a46
|
hydrolase |
X-ray (2.2 Å) |
Imamura K, Wallace SS, Doublie S |
(2009) "Structural
Characterization of a Viral NEIL1 Ortholog Unliganded
and Bound to Abasic Site-containing DNA."
J.Biol.Chem., 284,
26174-26183. doi: 10.1074/jbc.M109.021907.
|
Crystal structure of mvnei1-thf complex . SNAP output
|
|
3a4k
|
hydrolase-DNA |
X-ray (2.17 Å) |
Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I |
(2009) "Structures
of restriction endonuclease HindIII in complex with its
cognate DNA and divalent cations." Acta
Crystallogr.,Sect.D, 65,
1326-1333. doi: 10.1107/S0907444909041134.
|
Crystal structural analysis of hindiii restriction
endonuclease in complex with cognate DNA and divalent
cations at 2.17 angstrom resolution . SNAP output
|
|
3a5t
|
transcription regulator-DNA |
X-ray (2.8 Å) |
Kurokawa H, Motohashi H, Sueno S, Kimura M, Takagawa
H, Kanno Y, Yamamoto M, Tanaka T |
(2009) "Structural
Basis of Alternative DNA Recognition by Maf
Transcription Factors." Mol.Cell.Biol.,
29, 6232-6244. doi: 10.1128/MCB.00708-09.
|
Crystal structure of mafg-DNA complex . SNAP output
|
|
3a5u
|
DNA binding protein |
X-ray (2.8 Å) |
Kaushal PS, Manjunath GP, Sekar K, Muniyappa K,
Vijayan M |
(2009) "Promiscuity and specificity in DNA binding to
SSB: Insights from the structure of the Mycobacterium
smegmatis SSB-ssDNA complex." |
Promiscuity and specificity in DNA binding to ssb:
insights from the structure of the mycobacterium
smegmatis ssb-ssDNA complex . SNAP output
|
|
3a6n
|
structural protein-DNA |
X-ray (2.7 Å) |
Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga
T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H |
(2010) "Structural
basis of instability of the nucleosome containing a
testis-specific histone variant, human H3T."
Proc.Natl.Acad.Sci.USA, 107,
10454-10459. doi: 10.1073/pnas.1003064107.
|
The nucleosome containing a testis-specific histone
variant, human h3t . SNAP output
|
|
3aaf
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Kitano K, Kim SY, Hakoshima T |
(2010) "Structural
basis for DNA strand separation by the unconventional
winged-helix domain of RecQ helicase WRN."
Structure, 18, 177-187. doi:
10.1016/j.str.2009.12.011.
|
Structure of wrn rqc domain bound to double-stranded
DNA . SNAP output
|
|
3afa
|
structural protein-DNA |
X-ray (2.5 Å) |
Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga
T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H |
(2010) "Structural
basis of instability of the nucleosome containing a
testis-specific histone variant, human H3T."
Proc.Natl.Acad.Sci.USA, 107,
10454-10459. doi: 10.1073/pnas.1003064107.
|
The human nucleosome structure . SNAP output
|
|
3an2
|
structural protein-DNA |
X-ray (3.6 Å) |
Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y,
Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park S-Y,
Kimura H, Kurumizaka H |
(2011) "Crystal
structure of the human centromeric nucleosome
containing CENP-A." Nature,
476, 232-235. doi: 10.1038/nature10258.
|
The structure of the centromeric nucleosome containing
cenp-a . SNAP output
|
|
3aoh
|
transcription, transferase-DNA-RNA |
X-ray (4.1 Å) |
Tagami S, Sekine SI, Kumarevel T, Hino N, Murayama Y,
Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S |
(2010) "Crystal
structure of bacterial RNA polymerase bound with a
transcription inhibitor protein." Nature,
468, 978-982. doi: 10.1038/nature09573.
|
RNA polymerase-gfh1 complex (crystal type 1) . SNAP output
|
|
3aoi
|
transcription, transferase-DNA-RNA |
X-ray (4.3 Å) |
Tagami S, Sekine SI, Kumarevel T, Hino N, Murayama Y,
Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S |
(2010) "Crystal
structure of bacterial RNA polymerase bound with a
transcription inhibitor protein." Nature,
468, 978-982. doi: 10.1038/nature09573.
|
RNA polymerase-gfh1 complex (crystal type 2) . SNAP output
|
|
3au6
|
transferase-DNA |
X-ray (3.3 Å) |
Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui
R |
(2012) "The
structural basis of the kinetic mechanism of a
gap-filling X-family DNA polymerase that binds
Mg(2+)-dNTP before binding to DNA."
J.Mol.Biol., 417, 179-196.
doi: 10.1016/j.jmb.2012.01.025.
|
DNA polymerase x from thermus thermophilus hb8 ternary
complex with primer-template DNA and ddgtp . SNAP output
|
|
3auo
|
transferase-DNA |
X-ray (2.7 Å) |
Nakane S, Ishikawa H, Nakagawa N, Kuramitsu S, Masui
R |
(2012) "The
structural basis of the kinetic mechanism of a
gap-filling X-family DNA polymerase that binds
Mg(2+)-dNTP before binding to DNA."
J.Mol.Biol., 417, 179-196.
doi: 10.1016/j.jmb.2012.01.025.
|
DNA polymerase x from thermus thermophilus hb8 ternary
complex with 1-nt gapped DNA and ddgtp . SNAP output
|
|
3av1
|
structural protein-DNA |
X-ray (2.5 Å) |
Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H,
Kagawa W, Kurumizaka H |
(2011) "Structures
of human nucleosomes containing major histone H3
variants." Acta Crystallogr.,Sect.D,
67, 578-583. doi: 10.1107/S0907444911014818.
|
The human nucleosome structure containing the histone
variant h3.2 . SNAP
output
|
|
3av2
|
structural protein-DNA |
X-ray (2.8 Å) |
Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H,
Kagawa W, Kurumizaka H |
(2011) "Structures
of human nucleosomes containing major histone H3
variants." Acta Crystallogr.,Sect.D,
67, 578-583. doi: 10.1107/S0907444911014818.
|
The human nucleosome structure containing the histone
variant h3.3 . SNAP
output
|
|
3ayw
|
structural protein-DNA |
X-ray (2.9 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h3k56q mutation . SNAP output
|
|
3aze
|
structural protein-DNA |
X-ray (3.0 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h3k64q mutation . SNAP output
|
|
3azf
|
structural protein-DNA |
X-ray (2.7 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h3k79q mutation . SNAP output
|
|
3azg
|
structural protein-DNA |
X-ray (2.4 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h3k115q mutation . SNAP output
|
|
3azh
|
structural protein-DNA |
X-ray (3.49 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h3k122q mutation . SNAP output
|
|
3azi
|
structural protein-DNA |
X-ray (2.7 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h4k31q mutation . SNAP output
|
|
3azj
|
structural protein-DNA |
X-ray (2.89 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h4k44q mutation . SNAP output
|
|
3azk
|
structural protein-DNA |
X-ray (3.2 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h4k59q mutation . SNAP output
|
|
3azl
|
structural protein-DNA |
X-ray (2.7 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h4k77q mutation . SNAP output
|
|
3azm
|
structural protein-DNA |
X-ray (2.89 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h4k79q mutation . SNAP output
|
|
3azn
|
structural protein-DNA |
X-ray (3.0 Å) |
Iwasaki W, Tachiwana H, Kawaguchi K, Shibata T,
Kagawa W, Kurumizaka H |
(2011) "Comprehensive
Structural Analysis of Mutant Nucleosomes Containing
Lysine to Glutamine (KQ) Substitutions in the H3 and H4
Histone-Fold Domains." Biochemistry,
50, 7822-7832. doi: 10.1021/bi201021h.
|
Crystal structure of human nucleosome core particle
containing h4k91q mutation . SNAP output
|
|
3b39
|
transferase-DNA |
X-ray (2.35 Å) |
Corn JE, Pelton JG, Berger JM |
(2008) "Identification
of a DNA primase template tracking site redefines the
geometry of primer synthesis."
Nat.Struct.Mol.Biol., 15,
163-169. doi: 10.1038/nsmb.1373.
|
Structure of the dnag primase catalytic domain bound to
ssDNA . SNAP output
|
|
3b6f
|
structural protein-DNA |
X-ray (3.45 Å) |
Wu B, Droge P, Davey CA |
(2008) "Site
selectivity of platinum anticancer therapeutics."
Nat.Chem.Biol., 4, 110-112.
doi: 10.1038/nchembio.2007.58.
|
Nucleosome core particle treated with cisplatin .
SNAP output
|
|
3b6g
|
structural protein-DNA |
X-ray (3.45 Å) |
Wu B, Droge P, Davey CA |
(2008) "Site
selectivity of platinum anticancer therapeutics."
Nat.Chem.Biol., 4, 110-112.
doi: 10.1038/nchembio.2007.58.
|
Nucleosome core particle treated with oxaliplatin .
SNAP output
|
|
3bam
|
hydrolase-DNA |
X-ray (1.8 Å) |
Viadiu H, Aggarwal AK |
(1998) "The role
of metals in catalysis by the restriction endonuclease
BamHI." Nat.Struct.Biol.,
5, 910-916. doi: 10.1038/2352.
|
Restriction endonuclease bamhi complex with DNA and
manganese ions (post-reactive complex) . SNAP output
|
|
3bbb
|
transferase |
X-ray (1.3 Å) |
Dexheimer TS, Carey SS, Zuohe S, Gokhale VM, Hu X,
Murata LB, Maes EM, Weichsel A, Sun D, Meuillet EJ,
Montfort WR, Hurley LH |
(2009) "NM23-H2
may play an indirect role in transcriptional activation
of c-myc gene expression but does not cleave the
nuclease hypersensitive element III1."
Mol.Cancer Ther., 8,
1363-1377. doi: 10.1158/1535-7163.MCT-08-1093.
|
Crystal structure of the nm23-h2 transcription factor
complex with dinucleotide d(ag) . SNAP output
|
|
3bbx
|
ribosome |
cryo-EM (10.0 Å) |
Jiang L, Schaffitzel C, Bingel-Erlenmeyer R, Ban N,
Korber P, Koning RI, de Geus DC, Plaisier JR, Abrahams
JP |
(2009) "Recycling
of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA
Complexes by the Heat Shock Protein Hsp15."
J.Mol.Biol., 386, 1357-1367.
doi: 10.1016/j.jmb.2008.10.079.
|
The hsp15 protein fitted into the low resolution
cryo-EM map of the 50s.nc-trna.hsp15 complex . SNAP output
|
|
3bdn
|
transcription-DNA |
X-ray (3.909 Å) |
Stayrook SE, Jaru-Ampornpan P, Ni J, Hochschild A,
Lewis M |
(2008) "Crystal
structure of the lambda repressor and a model for
pairwise cooperative operator binding."
Nature, 452, 1022-1025. doi:
10.1038/nature06831.
|
Crystal structure of the lambda repressor . SNAP output
|
|
3bdp
|
transferase-DNA |
X-ray (1.9 Å) |
Kiefer JR, Mao C, Braman JC, Beese LS |
(1998) "Visualizing
DNA replication in a catalytically active Bacillus DNA
polymerase crystal." Nature,
391, 304-307. doi: 10.1038/34693.
|
DNA polymerase i-DNA complex . SNAP output
|
|
3bep
|
transferase, transcription-DNA |
X-ray (1.92 Å) |
Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong X-P,
O'Donnell M |
(2008) "Structure
of a sliding clamp on DNA."
Cell(Cambridge,Mass.), 132,
43-54. doi: 10.1016/j.cell.2007.11.045.
|
Structure of a sliding clamp on DNA . SNAP output
|
|
3bi3
|
oxidoreductase-DNA |
X-ray (1.9 Å) |
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
X-ray structure of alkb protein bound to dsDNA
containing 1mea-a with cofactors . SNAP output
|
|
3bie
|
oxidoreductase-DNA |
X-ray (1.68 Å) |
Yang C-G, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
X-ray structure of e coli alkb bound to dsDNA
containing 1mea-t with mn and 2kg . SNAP output
|
|
3bjy
|
transferase-DNA |
X-ray (2.41 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2008) "Protein-template-directed
synthesis across an acrolein-derived DNA adduct by
yeast Rev1 DNA polymerase." Structure,
16, 239-245. doi: 10.1016/j.str.2007.12.009.
|
Catalytic core of rev1 in complex with DNA (modified
template guanine) and incoming nucleotide . SNAP output
|
|
3bkz
|
DNA repair,oxidoreductase-DNA |
X-ray (1.65 Å) |
Yang C-G, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
X-ray structure of e coli alkb crosslinked to dsDNA in
the active site . SNAP
output
|
|
3bm3
|
hydrolase-DNA |
X-ray (1.7 Å) |
Szczepanowski RH, Carpenter M, Czapinska H,
Tamulaitis G, Siksnys V, Bhagwat A, Bochtler M |
"A direct crystallographic demonstration that Type II
restriction endonuclease PspGI flips nucleotides." |
Restriction endonuclease pspgi-substrate DNA complex .
SNAP output
|
|
3bq0
|
transferase-DNA |
X-ray (2.6 Å) |
Wilson RC, Pata JD |
(2008) "Structural
insights into the generation of single-base deletions
by the Y family DNA polymerase dbh."
Mol.Cell, 29, 767-779. doi:
10.1016/j.molcel.2008.01.014.
|
Pre-insertion binary complex of dbh DNA polymerase .
SNAP output
|
|
3bq1
|
transferase-DNA |
X-ray (2.7 Å) |
Wilson RC, Pata JD |
(2008) "Structural
insights into the generation of single-base deletions
by the Y family DNA polymerase dbh."
Mol.Cell, 29, 767-779. doi:
10.1016/j.molcel.2008.01.014.
|
Insertion ternary complex of dbh DNA polymerase .
SNAP output
|
|
3bq2
|
transferase-DNA |
X-ray (2.7 Å) |
Wilson RC, Pata JD |
(2008) "Structural
insights into the generation of single-base deletions
by the Y family DNA polymerase dbh."
Mol.Cell, 29, 767-779. doi:
10.1016/j.molcel.2008.01.014.
|
Post-insertion binary complex of dbh DNA polymerase .
SNAP output
|
|
3brd
|
DNA binding protein-DNA |
X-ray (2.21 Å) |
Friedmann DR, Wilson JJ, Kovall RA |
(2008) "RAM-induced
Allostery Facilitates Assembly of a Notch Pathway
Active Transcription Complex."
J.Biol.Chem., 283,
14781-14791. doi: 10.1074/jbc.M709501200.
|
Csl (lag-1) bound to DNA with lin-12 ram peptide,
p212121 . SNAP
output
|
|
3brf
|
DNA binding protein-DNA |
X-ray (2.47 Å) |
Friedmann DR, Wilson JJ, Kovall RA |
(2008) "RAM-induced
Allostery Facilitates Assembly of a Notch Pathway
Active Transcription Complex."
J.Biol.Chem., 283,
14781-14791. doi: 10.1074/jbc.M709501200.
|
Csl (lag-1) bound to DNA with lin-12 ram peptide, c2221
. SNAP output
|
|
3brg
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Friedmann DR, Wilson JJ, Kovall RA |
(2008) "RAM-induced
Allostery Facilitates Assembly of a Notch Pathway
Active Transcription Complex."
J.Biol.Chem., 283,
14781-14791. doi: 10.1074/jbc.M709501200.
|
Csl (rbp-jk) bound to DNA . SNAP output
|
|
3bs1
|
transcription regulator |
X-ray (1.6 Å) |
Sidote DJ, Barbieri CM, Wu T, Stock AM |
(2008) "Structure
of the Staphylococcus aureus AgrA LytTR Domain Bound to
DNA Reveals a Beta Fold with an Unusual Mode of
Binding." Structure, 16,
727-735. doi: 10.1016/j.str.2008.02.011.
|
Structure of the staphylococcus aureus agra lyttr
domain bound to DNA reveals a beta fold with a novel
mode of binding . SNAP
output
|
|
3bsu
|
hydrolase-RNA-DNA |
X-ray (2.1 Å) |
Nowotny M, Cerritelli SM, Ghirlando R, Gaidamakov SA,
Crouch RJ, Yang W |
(2008) "Specific
recognition of RNA/DNA hybrid and enhancement of human
RNase H1 activity by HBD." Embo J.,
27, 1172-1181. doi: 10.1038/emboj.2008.44.
|
Hybrid-binding domain of human rnase h1 in complex with
12-mer RNA-DNA . SNAP
output
|
|
3btx
|
oxidoreductase-DNA |
X-ray (2.0 Å) |
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
X-ray structure of human abh2 bound to dsDNA through
active site cross-linking . SNAP output
|
|
3bty
|
oxidoreductase-DNA |
X-ray (2.35 Å) |
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
Crystal structure of human abh2 bound to dsDNA
containing 1mea through cross-linking away from active
site . SNAP output
|
|
3btz
|
oxidoreductase-DNA |
X-ray (3.0 Å) |
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
Crystal structure of human abh2 cross-linked to dsDNA .
SNAP output
|
|
3bu0
|
oxidoreductase-DNA |
X-ray (2.5 Å) |
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
Crystal structure of human abh2 cross-linked to dsDNA
with cofactors . SNAP
output
|
|
3buc
|
oxidoreductase-DNA |
X-ray (2.59 Å) |
Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice
PA, He C |
(2008) "Crystal
structures of DNA/RNA repair enzymes AlkB and ABH2
bound to dsDNA." Nature,
452, 961-965. doi: 10.1038/nature06889.
|
X-ray structure of human abh2 bound to dsDNA with
mn(ii) and 2kg . SNAP
output
|
|
3c0w
|
hydrolase-DNA |
X-ray (2.2 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2008) "Crystal
structures of I-SceI complexed to nicked DNA
substrates: snapshots of intermediates along the DNA
cleavage reaction pathway." Nucleic Acids
Res., 36, 3287-3296. doi:
10.1093/nar/gkn178.
|
I-scei in complex with a bottom nicked DNA substrate .
SNAP output
|
|
3c0x
|
hydrolase-DNA |
X-ray (2.3 Å) |
Moure CM, Gimble FS, Quiocho FA |
(2008) "Crystal
structures of I-SceI complexed to nicked DNA
substrates: snapshots of intermediates along the DNA
cleavage reaction pathway." Nucleic Acids
Res., 36, 3287-3296. doi:
10.1093/nar/gkn178.
|
I-scei in complex with a top nicked DNA substrate .
SNAP output
|
|
3c1b
|
structural protein-DNA |
X-ray (2.2 Å) |
Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat
KM, Luger K |
(2008) "The
effect of H3K79 dimethylation and H4K20 trimethylation
on nucleosome and chromatin structure."
Nat.Struct.Mol.Biol., 15,
1122-1124. doi: 10.1038/nsmb.1489.
|
The effect of h3 k79 dimethylation and h4 k20
trimethylation on nucleosome and chromatin structure .
SNAP output
|
|
3c1c
|
structural protein-DNA |
X-ray (3.15 Å) |
Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat
KM, Luger K |
(2008) "The
effect of H3K79 dimethylation and H4K20 trimethylation
on nucleosome and chromatin structure."
Nat.Struct.Mol.Biol., 15,
1122-1124. doi: 10.1038/nsmb.1489.
|
The effect of h3 k79 dimethylation and h4 k20
trimethylation on nucleosome and chromatin structure .
SNAP output
|
|
3c25
|
hydrolase-DNA |
X-ray (2.5 Å) |
Lambert AR, Sussman D, Shen B, Maunus R, Nix J,
Samuelson J, Xu SY, Stoddard BL |
(2008) "Structures
of the Rare-Cutting Restriction Endonuclease NotI
Reveal a Unique Metal Binding Fold Involved in DNA
Binding." Structure, 16,
558-569. doi: 10.1016/j.str.2008.01.017.
|
Crystal structure of noti restriction endonuclease
bound to cognate DNA . SNAP output
|
|
3c28
|
recombination-DNA |
X-ray (2.6 Å) |
Ghosh K, Van Duyne GD |
"Detailed study on Synapsis in Cre-loxP recombination
reaction." |
Crystal structure of the product synapse complex .
SNAP output
|
|
3c29
|
recombination-DNA |
X-ray (2.2 Å) |
Ghosh K, Van Duyne GD |
"Synapsis study in detail." |
Cre-loxp synaptic structure . SNAP output
|
|
3c2i
|
transcription regulator |
X-ray (2.5 Å) |
Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP,
Walkinshaw MD |
(2008) "MeCP2
binding to DNA depends upon hydration at
methyl-CpG." Mol.Cell,
29, 525-531. doi: 10.1016/j.molcel.2007.12.028.
|
The crystal structure of methyl-cpg binding domain of
human mecp2 in complex with a methylated DNA sequence
from bdnf . SNAP
output
|
|
3c2k
|
transferase-DNA |
X-ray (2.4 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2008) "Structures
of DNA polymerase beta with active-site mismatches
suggest a transient abasic site intermediate during
misincorporation." Mol.Cell,
30, 315-324. doi: 10.1016/j.molcel.2008.02.025.
|
DNA polymerase beta with a gapped DNA substrate and
dumpnpp with manganese in the active site . SNAP output
|
|
3c2l
|
transferase-DNA |
X-ray (2.6 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2008) "Structures
of DNA polymerase beta with active-site mismatches
suggest a transient abasic site intermediate during
misincorporation." Mol.Cell,
30, 315-324. doi: 10.1016/j.molcel.2008.02.025.
|
Ternary complex of DNA polymerase beta with a c:dapcpp
mismatch in the active site . SNAP output
|
|
3c2m
|
transferase, lyase-DNA |
X-ray (2.15 Å) |
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson
SH |
(2008) "Structures
of DNA polymerase beta with active-site mismatches
suggest a transient abasic site intermediate during
misincorporation." Mol.Cell,
30, 315-324. doi: 10.1016/j.molcel.2008.02.025.
|
Ternary complex of DNA polymerase beta with a g:dapcpp
mismatch in the active site . SNAP output
|
|
3c2p
|
transferase-DNA |
X-ray (2.0 Å) |
Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami
KS |
(2008) "Structural
basis for DNA-hairpin promoter recognition by the
bacteriophage N4 virion RNA polymerase."
Mol.Cell, 32, 707-717. doi:
10.1016/j.molcel.2008.11.010.
|
X-ray crystal structure of the n4 mini-vrnap p1
promoter complex . SNAP
output
|
|
3c3l
|
transferase-DNA |
X-ray (2.4 Å) |
Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami
KS |
(2008) "Structural
basis for DNA-hairpin promoter recognition by the
bacteriophage N4 virion RNA polymerase."
Mol.Cell, 32, 707-717. doi:
10.1016/j.molcel.2008.11.010.
|
X-ray crystal structure of the n4 mini-vrnap p2
promoter complex . SNAP
output
|
|
3c46
|
transferase-DNA |
X-ray (2.0 Å) |
Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami
KS |
(2008) "Structural
basis for DNA-hairpin promoter recognition by the
bacteriophage N4 virion RNA polymerase."
Mol.Cell, 32, 707-717. doi:
10.1016/j.molcel.2008.11.010.
|
X-ray crystal structure of the n4 mini-vrnap p2_7a
promoter complex soaked with mgcl2 . SNAP output
|
|
3c58
|
hydrolase-DNA |
X-ray (1.9 Å) |
Coste F, Ober M, Le Bihan YV, Izquierdo MA, Hervouet
N, Mueller H, Carell T, Castaing B |
(2008) "Bacterial
base excision repair enzyme Fpg recognizes bulky
N7-substituted-FapydG lesion via unproductive binding
mode." Chem.Biol., 15,
706-717. doi: 10.1016/j.chembiol.2008.05.014.
|
Crystal structure of a complex between the wild-type
lactococcus lactis fpg (mutm) and a n7-benzyl-fapy-dg
containing DNA . SNAP
output
|
|
3c5f
|
transferase, lyase-DNA |
X-ray (2.25 Å) |
Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC,
Schlick T, Kunkel TA |
(2008) "Substrate-induced
DNA strand misalignment during catalytic cycling by DNA
polymerase lambda." Embo Rep.,
9, 459-464. doi: 10.1038/embor.2008.33.
|
Structure of a binary complex of the r517a pol lambda
mutant . SNAP output
|
|
3c5g
|
transferase-DNA, lyase-DNA |
X-ray (2.2 Å) |
Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC,
Schlick T, Kunkel TA |
(2008) "Substrate-induced
DNA strand misalignment during catalytic cycling by DNA
polymerase lambda." Embo Rep.,
9, 459-464. doi: 10.1038/embor.2008.33.
|
Structure of a ternary complex of the r517k pol lambda
mutant . SNAP output
|
|
3cbb
|
transcription-DNA |
X-ray (2.0 Å) |
Lu P, Rha GB, Melikishvili M, Wu G, Adkins BC, Fried
MG, Chi YI |
(2008) "Structural
basis of natural promoter recognition by a unique
nuclear receptor, HNF4alpha. Diabetes gene
product." J.Biol.Chem.,
283, 33685-33697. doi: 10.1074/jbc.M806213200.
|
Crystal structure of hepatocyte nuclear factor 4alpha
in complex with DNA: diabetes gene product . SNAP output
|
|
3cfp
|
transferase-DNA |
X-ray (2.5 Å) |
Klimenko D, Wang M, Steitz TA, Konigsberg WH, Wang
J |
"Insights into base selectivity from the structures
of an RB69 DNA Polymerase triple mutant." |
Structure of the replicating complex of a pol alpha
family DNA polymerase, ternary complex 1 . SNAP output
|
|
3cfr
|
transferase-DNA |
X-ray (2.4 Å) |
Klimenko D, Wang M, Steitz TA, Konigsberg WH, Wang
J |
"Insights into base selectivity from the structures
of an RB69 DNA Polymerase triple mutant." |
Structure of the replicating complex of a pol alpha
family DNA polymerase, ternary complex 2 . SNAP output
|
|
3clc
|
transcription regulator-DNA |
X-ray (2.8 Å) |
McGeehan JE, Streeter SD, Thresh SJ, Ball N, Ravelli
RB, Kneale GG |
(2008) "Structural
analysis of the genetic switch that regulates the
expression of restriction-modification genes."
Nucleic Acids Res., 36,
4778-4787. doi: 10.1093/nar/gkn448.
|
Crystal structure of the restriction-modification
controller protein c.esp1396i tetramer in complex with
its natural 35 base-pair operator . SNAP output
|
|
3clz
|
ligase |
X-ray (2.2 Å) |
Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner
C, Arrowsmith CH, Dhe-Paganon S |
(2008) "Structural
basis for recognition of hemi-methylated DNA by the SRA
domain of human UHRF1." Nature,
455, 822-825. doi: 10.1038/nature07273.
|
The set and ring associated (sra) domain of uhrf1 bound
to methylated DNA . SNAP
output
|
|
3cmt
|
recombination-DNA |
X-ray (3.15 Å) |
Chen Z, Yang H, Pavletich NP |
(2008) "Mechanism
of homologous recombination from the RecA-ssDNA/dsDNA
structures." Nature, 453,
489-494. doi: 10.1038/nature06971.
|
Mechanism of homologous recombination from the
reca-ssDNA-dsDNA structures . SNAP output
|
|
3cmu
|
recombination-DNA |
X-ray (4.2 Å) |
Chen Z, Yang H, Pavletich NP |
(2008) "Mechanism
of homologous recombination from the RecA-ssDNA/dsDNA
structures." Nature, 453,
489-494. doi: 10.1038/nature06971.
|
Mechanism of homologous recombination from the
reca-ssDNA-dsDNA structures . SNAP output
|
|
3cmw
|
recombination-DNA |
X-ray (2.8 Å) |
Chen Z, Yang H, Pavletich NP |
(2008) "Mechanism
of homologous recombination from the RecA-ssDNA/dsDNA
structures." Nature, 453,
489-494. doi: 10.1038/nature06971.
|
Mechanism of homologous recombination from the
reca-ssDNA-dsDNA structures . SNAP output
|
|
3cmx
|
recombination-DNA |
X-ray (3.4 Å) |
Chen Z, Yang H, Pavletich NP |
(2008) "Mechanism
of homologous recombination from the RecA-ssDNA/dsDNA
structures." Nature, 453,
489-494. doi: 10.1038/nature06971.
|
Mechanism of homologous recombination from the
reca-ssDNA-dsDNA structures . SNAP output
|
|
3cmy
|
transcription regulator-DNA |
X-ray (1.95 Å) |
Birrane G, Soni A, Ladias JA |
(2009) "Structural
Basis for DNA Recognition by the Human PAX3
Homeodomain." Biochemistry,
48, 1148-1155. doi: 10.1021/bi802052y.
|
Structure of a homeodomain in complex with DNA .
SNAP output
|
|
3co6
|
transcription-DNA |
X-ray (2.1 Å) |
Brent MM, Anand R, Marmorstein R |
(2008) "Structural
Basis for DNA Recognition by FoxO1 and Its Regulation
by Posttranslational Modification."
Structure, 16, 1407-1416.
doi: 10.1016/j.str.2008.06.013.
|
Crystal structure of foxo1 dbd bound to dbe1 DNA .
SNAP output
|
|
3co7
|
transcription-DNA |
X-ray (2.91 Å) |
Brent MM, Anand R, Marmorstein R |
(2008) "Structural
Basis for DNA Recognition by FoxO1 and Its Regulation
by Posttranslational Modification."
Structure, 16, 1407-1416.
doi: 10.1016/j.str.2008.06.013.
|
Crystal structure of foxo1 dbd bound to dbe2 DNA .
SNAP output
|
|
3coa
|
transcription-DNA |
X-ray (2.2 Å) |
Brent MM, Anand R, Marmorstein R |
(2008) "Structural
Basis for DNA Recognition by FoxO1 and Its Regulation
by Posttranslational Modification."
Structure, 16, 1407-1416.
doi: 10.1016/j.str.2008.06.013.
|
Crystal structure of foxo1 dbd bound to ire DNA .
SNAP output
|
|
3coq
|
transcription-DNA |
X-ray (2.4 Å) |
Hong M, Fitzgerald MX, Harper S, Luo C, Speicher DW,
Marmorstein R |
(2008) "Structural
basis for dimerization in DNA recognition by gal4."
Structure, 16, 1019-1026.
doi: 10.1016/j.str.2008.03.015.
|
Structural basis for dimerization in DNA recognition by
gal4 . SNAP output
|
|
3cq8
|
transferase-DNA |
X-ray (2.5 Å) |
Zhong X, Pedersen LC, Kunkel TA |
(2008) "Characterization
of a replicative DNA polymerase mutant with reduced
fidelity and increased translesion synthesis
capacity." Nucleic Acids Res.,
36, 3892-3904. doi: 10.1093/nar/gkn312.
|
Ternary complex of the l415f mutant rb69
exo(-)polymerase . SNAP
output
|
|
3cro
|
transcription-DNA |
X-ray (2.5 Å) |
Mondragon A, Harrison SC |
(1991) "The phage
434 Cro/OR1 complex at 2.5 A resolution."
J.Mol.Biol., 219, 321-334.
doi: 10.1016/0022-2836(91)90568-Q.
|
The phage 434 cro-or1 complex at 2.5 angstroms
resolution . SNAP
output
|
|
3crx
|
hydrolase, ligase-DNA |
X-ray (2.5 Å) |
Gopaul DN, Guo F, Van Duyne GD |
(1998) "Structure
of the Holliday junction intermediate in Cre-loxP
site-specific recombination." EMBO J.,
17, 4175-4187. doi: 10.1093/emboj/17.14.4175.
|
Cre recombinase-DNA complex intermediate i . SNAP output
|
|
3cvs
|
hydrolase-DNA |
X-ray (2.4 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
8oxoguanine:adenine base pair . SNAP output
|
|
3cvt
|
hydrolase-DNA |
X-ray (2.5 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
8oxoguanine:cytosine base pair . SNAP output
|
|
3cvu
|
lyase-DNA |
X-ray (2.0 Å) |
Maul MJ, Barends TR, Glas AF, Cryle MJ, Domratcheva
T, Schneider S, Schlichting I, Carell T |
(2008) "Crystal
structure and mechanism of a DNA (6-4) photolyase."
Angew.Chem.Int.Ed.Engl., 47,
10076-10080. doi: 10.1002/anie.200804268.
|
Drosophila melanogaster (6-4) photolyase bound to ds
DNA with a t-t (6-4) photolesion . SNAP output
|
|
3cvv
|
lyase-DNA |
X-ray (2.1 Å) |
Glas AF, Maul MJ, Cryle M, Barends TR, Schneider S,
Kaya E, Schlichting I, Carell T |
(2009) "The
archaeal cofactor F0 is a light-harvesting antenna
chromophore in eukaryotes."
Proc.Natl.Acad.Sci.USA, 106,
11540-11545. doi: 10.1073/pnas.0812665106.
|
Drosophila melanogaster (6-4) photolyase bound to ds
DNA with a t-t (6-4) photolesion and f0 cofactor .
SNAP output
|
|
3cvw
|
lyase-DNA |
X-ray (3.2 Å) |
Maul MJ, Barends T, Glas AF, Cryle MJ, Schneider S,
Domratcheva T, Schlichting I, Carell T |
"Structure and mechanism of a cofactor f0 accelerated
(6-4) photolyase from the fruit fly." |
Drosophila melanogaster (6-4) photolyase h365n mutant
bound to ds DNA with a t-t (6-4) photolesion and
cofactor f0 . SNAP
output
|
|
3cvx
|
lyase-DNA |
X-ray (3.2 Å) |
Maul MJ, Barends T, Glas AF, Cryle MJ, Schneider S,
Domratcheva T, Schlichting I, Carell T |
"Structure and mechanism of a coenzyme F0 accelerated
(6-4) photolyase from the fruit fly." |
Drosophila melanogaster (6-4) photolyase h369m mutant
bound to ds DNA with a t-t (6-4) photolesion . SNAP output
|
|
3cvy
|
lyase-DNA |
X-ray (2.7 Å) |
Maul MJ, Barends TR, Glas AF, Cryle MJ, Domratcheva
T, Schneider S, Schlichting I, Carell T |
(2008) "Crystal
structure and mechanism of a DNA (6-4) photolyase."
Angew.Chem.Int.Ed.Engl., 47,
10076-10080. doi: 10.1002/anie.200804268.
|
Drosophila melanogaster (6-4) photolyase bound to
repaired ds DNA . SNAP
output
|
|
3cw7
|
hydrolase-DNA |
X-ray (2.3 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
8oxoguanine:cytosine base pair . SNAP output
|
|
3cwa
|
hydrolase-DNA |
X-ray (2.4 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
8oxoguanine:cytosine base pair . SNAP output
|
|
3cws
|
hydrolase-DNA |
X-ray (2.3 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
2'-fluoro-2'-deoxyinosine:thymine base pair . SNAP output
|
|
3cwt
|
hydrolase-DNA |
X-ray (2.3 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
2'-fluoro-2'-deoxyinosine:adenine base pair . SNAP output
|
|
3cwu
|
hydrolase-DNA |
X-ray (2.8 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2008) "Structure
of the E. coli DNA Glycosylase AlkA Bound to the Ends
of Duplex DNA: A System for the Structure Determination
of Lesion-Containing DNA." Structure,
16, 1166-1174. doi: 10.1016/j.str.2008.04.012.
|
Crystal structure of an alka host-guest complex
2'-fluoro-2'-deoxy-1,n6-ethenoadenine:thymine base pair
. SNAP output
|
|
3d0a
|
transcription-DNA |
X-ray (1.8 Å) |
Suad O, Rozenberg H, Brosh R, Diskin-Posner Y,
Kessler N, Shimon LJW, Frolow F, Liran A, Rotter V,
Shakked Z |
(2009) "Structural
basis of restoring sequence-specific DNA binding and
transactivation to mutant p53 by suppressor
mutations." J.Mol.Biol.,
385, 249-265. doi: 10.1016/j.jmb.2008.10.063.
|
Human p53 core domain with hot spot mutation r249s and
second site suppressor mutation h168r in
sequence-specific complex with DNA . SNAP output
|
|
3d0p
|
hydrolase-DNA |
X-ray (1.8 Å) |
Pallan PS, Egli M |
(2008) "Insights
into RNA/DNA hybrid recognition and processing by RNase
H from the crystal structure of a non-specific
enzyme-dsDNA complex." Cell Cycle,
7, 2562-2569.
|
Insights into RNA-DNA hybrid recognition and processing
by rnase h from the crystal structure of a non-specific
enzyme-dsDNA complex . SNAP output
|
|
3d1n
|
transcription regulator-DNA |
X-ray (2.51 Å) |
Pereira JH, Kim SH |
(2009) "Structure
of human Brn-5 transcription factor in complex with CRH
gene promoter." J.Struct.Biol.,
167, 159-165. doi: 10.1016/j.jsb.2009.05.003.
|
Structure of human brn-5 transcription factor in
complex with corticotrophin-releasing hormone gene
promoter . SNAP
output
|
|
3d2s
|
metal binding protein-RNA |
X-ray (1.7 Å) |
Teplova M, Patel DJ |
(2008) "Structural
insights into RNA recognition by the
alternative-splicing regulator muscleblind-like
MBNL1." Nat.Struct.Mol.Biol.,
15, 1343-1351. doi: 10.1038/nsmb.1519.
|
Crystal structure of mbnl1 tandem zinc finger 3 and 4
domain in complex with cgcugu RNA . SNAP output
|
|
3d2w
|
DNA-RNA binding protein |
X-ray (1.65 Å) |
Kuo PH, Doudeva LG, Wang YT, Shen CK, Yuan HS |
(2009) "Structural
insights into TDP-43 in nucleic-acid binding and domain
interactions." Nucleic Acids Res.,
37, 1799-1808. doi: 10.1093/nar/gkp013.
|
Crystal structure of mouse tdp-43 rrm2 domain in
complex with DNA . SNAP
output
|
|
3d4v
|
hydrolase-DNA |
X-ray (2.9 Å) |
Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL |
(2008) "Synthesis
and structure of duplex DNA containing the genotoxic
nucleobase lesion N7-methylguanine."
J.Am.Chem.Soc., 130,
11570-11571. doi: 10.1021/ja8025328.
|
Crystal structure of an alka host-guest complex
n7methylguanine:cytosine base pair . SNAP output
|
|
3d6y
|
transcription regulator-DNA |
X-ray (2.7 Å) |
Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N,
Neyfakh AA, Brennan RG |
(2008) "Structures
of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding
Pocket and Transcription Activation through Tyrosine
Expulsion." J.Biol.Chem.,
283, 26795-26804. doi: 10.1074/jbc.M804191200.
|
Crystal structure of r275e mutant of bmrr bound to DNA
and berberine . SNAP
output
|
|
3d6z
|
transcription regulator-DNA |
X-ray (2.6 Å) |
Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N,
Neyfakh AA, Brennan RG |
(2008) "Structures
of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding
Pocket and Transcription Activation through Tyrosine
Expulsion." J.Biol.Chem.,
283, 26795-26804. doi: 10.1074/jbc.M804191200.
|
Crystal structure of r275e mutant of bmrr bound to DNA
and rhodamine . SNAP
output
|
|
3d70
|
transcription regulator-DNA |
X-ray (2.8 Å) |
Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N,
Neyfakh AA, Brennan RG |
(2008) "Structures
of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding
Pocket and Transcription Activation through Tyrosine
Expulsion." J.Biol.Chem.,
283, 26795-26804. doi: 10.1074/jbc.M804191200.
|
Crystal structure of e253a mutant of bmrr bound to
22-bp oligonucleotide . SNAP output
|
|
3d71
|
transcription regulator-DNA |
X-ray (2.8 Å) |
Newberry KJ, Huffman JL, Miller MC, Vazquez-Laslop N,
Neyfakh AA, Brennan RG |
(2008) "Structures
of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding
Pocket and Transcription Activation through Tyrosine
Expulsion." J.Biol.Chem.,
283, 26795-26804. doi: 10.1074/jbc.M804191200.
|
Crystal structure of e253q bmrr bound to 22 base pair
promoter site . SNAP
output
|
|
3dfv
|
transcription-DNA |
X-ray (3.1 Å) |
Bates DL, Chen Y, Kim G, Guo L, Chen L |
(2008) "Crystal
structures of multiple GATA zinc fingers bound to DNA
reveal new insights into DNA recognition and
self-association by GATA." J.Mol.Biol.,
381, 1292-1306. doi: 10.1016/j.jmb.2008.06.072.
|
Adjacent gata DNA binding . SNAP output
|
|
3dfx
|
transcription-DNA |
X-ray (2.7 Å) |
Bates DL, Chen Y, Kim G, Guo L, Chen L |
(2008) "Crystal
structures of multiple GATA zinc fingers bound to DNA
reveal new insights into DNA recognition and
self-association by GATA." J.Mol.Biol.,
381, 1292-1306. doi: 10.1016/j.jmb.2008.06.072.
|
Opposite gata DNA binding . SNAP output
|
|
3dlb
|
nucleic acid binding protein-DNA |
X-ray (2.7 Å) |
Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ |
(2008) "Structure
of the guide-strand-containing argonaute silencing
complex." Nature, 456,
209-213. doi: 10.1038/nature07315.
|
Crystal structure of the guide-strand-containing
argonaute protein silencing complex . SNAP output
|
|
3dlh
|
nucleic acid binding protein-DNA |
X-ray (3.0 Å) |
Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ |
(2008) "Structure
of the guide-strand-containing argonaute silencing
complex." Nature, 456,
209-213. doi: 10.1038/nature07315.
|
Crystal structure of the guide-strand-containing
argonaute protein silencing complex . SNAP output
|
|
3dnv
|
transcription-DNA |
X-ray (2.68 Å) |
Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K,
Brennan RG |
(2009) "Molecular
mechanisms of HipA-mediated multidrug tolerance and its
neutralization by HipB." Science,
323, 396-401. doi: 10.1126/science.1163806.
|
Mdt protein . SNAP
output
|
|
3do7
|
transcription-DNA |
X-ray (3.05 Å) |
Fusco A, Huang DB, Miller D, Vu D, Ghosh G |
"NF-kapppaB p52:RelB heterodimer uses different
binding modes to recognize different kappaB DNA." |
X-ray structure of a nf-kb p52-relb-DNA complex .
SNAP output
|
|
3dpg
|
hydrolase-DNA |
X-ray (1.91 Å) |
Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton
M, Hough D, Bitinaite J, Horton NC |
(2008) "The
structure of SgrAI bound to DNA; recognition of an 8
base pair target." Nucleic Acids Res.,
36, 5405-5416. doi: 10.1093/nar/gkn510.
|
Sgrai with noncognate DNA bound . SNAP output
|
|
3dsc
|
hydrolase-DNA |
X-ray (2.7 Å) |
Williams RS, Moncalian G, Williams JS, Yamada Y,
Limbo O, Shin DS, Groocock LM, Cahill D, Hitomi C,
Guenther G, Moiani D, Carney JP, Russell P, Tainer
JA |
(2008) "Mre11
dimers coordinate DNA end bridging and nuclease
processing in double-strand-break repair."
Cell(Cambridge,Mass.), 135,
97-109. doi: 10.1016/j.cell.2008.08.017.
|
Crystal structure of p. furiosus mre11 DNA synaptic
complex . SNAP
output
|
|
3dsd
|
hydrolase-DNA |
X-ray (2.2 Å) |
Williams RS, Moncalian G, Williams JS, Yamada Y,
Limbo O, Shin DS, Groocock LM, Cahill D, Hitomi C,
Guenther G, Moiani D, Carney JP, Russell P, Tainer
JA |
(2008) "Mre11
dimers coordinate DNA end bridging and nuclease
processing in double-strand-break repair."
Cell(Cambridge,Mass.), 135,
97-109. doi: 10.1016/j.cell.2008.08.017.
|
Crystal structure of p. furiosus mre11-h85s bound to a
branched DNA and manganese . SNAP output
|
|
3dvo
|
hydrolase-DNA |
X-ray (1.892 Å) |
Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton
M, Hough D, Bitinaite J, Horton NC |
(2008) "The
structure of SgrAI bound to DNA; recognition of an 8
base pair target." Nucleic Acids Res.,
36, 5405-5416. doi: 10.1093/nar/gkn510.
|
Sgrai with cognate DNA and calcium bound . SNAP output
|
|
3dw9
|
hydrolase-DNA |
X-ray (2.2 Å) |
Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton
M, Hough D, Bitinaite J, Horton NC |
(2008) "The
structure of SgrAI bound to DNA; recognition of an 8
base pair target." Nucleic Acids Res.,
36, 5405-5416. doi: 10.1093/nar/gkn510.
|
Sgrai with cognate DNA and manganese bound . SNAP output
|
|
3dzu
|
transcription-DNA |
X-ray (3.2 Å) |
Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y,
Burris TP, Rastinejad F |
(2008) "Structure
of the intact PPAR-gamma-RXR- nuclear receptor complex
on DNA." Nature, 456,
350-356. doi: 10.1038/nature07413.
|
Intact ppar gamma - rxr alpha nuclear receptor complex
on DNA bound with bvt.13, 9-cis retinoic acid and ncoa2
peptide . SNAP
output
|
|
3dzy
|
transcription-DNA |
X-ray (3.1 Å) |
Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y,
Burris TP, Rastinejad F |
(2008) "Structure
of the intact PPAR-gamma-RXR- nuclear receptor complex
on DNA." Nature, 456,
350-356. doi: 10.1038/nature07413.
|
Intact ppar gamma - rxr alpha nuclear receptor complex
on DNA bound with rosiglitazone, 9-cis retinoic acid
and ncoa2 peptide . SNAP
output
|
|
3e00
|
transcription-DNA |
X-ray (3.1 Å) |
Chandra V, Huang P, Hamuro Y, Raghuram S, Wang Y,
Burris TP, Rastinejad F |
(2008) "Structure
of the intact PPAR-gamma-RXR- nuclear receptor complex
on DNA." Nature, 456,
350-356. doi: 10.1038/nature07413.
|
Intact ppar gamma - rxr alpha nuclear receptor complex
on DNA bound with gw9662, 9-cis retinoic acid and ncoa2
peptide . SNAP
output
|
|
3e0d
|
transferase-DNA |
X-ray (4.6 Å) |
Wing RA, Bailey S, Steitz TA |
(2008) "Insights
into the Replisome from the Structure of a Ternary
Complex of the DNA Polymerase III alpha-Subunit."
J.Mol.Biol., 382, 859-869.
doi: 10.1016/j.jmb.2008.07.058.
|
Insights into the replisome from the crystral structure
of the ternary complex of the eubacterial DNA
polymerase iii alpha-subunit . SNAP output
|
|
3e2e
|
transferase-RNA-DNA |
X-ray (3.0 Å) |
Durniak KJ, Bailey S, Steitz TA |
(2008) "The
structure of a transcribing t7 RNA polymerase in
transition from initiation to elongation."
Science, 322, 553-557. doi:
10.1126/science.1163433.
|
Crystal structure of an intermediate complex of t7 rnap
and 7nt of RNA . SNAP
output
|
|
3e3j
|
transferase-RNA-DNA |
X-ray (6.7 Å) |
Durniak KJ, Bailey S, Steitz TA |
(2008) "The
structure of a transcribing t7 RNA polymerase in
transition from initiation to elongation."
Science, 322, 553-557. doi:
10.1126/science.1163433.
|
Crystal structure of an intermediate complex of t7 rnap
and 8nt of RNA . SNAP
output
|
|
3e3y
|
hydrolase-DNA |
X-ray (2.13 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to gttaac and cocrystallized with 5
mm ca2+ . SNAP
output
|
|
3e40
|
hydrolase-DNA |
X-ray (2.1 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to gttaac and cocrystallized with 5
mm ca2+ . SNAP
output
|
|
3e41
|
hydrolase-DNA |
X-ray (2.73 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to gtcgac and 5 mm ca2+ . SNAP output
|
|
3e42
|
hydrolase-DNA |
X-ray (2.68 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to gtcgac and ca2+ (cocrystallized)
. SNAP output
|
|
3e43
|
hydrolase-DNA |
X-ray (2.73 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to gttaac and cocrystallized with
2.5 mm mgcl2 . SNAP
output
|
|
3e44
|
hydrolase-DNA |
X-ray (2.52 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to cleaved DNA (gtt | aac) and mn2+
. SNAP output
|
|
3e45
|
hydrolase-DNA |
X-ray (2.78 Å) |
Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton
NC |
(2008) "DNA
distortion and specificity in a sequence-specific
endonuclease." J.Mol.Biol.,
383, 186-204. doi: 10.1016/j.jmb.2008.08.032.
|
Q138f hincii bound to noncognate DNA (gtgcac) and ca2+
. SNAP output
|
|
3e54
|
hydrolase-DNA |
X-ray (2.5 Å) |
Nomura N, Nomura Y, Sussman D, Klein D, Stoddard
BL |
(2008) "Recognition
of a common rDNA target site in archaea and eukarya by
analogous LAGLIDADG and His-Cys box homing
endonucleases." Nucleic Acids Res.,
36, 6988-6998. doi: 10.1093/nar/gkn846.
|
Archaeal intron-encoded homing endonuclease i-vdi141i
complexed with DNA . SNAP output
|
|
3e6c
|
transcription regulation-DNA |
X-ray (1.8 Å) |
Levy C, Pike K, Heyes DJ, Joyce MG, Gabor K, Smidt H,
van der Oost J, Leys D |
(2008) "Molecular
basis of halorespiration control by CprK, a CRP-FNR
type transcriptional regulator."
Mol.Microbiol., 70, 151-167.
doi: 10.1111/j.1365-2958.2008.06399.x.
|
Cprk ocpa DNA complex . SNAP output
|
|
3ebc
|
hydrolase-DNA |
X-ray (2.55 Å) |
Little EJ, Babic AC, Horton NC |
(2008) "Early
Interrogation and Recognition of DNA Sequence by
Indirect Readout." Structure,
16, 1828-1837.
|
Structure of n141a hincii with cognate DNA . SNAP output
|
|
3ecp
|
DNA recombination-DNA |
X-ray (2.5 Å) |
Klenchin VA, Czyz A, Goryshin IY, Gradman R, Lovell
S, Rayment I, Reznikoff WS |
(2008) "Phosphate
coordination and movement of DNA in the Tn5 synaptic
complex: role of the (R)YREK motif." Nucleic
Acids Res., 36, 5855-5862. doi:
10.1093/nar/gkn577.
|
Crystal structure of tn5 transposase complexed with 5'
phosphorylated transposon end DNA . SNAP output
|
|
3eeo
|
transferase-DNA |
X-ray (1.94 Å) |
Porta JC, Christman JK, Borgstahl GEO |
"M. HhaI co-crystallized with synthetic dsDNA
containing a propane diol in place of the deoxycytidine
residue targeted for methylation." |
M. hhai co-crystallized with synthetic dsDNA containing
a propane diol in place of the deoxycytidine residue
targeted for methylation. . SNAP output
|
|
3eh8
|
hydrolase-DNA |
X-ray (2.7 Å) |
Takeuchi R, Certo M, Caprara MG, Scharenberg AM,
Stoddard BL |
(2009) "Optimization
of in vivo activity of a bifunctional homing
endonuclease and maturase reverses evolutionary
degradation." Nucleic Acids Res.,
37, 877-890. doi: 10.1093/nar/gkn1007.
|
Crystal structure of y2 i-anii variant (f13y-s111y)-DNA
complex with calcium . SNAP output
|
|
3ei1
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Scrima A, Konickova R, Czyzewski BK, Kawasaki Y,
Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP,
Thoma NH |
(2008) "Structural
basis of UV DNA-damage recognition by the DDB1-DDB2
complex." Cell(Cambridge,Mass.),
135, 1213-1223. doi: 10.1016/j.cell.2008.10.045.
|
Structure of hsddb1-drddb2 bound to a 14 bp 6-4
photoproduct containing DNA-duplex . SNAP output
|
|
3ei2
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Scrima A, Konickova R, Czyzewski BK, Kawasaki Y,
Jeffrey PD, Groisman R, Nakatani Y, Iwai S, Pavletich NP,
Thoma NH |
(2008) "Structural
basis of UV DNA-damage recognition by the DDB1-DDB2
complex." Cell(Cambridge,Mass.),
135, 1213-1223. doi: 10.1016/j.cell.2008.10.045.
|
Structure of hsddb1-drddb2 bound to a 16 bp abasic site
containing DNA-duplex . SNAP output
|
|
3epg
|
transferase-DNA |
X-ray (2.5 Å) |
Pence MG, Blans P, Zink CN, Hollis T, Fishbein JC,
Perrino FW |
(2009) "Lesion
bypass of N2-ethylguanine by human DNA polymerase
iota." J.Biol.Chem., 284,
1732-1740. doi: 10.1074/jbc.M807296200.
|
Structure of human DNA polymerase iota complexed with
n2-ethylguanine . SNAP
output
|
|
3epi
|
transferase-DNA |
X-ray (2.9 Å) |
Pence MG, Blans P, Zink CN, Hollis T, Fishbein JC,
Perrino FW |
(2009) "Lesion
bypass of N2-ethylguanine by human DNA polymerase
iota." J.Biol.Chem., 284,
1732-1740. doi: 10.1074/jbc.M807296200.
|
Structure of human DNA polymerase iota complexed with
n2-ethylguanine and incoming ttp . SNAP output
|
|
3er8
|
transcription, transferase-DNA, RNA |
X-ray (3.18 Å) |
Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL,
Gershon PD |
(2009) "Polymerase
Translocation with Respect to Single-Stranded Nucleic
Acid: Looping or Wrapping of Primer around a Poly(A)
Polymerase." Structure,
17, 680-689. doi: 10.1016/j.str.2009.03.012.
|
Crystal structure of the heterodimeric vaccinia virus
mrna polyadenylate polymerase complex with two
fragments of RNA . SNAP
output
|
|
3erc
|
transcription, transferase-DNA, RNA |
X-ray (3.21 Å) |
Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL,
Gershon PD |
(2009) "Polymerase
Translocation with Respect to Single-Stranded Nucleic
Acid: Looping or Wrapping of Primer around a Poly(A)
Polymerase." Structure,
17, 680-689. doi: 10.1016/j.str.2009.03.012.
|
Crystal structure of the heterodimeric vaccinia virus
mrna polyadenylate polymerase with three fragments of
RNA and 3'-deoxy atp . SNAP output
|
|
3ere
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Cherney LT, Cherney MM, Garen CR, Lu GJ, James
MN |
(2008) "Crystal
structure of the arginine repressor protein in complex
with the DNA operator from Mycobacterium
tuberculosis." J.Mol.Biol.,
384, 1330-1340. doi: 10.1016/j.jmb.2008.10.015.
|
Crystal structure of the arginine repressor protein
from mycobacterium tuberculosis in complex with the DNA
operator . SNAP
output
|
|
3exj
|
transcription-DNA |
X-ray (2.0 Å) |
Malecka KA, Ho WC, Marmorstein R |
(2009) "Crystal
structure of a p53 core tetramer bound to DNA."
Oncogene, 28, 325-333. doi:
10.1038/onc.2008.400.
|
Crystal structure of a p53 core tetramer bound to DNA .
SNAP output
|
|
3exl
|
transcription-DNA |
X-ray (2.2 Å) |
Malecka KA, Ho WC, Marmorstein R |
(2009) "Crystal
structure of a p53 core tetramer bound to DNA."
Oncogene, 28, 325-333. doi:
10.1038/onc.2008.400.
|
Crystal structure of a p53 core tetramer bound to DNA .
SNAP output
|
|
3ey1
|
hydrolase-DNA |
X-ray (1.6 Å) |
Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M,
Egli M |
(2009) "A
conformational transition in the structure of a
2'-thiomethyl-modified DNA visualized at high
resolution." Chem.Commun.(Camb.),
15, 2017-2019. doi: 10.1039/b822781k.
|
A conformational transition in the structure of a
2'-thiomethyl-modified DNA visualized at high
resolution . SNAP
output
|
|
3eyi
|
DNA binding protein-DNA |
X-ray (1.45 Å) |
Ha SC, Kim D, Hwang HY, Rich A, Kim YG, Kim KK |
(2008) "The
crystal structure of the second Z-DNA binding domain of
human DAI (ZBP1) in complex with Z-DNA reveals an
unusual binding mode to Z-DNA."
Proc.Natl.Acad.Sci.USA, 105,
20671-20676. doi: 10.1073/pnas.0810463106.
|
The crystal structure of the second z-DNA binding
domain of human dai (zbp1) in complex with z-DNA .
SNAP output
|
|
3eyz
|
transferase-DNA |
X-ray (2.1 Å) |
Golosov AA, Warren JJ, Beese LS, Karplus M |
(2010) "The
Mechanism of the Translocation Step in DNA Replication
by DNA Polymerase I: A Computer Simulation
Analysis." Structure, 18,
83-93. doi: 10.1016/j.str.2009.10.014.
|
Cocrystal structure of bacillus fragment DNA polymerase
i with duplex DNA (open form) . SNAP output
|
|
3ez5
|
transferase-DNA |
X-ray (1.9 Å) |
Golosov AA, Warren JJ, Beese LS, Karplus M |
(2010) "The
Mechanism of the Translocation Step in DNA Replication
by DNA Polymerase I: A Computer Simulation
Analysis." Structure, 18,
83-93. doi: 10.1016/j.str.2009.10.014.
|
Cocrystal structure of bacillus fragment DNA polymerase
i with duplex DNA , dctp, and zinc (closed form). .
SNAP output
|
|
3f21
|
hydrolase |
X-ray (2.2 Å) |
Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK |
(2009) "The
structures of non-CG-repeat Z-DNAs co-crystallized with
the Z-DNA-binding domain, hZ{alpha}ADAR1."
Nucleic Acids Res., 37,
629-637. doi: 10.1093/nar/gkn976.
|
Crystal structure of zalpha in complex with d(cacgtg) .
SNAP output
|
|
3f22
|
hydrolase |
X-ray (2.5 Å) |
Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK |
(2009) "The
structures of non-CG-repeat Z-DNAs co-crystallized with
the Z-DNA-binding domain, hZ{alpha}ADAR1."
Nucleic Acids Res., 37,
629-637. doi: 10.1093/nar/gkn976.
|
Crystal structure of zalpha in complex with d(cgtacg) .
SNAP output
|
|
3f23
|
hydrolase |
X-ray (2.7 Å) |
Ha SC, Choi J, Hwang HY, Rich A, Kim YG, Kim KK |
(2009) "The
structures of non-CG-repeat Z-DNAs co-crystallized with
the Z-DNA-binding domain, hZ{alpha}ADAR1."
Nucleic Acids Res., 37,
629-637. doi: 10.1093/nar/gkn976.
|
Crystal structure of zalpha in complex with d(cggccg) .
SNAP output
|
|
3f27
|
transcription-DNA |
X-ray (2.75 Å) |
Palasingam P, Jauch R, Ng CKL, Kolatkar PR |
(2009) "The
Structure of Sox17 Bound to DNA Reveals a Conserved
Bending Topology but Selective Protein Interaction
Platforms." J.Mol.Biol.,
388, 619-630. doi: 10.1016/j.jmb.2009.03.055.
|
Structure of sox17 bound to DNA . SNAP output
|
|
3f2b
|
transferase-DNA |
X-ray (2.39 Å) |
Evans RJ, Davies DR, Bullard JM, Christensen J, Green
LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis
TC |
(2008) "Structure
of PolC reveals unique DNA binding and fidelity
determinants." Proc.Natl.Acad.Sci.USA,
105, 20695-20700. doi: 10.1073/pnas.0809989106.
|
DNA polymerase polc from geobacillus kaustophilus
complex with DNA, dgtp, mg and zn . SNAP output
|
|
3f2c
|
transferase-DNA |
X-ray (2.5 Å) |
Evans RJ, Davies DR, Bullard JM, Christensen J, Green
LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis
TC |
(2008) "Structure
of PolC reveals unique DNA binding and fidelity
determinants." Proc.Natl.Acad.Sci.USA,
105, 20695-20700. doi: 10.1073/pnas.0809989106.
|
DNA polymerase polc from geobacillus kaustophilus
complex with DNA, dgtp and mn . SNAP output
|
|
3f2d
|
transferase-DNA |
X-ray (2.51 Å) |
Evans RJ, Davies DR, Bullard JM, Christensen J, Green
LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis
TC |
(2008) "Structure
of PolC reveals unique DNA binding and fidelity
determinants." Proc.Natl.Acad.Sci.USA,
105, 20695-20700. doi: 10.1073/pnas.0809989106.
|
DNA polymerase polc from geobacillus kaustophilus
complex with DNA, dgtp, mn and zn . SNAP output
|
|
3f73
|
nucleic acid binding protein-DNA-RNA |
X-ray (3.0 Å) |
Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel
DJ |
(2008) "Structure
of an argonaute silencing complex with a
seed-containing guide DNA and target RNA duplex."
Nature, 456, 921-926. doi:
10.1038/nature07666.
|
Alignment of guide-target seed duplex within an
argonaute silencing complex . SNAP output
|
|
3f8i
|
ligase-DNA |
X-ray (2.29 Å) |
Hashimoto H, Horton JR, Zhang X, Cheng X |
(2009) "UHRF1, a
modular multi-domain protein, regulates
replication-coupled crosstalk between DNA methylation
and histone modifications." Epigenetics,
4, 8-14.
|
Mouse uhrf1 sra domain bound with hemi-methylated cpg,
crystal structure in space group p21 . SNAP output
|
|
3f8j
|
ligase-DNA |
X-ray (1.99 Å) |
Hashimoto H, Horton JR, Zhang X, Cheng X |
(2009) "UHRF1, a
modular multi-domain protein, regulates
replication-coupled crosstalk between DNA methylation
and histone modifications." Epigenetics,
4, 8-14.
|
Mouse uhrf1 sra domain bound with hemi-methylated cpg,
crystal structure in space group c222(1) . SNAP output
|
|
3fbd
|
hydrolase-DNA |
X-ray (2.9 Å) |
Wang YT, Wright JD, Doudeva LG, Jhang HC, Lim C, Yuan
HS |
"Redesign of high-affinity nonspecific nucleases with
altered sequence preference." |
Crystal structure of the nuclease domain of cole7(d493q
mutant) in complex with an 18-bp duplex DNA . SNAP output
|
|
3fc3
|
hydrolase-DNA |
X-ray (1.75 Å) |
Sokolowska M, Czapinska H, Bochtler M |
(2009) "Crystal
structure of the beta beta alpha-Me type II restriction
endonuclease Hpy99I with target DNA." Nucleic
Acids Res., 37, 3799-3810. doi:
10.1093/nar/gkp228.
|
Crystal structure of the beta-beta-alpha-me type ii
restriction endonuclease hpy99i . SNAP output
|
|
3fd2
|
hydrolase-DNA |
X-ray (2.69 Å) |
Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ |
(2009) "Generation
of single-chain LAGLIDADG homing endonucleases from
native homodimeric precursor proteins." Nucleic
Acids Res., 37, 1650-1662. doi:
10.1093/nar/gkp004.
|
Crystal structure of mmsoi-DNA complex with calcium .
SNAP output
|
|
3fde
|
ligase |
X-ray (1.41 Å) |
Hashimoto H, Horton JR, Zhang X, Cheng X |
(2009) "UHRF1, a
modular multi-domain protein, regulates
replication-coupled crosstalk between DNA methylation
and histone modifications." Epigenetics,
4, 8-14.
|
Mouse uhrf1 sra domain bound with hemi-methylated cpg
DNA, crystal structure in space group c222(1) at 1.4 Å
resolution . SNAP
output
|
|
3fdq
|
DNA binding protein-DNA |
X-ray (1.75 Å) |
Shen A, Higgins DE, Panne D |
(2009) "Recognition
of AT-Rich DNA Binding Sites by the MogR
Repressor." Structure,
17, 769-777. doi: 10.1016/j.str.2009.02.018.
|
Recognition of at-rich DNA binding sites by the mogr
repressor . SNAP
output
|
|
3fhz
|
DNA binding protein-DNA |
X-ray (3.27 Å) |
Cherney LT, Cherney MM, Garen CR, James MN |
(2009) "The
structure of the arginine repressor from Mycobacterium
tuberculosis bound with its DNA operator and
Co-repressor, L-arginine." J.Mol.Biol.,
388, 85-97. doi: 10.1016/j.jmb.2009.02.053.
|
Crystal structure of the arginine repressor from
mycobacterium tuberculosis bound with its DNA operator
and co-repressor, l-arginine . SNAP output
|
|
3fmt
|
replication inhibitor-DNA |
X-ray (2.983 Å) |
Chung YS, Brendler T, Austin S, Guarne A |
(2009) "Structural
insights into the cooperative binding of SeqA to a
tandem GATC repeat." Nucleic Acids Res.,
37, 3143-3152. doi: 10.1093/nar/gkp151.
|
Crystal structure of seqa bound to DNA . SNAP output
|
|
3foe
|
isomerase-DNA |
X-ray (4.001 Å) |
Laponogov I, Sohi MK, Veselkov DA, Pan X-S, Sawhney
R, Thompson AW, McAuley KE, Fisher LM, Sanderson MR |
(2009) "Structural
insight into the quinolone-DNA cleavage complex of type
IIA topoisomerases." Nat.Struct.Mol.Biol.,
16, 667-669. doi: 10.1038/nsmb.1604.
|
Structural insight into the quinolone-DNA cleavage
complex of type iia topoisomerases . SNAP output
|
|
3fof
|
isomerase-DNA |
X-ray (4.0 Å) |
Laponogov I, Sohi MK, Veselkov DA, Pan X-S, Sawhney
R, Thompson AW, McAuley KE, Fisher LM, Sanderson MR |
(2009) "Structural
insight into the quinolone-DNA cleavage complex of type
IIA topoisomerases." Nat.Struct.Mol.Biol.,
16, 667-669. doi: 10.1038/nsmb.1604.
|
Structural insight into the quinolone-DNA cleavage
complex of type iia topoisomerases . SNAP output
|
|
3fsi
|
transferase-DNA |
X-ray (1.75 Å) |
Glass LS, Nguyen B, Goodwin KD, Dardonville C, Wilson
WD, Long EC, Georgiadis MM |
(2009) "Crystal
structure of a trypanocidal
4,4'-bis(imidazolinylamino)diphenylamine bound to
DNA." Biochemistry, 48,
5943-5952. doi: 10.1021/bi900204w.
|
Crystal structure of a trypanocidal
4,4'-bis(imidazolinylamino)diphenylamine bound to DNA .
SNAP output
|
|
3fyl
|
transcription-DNA |
X-ray (1.63 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:cgt complex . SNAP output
|
|
3g00
|
hydrolase-DNA |
X-ray (1.74 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Mth0212 in complex with a 9bp blunt end dsDNA at 1.7
angstrom . SNAP
output
|
|
3g0q
|
hydrolase-DNA |
X-ray (2.2 Å) |
Lee S, Verdine GL |
(2009) "Atomic
substitution reveals the structural basis for substrate
adenine recognition and removal by adenine DNA
glycosylase." Proc.Natl.Acad.Sci.Usa,
106, 18497-18502. doi: 10.1073/pnas.0902908106.
|
Crystal structure of muty bound to its inhibitor DNA .
SNAP output
|
|
3g0r
|
hydrolase-DNA |
X-ray (2.4 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Complex of mth0212 and an 8bp dsDNA with distorted ends
. SNAP output
|
|
3g2c
|
hydrolase-DNA |
X-ray (2.3 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Mth0212 in complex with a short ssDNA (cgta) . SNAP output
|
|
3g2d
|
hydrolase-DNA |
X-ray (2.3 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Complex of mth0212 and a 4 bp dsDNA with 3'-overhang .
SNAP output
|
|
3g38
|
hydrolase-DNA |
X-ray (3.04 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
The catalytically inactive mutant mth0212 (d151n) in
complex with an 8 bp dsDNA . SNAP output
|
|
3g3c
|
hydrolase-DNA |
X-ray (3.04 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Mth0212 (wt) in complex with a 6bp dsDNA containing a
single one nucleotide long 3'-overhang . SNAP output
|
|
3g3y
|
hydrolase-DNA |
X-ray (2.5 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Mth0212 in complex with ssDNA in space group p32 .
SNAP output
|
|
3g4t
|
hydrolase-DNA |
X-ray (2.64 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Mth0212 (wt) in complex with a 7bp dsDNA . SNAP output
|
|
3g6p
|
transcription-DNA |
X-ray (1.985 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:fkbp5 complex, 18bp . SNAP output
|
|
3g6q
|
transcription-DNA |
X-ray (2.26 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:fkbp5 binding site complex-9 .
SNAP output
|
|
3g6r
|
transcription-DNA |
X-ray (2.3 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:fkbp5 complex-52, 18bp . SNAP output
|
|
3g6t
|
transcription-DNA |
X-ray (1.9 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr gamma DNA-binding domain:fkbp5 16bp complex-34 .
SNAP output
|
|
3g6u
|
transcription-DNA |
X-ray (1.9 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA-binding domain:fkbp5 16bp complex-49 . SNAP output
|
|
3g6v
|
replication-DNA |
X-ray (2.2 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2009) "DNA
Synthesis across an Abasic Lesion by Human DNA
Polymerase iota." Structure,
17, 530-537. doi: 10.1016/j.str.2009.02.015.
|
DNA synthesis across an abasic lesion by human DNA
polymerase-iota . SNAP
output
|
|
3g6x
|
replication-DNA |
X-ray (2.08 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2009) "DNA
Synthesis across an Abasic Lesion by Human DNA
Polymerase iota." Structure,
17, 530-537. doi: 10.1016/j.str.2009.02.015.
|
Ternary complex of DNA polymerase iota:DNA:dgtp with an
abasic site at the templating position . SNAP output
|
|
3g6y
|
replication-DNA |
X-ray (2.1 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2009) "DNA
Synthesis across an Abasic Lesion by Human DNA
Polymerase iota." Structure,
17, 530-537. doi: 10.1016/j.str.2009.02.015.
|
Ternary complex of DNA polymerase iota:DNA:dttp with an
abasic site at the templating position . SNAP output
|
|
3g73
|
transcription-DNA |
X-ray (2.21 Å) |
Littler DR, Alvarez-Fernandez M, Stein A, Hibbert RG,
Heidebrecht T, Aloy P, Medema RH, Perrakis A |
(2010) "Structure
of the FoxM1 DNA-recognition domain bound to a promoter
sequence." Nucleic Acids Res. doi:
10.1093/nar/gkq194.
|
Structure of the foxm1 DNA binding . SNAP output
|
|
3g8u
|
transcription-DNA |
X-ray (1.9 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
DNA binding domain:gilz 16bp complex-5 . SNAP output
|
|
3g8x
|
transcription-DNA |
X-ray (2.05 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:gilz 16bp complex-65 . SNAP output
|
|
3g97
|
transcription-DNA |
X-ray (2.08 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA-binding domain:gilz 16bp complex-9 . SNAP output
|
|
3g99
|
transcription-DNA |
X-ray (1.81 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:pal complex-9 . SNAP output
|
|
3g9i
|
transcription-DNA |
X-ray (1.85 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain: pal complex-35 . SNAP output
|
|
3g9j
|
transcription-DNA |
X-ray (2.32 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:pal, 18bp complex-36 . SNAP output
|
|
3g9m
|
transcription-DNA |
X-ray (1.61 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA-binding domain:sgk 16bp complex-44 . SNAP output
|
|
3g9o
|
transcription-DNA |
X-ray (1.65 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA-binding domain:sgk 16bp complex-9 . SNAP output
|
|
3g9p
|
transcription-DNA |
X-ray (1.652 Å) |
Meijsing SH, Pufall MA, So AY, Bates DL, Chen L,
Yamamoto KR |
(2009) "DNA
binding site sequence directs glucocorticoid receptor
structure and activity." Science,
324, 407-410. doi: 10.1126/science.1164265.
|
Gr DNA binding domain:sgk 16bp complex-7 . SNAP output
|
|
3ga6
|
hydrolase-DNA |
X-ray (1.898 Å) |
Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L,
Ficner R |
(2010) "Crystal
Structure Analysis of DNA Uridine Endonuclease Mth212
Bound to DNA." J.Mol.Biol.,
399, 604-617. doi: 10.1016/j.jmb.2010.04.044.
|
Mth0212 in complex with two DNA helices . SNAP output
|
|
3gat
|
transcription-DNA |
NMR |
Tjandra N, Omichinski JG, Gronenborn AM, Clore GM,
Bax A |
(1997) "Use of
dipolar 1H-15N and 1H-13C couplings in the structure
determination of magnetically oriented macromolecules
in solution." Nat.Struct.Biol.,
4, 732-738. doi: 10.1038/nsb0997-732.
|
Solution NMR structure of the c-terminal domain of
chicken gata-1 bound to DNA, 34 structures . SNAP output
|
|
3gdx
|
transferase-DNA |
X-ray (2.2 Å) |
Upton TG, Kashemirov BA, McKenna CE, Goodman MF,
Prakash GK, Kultyshev R, Batra VK, Shock DD, Pedersen LC,
Beard WA, Wilson SH |
(2009) "Alpha,beta-difluoromethylene
deoxynucleoside 5'-triphosphates: a convenient
synthesis of useful probes for DNA polymerase beta
structure and function." Org.Lett.,
11, 1883-1886. doi: 10.1021/ol701755k.
|
DNA polymerase beta with a gapped dnd substrate and
dtmp(cf2)pp . SNAP
output
|
|
3gfi
|
transcription-DNA |
X-ray (2.1 Å) |
Kumarevel T, Tanaka T, Umehara T, Yokoyama S |
(2009) "ST1710-DNA
complex crystal structure reveals the DNA binding
mechanism of the MarR family of regulators."
Nucleic Acids Res., 37,
4723-4735. doi: 10.1093/nar/gkp496.
|
Crystal structure of st1710 complexed with its promoter
DNA . SNAP output
|
|
3gii
|
transferase-DNA |
X-ray (2.6 Å) |
Rechkoblit O, Malinina L, Cheng Y, Geacintov NE,
Broyde S, Patel DJ |
(2009) "Impact
of conformational heterogeneity of OxoG lesions and
their pairing partners on bypass fidelity by Y family
polymerases." Structure,
17, 725-736. doi: 10.1016/j.str.2009.03.011.
|
Dpo4 extension ternary complex with disordered a
opposite an oxog in anti conformation . SNAP output
|
|
3gij
|
transferase-DNA |
X-ray (2.4 Å) |
Rechkoblit O, Malinina L, Cheng Y, Geacintov NE,
Broyde S, Patel DJ |
(2009) "Impact
of conformational heterogeneity of OxoG lesions and
their pairing partners on bypass fidelity by Y family
polymerases." Structure,
17, 725-736. doi: 10.1016/j.str.2009.03.011.
|
Dpo4 extension ternary complex with oxog(syn)-a(anti)
and oxog(anti)-a(syn) pairs . SNAP output
|
|
3gik
|
transferase-DNA |
X-ray (2.9 Å) |
Rechkoblit O, Malinina L, Cheng Y, Geacintov NE,
Broyde S, Patel DJ |
(2009) "Impact
of conformational heterogeneity of OxoG lesions and
their pairing partners on bypass fidelity by Y family
polymerases." Structure,
17, 725-736. doi: 10.1016/j.str.2009.03.011.
|
Dpo4 extension ternary complex with the
oxog(anti)-c(anti) pair . SNAP output
|
|
3gil
|
transferase-DNA |
X-ray (2.71 Å) |
Rechkoblit O, Malinina L, Cheng Y, Geacintov NE,
Broyde S, Patel DJ |
(2009) "Impact
of conformational heterogeneity of OxoG lesions and
their pairing partners on bypass fidelity by Y family
polymerases." Structure,
17, 725-736. doi: 10.1016/j.str.2009.03.011.
|
Dpo4 extension ternary complex with oxog(anti)-t(anti)
pair . SNAP output
|
|
3gim
|
transferase-DNA |
X-ray (2.7 Å) |
Rechkoblit O, Malinina L, Cheng Y, Geacintov NE,
Broyde S, Patel DJ |
(2009) "Impact
of conformational heterogeneity of OxoG lesions and
their pairing partners on bypass fidelity by Y family
polymerases." Structure,
17, 725-736. doi: 10.1016/j.str.2009.03.011.
|
Dpo4 extension ternary complex with oxog(anti)-g(syn)
pair . SNAP output
|
|
3glf
|
transferase-DNA |
X-ray (3.388 Å) |
Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ,
Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M,
Kuriyan J |
(2009) "The
mechanism of ATP-dependent primer-template recognition
by a clamp loader complex."
Cell(Cambridge,Mass.), 137,
659-671. doi: 10.1016/j.cell.2009.03.044.
|
Crystal structure of the ecoli clamp loader bound to
primer-template DNA . SNAP output
|
|
3glg
|
transferase-DNA |
X-ray (3.25 Å) |
Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ,
Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M,
Kuriyan J |
(2009) "The
mechanism of ATP-dependent primer-template recognition
by a clamp loader complex."
Cell(Cambridge,Mass.), 137,
659-671. doi: 10.1016/j.cell.2009.03.044.
|
Crystal structure of a mutant (gammat157a) e. coli
clamp loader bound to primer-template DNA . SNAP output
|
|
3gli
|
transferase-DNA |
X-ray (3.5 Å) |
Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ,
Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M,
Kuriyan J |
(2009) "The
mechanism of ATP-dependent primer-template recognition
by a clamp loader complex."
Cell(Cambridge,Mass.), 137,
659-671. doi: 10.1016/j.cell.2009.03.044.
|
Crystal structure of the e. coli clamp loader bound to
primer-template DNA and psi peptide . SNAP output
|
|
3gna
|
recombination |
X-ray (2.4 Å) |
Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S,
Steitz TA, Schatz DG |
(2009) "Structure
of the RAG1 nonamer binding domain with DNA reveals a
dimer that mediates DNA synapsis."
Nat.Struct.Mol.Biol., 16,
499-508. doi: 10.1038/nsmb.1593.
|
Crystal structure of the rag1 nonamer-binding domain
with DNA . SNAP
output
|
|
3gnb
|
recombination |
X-ray (3.0 Å) |
Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S,
Steitz TA, Schatz DG |
(2009) "Structure
of the RAG1 nonamer binding domain with DNA reveals a
dimer that mediates DNA synapsis."
Nat.Struct.Mol.Biol., 16,
499-508. doi: 10.1038/nsmb.1593.
|
Crystal structure of the rag1 nonamer-binding domain
with DNA . SNAP
output
|
|
3go3
|
DNA-antibiotic |
X-ray (1.1 Å) |
Pfoh R, Cuesta-Seijo JA, Sheldrick GM |
(2009) "Interaction
of an Echinomycin-DNA Complex with Manganese Ion."
Acta Crystallogr.,Sect.F, 65,
660. doi: 10.1107/S1744309109019654.
|
Interactions of an echinomycin-DNA complex with
manganese(ii) ions . SNAP output
|
|
3go8
|
lyase-DNA |
X-ray (1.89 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Mutm encountering an intrahelical 8-oxoguanine (oxog)
lesion in ec3-loop deletion complex . SNAP output
|
|
3gox
|
hydrolase-DNA |
X-ray (1.5 Å) |
Sokolowska M, Czapinska H, Bochtler M |
(2009) "Crystal
structure of the beta beta alpha-Me type II restriction
endonuclease Hpy99I with target DNA." Nucleic
Acids Res., 37, 3799-3810. doi:
10.1093/nar/gkp228.
|
Crystal structure of the beta-beta-alpha-me type ii
restriction endonuclease hpy99i in the absence of edta
. SNAP output
|
|
3gp1
|
hydrolase-DNA |
X-ray (2.05 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Mutm encountering an intrahelical 8-oxoguanine (oxog)
lesion in ec3-v222p complex . SNAP output
|
|
3gp8
|
hydrolase-DNA |
X-ray (2.5 Å) |
Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley
DB |
(2009) "Mechanistic
basis of 5'-3' translocation in SF1B helicases."
Cell(Cambridge,Mass.), 137,
849-859. doi: 10.1016/j.cell.2009.03.036.
|
Crystal structure of the binary complex of recd2 with
DNA . SNAP output
|
|
3gpl
|
hydrolase-DNA |
X-ray (2.5 Å) |
Saikrishnan K, Powell B, Cook NJ, Webb MR, Wigley
DB |
(2009) "Mechanistic
basis of 5'-3' translocation in SF1B helicases."
Cell(Cambridge,Mass.), 137,
849-859. doi: 10.1016/j.cell.2009.03.036.
|
Crystal structure of the ternary complex of recd2 with
DNA and adpnp . SNAP
output
|
|
3gpp
|
lyase-DNA |
X-ray (2.15 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Mutm encountering an intrahelical 8-oxoguanine (oxog)
lesion in ec3-t224p complex . SNAP output
|
|
3gpu
|
lyase-DNA |
X-ray (1.62 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Mutm encountering an intrahelical 8-oxoguanine (oxog)
lesion in ec4-loop deletion complex . SNAP output
|
|
3gpx
|
lyase-DNA |
X-ray (1.78 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Sequence-matched mutm interrogation complex 4 (ic4) .
SNAP output
|
|
3gpy
|
lyase-DNA |
X-ray (1.85 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Sequence-matched mutm lesion recognition complex 3
(lrc3) . SNAP output
|
|
3gq3
|
lyase-DNA |
X-ray (1.83 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Mutm encountering an intrahelical 8-oxoguanine (oxog)
lesion in ec5-loop deletion complex . SNAP output
|
|
3gq4
|
lyase-DNA |
X-ray (1.7 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Sequence-matched mutm lesion recognition complex 5
(lrc5) . SNAP output
|
|
3gq5
|
lyase-DNA |
X-ray (1.9 Å) |
Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S,
Karplus M, Verdine GL |
(2009) "Encounter
and extrusion of an intrahelical lesion by a DNA repair
enzyme." Nature, 462,
762-766. doi: 10.1038/nature08561.
|
Sequence-matched mutm interrogation complex 5 (ic5) .
SNAP output
|
|
3gqc
|
transferase-DNA |
X-ray (2.5 Å) |
Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2009) "Structure
of the human Rev1-DNA-dNTP ternary complex."
J.Mol.Biol., 390, 699-709.
doi: 10.1016/j.jmb.2009.05.026.
|
Structure of human rev1-DNA-dntp ternary complex .
SNAP output
|
|
3gtg
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.78 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex with 12mer RNA .
SNAP output
|
|
3gtj
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.42 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex with 13mer RNA .
SNAP output
|
|
3gtk
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.8 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex with 18mer RNA .
SNAP output
|
|
3gtl
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.38 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex with 13mer with
g<>u mismatch . SNAP output
|
|
3gtm
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.8 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Co-complex of backtracked RNA polymerase ii with tfiis
. SNAP output
|
|
3gto
|
transcription, transferase-DNA-RNA hybrid |
X-ray (4.0 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex with 15mer RNA .
SNAP output
|
|
3gtp
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.9 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex with 24mer RNA .
SNAP output
|
|
3gtq
|
transcription, transferase-DNA-RNA hybrid |
X-ray (3.8 Å) |
Wang D, Bushnell DA, Huang X, Westover KD, Levitt M,
Kornberg RD |
(2009) "Structural
basis of transcription: backtracked RNA polymerase II
at 3.4 angstrom resolution." Science,
324, 1203-1206. doi: 10.1126/science.1168729.
|
Backtracked RNA polymerase ii complex induced by damage
. SNAP output
|
|
3gut
|
transcription-DNA |
X-ray (3.59 Å) |
Stroud JC, Oltman A, Han A, Bates DL, Chen L |
(2009) "Structural
basis of HIV-1 activation by NF-kappaB--a higher-order
complex of p50:RelA bound to the HIV-1 LTR."
J.Mol.Biol., 393, 98-112.
doi: 10.1016/j.jmb.2009.08.023.
|
Crystal structure of a higher-order complex of p50:rela
bound to the hiv-1 ltr . SNAP output
|
|
3gv5
|
transferase-DNA |
X-ray (2.0 Å) |
Kirouac KN, Ling H |
(2009) "Structural
basis of error-prone replication and stalling at a
thymine base by human DNA polymerase iota."
Embo J., 28, 1644-1654. doi:
10.1038/emboj.2009.122.
|
Human DNA polymerase iota in complex with t template
DNA and incoming ddadp . SNAP output
|
|
3gv7
|
transferase-DNA |
X-ray (2.2 Å) |
Kirouac KN, Ling H |
(2009) "Structural
basis of error-prone replication and stalling at a
thymine base by human DNA polymerase iota."
Embo J., 28, 1644-1654. doi:
10.1038/emboj.2009.122.
|
Human DNA polymerase iota in complex with t template
DNA and incoming dttp . SNAP output
|
|
3gv8
|
transferase-DNA |
X-ray (2.0 Å) |
Kirouac KN, Ling H |
(2009) "Structural
basis of error-prone replication and stalling at a
thymine base by human DNA polymerase iota."
Embo J., 28, 1644-1654. doi:
10.1038/emboj.2009.122.
|
Human DNA polymerase iota in complex with t template
DNA and incoming dgtp . SNAP output
|
|
3gx4
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili
M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ,
Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF,
Millington C, Arvai AS, Kroeger MD, Peterson LA, Williams
DM, Fried MG, Margison GP, Pegg AE, Tainer JA |
(2009) "Flipping
of alkylated DNA damage bridges base and nucleotide
excision repair." Nature,
459, 808-813. doi: 10.1038/nature08076.
|
Crystal structure analysis of s. pombe atl in complex
with DNA . SNAP
output
|
|
3gxq
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Ni L, Jensen SO, Ky Tonthat N, Berg T, Kwong SM, Guan
FH, Brown MH, Skurray RA, Firth N, Schumacher MA |
(2009) "The
Staphylococcus aureus pSK41 plasmid-encoded ArtA
protein is a master regulator of plasmid transmission
genes and contains a RHH motif used in alternate
DNA-binding modes." Nucleic Acids Res.,
37, 6970-6983. doi: 10.1093/nar/gkp756.
|
Structure of arta and DNA complex . SNAP output
|
|
3gyh
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili
M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ,
Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF,
Millington C, Arvai AS, Kroeger MD, Peterson LA, Williams
DM, Fried MG, Margison GP, Pegg AE, Tainer JA |
(2009) "Flipping
of alkylated DNA damage bridges base and nucleotide
excision repair." Nature,
459, 808-813. doi: 10.1038/nature08076.
|
Crystal structure analysis of s. pombe atl in complex
with damaged DNA containing pob . SNAP output
|
|
3gz6
|
DNA binding protein-DNA |
X-ray (2.901 Å) |
Huang N, De Ingeniis J, Galeazzi L, Mancini C,
Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA,
Raffaelli N, Zhang H |
(2009) "Structure
and function of an ADP-ribose-dependent transcriptional
regulator of NAD metabolism." Structure,
17, 939-951. doi: 10.1016/j.str.2009.05.012.
|
Crystal structure of shewanella oneidensis nrtr
complexed with a 27mer DNA . SNAP output
|
|
3h0d
|
transcription-DNA |
X-ray (2.4 Å) |
Fuhrmann J, Schmidt A, Spiess S, Lehner A, Turgay K,
Mechtler K, Charpentier E, Clausen T |
(2009) "McsB is
a protein arginine kinase that phosphorylates and
inhibits the heat-shock regulator CtsR."
Science, 324, 1323-1327. doi:
10.1126/science.1170088.
|
Crystal structure of ctsr in complex with a 26bp DNA
duplex . SNAP output
|
|
3h15
|
replication-DNA |
X-ray (2.72 Å) |
Warren EM, Huang H, Fanning E, Chazin WJ, Eichman
BF |
(2009) "Physical
Interactions between Mcm10, DNA, and DNA Polymerase
{alpha}." J.Biol.Chem.,
284, 24662-24672. doi: 10.1074/jbc.M109.020438.
|
Crystal structure of replication initiation factor
mcm10-id bound to ssDNA . SNAP output
|
|
3h25
|
replication-DNA |
X-ray (2.7 Å) |
Geibel S, Banchenko S, Engel M, Lanka E, Saenger
W |
(2009) "Structure
and function of primase RepB' encoded by
broad-host-range plasmid RSF1010 that replicates
exclusively in leading-strand mode."
Proc.Natl.Acad.Sci.USA, 106,
7810-7815. doi: 10.1073/pnas.0902910106.
|
Crystal structure of the catalytic domain of primase
repb' in complex with initiator DNA . SNAP output
|
|
3h3v
|
transferase-DNA-RNA |
X-ray (4.0 Å) |
Dengl S, Cramer P |
(2009) "Torpedo
Nuclease Rat1 Is Insufficient to Terminate RNA
Polymerase II in Vitro." J.Biol.Chem.,
284, 21270-21279. doi: 10.1074/jbc.M109.013847.
|
Yeast rnap ii containing poly(a)-signal sequence in the
active site . SNAP
output
|
|
3h40
|
replication-DNA |
X-ray (2.3 Å) |
Jain R, Nair DT, Johnson RE, Prakash L, Prakash S,
Aggarwal AK |
(2009) "Replication
across template T/U by human DNA polymerase-iota."
Structure, 17, 974-980. doi:
10.1016/j.str.2009.04.011.
|
Binary complex of human DNA polymerase iota with
template u-t . SNAP
output
|
|
3h4b
|
replication-DNA |
X-ray (2.85 Å) |
Jain R, Nair DT, Johnson RE, Prakash L, Prakash S,
Aggarwal AK |
(2009) "Replication
across template T/U by human DNA polymerase-iota."
Structure, 17, 974-980. doi:
10.1016/j.str.2009.04.011.
|
Ternary complex of human DNA polymerase iota with
template u-t and incoming datp . SNAP output
|
|
3h4d
|
replication-DNA |
X-ray (2.2 Å) |
Jain R, Nair DT, Johnson RE, Prakash L, Prakash S,
Aggarwal AK |
(2009) "Replication
across template T/U by human DNA polymerase-iota."
Structure, 17, 974-980. doi:
10.1016/j.str.2009.04.011.
|
Ternary complex of human DNA polymerase iota with
template u-t and incoming dgtp . SNAP output
|
|
3h8o
|
oxidoreductase-DNA |
X-ray (2.0 Å) |
Lu L, Yi C, Jian X, Zheng G, He C |
(2010) "Structure
determination of DNA methylation lesions N1-meA and
N3-meC in duplex DNA using a cross-linked protein-DNA
system." Nucleic Acids Res.,
38, 4415-4425. doi: 10.1093/nar/gkq129.
|
Structure determination of DNA methylation lesions
n1-mea and n3-mec in duplex DNA using a cross-linked
host-guest system . SNAP
output
|
|
3h8r
|
oxidoreductase-DNA |
X-ray (1.77 Å) |
Lu L, Yi C, Jian X, Zheng G, He C |
(2010) "Structure
determination of DNA methylation lesions N1-meA and
N3-meC in duplex DNA using a cross-linked protein-DNA
system." Nucleic Acids Res.,
38, 4415-4425. doi: 10.1093/nar/gkq129.
|
Structure determination of DNA methylation lesions
n1-mea and n3-mec in duplex DNA using a cross-linked
host-guest system . SNAP
output
|
|
3h8x
|
oxidoreductase-DNA |
X-ray (1.95 Å) |
Lu L, Yi C, Jian X, Zheng G, He C |
(2010) "Structure
determination of DNA methylation lesions N1-meA and
N3-meC in duplex DNA using a cross-linked protein-DNA
system." Nucleic Acids Res.,
38, 4415-4425. doi: 10.1093/nar/gkq129.
|
Structure determination of DNA methylation lesions
n1-mea and n3-mec in duplex DNA using a cross-linked
host-guest system . SNAP
output
|
|
3hax
|
isomerase-biosynthetic protein-RNA |
X-ray (2.11 Å) |
Duan J, Li L, Lu J, Wang W, Ye K |
(2009) "Structural
mechanism of substrate RNA recruitment in H/ACA
RNA-guided pseudouridine synthase."
Mol.Cell, 34, 427-439. doi:
10.1016/j.molcel.2009.05.005.
|
Crystal structure of a substrate-bound gar1-minus h-aca
rnp from pyrococcus furiosus . SNAP output
|
|
3hdd
|
transcription-DNA |
X-ray (2.2 Å) |
Fraenkel E, Rould MA, Chambers KA, Pabo CO |
(1998) "Engrailed
homeodomain-DNA complex at 2.2 A resolution: a detailed
view of the interface and comparison with other
engrailed structures." J.Mol.Biol.,
284, 351-361. doi: 10.1006/jmbi.1998.2147.
|
Engrailed homeodomain DNA complex . SNAP output
|
|
3hjf
|
nucleic acid binding protein-DNA-RNA |
X-ray (3.056 Å) |
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl
T, Patel DJ |
(2009) "Nucleation,
propagation and cleavage of target RNAs in Ago
silencing complexes." Nature,
461, 754-761. doi: 10.1038/nature08434.
|
Crystal structure of t. thermophilus argonaute e546
mutant protein complexed with DNA guide strand and
15-nt RNA target strand . SNAP output
|
|
3hk2
|
nucleic acid binding protein-DNA-RNA |
X-ray (2.8 Å) |
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl
T, Patel DJ |
(2009) "Nucleation,
propagation and cleavage of target RNAs in Ago
silencing complexes." Nature,
461, 754-761. doi: 10.1038/nature08434.
|
Crystal structure of t. thermophilus argonaute n478
mutant protein complexed with DNA guide strand and
19-nt RNA target strand . SNAP output
|
|
3hm9
|
nucleic acid binding protein-DNA-RNA |
X-ray (3.3 Å) |
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl
T, Patel DJ |
(2009) "Nucleation,
propagation and cleavage of target RNAs in Ago
silencing complexes." Nature,
461, 754-761. doi: 10.1038/nature08434.
|
Crystal structure of t. thermophilus argonaute
complexed with DNA guide strand and 19-nt RNA target
strand . SNAP output
|
|
3ho1
|
nucleic acid binding protein-DNA-RNA |
X-ray (2.6 Å) |
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl
T, Patel DJ |
(2009) "Nucleation,
propagation and cleavage of target RNAs in Ago
silencing complexes." Nature,
461, 754-761. doi: 10.1038/nature08434.
|
Crystal structure of t. thermophilus argonaute n546
mutant protein complexed with DNA guide strand and
12-nt RNA target strand . SNAP output
|
|
3hos
|
transferase, DNA binding protein-DNA |
X-ray (3.5 Å) |
Richardson JM, Colloms SD, Finnegan DJ, Walkinshaw
MD |
(2009) "Molecular
architecture of the Mos1 paired-end complex: the
structural basis of DNA transposition in a
eukaryote." Cell(Cambridge,Mass.),
138, 1096-1108. doi: 10.1016/j.cell.2009.07.012.
|
Crystal structure of the mariner mos1 paired end
complex with mg . SNAP
output
|
|
3hot
|
transferase, DNA binding protein-DNA |
X-ray (3.25 Å) |
Richardson JM, Colloms SD, Finnegan DJ, Walkinshaw
MD |
(2009) "Molecular
architecture of the Mos1 paired-end complex: the
structural basis of DNA transposition in a
eukaryote." Cell(Cambridge,Mass.),
138, 1096-1108. doi: 10.1016/j.cell.2009.07.012.
|
Crystal structure of the mos1 mariner paired end
complex with mn . SNAP
output
|
|
3hou
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.2 Å) |
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl
S, Lehmann E, Vassylyev D, Cramer P |
(2009) "Structural
basis of transcription: mismatch-specific fidelity
mechanisms and paused RNA polymerase II with frayed
RNA." Mol.Cell, 34,
710-721. doi: 10.1016/j.molcel.2009.06.002.
|
Complete RNA polymerase ii elongation complex i with a
t-u mismatch . SNAP
output
|
|
3hov
|
transcription, transferase-DNA-RNA |
X-ray (3.5 Å) |
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl
S, Lehmann E, Vassylyev D, Cramer P |
(2009) "Structural
basis of transcription: mismatch-specific fidelity
mechanisms and paused RNA polymerase II with frayed
RNA." Mol.Cell, 34,
710-721. doi: 10.1016/j.molcel.2009.06.002.
|
Complete RNA polymerase ii elongation complex ii .
SNAP output
|
|
3how
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.6 Å) |
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl
S, Lehmann E, Vassylyev D, Cramer P |
(2009) "Structural
basis of transcription: mismatch-specific fidelity
mechanisms and paused RNA polymerase II with frayed
RNA." Mol.Cell, 34,
710-721. doi: 10.1016/j.molcel.2009.06.002.
|
Complete RNA polymerase ii elongation complex iii with
a t-u mismatch and a frayed RNA 3'-uridine . SNAP output
|
|
3hox
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.65 Å) |
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl
S, Lehmann E, Vassylyev D, Cramer P |
(2009) "Structural
basis of transcription: mismatch-specific fidelity
mechanisms and paused RNA polymerase II with frayed
RNA." Mol.Cell, 34,
710-721. doi: 10.1016/j.molcel.2009.06.002.
|
Complete RNA polymerase ii elongation complex v .
SNAP output
|
|
3hoy
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.4 Å) |
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl
S, Lehmann E, Vassylyev D, Cramer P |
(2009) "Structural
basis of transcription: mismatch-specific fidelity
mechanisms and paused RNA polymerase II with frayed
RNA." Mol.Cell, 34,
710-721. doi: 10.1016/j.molcel.2009.06.002.
|
Complete RNA polymerase ii elongation complex vi .
SNAP output
|
|
3hoz
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.65 Å) |
Sydow JF, Brueckner F, Cheung ACM, Damsma GE, Dengl
S, Lehmann E, Vassylyev D, Cramer P |
(2009) "Structural
basis of transcription: mismatch-specific fidelity
mechanisms and paused RNA polymerase II with frayed
RNA." Mol.Cell, 34,
710-721. doi: 10.1016/j.molcel.2009.06.002.
|
Complete RNA polymerase ii elongation complex iv with a
t-u mismatch and a frayed RNA 3'-guanine . SNAP output
|
|
3hp6
|
transferase-DNA |
X-ray (1.81 Å) |
Wu EY, Beese LS |
(2011) "The
structure of a high fidelity DNA polymerase bound to a
mismatched nucleotide reveals an "ajar" intermediate
conformation in the nucleotide selection
mechanism." J.Biol.Chem.,
286, 19758-19767. doi: 10.1074/jbc.M110.191130.
|
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus f710y mutant bound to g:t
mismatch . SNAP
output
|
|
3hpo
|
transferase-DNA |
X-ray (1.75 Å) |
Wu EY, Beese LS |
(2011) "The
structure of a high fidelity DNA polymerase bound to a
mismatched nucleotide reveals an "ajar" intermediate
conformation in the nucleotide selection
mechanism." J.Biol.Chem.,
286, 19758-19767. doi: 10.1074/jbc.M110.191130.
|
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus y714s mutant bound to g:t
mismatch . SNAP
output
|
|
3hqf
|
hydrolase-DNA |
X-ray (2.51 Å) |
Golovenko D, Manakova E, Tamulaitiene G, Grazulis S,
Siksnys V |
(2009) "Structural
mechanisms for the 5'-CCWGG sequence recognition by the
N- and C-terminal domains of EcoRII." Nucleic
Acids Res., 37, 6613-6624. doi:
10.1093/nar/gkp699.
|
Crystal structure of restriction endonuclease ecorii
n-terminal effector-binding domain in complex with
cognate DNA . SNAP
output
|
|
3hqg
|
hydrolase-DNA |
X-ray (2.6 Å) |
Golovenko D, Manakova E, Tamulaitiene G, Grazulis S,
Siksnys V |
(2009) "Structural
mechanisms for the 5'-CCWGG sequence recognition by the
N- and C-terminal domains of EcoRII." Nucleic
Acids Res., 37, 6613-6624. doi:
10.1093/nar/gkp699.
|
Crystal structure of restriction endonuclease ecorii
catalytic c-terminal domain in complex with cognate DNA
. SNAP output
|
|
3ht3
|
transferase-DNA |
X-ray (1.7 Å) |
Wu EY, Beese LS |
(2011) "The
structure of a high fidelity DNA polymerase bound to a
mismatched nucleotide reveals an "ajar" intermediate
conformation in the nucleotide selection
mechanism." J.Biol.Chem.,
286, 19758-19767. doi: 10.1074/jbc.M110.191130.
|
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus v713p mutant bound to
g:dctp . SNAP output
|
|
3hts
|
transcription-DNA |
X-ray (1.75 Å) |
Littlefield O, Nelson HC |
(1999) "A new
use for the 'wing' of the 'winged' helix-turn-helix
motif in the HSF-DNA cocrystal."
Nat.Struct.Biol., 6, 464-470.
doi: 10.1038/8269.
|
Heat shock transcription factor-DNA complex . SNAP output
|
|
3hvr
|
nucleic acid binding protein-DNA-RNA |
X-ray (3.211 Å) |
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl
T, Patel DJ |
(2009) "Nucleation,
propagation and cleavage of target RNAs in Ago
silencing complexes." Nature,
461, 754-761. doi: 10.1038/nature08434.
|
Crystal structure of t. thermophilus argonaute
complexed with DNA guide strand and 19-nt RNA target
strand with two mg2+ at the cleavage site . SNAP output
|
|
3hw8
|
transferase-DNA |
X-ray (1.95 Å) |
Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM,
Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel
TA |
"Scrunching Durning DNA Repair Synthesis." |
Ternary complex of DNA polymerase lambda of a two
nucleotide gapped DNA substrate with a c in the scrunch
site . SNAP output
|
|
3hwt
|
transferase-DNA |
X-ray (1.95 Å) |
Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM,
Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel
TA |
"Scrunching during DNA repair synthesis." |
Ternary complex of DNA polymerase lambda bound to a two
nucleotide gapped DNA substrate with a scrunched da .
SNAP output
|
|
3hx0
|
transferase-DNA |
X-ray (3.0 Å) |
Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM,
Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel
TA |
"Scrunching During DNA Repair Synthesis." |
Ternary complex of l277a, h511a, r514 mutant pol lambda
bound to a 2 nucleotide gapped DNA substrate with a
scrunched da . SNAP
output
|
|
3hxm
|
nucleic acid binding protein-DNA-RNA |
X-ray (3.1 Å) |
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl
T, Patel DJ |
(2009) "Nucleation,
propagation and cleavage of target RNAs in Ago
silencing complexes." Nature,
461, 754-761. doi: 10.1038/nature08434.
|
Structure of an argonaute complexed with guide DNA and
target RNA duplex containing two mismatches. . SNAP output
|
|
3hxo
|
blood clotting-blood clotting regulator |
X-ray (2.4 Å) |
Huang RH, Fremont DH, Diener JL, Schaub RG, Sadler
JE |
(2009) "A
structural explanation for the antithrombotic activity
of ARC1172, a DNA aptamer that binds von Willebrand
factor domain A1." Structure,
17, 1476-1484. doi: 10.1016/j.str.2009.09.011.
|
Crystal structure of von willebrand factor (vwf) a1
domain in complex with DNA aptamer arc1172, an
inhibitor of vwf-platelet binding . SNAP output
|
|
3hxq
|
blood clotting-blood clotting regulator |
X-ray (2.694 Å) |
Huang RH, Fremont DH, Diener JL, Schaub RG, Sadler
JE |
(2009) "A
structural explanation for the antithrombotic activity
of ARC1172, a DNA aptamer that binds von Willebrand
factor domain A1." Structure,
17, 1476-1484. doi: 10.1016/j.str.2009.09.011.
|
Crystal structure of von willebrand factor (vwf) a1
domain in complex with DNA aptamer arc1172, an
inhibitor of vwf-platelet binding . SNAP output
|
|
3hzi
|
transcription-DNA |
X-ray (2.98 Å) |
Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K,
Brennan RG |
(2009) "Molecular
mechanisms of HipA-mediated multidrug tolerance and its
neutralization by HipB." Science,
323, 396-401. doi: 10.1126/science.1163806.
|
Structure of mdt protein . SNAP output
|
|
3i0w
|
hydrolase,lyase-DNA |
X-ray (1.73 Å) |
Faucher F, Wallace SS, Doublie S |
(2009) "Structural
basis for the lack of opposite base specificity of
Clostridium acetobutylicum 8-oxoguanine DNA
glycosylase." Dna Repair,
8, 1283-1289. doi: 10.1016/j.dnarep.2009.08.002.
|
Crystal structure of clostridium acetobutylicum
8-oxoguanine glycosylase-lyase in complex with dsDNA
containing cytosine opposite to 8-oxog . SNAP output
|
|
3i0x
|
hydrolase,lyase-DNA |
X-ray (1.8 Å) |
Faucher F, Wallace SS, Doublie S |
(2009) "Structural
basis for the lack of opposite base specificity of
Clostridium acetobutylicum 8-oxoguanine DNA
glycosylase." Dna Repair,
8, 1283-1289. doi: 10.1016/j.dnarep.2009.08.002.
|
Crystal structure of clostridium acetobutylicum
8-oxoguanine glycosylase-lyase in complex with dsDNA
containing adenine opposite to 8-oxog . SNAP output
|
|
3i2o
|
oxidoreductase-DNA |
X-ray (1.7 Å) |
Yu B, Hunt JF |
(2009) "Enzymological
and structural studies of the mechanism of promiscuous
substrate recognition by the oxidative DNA repair
enzyme AlkB." Proc.Natl.Acad.Sci.USA,
106, 14315-14320. doi: 10.1073/pnas.0812938106.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate and methylated trinucleotide t-mea-t .
SNAP output
|
|
3i3m
|
oxidoreductase-DNA |
X-ray (1.5 Å) |
Yu B, Hunt JF |
(2009) "Enzymological
and structural studies of the mechanism of promiscuous
substrate recognition by the oxidative DNA repair
enzyme AlkB." Proc.Natl.Acad.Sci.USA,
106, 14315-14320. doi: 10.1073/pnas.0812938106.
|
Crystal structure of alkb in complex with mn(ii),
2-oxoglutarate and methylated trinucleotide t-mec-t .
SNAP output
|
|
3i49
|
oxidoreductase-DNA |
X-ray (1.6 Å) |
Yu B, Hunt JF |
(2009) "Enzymological
and structural studies of the mechanism of promiscuous
substrate recognition by the oxidative DNA repair
enzyme AlkB." Proc.Natl.Acad.Sci.USA,
106, 14315-14320. doi: 10.1073/pnas.0812938106.
|
Crystal structure of alkb in complex with fe(ii),
2-oxoglutarate and methylated trinucleotide t-mec-t .
SNAP output
|
|
3i4m
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.7 Å) |
Damsma GE, Cramer P |
(2009) "Molecular
basis of transcriptional mutagenesis at
8-oxoguanine." J.Biol.Chem.,
284, 31658-31663. doi: 10.1074/jbc.M109.022764.
|
8-oxoguanine containing RNA polymerase ii elongation
complex d . SNAP
output
|
|
3i4n
|
transcription,transferase-DNA-RNA hybrid |
X-ray (3.9 Å) |
Damsma GE, Cramer P |
(2009) "Molecular
basis of transcriptional mutagenesis at
8-oxoguanine." J.Biol.Chem.,
284, 31658-31663. doi: 10.1074/jbc.M109.022764.
|
8-oxoguanine containing RNA polymerase ii elongation
complex e . SNAP
output
|
|
3i8d
|
hydrolase-DNA |
X-ray (1.61 Å) |
Pallan PS, Egli M |
(2009) "Pairing
geometry of the hydrophobic thymine analogue
2,4-difluorotoluene in duplex DNA as analyzed by X-ray
crystallography." J.Am.Chem.Soc.,
131, 12548-12549. doi: 10.1021/ja905739j.
|
The pairing geometry of the hydrophobic thymine analog
2,4-difluorotoluene in duplex DNA as analyzed by x-ray
crystallography . SNAP
output
|
|
3iag
|
transcription-DNA |
X-ray (2.0 Å) |
Friedmann DR, Kovall RA |
(2010) "Thermodynamic
and structural insights into CSL-DNA complexes."
Protein Sci., 19, 34-46. doi:
10.1002/pro.280.
|
Csl (rbp-jk) bound to hes-1 nonconsensus site .
SNAP output
|
|
3iay
|
transferase-DNA |
X-ray (2.0 Å) |
Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2009) "Structural
basis of high-fidelity DNA synthesis by yeast DNA
polymerase delta." Nat.Struct.Mol.Biol.,
16, 979-986. doi: 10.1038/nsmb.1663.
|
Ternary complex of DNA polymerase delta . SNAP output
|
|
3igc
|
isomerase-DNA |
X-ray (2.1 Å) |
Perry K, Hwang Y, Bushman FD, Van Duyne GD |
(2010) "Insights
from the Structure of a Smallpox Virus
Topoisomerase-DNA Transition State Mimic."
Structure, 18, 127-137. doi:
10.1016/j.str.2009.10.020.
|
Smallpox virus topoisomerase-DNA transition state .
SNAP output
|
|
3igk
|
transcription-DNA |
X-ray (1.7 Å) |
Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich
D, Honig B, Shakked Z |
(2010) "Diversity
in DNA recognition by p53 revealed by crystal
structures with Hoogsteen base pairs."
Nat.Struct.Mol.Biol., 17,
423-429. doi: 10.1038/nsmb.1800.
|
Diversity in DNA recognition by p53 revealed by crystal
structures with hoogsteen base pairs (p53-DNA complex
2) . SNAP output
|
|
3igl
|
transcription-DNA |
X-ray (1.8 Å) |
Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich
D, Honig B, Shakked Z |
(2010) "Diversity
in DNA recognition by p53 revealed by crystal
structures with Hoogsteen base pairs."
Nat.Struct.Mol.Biol., 17,
423-429. doi: 10.1038/nsmb.1800.
|
Diversity in DNA recognition by p53 revealed by crystal
structures with hoogsteen base pairs (p53-DNA complex
1) . SNAP output
|
|
3igm
|
transcription-DNA |
X-ray (2.2 Å) |
Lindner SE, De Silva EK, Keck JL, Llinas M |
(2010) "Structural
Determinants of DNA Binding by a P. falciparum ApiAP2
Transcriptional Regulator." J.Mol.Biol.,
395, 558-567. doi: 10.1016/j.jmb.2009.11.004.
|
A 2.2a crystal structure of the ap2 domain of pf14_0633
from p. falciparum, bound as a domain-swapped dimer to
its cognate DNA . SNAP
output
|
|
3ih7
|
(hydrolase,lyase)-DNA |
X-ray (3.1 Å) |
Crenshaw CM, Oo KS, Kutchukian PS, Verdine GL |
"A Catalytic Checkpoint in Base Excision by the Human
8-Oxoguanine DNA Glycosylase hOGG1." |
Crystal structure of catalytically active human
8-oxoguanine glycosylase distally crosslinked to
guanine-containing DNA . SNAP output
|
|
3iin
|
RNA binding protein-DNA-RNA |
X-ray (4.18 Å) |
Antonioli AH, Cochrane JC, Lipchock SV, Strobel
SA |
(2010) "Plasticity
of the RNA kink turn structural motif."
Rna, 16, 762-768. doi:
10.1261/rna.1883810.
|
Plasticity of the kink turn structural motif . SNAP output
|
|
3ikt
|
DNA binding protein-DNA |
X-ray (2.26 Å) |
McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D,
Soares AS, Paget MS, Kielkopf CL |
(2010) "Structural
basis for NADH/NAD+ redox sensing by a Rex family
repressor." Mol.Cell, 38,
563-575. doi: 10.1016/j.molcel.2010.05.006.
|
Crystal structure of a rex-family repressor-DNA-nad+
complex from thermus aquaticus . SNAP output
|
|
3il2
|
DNA binding protein-DNA |
X-ray (2.49 Å) |
McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D,
Soares AS, Paget MS, Kielkopf CL |
(2010) "Structural
basis for NADH/NAD+ redox sensing by a Rex family
repressor." Mol.Cell, 38,
563-575. doi: 10.1016/j.molcel.2010.05.006.
|
Crystal structure of a rex-family repressor r90d
mutant-DNA complex from thermus aquaticus . SNAP output
|
|
3imb
|
hydrolase-DNA |
X-ray (1.89 Å) |
Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis
G, Szczepanowski RH, Siksnys V, Bochtler M |
"How BcnI and MvaI distinguish W from S." |
Alternative binding mode of restriction endonuclease
bcni to cognate DNA . SNAP output
|
|
3in5
|
transferase-DNA |
X-ray (3.2 Å) |
Vasquez-Del Carpio R, Silverstein TD, Lone S, Swan
MK, Choudhury JR, Johnson RE, Prakash S, Prakash L,
Aggarwal AK |
(2009) "Structure
of human DNA polymerase kappa inserting dATP opposite
an 8-oxoG DNA lesion." PLOS ONE,
4, e5766. doi: 10.1371/journal.pone.0005766.
|
Structure of human DNA polymerase kappa inserting datp
opposite an 8-oxog DNA lesion . SNAP output
|
|
3irq
|
hydrolase-DNA |
X-ray (2.8 Å) |
de Rosa M, de Sanctis D, Rosario AL, Archer M, Rich
A, Athanasiadis A, Carrondo MA |
(2010) "Crystal
structure of a junction between two Z-DNA helices."
Proc.Natl.Acad.Sci.USA, 107,
9088-9092. doi: 10.1073/pnas.1003182107.
|
Crystal structure of a z-z junction . SNAP output
|
|
3irr
|
hydrolase-DNA |
X-ray (2.65 Å) |
de Rosa M, de Sanctis D, Rosario AL, Archer M, Rich
A, Athanasiadis A, Carrondo MA |
(2010) "Crystal
structure of a junction between two Z-DNA helices."
Proc.Natl.Acad.Sci.USA, 107,
9088-9092. doi: 10.1073/pnas.1003182107.
|
Crystal structure of a z-z junction (with hepes
intercalating) . SNAP
output
|
|
3isb
|
transferase-DNA |
X-ray (2.0 Å) |
Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson
SH |
(2009) "DNA
polymerase beta substrate specificity: side chain
modulation of the "A-rule"." J.Biol.Chem.,
284, 31680-31689. doi: 10.1074/jbc.M109.029843.
|
Binary complex of human DNA polymerase beta with a
gapped DNA . SNAP
output
|
|
3isc
|
transferase-DNA |
X-ray (2.0 Å) |
Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson
SH |
(2009) "DNA
polymerase beta substrate specificity: side chain
modulation of the "A-rule"." J.Biol.Chem.,
284, 31680-31689. doi: 10.1074/jbc.M109.029843.
|
Binary complex of human DNA polymerase beta with an
abasic site (thf) in the gapped DNA . SNAP output
|
|
3isd
|
transferase-DNA |
X-ray (2.6 Å) |
Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson
SH |
(2009) "DNA
polymerase beta substrate specificity: side chain
modulation of the "A-rule"." J.Biol.Chem.,
284, 31680-31689. doi: 10.1074/jbc.M109.029843.
|
Ternary complex of human DNA polymerase beta with an
abasic site (thf): dapcpp mismatch . SNAP output
|
|
3iv5
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp optimal binding
sequence f1 . SNAP
output
|
|
3iyd
|
transcription-DNA |
cryo-EM (19.8 Å) |
Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman
HM, Arnold E, Ebright RH, Lawson CL |
(2009) "Three-dimensional
EM structure of an intact activator-dependent
transcription initiation complex."
Proc.Natl.Acad.Sci.USA, 106,
19830-19835. doi: 10.1073/pnas.0908782106.
|
Three-dimensional em structure of an intact
activator-dependent transcription initiation complex .
SNAP output
|
|
3j6x
|
ribosome |
cryo-EM (6.1 Å) |
Koh CS, Brilot AF, Grigorieff N, Korostelev AA |
(2014) "Taura
syndrome virus IRES initiates translation by binding
its tRNA-mRNA-like structural element in the ribosomal
decoding center." Proc.Natl.Acad.Sci.USA,
111, 9139-9144. doi: 10.1073/pnas.1406335111.
|
S. cerevisiae 80s ribosome bound with taura syndrome
virus (tsv) ires, 5 degree rotation (class ii) .
SNAP output
|
|
3j6y
|
ribosome |
cryo-EM (6.1 Å) |
Koh CS, Brilot AF, Grigorieff N, Korostelev AA |
(2014) "Taura
syndrome virus IRES initiates translation by binding
its tRNA-mRNA-like structural element in the ribosomal
decoding center." Proc.Natl.Acad.Sci.USA,
111, 9139-9144. doi: 10.1073/pnas.1406335111.
|
S. cerevisiae 80s ribosome bound with taura syndrome
virus (tsv) ires, 2 degree rotation (class i) .
SNAP output
|
|
3j7o
|
ribosome |
cryo-EM (3.4 Å) |
Voorhees RM, Fernandez IS, Scheres SH, Hegde RS |
(2014) "Structure
of the Mammalian ribosome-sec61 complex to 3.4 a
resolution." Cell(Cambridge,Mass.),
157, 1632-1643. doi: 10.1016/j.cell.2014.05.024.
|
Structure of the mammalian 60s ribosomal subunit .
SNAP output
|
|
3j7p
|
ribosome |
cryo-EM (3.5 Å) |
Voorhees RM, Fernandez IS, Scheres SH, Hegde RS |
(2014) "Structure
of the Mammalian ribosome-sec61 complex to 3.4 a
resolution." Cell(Cambridge,Mass.),
157, 1632-1643. doi: 10.1016/j.cell.2014.05.024.
|
Structure of the 80s mammalian ribosome bound to eef2 .
SNAP output
|
|
3j7q
|
ribosome |
cryo-EM (3.4 Å) |
Voorhees RM, Fernandez IS, Scheres SH, Hegde RS |
(2014) "Structure
of the Mammalian ribosome-sec61 complex to 3.4 a
resolution." Cell(Cambridge,Mass.),
157, 1632-1643. doi: 10.1016/j.cell.2014.05.024.
|
Structure of the idle mammalian ribosome-sec61 complex
. SNAP output
|
|
3j7r
|
ribosome |
cryo-EM (3.9 Å) |
Voorhees RM, Fernandez IS, Scheres SH, Hegde RS |
(2014) "Structure
of the Mammalian ribosome-sec61 complex to 3.4 a
resolution." Cell(Cambridge,Mass.),
157, 1632-1643. doi: 10.1016/j.cell.2014.05.024.
|
Structure of the translating mammalian ribosome-sec61
complex . SNAP
output
|
|
3j92
|
ribosome-ligase |
cryo-EM (3.6 Å) |
Shao S, Brown A, Santhanam B, Hegde RS |
(2015) "Structure
and Assembly Pathway of the Ribosome Quality Control
Complex." Mol.Cell, 57,
433-444. doi: 10.1016/j.molcel.2014.12.015.
|
Structure and assembly pathway of the ribosome quality
control complex . SNAP
output
|
|
3j9x
|
virus |
cryo-EM (3.8 Å) |
DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D,
Egelman EH |
(2015) "A virus
that infects a hyperthermophile encapsidates A-form
DNA." Science, 348,
914-917. doi: 10.1126/science.aaa4181.
|
A virus that infects a hyperthermophile encapsidates
a-form DNA . SNAP
output
|
|
3jaa
|
transferase-DNA |
cryo-EM (22.0 Å) |
Lau WC, Li Y, Zhang Q, Huen MS |
(2015) "Molecular
architecture of the Ub-PCNA/Pol eta complex bound to
DNA." Sci Rep, 5, 15759.
doi: 10.1038/srep15759.
|
Human DNA polymerase eta in complex with normal DNA and
inco nucleotide (nrm) . SNAP output
|
|
3jag
|
ribosome |
cryo-EM (3.65 Å) |
Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan
V |
(2015) "Structural
basis for stop codon recognition in eukaryotes."
Nature, 524, 493-496. doi:
10.1038/nature14896.
|
Structure of a mammalian ribosomal termination complex
with abce1, erf1(aaq), and the uaa stop codon .
SNAP output
|
|
3jah
|
ribosome |
cryo-EM (3.45 Å) |
Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan
V |
(2015) "Structural
basis for stop codon recognition in eukaryotes."
Nature, 524, 493-496. doi:
10.1038/nature14896.
|
Structure of a mammalian ribosomal termination complex
with abce1, erf1(aaq), and the uag stop codon .
SNAP output
|
|
3jai
|
ribosome |
cryo-EM (3.65 Å) |
Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan
V |
(2015) "Structural
basis for stop codon recognition in eukaryotes."
Nature, 524, 493-496. doi:
10.1038/nature14896.
|
Structure of a mammalian ribosomal termination complex
with abce1, erf1(aaq), and the uga stop codon .
SNAP output
|
|
3jaj
|
ribosome |
cryo-EM (3.75 Å) |
Voorhees RM, Hegde RS |
(2015) "Structures
of the scanning and engaged states of the mammalian
SRP-ribosome complex." Elife,
4. doi: 10.7554/eLife.07975.
|
Structure of the engaged state of the mammalian
srp-ribosome complex . SNAP output
|
|
3jan
|
ribosome |
cryo-EM (3.75 Å) |
Voorhees RM, Hegde RS |
(2015) "Structures
of the scanning and engaged states of the mammalian
SRP-ribosome complex." Elife,
4. doi: 10.7554/eLife.07975.
|
Structure of the scanning state of the mammalian
srp-ribosome complex . SNAP output
|
|
3jbw
|
recombination-DNA |
cryo-EM (4.6 Å) |
Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H |
(2015) "Molecular
Mechanism of V(D)J Recombination from Synaptic
RAG1-RAG2 Complex Structures."
Cell(Cambridge,Mass.), 163,
1138-1152. doi: 10.1016/j.cell.2015.10.055.
|
Cryo-electron microscopy structure of rag paired
complex (with nbd, no symmetry) . SNAP output
|
|
3jbx
|
recombination-DNA |
cryo-EM (3.4 Å) |
Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H |
(2015) "Molecular
Mechanism of V(D)J Recombination from Synaptic
RAG1-RAG2 Complex Structures."
Cell(Cambridge,Mass.), 163,
1138-1152. doi: 10.1016/j.cell.2015.10.055.
|
Cryo-electron microscopy structure of rag signal end
complex (c2 symmetry) . SNAP output
|
|
3jby
|
recombination-DNA |
cryo-EM (3.7 Å) |
Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H |
(2015) "Molecular
Mechanism of V(D)J Recombination from Synaptic
RAG1-RAG2 Complex Structures."
Cell(Cambridge,Mass.), 163,
1138-1152. doi: 10.1016/j.cell.2015.10.055.
|
Cryo-electron microscopy structure of rag paired
complex (c2 symmetry) . SNAP output
|
|
3jca
|
viral protein |
cryo-EM (4.8 Å) |
Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG,
Demeler B, Cherepanov P, Lyumkis D, Engelman AN |
(2016) "Cryo-EM
reveals a novel octameric integrase structure for
betaretroviral intasome function." Nature,
530, 358-361. doi: 10.1038/nature16955.
|
Core model of the mouse mammary tumor virus intasome .
SNAP output
|
|
3jpn
|
transferase-DNA |
X-ray (2.15 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-dichloro methylene triphosphate . SNAP output
|
|
3jpo
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monochloromethylene triphosphate . SNAP output
|
|
3jpp
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monomethyl methylene triphosphate . SNAP output
|
|
3jpq
|
transferase-DNA |
X-ray (1.9 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monobromo methylene triphosphate . SNAP output
|
|
3jpr
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-dimethyl methylene triphosphate . SNAP output
|
|
3jps
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-fluoro methyl methylene triphosphate . SNAP output
|
|
3jpt
|
transferase-DNA |
X-ray (2.15 Å) |
Batra VK, Pedersen LC, Beard WA, Wilson SH,
Kashemirov BA, Upton TG, Goodman MF, McKenna CE |
(2010) "Halogenated
beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary
Complexes with DNA Polymerase beta: Structural Evidence
for Stereospecific Binding of the Fluoromethylene
Analogues." J.Am.Chem.Soc.,
132, 7617-7625. doi: 10.1021/ja909370k.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-fluoro chloro methylene triphosphate . SNAP output
|
|
3jr4
|
lyase-DNA |
X-ray (2.601 Å) |
Qi Y, Spong MC, Nam K, Karplus M, Verdine GL |
(2010) "Entrapment
and structure of an extrahelical guanine attempting to
enter the active site of a bacterial DNA glycosylase,
MutM." J.Biol.Chem., 285,
1468-1478. doi: 10.1074/jbc.M109.069799.
|
Mutm interrogating an extrahelical g . SNAP output
|
|
3jr5
|
lyase-DNA |
X-ray (1.704 Å) |
Qi Y, Spong MC, Nam K, Karplus M, Verdine GL |
(2010) "Entrapment
and structure of an extrahelical guanine attempting to
enter the active site of a bacterial DNA glycosylase,
MutM." J.Biol.Chem., 285,
1468-1478. doi: 10.1074/jbc.M109.069799.
|
Mutm lesion recognition control complex with n174c
crosslinking site . SNAP
output
|
|
3jr9
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp optimal binding
sequence f2 . SNAP
output
|
|
3jra
|
DNA binding protein-DNA |
X-ray (3.11 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27bp non consensus
sequence DNA f6 . SNAP
output
|
|
3jrb
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp DNA f24
containing t-tract at center . SNAP output
|
|
3jrc
|
DNA binding protein-DNA |
X-ray (3.08 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp DNA f29
containing 5 g-cs at center . SNAP output
|
|
3jrd
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp DNA f25
containing t2a3 sequence at center . SNAP output
|
|
3jre
|
DNA binding protein-DNA |
X-ray (3.17 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp DNA f26
containing a-tract at center . SNAP output
|
|
3jrf
|
DNA binding protein-DNA |
X-ray (3.05 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp DNA f27
containing a c-g at center . SNAP output
|
|
3jrg
|
DNA binding protein-DNA |
X-ray (3.11 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp non consensus
sequence DNA f18 . SNAP
output
|
|
3jrh
|
DNA binding protein-DNA |
X-ray (2.88 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp non consensus
sequence DNA f21 . SNAP
output
|
|
3jri
|
DNA binding protein-DNA |
X-ray (3.11 Å) |
Stella S, Cascio D, Johnson RC |
(2010) "The
shape of the DNA minor groove directs binding by the
DNA-bending protein Fis." Genes Dev.,
24, 814-826. doi: 10.1101/gad.1900610.
|
Crystal structure of fis bound to 27 bp non consensus
sequence DNA f23 . SNAP
output
|
|
3jsm
|
transferase-DNA complex |
X-ray (3.0 Å) |
Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG,
Tuske S, Tu X, Clark AD, Boyer PL, Hou X, Gaffney BL,
Jones RA, Miller MD, Hughes SH, Arnold E |
(2009) "Structural
basis for the role of the K65r mutation in HIV-1
reverse transcriptase polymerization, excision
antagonism, and tenofovir resistance."
J.Biol.Chem., 284,
35092-35100. doi: 10.1074/jbc.M109.022525.
|
K65r mutant hiv-1 reverse transcriptase cross-linked to
ds-DNA and complexed with tenofovir-diphosphate as the
incoming nucleotide substrate . SNAP output
|
|
3jso
|
hydrolase-DNA |
X-ray (2.29 Å) |
Zhang AP, Pigli YZ, Rice PA |
(2010) "Structure
of the LexA-DNA complex and implications for SOS box
measurement." Nature,
466, 883-886. doi: 10.1038/nature09200.
|
Classic protein with a new twist: crystal structure of
a lexa repressor DNA complex . SNAP output
|
|
3jsp
|
hydrolase-DNA |
X-ray (2.9 Å) |
Zhang AP, Pigli YZ, Rice PA |
(2010) "Structure
of the LexA-DNA complex and implications for SOS box
measurement." Nature,
466, 883-886. doi: 10.1038/nature09200.
|
Classic protein with a new twist: crystal structure of
a lexa repressor DNA complex . SNAP output
|
|
3jtg
|
transcription |
X-ray (2.2 Å) |
Agarkar VB, Babayeva ND, Wilder PJ, Rizzino A,
Tahirov TH |
(2010) "Crystal
structure of mouse Elf3 C-terminal DNA-binding domain
in complex with type II TGF-beta receptor promoter
DNA." J.Mol.Biol., 397,
278-289. doi: 10.1016/j.jmb.2010.01.017.
|
Crystal structure of mouse elf3 c-terminal DNA-binding
domain in complex with type ii tgf-beta receptor
promoter DNA . SNAP
output
|
|
3jx7
|
hydrolase-DNA |
X-ray (1.6 Å) |
Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman
BF |
(2010) "An
unprecedented nucleic acid capture mechanism for
excision of DNA damage." Nature,
468, 406-411. doi: 10.1038/nature09428.
|
Bacillus cereus alkylpurine DNA glycosylase alkd bound
to DNA containing a 3-methyladenine analog . SNAP output
|
|
3jxb
|
transcription regulator |
X-ray (1.67 Å) |
Watkins D, Mohan S, Koudelka GB, Williams LD |
(2010) "Sequence
Recognition of DNA by Protein-Induced Conformational
Transitions." J.Mol.Biol.,
396, 1145-1164. doi: 10.1016/j.jmb.2009.12.050.
|
Crystal structure of the p22 c2 repressor protein in
complex with synthetic operator 9c . SNAP output
|
|
3jxc
|
transcription regulator |
X-ray (1.9 Å) |
Watkins D, Mohan S, Koudelka GB, Williams LD |
(2010) "Sequence
Recognition of DNA by Protein-Induced Conformational
Transitions." J.Mol.Biol.,
396, 1145-1164. doi: 10.1016/j.jmb.2009.12.050.
|
Crystal structure of the p22 c2 repressor protein in
complex with synthetic operator 9t in the presence of
tl+ . SNAP output
|
|
3jxd
|
transcription regulator |
X-ray (2.1 Å) |
Watkins D, Mohan S, Koudelka GB, Williams LD |
(2010) "Sequence
Recognition of DNA by Protein-Induced Conformational
Transitions." J.Mol.Biol.,
396, 1145-1164. doi: 10.1016/j.jmb.2009.12.050.
|
Crystal structure of the p22 c2 repressor protein in
complex with synthetic operator 9c in the presence of
rb+ . SNAP output
|
|
3jxy
|
hydrolase-DNA |
X-ray (1.5 Å) |
Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman
BF |
(2010) "An
unprecedented nucleic acid capture mechanism for
excision of DNA damage." Nature,
468, 406-411. doi: 10.1038/nature09428.
|
Bacillus cereus alkylpurine DNA glycosylase alkd bound
to DNA containing a gt mismatch . SNAP output
|
|
3jxz
|
hydrolase-DNA |
X-ray (1.75 Å) |
Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman
BF |
(2010) "An
unprecedented nucleic acid capture mechanism for
excision of DNA damage." Nature,
468, 406-411. doi: 10.1038/nature09428.
|
Bacillus cereus alkylpurine DNA glycosylase alkd bound
to DNA containing an abasic site (across from t) .
SNAP output
|
|
3jy1
|
hydrolase-DNA |
X-ray (1.754 Å) |
Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman
BF |
(2010) "An
unprecedented nucleic acid capture mechanism for
excision of DNA damage." Nature,
468, 406-411. doi: 10.1038/nature09428.
|
Bacillus cereus alkylpurine DNA glycosylase alkd bound
to DNA containing an abasic site (across from c) .
SNAP output
|
|
3jyt
|
transferase-DNA complex |
X-ray (3.3 Å) |
Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG,
Tuske S, Tu X, Clark AD, Boyer PL, Hou X, Gaffney BL,
Jones RA, Miller MD, Hughes SH, Arnold E |
(2009) "Structural
basis for the role of the K65r mutation in HIV-1
reverse transcriptase polymerization, excision
antagonism, and tenofovir resistance."
J.Biol.Chem., 284,
35092-35100. doi: 10.1074/jbc.M109.022525.
|
K65r mutant hiv-1 reverse transcriptase cross-linked to
ds-DNA and complexed with datp as the incoming
nucleotide substrate . SNAP output
|
|
3k0s
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Lebbink JH, Fish A, Reumer A, Natrajan G, Winterwerp
HH, Sixma TK |
(2010) "Magnesium
coordination controls the molecular switch function of
DNA mismatch repair protein MutS."
J.Biol.Chem., 285,
13131-13141. doi: 10.1074/jbc.M109.066001.
|
Crystal structure of e.coli DNA mismatch repair protein
muts, d693n mutant, in complex with gt mismatched DNA .
SNAP output
|
|
3k4x
|
DNA binding protein-DNA |
X-ray (2.98 Å) |
McNally R, Bowman GD, Goedken ER, O'Donnell M,
Kuriyan J |
(2010) "Analysis
of the role of PCNA-DNA contacts during clamp
loading." Bmc Struct.Biol.,
10, 3. doi: 10.1186/1472-6807-10-3.
|
Eukaryotic sliding clamp pcna bound to DNA . SNAP output
|
|
3k57
|
transferase-DNA |
X-ray (2.08 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-normal DNA-datp
ternary complex . SNAP
output
|
|
3k58
|
transferase-DNA |
X-ray (2.05 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-normal DNA-dttp
ternary complex . SNAP
output
|
|
3k59
|
transferase-DNA |
X-ray (1.92 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-normal DNA-dctp
ternary complex . SNAP
output
|
|
3k5l
|
transferase-DNA |
X-ray (2.7 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-abasic DNA-datp
lt(0, 3) ternary complex . SNAP output
|
|
3k5m
|
transferase-DNA |
X-ray (2.04 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-abasic DNA-ddgtp
lt(-2, 2) ternary complex . SNAP output
|
|
3k5n
|
transferase-DNA |
X-ray (3.15 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-abasic DNA binary
complex . SNAP
output
|
|
3k70
|
hydrolase-DNA |
X-ray (3.59 Å) |
Saikrishnan K, Griffiths SP, Cook N, Court R, Wigley
DB |
(2008) "DNA
binding to RecD: role of the 1B domain in SF1B helicase
activity." Embo J., 27,
2222-2229.
|
Crystal structure of the complete initiation complex of
recbcd . SNAP output
|
|
3k9f
|
isomerase-DNA |
X-ray (2.9 Å) |
Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher
LM, Sanderson MR |
(2010) "Structural
Basis of Gate-DNA Breakage and Resealing by Type II
Topoisomerases." Plos One,
5, e11338. doi: 10.1371/journal.pone.0011338.
|
Detailed structural insight into the quinolone-DNA
cleavage complex of type iia topoisomerases . SNAP output
|
|
3kd1
|
transferase-DNA |
X-ray (2.66 Å) |
Zahn KE, Tchesnokov EP, Gotte M, Doublie S |
(2011) "Phosphonoformic
acid inhibits viral replication by trapping the closed
form of the DNA polymerase." J.Biol.Chem.,
286, 25246-25255. doi: 10.1074/jbc.M111.248864.
|
Closed binary complex of an rb69 gp43 fingers domain
mutant complexed with an acyclic gmp terminated primer
template pair. . SNAP
output
|
|
3kd5
|
transferase-DNA |
X-ray (2.69 Å) |
Zahn KE, Tchesnokov EP, Gotte M, Doublie S |
(2011) "Phosphonoformic
acid inhibits viral replication by trapping the closed
form of the DNA polymerase." J.Biol.Chem.,
286, 25246-25255. doi: 10.1074/jbc.M111.248864.
|
Closed ternary complex of an rb69 gp43 fingers domain
mutant complexed with an acyclic gmp terminated primer
template pair and phosphonoformic acid. . SNAP output
|
|
3kde
|
DNA binding protein-DNA |
X-ray (1.74 Å) |
Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio
DC |
(2010) "THAP
proteins target specific DNA sites through bipartite
recognition of adjacent major and minor grooves."
Nat.Struct.Mol.Biol., 17,
117-123. doi: 10.1038/nsmb.1742.
|
Crystal structure of the thap domain from d.
melanogaster p-element transposase in complex with its
natural DNA binding site . SNAP output
|
|
3ket
|
transcription-DNA |
X-ray (2.4 Å) |
Franza T, Rogstam A, Thiyagarajan S, Sullivan MJ,
Derre-Bobillot A, Bauer MC, Goh KGK, Da Cunha V, Glaser
P, Logan DT, Ulett GC, von Wachenfeldt C, Gaudu P |
(2021) "NAD+
pool depletion as a signal for the Rex regulon involved
in Streptococcus agalactiae virulence." Plos
Pathog., 17, e1009791. doi:
10.1371/journal.ppat.1009791.
|
Crystal structure of a rex-family transcriptional
regulatory protein from streptococcus agalactiae bound
to a palindromic operator . SNAP output
|
|
3khc
|
oxidoreductase-DNA |
X-ray (2.2 Å) |
Holland PJ, Hollis T |
(2010) "Structural
and mutational analysis of Escherichia coli AlkB
provides insight into substrate specificity and DNA
damage searching." Plos One,
5, e8680. doi: 10.1371/journal.pone.0008680.
|
Crystal structure of escherichia coli alkb in complex
with ssDNA containing a 1-methylguanine lesion .
SNAP output
|
|
3khg
|
transferase-DNA |
X-ray (2.96 Å) |
Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov
NE, Broyde S, Patel DJ |
(2010) "Mechanism
of error-free and semitargeted mutagenic bypass of an
aromatic amine lesion by Y-family polymerase Dpo4."
Nat.Struct.Mol.Biol., 17,
379-388. doi: 10.1038/nsmb.1771.
|
Dpo4 extension ternary complex with misinserted a
opposite the 2-aminofluorene-guanine [af]g lesion .
SNAP output
|
|
3khh
|
transferase-DNA |
X-ray (2.7 Å) |
Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov
NE, Broyde S, Patel DJ |
(2010) "Mechanism
of error-free and semitargeted mutagenic bypass of an
aromatic amine lesion by Y-family polymerase Dpo4."
Nat.Struct.Mol.Biol., 17,
379-388. doi: 10.1038/nsmb.1771.
|
Dpo4 extension ternary complex with a c base opposite
the 2-aminofluorene-guanine [af]g lesion . SNAP output
|
|
3khl
|
transferase-DNA |
X-ray (2.1 Å) |
Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov
NE, Broyde S, Patel DJ |
(2010) "Mechanism
of error-free and semitargeted mutagenic bypass of an
aromatic amine lesion by Y-family polymerase Dpo4."
Nat.Struct.Mol.Biol., 17,
379-388. doi: 10.1038/nsmb.1771.
|
Dpo4 post-extension ternary complex with misinserted a
opposite the 2-aminofluorene-guanine [af]g lesion .
SNAP output
|
|
3khr
|
transferase-DNA |
X-ray (2.01 Å) |
Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov
NE, Broyde S, Patel DJ |
(2010) "Mechanism
of error-free and semitargeted mutagenic bypass of an
aromatic amine lesion by Y-family polymerase Dpo4."
Nat.Struct.Mol.Biol., 17,
379-388. doi: 10.1038/nsmb.1771.
|
Dpo4 post-extension ternary complex with the correct c
opposite the 2-aminofluorene-guanine [af]g lesion .
SNAP output
|
|
3kjo
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Nandakumar J, Podell ER, Cech TR |
(2010) "How
telomeric protein POT1 avoids RNA to achieve
specificity for single-stranded DNA."
Proc.Natl.Acad.Sci.USA, 107,
651-656. doi: 10.1073/pnas.0911099107.
|
Crystal structure of hpot1v2-dtrud(agggttag) . SNAP output
|
|
3kjp
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Nandakumar J, Podell ER, Cech TR |
(2010) "How
telomeric protein POT1 avoids RNA to achieve
specificity for single-stranded DNA."
Proc.Natl.Acad.Sci.USA, 107,
651-656. doi: 10.1073/pnas.0911099107.
|
Crystal structure of hpot1v2-ggttagggttag . SNAP output
|
|
3kjv
|
transferase-DNA |
X-ray (3.1 Å) |
Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White
KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray
AS, McGrath ME, Swaminathan S |
(2010) "Visualizing
the molecular interactions of a nucleotide analog,
GS-9148, with HIV-1 reverse transcriptase-DNA
complex." J.Mol.Biol.,
397, 967-978. doi: 10.1016/j.jmb.2010.02.019.
|
Hiv-1 reverse transcriptase in complex with DNA .
SNAP output
|
|
3kk1
|
transferase-DNA |
X-ray (2.7 Å) |
Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White
KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray
AS, McGrath ME, Swaminathan S |
(2010) "Visualizing
the molecular interactions of a nucleotide analog,
GS-9148, with HIV-1 reverse transcriptase-DNA
complex." J.Mol.Biol.,
397, 967-978. doi: 10.1016/j.jmb.2010.02.019.
|
Hiv-1 reverse transcriptase-DNA complex with nuceotide
inhibitor gs-9148-diphosphate bound in nucleotide site
. SNAP output
|
|
3kk2
|
transferase-DNA |
X-ray (2.9 Å) |
Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White
KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray
AS, McGrath ME, Swaminathan S |
(2010) "Visualizing
the molecular interactions of a nucleotide analog,
GS-9148, with HIV-1 reverse transcriptase-DNA
complex." J.Mol.Biol.,
397, 967-978. doi: 10.1016/j.jmb.2010.02.019.
|
Hiv-1 reverse transcriptase-DNA complex with datp bound
in the nucleotide binding site . SNAP output
|
|
3kk3
|
transferase-DNA |
X-ray (2.9 Å) |
Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White
KL, Hung M, Liu X, Boojamra CG, Mackman RL, Cihlar T, Ray
AS, McGrath ME, Swaminathan S |
(2010) "Visualizing
the molecular interactions of a nucleotide analog,
GS-9148, with HIV-1 reverse transcriptase-DNA
complex." J.Mol.Biol.,
397, 967-978. doi: 10.1016/j.jmb.2010.02.019.
|
Hiv-1 reverse transcriptase-DNA complex with gs-9148
terminated primer . SNAP
output
|
|
3kle
|
transferase-DNA |
X-ray (3.2 Å) |
Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X,
Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH,
Sarafianos SG, Arnold E |
(2010) "Structural
basis of HIV-1 resistance to AZT by excision."
Nat.Struct.Mol.Biol., 17,
1202-1209. doi: 10.1038/nsmb.1908.
|
Crystal structure of azt-resistant hiv-1 reverse
transcriptase crosslinked to a dsDNA with a bound
excision product, aztppppa . SNAP output
|
|
3klf
|
transferase-DNA |
X-ray (3.15 Å) |
Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X,
Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH,
Sarafianos SG, Arnold E |
(2010) "Structural
basis of HIV-1 resistance to AZT by excision."
Nat.Struct.Mol.Biol., 17,
1202-1209. doi: 10.1038/nsmb.1908.
|
Crystal structure of wild-type hiv-1 reverse
transcriptase crosslinked to a dsDNA with a bound
excision product, aztppppa . SNAP output
|
|
3klg
|
transferase-DNA |
X-ray (3.65 Å) |
Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X,
Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH,
Sarafianos SG, Arnold E |
(2010) "Structural
basis of HIV-1 resistance to AZT by excision."
Nat.Struct.Mol.Biol., 17,
1202-1209. doi: 10.1038/nsmb.1908.
|
Crystal structure of azt-resistant hiv-1 reverse
transcriptase crosslinked to pre-translocation
aztmp-terminated DNA (complex n) . SNAP output
|
|
3klh
|
transferase-DNA |
X-ray (2.9 Å) |
Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X,
Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH,
Sarafianos SG, Arnold E |
(2010) "Structural
basis of HIV-1 resistance to AZT by excision."
Nat.Struct.Mol.Biol., 17,
1202-1209. doi: 10.1038/nsmb.1908.
|
Crystal structure of azt-resistant hiv-1 reverse
transcriptase crosslinked to post-translocation
aztmp-terminated DNA (complex p) . SNAP output
|
|
3kmd
|
DNA binding protein-DNA |
X-ray (2.15 Å) |
Chen Y, Dey R, Chen L |
(2010) "Crystal
structure of the p53 core domain bound to a full
consensus site as a self-assembled tetramer."
Structure, 18, 246-256. doi:
10.1016/j.str.2009.11.011.
|
Crystal structure of the p53 core domain bound to a
full consensus site as a self-assembled tetramer .
SNAP output
|
|
3kmp
|
transcription regulator-DNA |
X-ray (2.7 Å) |
BabuRajendran N, Palasingam P, Narasimhan K, Sun W,
Prabhakar S, Jauch R, Kolatkar PR |
(2010) "Structure
of Smad1 MH1/DNA complex reveals distinctive
rearrangements of BMP and TGF-beta effectors."
Nucleic Acids Res., 38,
3477-3488. doi: 10.1093/nar/gkq046.
|
Crystal structure of smad1-mh1-DNA complex . SNAP output
|
|
3knt
|
hydrolase, lyase-DNA |
X-ray (2.7 Å) |
Faucher F, Wallace SS, Doublie S |
(2010) "The
C-terminal Lysine of Ogg2 DNA Glycosylases is a Major
Molecular Determinant for Guanine/8-Oxoguanine
Distinction." J.Mol.Biol.,
397, 46-56. doi: 10.1016/j.jmb.2010.01.024.
|
Crystal structure of methanocaldococcus jannaschii
8-oxoguanine glycosylase-lyase in complex with 15mer
DNA containing 8-oxoguanine . SNAP output
|
|
3ko2
|
hydrolase-DNA |
X-ray (2.9 Å) |
Ashworth J, Taylor GK, Havranek JJ, Quadri SA,
Stoddard BL, Baker D |
(2010) "Computational
reprogramming of homing endonuclease specificity at
multiple adjacent base pairs." Nucleic Acids
Res., 38, 5601-5608. doi:
10.1093/nar/gkq283.
|
I-msoi re-designed for altered DNA cleavage specificity
(-7c) . SNAP output
|
|
3kov
|
transcription-DNA |
X-ray (2.9 Å) |
Wu Y, Dey R, Han A, Jayathilaka N, Philips M, Ye J,
Chen L |
(2010) "Structure
of the MADS-box/MEF2 Domain of MEF2A Bound to DNA and
Its Implication for Myocardin Recruitment."
J.Mol.Biol., 397, 520-533.
doi: 10.1016/j.jmb.2010.01.067.
|
Structure of mef2a bound to DNA reveals a completely
folded mads-box-mef2 domain that recognizes DNA and
recruits transcription co-factors . SNAP output
|
|
3kqh
|
hydrolase-DNA |
X-ray (2.4 Å) |
Gu M, Rice CM |
(2010) "Three
conformational snapshots of the hepatitis C virus NS3
helicase reveal a ratchet translocation mechanism."
Proc.Natl.Acad.Sci.USA, 107,
521-528. doi: 10.1073/pnas.0913380107.
|
Three conformational snapshots of the hepatitis c virus
ns3 helicase reveal a ratchet translocation mechanism .
SNAP output
|
|
3kqk
|
hydrolase-DNA |
X-ray (2.8 Å) |
Gu M, Rice CM |
(2010) "Three
conformational snapshots of the hepatitis C virus NS3
helicase reveal a ratchet translocation mechanism."
Proc.Natl.Acad.Sci.USA, 107,
521-528. doi: 10.1073/pnas.0913380107.
|
Three conformational snapshots of the hepatitis c virus
ns3 helicase reveal a ratchet translocation mechanism .
SNAP output
|
|
3kql
|
hydrolase-DNA |
X-ray (2.5 Å) |
Gu M, Rice CM |
(2010) "Three
conformational snapshots of the hepatitis C virus NS3
helicase reveal a ratchet translocation mechanism."
Proc.Natl.Acad.Sci.USA, 107,
521-528. doi: 10.1073/pnas.0913380107.
|
Three conformational snapshots of the hepatitis c virus
ns3 helicase reveal a ratchet translocation mechanism .
SNAP output
|
|
3kqn
|
hydrolase-DNA |
X-ray (2.05 Å) |
Gu M, Rice CM |
(2010) "Three
conformational snapshots of the hepatitis C virus NS3
helicase reveal a ratchet translocation mechanism."
Proc.Natl.Acad.Sci.USA, 107,
521-528. doi: 10.1073/pnas.0913380107.
|
Three conformational snapshots of the hepatitis c virus
ns3 helicase reveal a ratchet translocation mechanism .
SNAP output
|
|
3kqu
|
hydrolase-DNA |
X-ray (2.4 Å) |
Gu M, Rice CM |
(2010) "Inaugural
Article: Three conformational snapshots of the
hepatitis C virus NS3 helicase reveal a ratchet
translocation mechanism."
Proc.Natl.Acad.Sci.USA, 107,
521-528. doi: 10.1073/pnas.0913380107.
|
Three conformational snapshots of the hepatitis c virus
ns3 helicase reveal a ratchet translocation mechanism .
SNAP output
|
|
3ksa
|
isomerase-DNA |
X-ray (3.3 Å) |
Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher
LM, Sanderson MR |
(2010) "Structural
Basis of Gate-DNA Breakage and Resealing by Type II
Topoisomerases." Plos One,
5, e11338. doi: 10.1371/journal.pone.0011338.
|
Detailed structural insight into the DNA cleavage
complex of type iia topoisomerases (cleaved form) .
SNAP output
|
|
3ksb
|
isomerase-DNA |
X-ray (3.5 Å) |
Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher
LM, Sanderson MR |
(2010) "Structural
Basis of Gate-DNA Breakage and Resealing by Type II
Topoisomerases." Plos One,
5, e11338. doi: 10.1371/journal.pone.0011338.
|
Detailed structural insight into the DNA cleavage
complex of type iia topoisomerases (re-sealed form) .
SNAP output
|
|
3ktq
|
transferase-DNA |
X-ray (2.3 Å) |
Li Y, Korolev S, Waksman G |
(1998) "Crystal
structures of open and closed forms of binary and
ternary complexes of the large fragment of Thermus
aquaticus DNA polymerase I: structural basis for
nucleotide incorporation." EMBO J.,
17, 7514-7525. doi: 10.1093/emboj/17.24.7514.
|
Crystal structure of an active ternary complex of the
large fragment of DNA polymerase i from thermus
aquaticus . SNAP
output
|
|
3ktu
|
hydrolase,lyase-DNA |
X-ray (2.3 Å) |
Verdine GL, Lee SM |
"Structural investigation of hOGG1 bound to a
fluorinated oxoG analog." |
Structure of human 8-oxoguanine glycosylase 1 bound to
fluorninated oxog-containing DNA . SNAP output
|
|
3kuy
|
structural protein-DNA |
X-ray (2.9 Å) |
Davey GE, Wu B, Dong Y, Surana U, Davey CA |
(2010) "DNA
stretching in the nucleosome facilitates alkylation by
an intercalating antitumour agent." Nucleic
Acids Res., 38, 2081-2088. doi:
10.1093/nar/gkp1174.
|
DNA stretching in the nucleosome facilitates alkylation
by an intercalating antitumor agent . SNAP output
|
|
3kwq
|
structural protein-DNA |
X-ray (3.5 Å) |
Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen
JC, Peterson C, Luger K |
"Structural
characterization of H3K56Q nucleosomes and nucleosomal
arrays." Biochim.Biophys.Acta,
1799, 480-486. doi: 10.1016/j.bbagrm.2010.01.009.
|
Structural characterization of h3k56q nucleosomes and
nucleosomal arrays . SNAP output
|
|
3kxb
|
transcription-DNA |
X-ray (3.2 Å) |
Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen
JC, Peterson C, Luger K |
(2010) "Structural
characterization of H3K56Q nucleosomes and nucleosomal
arrays." Biochim.Biophys.Acta,
1799, 480-486. doi: 10.1016/j.bbagrm.2010.01.009.
|
Structural characterization of h3k56q nucleosomes and
nucleosomal arrays . SNAP output
|
|
3kxt
|
DNA binding protein-DNA |
X-ray (1.602 Å) |
Feng Y, Yao H, Wang J |
(2010) "Crystal
structure of the crenarchaeal conserved chromatin
protein Cren7 and double-stranded DNA complex."
Protein Sci., 19, 1253-1257.
doi: 10.1002/pro.385.
|
Crystal structure of sulfolobus cren7-dsDNA complex .
SNAP output
|
|
3kyl
|
nucleic acid binding protein-DNA-RNA |
X-ray (2.7 Å) |
Mitchell M, Gillis A, Futahashi M, Fujiwara H,
Skordalakes E |
(2010) "Structural
basis for telomerase catalytic subunit TERT binding to
RNA template and telomeric DNA."
Nat.Struct.Mol.Biol., 17,
513-518. doi: 10.1038/nsmb.1777.
|
Structure of the catalytic subunit of telomerase bound
to its RNA template and telomeric DNA . SNAP output
|
|
3kz8
|
transcription-DNA |
X-ray (1.91 Å) |
Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich
D, Honig B, Shakked Z |
(2010) "Diversity
in DNA recognition by p53 revealed by crystal
structures with Hoogsteen base pairs."
Nat.Struct.Mol.Biol., 17,
423-429. doi: 10.1038/nsmb.1800.
|
Diversity in DNA recognition by p53 revealed by crystal
structures with hoogsteen base pairs (p53-DNA complex
3) . SNAP output
|
|
3l1p
|
transcription-DNA |
X-ray (2.8 Å) |
Esch D, Vahokoski J, Groves MR, Pogenberg V, Cojocaru
V, Vom Bruch H, Han D, Drexler HCA, Arauzo-Bravo MJ, Ng
CKL, Jauch R, Wilmanns M, Scholer HR |
(2013) "A unique
Oct4 interface is crucial for reprogramming to
pluripotency." Nat.Cell Biol.,
15, 295-301. doi: 10.1038/ncb2680.
|
Pou protein:DNA complex . SNAP output
|
|
3l2c
|
transcription-DNA |
X-ray (1.868 Å) |
Boura E, Rezabkova L, Brynda J, Obsilova V, Obsil
T |
(2010) "Structure
of the human FOXO4-DBD-DNA complex at 1.9 A resolution
reveals new details of FOXO binding to the DNA."
Acta Crystallogr.,Sect.D, 66,
1351-1357. doi: 10.1107/S0907444910042228.
|
Crystal structure of the DNA binding domain of foxo4
bound to DNA . SNAP
output
|
|
3l2p
|
ligase-DNA |
X-ray (3.0 Å) |
Cotner-Gohara E, Kim IK, Hammel M, Tainer JA,
Tomkinson AE, Ellenberger T |
(2010) "Human
DNA Ligase III Recognizes DNA Ends by Dynamic Switching
between Two DNA-Bound States."
Biochemistry, 49, 6165-6176.
doi: 10.1021/bi100503w.
|
Human DNA ligase iii recognizes DNA ends by dynamic
switching between two DNA bound states . SNAP output
|
|
3l2q
|
recombination-DNA |
X-ray (3.25 Å) |
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov
P |
(2010) "Retroviral
intasome assembly and inhibition of DNA strand
transfer." Nature, 464,
232-236. doi: 10.1038/nature08784.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in apo form . SNAP output
|
|
3l2r
|
recombination-DNA |
X-ray (2.88 Å) |
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov
P |
(2010) "Retroviral
intasome assembly and inhibition of DNA strand
transfer." Nature, 464,
232-236. doi: 10.1038/nature08784.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium . SNAP output
|
|
3l2u
|
recombination-DNA |
X-ray (3.15 Å) |
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov
P |
(2010) "Retroviral
intasome assembly and inhibition of DNA strand
transfer." Nature, 464,
232-236. doi: 10.1038/nature08784.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and gs9137
(elvitegravir) . SNAP
output
|
|
3l2v
|
recombination-DNA |
X-ray (3.2 Å) |
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov
P |
(2010) "Retroviral
intasome assembly and inhibition of DNA strand
transfer." Nature, 464,
232-236. doi: 10.1038/nature08784.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with manganese and mk0518
(raltegravir) . SNAP
output
|
|
3l2w
|
recombination-DNA |
X-ray (3.2 Å) |
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov
P |
(2010) "Retroviral
intasome assembly and inhibition of DNA strand
transfer." Nature, 464,
232-236. doi: 10.1038/nature08784.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with manganese and gs9137
(elvitegravir) . SNAP
output
|
|
3l4j
|
isomerase-DNA |
X-ray (2.48 Å) |
Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger
JM |
(2010) "A novel
and unified two-metal mechanism for DNA cleavage by
type II and IA topoisomerases." Nature,
465, 641-644. doi: 10.1038/nature08974.
|
Topoisomerase ii-DNA cleavage complex, apo . SNAP output
|
|
3l4k
|
isomerase-DNA |
X-ray (2.98 Å) |
Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger
JM |
(2010) "A novel
and unified two-metal mechanism for DNA cleavage by
type II and IA topoisomerases." Nature,
465, 641-644. doi: 10.1038/nature08974.
|
Topoisomerase ii-DNA cleavage complex, metal-bound .
SNAP output
|
|
3l8b
|
transferase-DNA |
X-ray (2.15 Å) |
Aller P, Ye Y, Wallace SS, Burrows CJ, Doublie S |
(2010) "Crystal
structure of a replicative DNA polymerase bound to the
oxidized guanine lesion guanidinohydantoin."
Biochemistry, 49, 2502-2509.
doi: 10.1021/bi902195p.
|
Crystal structure of a replicative DNA polymerase bound
to the oxidized guanine lesion guanidinohydantoin .
SNAP output
|
|
3laj
|
transcription regulator |
X-ray (2.306 Å) |
Cherney LT, Cherney MM, Garen CR, James MN |
(2010) "crystal
structure of the intermediate complex of the arginine
repressor from Mycobacterium tuberculosis bound with
its DNA operator reveals detailed mechanism of arginine
repression." J.Mol.Biol.,
399, 240-254. doi: 10.1016/j.jmb.2010.03.065.
|
The structure of the intermediate complex of the
arginine repressor from mycobacterium tuberculosis
bound to its DNA operator and l-arginine. . SNAP output
|
|
3lap
|
transcription regulator-DNA |
X-ray (2.15 Å) |
Cherney LT, Cherney MM, Garen CR, James MN |
(2010) "crystal
structure of the intermediate complex of the arginine
repressor from Mycobacterium tuberculosis bound with
its DNA operator reveals detailed mechanism of arginine
repression." J.Mol.Biol.,
399, 240-254. doi: 10.1016/j.jmb.2010.03.065.
|
The structure of the intermediate complex of the
arginine repressor from mycobacterium tuberculosis
bound to its DNA operator and l-canavanine. . SNAP output
|
|
3lds
|
transferase-DNA |
X-ray (3.0 Å) |
Hogg M, Rudnicki J, Midkiff J, Reha-Krantz L, Doublie
S, Wallace SS |
(2010) "Kinetics
of mismatch formation opposite lesions by the
replicative DNA polymerase from bacteriophage
RB69." Biochemistry, 49,
2317-2325. doi: 10.1021/bi901488d.
|
Crystal structure of rb69 gp43 with DNA and datp
opposite 8-oxog . SNAP
output
|
|
3ldy
|
hydrolase-DNA |
X-ray (1.97 Å) |
Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan
RD, Wilson GG, Stoddard BL |
(2010) "Unusual
target site disruption by the rare-cutting HNH
restriction endonuclease PacI." Structure,
18, 734-743. doi: 10.1016/j.str.2010.03.009.
|
An extraordinary mechanism of DNA perturbation
exhibited by the rare-cutting hnh restriction
endonuclease paci . SNAP
output
|
|
3lel
|
structural protein-DNA |
X-ray (2.95 Å) |
Wu B, Mohideen K, Vasudevan D, Davey CA |
(2010) "Structural
insight into the sequence dependence of nucleosome
positioning." Structure,
18, 528-536. doi: 10.1016/j.str.2010.01.015.
|
Structural insight into the sequence-dependence of
nucleosome positioning . SNAP output
|
|
3lja
|
structural protein-DNA |
X-ray (2.75 Å) |
Wu B, Davey CA |
(2010) "Using
soft X-rays for a detailed picture of divalent metal
binding in the nucleosome." J.Mol.Biol.,
398, 633-640. doi: 10.1016/j.jmb.2010.03.038.
|
Using soft x-rays for a detailed picture of divalent
metal binding in the nucleosome . SNAP output
|
|
3lk9
|
lyase,transferase-DNA |
X-ray (2.5 Å) |
Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov
BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen
LC, Beard WA, Shock DD, Wilson SH, Olah GA |
(2010) "Synthesis
and biological evaluation of fluorinated
deoxynucleotide analogs based on
bis-(difluoromethylene)triphosphoric acid."
Proc.Natl.Acad.Sci.USA, 107,
15693-15698. doi: 10.1073/pnas.1007430107.
|
DNA polymerase beta with a gapped DNA substrate and
dtmp(cf2)p(cf2)p . SNAP
output
|
|
3lnq
|
gene regulation-DNA |
X-ray (2.25 Å) |
Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K,
Kojima T, Tanokura M |
(2010) "Cooperative
DNA-binding and sequence-recognition mechanism of
aristaless and clawless." Embo J.,
29, 1613-1623. doi: 10.1038/emboj.2010.53.
|
Structure of aristaless homeodomain in complex with DNA
. SNAP output
|
|
3lsp
|
transcription-DNA |
X-ray (2.66 Å) |
Miller DJ, Zhang YM, Subramanian C, Rock CO, White
SW |
(2010) "Structural
basis for the transcriptional regulation of membrane
lipid homeostasis." Nat.Struct.Mol.Biol.,
17, 971-975. doi: 10.1038/nsmb.1847.
|
Crystal structure of dest bound to descb promoter and
oleoyl-coa . SNAP
output
|
|
3lsr
|
transcription-DNA |
X-ray (2.55 Å) |
Miller DJ, Zhang YM, Subramanian C, Rock CO, White
SW |
(2010) "Structural
basis for the transcriptional regulation of membrane
lipid homeostasis." Nat.Struct.Mol.Biol.,
17, 971-975. doi: 10.1038/nsmb.1847.
|
Crystal structure of dest in complex with duplex DNA .
SNAP output
|
|
3ltn
|
isomerase-DNA |
X-ray (3.1 Å) |
Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher
LM, Sanderson MR |
(2010) "Structural
Basis of Gate-DNA Breakage and Resealing by Type II
Topoisomerases." Plos One,
5, e11338. doi: 10.1371/journal.pone.0011338.
|
Inhibitor-stabilized topoisomerase iv-DNA cleavage
complex (s. pneumoniae) . SNAP output
|
|
3lwh
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Zhang ZF, Gong Y, Guo L, Jiang T, Huang L |
(2010) "Structural
insights into the interaction of the crenarchaeal
chromatin protein Cren7 with DNA."
Mol.Microbiol., 76, 749-759.
doi: 10.1111/j.1365-2958.2010.07136.x.
|
Crystal structure of cren7-dsDNA complex . SNAP output
|
|
3lwi
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Zhang ZF, Gong Y, Guo L, Jiang T, Huang L |
(2010) "Structural
insights into the interaction of the crenarchaeal
chromatin protein Cren7 with DNA."
Mol.Microbiol., 76, 749-759.
doi: 10.1111/j.1365-2958.2010.07136.x.
|
Crystal structure of cren7-dsDNA complex . SNAP output
|
|
3lwl
|
transferase-DNA |
X-ray (2.25 Å) |
Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs
K, Welte W, Marx A |
(2010) "Replication
through an abasic DNA lesion: structural basis for
adenine selectivity." Embo J.,
29, 1738-1747. doi: 10.1038/emboj.2010.64.
|
Structure of klenow fragment of taq polymerase in
complex with an abasic site . SNAP output
|
|
3lwm
|
transferase-DNA |
X-ray (2.186 Å) |
Obeid S, Blatter N, Kranaster R, Schnur A, Diederichs
K, Welte W, Marx A |
(2010) "Replication
through an abasic DNA lesion: structural basis for
adenine selectivity." Embo J.,
29, 1738-1747. doi: 10.1038/emboj.2010.64.
|
Structure of the large fragment of thermus aquaticus
DNA polymerase i in complex with a blunt-ended DNA and
ddatp . SNAP output
|
|
3lz0
|
structural protein-DNA |
X-ray (2.5 Å) |
Vasudevan D, Chua EY, Davey CA |
(2010) "Crystal
structures of nucleosome core particles containing the
'601' strong positioning sequence."
J.Mol.Biol., 403, 1-10. doi:
10.1016/j.jmb.2010.08.039.
|
Crystal structure of nucleosome core particle composed
of the widom 601 DNA sequence (orientation 1) .
SNAP output
|
|
3lz1
|
structural protein-DNA |
X-ray (2.5 Å) |
Vasudevan D, Chua EY, Davey CA |
(2010) "Crystal
structures of nucleosome core particles containing the
'601' strong positioning sequence."
J.Mol.Biol., 403, 1-10. doi:
10.1016/j.jmb.2010.08.039.
|
Crystal structure of nucleosome core particle composed
of the widom 601 DNA sequence (orientation 2) .
SNAP output
|
|
3lzi
|
transferase-DNA |
X-ray (2.3 Å) |
Beckman J, Wang M, Blaha G, Wang J, Konigsberg
WH |
(2010) "Substitution
of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to
be inserted opposite 7,8-dihydro-8-oxoguanine ."
Biochemistry, 49, 4116-4125.
doi: 10.1021/bi100102s.
|
Rb69 DNA polymerase (y567a) ternary complex with datp
opposite 7,8-dihydro-8-oxoguanine . SNAP output
|
|
3lzj
|
transferase-DNA |
X-ray (2.05 Å) |
Beckman J, Wang M, Blaha G, Wang J, Konigsberg
WH |
(2010) "Substitution
of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to
be inserted opposite 7,8-dihydro-8-oxoguanine ."
Biochemistry, 49, 4116-4125.
doi: 10.1021/bi100102s.
|
Rb69 DNA polymerase (y567a) ternary complex with dctp
opposite 7,8-dihydro-8-oxoguanine . SNAP output
|
|
3m3y
|
transferase-DNA-RNA hybrid |
X-ray (3.18 Å) |
Wang D, Zhu G, Huang X, Lippard SJ |
(2010) "X-ray
structure and mechanism of RNA polymerase II stalled at
an antineoplastic monofunctional platinum-DNA
adduct." Proc.Natl.Acad.Sci.USA,
107, 9584-9589. doi: 10.1073/pnas.1002565107.
|
RNA polymerase ii elongation complex c . SNAP output
|
|
3m4a
|
isomerase-DNA |
X-ray (1.65 Å) |
Patel A, Yakovleva L, Shuman S, Mondragon A |
(2010) "Crystal
structure of a bacterial topoisomerase IB in complex
with DNA reveals a secondary DNA binding site."
Structure, 18, 725-733. doi:
10.1016/j.str.2010.03.007.
|
Crystal structure of a bacterial topoisomerase ib in
complex with DNA reveals a secondary DNA binding site .
SNAP output
|
|
3m4o
|
transferase-DNA-RNA hybrid |
X-ray (3.57 Å) |
Wang D, Zhu G, Huang X, Lippard SJ |
(2010) "X-ray
structure and mechanism of RNA polymerase II stalled at
an antineoplastic monofunctional platinum-DNA
adduct." Proc.Natl.Acad.Sci.USA,
107, 9584-9589. doi: 10.1073/pnas.1002565107.
|
RNA polymerase ii elongation complex b . SNAP output
|
|
3m7k
|
hydrolase-DNA |
X-ray (1.92 Å) |
Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan
RD, Wilson GG, Stoddard BL |
(2010) "Unusual
target site disruption by the rare-cutting HNH
restriction endonuclease PacI." Structure,
18, 734-743. doi: 10.1016/j.str.2010.03.009.
|
Crystal structure of paci-DNA enzyme product complex .
SNAP output
|
|
3m8r
|
transferase-DNA |
X-ray (2.0 Å) |
Betz K, Streckenbach F, Schnur A, Exner T, Welte W,
Diederichs K, Marx A |
(2010) "Structures
of DNA polymerases caught processing size-augmented
nucleotide probes."
Angew.Chem.Int.Ed.Engl., 49,
5181-5184. doi: 10.1002/anie.200905724.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with trapped 4'-ethylated dttp . SNAP output
|
|
3m8s
|
transferase-DNA |
X-ray (2.2 Å) |
Betz K, Streckenbach F, Schnur A, Exner T, Welte W,
Diederichs K, Marx A |
(2010) "Structures
of DNA polymerases caught processing size-augmented
nucleotide probes."
Angew.Chem.Int.Ed.Engl., 49,
5181-5184. doi: 10.1002/anie.200905724.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with trapped 4'-methylated dttp . SNAP output
|
|
3m9e
|
transcription-DNA |
X-ray (2.406 Å) |
Chen Y, Young MA |
(2010) "Structure
of a thyroid hormone receptor DNA-binding domain
homodimer bound to an inverted palindrome DNA response
element." Mol.Endocrinol.,
24, 1650-1664. doi: 10.1210/me.2010-0129.
|
Thyroid hormone beta DNA binding domain homodimer with
inverted palindrome tre . SNAP output
|
|
3m9m
|
transferase-DNA |
X-ray (2.9 Å) |
Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling
H |
(2010) "Structural
insight into dynamic bypass of the major cisplatin-DNA
adduct by Y-family polymerase Dpo4." Embo
J., 29, 2059-2069. doi: 10.1038/emboj.2010.101.
|
Crystal structure of dpo4 in complex with DNA
containing the major cisplatin lesion . SNAP output
|
|
3m9n
|
transferase-DNA |
X-ray (1.93 Å) |
Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling
H |
(2010) "Structural
insight into dynamic bypass of the major cisplatin-DNA
adduct by Y-family polymerase Dpo4." Embo
J., 29, 2059-2069. doi: 10.1038/emboj.2010.101.
|
Crystal structure of dpo4 in complex with DNA
containing the major cisplatin lesion . SNAP output
|
|
3m9o
|
transferase-DNA |
X-ray (2.0 Å) |
Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling
H |
(2010) "Structural
insight into dynamic bypass of the major cisplatin-DNA
adduct by Y-family polymerase Dpo4." Embo
J., 29, 2059-2069. doi: 10.1038/emboj.2010.101.
|
Crystal structure of dpo4 in complex with DNA
containing the major cisplatin lesion . SNAP output
|
|
3maq
|
transferase-DNA |
X-ray (2.4 Å) |
Wang F, Yang W |
(2009) "Structural
insight into translesion synthesis by DNA Pol II."
Cell(Cambridge,Mass.), 139,
1279-1289. doi: 10.1016/j.cell.2009.11.043.
|
Crystal structure of e.coli pol ii-normal DNA-dgtp
ternary complex . SNAP
output
|
|
3mby
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Hou EW, Pedersen LC, Prasad R,
Wilson SH |
(2010) "Mutagenic
conformation of 8-oxo-7,8-dihydro-2'-dGTP in the
confines of a DNA polymerase active site."
Nat.Struct.Mol.Biol., 17,
889-890. doi: 10.1038/nsmb.1852.
|
Ternary complex of DNA polymerase beta with template
base a and 8oxodgtp in the active site with a dideoxy
terminated primer . SNAP
output
|
|
3mda
|
lyase,transferase-DNA |
X-ray (2.031 Å) |
Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM |
(2010) "Interaction
between DNA Polymerase lambda and anticancer nucleoside
analogs." J.Biol.Chem.,
285, 16874-16879. doi: 10.1074/jbc.M109.094391.
|
DNA polymerase lambda in complex with arac . SNAP output
|
|
3mdc
|
lyase,transferase-DNA |
X-ray (1.999 Å) |
Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM |
(2010) "Interaction
between DNA Polymerase lambda and anticancer nucleoside
analogs." J.Biol.Chem.,
285, 16874-16879. doi: 10.1074/jbc.M109.094391.
|
DNA polymerase lambda in complex with dfdctp . SNAP output
|
|
3mfh
|
transferase-DNA |
X-ray (2.0 Å) |
Silverstein TD, Johnson RE, Jain R, Prakash L,
Prakash S, Aggarwal AK |
(2010) "Structural
basis for the suppression of skin cancers by DNA
polymerase eta." Nature,
465, 1039-1043. doi: 10.1038/nature09104.
|
DNA polymerase eta in complex with undamaged DNA .
SNAP output
|
|
3mfi
|
transferase-DNA |
X-ray (1.76 Å) |
Silverstein TD, Johnson RE, Jain R, Prakash L,
Prakash S, Aggarwal AK |
(2010) "Structural
basis for the suppression of skin cancers by DNA
polymerase eta." Nature,
465, 1039-1043. doi: 10.1038/nature09104.
|
DNA polymerase eta in complex with a cis-syn thymidine
dimer . SNAP output
|
|
3mfk
|
transcription-DNA |
X-ray (3.0 Å) |
Babayeva ND, Wilder PJ, Shiina M, Mino K, Desler M,
Ogata K, Rizzino A, Tahirov TH |
(2010) "Structural
basis of Ets1 cooperative binding to palindromic
sequences on stromelysin-1 promoter DNA." Cell
Cycle, 9, 3054-3062.
|
Ets1 complex with stromelysin-1 promoter DNA . SNAP output
|
|
3mgh
|
lyase,transferase-DNA |
X-ray (2.4 Å) |
Bebenek K, Garcia-Diaz M, Zhou RZ, Povirk LF, Kunkel
TA |
(2010) "Loop 1
modulates the fidelity of DNA polymerase lambda."
Nucleic Acids Res., 38,
5419-5431. doi: 10.1093/nar/gkq261.
|
Binary complex of a DNA polymerase lambda loop mutant .
SNAP output
|
|
3mgi
|
lyase,transferase-DNA |
X-ray (2.603 Å) |
Bebenek K, Garcia-Diaz M, Zhou RZ, Povirk LF, Kunkel
TA |
(2010) "Loop 1
modulates the fidelity of DNA polymerase lambda."
Nucleic Acids Res., 38,
5419-5431. doi: 10.1093/nar/gkq261.
|
Ternary complex of a DNA polymerase lambda loop mutant
. SNAP output
|
|
3mgp
|
structural protein-DNA |
X-ray (2.44 Å) |
Mohideen K, Muhammad R, Davey CA |
(2010) "Perturbations
in nucleosome structure from heavy metal
association." Nucleic Acids Res.,
38, 6301-6311. doi: 10.1093/nar/gkq420.
|
Binding of cobalt ions to the nucleosome core particle
. SNAP output
|
|
3mgq
|
structural protein-DNA |
X-ray (2.65 Å) |
Mohideen K, Muhammad R, Davey CA |
(2010) "Perturbations
in nucleosome structure from heavy metal
association." Nucleic Acids Res.,
38, 6301-6311. doi: 10.1093/nar/gkq420.
|
Binding of nickel ions to the nucleosome core particle
. SNAP output
|
|
3mgr
|
structural protein-DNA |
X-ray (2.3 Å) |
Mohideen K, Muhammad R, Davey CA |
(2010) "Perturbations
in nucleosome structure from heavy metal
association." Nucleic Acids Res.,
38, 6301-6311. doi: 10.1093/nar/gkq420.
|
Binding of rubidium ions to the nucleosome core
particle . SNAP
output
|
|
3mgs
|
structural protein-DNA |
X-ray (3.15 Å) |
Mohideen K, Muhammad R, Davey CA |
(2010) "Perturbations
in nucleosome structure from heavy metal
association." Nucleic Acids Res. doi:
10.1093/nar/gkq420.
|
Binding of cesium ions to the nucleosome core particle
. SNAP output
|
|
3mgv
|
isomerase-DNA |
X-ray (2.29 Å) |
Gibb B, Gupta K, Ghosh K, Sharp R, Chen J, Van Duyne
GD |
(2010) "Requirements
for catalysis in the Cre recombinase active site."
Nucleic Acids Res., 38,
5817-5832. doi: 10.1093/nar/gkq384.
|
Cre recombinase-DNA transition state . SNAP output
|
|
3mht
|
transferase-DNA |
X-ray (2.7 Å) |
O'Gara M, Klimasauskas S, Roberts RJ, Cheng X |
(1996) "Enzymatic
C5-cytosine methylation of DNA: mechanistic
implications of new crystal structures for HhaL
methyltransferase-DNA-AdoHcy complexes."
J.Mol.Biol., 261, 634-645.
doi: 10.1006/jmbi.1996.0489.
|
Ternary structure of hhai methyltransferase with
unmodified DNA and adohcy . SNAP output
|
|
3mip
|
de novo protein-DNA |
X-ray (2.4 Å) |
Ashworth J, Taylor GK, Havranek JJ, Quadri SA,
Stoddard BL, Baker D |
(2010) "Computational
reprogramming of homing endonuclease specificity at
multiple adjacent base pairs." Nucleic Acids
Res., 38, 5601-5608. doi:
10.1093/nar/gkq283.
|
I-msoi re-designed for altered DNA cleavage specificity
(-8gcg) . SNAP
output
|
|
3mis
|
de novo protein-DNA |
X-ray (2.3 Å) |
Ashworth J, Taylor GK, Havranek JJ, Quadri SA,
Stoddard BL, Baker D |
(2010) "Computational
reprogramming of homing endonuclease specificity at
multiple adjacent base pairs." Nucleic Acids
Res., 38, 5601-5608. doi:
10.1093/nar/gkq283.
|
I-msoi re-designed for altered DNA cleavage specificity
(-8g) . SNAP output
|
|
3mkw
|
DNA binding protein-DNA |
X-ray (2.99 Å) |
Schumacher MA, Piro KM, Xu W |
(2010) "Insight
into F plasmid DNA segregation revealed by structures
of SopB and SopB-DNA complexes." Nucleic Acids
Res., 38, 4514-4526. doi:
10.1093/nar/gkq161.
|
Structure of sopb(155-272)-18mer complex, i23 form .
SNAP output
|
|
3mky
|
DNA binding protein-DNA |
X-ray (2.86 Å) |
Schumacher MA, Piro KM, Xu W |
(2010) "Insight
into F plasmid DNA segregation revealed by structures
of SopB and SopB-DNA complexes." Nucleic Acids
Res., 38, 4514-4526. doi:
10.1093/nar/gkq161.
|
Structure of sopb(155-323)-18mer DNA complex, i23 form
. SNAP output
|
|
3mkz
|
DNA-binding protein-DNA |
X-ray (2.98 Å) |
Schumacher MA, Piro KM, Xu W |
(2010) "Insight
into F plasmid DNA segregation revealed by structures
of SopB and SopB-DNA complexes." Nucleic Acids
Res., 38, 4514-4526. doi:
10.1093/nar/gkq161.
|
Structure of sopb(155-272)-18mer complex, p21 form .
SNAP output
|
|
3mln
|
transcription-DNA |
X-ray (2.4 Å) |
Treiber N, Treiber T, Zocher G, Grosschedl R |
(2010) "Structure
of an Ebf1:DNA complex reveals unusual DNA recognition
and structural homology with Rel proteins."
Genes Dev., 24, 2270-2275.
doi: 10.1101/gad.1976610.
|
DNA binding domain of early b-cell factor 1 (ebf1)
bound to DNA (crystal form ii) . SNAP output
|
|
3mlo
|
transcription-DNA |
X-ray (3.01 Å) |
Treiber N, Treiber T, Zocher G, Grosschedl R |
(2010) "Structure
of an Ebf1:DNA complex reveals unusual DNA recognition
and structural homology with Rel proteins."
Genes Dev., 24, 2270-2275.
doi: 10.1101/gad.1976610.
|
DNA binding domain of early b-cell factor 1 (ebf1)
bound to DNA (crystal form i) . SNAP output
|
|
3mlp
|
transcription-DNA |
X-ray (2.8 Å) |
Treiber N, Treiber T, Zocher G, Grosschedl R |
(2010) "Structure
of an Ebf1:DNA complex reveals unusual DNA recognition
and structural homology with Rel proteins."
Genes Dev., 24, 2270-2275.
doi: 10.1101/gad.1976610.
|
Early b-cell factor 1 (ebf1) bound to DNA . SNAP output
|
|
3mnn
|
structural protein-DNA |
X-ray (2.5 Å) |
Wu B, Ong MS, Groessl M, Adhireksan Z, Hartinger CG,
Dyson PJ, Davey CA |
(2011) "A
ruthenium antimetastasis agent forms specific histone
protein adducts in the nucleosome core."
Chemistry, 17, 3562-3566.
doi: 10.1002/chem.201100298.
|
A ruthenium antitumour agent forms specific histone
protein adducts in the nucleosome core . SNAP output
|
|
3mq6
|
hydrolase-DNA |
X-ray (2.0 Å) |
Park CK, Joshi HK, Agrawal A, Ghare MI, Little EJ,
Dunten PW, Bitinaite J, Horton NC |
(2010) "Domain
swapping in allosteric modulation of DNA
specificity." Plos Biol.,
8, e1000554. doi: 10.1371/journal.pbio.1000554.
|
Domain swapped sgrai with DNA and calcium bound .
SNAP output
|
|
3mqy
|
hydrolase-DNA |
X-ray (2.0 Å) |
Little EJ, Dunten PW, Bitinaite J, Horton NC |
(2011) "New
clues in the allosteric activation of DNA cleavage by
SgrAI: structures of SgrAI bound to cleaved
primary-site DNA and uncleaved secondary-site DNA."
Acta Crystallogr.,Sect.D, 67,
67-74. doi: 10.1107/S0907444910047785.
|
Sgrai with cleaved DNA and magnesium bound . SNAP output
|
|
3mr2
|
transferase-DNA |
X-ray (1.83 Å) |
Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S,
Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F,
Yang W |
(2010) "Structure
and mechanism of human DNA polymerase eta."
Nature, 465, 1044-1048. doi:
10.1038/nature09196.
|
Human DNA polymerase eta in complex with normal DNA and
incoming nucleotide (nrm) . SNAP output
|
|
3mr3
|
transferase-DNA |
X-ray (1.75 Å) |
Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S,
Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F,
Yang W |
(2010) "Structure
and mechanism of human DNA polymerase eta."
Nature, 465, 1044-1048. doi:
10.1038/nature09196.
|
Human DNA polymerase eta - DNA ternary complex with the
3't of a cpd in the active site (tt1) . SNAP output
|
|
3mr5
|
transferase-DNA |
X-ray (1.8 Å) |
Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S,
Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F,
Yang W |
(2010) "Structure
and mechanism of human DNA polymerase eta."
Nature, 465, 1044-1048. doi:
10.1038/nature09196.
|
Human DNA polymerase eta - DNA ternary complex with a
cpd 1bp upstream of the active site (tt3) . SNAP output
|
|
3mr6
|
transferase-DNA |
X-ray (1.9 Å) |
Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S,
Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F,
Yang W |
(2010) "Structure
and mechanism of human DNA polymerase eta."
Nature, 465, 1044-1048. doi:
10.1038/nature09196.
|
Human DNA polymerase eta - DNA ternary complex with a
cpd 2bp upstream of the active site (tt4) . SNAP output
|
|
3mu6
|
DNA binding protein-DNA |
X-ray (2.434 Å) |
Jayathilaka N, Han A, Gaffney KJ, Dey R, Jarusiewicz
JA, Noridomi K, Philips MA, Lei X, He J, Ye J, Gao T,
Petasis NA, Chen L |
(2012) "Inhibition
of the function of class IIa HDACs by blocking their
interaction with MEF2." Nucleic Acids
Res., 40, 5378-5388. doi:
10.1093/nar/gks189.
|
Inhibiting the binding of class iia histone
deacetylases to myocyte enhancer factor-2 by small
molecules . SNAP
output
|
|
3mva
|
transcription-DNA |
X-ray (2.2 Å) |
Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E,
Garcia-Diaz M |
(2010) "Helix
unwinding and base flipping enable human MTERF1 to
terminate mitochondrial transcription."
Cell(Cambridge,Mass.), 141,
982-993. doi: 10.1016/j.cell.2010.05.018.
|
Crystal structure of human mterf1 bound to the
termination sequence . SNAP output
|
|
3mvb
|
transcription-DNA |
X-ray (2.786 Å) |
Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E,
Garcia-Diaz M |
(2010) "Helix
unwinding and base flipping enable human MTERF1 to
terminate mitochondrial transcription."
Cell(Cambridge,Mass.), 141,
982-993. doi: 10.1016/j.cell.2010.05.018.
|
Crystal structure of a triple rfy mutant of human
mterf1 bound to the termination sequence . SNAP output
|
|
3mvd
|
signaling protein-structural protein-DNA |
X-ray (2.9 Å) |
Makde RD, England JR, Yennawar HP, Tan S |
(2010) "Structure
of RCC1 chromatin factor bound to the nucleosome core
particle." Nature, 467,
562-566. doi: 10.1038/nature09321.
|
Crystal structure of the chromatin factor rcc1 in
complex with the nucleosome core particle . SNAP output
|
|
3mx4
|
hydrolase-DNA |
X-ray (2.5 Å) |
Mak AN, Lambert AR, Stoddard BL |
(2010) "Folding,
DNA Recognition, and Function of GIY-YIG Endonucleases:
Crystal Structures of R.Eco29kI."
Structure, 18, 1321-1331.
doi: 10.1016/j.str.2010.07.006.
|
DNA binding and cleavage by the giy-yig endonuclease
r.eco29ki inactive variant e142q . SNAP output
|
|
3mx9
|
hydrolase-DNA |
X-ray (2.6 Å) |
Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo
P, Villate M, Merino N, Marenchino M, D'Abramo M,
Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel
I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano
L, Blanco FJ, Montoya G |
(2011) "Molecular
basis of engineered meganuclease targeting of the
endogenous human RAG1 locus." Nucleic Acids
Res., 39, 729-743. doi: 10.1093/nar/gkq801.
|
Molecular basis of engineered meganuclease targeting of
the endogenous human rag1 locus . SNAP output
|
|
3mxa
|
hydrolase-DNA |
X-ray (2.3 Å) |
Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo
P, Villate M, Merino N, Marenchino M, D'Abramo M,
Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel
I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano
L, Blanco FJ, Montoya G |
(2011) "Molecular
basis of engineered meganuclease targeting of the
endogenous human RAG1 locus." Nucleic Acids
Res., 39, 729-743. doi: 10.1093/nar/gkq801.
|
Molecular basis of engineered meganuclease targeting of
the endogenous human rag1 locus . SNAP output
|
|
3mxb
|
hydrolase-DNA |
X-ray (2.3 Å) |
Munoz IG, Prieto J, Subramanian S, Coloma J, Redondo
P, Villate M, Merino N, Marenchino M, D'Abramo M,
Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel
I, Paques F, Duchateau P, Alibes A, Stricher F, Serrano
L, Blanco FJ, Montoya G |
(2011) "Molecular
basis of engineered meganuclease targeting of the
endogenous human RAG1 locus." Nucleic Acids
Res., 39, 729-743. doi: 10.1093/nar/gkq801.
|
Molecular basis of engineered meganuclease targeting of
the endogenous human rag1 locus . SNAP output
|
|
3mxi
|
hydrolase-DNA |
X-ray (2.55 Å) |
Bailey SL, Harvey S, Perrino FW, Hollis T |
"X-ray Crystal Structures of TREX1 3' Exonuclease
Autoimmune Disease Mutants." |
Trex1 3' exonuclease d18n familial chilblain lupus
mutant . SNAP output
|
|
3mxm
|
hydrolase-DNA |
X-ray (1.75 Å) |
Bailey SL, Harvey S, Perrino FW, Hollis T |
"X-ray Crystal Structures of TREX1 3' Exonuclease
Autoimmune Disease Mutants." |
Trex1 3' exonuclease v201d aicardi-goutieres syndrome
mutant . SNAP output
|
|
3mzh
|
transcription-DNA |
X-ray (2.9 Å) |
Akhter Y, Pogenberg V, Hasnain SE, Wilmanns M |
"Crystal Structure of Camp Receptor Protein from
Mycobacterium Tuberculosis in Complex with DNA and
cAMP." |
Crystal structure of camp receptor protein from
mycobacterium tuberculosis in complex with camp and its
DNA binding element . SNAP output
|
|
3n1i
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Cappadocia L, Marechal A, Parent JS, Lepage E,
Sygusch J, Brisson N |
(2010) "Crystal
Structures of DNA-Whirly Complexes and Their Role in
Arabidopsis Organelle Genome Repair." Plant
Cell, 22, 1849-1867. doi:
10.1105/tpc.109.071399.
|
Crystal structure of a stwhy2-ere32 complex . SNAP output
|
|
3n1j
|
DNA binding protein-DNA |
X-ray (2.65 Å) |
Cappadocia L, Marechal A, Parent JS, Lepage E,
Sygusch J, Brisson N |
(2010) "Crystal
Structures of DNA-Whirly Complexes and Their Role in
Arabidopsis Organelle Genome Repair." Plant
Cell, 22, 1849-1867. doi:
10.1105/tpc.109.071399.
|
Crystal structure of a stwhy2-dt32 complex . SNAP output
|
|
3n1k
|
DNA binding protein-DNA |
X-ray (2.702 Å) |
Cappadocia L, Marechal A, Parent JS, Lepage E,
Sygusch J, Brisson N |
(2010) "Crystal
Structures of DNA-Whirly Complexes and Their Role in
Arabidopsis Organelle Genome Repair." Plant
Cell, 22, 1849-1867. doi:
10.1105/tpc.109.071399.
|
Crystal structure of a stwhy2-cere32 complex . SNAP output
|
|
3n1l
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Cappadocia L, Marechal A, Parent JS, Lepage E,
Sygusch J, Brisson N |
(2010) "Crystal
Structures of DNA-Whirly Complexes and Their Role in
Arabidopsis Organelle Genome Repair." Plant
Cell, 22, 1849-1867. doi:
10.1105/tpc.109.071399.
|
Crystal structure of a stwhy2-rcere32 complex .
SNAP output
|
|
3n4m
|
gene regulation-DNA |
X-ray (2.987 Å) |
Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA,
Birktoft J, Di Felice R, Rohs R, Lawson CL |
(2020) "The RNA
Polymerase alpha Subunit Recognizes the DNA Shape of
the Upstream Promoter Element."
Biochemistry, 59, 4523-4532.
doi: 10.1021/acs.biochem.0c00571.
|
E. coli RNA polymerase alpha subunit c-terminal domain
in complex with cap and DNA . SNAP output
|
|
3n6s
|
transcription, replication-DNA |
X-ray (3.1 Å) |
Jimenez-Menendez N, Fernandez-Millan P, Rubio-Cosials
A, Arnan C, Montoya J, Jacobs HT, Bernado P, Coll M, Uson
I, Sola M |
(2010) "Human
mitochondrial mTERF wraps around DNA through a
left-handed superhelical tandem repeat."
Nat.Struct.Mol.Biol., 17,
891-893. doi: 10.1038/nsmb.1859.
|
Crystal structure of human mitochondrial mterf in
complex with a 15-mer DNA encompassing the trnaleu(uur)
binding sequence . SNAP
output
|
|
3n78
|
hydrolase-DNA |
X-ray (2.95 Å) |
Little EJ, Dunten PW, Bitinaite J, Horton NC |
(2011) "New
clues in the allosteric activation of DNA cleavage by
SgrAI: structures of SgrAI bound to cleaved
primary-site DNA and uncleaved secondary-site DNA."
Acta Crystallogr.,Sect.D, 67,
67-74. doi: 10.1107/S0907444910047785.
|
Sgrai bound to secondary site DNA and mg(ii) . SNAP output
|
|
3n7b
|
hydrolase-DNA |
X-ray (2.65 Å) |
Little EJ, Dunten PW, Bitinaite J, Horton NC |
(2011) "New
clues in the allosteric activation of DNA cleavage by
SgrAI: structures of SgrAI bound to cleaved
primary-site DNA and uncleaved secondary-site DNA."
Acta Crystallogr.,Sect.D, 67,
67-74. doi: 10.1107/S0907444910047785.
|
Sgrai bound to secondary site DNA and ca(ii) . SNAP output
|
|
3n7q
|
transcription, replication-DNA |
X-ray (2.4 Å) |
Jimenez-Menendez N, Fernandez-Millan P, Rubio-Cosials
A, Arnan C, Montoya J, Jacobs HT, Bernado P, Coll M, Uson
I, Sola M |
(2010) "Human
mitochondrial mTERF wraps around DNA through a
left-handed superhelical tandem repeat."
Nat.Struct.Mol.Biol., 17,
891-893. doi: 10.1038/nsmb.1859.
|
Crystal structure of human mitochondrial mterf fragment
(aa 99-399) in complex with a 12-mer DNA encompassing
the trnaleu(uur) binding sequence . SNAP output
|
|
3n97
|
gene regulation-DNA |
X-ray (3.252 Å) |
Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA,
Birktoft J, Di Felice R, Rohs R, Lawson CL |
(2020) "The RNA
Polymerase alpha Subunit Recognizes the DNA Shape of
the Upstream Promoter Element."
Biochemistry, 59, 4523-4532.
doi: 10.1021/acs.biochem.0c00571.
|
RNA polymerase alpha c-terminal domain (e. coli) and
sigma region 4 (t. aq. mutant) bound to (up,-35
element) DNA . SNAP
output
|
|
3nae
|
transferase-DNA |
X-ray (2.003 Å) |
Beckman J, Wang M, Blaha G, Wang J, Konigsberg
WH |
(2010) "Substitution
of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP
and dGMP To Be Inserted opposite Guanidinohydantoin
." Biochemistry, 49,
8554-8563. doi: 10.1021/bi100913v.
|
Rb69 DNA polymerase (y567a) ternary complex with datp
opposite guanidinohydantoin . SNAP output
|
|
3nbn
|
transcription-DNA |
X-ray (3.45 Å) |
Arnett KL, Hass M, McArthur DG, Ilagan MX, Aster JC,
Kopan R, Blacklow SC |
(2010) "Structural
and mechanistic insights into cooperative assembly of
dimeric Notch transcription complexes."
Nat.Struct.Mol.Biol., 17,
1312-1317. doi: 10.1038/nsmb.1938.
|
Crystal structure of a dimer of notch transcription
complex trimers on hes1 DNA . SNAP output
|
|
3nci
|
transferase-DNA |
X-ray (1.79 Å) |
Wang M, Xia S, Blaha G, Steitz TA, Konigsberg WH,
Wang J |
(2011) "Insights
into base selectivity from the 1.8 A resolution
structure of an RB69 DNA polymerase ternary
complex." Biochemistry,
50, 581-590. doi: 10.1021/bi101192f.
|
Rb69 DNA polymerase ternary complex with dctp opposite
dg at 1.8 angstrom resolution . SNAP output
|
|
3ndh
|
hydrolase-DNA |
X-ray (1.3 Å) |
Firczuk M, Wojciechowski M, Czapinska H, Bochtler
M |
(2011) "DNA
intercalation without flipping in the specific ThaI-DNA
complex." Nucleic Acids Res.,
39, 744-754. doi: 10.1093/nar/gkq834.
|
Restriction endonuclease in complex with substrate DNA
. SNAP output
|
|
3ndk
|
transferase-DNA |
X-ray (2.0 Å) |
Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T,
Wang J, Konigsberg W |
(2011) "Variation
in Mutation Rates Caused by RB69pol Fidelity Mutants
Can Be Rationalized on the Basis of Their Kinetic
Behavior and Crystal Structures."
J.Mol.Biol., 406, 558-570.
doi: 10.1016/j.jmb.2010.12.033.
|
Rb69 DNA polymerase (y567a) ternary complex with dctp
opposite dg . SNAP
output
|
|
3ne6
|
transferase-DNA |
X-ray (2.001 Å) |
Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T,
Wang J, Konigsberg W |
(2011) "Variation
in Mutation Rates Caused by RB69pol Fidelity Mutants
Can Be Rationalized on the Basis of Their Kinetic
Behavior and Crystal Structures."
J.Mol.Biol., 406, 558-570.
doi: 10.1016/j.jmb.2010.12.033.
|
Rb69 DNA polymerase (s565g-y567a) ternary complex with
dctp opposite dg . SNAP
output
|
|
3ngd
|
transferase-DNA |
X-ray (2.8 Å) |
Pence MG, Choi JY, Egli M, Guengerich FP |
(2010) "Structural
Basis for Proficient Incorporation of dTTP Opposite
O6-Methylguanine by Human DNA Polymerase {iota}."
J.Biol.Chem., 285,
40666-40672. doi: 10.1074/jbc.M110.183665.
|
Structural basis for proficient incorporation of dttp
opposite o6-methylguanine by human DNA polymerase iota
. SNAP output
|
|
3ngi
|
transferase-DNA |
X-ray (1.886 Å) |
Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T,
Wang J, Konigsberg W |
(2011) "Variation
in Mutation Rates Caused by RB69pol Fidelity Mutants
Can Be Rationalized on the Basis of Their Kinetic
Behavior and Crystal Structures."
J.Mol.Biol., 406, 558-570.
doi: 10.1016/j.jmb.2010.12.033.
|
Rb69 DNA polymerase (y567a) ternary complex with dttp
opposite dg . SNAP
output
|
|
3ngo
|
hydrolase-DNA |
X-ray (2.2 Å) |
Wang H, Morita M, Yang X, Suzuki T, Yang W, Wang J,
Ito K, Wang Q, Zhao C, Bartlam M, Yamamoto T, Rao Z |
(2010) "Crystal
structure of the human CNOT6L nuclease domain reveals
strict poly(A) substrate specificity." Embo
J. doi: 10.1038/emboj.2010.152.
|
Crystal structure of the human cnot6l nuclease domain
in complex with poly(a) DNA . SNAP output
|
|
3ngz
|
hydrolase-DNA |
X-ray (2.1 Å) |
Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan
HS |
(2011) "Structural
basis for RNA trimming by RNase T in stable RNA 3'-end
maturation." Nat.Chem.Biol.,
7, 236-243. doi: 10.1038/nchembio.524.
|
Crystal structure of rnase t in complex with a
non-preferred ssDNA (gc) with one mg in the active site
. SNAP output
|
|
3nh0
|
hydrolase-DNA |
X-ray (2.3 Å) |
Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan
HS |
(2011) "Structural
basis for RNA trimming by RNase T in stable RNA 3'-end
maturation." Nat.Chem.Biol.,
7, 236-243. doi: 10.1038/nchembio.524.
|
Crystal structure of rnase t in complex with a
non-preferred ssDNA (aac) . SNAP output
|
|
3nh1
|
hydrolase-DNA |
X-ray (2.107 Å) |
Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan
HS |
(2011) "Structural
basis for RNA trimming by RNase T in stable RNA 3'-end
maturation." Nat.Chem.Biol.,
7, 236-243. doi: 10.1038/nchembio.524.
|
Crystal structure of rnase t in complex with a
preferred ssDNA (tagg) with two mg in the active site .
SNAP output
|
|
3nh2
|
hydrolase-DNA |
X-ray (2.3 Å) |
Hsiao Y-Y, Yang C-C, Lin CL, Lin JLJ, Duh Y, Yuan
HS |
(2011) "Structural
basis for RNA trimming by RNase T in stable RNA 3'-end
maturation." Nat.Chem.Biol.,
7, 236-243. doi: 10.1038/nchembio.524.
|
Crystal structure of rnase t in complex with a stem DNA
with a 3' overhang . SNAP output
|
|
3nhg
|
transferase-DNA |
X-ray (2.5 Å) |
Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T,
Wang J, Konigsberg W |
(2011) "Variation
in Mutation Rates Caused by RB69pol Fidelity Mutants
Can Be Rationalized on the Basis of Their Kinetic
Behavior and Crystal Structures."
J.Mol.Biol., 406, 558-570.
doi: 10.1016/j.jmb.2010.12.033.
|
Rb69 DNA polymerase (s565g-y567a) ternary complex with
dttp opposite dg . SNAP
output
|
|
3nic
|
hydrolase-DNA |
X-ray (2.8 Å) |
Mak AN, Lambert AR, Stoddard BL |
(2010) "Folding,
DNA Recognition, and Function of GIY-YIG Endonucleases:
Crystal Structures of R.Eco29kI."
Structure, 18, 1321-1331.
doi: 10.1016/j.str.2010.07.006.
|
DNA binding and cleavage by the giy-yig endonuclease
r.eco29ki inactive variant y49f . SNAP output
|
|
3nm9
|
gene regulation-DNA |
X-ray (2.85 Å) |
Churchill ME, Klass J, Zoetewey DL |
(2010) "Structural
analysis of HMGD-DNA complexes reveals influence of
intercalation on sequence selectivity and DNA
bending." J.Mol.Biol.,
403, 88-102. doi: 10.1016/j.jmb.2010.08.031.
|
Hmgd(m13a)-DNA complex . SNAP output
|
|
3o1m
|
oxidoreductase |
X-ray (1.75 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1o
|
oxidoreductase |
X-ray (1.92 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang C-G, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1p
|
oxidoreductase |
X-ray (1.51 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1r
|
oxidoreductase |
X-ray (1.77 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1s
|
oxidoreductase |
X-ray (1.58 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1t
|
oxidoreductase |
X-ray (1.48 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1u
|
oxidoreductase |
X-ray (1.54 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o1v
|
oxidoreductase |
X-ray (1.9 Å) |
Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X,
Yang CG, Cui Q, He C |
(2010) "Iron-catalysed
oxidation intermediates captured in a DNA repair
dioxygenase." Nature,
468, 330-333. doi: 10.1038/nature09497.
|
Iron-catalyzed oxidation intermediates captured in a
DNA repair dioxygenase . SNAP output
|
|
3o3f
|
hydrolase-DNA-RNA hybrid |
X-ray (2.0 Å) |
Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch
RJ, Nowotny M |
(2010) "Crystal
Structures of RNase H2 in Complex with Nucleic Acid
Reveal the Mechanism of RNA-DNA Junction Recognition
and Cleavage." Mol.Cell,
40, 658-670. doi: 10.1016/j.molcel.2010.11.001.
|
T. maritima rnase h2 d107n in complex with nucleic acid
substrate and magnesium ions . SNAP output
|
|
3o3g
|
hydrolase-DNA-RNA hybrid |
X-ray (2.1 Å) |
Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch
RJ, Nowotny M |
(2010) "Crystal
Structures of RNase H2 in Complex with Nucleic Acid
Reveal the Mechanism of RNA-DNA Junction Recognition
and Cleavage." Mol.Cell,
40, 658-670. doi: 10.1016/j.molcel.2010.11.001.
|
T. maritima rnase h2 in complex with nucleic acid
substrate and calcium ions . SNAP output
|
|
3o3h
|
hydrolase-DNA-RNA hybrid |
X-ray (2.8 Å) |
Rychlik MP, Chon H, Cerritelli SM, Klimek P, Crouch
RJ, Nowotny M |
(2010) "Crystal
Structures of RNase H2 in Complex with Nucleic Acid
Reveal the Mechanism of RNA-DNA Junction Recognition
and Cleavage." Mol.Cell,
40, 658-670. doi: 10.1016/j.molcel.2010.11.001.
|
T. maritima rnase h2 d107n in complex with nucleic acid
substrate and manganese ions . SNAP output
|
|
3o62
|
structural protein-DNA |
X-ray (3.216 Å) |
Todd RC, Lippard SJ |
(2010) "Consequences
of Cisplatin binding on nucleosome structure and
dynamics." Chem.Biol.,
17, 1334-1343. doi: 10.1016/j.chembiol.2010.10.018.
|
Nucleosome core particle modified with a cisplatin
1,3-cis-{pt(nh3)2}2+-d(gptpg) intrastrand cross-link .
SNAP output
|
|
3o9x
|
transcription regulator-DNA |
X-ray (2.1 Å) |
Brown BL, Wood TK, Peti W, Page R |
(2011) "Structure
of the Escherichia coli Antitoxin MqsA (YgiT/b3021)
Bound to Its Gene Promoter Reveals Extensive Domain
Rearrangements and the Specificity of Transcriptional
Regulation." J.Biol.Chem.,
286, 2285-2296. doi: 10.1074/jbc.M110.172643.
|
Structure of the e. coli antitoxin mqsa (ygit-b3021) in
complex with its gene promoter . SNAP output
|
|
3oa6
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Kim D, Blus BJ, Chandra V, Huang P, Rastinejad F,
Khorasanizadeh S |
(2010) "Corecognition
of DNA and a methylated histone tail by the MSL3
chromodomain." Nat.Struct.Mol.Biol.,
17, 1027-1029. doi: 10.1038/nsmb.1856.
|
Human msl3 chromodomain bound to DNA and h4k20me1
peptide . SNAP
output
|
|
3od8
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Langelier MF, Planck JL, Roy S, Pascal JM |
(2011) "Crystal
Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1)
Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL
INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY."
J.Biol.Chem., 286,
10690-10701. doi: 10.1074/jbc.M110.202507.
|
Human parp-1 zinc finger 1 (zn1) bound to DNA .
SNAP output
|
|
3oda
|
DNA binding protein-DNA |
X-ray (2.64 Å) |
Langelier MF, Planck JL, Roy S, Pascal JM |
(2011) "Crystal
Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1)
Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL
INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY."
J.Biol.Chem., 286,
10690-10701. doi: 10.1074/jbc.M110.202507.
|
Human parp-1 zinc finger 1 (zn1) bound to DNA .
SNAP output
|
|
3odc
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Langelier MF, Planck JL, Roy S, Pascal JM |
(2011) "Crystal
Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1)
Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL
INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY."
J.Biol.Chem., 286,
10690-10701. doi: 10.1074/jbc.M110.202507.
|
Human parp-1 zinc finger 2 (zn2) bound to DNA .
SNAP output
|
|
3ode
|
DNA binding protein-DNA |
X-ray (2.95 Å) |
Langelier MF, Planck JL, Roy S, Pascal JM |
(2011) "Crystal
Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1)
Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL
INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY."
J.Biol.Chem., 286,
10690-10701. doi: 10.1074/jbc.M110.202507.
|
Human parp-1 zinc finger 2 (zn2) bound to DNA .
SNAP output
|
|
3odh
|
hydrolase-DNA |
X-ray (2.3 Å) |
Vanamee ES, Viadiu H, Chan SH, Ummat A, Hartline AM,
Xu SY, Aggarwal AK |
(2011) "Asymmetric
DNA recognition by the OkrAI endonuclease, an
isoschizomer of BamHI." Nucleic Acids
Res., 39, 712-719. doi: 10.1093/nar/gkq779.
|
Structure of okrai-DNA complex . SNAP output
|
|
3ogd
|
hydrolase-DNA |
X-ray (2.8 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2010) "Structure
of Escherichia coli AlkA in Complex with Undamaged
DNA." J.Biol.Chem., 285,
35783-35791. doi: 10.1074/jbc.M110.155663.
|
Alka undamaged DNA complex: interrogation of a g*:c
base pair . SNAP
output
|
|
3ogu
|
transferase-DNA |
X-ray (1.845 Å) |
Gieseking S, Bergen K, Di Pasquale F, Diederichs K,
Welte W, Marx A |
(2011) "Human
DNA polymerase beta mutations allowing efficient abasic
site bypass." J.Biol.Chem.,
286, 4011-4020. doi: 10.1074/jbc.M110.176826.
|
DNA polymerase beta mutant 5p20 complexed with 6bp of
DNA . SNAP output
|
|
3oh6
|
hydrolase-DNA |
X-ray (2.894 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2010) "Structure
of Escherichia coli AlkA in Complex with Undamaged
DNA." J.Biol.Chem., 285,
35783-35791. doi: 10.1074/jbc.M110.155663.
|
Alka undamaged DNA complex: interrogation of a c:g base
pair . SNAP output
|
|
3oh9
|
hydrolase-DNA |
X-ray (2.802 Å) |
Bowman BR, Lee S, Wang S, Verdine GL |
(2010) "Structure
of Escherichia coli AlkA in Complex with Undamaged
DNA." J.Biol.Chem., 285,
35783-35791. doi: 10.1074/jbc.M110.155663.
|
Alka undamaged DNA complex: interrogation of a t:a base
pair . SNAP output
|
|
3oha
|
transferase-DNA |
X-ray (2.0 Å) |
Silverstein TD, Jain R, Johnson RE, Prakash L,
Prakash S, Aggarwal AK |
(2010) "Structural
basis for error-free replication of oxidatively damaged
DNA by yeast DNA polymerase eta."
Structure, 18, 1463-1470.
doi: 10.1016/j.str.2010.08.019.
|
Yeast DNA polymerase eta inserting dctp opposite an
8oxog lesion . SNAP
output
|
|
3ohb
|
transferase-DNA |
X-ray (2.0 Å) |
Silverstein TD, Jain R, Johnson RE, Prakash L,
Prakash S, Aggarwal AK |
(2010) "Structural
basis for error-free replication of oxidatively damaged
DNA by yeast DNA polymerase eta."
Structure, 18, 1463-1470.
doi: 10.1016/j.str.2010.08.019.
|
Yeast DNA polymerase eta extending from an 8-oxog
lesion . SNAP output
|
|
3ojs
|
transferase-DNA |
X-ray (1.9 Å) |
Obeid S, Baccaro A, Welte W, Diederichs K, Marx
A |
(2010) "Structural
basis for the synthesis of nucleobase modified DNA by
Thermus aquaticus DNA polymerase."
Proc.Natl.Acad.Sci.USA, 107,
21327-21331. doi: 10.1073/pnas.1013804107.
|
Snapshots of the large fragment of DNA polymerase i
from thermus aquaticus processing c5 modified
thymidines . SNAP
output
|
|
3oju
|
transferase-DNA |
X-ray (2.0 Å) |
Obeid S, Baccaro A, Welte W, Diederichs K, Marx
A |
(2010) "Structural
basis for the synthesis of nucleobase modified DNA by
Thermus aquaticus DNA polymerase."
Proc.Natl.Acad.Sci.USA, 107,
21327-21331. doi: 10.1073/pnas.1013804107.
|
Snapshot of the large fragment of DNA polymerase i from
thermus aquaticus processing c5 modified thymidies .
SNAP output
|
|
3on0
|
DNA binding protein-DNA |
X-ray (2.874 Å) |
Wong JJ, Lu J, Edwards RA, Frost LS, Glover JN |
(2011) "Structural
basis of cooperative DNA recognition by the plasmid
conjugation factor, TraM." Nucleic Acids
Res., 39, 6775-6788. doi:
10.1093/nar/gkr296.
|
Crystal structure of the ped208 tram-sbma complex .
SNAP output
|
|
3ool
|
hydrolase-DNA |
X-ray (2.3 Å) |
Joshi R, Ho KK, Tenney K, Chen JH, Golden BL, Gimble
FS |
(2011) "Evolution
of I-SceI Homing Endonucleases with Increased DNA
Recognition Site Specificity."
J.Mol.Biol., 405, 185-200.
doi: 10.1016/j.jmb.2010.10.029.
|
I-scei complexed with c-g+4 DNA substrate . SNAP output
|
|
3oor
|
hydrolase-DNA |
X-ray (2.5 Å) |
Joshi R, Ho KK, Tenney K, Chen JH, Golden BL, Gimble
FS |
(2011) "Evolution
of I-SceI Homing Endonucleases with Increased DNA
Recognition Site Specificity."
J.Mol.Biol., 405, 185-200.
doi: 10.1016/j.jmb.2010.10.029.
|
I-scei mutant (k86r-g100t)complexed with c-g+4 DNA
substrate . SNAP
output
|
|
3oqg
|
hydrolase-DNA |
X-ray (1.75 Å) |
Sokolowska M, Czapinska H, Bochtler M |
(2011) "Hpy188I-DNA
pre- and post-cleavage complexes--snapshots of the
GIY-YIG nuclease mediated catalysis." Nucleic
Acids Res., 39, 1554-1564. doi:
10.1093/nar/gkq821.
|
Restriction endonuclease hpy188i in complex with
substrate DNA . SNAP
output
|
|
3oqm
|
transcription-transferase-DNA |
X-ray (2.96 Å) |
Schumacher MA, Sprehe M, Bartholomae M, Hillen W,
Brennan RG |
(2011) "Structures
of carbon catabolite protein A-(HPr-Ser46-P) bound to
diverse catabolite response element sites reveal the
basis for high-affinity binding to degenerate DNA
operators." Nucleic Acids Res.,
39, 2931-2942. doi: 10.1093/nar/gkq1177.
|
Structure of ccpa-hpr-ser46p-acka2 complex . SNAP output
|
|
3oqn
|
transcription-transferase-DNA |
X-ray (3.3 Å) |
Schumacher MA, Sprehe M, Bartholomae M, Hillen W,
Brennan RG |
(2011) "Structures
of carbon catabolite protein A-(HPr-Ser46-P) bound to
diverse catabolite response element sites reveal the
basis for high-affinity binding to degenerate DNA
operators." Nucleic Acids Res.,
39, 2931-2942. doi: 10.1093/nar/gkq1177.
|
Structure of ccpa-hpr-ser46-p-gntr-down cre . SNAP output
|
|
3oqo
|
transcription-transferase-DNA |
X-ray (2.97 Å) |
Schumacher MA, Sprehe M, Bartholomae M, Hillen W,
Brennan RG |
(2011) "Structures
of carbon catabolite protein A-(HPr-Ser46-P) bound to
diverse catabolite response element sites reveal the
basis for high-affinity binding to degenerate DNA
operators." Nucleic Acids Res.,
39, 2931-2942. doi: 10.1093/nar/gkq1177.
|
Ccpa-hpr-ser46p-syn cre . SNAP output
|
|
3or3
|
hydrolase-DNA |
X-ray (1.95 Å) |
Sokolowska M, Czapinska H, Bochtler M |
(2011) "Hpy188I-DNA
pre- and post-cleavage complexes--snapshots of the
GIY-YIG nuclease mediated catalysis." Nucleic
Acids Res., 39, 1554-1564. doi:
10.1093/nar/gkq821.
|
Restriction endonuclease hpy188i in complex with
product DNA . SNAP
output
|
|
3orc
|
gene regulation-DNA |
X-ray (3.0 Å) |
Albright RA, Mossing MC, Matthews BW |
(1998) "Crystal
structure of an engineered Cro monomer bound
nonspecifically to DNA: possible implications for
nonspecific binding by the wild-type protein."
Protein Sci., 7, 1485-1494.
|
Crystal structure of an engineered cro monomer bound
nonspecifically to DNA . SNAP output
|
|
3os0
|
recombination-DNA |
X-ray (2.81 Å) |
Maertens GN, Hare S, Cherepanov P |
(2010) "The
mechanism of retroviral integration from X-ray
structures of its key intermediates."
Nature, 468, 326-329. doi:
10.1038/nature09517.
|
Pfv strand transfer complex (stc) at 2.81 Å resolution
. SNAP output
|
|
3os1
|
recombination-DNA |
X-ray (2.97 Å) |
Maertens GN, Hare S, Cherepanov P |
(2010) "The
mechanism of retroviral integration from X-ray
structures of its key intermediates."
Nature, 468, 326-329. doi:
10.1038/nature09517.
|
Pfv target capture complex (tcc) at 2.97 Å resolution .
SNAP output
|
|
3os2
|
recombination-DNA |
X-ray (3.32 Å) |
Maertens GN, Hare S, Cherepanov P |
(2010) "The
mechanism of retroviral integration from X-ray
structures of its key intermediates."
Nature, 468, 326-329. doi:
10.1038/nature09517.
|
Pfv target capture complex (tcc) at 3.32 Å resolution .
SNAP output
|
|
3osf
|
transcription-DNA |
X-ray (2.032 Å) |
Jiang I, Tsai CK, Chen SC, Wang SH, Amiraslanov I,
Chang CF, Wu WJ, Tai JH, Liaw YC, Huang TH |
(2011) "Molecular
basis of the recognition of the ap65-1 gene
transcription promoter elements by a Myb protein from
the protozoan parasite Trichomonas vaginalis."
Nucleic Acids Res., 39,
8992-9008. doi: 10.1093/nar/gkr558.
|
The structure of protozoan parasite trichomonas
vaginalis myb2 in complex with mre-2f-13 DNA . SNAP output
|
|
3osg
|
transcription-DNA |
X-ray (1.997 Å) |
Jiang I, Tsai CK, Chen SC, Wang SH, Amiraslanov I,
Chang CF, Wu WJ, Tai JH, Liaw YC, Huang TH |
(2011) "Molecular
basis of the recognition of the ap65-1 gene
transcription promoter elements by a Myb protein from
the protozoan parasite Trichomonas vaginalis."
Nucleic Acids Res., 39,
8992-9008. doi: 10.1093/nar/gkr558.
|
The structure of protozoan parasite trichomonas
vaginalis myb2 in complex with mre-1-12 DNA . SNAP output
|
|
3osn
|
transferase-DNA |
X-ray (1.9 Å) |
Pence MG, Choi JY, Egli M, Guengerich FP |
(2010) "Structural
Basis for Proficient Incorporation of dTTP Opposite
O6-Methylguanine by Human DNA Polymerase {iota}."
J.Biol.Chem., 285,
40666-40672. doi: 10.1074/jbc.M110.183665.
|
Structural basis for proficient incorporation of dttp
opposite o6-methylguanine by human DNA polymerase iota
. SNAP output
|
|
3osp
|
transferase-DNA |
X-ray (2.5 Å) |
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2011) "DNA
synthesis across an abasic lesion by yeast REV1 DNA
polymerase." J.Mol.Biol.,
406, 18-28. doi: 10.1016/j.jmb.2010.12.016.
|
Structure of rev1 . SNAP
output
|
|
3oy9
|
recombination,viral protein-DNA |
X-ray (2.55 Å) |
Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov
P |
(2010) "Retroviral
intasome assembly and inhibition of DNA strand
transfer." Nature, 464,
232-236. doi: 10.1038/nature08784.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with manganese at 2.55 resolution .
SNAP output
|
|
3oya
|
recombination,viral protein-DNA |
X-ray (2.65 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and raltegravir at
2.65 resolution . SNAP
output
|
|
3oyb
|
recombination,viral protein-DNA |
X-ray (2.54 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti mk2048
. SNAP output
|
|
3oyc
|
recombination,viral protein-DNA |
X-ray (2.66 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti pica .
SNAP output
|
|
3oyd
|
recombination,viral protein-DNA |
X-ray (2.54 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti gs9160
. SNAP output
|
|
3oye
|
recombination,viral protein-DNA |
X-ray (2.74 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti
compound2 . SNAP
output
|
|
3oyf
|
recombination,viral protein-DNA |
X-ray (2.51 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti
l-870,810 . SNAP
output
|
|
3oyg
|
recombination,viral protein-DNA |
X-ray (2.56 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti
compound1 (compoundg) . SNAP output
|
|
3oyh
|
recombination,viral protein-DNA |
X-ray (2.74 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti mk0536
. SNAP output
|
|
3oyi
|
recombination,viral protein-DNA |
X-ray (2.72 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the pfv s217q mutant intasome in
complex with manganese . SNAP output
|
|
3oyj
|
recombination,viral protein-DNA |
X-ray (2.68 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the pfv s217q mutant intasome in
complex with magnesium and the insti mk2048 . SNAP output
|
|
3oyk
|
recombination,viral protein-DNA |
X-ray (2.72 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the pfv s217h mutant intasome
bound to manganese . SNAP output
|
|
3oyl
|
recombination,viral protein-DNA |
X-ray (2.54 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the pfv s217h mutant intasome
bound to magnesium and the insti mk2048 . SNAP output
|
|
3oym
|
recombination,viral protein-DNA |
X-ray (2.02 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the pfv n224h mutant intasome
bound to manganese . SNAP output
|
|
3oyn
|
recombination,viral protein-DNA |
X-ray (2.68 Å) |
Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD,
Cherepanov P |
(2010) "Molecular
mechanisms of retroviral integrase inhibition and the
evolution of viral resistance."
Proc.Natl.Acad.Sci.USA, 107,
20057-20062. doi: 10.1073/pnas.1010246107.
|
Crystal structure of the pfv n224h mutant intasome
bound to magnesium and the insti mk2048 . SNAP output
|
|
3p57
|
transferase-transcription activator-DNA |
X-ray (2.19 Å) |
He J, Ye J, Cai Y, Riquelme C, Liu JO, Liu X, Han A,
Chen L |
(2011) "Structure
of p300 bound to MEF2 on DNA reveals a mechanism of
enhanceosome assembly." Nucleic Acids
Res., 39, 4464-4474. doi:
10.1093/nar/gkr030.
|
Crystal structure of the p300 taz2 domain bound to mef2
on DNA . SNAP output
|
|
3p6y
|
RNA binding protein-RNA |
X-ray (2.9 Å) |
Li H, Tong S, Li X, Shi H, Gao Y, Ge H, Niu L, Teng
M |
"Structural basis of pre-mRNA recognition by the
human cleavage factor Im complex." |
Cf im25-cf im68-uguaa complex . SNAP output
|
|
3pih
|
hydrolase-DNA |
X-ray (2.9 Å) |
Jaciuk M, Nowak E, Skowronek K, Tanska A, Nowotny
M |
(2011) "Structure
of UvrA nucleotide excision repair protein in complex
with modified DNA." Nat.Struct.Mol.Biol.,
18, 191-197. doi: 10.1038/nsmb.1973.
|
T. maritima uvra in complex with fluorescein-modified
DNA . SNAP output
|
|
3pjr
|
hydrolase-DNA |
X-ray (3.3 Å) |
Velankar SS, Soultanas P, Dillingham MS, Subramanya
HS, Wigley DB |
(1999) "Crystal
structures of complexes of PcrA DNA helicase with a DNA
substrate indicate an inchworm mechanism."
Cell(Cambridge,Mass.), 97,
75-98. doi: 10.1016/S0092-8674(00)80716-3.
|
Helicase substrate complex . SNAP output
|
|
3pky
|
transferase-DNA |
X-ray (3.1 Å) |
Brissett NC, Martin MJ, Pitcher RS, Bianchi J, Juarez
R, Green AJ, Fox GC, Blanco L, Doherty AJ |
(2011) "Structure
of a Preternary Complex Involving a Prokaryotic NHEJ
DNA Polymerase." Mol.Cell,
41, 221-231. doi: 10.1016/j.molcel.2010.12.026.
|
Polymerase domain from mycobacterium tuberculosis
ligase d in complex with DNA, utp and manganese. .
SNAP output
|
|
3pml
|
lyase,transferase-DNA |
X-ray (2.6 Å) |
Bebenek K, Pedersen LC, Kunkel TA |
(2011) "Replication
infidelity via a mismatch with Watson-Crick
geometry." Proc.Natl.Acad.Sci.USA,
108, 1862-1867. doi: 10.1073/pnas.1012825108.
|
Crystal structure of a polymerase lambda variant with a
dgtp analog opposite a templating t . SNAP output
|
|
3pmn
|
lyase,transferase-DNA |
X-ray (2.2 Å) |
Bebenek K, Pedersen LC, Kunkel TA |
(2011) "Replication
infidelity via a mismatch with Watson-Crick
geometry." Proc.Natl.Acad.Sci.USA,
108, 1862-1867. doi: 10.1073/pnas.1012825108.
|
Ternary crystal structure of polymerase lambda variant
with a gt mispair at the primer terminus with mn2+ in
the active site . SNAP
output
|
|
3pnc
|
lyase,transferase-DNA |
X-ray (2.0 Å) |
Bebenek K, Pedersen LC, Kunkel TA |
(2011) "Replication
infidelity via a mismatch with Watson-Crick
geometry." Proc.Natl.Acad.Sci.USA,
108, 1862-1867. doi: 10.1073/pnas.1012825108.
|
Ternary crystal structure of a polymerase lambda
variant with a gt mispair at the primer terminus and
sodium at catalytic metal site . SNAP output
|
|
3po2
|
transferase-DNA-RNA |
X-ray (3.3 Å) |
Cheung AC, Cramer P |
(2011) "Structural
basis of RNA polymerase II backtracking, arrest and
reactivation." Nature,
471, 249-253. doi: 10.1038/nature09785.
|
Arrested RNA polymerase ii elongation complex .
SNAP output
|
|
3po3
|
transferase-DNA-RNA |
X-ray (3.3 Å) |
Cheung AC, Cramer P |
(2011) "Structural
basis of RNA polymerase II backtracking, arrest and
reactivation." Nature,
471, 249-253. doi: 10.1038/nature09785.
|
Arrested RNA polymerase ii reactivation intermediate .
SNAP output
|
|
3po4
|
transferase-DNA |
X-ray (1.8 Å) |
Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W,
Diederichs K, Marx A |
(2011) "Learning
from Directed Evolution: Thermus aquaticus DNA
Polymerase Mutants with Translesion Synthesis
Activity." Chembiochem,
12, 1574-1580. doi: 10.1002/cbic.201000783.
|
Structure of a mutant of the large fragment of DNA
polymerase i from thermus aquaticus in complex with a
blunt-ended DNA and ddatp . SNAP output
|
|
3po5
|
transferase-DNA |
X-ray (2.39 Å) |
Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W,
Diederichs K, Marx A |
(2011) "Learning
from Directed Evolution: Thermus aquaticus DNA
Polymerase Mutants with Translesion Synthesis
Activity." Chembiochem,
12, 1574-1580. doi: 10.1002/cbic.201000783.
|
Structure of a mutant of the large fragment of DNA
polymerase i from thermus auqaticus in complex with an
abasic site and ddatp . SNAP output
|
|
3pov
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Bagneris C, Briggs LC, Savva R, Ebrahimi B, Barrett
TE |
(2011) "Crystal
structure of a KSHV-SOX-DNA complex: insights into the
molecular mechanisms underlying DNase activity and host
shutoff." Nucleic Acids Res.,
39, 5744-5756. doi: 10.1093/nar/gkr111.
|
Crystal structure of a sox-DNA complex . SNAP output
|
|
3pr4
|
transferase-DNA |
X-ray (2.65 Å) |
Kirouac KN, Suo Z, Ling H |
(2011) "Structural
mechanism of ribonucleotide discrimination by a
Y-family DNA polymerase." J.Mol.Biol.,
407, 382-390. doi: 10.1016/j.jmb.2011.01.037.
|
Dpo4 y12a mutant incorporating dadp opposite template
dt . SNAP output
|
|
3pr5
|
transferase-DNA |
X-ray (2.4 Å) |
Kirouac KN, Suo Z, Ling H |
(2011) "Structural
mechanism of ribonucleotide discrimination by a
Y-family DNA polymerase." J.Mol.Biol.,
407, 382-390. doi: 10.1016/j.jmb.2011.01.037.
|
Dpo4 y12a mutant incorporating adp opposite template dt
. SNAP output
|
|
3pt6
|
transferase-DNA |
X-ray (3.0 Å) |
Song J, Rechkoblit O, Bestor TH, Patel DJ |
(2011) "Structure
of DNMT1-DNA complex reveals a role for autoinhibition
in maintenance DNA methylation." Science,
331, 1036-1040. doi: 10.1126/science.1195380.
|
Crystal structure of mouse dnmt1(650-1602) in complex
with DNA . SNAP
output
|
|
3pta
|
transferase-DNA |
X-ray (3.6 Å) |
Song J, Rechkoblit O, Bestor TH, Patel DJ |
(2011) "Structure
of DNMT1-DNA complex reveals a role for autoinhibition
in maintenance DNA methylation." Science,
331, 1036-1040. doi: 10.1126/science.1195380.
|
Crystal structure of human dnmt1(646-1600) in complex
with DNA . SNAP
output
|
|
3pv8
|
transferase-DNA |
X-ray (1.52 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to DNA and ddttp-da in closed
conformation . SNAP
output
|
|
3pvi
|
hydrolase-DNA |
X-ray (1.59 Å) |
Horton JR, Nastri HG, Riggs PD, Cheng X |
(1998) "Asp34 of
PvuII endonuclease is directly involved in DNA minor
groove recognition and indirectly involved in
catalysis." J.Mol.Biol.,
284, 1491-1504. doi: 10.1006/jmbi.1998.2269.
|
D34g mutant of pvuii endonuclease complexed with
cognate DNA shows that asp34 is directly involved in
DNA recognition and indirectly involved in catalysis .
SNAP output
|
|
3pvp
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Tsodikov OV, Biswas T |
(2011) "Structural
and Thermodynamic Signatures of DNA Recognition by
Mycobacterium tuberculosis DnaA."
J.Mol.Biol., 410, 461-476.
doi: 10.1016/j.jmb.2011.05.007.
|
Structure of mycobacterium tuberculosis dnaa-dbd in
complex with box2 DNA . SNAP output
|
|
3pvv
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Tsodikov OV, Biswas T |
(2011) "Structural
and Thermodynamic Signatures of DNA Recognition by
Mycobacterium tuberculosis DnaA."
J.Mol.Biol., 410, 461-476.
doi: 10.1016/j.jmb.2011.05.007.
|
Structure of mycobacterium tuberculosis dnaa-dbd in
complex with box1 DNA . SNAP output
|
|
3pvx
|
transferase-DNA |
X-ray (3.03 Å) |
Banerjee S, Brown KL, Egli M, Stone MP |
(2011) "Bypass
of Aflatoxin B(1) Adducts by the Sulfolobus
solfataricus DNA Polymerase IV."
J.Am.Chem.Soc., 133,
12556-12568. doi: 10.1021/ja2015668.
|
Binary complex of aflatoxin b1 adduct modified DNA
(afb1-fapy) with DNA polymerase iv . SNAP output
|
|
3pw0
|
transferase-DNA |
X-ray (2.91 Å) |
Banerjee S, Brown KL, Egli M, Stone MP |
(2011) "Bypass
of Aflatoxin B(1) Adducts by the Sulfolobus
solfataricus DNA Polymerase IV."
J.Am.Chem.Soc., 133,
12556-12568. doi: 10.1021/ja2015668.
|
Ternary complex of aflatoxin b1 adduct modified DNA
(afb1-fapy) with DNA polymerase iv and incoming datp .
SNAP output
|
|
3pw2
|
transferase-DNA |
X-ray (2.74 Å) |
Banerjee S, Brown KL, Egli M, Stone MP |
(2011) "Bypass
of Aflatoxin B(1) Adducts by the Sulfolobus
solfataricus DNA Polymerase IV."
J.Am.Chem.Soc., 133,
12556-12568. doi: 10.1021/ja2015668.
|
Ternary complex of aflatoxin b1 adduct modified DNA
(afb1-fapy) with DNA polymerase iv and incoming dttp .
SNAP output
|
|
3pw4
|
transferase-DNA |
X-ray (2.9 Å) |
Banerjee S, Brown KL, Egli M, Stone MP |
(2011) "Bypass
of Aflatoxin B(1) Adducts by the Sulfolobus
solfataricus DNA Polymerase IV."
J.Am.Chem.Soc., 133,
12556-12568. doi: 10.1021/ja2015668.
|
Ternary complex of aflatoxin b1 adduct modified DNA
(afb1-n7-gua) with DNA polymerase iv and incoming datp
. SNAP output
|
|
3pw5
|
transferase-DNA |
X-ray (3.0 Å) |
Banerjee S, Brown KL, Egli M, Stone MP |
(2011) "Bypass
of Aflatoxin B(1) Adducts by the Sulfolobus
solfataricus DNA Polymerase IV."
J.Am.Chem.Soc., 133,
12556-12568. doi: 10.1021/ja2015668.
|
Ternary complex of aflatoxin b1 adduct modified DNA
(afb1-n7-gua) with DNA polymerase iv and incoming dttp
. SNAP output
|
|
3pw7
|
transferase-DNA |
X-ray (2.9 Å) |
Banerjee S, Brown KL, Egli M, Stone MP |
(2011) "Bypass
of Aflatoxin B(1) Adducts by the Sulfolobus
solfataricus DNA Polymerase IV."
J.Am.Chem.Soc., 133,
12556-12568. doi: 10.1021/ja2015668.
|
Ternary complex of aflatoxin b1 adduct modified DNA
(afb1-n7-gua) with DNA polymerase iv and incoming dctp
. SNAP output
|
|
3px0
|
transferase-DNA |
X-ray (1.73 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to DNA and dctp-da mismatch (tautomer)
in closed conformation . SNAP output
|
|
3px4
|
transferase-DNA |
X-ray (1.582 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to DNA and ddctp-da mismatch (wobble) in
ajar conformation . SNAP
output
|
|
3px6
|
transferase-DNA |
X-ray (1.59 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to DNA and ddctp-da mismatch (tautomer)
in closed conformation . SNAP output
|
|
3px7
|
isomerase-DNA |
X-ray (2.3 Å) |
Tse-Dinh YC, Zhang Z, Cheng B |
"Structure of E. coli Topoisomerase I Trapped as
Covalent Complex Intermediate with Cleaved DNA." |
Crystal structure of covalent complex of topoisomerase
1a with substrate . SNAP
output
|
|
3py8
|
transferase-DNA |
X-ray (1.74 Å) |
Obeid S, Schnur A, Gloeckner C, Blatter N, Welte W,
Diederichs K, Marx A |
(2011) "Learning
from Directed Evolution: Thermus aquaticus DNA
Polymerase Mutants with Translesion Synthesis
Activity." Chembiochem,
12, 1574-1580. doi: 10.1002/cbic.201000783.
|
Crystal structure of a mutant of the large fragment of
DNA polymerase i from thermus aquaticus in a closed
ternary complex with DNA and ddctp . SNAP output
|
|
3pzp
|
transferase-DNA |
X-ray (3.336 Å) |
Vasquez-Del Carpio R, Silverstein TD, Lone S, Johnson
RE, Prakash L, Prakash S, Aggarwal AK |
(2011) "Role of
human DNA polymerase kappa in extension opposite from a
cis-syn thymine dimer." J.Mol.Biol.,
408, 252-261. doi: 10.1016/j.jmb.2011.02.042.
|
Human DNA polymerase kappa extending opposite a cis-syn
thymine dimer . SNAP
output
|
|
3q05
|
antitumor protein-DNA |
X-ray (2.4 Å) |
Petty TJ, Emamzadah S, Costantino L, Petkova I,
Stavridi ES, Saven JG, Vauthey E, Halazonetis TD |
(2011) "An
induced fit mechanism regulates p53 DNA binding
kinetics to confer sequence specificity." Embo
J., 30, 2167-2176. doi: 10.1038/emboj.2011.127.
|
An induced fit mechanism regulates p53 DNA binding
kinetics to confer sequence specificity . SNAP output
|
|
3q06
|
cell cycle-DNA |
X-ray (3.2 Å) |
Petty TJ, Emamzadah S, Costantino L, Petkova I,
Stavridi ES, Saven JG, Vauthey E, Halazonetis TD |
(2011) "An
induced fit mechanism regulates p53 DNA binding
kinetics to confer sequence specificity." Embo
J., 30, 2167-2176. doi: 10.1038/emboj.2011.127.
|
An induced fit mechanism regulates p53 DNA binding
kinetics to confer sequence specificity . SNAP output
|
|
3q0a
|
transcription-DNA |
X-ray (2.69 Å) |
Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB,
Murakami KS |
(2011) "X-ray
crystal structures elucidate the nucleotidyl transfer
reaction of transcript initiation using two
nucleotides." Proc.Natl.Acad.Sci.USA,
108, 3566-3571. doi: 10.1073/pnas.1016691108.
|
X-ray crystal structure of the transcription initiation
complex of the n4 mini-vrnap with p2 promoter: mismatch
complex . SNAP
output
|
|
3q0b
|
transferase-DNA |
X-ray (2.2 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra- fully methylated cg DNA
complex in space group p42212 . SNAP output
|
|
3q0c
|
transferase-DNA |
X-ray (2.66 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra-fully methylated cg DNA
complex in space group p6122 . SNAP output
|
|
3q0d
|
transferase-DNA |
X-ray (2.37 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra- hemi methylated cg DNA
complex . SNAP
output
|
|
3q0f
|
transferase-DNA |
X-ray (2.75 Å) |
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson
LM, Reinberg D, Patel DJ, Jacobsen SE |
(2011) "A dual
flip-out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA
methylation and H3K9 dimethylation in vivo."
Genes Dev., 25, 137-152. doi:
10.1101/gad.1980311.
|
Crystal structure of suvh5 sra- methylated chh DNA
complex . SNAP
output
|
|
3q1m
|
transcription-DNA |
X-ray (3.2 Å) |
Bachas S, Eginton C, Gunio D, Wade H |
(2011) "Structural
contributions to multidrug recognition in the multidrug
resistance (MDR) gene regulator, BmrR."
Proc.Natl.Acad.Sci.USA, 108,
11046-11051. doi: 10.1073/pnas.1104850108.
|
Crystal structure of bmrr dimer bound to DNA and the
ligand 4-amino-quinaldine . SNAP output
|
|
3q1q
|
hydrolase-RNA |
X-ray (3.8 Å) |
Reiter NJ, Osterman A, Torres-Larios A, Swinger KK,
Pan T, Mondragon A |
(2010) "Structure
of a Bacterial Ribonuclease P Holoenzyme in Complex
with tRNA." Nature, 468,
784-789. doi: 10.1038/NATURE09516.
|
Structure of a bacterial ribonuclease p holoenzyme in
complex with trna . SNAP
output
|
|
3q1r
|
hydrolase-RNA |
X-ray (4.21 Å) |
Reiter NJ, Osterman A, Torres-Larios A, Swinger KK,
Pan T, Mondragon A |
(2010) "Structure
of a Bacterial Ribonuclease P Holoenzyme in Complex
with tRNA." Nature, 468,
784-789. doi: 10.1038/NATURE09516.
|
Crystal structure of a bacterial rnase p holoenzyme in
complex with trna and in the presence of 5' leader .
SNAP output
|
|
3q22
|
transferase-DNA |
X-ray (2.11 Å) |
Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB,
Murakami KS |
(2011) "X-ray
crystal structures elucidate the nucleotidyl transfer
reaction of transcript initiation using two
nucleotides." Proc.Natl.Acad.Sci.USA,
108, 3566-3571. doi: 10.1073/pnas.1016691108.
|
X-ray crystal structure of the n4 mini-vrnap and p2_7a
promoter transcription initiation complex with gtp and
magnesium: substrate complex i . SNAP output
|
|
3q23
|
transferase-DNA |
X-ray (1.8 Å) |
Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB,
Murakami KS |
(2011) "X-ray
crystal structures elucidate the nucleotidyl transfer
reaction of transcript initiation using two
nucleotides." Proc.Natl.Acad.Sci.USA,
108, 3566-3571. doi: 10.1073/pnas.1016691108.
|
X-ray crystal structure of the n4 mini-vrnap and p2_7a
promoter transcription initiation complex with gmpcpp
and manganese: sustrate complex ii . SNAP output
|
|
3q24
|
transferase-DNA-RNA |
X-ray (1.81 Å) |
Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB,
Murakami KS |
(2011) "X-ray
crystal structures elucidate the nucleotidyl transfer
reaction of transcript initiation using two
nucleotides." Proc.Natl.Acad.Sci.USA,
108, 3566-3571. doi: 10.1073/pnas.1016691108.
|
X-ray crystal structure of the n4 mini-vrnap and p2_7a
promoter transcription initiation complex with pppgpg
and pyrophosphate: product complex . SNAP output
|
|
3q2y
|
transcription-DNA |
X-ray (2.95 Å) |
Bachas S, Eginton C, Gunio D, Wade H |
(2011) "Structural
contributions to multidrug recognition in the multidrug
resistance (MDR) gene regulator, BmrR."
Proc.Natl.Acad.Sci.USA, 108,
11046-11051. doi: 10.1073/pnas.1104850108.
|
Crystal structure of bmrr bound to ethidium . SNAP output
|
|
3q3d
|
transcription regulator-DNA-antibiotic |
X-ray (2.79 Å) |
Bachas S, Eginton C, Gunio D, Wade H |
(2011) "Structural
contributions to multidrug recognition in the multidrug
resistance (MDR) gene regulator, BmrR."
Proc.Natl.Acad.Sci.USA, 108,
11046-11051. doi: 10.1073/pnas.1104850108.
|
Crystal structure of bmrr bound to puromycin . SNAP output
|
|
3q5f
|
transcription-DNA |
X-ray (2.96 Å) |
Dolan KT, Duguid EM, He C |
(2011) "Crystal
Structures of SlyA Protein, a Master Virulence
Regulator of Salmonella, in Free and DNA-bound
States." J.Biol.Chem.,
286, 22178-22185. doi: 10.1074/jbc.M111.245258.
|
Crystal structure of the salmonella transcriptional
regulator slya in complex with DNA . SNAP output
|
|
3q5p
|
transcription-DNA-antibiotic |
X-ray (2.942 Å) |
Bachas S, Eginton C, Gunio D, Wade H |
(2011) "Structural
contributions to multidrug recognition in the multidrug
resistance (MDR) gene regulator, BmrR."
Proc.Natl.Acad.Sci.USA, 108,
11046-11051. doi: 10.1073/pnas.1104850108.
|
Crystal structure of bmrr bound to tetracycline .
SNAP output
|
|
3q5r
|
transcription-RNA-antibiotic |
X-ray (3.05 Å) |
Bachas S, Eginton C, Gunio D, Wade H |
(2011) "Structural
contributions to multidrug recognition in the multidrug
resistance (MDR) gene regulator, BmrR."
Proc.Natl.Acad.Sci.USA, 108,
11046-11051. doi: 10.1073/pnas.1104850108.
|
Crystal structure of bmrr bound to kanamycin . SNAP output
|
|
3q5s
|
transcription-DNA |
X-ray (3.1 Å) |
Bachas S, Eginton C, Gunio D, Wade H |
(2011) "Structural
contributions to multidrug recognition in the multidrug
resistance (MDR) gene regulator, BmrR."
Proc.Natl.Acad.Sci.USA, 108,
11046-11051. doi: 10.1073/pnas.1104850108.
|
Crystal structure of bmrr bound to acetylcholine .
SNAP output
|
|
3q8k
|
hydrolase-DNA |
X-ray (2.2 Å) |
Tsutakawa SE, Classen S, Chapados BR, Arvai AS,
Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker
AH, Shen B, Cooper PK, Grasby JA, Tainer JA |
(2011) "Human
Flap Endonuclease Structures, DNA Double-Base Flipping,
and a Unified Understanding of the FEN1
Superfamily." Cell(Cambridge,Mass.),
145, 198-211. doi: 10.1016/j.cell.2011.03.004.
|
Crystal structure of human flap endonuclease fen1 (wt)
in complex with product 5'-flap DNA, sm3+, and k+ .
SNAP output
|
|
3q8l
|
hydrolase-DNA |
X-ray (2.319 Å) |
Tsutakawa SE, Classen S, Chapados BR, Arvai AS,
Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker
AH, Shen B, Cooper PK, Grasby JA, Tainer JA |
(2011) "Human
Flap Endonuclease Structures, DNA Double-Base Flipping,
and a Unified Understanding of the FEN1
Superfamily." Cell(Cambridge,Mass.),
145, 198-211. doi: 10.1016/j.cell.2011.03.004.
|
Crystal structure of human flap endonuclease fen1 (wt)
in complex with substrate 5'-flap DNA, sm3+, and k+ .
SNAP output
|
|
3q8m
|
hydrolase-DNA |
X-ray (2.6 Å) |
Tsutakawa SE, Classen S, Chapados BR, Arvai AS,
Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker
AH, Shen B, Cooper PK, Grasby JA, Tainer JA |
(2011) "Human
Flap Endonuclease Structures, DNA Double-Base Flipping,
and a Unified Understanding of the FEN1
Superfamily." Cell(Cambridge,Mass.),
145, 198-211. doi: 10.1016/j.cell.2011.03.004.
|
Crystal structure of human flap endonuclease fen1
(d181a) in complex with substrate 5'-flap DNA and k+ .
SNAP output
|
|
3q8p
|
transferase-DNA |
X-ray (1.95 Å) |
Kirouac KN, Ling H |
(2011) "Unique
active site promotes error-free replication opposite an
8-oxo-guanine lesion by human DNA polymerase iota."
Proc.Natl.Acad.Sci.USA, 108,
3210-3215. doi: 10.1073/pnas.1013909108.
|
Human DNA polymerase iota incorporating dctp opposite
8-oxo-guanine . SNAP
output
|
|
3q8q
|
transferase-DNA |
X-ray (2.031 Å) |
Kirouac KN, Ling H |
(2011) "Unique
active site promotes error-free replication opposite an
8-oxo-guanine lesion by human DNA polymerase iota."
Proc.Natl.Acad.Sci.USA, 108,
3210-3215. doi: 10.1073/pnas.1013909108.
|
Human DNA polymerase iota incorporating datp opposite
8-oxo-guanine . SNAP
output
|
|
3q8r
|
transferase-DNA |
X-ray (2.45 Å) |
Kirouac KN, Ling H |
(2011) "Unique
active site promotes error-free replication opposite an
8-oxo-guanine lesion by human DNA polymerase iota."
Proc.Natl.Acad.Sci.USA, 108,
3210-3215. doi: 10.1073/pnas.1013909108.
|
Human DNA polymerase iota incorporating dgtp opposite
8-oxo-guanine . SNAP
output
|
|
3q8s
|
transferase-DNA |
X-ray (2.09 Å) |
Kirouac KN, Ling H |
"Human DNA polymerase iota incorporating dTTP
opposite 8-oxo-guanine." |
Human DNA polymerase iota incorporating dttp opposite
8-oxo-guanine . SNAP
output
|
|
3qe9
|
hydrolase-DNA |
X-ray (2.51 Å) |
Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW,
Modrich P, Beese LS |
(2011) "Structures
of human exonuclease 1 DNA complexes suggest a unified
mechanism for nuclease family."
Cell(Cambridge,Mass.), 145,
212-223. doi: 10.1016/j.cell.2011.03.005.
|
Crystal structure of human exonuclease 1 exo1 (d173a)
in complex with DNA (complex i) . SNAP output
|
|
3qea
|
hydrolase-DNA |
X-ray (3.1 Å) |
Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW,
Modrich P, Beese LS |
(2011) "Structures
of human exonuclease 1 DNA complexes suggest a unified
mechanism for nuclease family."
Cell(Cambridge,Mass.), 145,
212-223. doi: 10.1016/j.cell.2011.03.005.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with DNA (complex ii) . SNAP output
|
|
3qeb
|
hydrolase-DNA |
X-ray (3.0 Å) |
Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW,
Modrich P, Beese LS |
(2011) "Structures
of human exonuclease 1 DNA complexes suggest a unified
mechanism for nuclease family."
Cell(Cambridge,Mass.), 145,
212-223. doi: 10.1016/j.cell.2011.03.005.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with DNA and mn2+ (complex iii) . SNAP output
|
|
3qei
|
transferase-DNA |
X-ray (2.178 Å) |
Xia S, Eom SH, Konigsberg WH, Wang J |
(2012) "Structural
Basis for Differential Insertion Kinetics of dNMPs
Opposite a Difluorotoluene Nucleotide Residue."
Biochemistry, 51, 1476-1485.
doi: 10.1021/bi2016487.
|
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dctp opposite difluorotoluene nucleoside .
SNAP output
|
|
3qep
|
transferase-DNA |
X-ray (1.8 Å) |
Xia S, Konigsberg WH, Wang J |
(2011) "Hydrogen-bonding
capability of a templating difluorotoluene nucleotide
residue in an RB69 DNA polymerase ternary complex."
J.Am.Chem.Soc., 133,
10003-10005. doi: 10.1021/ja2021735.
|
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dttp opposite difluorotoluene nucleoside .
SNAP output
|
|
3qer
|
transferase-DNA |
X-ray (1.96 Å) |
Xia S, Eom SH, Konigsberg WH, Wang J |
(2012) "Structural
Basis for Differential Insertion Kinetics of dNMPs
Opposite a Difluorotoluene Nucleotide Residue."
Biochemistry, 51, 1476-1485.
doi: 10.1021/bi2016487.
|
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with datp opposite difluorotoluene nucleoside .
SNAP output
|
|
3qes
|
transferase-DNA |
X-ray (1.98 Å) |
Xia S, Eom SH, Konigsberg WH, Wang J |
(2012) "Structural
Basis for Differential Insertion Kinetics of dNMPs
Opposite a Difluorotoluene Nucleotide Residue."
Biochemistry, 51, 1476-1485.
doi: 10.1021/bi2016487.
|
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dgtp opposite difluorotoluene nucleoside .
SNAP output
|
|
3qet
|
transferase-DNA |
X-ray (2.08 Å) |
Xia S, Konigsberg WH, Wang J |
"Hydrogen-Bonding Capability of Difluorotoluene
Nucleoside in Replication Complexes." |
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dttp opposite dt . SNAP output
|
|
3qev
|
transferase-DNA |
X-ray (1.77 Å) |
Xia S, Konigsberg WH, Wang J |
"Hydrogen-Bonding Capability of Difluorotoluene
Nucleoside in Replication Complexes." |
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dctp opposite dt . SNAP output
|
|
3qew
|
transferase-DNA |
X-ray (1.84 Å) |
Xia S, Konigsberg WH, Wang J |
"Hydrogen-Bonding Capability of Difluorotoluene
Nucleoside in Replication Complexes." |
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with ddtp opposite dt . SNAP output
|
|
3qex
|
transferase-DNA |
X-ray (1.73 Å) |
Xia S, Konigsberg WH, Wang J |
"Hydrogen-Bonding Capability of Difluorotoluene
Nucleoside in Replication Complexes." |
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dgtp opposite dt . SNAP output
|
|
3qfq
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Harrison CJ, Meinke G, Kwun HJ, Rogalin H, Phelan PJ,
Bullock PA, Chang Y, Moore PS, Bohm A |
(2011) "Asymmetric
assembly of merkel cell polyomavirus large T-antigen
origin binding domains at the viral origin."
J.Mol.Biol., 409, 529-542.
doi: 10.1016/j.jmb.2011.03.051.
|
Asymmetric assembly of merkel cell polyomavirus large
t-antigen origin binding domains at the viral origin .
SNAP output
|
|
3qi5
|
hydrolase-DNA |
X-ray (2.2 Å) |
Lingaraju GM, Davis CA, Setser JW, Samson LD, Drennan
CL |
(2011) "Structural
Basis for the Inhibition of Human Alkyladenine DNA
Glycosylase (AAG) by 3,N4-Ethenocytosine-containing
DNA." J.Biol.Chem., 286,
13205-13213. doi: 10.1074/jbc.M110.192435.
|
Crystal structure of human alkyladenine DNA glycosylase
in complex with 3,n4-ethenocystosine containing duplex
DNA . SNAP output
|
|
3qlp
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.14 Å) |
Russo Krauss I, Merlino A, Giancola C, Randazzo A,
Mazzarella L, Sica F |
(2011) "Thrombin-aptamer
recognition: a revealed ambiguity." Nucleic
Acids Res., 39, 7858-7867. doi:
10.1093/nar/gkr522.
|
X-ray structure of the complex between human alpha
thrombin and a modified thrombin binding aptamer (mtba)
. SNAP output
|
|
3qmb
|
DNA binding protein-DNA |
X-ray (2.06 Å) |
Xu C, Bian C, Lam R, Dong A, Min J |
(2011) "The
structural basis for selective binding of
non-methylated CpG islands by the CFP1 CXXC
domain." Nat Commun, 2,
227. doi: 10.1038/ncomms1237.
|
Structural basis of selective binding of nonmethylated
cpg islands by the cxxc domain of cfp1 . SNAP output
|
|
3qmc
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Xu C, Bian C, Lam R, Dong A, Min J |
(2011) "The
structural basis for selective binding of
non-methylated CpG islands by the CFP1 CXXC
domain." Nat Commun, 2,
227. doi: 10.1038/ncomms1237.
|
Structural basis of selective binding of nonmethylated
cpg islands by the cxxc domain of cfp1 . SNAP output
|
|
3qmd
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Xu C, Bian C, Lam R, Dong A, Min J |
(2011) "The
structural basis for selective binding of
non-methylated CpG islands by the CFP1 CXXC
domain." Nat Commun, 2,
227. doi: 10.1038/ncomms1237.
|
Structural basis of selective binding of nonmethylated
cpg islands by the cxxc domain of cfp1 . SNAP output
|
|
3qmg
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Xu C, Bian C, Lam R, Dong A, Min J |
(2011) "The
structural basis for selective binding of
non-methylated CpG islands by the CFP1 CXXC
domain." Nat Commun, 2,
227. doi: 10.1038/ncomms1237.
|
Structural basis of selective binding of non-methylated
cpg islands by the cxxc domain of cfp1 . SNAP output
|
|
3qmh
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Xu C, Bian C, Lam R, Dong A, Min J |
(2011) "The
structural basis for selective binding of
non-methylated CpG islands by the CFP1 CXXC
domain." Nat Commun, 2,
227. doi: 10.1038/ncomms1237.
|
Structural basis of selective binding of non-methylated
cpg islands (DNA-tcga) by the cxxc domain of cfp1 .
SNAP output
|
|
3qmi
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Xu C, Bian C, Lam R, Dong A, Min J |
(2011) "The
structural basis for selective binding of
non-methylated CpG islands by the CFP1 CXXC
domain." Nat Commun, 2,
227. doi: 10.1038/ncomms1237.
|
Structural basis of selective binding of non-methylated
cpg islands (DNA-acgt) by the cxxc domain of cfp1 .
SNAP output
|
|
3qnn
|
transferase-DNA |
X-ray (1.92 Å) |
Xia S, Beckman J, Wang J, Konigsberg WH |
(2012) "Using a
Fluorescent Cytosine Analogue tC(o) To Probe the Effect
of the Y567 to Ala Substitution on the Preinsertion
Steps of dNMP Incorporation by RB69 DNA
Polymerase." Biochemistry,
51, 4609-4617. doi: 10.1021/bi300241m.
|
Rb69 DNA polymerase (y567a) ternary complex with dgt
opposite 3tco . SNAP
output
|
|
3qno
|
transferase-DNA |
X-ray (1.88 Å) |
Xia S, Beckman J, Wang J, Konigsberg WH |
(2012) "Using a
Fluorescent Cytosine Analogue tC(o) To Probe the Effect
of the Y567 to Ala Substitution on the Preinsertion
Steps of dNMP Incorporation by RB69 DNA
Polymerase." Biochemistry,
51, 4609-4617. doi: 10.1021/bi300241m.
|
Rb69 DNA polymerase (y567a) ternary complex with datp
opposite 3tco . SNAP
output
|
|
3qoq
|
transcription-DNA |
X-ray (3.1 Å) |
Pryor Jr EE, Waligora EA, Xu B, Dellos-Nolan S,
Wozniak DJ, Hollis T |
(2012) "The
Transcription Factor AmrZ Utilizes Multiple DNA Binding
Modes to Recognize Activator and Repressor Sequences of
Pseudomonas aeruginosa Virulence Genes." Plos
Pathog., 8, e1002648. doi:
10.1371/journal.ppat.1002648.
|
Crystal structure of the transcription factor amrz in
complex with the 18 base pair amrz1 binding site .
SNAP output
|
|
3qqy
|
hydrolase-DNA |
X-ray (2.401 Å) |
Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ,
Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL |
(2011) "Tapping
natural reservoirs of homing endonucleases for targeted
gene modification."
Proc.Natl.Acad.Sci.USA, 108,
13077-13082. doi: 10.1073/pnas.1107719108.
|
Crystal structure of a novel laglidadg homing
endonuclease, i-onui (from ophiostoma novo-ulmi subsp.
americana) . SNAP
output
|
|
3qrf
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Bandukwala HS, Wu Y, Feuerer M, Chen Y, Barboza B,
Ghosh S, Stroud JC, Benoist C, Mathis D, Rao A, Chen
L |
(2011) "Structure
of a Domain-Swapped FOXP3 Dimer on DNA and Its Function
in Regulatory T Cells." Immunity,
34, 479-491. doi: 10.1016/j.immuni.2011.02.017.
|
Structure of a domain-swapped foxp3 dimer . SNAP output
|
|
3qsv
|
transcription-DNA |
X-ray (2.708 Å) |
Baburajendran N, Jauch R, Zhen CTY, Kolatkar PR |
"Structural basis for DNA recognition by constitutive
Smad4 MH1 dimers." |
Structural basis for DNA recognition by constitutive
smad4 mh1 dimers . SNAP
output
|
|
3qx3
|
isomerase-DNA-isomerase inhibitor |
X-ray (2.162 Å) |
Wu CC, Li TK, Farh L, Lin LY, Lin TS, Yu YJ, Yen TJ,
Chiang CW, Chan NL |
(2011) "Structural
basis of type II topoisomerase inhibition by the
anticancer drug etoposide." Science,
333, 459-462. doi: 10.1126/science.1204117.
|
Human topoisomerase iibeta in complex with DNA and
etoposide . SNAP
output
|
|
3qym
|
transcription activator-DNA |
X-ray (3.2 Å) |
Chen C, Gorlatova N, Kelman Z, Herzberg O |
(2011) "Structures
of p63 DNA binding domain in complexes with half-site
and with spacer-containing full response elements."
Proc.Natl.Acad.Sci.USA, 108,
6456-6461. doi: 10.1073/pnas.1013657108.
|
Structure of p63 DNA binding domain in complex with a
10 base pair a-t rich response element half site .
SNAP output
|
|
3qyn
|
transcription activator-DNA |
X-ray (2.5 Å) |
Chen C, Gorlatova N, Kelman Z, Herzberg O |
(2011) "Structures
of p63 DNA binding domain in complexes with half-site
and with spacer-containing full response elements."
Proc.Natl.Acad.Sci.USA, 108,
6456-6461. doi: 10.1073/pnas.1013657108.
|
Structure of p63 DNA binding domain in complex with a
22 base pair a-t rich response element containing 2
base pair spacer between half sites . SNAP output
|
|
3qyx
|
transcription-DNA |
X-ray (3.75 Å) |
Blasco B, Stenta M, Alonso-Sarduy L, Dietler G,
Peraro MD, Cole ST, Pojer F |
(2011) "Atypical
DNA recognition mechanism used by the EspR virulence
regulator of Mycobacterium tuberculosis."
Mol.Microbiol., 82, 251-264.
doi: 10.1111/j.1365-2958.2011.07813.x.
|
Crystal structure of mycobacterium tuberculosis espr in
complex with a small DNA fragment . SNAP output
|
|
3qz7
|
transferase-DNA |
X-ray (1.998 Å) |
Wu Y, Wilson RC, Pata JD |
(2011) "The
y-family DNA polymerase dpo4 uses a template slippage
mechanism to create single-base deletions."
J.Bacteriol., 193, 2630-2636.
doi: 10.1128/JB.00012-11.
|
T-3 ternary complex of dpo4 . SNAP output
|
|
3qz8
|
transferase-DNA |
X-ray (1.999 Å) |
Wu Y, Wilson RC, Pata JD |
(2011) "The
y-family DNA polymerase dpo4 uses a template slippage
mechanism to create single-base deletions."
J.Bacteriol., 193, 2630-2636.
doi: 10.1128/JB.00012-11.
|
Tt-4 ternary complex of dpo4 . SNAP output
|
|
3r7p
|
hydrolase-DNA |
X-ray (2.704 Å) |
Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ,
Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL |
(2011) "Tapping
natural reservoirs of homing endonucleases for targeted
gene modification."
Proc.Natl.Acad.Sci.USA, 108,
13077-13082. doi: 10.1073/pnas.1107719108.
|
The crystal structure of i-ltri . SNAP output
|
|
3r8f
|
replication activator-DNA |
X-ray (3.366 Å) |
Duderstadt KE, Chuang K, Berger JM |
(2011) "DNA
stretching by bacterial initiators promotes replication
origin opening." Nature,
478, 209-213. doi: 10.1038/nature10455.
|
Replication initiator dnaa bound to amppcp and
single-stranded DNA . SNAP output
|
|
3ra0
|
DNA binding protein-DNA |
X-ray (2.451 Å) |
Cappadocia L, Parent JS, Zampini E, Lepage E, Sygusch
J, Brisson N |
(2012) "A
conserved lysine residue of plant Whirly proteins is
necessary for higher order protein assembly and
protection against DNA damage." Nucleic Acids
Res., 40, 258-269. doi: 10.1093/nar/gkr740.
|
Crystal structure of a stwhy2 k67a-dt32 complex .
SNAP output
|
|
3ra4
|
virus |
X-ray (2.7 Å) |
Nam HJ, Gurda BL, McKenna R, Potter M, Byrne B,
Salganik M, Muzyczka N, Agbandje-McKenna M |
(2011) "Structural
studies of adeno-associated virus serotype 8 capsid
transitions associated with endosomal trafficking."
J.Virol., 85, 11791-11799.
doi: 10.1128/JVI.05305-11.
|
Structural studies of aav8 capsid transitions
associated with endosomal trafficking . SNAP output
|
|
3ra9
|
virus |
X-ray (2.7 Å) |
Nam HJ, Gurda BL, McKenna R, Potter M, Byrne B,
Salganik M, Muzyczka N, Agbandje-McKenna M |
(2011) "Structural
studies of adeno-associated virus serotype 8 capsid
transitions associated with endosomal trafficking."
J.Virol., 85, 11791-11799.
doi: 10.1128/JVI.05305-11.
|
Structural studies of aav8 capsid transitions
associated with endosomal trafficking . SNAP output
|
|
3rad
|
isomerase-DNA-antibiotic |
X-ray (3.35 Å) |
Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A,
Moser HE, Fisher LM, Sanderson MR |
(2016) "Exploring
the active site of the Streptococcus pneumoniae
topoisomerase IV-DNA cleavage complex with novel
7,8-bridged fluoroquinolones." Open Biol,
6. doi: 10.1098/rsob.160157.
|
Quinolone(clinafloxacin)-DNA cleavage complex of type
iv topoisomerase from s. pneumoniae . SNAP output
|
|
3rae
|
isomerase-DNA-antibiotic |
X-ray (2.9 Å) |
Veselkov DA, Laponogov I, Pan XS, Selvarajah J,
Skamrova GB, Branstrom A, Narasimhan J, Prasad JV, Fisher
LM, Sanderson MR |
(2016) "Structure
of a quinolone-stabilized cleavage complex of
topoisomerase IV from Klebsiella pneumoniae and
comparison with a related Streptococcus pneumoniae
complex." Acta Crystallogr.,Sect.D,
72, 488-496. doi: 10.1107/S2059798316001212.
|
Quinolone(levofloxacin)-DNA cleavage complex of type iv
topoisomerase from s. pneumoniae . SNAP output
|
|
3raf
|
isomerase-DNA-antibiotic |
X-ray (3.24 Å) |
Laponogov I, Pan X-S, Veselkov DA, McAuley KE, Fisher
LM, Sanderson MR |
"Inhibitor-stabilised cleavage complexes of
topoisomerase IIa: structural analysis of drug-dependent
inter- and intramolecular interactions." |
Quinazolinedione-DNA cleavage complex of type iv
topoisomerase from s. pneumoniae . SNAP output
|
|
3raq
|
transferase-DNA |
X-ray (2.25 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
c base opposite the 1-methylguanine (mg1) lesion .
SNAP output
|
|
3rax
|
transferase-DNA |
X-ray (1.891 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
t base opposite the 1-methylguanine (m1g) lesion .
SNAP output
|
|
3rb0
|
transferase-DNA |
X-ray (3.225 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
g base opposite the 1-methylguanine (m1g) lesion .
SNAP output
|
|
3rb3
|
transferase-DNA |
X-ray (2.8 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
a base opposite the 1-methylguanine (m1g) lesion .
SNAP output
|
|
3rb4
|
transferase-DNA |
X-ray (2.805 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
g base opposite the 3-methylcytosine (m3c) lesion .
SNAP output
|
|
3rb6
|
transferase-DNA |
X-ray (2.7 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
a base opposite the 3-methylcytosine (m3c) lesion .
SNAP output
|
|
3rbd
|
transferase-DNA |
X-ray (2.502 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
c base opposite the 3-methylcytosine (m3c) lesion .
SNAP output
|
|
3rbe
|
transferase-DNA |
X-ray (2.8 Å) |
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ |
(2011) "Implications
for damage recognition during Dpo4-mediated mutagenic
bypass of m1G and m3C lesions." Structure,
19, 821-832. doi: 10.1016/j.str.2011.03.020.
|
Dpo4 extension ternary complex with 3'-terminal primer
t base opposite the 3-methylcytosine (m3c) lesion .
SNAP output
|
|
3reh
|
structural protein-DNA |
X-ray (2.5 Å) |
Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA |
(2011) "Specific
DNA structural attributes modulate platinum anticancer
drug site selection and cross-link generation."
Nucleic Acids Res., 39,
8200-8212. doi: 10.1093/nar/gkr491.
|
2.5 angstrom crystal structure of the nucleosome core
particle assembled with a 145 bp alpha-satellite DNA
(ncp145) . SNAP
output
|
|
3rei
|
structural protein-DNA |
X-ray (2.65 Å) |
Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA |
(2011) "Specific
DNA structural attributes modulate platinum anticancer
drug site selection and cross-link generation."
Nucleic Acids Res., 39,
8200-8212. doi: 10.1093/nar/gkr491.
|
2.65 angstrom crystal structure of the nucleosome core
particle assembled with a 145 bp alpha-satellite DNA
(ncp145) derivatized with triamminechloroplatinum(ii)
chloride . SNAP
output
|
|
3rej
|
structural protein-DNA |
X-ray (2.55 Å) |
Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA |
(2011) "Specific
DNA structural attributes modulate platinum anticancer
drug site selection and cross-link generation."
Nucleic Acids Res., 39,
8200-8212. doi: 10.1093/nar/gkr491.
|
2.55 angstrom crystal structure of the nucleosome core
particle assembled with a 146 bp alpha-satellite DNA
(ncp146b) . SNAP
output
|
|
3rek
|
structural protein-DNA |
X-ray (2.6 Å) |
Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA |
(2011) "Specific
DNA structural attributes modulate platinum anticancer
drug site selection and cross-link generation."
Nucleic Acids Res., 39,
8200-8212. doi: 10.1093/nar/gkr491.
|
2.6 angstrom crystal structure of the nucleosome core
particle assembled with a 146 bp alpha-satellite DNA
(ncp146b) derivatized with oxaliplatin . SNAP output
|
|
3rel
|
structural protein-DNA |
X-ray (2.7 Å) |
Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA |
(2011) "Specific
DNA structural attributes modulate platinum anticancer
drug site selection and cross-link generation."
Nucleic Acids Res., 39,
8200-8212. doi: 10.1093/nar/gkr491.
|
2.7 angstrom crystal structure of the nucleosome core
particle assembled with a 146 bp alpha-satellite DNA
(ncp146b) derivatized with triamminechloroplatinum(ii)
chloride . SNAP
output
|
|
3rh4
|
transferase-DNA |
X-ray (1.918 Å) |
Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen
LG, Wilson SH |
(2011) "Molecular
insights into DNA polymerase deterrents for
ribonucleotide insertion." J.Biol.Chem.,
286, 31650-31660. doi: 10.1074/jbc.M111.253401.
|
DNA polymerase beta with a dideoxy-terminated primer
with an incoming ribonucleotide (rctp) . SNAP output
|
|
3rh5
|
transferase-DNA |
X-ray (2.096 Å) |
Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen
LG, Wilson SH |
(2011) "Molecular
insights into DNA polymerase deterrents for
ribonucleotide insertion." J.Biol.Chem.,
286, 31650-31660. doi: 10.1074/jbc.M111.253401.
|
DNA polymerase beta mutant (y271) with a
dideoxy-terminated primer with an incoming
deoxynucleotide (dctp) . SNAP output
|
|
3rh6
|
transferase-DNA |
X-ray (2.048 Å) |
Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen
LG, Wilson SH |
(2011) "Molecular
insights into DNA polymerase deterrents for
ribonucleotide insertion." J.Biol.Chem.,
286, 31650-31660. doi: 10.1074/jbc.M111.253401.
|
DNA polymerase beta mutant (y271) with a
dideoxy-terminated primer with an incoming
ribonucleotide (rctp) . SNAP output
|
|
3ri4
|
transcription-DNA |
X-ray (3.0 Å) |
Babayeva ND, Baranovskaya OI, Tahirov TH |
(2012) "Structural
basis of ets1 cooperative binding to widely separated
sites on promoter DNA." Plos One,
7, e33698. doi: 10.1371/journal.pone.0033698.
|
Ets1 cooperative binding to widely separated sites on
promoter DNA . SNAP
output
|
|
3rje
|
transferase, lyase-DNA |
X-ray (2.1 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Ternary complex of DNA polymerase beta with a gapped
DNA containing 8odg at template position . SNAP output
|
|
3rjf
|
transferase, lyase-DNA |
X-ray (2.3 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Ternary complex of DNA polymerase beta with a gapped
DNA containing (syn)8odg at template position paired
with non-hydrolyzable datp analog (dapcpp) . SNAP output
|
|
3rjg
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Binary complex of DNA polymerase beta with a gapped DNA
containing 8odg:da base-pair at primer terminus .
SNAP output
|
|
3rjh
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Ternary complex of DNA polymerase beta with a gapped
DNA containing (syn)8odg:da at primer terminus and
dg:dcmp(cf2)ppin the active site . SNAP output
|
|
3rji
|
transferase, lyase-DNA |
X-ray (2.3 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Ternary complex of DNA polymerase beta with a gapped
DNA containing 8odg at template position paired with
non-hydrolyzable dctp analog (dcmp(cf2)pp) . SNAP output
|
|
3rjj
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Ternary complex crystal structure of DNA polymerase
beta with template 8odg provides insight into mutagenic
lesion bypass . SNAP
output
|
|
3rjk
|
transferase, lyase-DNA |
X-ray (2.1 Å) |
Batra VK, Shock DD, Beard WA, McKenna CE, Wilson
SH |
(2012) "Binary
complex crystal structure of DNA polymerase beta
reveals multiple conformations of the templating
8-oxoguanine lesion."
Proc.Natl.Acad.Sci.USA, 109,
113-118. doi: 10.1073/pnas.1112235108.
|
Ternary complex of DNA polymerase beta with a gapped
DNA containing 8odg:dc base pair at primer terminus and
dg:dcmp(cf2)pp in the active site . SNAP output
|
|
3rkq
|
transcription-DNA |
X-ray (1.7 Å) |
Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H,
Nam HJ |
(2012) "Crystal
structure of the human NKX2.5 homeodomain in complex
with DNA target." Biochemistry,
51, 6312-6319. doi: 10.1021/bi300849c.
|
Nkx2.5 homeodomain dimer bound to anf-242 DNA .
SNAP output
|
|
3rma
|
transferase-DNA |
X-ray (2.84 Å) |
Aller P, Duclos S, Wallace SS, Doublie S |
(2011) "A
crystallographic study of the role of sequence context
in thymine glycol bypass by a replicative DNA
polymerase serendipitously sheds light on the
exonuclease complex." J.Mol.Biol.,
412, 22-34. doi: 10.1016/j.jmb.2011.07.007.
|
Crystal structure of a replicative DNA polymerase bound
to DNA containing thymine glycol . SNAP output
|
|
3rmb
|
transferase-DNA |
X-ray (2.65 Å) |
Aller P, Duclos S, Wallace SS, Doublie S |
(2011) "A
crystallographic study of the role of sequence context
in thymine glycol bypass by a replicative DNA
polymerase serendipitously sheds light on the
exonuclease complex." J.Mol.Biol.,
412, 22-34. doi: 10.1016/j.jmb.2011.07.007.
|
Crystal structure of a replicative DNA polymerase bound
to DNA containing thymine glycol . SNAP output
|
|
3rmc
|
transferase-DNA |
X-ray (3.0 Å) |
Aller P, Duclos S, Wallace SS, Doublie S |
(2011) "A
crystallographic study of the role of sequence context
in thymine glycol bypass by a replicative DNA
polymerase serendipitously sheds light on the
exonuclease complex." J.Mol.Biol.,
412, 22-34. doi: 10.1016/j.jmb.2011.07.007.
|
Crystal structure of a replicative DNA polymerase bound
to DNA containing thymine glycol . SNAP output
|
|
3rmd
|
transferase-DNA |
X-ray (2.98 Å) |
Aller P, Duclos S, Wallace SS, Doublie S |
(2011) "A
crystallographic study of the role of sequence context
in thymine glycol bypass by a replicative DNA
polymerase serendipitously sheds light on the
exonuclease complex." J.Mol.Biol.,
412, 22-34. doi: 10.1016/j.jmb.2011.07.007.
|
Crystal structure of a replicative DNA polymerase bound
to DNA containing thymine glycol . SNAP output
|
|
3rmp
|
DNA binding protein-DNA |
X-ray (2.21 Å) |
Szwagierczak A, Popowicz GM, Holak TA, Rakin A,
Antonenka U |
"Structural basis for the recognition of attP
substrates by P4-like integrases." |
Structural basis for the recognition of attp substrates
by p4-like integrases . SNAP output
|
|
3rn2
|
immune system-DNA |
X-ray (2.55 Å) |
Jin T, Perry A, Jiang J, Smith P, Curry JA,
Unterholzner L, Jiang Z, Horvath G, Rathinam VA,
Johnstone RW, Hornung V, Latz E, Bowie AG, Fitzgerald KA,
Xiao TS |
(2012) "Structures
of the HIN Domain:DNA Complexes Reveal Ligand Binding
and Activation Mechanisms of the AIM2 Inflammasome and
IFI16 Receptor." Immunity,
36, 561-571. doi: 10.1016/j.immuni.2012.02.014.
|
Structural basis of cytosolic DNA recognition by innate
immune receptors . SNAP
output
|
|
3rn5
|
immune system-DNA |
X-ray (2.5 Å) |
Jin T, Perry A, Jiang J, Smith P, Curry JA,
Unterholzner L, Jiang Z, Horvath G, Rathinam VA,
Johnstone RW, Hornung V, Latz E, Bowie AG, Fitzgerald KA,
Xiao TS |
(2012) "Structures
of the HIN Domain:DNA Complexes Reveal Ligand Binding
and Activation Mechanisms of the AIM2 Inflammasome and
IFI16 Receptor." Immunity,
36, 561-571. doi: 10.1016/j.immuni.2012.02.014.
|
Structural basis of cytosolic DNA recognition by innate
immune receptors . SNAP
output
|
|
3rnu
|
transcription activator-DNA |
X-ray (2.502 Å) |
Jin T, Perry A, Jiang J, Smith P, Curry JA,
Unterholzner L, Jiang Z, Horvath G, Rathinam VA,
Johnstone RW, Hornung V, Latz E, Bowie AG, Fitzgerald KA,
Xiao TS |
(2012) "Structures
of the HIN Domain:DNA Complexes Reveal Ligand Binding
and Activation Mechanisms of the AIM2 Inflammasome and
IFI16 Receptor." Immunity,
36, 561-571. doi: 10.1016/j.immuni.2012.02.014.
|
Structural basis of cytosolic DNA sensing by innate
immune receptors . SNAP
output
|
|
3rr7
|
transferase-DNA |
X-ray (1.95 Å) |
Obeid S, Welte W, Diederichs K, Marx A |
(2012) "Amino
Acid templating mechanisms in selection of nucleotides
opposite abasic sites by a family a DNA
polymerase." J.Biol.Chem.,
287, 14099-14108. doi: 10.1074/jbc.M111.334904.
|
Binary structure of the large fragment of taq DNA
polymerase bound to an abasic site . SNAP output
|
|
3rr8
|
transferase-DNA |
X-ray (2.4 Å) |
Obeid S, Welte W, Diederichs K, Marx A |
(2012) "Amino
Acid templating mechanisms in selection of nucleotides
opposite abasic sites by a family a DNA
polymerase." J.Biol.Chem.,
287, 14099-14108. doi: 10.1074/jbc.M111.334904.
|
Ternary structure of the large fragment of taq DNA
polymerase bound to an abasic site and a ddgtp .
SNAP output
|
|
3rrg
|
transferase-DNA |
X-ray (2.3 Å) |
Obeid S, Welte W, Diederichs K, Marx A |
(2012) "Amino
Acid templating mechanisms in selection of nucleotides
opposite abasic sites by a family a DNA
polymerase." J.Biol.Chem.,
287, 14099-14108. doi: 10.1074/jbc.M111.334904.
|
Ternary structure of the large fragment of taq DNA
polymerase bound to an abasic site and a ddgtp .
SNAP output
|
|
3rrh
|
transferase-DNA |
X-ray (1.8 Å) |
Obeid S, Welte W, Diederichs K, Marx A |
(2012) "Amino
Acid templating mechanisms in selection of nucleotides
opposite abasic sites by a family a DNA
polymerase." J.Biol.Chem.,
287, 14099-14108. doi: 10.1074/jbc.M111.334904.
|
Ternary structure of the large fragment of taq DNA
polymerase bound to an abasic site and a ddttp .
SNAP output
|
|
3rtv
|
transferase-DNA |
X-ray (1.9 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A |
(2012) "KlenTaq
polymerase replicates unnatural base pairs by inducing
a Watson-Crick geometry." Nat.Chem.Biol.,
8, 612-614. doi: 10.1038/nchembio.966.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with natural primer-template DNA . SNAP output
|
|
3rwu
|
transferase-DNA |
X-ray (2.33 Å) |
Xia S, Konigsberg WH, Wang J |
(2011) "Hydrogen-Bonding
Capability of a Templating Difluorotoluene Nucleotide
Residue in an RB69 DNA Polymerase Ternary Complex."
J.Am.Chem.Soc., 133,
10003-10005. doi: 10.1021/ja2021735.
|
Rb69 DNA polymerase (y567a) ternary complex with datp
opposite difluorotoluene nucleoside . SNAP output
|
|
3rzd
|
transcription-RNA-DNA |
X-ray (3.3 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 5-nt RNA .
SNAP output
|
|
3rzg
|
oxidoreductase-DNA |
X-ray (1.62 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Duplex interrogation by a direct DNA repair protein in
the search of damage . SNAP output
|
|
3rzh
|
oxidoreductase-DNA |
X-ray (2.25 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Duplex interrogation by a direct DNA repair protein in
the search of damage . SNAP output
|
|
3rzj
|
oxidoreductase-DNA |
X-ray (2.5 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Duplex interrogation by a direct DNA repair protein in
the search of damage . SNAP output
|
|
3rzk
|
oxidoreductase-DNA |
X-ray (2.78 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Duplex interrogation by a direct DNA repair protein in
the search of damage . SNAP output
|
|
3rzl
|
oxidoreductase-DNA |
X-ray (2.6 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Duplex interrogation by a direct DNA repair protein in
the search of damage . SNAP output
|
|
3rzm
|
oxidoreductase-DNA |
X-ray (3.06 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Duplex interrogation by a direct DNA repair protein in
the search of damage . SNAP output
|
|
3rzo
|
transcription-RNA-DNA |
X-ray (3.0 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 4-nt RNA .
SNAP output
|
|
3s14
|
transcription-RNA-DNA |
X-ray (2.85 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 6-nt RNA .
SNAP output
|
|
3s15
|
transcription-RNA-DNA |
X-ray (3.3 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 7-nt RNA .
SNAP output
|
|
3s16
|
transcription-RNA-DNA |
X-ray (3.241 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with an 8-nt RNA .
SNAP output
|
|
3s17
|
transcription-RNA-DNA |
X-ray (3.2 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 9-nt RNA .
SNAP output
|
|
3s1m
|
transcription-RNA-DNA |
X-ray (3.13 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 5-nt RNA
(variant 1) . SNAP
output
|
|
3s1n
|
transcription-RNA-DNA |
X-ray (3.1 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 5-nt RNA
(variant 2) . SNAP
output
|
|
3s1q
|
transcription-RNA-DNA |
X-ray (3.3 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 5-nt
3'-deoxy RNA soaked with atp . SNAP output
|
|
3s1r
|
transcription-RNA-DNA |
X-ray (3.2 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 5-nt
3'-deoxy RNA soaked with gtp . SNAP output
|
|
3s2d
|
transcription-RNA-DNA |
X-ray (3.2 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 5-nt RNA
containing a 5br-u . SNAP output
|
|
3s2h
|
transcription-RNA-DNA |
X-ray (3.3 Å) |
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg
RD |
(2011) "Initiation
complex structure and promoter proofreading."
Science, 333, 633-637. doi:
10.1126/science.1206629.
|
RNA polymerase ii initiation complex with a 6-nt RNA
containing a 2[prime]-iodo atp . SNAP output
|
|
3s3m
|
recombination-inhibitor-DNA |
X-ray (2.49 Å) |
Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier
Y, Hughes SH, Cherepanov P |
(2011) "Structural
and Functional Analyses of the Second-Generation
Integrase Strand Transfer Inhibitor Dolutegravir
(S/GSK1349572)." Mol.Pharmacol.,
80, 565-572. doi: 10.1124/mol.111.073189.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and dolutegravir
(s-gsk1349572) . SNAP
output
|
|
3s3n
|
transferase-inhibitor-DNA |
X-ray (2.49 Å) |
Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier
Y, Hughes SH, Cherepanov P |
(2011) "Structural
and Functional Analyses of the Second-Generation
Integrase Strand Transfer Inhibitor Dolutegravir
(S/GSK1349572)." Mol.Pharmacol.,
80, 565-572. doi: 10.1124/mol.111.073189.
|
Crystal structure of the prototype foamy virus (pfv)
s217h mutant intasome in complex with magnesium and
dolutegravir (s-gsk1349572) . SNAP output
|
|
3s3o
|
recombination-inhibitor-DNA |
X-ray (2.55 Å) |
Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier
Y, Hughes SH, Cherepanov P |
(2011) "Structural
and Functional Analyses of the Second-Generation
Integrase Strand Transfer Inhibitor Dolutegravir
(S/GSK1349572)." Mol.Pharmacol.,
80, 565-572. doi: 10.1124/mol.111.073189.
|
Crystal structure of the prototype foamy virus (pfv)
n224h mutant intasome in complex with magnesium and
dolutegravir (s-gsk1349572) . SNAP output
|
|
3s57
|
oxidoreductase-DNA |
X-ray (1.6 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Abh2 cross-linked with undamaged dsDNA-1 containing
cofactors . SNAP
output
|
|
3s5a
|
oxidoreductase-DNA |
X-ray (1.7 Å) |
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ,
Dinner AR, Yang CG, He C |
(2012) "Duplex
interrogation by a direct DNA repair protein in search
of base damage." Nat.Struct.Mol.Biol.,
19, 671-676. doi: 10.1038/nsmb.2320.
|
Abh2 cross-linked to undamaged dsDNA-2 with cofactors .
SNAP output
|
|
3s6i
|
hydrolase-DNA |
X-ray (2.28 Å) |
Adhikary S, Eichman BF |
(2011) "Analysis
of substrate specificity of Schizosaccharomyces pombe
Mag1 alkylpurine DNA glycosylase." Embo
Rep., 12, 1286-1292. doi:
10.1038/embor.2011.189.
|
Schizosaccaromyces pombe 3-methyladenine DNA
glycosylase (mag1) in complex with abasic-DNA. .
SNAP output
|
|
3s8q
|
protein binding-DNA |
X-ray (2.1 Å) |
McGeehan JE, Ball NJ, Streeter SD, Thresh SJ, Kneale
GG |
(2012) "Recognition
of dual symmetry by the controller protein C.Esp1396I
based on the structure of the transcriptional
activation complex." Nucleic Acids Res.,
40, 4158-4167. doi: 10.1093/nar/gkr1250.
|
Crystal structure of the r-m controller protein
c.esp1396i ol operator complex . SNAP output
|
|
3s9h
|
transferase-DNA |
X-ray (1.95 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase triple mutant(l561a-s565g-y567a)
ternary complex with dupnpp and a dideoxy-terminated
primer in the presence of ca2+ . SNAP output
|
|
3sar
|
hydrolase-DNA |
X-ray (1.95 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm slanted complex 1 . SNAP output
|
|
3sas
|
hydrolase-DNA |
X-ray (2.05 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm slanted complex 4 with r112a mutation . SNAP output
|
|
3sat
|
hydrolase-DNA |
X-ray (2.15 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm slanted complex 6 with r112a mutation . SNAP output
|
|
3sau
|
hydrolase-DNA |
X-ray (1.65 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm interrogation complex 6 . SNAP output
|
|
3sav
|
hydrolase-DNA |
X-ray (2.125 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm slanted complex 8 . SNAP output
|
|
3saw
|
hydrolase-DNA |
X-ray (2.35 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm slanted complex 8 with r112a mutation . SNAP output
|
|
3sbj
|
hydrolase-DNA |
X-ray (2.1 Å) |
Qi Y, Nam K, Spong MC, Banerjee A, Sung RJ, Zhang M,
Karplus M, Verdine GL |
(2012) "Strandwise
translocation of a DNA glycosylase on undamaged
DNA." Proc.Natl.Acad.Sci.USA,
109, 1086-1091. doi: 10.1073/pnas.1111237108.
|
Mutm slanted complex 7 . SNAP output
|
|
3scx
|
transferase-DNA |
X-ray (2.35 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase triple mutant(l561a-s565g-y567a)
ternary complex with dupnpp and a deoxy-terminated
primer in the presence of ca2+ . SNAP output
|
|
3si6
|
transferase-DNA |
X-ray (1.85 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase triple mutant (l561a-s565g-y567a)
ternary complex with dupnpp and a deoxy-terminated
primer in the presence of mg2+ . SNAP output
|
|
3si8
|
transferase-DNA |
X-ray (2.15 Å) |
Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S,
Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F,
Yang W |
(2010) "Structure
and mechanism of human DNA polymerase eta."
Nature, 465, 1044-1048. doi:
10.1038/nature09196.
|
Human DNA polymerase eta - DNA ternary complex with the
5't of a cpd in the active site (tt2) . SNAP output
|
|
3sjj
|
transferase-DNA |
X-ray (2.38 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase triple mutant (l561a-s565g-y567a)
ternary complex with dupnpp and a deoxy-terminated
primer in the presence of mn2+ . SNAP output
|
|
3sjm
|
DNA-DNA binding protein |
X-ray (1.35 Å) |
Nair SK, Sliverman SK, Chen JH, Xiao Y |
"Crystal Structure Analysis of TRF2-Dbd-DNA
complex." |
Crystal structure analysis of trf2-dbd-DNA complex .
SNAP output
|
|
3slp
|
hydrolase-DNA |
X-ray (2.3 Å) |
Zhang J, McCabe KA, Bell CE |
(2011) "Crystal
structures of {lambda} exonuclease in complex with DNA
suggest an electrostatic ratchet mechanism for
processivity." Proc.Natl.Acad.Sci.USA,
108, 11872-11877. doi: 10.1073/pnas.1103467108.
|
Crystal structure of lambda exonuclease in complex with
a 12 bp symmetric DNA duplex . SNAP output
|
|
3sm4
|
hydrolase-DNA |
X-ray (1.88 Å) |
Zhang J, McCabe KA, Bell CE |
(2011) "Crystal
structures of {lambda} exonuclease in complex with DNA
suggest an electrostatic ratchet mechanism for
processivity." Proc.Natl.Acad.Sci.USA,
108, 11872-11877. doi: 10.1073/pnas.1103467108.
|
Crystal structure of the k131a mutant of lambda
exonuclease in complex with a 5'-phosphorylated
14-mer-12-mer duplex and magnesium . SNAP output
|
|
3snn
|
transferase-DNA |
X-ray (2.0 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase (l561a-s565g-y567a) ternary complex
with dctp opposite dg in the presence of mg2+ .
SNAP output
|
|
3spd
|
hydrolase-DNA |
X-ray (1.912 Å) |
Gong Y, Zhu D, Ding J, Dou C, Ren X, Gu L, Jiang T,
Wang D |
(2011) "Crystal
structures of aprataxin ortholog Hnt3 reveal the
mechanism for reversal of 5'-adenylated DNA."
Nat.Struct.Mol.Biol., 18,
1297-1299. doi: 10.1038/nsmb.2145.
|
Crystal structure of aprataxin ortholog hnt3 in complex
with DNA . SNAP
output
|
|
3spl
|
hydrolase-DNA |
X-ray (2.101 Å) |
Gong Y, Zhu D, Ding J, Dou C, Ren X, Gu L, Jiang T,
Wang D |
(2011) "Crystal
structures of aprataxin ortholog Hnt3 reveal the
mechanism for reversal of 5'-adenylated DNA."
Nat.Struct.Mol.Biol., 18,
1297-1299. doi: 10.1038/nsmb.2145.
|
Crystal structure of aprataxin ortholog hnt3 in complex
with DNA and amp . SNAP
output
|
|
3spy
|
transferase-DNA |
X-ray (2.14 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase(l415a-l561a-s565g-y567a) ternary
complex with dupcpp opposite da . SNAP output
|
|
3spz
|
transferase-DNA |
X-ray (2.43 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
DNA polymerase(l415a-l561a-s565g-y567a) ternary complex
with dupcpp opposite da (ca2+) . SNAP output
|
|
3sq0
|
transferase-DNA |
X-ray (2.0 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
DNA polymerase(l561a-s565g-y567a) ternary complex with
dupnpp opposite da (mn2+) . SNAP output
|
|
3sq1
|
transferase-DNA |
X-ray (1.82 Å) |
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J |
(2011) "Structural
Insights into Complete Metal Ion Coordination from
Ternary Complexes of B Family RB69 DNA Polymerase."
Biochemistry, 50, 9114-9124.
doi: 10.1021/bi201260h.
|
Rb69 DNA polymerase ternary complex with dupcpp
opposite da . SNAP
output
|
|
3sq2
|
transferase-DNA |
X-ray (2.1 Å) |
Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao
C, Beckman J, Christian T, Konigsberg W |
(2011) "Structure
of the 2-Aminopurine-Cytosine Base Pair Formed in the
Polymerase Active Site of the RB69 Y567A-DNA
Polymerase." Biochemistry,
50, 10136-10149. doi: 10.1021/bi2014618.
|
Rb69 DNA polymerase ternary complex with dttp opposite
2ap (at rich sequence) . SNAP output
|
|
3sq4
|
transferase-DNA |
X-ray (2.23 Å) |
Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao
C, Beckman J, Christian T, Konigsberg W |
(2011) "Structure
of the 2-Aminopurine-Cytosine Base Pair Formed in the
Polymerase Active Site of the RB69 Y567A-DNA
Polymerase." Biochemistry,
50, 10136-10149. doi: 10.1021/bi2014618.
|
Rb69 DNA polymerase ternary complex with dttp opposite
2ap (gc rich sequence) . SNAP output
|
|
3sqi
|
DNA binding protein-DNA |
X-ray (2.82 Å) |
Cho US, Harrison SC |
(2011) "Ndc10 is
a platform for inner kinetochore assembly in budding
yeast." Nat.Struct.Mol.Biol.,
19, 48-55. doi: 10.1038/nsmb.2178.
|
DNA binding domain of ndc10 . SNAP output
|
|
3sqx
|
hydrolase-RNA |
X-ray (2.112 Å) |
Mohr G, Del Campo M, Turner KG, Gilman B, Wolf RZ,
Lambowitz AM |
(2011) "High-Throughput
Genetic Identification of Functionally Important
Regions of the Yeast DEAD-Box Protein Mss116p."
J.Mol.Biol., 413, 952-972.
doi: 10.1016/j.jmb.2011.09.015.
|
Structure of mss116p (nte and c-tail double deletion)
bound to ssrna and amp-pnp . SNAP output
|
|
3ssc
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Sukackaite R, Grazulis S, Tamulaitis G, Siksnys
V |
(2012) "The
recognition domain of the methyl-specific endonuclease
McrBC flips out 5-methylcytosine." Nucleic
Acids Res., 40, 7552-7562. doi:
10.1093/nar/gks332.
|
DNA binding domain of restriction endonuclease bound to
DNA . SNAP output
|
|
3ssd
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Sukackaite R, Grazulis S, Tamulaitis G, Siksnys
V |
(2012) "The
recognition domain of the methyl-specific endonuclease
McrBC flips out 5-methylcytosine." Nucleic
Acids Res., 40, 7552-7562. doi:
10.1093/nar/gks332.
|
DNA binding domain of restriction endonuclease bound to
DNA . SNAP output
|
|
3sse
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Sukackaite R, Grazulis S, Tamulaitis G, Siksnys
V |
(2012) "The
recognition domain of the methyl-specific endonuclease
McrBC flips out 5-methylcytosine." Nucleic
Acids Res., 40, 7552-7562. doi:
10.1093/nar/gks332.
|
DNA binding domain of restriction endonuclease bound to
DNA . SNAP output
|
|
3sun
|
transferase-DNA |
X-ray (2.42 Å) |
Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao
C, Beckman J, Christian T, Konigsberg W |
(2011) "Structure
of the 2-Aminopurine-Cytosine Base Pair Formed in the
Polymerase Active Site of the RB69 Y567A-DNA
Polymerase." Biochemistry,
50, 10136-10149. doi: 10.1021/bi2014618.
|
Rb69 DNA polymerase (y567a) ternary complex with dttp
opposite 2ap (at rich sequence) . SNAP output
|
|
3suo
|
transferase-DNA |
X-ray (2.23 Å) |
Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao
C, Beckman J, Christian T, Konigsberg W |
(2011) "Structure
of the 2-Aminopurine-Cytosine Base Pair Formed in the
Polymerase Active Site of the RB69 Y567A-DNA
Polymerase." Biochemistry,
50, 10136-10149. doi: 10.1021/bi2014618.
|
Rb69 DNA polymerase (y567a) ternary complex with dttp
opposite 2ap (gc rich sequence) . SNAP output
|
|
3sup
|
transferase-DNA |
X-ray (2.32 Å) |
Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao
C, Beckman J, Christian T, Konigsberg W |
(2011) "Structure
of the 2-Aminopurine-Cytosine Base Pair Formed in the
Polymerase Active Site of the RB69 Y567A-DNA
Polymerase." Biochemistry,
50, 10136-10149. doi: 10.1021/bi2014618.
|
Rb69 DNA polymerase (y567a) ternary complex with dctp
opposite 2ap (gc rich sequence) . SNAP output
|
|
3suq
|
transferase-DNA |
X-ray (3.15 Å) |
Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao
C, Beckman J, Christian T, Konigsberg W |
(2011) "Structure
of the 2-Aminopurine-Cytosine Base Pair Formed in the
Polymerase Active Site of the RB69 Y567A-DNA
Polymerase." Biochemistry,
50, 10136-10149. doi: 10.1021/bi2014618.
|
Rb69 DNA polymerase (y567a) ternary complex with dctp
opposite 2ap (at rich sequence) . SNAP output
|
|
3sv3
|
transferase-DNA |
X-ray (2.1 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A |
(2012) "KlenTaq
polymerase replicates unnatural base pairs by inducing
a Watson-Crick geometry." Nat.Chem.Biol.,
8, 612-614. doi: 10.1038/nchembio.966.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with the artificial base pair dnam-d5sicstp .
SNAP output
|
|
3sv4
|
transferase-DNA |
X-ray (1.99 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A |
(2012) "KlenTaq
polymerase replicates unnatural base pairs by inducing
a Watson-Crick geometry." Nat.Chem.Biol.,
8, 612-614. doi: 10.1038/nchembio.966.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in an open binary
complex with dt as templating nucleobase . SNAP output
|
|
3swm
|
transcription-DNA |
X-ray (4.25 Å) |
Welner DH, Lindemose S, Grossmann JG, Mollegaard NE,
Olsen AN, Helgstrand C, Skriver K, Lo Leggio L |
(2012) "DNA
binding by the plant-specific NAC transcription factors
in crystal and solution: a firm link to WRKY and GCM
transcription factors." Biochem.J.,
444, 395-404. doi: 10.1042/BJ20111742.
|
The nac domain of anac019 in complex with DNA, gold
derivative . SNAP
output
|
|
3swp
|
transcription-DNA |
X-ray (4.113 Å) |
Welner DH, Lindemose S, Grossmann JG, Mollegaard NE,
Olsen AN, Helgstrand C, Skriver K, Lo Leggio L |
(2012) "DNA
binding by the plant-specific NAC transcription factors
in crystal and solution: a firm link to WRKY and GCM
transcription factors." Biochem.J.,
444, 395-404. doi: 10.1042/BJ20111742.
|
Anac019 nac domain in complex with DNA . SNAP output
|
|
3syz
|
transferase-DNA |
X-ray (1.952 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A |
(2012) "KlenTaq
polymerase replicates unnatural base pairs by inducing
a Watson-Crick geometry." Nat.Chem.Biol.,
8, 612-614. doi: 10.1038/nchembio.966.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in an open binary
complex with dnam as templating nucleobase . SNAP output
|
|
3sz2
|
transferase-DNA |
X-ray (2.15 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Dwyer TJ, Ordoukhanian P, Romesberg FE, Marx A |
(2012) "KlenTaq
polymerase replicates unnatural base pairs by inducing
a Watson-Crick geometry." Nat.Chem.Biol.,
8, 612-614. doi: 10.1038/nchembio.966.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in an open binary
complex with dg as templating nucleobase . SNAP output
|
|
3sz5
|
hydrolase-DNA |
X-ray (2.8 Å) |
Yang W, Chen WY, Wang H, Ho JW, Huang JD, Woo PC, Lau
SK, Yuen KY, Zhang Q, Zhou W, Bartlam M, Watt RM, Rao
Z |
(2011) "Structural
and functional insight into the mechanism of an
alkaline exonuclease from Laribacter
hongkongensis." Nucleic Acids Res.,
39, 9803-9819. doi: 10.1093/nar/gkr660.
|
Crystal structure of lhk-exo in complex with
5-phosphorylated oligothymidine (dt)4 . SNAP output
|
|
3szq
|
hydrolase-DNA |
X-ray (2.353 Å) |
Tumbale P, Appel CD, Kraehenbuehl R, Robertson PD,
Williams JS, Krahn J, Ahel I, Williams RS |
(2011) "Structure
of an aprataxin-DNA complex with insights into AOA1
neurodegenerative disease."
Nat.Struct.Mol.Biol., 18,
1189-1195. doi: 10.1038/nsmb.2146.
|
Structure of an s. pombe aptx-DNA-amp-zn complex .
SNAP output
|
|
3t3f
|
transferase-DNA |
X-ray (1.9 Å) |
Obeid S, Welte W, Diederichs K, Marx A |
(2012) "Amino
acid templating mechanisms in selection of nucleotides
opposite abasic sites by a family a DNA
polymerase." J.Biol.Chem.,
287, 14099-14108. doi: 10.1074/jbc.M111.334904.
|
Ternary structure of the large fragment of taq DNA
polymerase bound to an abasic site and dnitp . SNAP output
|
|
3t5h
|
DNA-transferase |
X-ray (2.35 Å) |
Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli
M, Stone MP |
(2012) "Replication
bypass of the trans-4-Hydroxynonenal-derived
(6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the
sulfolobus solfataricus DNA polymerase IV."
Chem.Res.Toxicol., 25,
422-435. doi: 10.1021/tx200460j.
|
Ternary complex of hne adduct modified DNA (5'-cxg-3'
vs 13-mer) with dpo4 and incoming ddgt . SNAP output
|
|
3t5j
|
DNA-transferase |
X-ray (2.4 Å) |
Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli
M, Stone MP |
(2012) "Replication
bypass of the trans-4-Hydroxynonenal-derived
(6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the
sulfolobus solfataricus DNA polymerase IV."
Chem.Res.Toxicol., 25,
422-435. doi: 10.1021/tx200460j.
|
Ternary complex of hne adduct modified DNA (5'-txg-3'
vs 13-mer) with dpo4 and incoming ddtp . SNAP output
|
|
3t5k
|
DNA-transferase |
X-ray (2.9 Å) |
Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli
M, Stone MP |
(2012) "Replication
bypass of the trans-4-Hydroxynonenal-derived
(6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the
sulfolobus solfataricus DNA polymerase IV."
Chem.Res.Toxicol., 25,
422-435. doi: 10.1021/tx200460j.
|
Ternary complex of hne adduct modified DNA (5'-txg-3'
vs 14-mer) with dpo4 and incoming ddtp . SNAP output
|
|
3t5l
|
DNA-transferase |
X-ray (2.9 Å) |
Banerjee S, Christov PP, Kozekova A, Rizzo CJ, Egli
M, Stone MP |
(2012) "Replication
bypass of the trans-4-Hydroxynonenal-derived
(6S,8R,11S)-1,N(2)-deoxyguanosine DNA adduct by the
sulfolobus solfataricus DNA polymerase IV."
Chem.Res.Toxicol., 25,
422-435. doi: 10.1021/tx200460j.
|
Ternary complex of hne adduct modified DNA (5'-cxg-3'
vs 14-mer) with dpo4 and incoming ddgt . SNAP output
|
|
3t79
|
DNA binding protein-DNA |
X-ray (3.61 Å) |
Cho US, Harrison SC |
(2011) "Ndc10 is
a platform for inner kinetochore assembly in budding
yeast." Nat.Struct.Mol.Biol.,
19, 48-55. doi: 10.1038/nsmb.2178.
|
Ndc10: a platform for inner kinetochore assembly in
budding yeast . SNAP
output
|
|
3tab
|
transferase-DNA |
X-ray (2.8 Å) |
Zahn KE, Averill A, Wallace SS, Doublie S |
(2011) "The
miscoding potential of 5-hydroxycytosine arises due to
template instability in the replicative polymerase
active site." Biochemistry,
50, 10350-10358. doi: 10.1021/bi201219s.
|
5-hydroxycytosine paired with dgmp in rb69 gp43 .
SNAP output
|
|
3tae
|
transferase-DNA |
X-ray (2.71 Å) |
Zahn KE, Averill A, Wallace SS, Doublie S |
(2011) "The
miscoding potential of 5-hydroxycytosine arises due to
template instability in the replicative polymerase
active site." Biochemistry,
50, 10350-10358. doi: 10.1021/bi201219s.
|
5-hydroxycytosine paired with damp in rb69 gp43 .
SNAP output
|
|
3taf
|
transferase-DNA |
X-ray (3.0 Å) |
Zahn KE, Averill A, Wallace SS, Doublie S |
(2011) "The
miscoding potential of 5-hydroxycytosine arises due to
template instability in the replicative polymerase
active site." Biochemistry,
50, 10350-10358. doi: 10.1021/bi201219s.
|
5-fluorocytosine paired with ddgmp in rb69 gp43 .
SNAP output
|
|
3tag
|
transferase-DNA |
X-ray (2.95 Å) |
Zahn KE, Averill A, Wallace SS, Doublie S |
(2011) "The
miscoding potential of 5-hydroxycytosine arises due to
template instability in the replicative polymerase
active site." Biochemistry,
50, 10350-10358. doi: 10.1021/bi201219s.
|
5-fluorocytosine paired with damp in rb69 gp43 .
SNAP output
|
|
3tan
|
transferase-DNA |
X-ray (1.53 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to duplex DNA with cytosine-adenine
mismatch at (n-1) position . SNAP output
|
|
3tap
|
transferase-DNA |
X-ray (1.655 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to duplex DNA with cytosine-adenine
mismatch at (n-3) position . SNAP output
|
|
3taq
|
transferase-DNA |
X-ray (1.65 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to duplex DNA with cytosine-adenine
mismatch at (n-4) position . SNAP output
|
|
3tar
|
transferase-DNA |
X-ray (1.6 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to duplex DNA with cytosine-adenine
mismatch at (n-6) position . SNAP output
|
|
3ted
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Sharma A, Jenkins KR, Heroux A, Bowman GD |
(2011) "DNA-binding domain of Chd1 in complex with a
DNA duplex." J.Biol.Chem. |
Crystal structure of the chd1 DNA-binding domain in
complex with a DNA duplex . SNAP output
|
|
3tfr
|
transferase-DNA |
X-ray (2.0 Å) |
Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock
DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH |
(2012) "Stereospecific
Formation of a Ternary Complex of (S)-alpha,
beta-Fluoromethylene-dATP with DNA Pol beta."
Chembiochem, 13, 528-530.
doi: 10.1002/cbic.201100738.
|
Ternary complex structure of DNA polymerase beta with a
gapped DNA substrate and a, b damp(cf2)pp in the active
site . SNAP output
|
|
3tfs
|
transferase-DNA |
X-ray (2.0 Å) |
Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock
DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH |
(2012) "Stereospecific
Formation of a Ternary Complex of (S)-alpha,
beta-Fluoromethylene-dATP with DNA Pol beta."
Chembiochem, 13, 528-530.
doi: 10.1002/cbic.201100738.
|
Ternary complex structure of DNA polymerase beta with a
gapped DNA substrate and a, b damp(cfh)pp in the active
site: stereoselective binding of (s) isomer . SNAP output
|
|
3thv
|
transferase-DNA |
X-ray (1.611 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to DNA and ddatp-dt in closed
conformation . SNAP
output
|
|
3thw
|
DNA binding protein-DNA |
X-ray (3.09 Å) |
Gupta S, Gellert M, Yang W |
(2012) "Mechanism
of mismatch recognition revealed by human MutSbeta
bound to unpaired DNA loops."
Nat.Struct.Mol.Biol., 19,
72-78. doi: 10.1038/nsmb.2175.
|
Human mutsbeta complexed with an idl of 4 bases (loop4)
and adp . SNAP
output
|
|
3thx
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Gupta S, Gellert M, Yang W |
(2012) "Mechanism
of mismatch recognition revealed by human MutSbeta
bound to unpaired DNA loops."
Nat.Struct.Mol.Biol., 19,
72-78. doi: 10.1038/nsmb.2175.
|
Human mutsbeta complexed with an idl of 3 bases (loop3)
and adp . SNAP
output
|
|
3thy
|
DNA binding protein-DNA |
X-ray (2.894 Å) |
Gupta S, Gellert M, Yang W |
(2012) "Mechanism
of mismatch repair revealed by human MutSbeta bound to
unpaired DNA loops." Nat.Struct.Mol.Biol.,
19, 72-78. doi: 10.1038/nsmb.2175.
|
Human mutsbeta complexed with an idl of 2 bases (loop2)
and adp . SNAP
output
|
|
3thz
|
DNA binding protein-DNA |
X-ray (4.3 Å) |
Gupta S, Gellert M, Yang W |
(2012) "Mechanism
of mismatch repair revealed by human MutS bound to
unpaired DNA loops." Nat.Struct.Mol.Biol.,
19, 72-78. doi: 10.1038/nsmb.2175.
|
Human mutsbeta complexed with an idl of 6 bases (loop6)
and adp . SNAP
output
|
|
3ti0
|
transferase-DNA |
X-ray (1.62 Å) |
Wang W, Hellinga HW, Beese LS |
(2011) "Structural
evidence for the rare tautomer hypothesis of
spontaneous mutagenesis."
Proc.Natl.Acad.Sci.USA, 108,
17644-17648. doi: 10.1073/pnas.1114496108.
|
Crystal structure of bacillus DNA polymerase i large
fragment bound to DNA and ddgtp-dc in closed
conformation . SNAP
output
|
|
3tmm
|
transcription-DNA |
X-ray (2.5 Å) |
Ngo HB, Kaiser JT, Chan DC |
(2011) "The
mitochondrial transcription and packaging factor Tfam
imposes a U-turn on mitochondrial DNA."
Nat.Struct.Mol.Biol., 18,
1290-1296. doi: 10.1038/nsmb.2159.
|
Tfam imposes a u-turn on mitochondrial DNA . SNAP output
|
|
3tq1
|
transferase-DNA |
X-ray (2.556 Å) |
Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE,
Prakash L, Prakash S, Aggarwal AK |
(2012) "Human
DNA Polymerase Eta Is Pre-Aligned for dNTP Binding and
Catalysis." J.Mol.Biol.,
415, 627-634. doi: 10.1016/j.jmb.2011.11.038.
|
Human DNA polymerase eta in binary complex with DNA .
SNAP output
|
|
3tq6
|
transcription-DNA |
X-ray (2.45 Å) |
Rubio-Cosials A, Sidow JF, Jimenez-Menendez N,
Fernandez-Millan P, Montoya J, Jacobs HT, Coll M, Bernado
P, Sola M |
(2011) "Human
mitochondrial transcription factor A induces a U-turn
structure in the light strand promoter."
Nat.Struct.Mol.Biol., 18,
1281-1289. doi: 10.1038/nsmb.2160.
|
Crystal structure of human mitochondrial transcription
factor a, tfam or mttfa, bound to the light strand
promoter lsp . SNAP
output
|
|
3ts8
|
antitumor protein-DNA |
X-ray (2.8 Å) |
Emamzadah S, Tropia L, Halazonetis TD |
(2011) "Crystal
Structure of a Multidomain Human p53 Tetramer Bound to
the Natural CDKN1A (p21) p53-Response Element."
Mol Cancer Res, 9, 1493-1499.
doi: 10.1158/1541-7786.MCR-11-0351.
|
Crystal structure of a multidomain human p53 tetramer
bound to the natural cdkn1a(p21) p53-response element .
SNAP output
|
|
3tu4
|
signaling protein-structural protein-DNA |
X-ray (3.0 Å) |
Armache KJ, Garlick JD, Canzio D, Narlikar GJ,
Kingston RE |
(2011) "Structural
basis of silencing: Sir3 BAH domain in complex with a
nucleosome at 3.0 A resolution." Science,
334, 977-982. doi: 10.1126/science.1210915.
|
Crystal structure of the sir3 bah domain in complex
with a nucleosome core particle. . SNAP output
|
|
3twh
|
hydrolase-RNA-DNA |
X-ray (1.79 Å) |
Abdur R, Gerlits OO, Gan J, Jiang J, Salon J,
Kovalevsky AY, Chumanevich AA, Weber IT, Huang Z |
(2014) "Novel
complex MAD phasing and RNase H structural insights
using selenium oligonucleotides." Acta
Crystallogr.,Sect.D, 70, 354-361.
doi: 10.1107/S1399004713027922.
|
Selenium derivatized RNA-DNA hybrid in complex with
rnase h catalytic domain d132n mutant . SNAP output
|
|
3twm
|
hydrolase-DNA |
X-ray (2.8 Å) |
Duclos S, Aller P, Jaruga P, Dizdaroglu M, Wallace
SS, Doublie S |
(2012) "Structural
and biochemical studies of a plant
formamidopyrimidine-DNA glycosylase reveal why
eukaryotic Fpg glycosylases do not excise
8-oxoguanine." Dna Repair,
11, 714-725. doi: 10.1016/j.dnarep.2012.06.004.
|
Crystal structure of arabidopsis thaliana fpg .
SNAP output
|
|
3u2b
|
transcription-DNA |
X-ray (2.402 Å) |
Jauch R, Ng CKL, Narasimhan K, Kolatkar PR |
(2012) "The
crystal structure of the Sox4 HMG domain-DNA complex
suggests a mechanism for positional interdependence in
DNA recognition." Biochem.J.,
443, 39-47. doi: 10.1042/BJ20111768.
|
Structure of the sox4 hmg domain bound to DNA .
SNAP output
|
|
3u3w
|
transcription activator-DNA |
X-ray (2.4 Å) |
Grenha R, Slamti L, Nicaise M, Refes Y, Lereclus D,
Nessler S |
(2013) "Structural
basis for the activation mechanism of the PlcR
virulence regulator by the quorum-sensing signal
peptide PapR." Proc.Natl.Acad.Sci.USA,
110, 1047-1052. doi: 10.1073/pnas.1213770110.
|
Crystal structure of bacillus thuringiensis plcr in
complex with the peptide papr7 and DNA . SNAP output
|
|
3u3y
|
hydrolase-DNA |
X-ray (2.28 Å) |
Bailey SL, Harvey S, Perrino FW, Hollis T |
(2012) "Defects
in DNA degradation revealed in crystal structures of
TREX1 exonuclease mutations linked to autoimmune
disease." Dna Repair, 11,
65-73. doi: 10.1016/j.dnarep.2011.10.007.
|
Mouse trex1 d200h mutant . SNAP output
|
|
3u44
|
hydrolase-DNA |
X-ray (3.201 Å) |
Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW,
Dillingham MS, Wigley DB |
(2012) "Insights
into Chi recognition from the structure of an
AddAB-type helicase-nuclease complex." Embo
J., 31, 1568-1578. doi: 10.1038/emboj.2012.9.
|
Crystal structure of addab-DNA complex . SNAP output
|
|
3u4q
|
hydrolase-DNA |
X-ray (2.8 Å) |
Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW,
Dillingham MS, Wigley DB |
(2012) "Insights
into Chi recognition from the structure of an
AddAB-type helicase-nuclease complex." Embo
J., 31, 1568-1578. doi: 10.1038/emboj.2012.9.
|
Structure of addab-DNA complex at 2.8 angstroms .
SNAP output
|
|
3u58
|
DNA binding protein-DNA |
X-ray (2.613 Å) |
Zeng Z, Min B, Huang J, Hong K, Yang Y, Collins K,
Lei M |
(2011) "Structural
basis for Tetrahymena telomerase processivity factor
Teb1 binding to single-stranded telomeric-repeat
DNA." Proc.Natl.Acad.Sci.USA,
108, 20357-20361. doi: 10.1073/pnas.1113624108.
|
Crystal structure of the tetrahymena telomerase
processivity factor teb1 ab . SNAP output
|
|
3u5z
|
DNA binding protein-DNA |
X-ray (3.5 Å) |
Kelch BA, Makino DL, O'Donnell M, Kuriyan J |
(2011) "How a
DNA polymerase clamp loader opens a sliding clamp."
Science, 334, 1675-1680. doi:
10.1126/science.1211884.
|
Structure of t4 bacteriophage clamp loader bound to the
t4 clamp, primer-template DNA, and atp analog .
SNAP output
|
|
3u60
|
DNA binding protein-DNA |
X-ray (3.34 Å) |
Kelch BA, Makino DL, O'Donnell M, Kuriyan J |
(2011) "How a
DNA polymerase clamp loader opens a sliding clamp."
Science, 334, 1675-1680. doi:
10.1126/science.1211884.
|
Structure of t4 bacteriophage clamp loader bound to
open clamp, DNA and atp analog . SNAP output
|
|
3u61
|
DNA binding protein-DNA |
X-ray (3.2 Å) |
Kelch BA, Makino DL, O'Donnell M, Kuriyan J |
(2011) "How a
DNA polymerase clamp loader opens a sliding clamp."
Science, 334, 1675-1680. doi:
10.1126/science.1211884.
|
Structure of t4 bacteriophage clamp loader bound to
closed clamp, DNA and atp analog and adp . SNAP output
|
|
3u6c
|
hydrolase-DNA |
X-ray (1.8 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 1 apgo . SNAP
output
|
|
3u6d
|
hydrolase-DNA |
X-ray (1.87 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 1 gpgo . SNAP
output
|
|
3u6e
|
hydrolase-DNA |
X-ray (1.7 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 1 tpgo . SNAP
output
|
|
3u6f
|
hydrolase-DNA |
X-ray (2.3 Å) |
Bailey SL, Harvey S, Perrino FW, Hollis T |
(2012) "Defects
in DNA degradation revealed in crystal structures of
TREX1 exonuclease mutations linked to autoimmune
disease." Dna Repair, 11,
65-73. doi: 10.1016/j.dnarep.2011.10.007.
|
Mouse trex1 d200n mutant . SNAP output
|
|
3u6l
|
hydrolase-DNA |
X-ray (1.97 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 2 cpgo . SNAP
output
|
|
3u6m
|
hydrolase-DNA |
X-ray (2.1 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Structural effects of sequence context on lesion
recognition by mutm . SNAP output
|
|
3u6o
|
hydrolase-DNA |
X-ray (1.9 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 1 apg . SNAP
output
|
|
3u6p
|
hydrolase-DNA |
X-ray (1.6 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 1 gpg . SNAP
output
|
|
3u6q
|
hydrolase-DNA |
X-ray (1.981 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 2 apgo . SNAP
output
|
|
3u6s
|
hydrolase-DNA |
X-ray (1.77 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2012) "Sequence-dependent
structural variation in DNA undergoing intrahelical
inspection by the DNA glycosylase MutM."
J.Biol.Chem., 287,
18044-18054. doi: 10.1074/jbc.M111.313635.
|
Mutm set 1 tpg . SNAP
output
|
|
3u6y
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Tanaka T, Padavattan S, Kumarevel T |
(2012) "Crystal
structure of archaeal chromatin protein
Alba2-double-stranded DNA complex from Aeropyrum pernix
K1." J.Biol.Chem., 287,
10394-10402. doi: 10.1074/jbc.M112.343210.
|
Crystal structure of alba2-DNA complex . SNAP output
|
|
3u7f
|
hydrolase,transferase-DNA |
X-ray (1.8 Å) |
Coquelle N, Havali-Shahriari Z, Bernstein N, Green R,
Glover JN |
(2011) "Structural
basis for the phosphatase activity of polynucleotide
kinase/phosphatase on single- and double-stranded DNA
substrates." Proc.Natl.Acad.Sci.USA,
108, 21022-21027. doi: 10.1073/pnas.1112036108.
|
Crystal structure of mpnkp catalytic fragment (d170a)
bound to single-stranded DNA (tcctcp) . SNAP output
|
|
3u7g
|
hydrolase,transferase-DNA |
X-ray (2.1 Å) |
Coquelle N, Havali-Shahriari Z, Bernstein N, Green R,
Glover JN |
(2011) "Structural
basis for the phosphatase activity of polynucleotide
kinase/phosphatase on single- and double-stranded DNA
substrates." Proc.Natl.Acad.Sci.USA,
108, 21022-21027. doi: 10.1073/pnas.1112036108.
|
Crystal structure of mpnkp catalytic fragment (d170a)
bound to single-stranded DNA (tcctap) . SNAP output
|
|
3u7h
|
hydrolase,transferase-DNA |
X-ray (2.0 Å) |
Coquelle N, Havali-Shahriari Z, Bernstein N, Green R,
Glover JN |
(2011) "Structural
basis for the phosphatase activity of polynucleotide
kinase/phosphatase on single- and double-stranded DNA
substrates." Proc.Natl.Acad.Sci.USA,
108, 21022-21027. doi: 10.1073/pnas.1112036108.
|
Crystal structure of mpnkp catalytic fragment (d170a)
bound to single-stranded DNA (tccttp) . SNAP output
|
|
3ubt
|
transferase-DNA |
X-ray (2.502 Å) |
Didovyk A, Verdine GL |
(2012) "Structural
origins of DNA target selection and nucleobase
extrusion by a DNA Cytosine methyltransferase."
J.Biol.Chem., 287,
40099-40105. doi: 10.1074/jbc.M112.413054.
|
Crystal structure of c71s mutant of DNA cytosine-5
methyltransferase m.haeiii bound to DNA . SNAP output
|
|
3uby
|
hydrolase-DNA |
X-ray (2.0 Å) |
Setser JW, Lingaraju GM, Davis CA, Samson LD, Drennan
CL |
(2012) "Searching
for DNA lesions: structural evidence for lower- and
higher-affinity DNA binding conformations of human
alkyladenine DNA glycosylase."
Biochemistry, 51, 382-390.
doi: 10.1021/bi201484k.
|
Crystal structure of human alklyadenine DNA glycosylase
in a lower and higher-affinity complex with DNA .
SNAP output
|
|
3udg
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
George NP, Ngo KV, Chitteni-Pattu S, Norais CA,
Battista JR, Cox MM, Keck JL |
(2012) "Structure
and Cellular Dynamics of Deinococcus radiodurans
Single-stranded DNA (ssDNA)-binding Protein (SSB)-DNA
Complexes." J.Biol.Chem.,
287, 22123-22132. doi: 10.1074/jbc.M112.367573.
|
Structure of deinococcus radiodurans ssb bound to ssDNA
. SNAP output
|
|
3ufd
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Ball NJ, McGeehan JE, Streeter SD, Thresh SJ, Kneale
GG |
(2012) "The
structural basis of differential DNA sequence
recognition by restriction-modification controller
proteins." Nucleic Acids Res.,
40, 10532-10542. doi: 10.1093/nar/gks718.
|
C.esp1396i bound to its highest affinity operator site
om . SNAP output
|
|
3ufj
|
hydrolase-DNA |
X-ray (2.967 Å) |
Maiti A, Noon MS, Mackerell AD, Pozharski E, Drohat
AC |
(2012) "Lesion
processing by a repair enzyme is severely curtailed by
residues needed to prevent aberrant activity on
undamaged DNA." Proc.Natl.Acad.Sci.USA,
109, 8091-8096. doi: 10.1073/pnas.1201010109.
|
Human thymine DNA glycosylase bound to substrate analog
2'-fluoro-2'-deoxyuridine . SNAP output
|
|
3ugm
|
transcription-DNA |
X-ray (3.0 Å) |
Mak AN, Bradley P, Cernadas RA, Bogdanove AJ,
Stoddard BL |
(2012) "The
Crystal Structure of TAL Effector PthXo1 Bound to Its
DNA Target." Science,
335, 716-719. doi: 10.1126/science.1216211.
|
Structure of tal effector pthxo1 bound to its DNA
target . SNAP output
|
|
3ugo
|
transcription-DNA |
X-ray (2.096 Å) |
Feklistov A, Darst SA |
(2011) "Structural
basis for promoter-10 element recognition by the
bacterial RNA polymerase sigma subunit."
Cell(Cambridge,Mass.), 147,
1257-1269. doi: 10.1016/j.cell.2011.10.041.
|
Crystal structure of RNA-polymerase sigma subunit
domain 2 complexed with -10 promoter element ssDNA
oligo (tacaat) . SNAP
output
|
|
3ugp
|
transcription-DNA |
X-ray (2.697 Å) |
Feklistov A, Darst SA |
(2011) "Structural
basis for promoter-10 element recognition by the
bacterial RNA polymerase sigma subunit."
Cell(Cambridge,Mass.), 147,
1257-1269. doi: 10.1016/j.cell.2011.10.041.
|
Crystal structure of RNA-polymerase sigma subunit
domain 2 complexed with -10 promoter element ssDNA
oligo (tataat) . SNAP
output
|
|
3uiq
|
transferase-DNA |
X-ray (1.879 Å) |
Xia S, Eom SH, Konigsberg WH, Wang J |
(2012) "Bidentate
and tridentate metal-ion coordination states within
ternary complexes of RB69 DNA polymerase."
Protein Sci., 21, 447-451.
doi: 10.1002/pro.2026.
|
Rb69 DNA polymerase ternary complex containing dupnpp .
SNAP output
|
|
3uk3
|
DNA-metal binding protein |
X-ray (2.1 Å) |
Vandevenne MS, Jacques DA, Guss JM, Mackay JP |
"Rediscovering DNA recognition by classical Zinc
Fingers." |
Crystal structure of znf217 bound to DNA . SNAP output
|
|
3ukg
|
DNA binding protein-DNA |
X-ray (2.95 Å) |
Matot B, Le Bihan YV, Lescasse R, Perez J, Miron S,
David G, Castaing B, Weber P, Raynal B, Zinn-Justin S,
Gasparini S, Le Du MH |
(2012) "The
orientation of the C-terminal domain of the
Saccharomyces cerevisiae Rap1 protein is determined by
its binding to DNA." Nucleic Acids Res.,
40, 3197-3207. doi: 10.1093/nar/gkr1166.
|
Crystal structure of rap1-DNA complex . SNAP output
|
|
3uld
|
hydrolase-RNA-DNA |
X-ray (1.6 Å) |
Gan JH, Abdur R, Huang Z |
"RNA/DNA hybrid in complex with RNase H catalytic
domain mutant D132N." |
High resolution structure of DNA-RNA hybrid in complex
with rnase h catalytic domain d132n mutant . SNAP output
|
|
3ulp
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Antony E, Weiland EA, Korolev S, Lohman TM |
(2012) "Plasmodium
falciparum SSB Tetramer Wraps Single-Stranded DNA with
Similar Topology but Opposite Polarity to E. coli
SSB." J.Mol.Biol., 420,
269-283. doi: 10.1016/j.jmb.2012.04.021.
|
Plasmodium falciparum ssb complex with ssDNA . SNAP output
|
|
3uo7
|
hydrolase-DNA |
X-ray (3.002 Å) |
Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C,
Jiang H, He C |
(2012) "Thymine
DNA glycosylase specifically recognizes
5-carboxylcytosine-modified DNA."
Nat.Chem.Biol., 8, 328-330.
doi: 10.1038/nchembio.914.
|
Crystal structure of human thymine DNA glycosylase
bound to substrate 5-carboxylcytosine . SNAP output
|
|
3uob
|
hydrolase-DNA |
X-ray (3.011 Å) |
Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C,
Jiang H, He C |
(2012) "Thymine
DNA glycosylase specifically recognizes
5-carboxylcytosine-modified DNA."
Nat.Chem.Biol., 8, 328-330.
doi: 10.1038/nchembio.914.
|
Crystal structure of human thymine DNA glycosylase
bound to substrate analog
2'-deoxy-2'-beta-fluoro-cytidine . SNAP output
|
|
3upq
|
transferase, lyase-DNA |
X-ray (1.95 Å) |
Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek
K |
(2012) "The
catalytic cycle for ribonucleotide incorporation by
human DNA Pol lambda." Nucleic Acids Res.,
40, 7518-7527. doi: 10.1093/nar/gks413.
|
Crystal structure of the pre-catalytic ternary complex
of polymerase lambda with an ratp analog opposite a
templating t. . SNAP
output
|
|
3upu
|
hydrolase-DNA |
X-ray (3.299 Å) |
He X, Byrd AK, Yun MK, Pemble CW, Harrison D, Yeruva
L, Dahl C, Kreuzer KN, Raney KD, White SW |
(2012) "The T4
Phage SF1B Helicase Dda Is Structurally Optimized to
Perform DNA Strand Separation." Structure,
20, 1189-1200. doi: 10.1016/j.str.2012.04.013.
|
Crystal structure of the t4 phage sf1b helicase dda .
SNAP output
|
|
3uq0
|
transferase, lyase-DNA |
X-ray (2.14 Å) |
Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek
K |
(2012) "The
catalytic cycle for ribonucleotide incorporation by
human DNA Pol lambda." Nucleic Acids Res.,
40, 7518-7527. doi: 10.1093/nar/gks413.
|
Crystal structure of the post-catalytic product complex
of polymerase lambda with an ramp at the primer
terminus. . SNAP
output
|
|
3uq2
|
transferase, lyase-DNA |
X-ray (2.25 Å) |
Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek
K |
(2012) "The
catalytic cycle for ribonucleotide incorporation by
human DNA Pol lambda." Nucleic Acids Res.,
40, 7518-7527. doi: 10.1093/nar/gks413.
|
Crystal structure of the post-catalytic product complex
of polymerase lambda with an rcmp inserted opposite a
templating g and damp inserted opposite a templating t
at the primer terminus. . SNAP output
|
|
3us0
|
transcription activator-DNA |
X-ray (2.5 Å) |
Chen C, Gorlatova N, Herzberg O |
(2012) "Pliable
DNA Conformation of Response Elements Bound to
Transcription Factor p63." J.Biol.Chem.,
287, 7477-7486. doi: 10.1074/jbc.M111.315820.
|
Structure of p63 DNA binding domain in complex with a
22 base pair a-t rich response element containing a two
base pair "at" spacer between half sites . SNAP output
|
|
3us1
|
transcription activator-DNA |
X-ray (2.8 Å) |
Chen C, Gorlatova N, Herzberg O |
(2012) "Pliable
DNA Conformation of Response Elements Bound to
Transcription Factor p63." J.Biol.Chem.,
287, 7477-7486. doi: 10.1074/jbc.M111.315820.
|
Structure of p63 DNA binding domain in complex with a
22 base pair response element containing a two base
pair "gc" spacer between half sites . SNAP output
|
|
3us2
|
transcription activator-DNA |
X-ray (4.2 Å) |
Chen C, Gorlatova N, Herzberg O |
(2012) "Pliable
DNA Conformation of Response Elements Bound to
Transcription Factor p63." J.Biol.Chem.,
287, 7477-7486. doi: 10.1074/jbc.M111.315820.
|
Structure of p63 DNA binding domain in complex with a
19 base pair a-t rich response element containing two
half sites with a single base pair overlap . SNAP output
|
|
3ut9
|
structural protein-DNA |
X-ray (2.2 Å) |
Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA |
(2012) "The
mechanics behind DNA sequence-dependent properties of
the nucleosome." Nucleic Acids Res.,
40, 6338-6352. doi: 10.1093/nar/gks261.
|
Crystal structure of nucleosome core particle assembled
with a palindromic widom '601' derivative (ncp-601l) .
SNAP output
|
|
3uta
|
structural protein-DNA |
X-ray (2.07 Å) |
Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA |
(2012) "The
mechanics behind DNA sequence-dependent properties of
the nucleosome." Nucleic Acids Res.,
40, 6338-6352. doi: 10.1093/nar/gks261.
|
Crystal structure of nucleosome core particle assembled
with an alpha-satellite sequence containing two ttaaa
elements (ncp-ta2) . SNAP output
|
|
3utb
|
structural protein-DNA |
X-ray (2.2 Å) |
Chua EYD, Vasudevan D, Davey GE, Wu B, Davey CA |
(2012) "The
mechanics behind DNA sequence-dependent properties of
the nucleosome." Nucleic Acids Res.,
40, 6338-6352. doi: 10.1093/nar/gks261.
|
Crystal structure of nucleosome core particle assembled
with the 146b alpha-satellite sequence (ncp146b) .
SNAP output
|
|
3uvf
|
hydrolase-DNA |
X-ray (3.0 Å) |
Jacoby K, Metzger M, Shen BW, Certo MT, Jarjour J,
Stoddard BL, Scharenberg AM |
(2012) "Expanding
LAGLIDADG endonuclease scaffold diversity by rapidly
surveying evolutionary sequence space." Nucleic
Acids Res., 40, 4954-4964. doi:
10.1093/nar/gkr1303.
|
Expanding lagalidadg endonuclease scaffold diversity by
rapidly surveying evolutionary sequence space .
SNAP output
|
|
3uxp
|
transferase, lyase-DNA |
X-ray (2.723 Å) |
Gridley CL, Rangarajan S, Firbank S, Dalal S, Sweasy
JB, Jaeger J |
(2013) "Structural
Changes in the Hydrophobic Hinge Region Adversely
Affect the Activity and Fidelity of the I260Q Mutator
DNA Polymerase beta." Biochemistry,
52, 4422-4432. doi: 10.1021/bi301368f.
|
Co-crystal structure of rat DNA polymerase beta mutator
i260q: enzyme-DNA-ddttp . SNAP output
|
|
3uxw
|
DNA-peptide |
X-ray (2.27 Å) |
Fonfria-Subiros E, Acosta-Reyes F, Saperas N, Pous J,
Subirana JA, Campos JL |
(2012) "Crystal
structure of a complex of DNA with one AT-hook of
HMGA1." Plos One, 7,
e37120. doi: 10.1371/journal.pone.0037120.
|
Crystal structures of an a-t-hook-DNA complex .
SNAP output
|
|
3v1z
|
hydrolase-DNA |
X-ray (2.2 Å) |
Manakova E, Grazulis S, Zaremba M, Tamulaitiene G,
Golovenko D, Siksnys V |
(2012) "Structural
mechanisms of the degenerate sequence recognition by
Bse634I restriction endonuclease." Nucleic
Acids Res., 40, 6741-6751. doi:
10.1093/nar/gks300.
|
Crystal structure of type iif restriction endonuclease
bse634i with cognate DNA . SNAP output
|
|
3v20
|
DNA binding protein, hydrolase-DNA |
X-ray (2.35 Å) |
Manakova E, Grazulis S, Zaremba M, Tamulaitiene G,
Golovenko D, Siksnys V |
(2012) "Structural
mechanisms of the degenerate sequence recognition by
Bse634I restriction endonuclease." Nucleic
Acids Res., 40, 6741-6751. doi:
10.1093/nar/gks300.
|
Crystal structure of type iif restriction endonuclease
bse634i with cognate DNA . SNAP output
|
|
3v21
|
DNA binding protein, hydrolase-DNA |
X-ray (2.7 Å) |
Manakova E, Grazulis S, Zaremba M, Tamulaitiene G,
Golovenko D, Siksnys V |
(2012) "Structural
mechanisms of the degenerate sequence recognition by
Bse634I restriction endonuclease." Nucleic
Acids Res., 40, 6741-6751. doi:
10.1093/nar/gks300.
|
Crystal structure of type iif restriction endonuclease
bse634i with cognate DNA . SNAP output
|
|
3v4i
|
transferase-DNA |
X-ray (2.8 Å) |
Das K, Martinez SE, Bauman JD, Arnold E |
(2012) "HIV-1
reverse transcriptase complex with DNA and nevirapine
reveals non-nucleoside inhibition mechanism."
Nat.Struct.Mol.Biol., 19,
253-259. doi: 10.1038/nsmb.2223.
|
Crystal structure of hiv-1 reverse transcriptase (rt)
with DNA and azttp . SNAP output
|
|
3v4r
|
hydrolase-DNA |
X-ray (3.25 Å) |
Webster MP, Jukes R, Zamfir VS, Kay CW, Bagneris C,
Barrett T |
(2012) "Crystal
structure of the UvrB dimer: insights into the nature
and functioning of the UvrAB damage engagement and
UvrB-DNA complexes." Nucleic Acids Res.,
40, 8743-8758. doi: 10.1093/nar/gks633.
|
Crystal structure of a uvrb dimer-DNA complex .
SNAP output
|
|
3v6d
|
transferase-DNA |
X-ray (2.7 Å) |
Das K, Martinez SE, Bauman JD, Arnold E |
(2012) "HIV-1
reverse transcriptase complex with DNA and nevirapine
reveals non-nucleoside inhibition mechanism."
Nat.Struct.Mol.Biol., 19,
253-259. doi: 10.1038/nsmb.2223.
|
Crystal structure of hiv-1 reverse transcriptase (rt)
cross-linked with azt-terminated DNA . SNAP output
|
|
3v6h
|
transferase-DNA |
X-ray (2.3 Å) |
Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS,
Rizzo CJ, Egli M, Guengerich FP |
(2012) "Replication
of n(2) ,3-ethenoguanine by DNA polymerases."
Angew.Chem.Int.Ed.Engl., 51,
5466-5469. doi: 10.1002/anie.201109004.
|
Replication of n2,3-ethenoguanine by DNA polymerases .
SNAP output
|
|
3v6j
|
transferase-DNA |
X-ray (2.3 Å) |
Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS,
Rizzo CJ, Egli M, Guengerich FP |
(2012) "Replication
of n(2) ,3-ethenoguanine by DNA polymerases."
Angew.Chem.Int.Ed.Engl., 51,
5466-5469. doi: 10.1002/anie.201109004.
|
Replication of n2,3-ethenoguanine by DNA polymerases .
SNAP output
|
|
3v6k
|
transferase-DNA |
X-ray (3.6 Å) |
Zhao L, Christov PP, Kozekov ID, Pence MG, Pallan PS,
Rizzo CJ, Egli M, Guengerich FP |
(2012) "Replication
of n(2) ,3-ethenoguanine by DNA polymerases."
Angew.Chem.Int.Ed.Engl., 51,
5466-5469. doi: 10.1002/anie.201109004.
|
Replication of n2,3-ethenoguanine by DNA polymerases .
SNAP output
|
|
3v6t
|
DNA binding protein-DNA |
X-ray (1.85 Å) |
Deng D, Yan CY, Pan XJ, Mahfouz M, Wang JW, Zhu JK,
Shi YG, Yan N |
(2012) "Structural
Basis for Sequence-Specific Recognition of DNA by TAL
Effectors." Science. doi: 10.1126/science.1215670.
|
Crystal structure of the DNA-bound dhax3, a tal
effector, at 1.85 angstrom . SNAP output
|
|
3v72
|
DNA binding protein-DNA |
X-ray (2.49 Å) |
Li Y, Gridley CL, Jaeger J, Sweasy JB, Schlick T |
(2012) "Unfavorable
Electrostatic and Steric Interactions in DNA Polymerase
beta E295K Mutant Interfere with the Enzyme s
Pathway." J.Am.Chem.Soc.,
134, 9999-10010. doi: 10.1021/ja300361r.
|
Crystal structure of rat DNA polymerase beta mutator
e295k: enzyme-dsDNA . SNAP output
|
|
3v79
|
transcription-DNA |
X-ray (3.85 Å) |
Choi SH, Wales TE, Nam Y, O'Donovan DJ, Sliz P, Engen
JR, Blacklow SC |
(2012) "Conformational
Locking upon Cooperative Assembly of Notch
Transcription Complexes." Structure,
20, 340-349. doi: 10.1016/j.str.2011.12.011.
|
Structure of human notch1 transcription complex
including csl, ram, ank, and maml-1 on hes-1 promoter
DNA sequence . SNAP
output
|
|
3v7j
|
transferase-DNA |
X-ray (2.25 Å) |
Rangarajan S, Gridley CL, Firbank S, Dalal S, Sweasy
JB, Jaeger J |
"Crystallographic studies of K72E mutant DNA
polymerase explain loss of lyase function and reveal
changes in the overall conformational state of the
polymerase domain." |
Co-crystal structure of wild type rat polymerase beta:
enzyme-DNA binary complex . SNAP output
|
|
3v7k
|
transferase-DNA |
X-ray (2.271 Å) |
Rangarajan S, Gridley CL, Firbank S, Dalal S, Sweasy
JB, Jaeger J |
"Crystallographic studies of K72E mutant DNA
polymerase explain loss of lyase function and reveal
changes in the overall conformational state of the
polymerase domain." |
Co-crystal structure of k72e variant of rat polymerase
beta: enzyme-DNA binary complex . SNAP output
|
|
3v81
|
transferase-DNA |
X-ray (2.85 Å) |
Das K, Martinez SE, Bauman JD, Arnold E |
(2012) "HIV-1
reverse transcriptase complex with DNA and nevirapine
reveals non-nucleoside inhibition mechanism."
Nat.Struct.Mol.Biol., 19,
253-259. doi: 10.1038/nsmb.2223.
|
Crystal structure of hiv-1 reverse transcriptase (rt)
with DNA and the nonnucleoside inhibitor nevirapine .
SNAP output
|
|
3v9s
|
hydrolase-DNA |
X-ray (2.1 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a product
ssDNA (aac) with one mg in the active site . SNAP output
|
|
3v9u
|
hydrolase-DNA |
X-ray (2.298 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a
preferred ssDNA (aat) with two mg in the active site .
SNAP output
|
|
3v9w
|
hydrolase-DNA |
X-ray (1.702 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a
preferred ssDNA (tta) with two mg in the active site .
SNAP output
|
|
3v9x
|
hydrolase-DNA |
X-ray (1.9 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a
preferred ssDNA (aaa) with two mg in the active site .
SNAP output
|
|
3v9z
|
hydrolase-DNA |
X-ray (1.8 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a product
ssDNA (acc) with one mg in the active site . SNAP output
|
|
3va0
|
hydrolase-DNA |
X-ray (2.201 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a
di-nucleotide product (gg) with one mg in the active
site . SNAP output
|
|
3va3
|
hydrolase-DNA |
X-ray (2.714 Å) |
Hsiao Y-Y, Duh Y, Chen YP, Wang YT, Yuan HS |
(2012) "How an
exonuclease decides where to stop in trimming of
nucleic acids: crystal structures of RNase T-product
complexes." Nucleic Acids Res.,
40, 8144-8154. doi: 10.1093/nar/gks548.
|
Crystal structure of rnase t in complex with a duplex
DNA product (stem loop DNA with 2 nucleotide 3'
overhang) . SNAP
output
|
|
3vaf
|
RNA binding protein-DNA |
X-ray (2.49 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru3 DNA . SNAP output
|
|
3vag
|
RNA binding protein-DNA |
X-ray (2.19 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru3c2 DNA . SNAP output
|
|
3vah
|
RNA binding protein-DNA |
X-ray (2.5 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru3c4 DNA . SNAP output
|
|
3vai
|
RNA binding protein-DNA |
X-ray (2.2 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru3c5 DNA . SNAP output
|
|
3vaj
|
RNA binding protein-DNA |
X-ray (1.9 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru5c6 DNA . SNAP output
|
|
3vak
|
RNA binding protein-DNA |
X-ray (2.17 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru5 DNA . SNAP output
|
|
3val
|
RNA binding protein-DNA |
X-ray (2.5 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru5c1 DNA . SNAP output
|
|
3vam
|
RNA binding protein-DNA |
X-ray (2.4 Å) |
Jenkins JL, Agrawal AA, Gupta A, Green MR, Kielkopf
CL |
(2013) "U2AF65
adapts to diverse pre-mRNA splice sites through
conformational selection of specific and promiscuous
RNA recognition motifs." Nucleic Acids
Res., 41, 3859-3873. doi:
10.1093/nar/gkt046.
|
Structure of u2af65 variant with bru5c2 DNA . SNAP output
|
|
3vd0
|
antitumor protein-DNA |
X-ray (2.95 Å) |
Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A,
Fronza G, Viadiu H |
(2012) "Structure
of p73 DNA-binding domain tetramer modulates p73
transactivation." Proc.Natl.Acad.Sci.USA,
109, 6066-6071. doi: 10.1073/pnas.1115463109.
|
Structure of p73 DNA binding domain tetramer modulates
p73 transactivation . SNAP output
|
|
3vd1
|
antitumor protein-DNA |
X-ray (2.95 Å) |
Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A,
Fronza G, Viadiu H |
(2012) "Structure
of p73 DNA-binding domain tetramer modulates p73
transactivation." Proc.Natl.Acad.Sci.USA,
109, 6066-6071. doi: 10.1073/pnas.1115463109.
|
Structure of p73 DNA binding domain tetramer modulates
p73 transactivation . SNAP output
|
|
3vd2
|
antitumor protein-DNA |
X-ray (4.0 Å) |
Ethayathulla AS, Tse PW, Monti P, Nguyen S, Inga A,
Fronza G, Viadiu H |
(2012) "Structure
of p73 DNA-binding domain tetramer modulates p73
transactivation." Proc.Natl.Acad.Sci.USA,
109, 6066-6071. doi: 10.1073/pnas.1115463109.
|
Structure of p73 DNA binding domain tetramer modulates
p73 transactivation . SNAP output
|
|
3vd6
|
transcription-DNA |
X-ray (1.98 Å) |
Wilkinson-White L, Lester KL, Ripin N, Jacques DA,
Mitchell Guss J, Matthews JM |
(2015) "GATA1
directly mediates interactions with closely spaced
pseudopalindromic but not distantly spaced double GATA
sites on DNA." Protein Sci.,
24, 1649-1659. doi: 10.1002/pro.2760.
|
Both zn fingers of gata1 bound to palindromic DNA
recognition site, p21 crystal form . SNAP output
|
|
3vdy
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Yadav T, Carrasco B, Myers AR, George NP, Keck JL,
Alonso JC |
(2012) "Genetic
recombination in Bacillus subtilis: a division of labor
between two single-strand DNA-binding proteins."
Nucleic Acids Res., 40,
5546-5559. doi: 10.1093/nar/gks173.
|
B. subtilis ssbb-ssDNA . SNAP output
|
|
3vea
|
DNA binding protein-DNA |
X-ray (2.55 Å) |
Dupaigne P, Tonthat NK, Espeli O, Whitfill T, Boccard
F, Schumacher MA |
(2012) "Molecular
basis for a protein-mediated DNA-bridging mechanism
that functions in condensation of the E. coli
chromosome." Mol.Cell,
48, 560-571. doi: 10.1016/j.molcel.2012.09.009.
|
Crystal structure of matp-mats23mer . SNAP output
|
|
3veb
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Dupaigne P, Tonthat NK, Espeli O, Whitfill T, Boccard
F, Schumacher MA |
(2012) "Molecular
basis for a protein-mediated DNA-bridging mechanism
that functions in condensation of the E. coli
chromosome." Mol.Cell,
48, 560-571. doi: 10.1016/j.molcel.2012.09.009.
|
Crystal structure of matp-mats . SNAP output
|
|
3vek
|
transcription-DNA |
X-ray (2.63 Å) |
Wilkinson-White L, Lester KL, Ripin N, Jacques DA,
Mitchell Guss J, Matthews JM |
(2015) "GATA1
directly mediates interactions with closely spaced
pseudopalindromic but not distantly spaced double GATA
sites on DNA." Protein Sci.,
24, 1649-1659. doi: 10.1002/pro.2760.
|
Both zn fingers of gata1 bound to palindromic DNA
recognition site, p1 crystal form . SNAP output
|
|
3vh0
|
protein binding-DNA |
X-ray (2.9 Å) |
Kagawa W, Sagawa T, Niki H, Kurumizaka H |
(2011) "Structural
basis for the DNA-binding activity of the bacterial
beta-propeller protein YncE." Acta
Crystallogr.,Sect.D, 67,
1045-1053. doi: 10.1107/S0907444911045033.
|
Crystal structure of e. coli ynce complexed with DNA .
SNAP output
|
|
3vk7
|
hydrolase-DNA |
X-ray (2.1 Å) |
Imamura K, Averill A, Wallace SS, Doublie S |
(2012) "Structural
characterization of viral ortholog of human DNA
glycosylase NEIL1 bound to thymine glycol or
5-hydroxyuracil-containing DNA."
J.Biol.Chem., 287, 4288-4298.
doi: 10.1074/jbc.M111.315309.
|
Crystal structure of DNA-glycosylase bound to DNA
containing 5-hydroxyuracil . SNAP output
|
|
3vk8
|
hydrolase-DNA |
X-ray (2.0 Å) |
Imamura K, Averill A, Wallace SS, Doublie S |
(2012) "Structural
characterization of viral ortholog of human DNA
glycosylase NEIL1 bound to thymine glycol or
5-hydroxyuracil-containing DNA."
J.Biol.Chem., 287, 4288-4298.
doi: 10.1074/jbc.M111.315309.
|
Crystal structure of DNA-glycosylase bound to DNA
containing thymine glycol . SNAP output
|
|
3vke
|
DNA binding protein-DNA |
X-ray (1.77 Å) |
Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR,
Barker A, Leedman PJ, Wilce JA, Wilce MCJ |
(2012) "Contribution
of the first K-homology domain of poly(C)-binding
protein 1 to its affinity and specificity for C-rich
oligonucleotides." Nucleic Acids Res.,
40, 5101-5114. doi: 10.1093/nar/gks058.
|
Contribution of the first k-homology domain of
poly(c)-binding protein 1 to its affinity and
specificity for c-rich oligonucleotides . SNAP output
|
|
3vok
|
transcription-DNA |
X-ray (2.0 Å) |
Sawai H, Yamanaka M, Sugimoto H, Shiro Y, Aono S |
(2012) "Structural
Basis for the Transcriptional Regulation of Heme
Homeostasis in Lactococcus lactis."
J.Biol.Chem., 287,
30755-30768. doi: 10.1074/jbc.M112.370916.
|
X-ray crystal structure of wild type hrtr in the apo
form with the target DNA. . SNAP output
|
|
3vw3
|
immune system-DNA |
X-ray (2.5 Å) |
Yokoyama H, Mizutani R, Satow Y |
(2013) "Structure
of a double-stranded DNA (6-4) photoproduct in complex
with the 64M-5 antibody Fab." Acta
Crystallogr.,Sect.D, 69, 504-512.
doi: 10.1107/S0907444912050007.
|
Antibody 64m-5 fab in complex with a double-stranded
DNA (6-4) photoproduct . SNAP output
|
|
3vw4
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Itou H, Yagura M, Shirakihara Y, Itoh T |
(2015) "Structural
Basis for Replication Origin Unwinding by An
Initiator-Primase of Plasmid ColE2-P9: Duplex DNA
Unwinding by A Single Protein."
J.Biol.Chem., 290, 3601-3611.
doi: 10.1074/jbc.M114.595645.
|
Crystal structure of the DNA-binding domain of cole2-p9
rep in complex with the replication origin . SNAP output
|
|
3vwb
|
transcription-DNA |
X-ray (2.416 Å) |
Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger
S, Wang MT, Cui S, Jin Q |
(2013) "Structural
insights into VirB-DNA complexes reveal mechanism of
transcriptional activation of virulence genes."
Nucleic Acids Res., 41,
10529-10541. doi: 10.1093/nar/gkt748.
|
Crystal structure of virb core domain (se-met
derivative) complexed with the cis-acting site (5-bru
modifications) upstream icsb promoter . SNAP output
|
|
3vxv
|
hydrolase-DNA |
X-ray (2.0 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of methyl cpg binding domain of mbd4
in complex with the 5mcg-tg sequence . SNAP output
|
|
3vxx
|
hydrolase-DNA |
X-ray (2.204 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of methyl cpg binding domain of mbd4
in complex with the 5mcg-5mcg sequence . SNAP output
|
|
3vyb
|
hydrolase-DNA |
X-ray (2.4 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of methyl cpg binding domain of mbd4
in complex with the 5mcg-hmcg sequence . SNAP output
|
|
3vyq
|
hydrolase-DNA |
X-ray (2.525 Å) |
Otani J, Arita K, Kato T, Kinoshita M, Kimura H,
Suetake I, Tajima S, Ariyoshi M, Shirakawa M |
(2013) "Structural
basis of the versatile DNA recognition ability of the
methyl-CpG binding domain of methyl-CpG binding domain
protein 4." J.Biol.Chem.,
288, 6351-6362. doi: 10.1074/jbc.M112.431098.
|
Crystal structure of the methyl cpg binding domain of
mbd4 in complex with the 5mcg-tg sequence in space
group p1 . SNAP
output
|
|
3w2a
|
transcription-DNA |
X-ray (2.775 Å) |
Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger
S, Wang MT, Cui S, Jin Q |
(2013) "Structural
insights into VirB-DNA complexes reveal mechanism of
transcriptional activation of virulence genes."
Nucleic Acids Res., 41,
10529-10541. doi: 10.1093/nar/gkt748.
|
Crystal structure of virb core domain complexed with
the cis-acting site upstream icsp promoter . SNAP output
|
|
3w3c
|
transcription-DNA |
X-ray (2.431 Å) |
Gao XP, Zou TT, Mu ZX, Qin B, Yang J, Waltersperger
S, Wang MT, Cui S, Jin Q |
(2013) "Structural
insights into VirB-DNA complexes reveal mechanism of
transcriptional activation of virulence genes."
Nucleic Acids Res., 41,
10529-10541. doi: 10.1093/nar/gkt748.
|
Crystal structure of virb core domain complexed with
the cis-acting site upstream icsb promoter . SNAP output
|
|
3w6v
|
transcription activator-DNA |
X-ray (2.95 Å) |
Yao MD, Ohtsuka J, Nagata K, Miyazono K, Zhi Y,
Ohnishi Y, Tanokura M |
(2013) "Complex
Structure of the DNA-binding Domain of AdpA, the Global
Transcription Factor in Streptomyces griseus, and a
Target Duplex DNA Reveals the Structural Basis of Its
Tolerant DNA Sequence Specificity."
J.Biol.Chem., 288,
31019-31029. doi: 10.1074/jbc.M113.473611.
|
Crystal structure of the DNA-binding domain of adpa,
the global transcriptional factor, in complex with a
target DNA . SNAP
output
|
|
3w96
|
structural protein-DNA |
X-ray (3.0 Å) |
Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H,
Tachiwana H, Shibata T, Kagawa W, Kurumizaka H |
(2013) "Contribution
of histone N-terminal tails to the structure and
stability of nucleosomes." FEBS Open Bio,
3, 363-369. doi: 10.1016/j.fob.2013.08.007.
|
Crystal structure of human nucleosome core particle
lacking h2a n-terminal region . SNAP output
|
|
3w97
|
structural protein-DNA |
X-ray (3.2 Å) |
Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H,
Tachiwana H, Shibata T, Kagawa W, Kurumizaka H |
(2013) "Contribution
of histone N-terminal tails to the structure and
stability of nucleosomes." FEBS Open Bio,
3, 363-369. doi: 10.1016/j.fob.2013.08.007.
|
Crystal structure of human nucleosome core particle
lacking h2b n-terminal region . SNAP output
|
|
3w98
|
structural protein-DNA |
X-ray (3.42 Å) |
Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H,
Tachiwana H, Shibata T, Kagawa W, Kurumizaka H |
(2013) "Contribution
of histone N-terminal tails to the structure and
stability of nucleosomes." FEBS Open Bio,
3, 363-369. doi: 10.1016/j.fob.2013.08.007.
|
Crystal structure of human nucleosome core particle
lacking h3.1 n-terminal region . SNAP output
|
|
3w99
|
structural protein-DNA |
X-ray (3.0 Å) |
Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H,
Tachiwana H, Shibata T, Kagawa W, Kurumizaka H |
(2013) "Contribution
of histone N-terminal tails to the structure and
stability of nucleosomes." FEBS Open Bio,
3, 363-369. doi: 10.1016/j.fob.2013.08.007.
|
Crystal structure of human nucleosome core particle
lacking h4 n-terminal region . SNAP output
|
|
3wa9
|
structural protein-DNA |
X-ray (3.07 Å) |
Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A,
Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W,
Harata M, Kimura H, Kurumizaka H |
(2013) "Structural
polymorphism in the L1 loop regions of human H2A.Z.1
and H2A.Z.2." Acta Crystallogr.,Sect.D,
69, 2431-2439. doi: 10.1107/S090744491302252X.
|
The nucleosome containing human h2a.z.1 . SNAP output
|
|
3waa
|
structural protein-DNA |
X-ray (3.2 Å) |
Horikoshi N, Sato K, Shimada K, Arimura Y, Osakabe A,
Tachiwana H, Hayashi-Takanaka Y, Iwasaki W, Kagawa W,
Harata M, Kimura H, Kurumizaka H |
(2013) "Structural
polymorphism in the L1 loop regions of human H2A.Z.1
and H2A.Z.2." Acta Crystallogr.,Sect.D,
69, 2431-2439. doi: 10.1107/S090744491302252X.
|
The nucleosome containing human h2a.z.2 . SNAP output
|
|
3waz
|
hydrolase-DNA |
X-ray (3.0 Å) |
Miyazono K, Furuta Y, Watanabe-Matsui M, Miyakawa T,
Ito T, Kobayashi I, Tanokura M |
(2014) "A
sequence-specific DNA glycosylase mediates
restriction-modification in Pyrococcus abyssi."
Nat Commun, 5, 3178. doi:
10.1038/ncomms4178.
|
Crystal structure of a restriction enzyme pabi in
complex with DNA . SNAP
output
|
|
3wgi
|
transcription-DNA |
X-ray (3.25 Å) |
Zheng Y, Ko T-P, Sun H, Huang C-H, Pei J, Qiu R, Wang
AH-J, Wiegel J, Shao W, Guo R-T |
(2014) "Distinct
structural features of Rex-family repressors to sense
redox levels in anaerobes and aerobes."
J.Struct.Biol., 188, 195-204.
doi: 10.1016/j.jsb.2014.11.001.
|
Crystal structure of rsp in complex with beta-nad+ and
operator DNA . SNAP
output
|
|
3wkj
|
structural protein-DNA |
X-ray (2.8 Å) |
Urahama T, Horikoshi N, Osakabe A, Tachiwana H,
Kurumizaka H |
(2014) "Structure
of human nucleosome containing the testis-specific
histone variant TSH2B." Acta
Crystallogr.,Sect.F, 70, 444-449.
doi: 10.1107/S2053230X14004695.
|
The nucleosome containing human tsh2b . SNAP output
|
|
3wpc
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E,
Uchiyama S, Miyake K, Shimizu T |
(2015) "Structural
basis of CpG and inhibitory DNA recognition by
Toll-like receptor 9." Nature,
520, 702-705. doi: 10.1038/nature14138.
|
Crystal structure of horse tlr9 in complex with
agonistic dna1668_12mer . SNAP output
|
|
3wpd
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E,
Uchiyama S, Miyake K, Shimizu T |
(2015) "Structural
basis of CpG and inhibitory DNA recognition by
Toll-like receptor 9." Nature,
520, 702-705. doi: 10.1038/nature14138.
|
Crystal structure of horse tlr9 in complex with
inhibitory dna4084 . SNAP output
|
|
3wpe
|
DNA binding protein-DNA |
X-ray (2.38 Å) |
Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E,
Uchiyama S, Miyake K, Shimizu T |
(2015) "Structural
basis of CpG and inhibitory DNA recognition by
Toll-like receptor 9." Nature,
520, 702-705. doi: 10.1038/nature14138.
|
Crystal structure of bovine tlr9 in complex with
agonistic dna1668_12mer . SNAP output
|
|
3wpg
|
DNA binding protein-DNA |
X-ray (2.246 Å) |
Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E,
Uchiyama S, Miyake K, Shimizu T |
(2015) "Structural
basis of CpG and inhibitory DNA recognition by
Toll-like receptor 9." Nature,
520, 702-705. doi: 10.1038/nature14138.
|
Crystal structure of mouse tlr9 in complex with
inhibitory dna4084 (form 1) . SNAP output
|
|
3wph
|
DNA binding protein-DNA |
X-ray (2.327 Å) |
Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E,
Uchiyama S, Miyake K, Shimizu T |
(2015) "Structural
basis of CpG and inhibitory DNA recognition by
Toll-like receptor 9." Nature,
520, 702-705. doi: 10.1038/nature14138.
|
Crystal structure of mouse tlr9 in complex with
inhibitory dna4084 (form 2) . SNAP output
|
|
3wpi
|
DNA binding protein-DNA |
X-ray (2.246 Å) |
Ohto U, Shibata T, Tanji H, Ishida H, Krayukhina E,
Uchiyama S, Miyake K, Shimizu T |
(2015) "Structural
basis of CpG and inhibitory DNA recognition by
Toll-like receptor 9." Nature,
520, 702-705. doi: 10.1038/nature14138.
|
Crystal structure of mouse tlr9 in complex with
inhibitory dna_super . SNAP output
|
|
3wtp
|
DNA binding protein-DNA |
X-ray (2.67 Å) |
Arimura Y, Shirayama K, Horikoshi N, Fujita R,
Taguchi H, Kagawa W, Fukagawa T, Almouzni G, Kurumizaka
H |
(2014) "Crystal
structure and stable property of the cancer-associated
heterotypic nucleosome containing CENP-A and H3.3."
Sci Rep, 4, 7115. doi:
10.1038/srep07115.
|
Crystal structure of the heterotypic nucleosome
containing human cenp-a and h3.3 . SNAP output
|
|
3wts
|
transcription-DNA |
X-ray (2.35 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of ets1,
runx1, cbfbeta, and the tcralpha gene enhancer DNA .
SNAP output
|
|
3wtt
|
transcription-DNA |
X-ray (2.35 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of
phosphorylated ets1, runx1, cbfbeta, and the tcralpha
gene enhancer DNA . SNAP
output
|
|
3wtu
|
transcription-DNA |
X-ray (2.7 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of ets1
(v170a), runx1, cbfbeta, and the tcralpha gene enhancer
DNA . SNAP output
|
|
3wtv
|
transcription-DNA |
X-ray (2.7 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of
ets1(v170g), runx1, cbfbeta, and the tcralpha gene
enhancer DNA . SNAP
output
|
|
3wtw
|
transcription-DNA |
X-ray (2.9 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of
ets1(k167a), runx1, cbfbeta, and the tcralpha gene
enhancer DNA . SNAP
output
|
|
3wtx
|
transcription-DNA |
X-ray (2.8 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of
ets1(y329a), runx1, cbfbeta, and the tcralpha gene
enhancer DNA . SNAP
output
|
|
3wty
|
transcription-DNA |
X-ray (2.7 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the complex comprised of
ets1(g333p), runx1, cbfbeta, and the tcralpha gene
enhancer DNA . SNAP
output
|
|
3wu1
|
transcription-DNA |
X-ray (2.4 Å) |
Shiina M, Hamada K, Inoue-Bungo T, Shimamura M,
Uchiyama A, Baba S, Sato K, Yamamoto M, Ogata K |
(2015) "A novel
allosteric mechanism on protein-DNA interactions
underlying the phosphorylation-dependent regulation of
Ets1 target gene expressions."
J.Mol.Biol., 427, 1655-1669.
doi: 10.1016/j.jmb.2014.07.020.
|
Crystal structure of the ets1-runx1-DNA ternary complex
. SNAP output
|
|
3wvg
|
hydrolase-DNA |
X-ray (2.25 Å) |
Kawamura T, Kobayashi T, Watanabe N |
(2015) "Analysis
of the HindIII-catalyzed reaction by time-resolved
crystallography." Acta
Crystallogr.,Sect.D, 71, 256-265.
doi: 10.1107/S1399004714025188.
|
Time-resolved crystal structure of hindiii with 0sec
soaking . SNAP
output
|
|
3wvh
|
hydrolase-DNA |
X-ray (2.54 Å) |
Kawamura T, Kobayashi T, Watanabe N |
(2015) "Analysis
of the HindIII-catalyzed reaction by time-resolved
crystallography." Acta
Crystallogr.,Sect.D, 71, 256-265.
doi: 10.1107/S1399004714025188.
|
Time-resolved crystal structure of hindiii with 25sec
soaking . SNAP
output
|
|
3wvi
|
hydrolase-DNA |
X-ray (2.55 Å) |
Kawamura T, Kobayashi T, Watanabe N |
(2015) "Analysis
of the HindIII-catalyzed reaction by time-resolved
crystallography." Acta
Crystallogr.,Sect.D, 71, 256-265.
doi: 10.1107/S1399004714025188.
|
Time-resolved crystal structure of hindiii with 40 sec
soaking . SNAP
output
|
|
3wvk
|
hydrolase-DNA |
X-ray (2.0 Å) |
Kawamura T, Kobayashi T, Watanabe N |
(2015) "Analysis
of the HindIII-catalyzed reaction by time-resolved
crystallography." Acta
Crystallogr.,Sect.D, 71, 256-265.
doi: 10.1107/S1399004714025188.
|
Time-resolved crystal structure of hindiii with 230sec
soaking . SNAP
output
|
|
3wvp
|
hydrolase-DNA |
X-ray (2.3 Å) |
Kawamura T, Kobayashi T, Watanabe N |
(2015) "Analysis
of the HindIII-catalyzed reaction by time-resolved
crystallography." Acta
Crystallogr.,Sect.D, 71, 256-265.
doi: 10.1107/S1399004714025188.
|
Time-resolved crystal structure of hindiii with 60sec
soaking . SNAP
output
|
|
3x1l
|
RNA binding protein-RNA-DNA |
X-ray (2.096 Å) |
Osawa T, Inanaga H, Sato C, Numata T |
(2015) "Crystal
structure of the CRISPR-Cas RNA silencing Cmr complex
bound to a target analog." Mol.Cell,
58, 418-430. doi: 10.1016/j.molcel.2015.03.018.
|
Crystal structure of the crispr-cas RNA silencing cmr
complex bound to a target analog . SNAP output
|
|
3x1s
|
structural protein-DNA |
X-ray (2.805 Å) |
Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T,
Ishii S, Kumarevel T |
(2015) "Structural
and functional analyses of nucleosome complexes with
mouse histone variants TH2a and TH2b, involved in
reprogramming."
Biochem.Biophys.Res.Commun.,
464, 929-935. doi: 10.1016/j.bbrc.2015.07.070.
|
Crystal structure of the nucleosome core particle .
SNAP output
|
|
3x1t
|
structural protein-DNA |
X-ray (2.808 Å) |
Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T,
Ishii S, Kumarevel T |
(2015) "Structural
and functional analyses of nucleosome complexes with
mouse histone variants TH2a and TH2b, involved in
reprogramming."
Biochem.Biophys.Res.Commun.,
464, 929-935. doi: 10.1016/j.bbrc.2015.07.070.
|
Crystal structure of nucleosome core particle
consisting of mouse testis specific histone variants
h2aa and h2ba . SNAP
output
|
|
3x1u
|
structural protein-DNA |
X-ray (3.25 Å) |
Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T,
Ishii S, Kumarevel T |
(2015) "Structural
and functional analyses of nucleosome complexes with
mouse histone variants TH2a and TH2b, involved in
reprogramming."
Biochem.Biophys.Res.Commun.,
464, 929-935. doi: 10.1016/j.bbrc.2015.07.070.
|
Crystal structure of nucleosome core particle in the
presence of histone variants involved in reprogramming
. SNAP output
|
|
3x1v
|
structural protein-DNA |
X-ray (2.921 Å) |
Padavattan S, Shinagawa T, Hasegawa K, Kumasaka T,
Ishii S, Kumarevel T |
(2015) "Structural
and functional analyses of nucleosome complexes with
mouse histone variants TH2a and TH2b, involved in
reprogramming."
Biochem.Biophys.Res.Commun.,
464, 929-935. doi: 10.1016/j.bbrc.2015.07.070.
|
Crystal structure of nucleosome core particle in the
presence of histone variant involved in reprogramming .
SNAP output
|
|
3zda
|
hydrolase-DNA |
X-ray (1.5 Å) |
Anstey-Gilbert CS, Hemsworth GR, Flemming CS,
Hodskinson MRG, Zhang J, Sedelnikova SE, Stillman TJ,
Sayers JR, Artymiuk PJ |
(2013) "The
Structure of E. Coli Exoix - Implications for DNA
Binding and Catalysis in Flap Endonucleases."
Nucleic Acids Res., 41, 8357.
doi: 10.1093/NAR/GKT591.
|
Structure of e. coli exoix in complex with a fragment
of the flap1 DNA oligonucleotide, potassium and
magnesium . SNAP
output
|
|
3zdb
|
hydrolase-DNA |
X-ray (1.47 Å) |
Anstey-Gilbert CS, Hemsworth GR, Flemming CS,
Hodskinson MRG, Zhang J, Sedelnikova SE, Stillman TJ,
Sayers JR, Artymiuk PJ |
(2013) "The
Structure of E. Coli Exoix - Implications for DNA
Binding and Catalysis in Flap Endonucleases."
Nucleic Acids Res., 41, 8357.
doi: 10.1093/NAR/GKT591.
|
Structure of e. coli exoix in complex with the
palindromic 5ov4 DNA oligonucleotide, di-magnesium and
potassium . SNAP
output
|
|
3zdc
|
hydrolase |
X-ray (1.53 Å) |
Anstey-Gilbert CS, Hemsworth GR, Flemming CS,
Hodskinson MRG, Zhang J, Sedelnikova SE, Stillman TJ,
Sayers JR, Artymiuk PJ |
(2013) "The
Structure of E. Coli Exoix - Implications for DNA
Binding and Catalysis in Flap Endonucleases."
Nucleic Acids Res., 41, 8357.
doi: 10.1093/NAR/GKT591.
|
Structure of e. coli exoix in complex with the
palindromic 5ov4 DNA oligonucleotide, potassium and
calcium . SNAP
output
|
|
3zdd
|
hydrolase-DNA |
X-ray (1.5 Å) |
Anstey-Gilbert CS, Hemsworth GR, Flemming CS,
Hodskinson MR, Zhang J, Sedelnikova SE, Stillman TJ,
Sayers JR, Artymiuk PJ |
(2013) "The
structure of Escherichia coli ExoIX--implications for
DNA binding and catalysis in flap endonucleases."
Nucleic Acids Res., 41,
8357-8367. doi: 10.1093/nar/gkt591.
|
Structure of e. coli exoix in complex with the
palindromic 5ov6 oligonucleotide and potassium .
SNAP output
|
|
3zgz
|
ligase-RNA |
X-ray (2.4 Å) |
Chopra S, Palencia A, Virus C, Tripathy A, Temple BR,
Velazquez-Campoy A, Cusack S, Reader JS |
(2013) "Plant
Tumour Biocontrol Agent Employs a tRNA-Dependent
Mechanism to Inhibit Leucyl-tRNA Synthetase."
Nat.Commun., 4, 1417. doi:
10.1038/NCOMMS2421.
|
Ternary complex of e. coli leucyl-trna synthetase,
trna(leu) and toxic moiety from agrocin 84 (tm84) in
aminoacylation-like conformation . SNAP output
|
|
3zh2
|
oxidoreductase |
X-ray (2.1 Å) |
Cheung YW, Kwok J, Law AWL, Watt RM, Kotaka M, Tanner
JA |
(2013) "Structural
Basis for Discriminatory Recognition of Plasmodium
Lactate Dehydrogenase by a DNA Aptamer."
Proc.Natl.Acad.Sci.USA, 110,
15967. doi: 10.1073/PNAS.1309538110.
|
Structure of plasmodium falciparum lactate
dehydrogenase in complex with a DNA aptamer . SNAP output
|
|
3zhm
|
transcription |
X-ray (2.6 Å) |
Frandsen KH, Rasmussen KK, Jensen MR, Hammer K,
Pedersen M, Poulsen JN, Arleth L, Lo Leggio L |
(2013) "Binding
of the N-Terminal Domain of the Lactococcal
Bacteriophage Tp901-1 Ci Repressor to its Target DNA: A
Crystallography, Small Angle Scattering, and Nuclear
Magnetic Resonance Study." Biochemistry,
52, 6892. doi: 10.1021/BI400439Y.
|
N-terminal domain of the ci repressor from
bacteriophage tp901-1 in complex with the ol2 operator
half-site . SNAP
output
|
|
3zi5
|
hydrolase-DNA |
X-ray (3.2 Å) |
Golovenko D, Grazulis S, Manakova E, Sasnauskas G,
Siksnys V, Zakrys L, Zaremba M |
(2014) "Structural
Insight Into the Specificity of the B3 DNA-Binding
Domains Provided by the Co-Crystal Structure of the
C-Terminal Fragment of Bfii Restriction Enzyme."
Nucleic Acids Res., 42, 4113.
doi: 10.1093/NAR/GKT1368.
|
Crystal structure of restriction endonuclease bfii
c-terminal recognition domain in complex with cognate
DNA . SNAP output
|
|
3zkc
|
transcription-DNA |
X-ray (3.0 Å) |
Newman JA, Rodrigues C, Lewis RJ |
(2013) "Molecular
Basis of the Activity of Sinr, the Master Regulator of
Biofilm Formation in Bacillus Subtilis."
J.Biol.Chem., 288, 10766.
doi: 10.1074/JBC.M113.455592.
|
Crystal structure of the master regulator for biofilm
formation sinr in complex with DNA. . SNAP output
|
|
3zlj
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Groothuizen FS, Fish A, Petoukhov MV, Reumer A,
Manelyte L, Winterwerp HHK, Marinus MG, Lebbink JHG,
Svergun DI, Friedhoff P, Sixma TK |
(2013) "Using
Stable Muts Dimers and Tetramers to Quantitatively
Analyze DNA Mismatch Recognition and Sliding Clamp
Formation." Nucleic Acids Res.,
41, 8166. doi: 10.1093/NAR/GKT582.
|
Crystal structure of full-length e.coli DNA mismatch
repair protein muts d835r mutant in complex with gt
mismatched DNA . SNAP
output
|
|
3zp5
|
transcription-DNA |
X-ray (2.0 Å) |
Cooper CDO, Newman JA, Aitkenhead H, Allerston CK,
Gileadi O |
(2015) "Structures
of the Ets Domains of Transcription Factors Etv1, Etv4,
Etv5 and Fev: Determinants of DNA Binding and Redox
Regulation by Disulfide Bond Formation."
J.Biol.Chem., 290, 13692.
doi: 10.1074/JBC.M115.646737.
|
Crystal structure of the DNA binding ets domain of the
human protein fev in complex with DNA . SNAP output
|
|
3zpl
|
transcription-DNA |
X-ray (2.8 Å) |
Stevenson CEM, Assaad A, Chandra G, Le TBK, Greive
SJ, Bibb MJ, Lawson DM |
(2013) "Investigation
of DNA Sequence Recognition by a Streptomycete Marr
Family Transcriptional Regulator Through Surface
Plasmon Resonance and X-Ray Crystallography."
Nucleic Acids Res., 41, 7009.
doi: 10.1093/NAR/GKT523.
|
Crystal structure of sco3205, a marr family
transcriptional regulator from streptomyces coelicolor,
in complex with DNA . SNAP output
|
|
3zqc
|
transcription-DNA |
X-ray (2.9 Å) |
Wei S-Y, Lou Y-C, Tsai J-Y, Ho MR, Chou CC,
Rajasekaran M, Hsu H-M, Tai J-H, Hsiao C-D, Chen C |
(2012) "Structure
of the Trichomonas Vaginalis Myb3 DNA-Binding Domain
Bound to a Promoter Sequence Reveals a Unique
C-Terminal Beta-Hairpin Conformation." Nucleic
Acids Res., 40, 449. doi:
10.1093/NAR/GKR707.
|
Structure of the trichomonas vaginalis myb3 DNA-binding
domain bound to a promoter sequence reveals a unique
c-terminal beta-hairpin conformation . SNAP output
|
|
3zql
|
protein-DNA complex |
X-ray (2.99 Å) |
Le TBK, Schumacher MA, Lawson DM, Brennan RG, Buttner
MJ |
(2011) "The
Crystal Structure of the Tetr Family Transcriptional
Repressor Simr Bound to DNA and the Role of a Flexible
N-Terminal Extension in Minor Groove Binding."
Nucleic Acids Res., 39, 9433.
doi: 10.1093/NAR/GKR640.
|
DNA-bound form of tetr-like repressor simr . SNAP output
|
|
3zvk
|
antitoxin-toxin-DNA |
X-ray (2.5 Å) |
Mate MJ, Vincentelli R, Foos N, Raoult D, Cambillau
C, Ortiz-Lombardia M |
(2012) "Crystal
Structure of the DNA-Bound Vapbc2 Antitoxin/Toxin Pair
from Rickettsia Felis." Nucleic Acids
Res., 40, 3245. doi: 10.1093/NAR/GKR1167.
|
Crystal structure of vapbc2 from rickettsia felis bound
to a DNA fragment from their promoter . SNAP output
|
|
3zvm
|
hydrolase-transferase-DNA |
X-ray (1.997 Å) |
Garces F, Pearl LH, Oliver AW |
(2011) "The
structural basis for substrate recognition by mammalian
polynucleotide kinase 3' phosphatase." Mol.
Cell, 44, 385-396. doi: 10.1016/j.molcel.2011.08.036.
|
The structural basis for substrate recognition by
mammalian polynucleotide kinase 3' phosphatase .
SNAP output
|
|
3zvn
|
hydrolase-transferase-DNA |
X-ray (2.15 Å) |
Garces F, Pearl LH, Oliver AW |
(2011) "The
structural basis for substrate recognition by mammalian
polynucleotide kinase 3' phosphatase." Mol.
Cell, 44, 385-396. doi: 10.1016/j.molcel.2011.08.036.
|
The structural basis for substrate recognition by
mammalian polynucleotide kinase 3' phosphatase .
SNAP output
|
|
4a04
|
transcription |
X-ray (2.58 Å) |
El Omari K, De Mesmaeker J, Karia D, Ginn H,
Bhattacharya S, Mancini EJ |
(2012) "Structure
of the DNA-Bound T-Box Domain of Human Tbx1, a
Transcription Factor Associated with the Digeorge
Syndrome." Proteins, 80,
655. doi: 10.1002/PROT.23208.
|
Structure of the DNA-bound t-box domain of human tbx1,
a transcription factor associated with the digeorge
syndrome . SNAP
output
|
|
4a08
|
DNA-binding protein-DNA |
X-ray (3.0 Å) |
Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH |
(2011) "The
Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase
Architecture, Targeting, and Activation."
Cell(Cambridge,Mass.), 147,
1024. doi: 10.1016/J.CELL.2011.10.035.
|
Structure of hsddb1-drddb2 bound to a 13 bp cpd-duplex
(purine at d-1 position) at 3.0 Å resolution (cpd 1) .
SNAP output
|
|
4a09
|
DNA-binding protein-DNA |
X-ray (3.1 Å) |
Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH |
(2011) "The
Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase
Architecture, Targeting, and Activation."
Cell(Cambridge,Mass.), 147,
1024. doi: 10.1016/J.CELL.2011.10.035.
|
Structure of hsddb1-drddb2 bound to a 15 bp cpd-duplex
(purine at d-1 position) at 3.1 Å resolution (cpd 2) .
SNAP output
|
|
4a0a
|
DNA binding protein-DNA |
X-ray (3.6 Å) |
Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH |
(2011) "The
Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase
Architecture, Targeting, and Activation."
Cell(Cambridge,Mass.), 147,
1024. doi: 10.1016/J.CELL.2011.10.035.
|
Structure of hsddb1-drddb2 bound to a 16 bp cpd-duplex
(pyrimidine at d-1 position) at 3.6 Å resolution (cpd
3) . SNAP output
|
|
4a0b
|
DNA binding protein-DNA |
X-ray (3.8 Å) |
Scrima A, Fischer ES, Iwai S, Gut H, Thoma NH |
(2011) "The
Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase
Architecture, Targeting, and Activation."
Cell(Cambridge,Mass.), 147,
1024. doi: 10.1016/J.CELL.2011.10.035.
|
Structure of hsddb1-drddb2 bound to a 16 bp cpd-duplex
(pyrimidine at d-1 position) at 3.8 Å resolution (cpd
4) . SNAP output
|
|
4a0k
|
ligase-DNA-binding protein-DNA |
X-ray (5.93 Å) |
Fischer ES, Scrima A, Bohm K, Matsumoto S, Lingaraju
GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F,
Iwai S, Gut H, Sugasawa K, Thoma NH |
(2011) "The
Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase
Architecture, Targeting, and Activation."
Cell(Cambridge,Mass.), 147,
1024. doi: 10.1016/J.CELL.2011.10.035.
|
Structure of ddb1-ddb2-cul4a-rbx1 bound to a 12 bp
abasic site containing DNA-duplex . SNAP output
|
|
4a0l
|
ligase-DNA-binding protein-DNA |
X-ray (7.4 Å) |
Fischer ES, Scrima A, Bohm K, Matsumoto S, Lingaraju
GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F,
Iwai S, Gut H, Sugasawa K, Thoma NH |
(2011) "The
Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase
Architecture, Targeting, and Activation."
Cell(Cambridge,Mass.), 147,
1024. doi: 10.1016/J.CELL.2011.10.035.
|
Structure of ddb1-ddb2-cul4b-rbx1 bound to a 12 bp
abasic site containing DNA-duplex . SNAP output
|
|
4a12
|
transcription |
X-ray (3.15 Å) |
Albanesi D, Reh G, Guerin ME, Schaeffer F,
Debarbouille M, Buschiazzo A, Schujman GE, De Mendoza D,
Alzari PM |
(2013) "Structural
Basis for Feed-Forward Transcriptional Regulation of
Membrane Lipid Homeostasis in Staphylococcus
Aureus." Plos Pathog., 9,
3108. doi: 10.1371/JOURNAL.PPAT.1003108.
|
Structure of the global transcription regulator fapr
from staphylococcus aureus in complex with DNA operator
. SNAP output
|
|
4a15
|
hydrolase |
X-ray (2.2 Å) |
Kuper J, Wolski SC, Michels G, Kisker C |
(2011) "Functional
and Structural Studies of the Nucleotide Excision
Repair Helicase Xpd Suggest a Polarity for DNA
Translocation." Embo J.,
31, 494. doi: 10.1038/EMBOJ.2011.374.
|
Crystal structure of an xpd DNA complex . SNAP output
|
|
4a3b
|
transcription |
X-ray (3.5 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
4nt DNA-RNA hybrid . SNAP output
|
|
4a3c
|
transcription |
X-ray (3.5 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
5nt DNA-RNA hybrid . SNAP output
|
|
4a3d
|
transcription |
X-ray (3.4 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
6nt DNA-RNA hybrid . SNAP output
|
|
4a3e
|
transcription |
X-ray (3.4 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
5nt DNA-RNA hybrid and soaked with ampcpp . SNAP output
|
|
4a3f
|
transcription |
X-ray (3.5 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
6nt DNA-RNA hybrid and soaked with ampcpp . SNAP output
|
|
4a3g
|
transcription |
X-ray (3.5 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
2nt DNA-RNA hybrid . SNAP output
|
|
4a3i
|
transcription |
X-ray (3.8 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii binary complex with DNA . SNAP output
|
|
4a3j
|
transcription |
X-ray (3.7 Å) |
Cheung ACM, Sainsbury S, Cramer P |
(2011) "Structural
Basis of Initial RNA Polymerase II Transcription."
Embo J., 30, 4755. doi:
10.1038/EMBOJ.2011.396.
|
RNA polymerase ii initial transcribing complex with a
2nt DNA-RNA hybrid and soaked with gmpcpp . SNAP output
|
|
4a3k
|
transcription |
X-ray (3.5 Å) |
Cheung ACM, Sainsbury S, Cramer P |
(2011) "Structural
Basis of Initial RNA Polymerase II Transcription."
Embo J., 30, 4755. doi:
10.1038/EMBOJ.2011.396.
|
RNA polymerase ii initial transcribing complex with a
7nt DNA-RNA hybrid . SNAP output
|
|
4a3l
|
transcription |
X-ray (3.5 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
7nt DNA-RNA hybrid and soaked with ampcpp . SNAP output
|
|
4a3m
|
transcription |
X-ray (3.9 Å) |
Cheung AC, Sainsbury S, Cramer P |
(2011) "Structural
basis of initial RNA polymerase II transcription."
EMBO J., 30, 4755-4763. doi:
10.1038/emboj.2011.396.
|
RNA polymerase ii initial transcribing complex with a
4nt DNA-RNA hybrid and soaked with ampcpp . SNAP output
|
|
4a75
|
chaperone-DNA |
X-ray (1.75 Å) |
Mayr F, Schutz A, Doge N, Heinemann U |
(2012) "The
Lin28 Cold-Shock Domain Remodels Pre-Let-7
Microrna." Nucleic Acids Res.,
40, 7492. doi: 10.1093/NAR/GKS355.
|
The lin28b cold shock domain in complex with
hexathymidine. . SNAP
output
|
|
4a76
|
chaperone-DNA |
X-ray (1.92 Å) |
Mayr F, Schutz A, Doge N, Heinemann U |
(2012) "The
Lin28 Cold-Shock Domain Remodels Pre-Let-7
Microrna." Nucleic Acids Res.,
40, 7492. doi: 10.1093/NAR/GKS355.
|
The lin28b cold shock domain in complex with
heptathymidine . SNAP
output
|
|
4a8f
|
transferase |
X-ray (3.3 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a8k
|
transferase-DNA |
X-ray (3.5 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a8m
|
transferase-DNA |
X-ray (2.92 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a8q
|
transferase-DNA |
X-ray (3.06 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a8s
|
transferase-DNA |
X-ray (2.9 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a8w
|
transferase-DNA |
X-ray (3.04 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a8y
|
transferase-DNA |
X-ray (3.41 Å) |
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes
JM |
(2012) "Noncatalytic
Ions Direct the RNA-Dependent RNA Polymerase of
Bacterial Double-Stranded RNA Virus Phi6 from De Novo
Initiation to Elongation." J.Virol.,
86, 2837. doi: 10.1128/JVI.05168-11.
|
Non-catalytic ions direct the RNA-dependent RNA
polymerase of bacterial dsrna virus phi6 from de novo
initiation to elongation . SNAP output
|
|
4a93
|
transcription |
X-ray (3.4 Å) |
Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C,
Gotte D, Strathern JN, Carell T, Cramer P, Kashlev M |
(2012) "Mechanism
of Translesion Transcription by RNA Polymerase II and
its Role in Cellular Resistance to DNA Damage."
Mol.Cell, 46, 18. doi:
10.1016/J.MOLCEL.2012.02.006.
|
RNA polymerase ii elongation complex containing a cpd
lesion . SNAP output
|
|
4aa6
|
transcription-DNA |
X-ray (2.6 Å) |
Schwabe JW, Chapman L, Rhodes D |
(1995) "The
oestrogen receptor recognizes an imperfectly
palindromic response element through an alternative
side-chain conformation." Structure,
3, 201-213. doi: 10.1016/s0969-2126(01)00150-2.
|
The oestrogen receptor recognizes an imperfectly
palindromic response element through an alternative
side-chain conformation . SNAP output
|
|
4aab
|
hydrolase-DNA |
X-ray (2.5 Å) |
Molina R, Redondo P, Stella S, Marenchino M, D'Abramo
M, Gervasio FL, Charles Epinat J, Valton J, Grizot S,
Duchateau P, Prieto J, Montoya G |
(2012) "Non-Specific
Protein-DNA Interactions Control I-Crei Target Binding
and Cleavage." Nucleic Acids Res.,
40, 6936-6945. doi: 10.1093/NAR/GKS320.
|
Crystal structure of the mutant d75n i-crei in complex
with its wild- type target (the four central bases, 2nn
region, are composed by gtac from 5' to 3') . SNAP output
|
|
4aad
|
hydrolase-DNA |
X-ray (3.1 Å) |
Molina R, Redondo P, Stella S, Marenchino M, D'Abramo
M, Gervasio FL, Charles Epinat J, Valton J, Grizot S,
Duchateau P, Prieto J, Montoya G |
(2012) "Non-Specific
Protein-DNA Interactions Control I-Crei Target Binding
and Cleavage." Nucleic Acids Res.,
40, 6936-6945. doi: 10.1093/NAR/GKS320.
|
Crystal structure of the mutant d75n i-crei in complex
with its wild- type target in absence of metal ions at
the active site (the four central bases, 2nn region,
are composed by gtac from 5' to 3') . SNAP output
|
|
4aae
|
hydrolase-DNA |
X-ray (2.6 Å) |
Molina R, Redondo P, Stella S, Marenchino M, D'Abramo
M, Gervasio FL, Charles Epinat J, Valton J, Grizot S,
Duchateau P, Prieto J, Montoya G |
(2012) "Non-Specific
Protein-DNA Interactions Control I-Crei Target Binding
and Cleavage." Nucleic Acids Res.,
40, 6936-6945. doi: 10.1093/NAR/GKS320.
|
Crystal structure of the mutant d75n i-crei in complex
with an altered target (the four central bases, 2nn
region, are composed by agcg from 5' to 3') . SNAP output
|
|
4aaf
|
hydrolase-DNA |
X-ray (2.5 Å) |
Molina R, Redondo P, Stella S, Marenchino M, D'Abramo
M, Gervasio FL, Charles Epinat J, Valton J, Grizot S,
Duchateau P, Prieto J, Montoya G |
(2012) "Non-Specific
Protein-DNA Interactions Control I-Crei Target Binding
and Cleavage." Nucleic Acids Res.,
40, 6936. doi: 10.1093/NAR/GKS320.
|
Crystal structure of the mutant d75n i-crei in complex
with an altered target (the four central bases, 2nn
region, are composed by tgca from 5' to 3') . SNAP output
|
|
4aag
|
hydrolase-DNA |
X-ray (2.8 Å) |
Molina R, Redondo P, Stella S, Marenchino M, D'Abramo
M, Gervasio FL, Charles Epinat J, Valton J, Grizot S,
Duchateau P, Prieto J, Montoya G |
(2012) "Non-Specific
Protein-DNA Interactions Control I-Crei Target Binding
and Cleavage." Nucleic Acids Res.,
40, 6936. doi: 10.1093/NAR/GKS320.
|
Crystal structure of the mutant d75n i-crei in complex
with its wild- type target in presence of ca at the
active site (the four central bases, 2nn region, are
composed by gtac from 5' to 3') . SNAP output
|
|
4abt
|
hydrolase-DNA |
X-ray (2.22 Å) |
Manakova EN, Grazulis S, Zaremba M, Tamulaitiene G,
Golovenko D, Siksnys V |
"Structure of Type Iif Restriction Endonuclease
Ngomiv with Cognate Uncleaved DNA." |
Crystal structure of type iif restriction endonuclease
ngomiv with cognate uncleaved DNA . SNAP output
|
|
4aij
|
transcription |
X-ray (2.05 Å) |
Quade N, Mendonca C, Herbst K, Heroven AK, Ritter C,
Heinz DW, Dersch P |
(2012) "Structural
Basis for Intrinsic Thermosensing by the Master
Virulence Regulator Rova of Yersinia."
J.Biol.Chem., 287, 35796.
doi: 10.1074/JBC.M112.379156.
|
Crystal structure of rova from yersinia in complex with
a rova promoter fragment . SNAP output
|
|
4aik
|
transcription |
X-ray (1.85 Å) |
Quade N, Mendonca C, Herbst K, Heroven AK, Ritter C,
Heinz DW, Dersch P |
(2012) "Structural
Basis for Intrinsic Thermosensing by the Master
Virulence Regulator Rova of Yersinia."
J.Biol.Chem., 287, 35796.
doi: 10.1074/JBC.M112.379156.
|
Crystal structure of rova from yersinia in complex with
an invasin promoter fragment . SNAP output
|
|
4ail
|
transferase |
X-ray (2.9 Å) |
Wynne SA, Pinheiro VB, Holliger P, Leslie AG |
(2013) "Structures
of an Apo and a Binary Complex of an Evolved Archeal B
Family DNA Polymerase Capable of Synthesising Highly
Cy-Dye Labelled DNA." Plos One,
8, 70892. doi: 10.1371/JOURNAL.PONE.0070892.
|
Crystal structure of an evolved replicating DNA
polymerase . SNAP
output
|
|
4al5
|
hydrolase-RNA |
X-ray (2.0 Å) |
Haurwitz RE, Sternberg SH, Doudna JA |
(2012) "Csy4
Relies on an Unusual Catalytic Dyad to Position and
Cleave Crispr RNA." Embo J.,
31, 2824. doi: 10.1038/EMBOJ.2012.107.
|
Crystal structure of the csy4-crrna product complex .
SNAP output
|
|
4am3
|
transferase-RNA |
X-ray (3.0 Å) |
Hardwick SW, Gubbey T, Hug I, Jenal U, Luisi BF |
(2012) "Crystal
Structure of Caulobacter Crescentus Polynucleotide
Phosphorylase Reveals a Mechanism of RNA Substrate
Channelling and RNA Degradosome Assembly." Open
Biol., 2, 20028. doi: 10.1098/RSOB.120028.
|
Crystal structure of c. crescentus pnpase bound to RNA
. SNAP output
|
|
4aqu
|
hydrolase |
X-ray (2.3 Å) |
Valton J, Daboussi F, Leduc S, Molina R, Redondo P,
Macmaster R, Montoya G, Duchateau P |
(2012) "5'-Cytosine-Phosphoguanine
(Cpg) Methylation Impacts the Activity of Natural and
Engineered Meganucleases." J.Biol.Chem.,
287, 30139. doi: 10.1074/JBC.M112.379966.
|
Crystal structure of i-crei complexed with its target
methylated at position plus 2 (in the b strand) in the
presence of calcium . SNAP output
|
|
4aqx
|
hydrolase |
X-ray (2.2 Å) |
Valton J, Daboussi F, Leduc S, Molina R, Redondo P,
Macmaster R, Montoya G, Duchateau P |
(2012) "5'-Cytosine-Phosphoguanine
(Cpg) Methylation Impacts the Activity of Natural and
Engineered Meganucleases." J.Biol.Chem.,
287, 30139. doi: 10.1074/JBC.M112.379966.
|
Crystal structure of i-crei complexed with its target
methylated at position plus 2 (in the b strand) in the
presence of magnesium . SNAP output
|
|
4aso
|
structural protein-DNA |
X-ray (7.0 Å) |
Aylett CHS, Lowe J |
(2012) "Superstructure
of the Centromeric Complex of Tubzrc Plasmid
Partitioning Systems."
Proc.Natl.Acad.Sci.USA, 109,
16522. doi: 10.1073/PNAS.1210899109.
|
Tubr bound to 24 bp of tubc from bacillus thuringiensis
serovar israelensis pbtoxis . SNAP output
|
|
4ass
|
structural protein-DNA |
X-ray (7.0 Å) |
Aylett CHS, Lowe J |
(2012) "Superstructure
of the Centromeric Complex of Tubzrc Plasmid
Partitioning Systems."
Proc.Natl.Acad.Sci.USA, 109,
16522. doi: 10.1073/PNAS.1210899109.
|
Tubr bound to tubc - 26 bp - from bacillus
thuringiensis serovar israelensis pbtoxis . SNAP output
|
|
4ati
|
DNA-binding protein-DNA |
X-ray (2.6 Å) |
Pogenberg V, Hogmundsdottir M, Bergsteinsdottir K,
Schepsky A, Phung B, Deineko V, Milewski M, Steingrimsson
E, Wilmanns M |
(2012) "Restricted
Leucine Zipper Dimerization and Specificity of DNA
Recognition of the Melanocyte Master Regulator
Mitf." Genes Dev., 26,
2647. doi: 10.1101/GAD.198192.112.
|
Mitf:m-box complex . SNAP output
|
|
4atk
|
DNA binding protein-DNA |
X-ray (2.95 Å) |
Pogenberg V, Hogmundsdottir M, Bergsteinsdottir K,
Schepsky A, Phung B, Deineko V, Milewski M, Steingrimsson
E, Wilmanns M |
(2012) "Restricted
Leucine Zipper Dimerization and Specificity of DNA
Recognition of the Melanocyte Master Regulator
Mitf." Genes Dev., 26,
2647. doi: 10.1101/GAD.198192.112.
|
Mitf:e-box complex . SNAP output
|
|
4auw
|
transcription |
X-ray (2.9 Å) |
Textor LC, Wilmanns M, Holton SJ |
(2007) "Expression,
purification, crystallization and preliminary
crystallographic analysis of the mouse transcription
factor MafB in complex with its DNA-recognition motif
Cmare." Acta Crystallogr Sect F Struct Biol
Cryst Commun., 63, 657-661. doi:
10.1107/S1744309107031260.
|
Crystal structure of the bzip homodimeric mafb in
complex with the c- mare binding site . SNAP output
|
|
4av1
|
transferase |
X-ray (3.1 Å) |
Ali AAE, Timinszky G, Arribas-Bosacoma R, Kozlowski
M, Hassa PO, Hassler M, Ladurner AG, Pearl LH, Oliver
AW |
(2012) "The
Zinc-Finger Domains of Parp1 Cooperate to Recognise DNA
Strand-Breaks." Nat.Struct.Mol.Biol.,
19, 685. doi: 10.1038/NSMB.2335.
|
Crystal structure of the human parp-1 DNA binding
domain in complex with DNA . SNAP output
|
|
4awl
|
transcription-DNA |
X-ray (3.08 Å) |
Nardini M, Gnesutta N, Donati G, Gatta R, Forni C,
Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M,
Mantovani R |
(2013) "Sequence-Specific
Transcription Factor NF-Y Displays Histone-Like DNA
Binding and H2B-Like Ubiquitination."
Cell(Cambridge,Mass.), 152,
132. doi: 10.1016/J.CELL.2012.11.047.
|
The nf-y transcription factor is structurally and
functionally a sequence specific histone . SNAP output
|
|
4b20
|
hydrolase |
X-ray (2.75 Å) |
Rosnes I, Rowe AD, Vik ES, Forstrom RJ, Alseth I,
Bjoras M, Dalhus B |
(2013) "Structural
Basis of DNA Loop Recognition by Endonuclease V."
Structure, 21, 257. doi:
10.1016/J.STR.2012.12.007.
|
Structural basis of DNA loop recognition by
endonuclease v . SNAP
output
|
|
4b21
|
hydrolase-DNA |
X-ray (1.45 Å) |
Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom
RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M |
(2013) "Sculpting
of DNA at Abasic Sites by DNA Glycosylase Homolog
Mag2." Structure, 21,
154. doi: 10.1016/J.STR.2012.11.004.
|
Unprecedented sculpting of DNA at abasic sites by DNA
glycosylase homolog mag2 . SNAP output
|
|
4b22
|
hydrolase |
X-ray (1.9 Å) |
Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom
RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M |
(2013) "Sculpting
of DNA at Abasic Sites by DNA Glycosylase Homolog
Mag2." Structure, 21,
154. doi: 10.1016/J.STR.2012.11.004.
|
Unprecedented sculpting of DNA at abasic sites by DNA
glycosylase homolog mag2 . SNAP output
|
|
4b23
|
hydrolase-DNA |
X-ray (2.0 Å) |
Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom
RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M |
(2013) "Sculpting
of DNA at Abasic Sites by DNA Glycosylase Homolog
Mag2." Structure, 21,
154. doi: 10.1016/J.STR.2012.11.004.
|
Unprecedented sculpting of DNA at abasic sites by DNA
glycosylase homolog mag2 . SNAP output
|
|
4b24
|
hydrolase-DNA |
X-ray (2.3 Å) |
Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrom
RJ, Mcmurray CT, Alseth I, Tainer JA, Bjoras M |
(2013) "Sculpting
of DNA at Abasic Sites by DNA Glycosylase Homolog
Mag2." Structure, 21,
154. doi: 10.1016/J.STR.2012.11.004.
|
Unprecedented sculpting of DNA at abasic sites by DNA
glycosylase homolog mag2 . SNAP output
|
|
4b3o
|
hydrolase-DNA-RNA |
X-ray (3.3 Å) |
Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang
W |
(2013) "Complexes
of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a
Structure Compatible with RNA Degradation."
Nat.Struct.Mol.Biol., 20,
230. doi: 10.1038/NSMB.2485.
|
Structures of hiv-1 rt and RNA-DNA complex reveal a
unique rt conformation and substrate interface .
SNAP output
|
|
4b3p
|
hydrolase-RNA-DNA |
X-ray (4.839 Å) |
Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang
W |
(2013) "Complexes
of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a
Structure Compatible with RNA Degradation."
Nat.Struct.Mol.Biol., 20,
230. doi: 10.1038/NSMB.2485.
|
Structures of hiv-1 rt and RNA-DNA complex reveal a
unique rt conformation and substrate interface .
SNAP output
|
|
4b3q
|
hydrolase-DNA-RNA |
X-ray (5.0 Å) |
Lapkouski M, Tian L, Miller JT, Le Grice SFJ, Yang
W |
(2013) "Complexes
of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a
Structure Compatible with RNA Degradation."
Nat.Struct.Mol.Biol., 20,
230. doi: 10.1038/NSMB.2485.
|
Structures of hiv-1 rt and RNA-DNA complex reveal a
unique rt conformation and substrate interface .
SNAP output
|
|
4b5f
|
hydrolase-DNA |
X-ray (2.005 Å) |
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K,
Tang CM, Baldwin GS, Freemont PS |
(2012) "Structural
basis for the recognition and cleavage of abasic DNA in
Neisseria meningitidis." Proc. Natl. Acad. Sci.
U.S.A., 109, 16852-16857. doi:
10.1073/pnas.1206563109.
|
Substrate bound neisseria ap endonuclease in absence of
metal ions (crystal form 1) . SNAP output
|
|
4b5g
|
hydrolase-DNA |
X-ray (2.75 Å) |
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K,
Tang CM, Baldwin GS, Freemont PS |
(2012) "Structural
basis for the recognition and cleavage of abasic DNA in
Neisseria meningitidis." Proc. Natl. Acad. Sci.
U.S.A., 109, 16852-16857. doi:
10.1073/pnas.1206563109.
|
Substrate bound neisseria ap endonuclease in absence of
metal ions (crystal form 2) . SNAP output
|
|
4b5h
|
hydrolase-DNA |
X-ray (3.05 Å) |
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K,
Tang CM, Baldwin GS, Freemont PS |
(2012) "Structural
basis for the recognition and cleavage of abasic DNA in
Neisseria meningitidis." Proc. Natl. Acad. Sci.
U.S.A., 109, 16852-16857. doi:
10.1073/pnas.1206563109.
|
Substate bound inactive mutant of neisseria ap
endonuclease in presence of metal ions . SNAP output
|
|
4b5i
|
hydrolase-DNA |
X-ray (2.555 Å) |
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K,
Tang CM, Baldwin GS, Freemont PS |
(2012) "Structural
basis for the recognition and cleavage of abasic DNA in
Neisseria meningitidis." Proc. Natl. Acad. Sci.
U.S.A., 109, 16852-16857. doi:
10.1073/pnas.1206563109.
|
Product complex of neisseria ap endonuclease in
presence of metal ions . SNAP output
|
|
4b5j
|
hydrolase-DNA |
X-ray (2.1 Å) |
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K,
Tang CM, Baldwin GS, Freemont PS |
(2012) "Structural
basis for the recognition and cleavage of abasic DNA in
Neisseria meningitidis." Proc. Natl. Acad. Sci.
U.S.A., 109, 16852-16857. doi:
10.1073/pnas.1206563109.
|
Neisseria ap endonuclease bound to the substrate with
an orphan adenine base . SNAP output
|
|
4b5m
|
hydrolase-DNA |
X-ray (2.758 Å) |
Lu D, Silhan J, MacDonald JT, Carpenter EP, Jensen K,
Tang CM, Baldwin GS, Freemont PS |
(2012) "Structural
basis for the recognition and cleavage of abasic DNA in
Neisseria meningitidis." Proc. Natl. Acad. Sci.
U.S.A., 109, 16852-16857. doi:
10.1073/pnas.1206563109.
|
Neisseria ap endonuclease bound to the substrate with a
cytosine orphan base . SNAP output
|
|
4b9l
|
transferase-DNA |
X-ray (2.05 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i with
the oxidative formamidopyrimidine-da DNA lesion in the
pre-insertion site. . SNAP output
|
|
4b9m
|
transferase-DNA |
X-ray (2.05 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i with an
oxidative formamidopyrimidine-da DNA lesion -thymine
basepair in the post- insertion site. . SNAP output
|
|
4b9n
|
transferase-DNA |
X-ray (2.2 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i
correctly bypassing the oxidative
formamidopyrimidine-da DNA lesion. . SNAP output
|
|
4b9s
|
transferase-DNA |
X-ray (1.73 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i with an
oxidative formamidopyrimidine-dg DNA lesion outside of
the pre-insertion site. . SNAP output
|
|
4b9t
|
transferase-DNA |
X-ray (2.65 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i with an
oxidative formamidopyrimidine-dg DNA lesion -dc
basepair in the post-insertion site. . SNAP output
|
|
4b9u
|
transferase-DNA |
X-ray (2.1 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i with an
oxidative formamidopyrimidine-dg DNA lesion -da
basepair in the post-insertion site. . SNAP output
|
|
4b9v
|
transferase-DNA |
X-ray (2.0 Å) |
Gehrke TH, Lischke U, Gasteiger KL, Schneider S,
Arnold S, Muller HC, Stephenson DS, Zipse H, Carell
T |
(2013) "Unexpected
Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA
Lesions." Nat.Chem.Biol.,
9, 455. doi: 10.1038/NCHEMBIO.1254.
|
Structure of the high fidelity DNA polymerase i with
extending from an oxidative formamidopyrimidine-dg DNA
lesion -da basepair. . SNAP output
|
|
4bac
|
transferase-DNA |
X-ray (3.263 Å) |
Yin Z, Lapkouski M, Yang W, Craigie R |
(2012) "Assembly
of Prototype Foamy Virus Strand Transfer Complexes on
Product DNA Bypassing Catalysis of Integration."
Protein Sci., 21, 1849. doi:
10.1002/PRO.2166.
|
Prototype foamy virus strand transfer complexes on
product DNA . SNAP
output
|
|
4bbs
|
transcription |
X-ray (3.6 Å) |
Sainsbury S, Niesser J, Cramer P |
(2013) "Structure
and Function of the Initially Transcribing RNA
Polymerase II-TFIIB Complex." Nature,
493, 437. doi: 10.1038/NATURE11715.
|
Structure of an initially transcribing RNA polymerase
ii-tfiib complex . SNAP
output
|
|
4bdp
|
transferase-DNA |
X-ray (1.8 Å) |
Kiefer JR, Mao C, Braman JC, Beese LS |
(1998) "Visualizing
DNA replication in a catalytically active Bacillus DNA
polymerase crystal." Nature,
391, 304-307. doi: 10.1038/34693.
|
Crystal structure of bacillus DNA polymerase i fragment
complexed to 11 base pairs of duplex DNA after addition
of two datp residues . SNAP output
|
|
4bdy
|
transferase-DNA |
X-ray (2.52 Å) |
Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ,
Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P,
Pommier Y |
(2013) "Activities,
Crystal Structures and Molecular Dynamics of
Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1
Integrase." Acs Chem.Biol.,
8, 209. doi: 10.1021/CB300471N.
|
Pfv intasome with inhibitor xz-89 . SNAP output
|
|
4bdz
|
transferase-DNA |
X-ray (2.85 Å) |
Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ,
Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P,
Pommier Y |
(2013) "Activities,
Crystal Structures and Molecular Dynamics of
Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1
Integrase." Acs Chem.Biol.,
8, 209. doi: 10.1021/CB300471N.
|
Pfv intasome with inhibitor xz-90 . SNAP output
|
|
4be0
|
transferase-DNA |
X-ray (2.68 Å) |
Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ,
Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P,
Pommier Y |
(2013) "Activities,
Crystal Structures and Molecular Dynamics of
Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1
Integrase." Acs Chem.Biol.,
8, 209. doi: 10.1021/CB300471N.
|
Pfv intasome with inhibitor xz-115 . SNAP output
|
|
4be1
|
transferase-DNA |
X-ray (2.71 Å) |
Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ,
Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P,
Pommier Y |
(2013) "Activities,
Crystal Structures and Molecular Dynamics of
Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1
Integrase." Acs Chem.Biol.,
8, 209. doi: 10.1021/CB300471N.
|
Pfv intasome with inhibitor xz-116 . SNAP output
|
|
4be2
|
transferase-DNA |
X-ray (2.38 Å) |
Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ,
Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P,
Pommier Y |
(2013) "Activities,
Crystal Structures and Molecular Dynamics of
Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1
Integrase." Acs Chem.Biol.,
8, 209. doi: 10.1021/CB300471N.
|
Pfv intasome with inhibitor xz-259 . SNAP output
|
|
4bhk
|
transcription-DNA |
X-ray (2.32 Å) |
Sayou C, Monniaux M, Nanao MH, Moyroud E, Brockington
SF, Thevenon E, Chahtane H, Warthmann N, Melkonian M,
Zhang Y, Wong GK, Weigel D, Parcy F, Dumas R |
(2014) "A
Promiscuous Intermediate Underlies the Evolution of
Leafy DNA Binding Specificity." Science,
343, 645. doi: 10.1126/SCIENCE.1248229.
|
Crystal structure of moss leafy bound to DNA . SNAP output
|
|
4bhm
|
transcription-DNA |
X-ray (2.7 Å) |
Huang J, Zhao Y, Liu H, Huang D, Cheng X, Zhao W,
Taylor IA, Liu J, Peng YL |
(2015) "Substitution
of Tryptophan 89 with Tyrosine Switches the DNA Binding
Mode of Pc4." Sci.Rep.,
5, 8789. doi: 10.1038/SREP08789.
|
The crystal structure of mosub1-DNA complex reveals a
novel DNA binding mode . SNAP output
|
|
4bnc
|
DNA binding protein |
X-ray (2.9 Å) |
Cooper CDO, Newman JA, Aitkenhead H, Allerston CK,
Gileadi O |
(2015) "Structures
of the Ets Domains of Transcription Factors Etv1, Etv4,
Etv5 and Fev: Determinants of DNA Binding and Redox
Regulation by Disulfide Bond Formation."
J.Biol.Chem., 290, 13692.
doi: 10.1074/JBC.M115.646737.
|
Crystal structure of the DNA-binding domain of human
etv1 complexed with DNA . SNAP output
|
|
4boc
|
transcription |
X-ray (2.65 Å) |
Schwinghammer K, Cheung ACM, Morozov YI, Agaronyan K,
Temiakov D, Cramer P |
(2013) "Structure
of Human Mitochondrial RNA Polymerase Elongation
Complex." Nat.Struct.Mol.Biol.,
20, 1298. doi: 10.1038/NSMB.2683.
|
Structure of mitochondrial RNA polymerase elongation
complex . SNAP
output
|
|
4bqa
|
transcription |
X-ray (2.5 Å) |
Newman JA, Cooper CDO, Aitkenhead H, Gileadi O |
(2015) "Structural
Insights Into the Autoregulation and Cooperativity of
the Human Transcription Factor Ets-2."
J.Biol.Chem., 290, 8539. doi:
10.1074/JBC.M114.619270.
|
Crystal structure of the ets domain of human ets2 in
complex with DNA . SNAP
output
|
|
4bul
|
isomerase |
X-ray (2.6 Å) |
Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS,
Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken
JM, Giordano I, Hoover JL, Huang J, Jones GE,
Kusalakumari Sukmar SK, Spitzfaden C, Markwell RE,
Minthorn EA, Rittenhouse S, Gwynn MN, Pearson ND |
(2013) "Novel
Hydroxyl Tricyclics (E.G., Gsk966587) as Potent
Inhibitors of Bacterial Type Iia Topoisomerases."
Bioorg.Med.Chem.Lett., 23,
5437. doi: 10.1016/J.BMCL.2013.07.013.
|
Novel hydroxyl tricyclics (e.g. gsk966587) as potent
inhibitors of bacterial type iia topoisomerases .
SNAP output
|
|
4bwj
|
transferase-DNA |
X-ray (1.55 Å) |
Blatter N, Bergen K, Nolte O, Welte W, Diederichs K,
Mayer J, Wieland M, Marx A |
(2013) "Structure
and Function of an RNA-Reading Thermostable DNA
Polymerase." Angew.Chem.Int.Ed.Engl.,
52, 11935. doi: 10.1002/ANIE.201306655.
|
Klentaq mutant in complex with DNA and ddctp . SNAP output
|
|
4bwm
|
transferase-DNA-RNA |
X-ray (1.749 Å) |
Blatter N, Bergen K, Nolte O, Welte W, Diederichs K,
Mayer J, Wieland M, Marx A |
(2013) "Structure
and Function of an RNA-Reading Thermostable DNA
Polymerase." Angew.Chem.Int.Ed.Engl.,
52, 11935. doi: 10.1002/ANIE.201306655.
|
Klentaq mutant in complex with a RNA-DNA hybrid .
SNAP output
|
|
4bxo
|
hydrolase-DNA |
X-ray (2.15 Å) |
Coulthard R, Deans AJ, Swuec P, Bowles M, Costa A,
West SC, Mcdonald NQ |
(2013) "Architecture
and DNA Recognition Elements of the Fanconi Anemia
Fancm-Faap24 Complex." Structure,
21, 1648. doi: 10.1016/J.STR.2013.07.006.
|
Architecture and DNA recognition elements of the
fanconi anemia fancm- faap24 complex . SNAP output
|
|
4bxx
|
transcription |
X-ray (3.28 Å) |
Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M,
Strahl BD, Cramer P |
(2013) "Structures
of RNA Polymerase II Complexes with Bye1, a
Chromatin-Binding Phf3/Dido1 Homologue."
Proc.Natl.Acad.Sci.USA, 110,
15277. doi: 10.1073/PNAS.1311010110.
|
Arrested RNA polymerase ii-bye1 complex . SNAP output
|
|
4by1
|
transcription |
X-ray (3.6 Å) |
Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M,
Strahl BD, Cramer P |
(2013) "Structures
of RNA Polymerase II Complexes with Bye1, a
Chromatin-Binding Phf3/Dido1 Homologue."
Proc.Natl.Acad.Sci.USA, 110,
15277. doi: 10.1073/PNAS.1311010110.
|
Elongating RNA polymerase ii-bye1 tld complex soaked
with ampcpp . SNAP
output
|
|
4by7
|
transcription |
X-ray (3.15 Å) |
Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M,
Strahl BD, Cramer P |
(2013) "Structures
of RNA polymerase II complexes with Bye1, a
chromatin-binding PHF3/DIDO homologue." Proc.
Natl. Acad. Sci. U.S.A., 110,
15277-15282. doi: 10.1073/pnas.1311010110.
|
Elongating RNA polymerase ii-bye1 tld complex .
SNAP output
|
|
4c2t
|
hydrolase-DNA |
X-ray (3.997 Å) |
Stelter M, Acajjaoui S, Mcsweeney S, Timmins J |
(2013) "Structural
and Mechanistic Insight Into DNA Unwinding by
Deinococcus Radiodurans Uvrd." Plos One,
8, 77364. doi: 10.1371/JOURNAL.PONE.0077364.
|
Crystal structure of full length deinococcus
radiodurans uvrd in complex with DNA . SNAP output
|
|
4c2u
|
hydrolase-DNA |
X-ray (2.55 Å) |
Stelter M, Acajjaoui S, Mcsweeney S, Timmins J |
(2013) "Structural
and Mechanistic Insight Into DNA Unwinding by
Deinococcus Radiodurans Uvrd." Plos One,
8, 77364. doi: 10.1371/JOURNAL.PONE.0077364.
|
Crystal structure of deinococcus radiodurans uvrd in
complex with DNA, form 1 . SNAP output
|
|
4c30
|
hydrolase-DNA |
X-ray (3.0 Å) |
Stelter M, Acajjaoui S, Mcsweeney S, Timmins J |
(2013) "Structural
and Mechanistic Insight Into DNA Unwinding by
Deinococcus Radiodurans Uvrd." Plos One,
8, 77364. doi: 10.1371/JOURNAL.PONE.0077364.
|
Crystal structure of deinococcus radiodurans uvrd in
complex with DNA, form 2 . SNAP output
|
|
4c8k
|
transferase-DNA |
X-ray (2.17 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Romesberg FE, Marx A |
(2013) "Structural
Insights Into DNA Replication without Hydrogen
Bonds." J.Am.Chem.Soc.,
135, 18637. doi: 10.1021/JA409609J.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a partially
closed complex with the artificial base pair
d5sics-dnamtp . SNAP
output
|
|
4c8l
|
transferase-DNA |
X-ray (1.7 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Romesberg FE, Marx A |
(2013) "Structural
Insights Into DNA Replication without Hydrogen
Bonds." J.Am.Chem.Soc.,
135, 18637. doi: 10.1021/JA409609J.
|
Binary complex of the large fragment of DNA polymerase
i from thermus aquaticus with the artificial base pair
dnam-d5sics at the postinsertion site (sequence context
1) . SNAP output
|
|
4c8m
|
transferase-DNA |
X-ray (1.568 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Romesberg FE, Marx A |
(2013) "Structural
Insights Into DNA Replication without Hydrogen
Bonds." J.Am.Chem.Soc.,
135, 18637. doi: 10.1021/JA409609J.
|
Binary complex of the large fragment of DNA polymerase
i from thermus aquaticus with the aritificial base pair
d5sics-dnam at the postinsertion site (sequence context
2) . SNAP output
|
|
4c8n
|
transferase-DNA |
X-ray (1.88 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Romesberg FE, Marx A |
(2013) "Structural
Insights Into DNA Replication without Hydrogen
Bonds." J.Am.Chem.Soc.,
135, 18637. doi: 10.1021/JA409609J.
|
Binary complex of the large fragment of DNA polymerase
i from thermus aquaticus with the aritificial base pair
dnam-d5sics at the postinsertion site (sequence context
3) . SNAP output
|
|
4c8o
|
transferase-DNA |
X-ray (1.75 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Romesberg FE, Marx A |
(2013) "Structural
Insights Into DNA Replication without Hydrogen
Bonds." J.Am.Chem.Soc.,
135, 18637. doi: 10.1021/JA409609J.
|
Binary complex of the large fragment of DNA polymerase
i from thermus aquaticus with the aritificial base pair
dnam-d5sics at the postinsertion site (sequence context
2) . SNAP output
|
|
4c8y
|
RNA binding protein-RNA |
X-ray (1.8 Å) |
Niewoehner O, Jinek M, Doudna JA |
(2014) "Evolution
of Crispr RNA Recognition and Processing by Cas6
Endonucleases." Nucleic Acids Res.,
42, 1341. doi: 10.1093/NAR/GKT922.
|
Cas6 (ttha0078) substrate mimic complex . SNAP output
|
|
4cch
|
transferase-DNA |
X-ray (2.55 Å) |
Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs
K, Romesberg FE, Marx A |
(2013) "Structural
Insights Into DNA Replication without Hydrogen
Bonds." J.Am.Chem.Soc.,
135, 18637. doi: 10.1021/JA409609J.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in an open binary
complex with d5sics as templating nucleotide . SNAP output
|
|
4ceh
|
hydrolase-DNA |
X-ray (3.24 Å) |
Krajewski WW, Fu X, Wilkinson M, Cronin NB,
Dillingham MS, Wigley DB |
(2014) "Structural
Basis for Translocation by Addab Helicase-Nuclease and
its Arrest at Chi Sites." Nature,
508, 416. doi: 10.1038/NATURE13037.
|
Crystal structure of addab with a forked DNA substrate
. SNAP output
|
|
4cei
|
hydrolase-DNA |
X-ray (2.8 Å) |
Krajewski WW, Fu X, Wilkinson M, Cronin NB,
Dillingham MS, Wigley DB |
(2014) "Structural
Basis for Translocation by Addab Helicase-Nuclease and
its Arrest at Chi Sites." Nature,
508, 416. doi: 10.1038/NATURE13037.
|
Crystal structure of adpnp-bound addab with a forked
DNA substrate . SNAP
output
|
|
4cej
|
hydrolase-DNA |
X-ray (3.0 Å) |
Krajewski WW, Fu X, Wilkinson M, Cronin NB,
Dillingham MS, Wigley DB |
(2014) "Structural
Basis for Translocation by Addab Helicase-Nuclease and
its Arrest at Chi Sites." Nature,
508, 416. doi: 10.1038/NATURE13037.
|
Crystal structure of addab-DNA-adpnp complex at 3
angstrom resolution . SNAP output
|
|
4cgz
|
hydrolase-DNA |
X-ray (3.2 Å) |
Newman JA, Savitsky P, Allerston CK, Bizard AH, Ozer
O, Sarlos K, Liu Y, Pardon E, Steyaert J, Hickson ID,
Gileadi O |
(2015) "Crystal
Structure of the Bloom'S Syndrome Helicase Indicates a
Role for the Hrdc Domain in Conformational
Changes." Nucleic Acids Res.,
43, 5221. doi: 10.1093/NAR/GKV373.
|
Crystal structure of the bloom's syndrome helicase blm
in complex with DNA . SNAP output
|
|
4ch1
|
transcription-DNA |
NMR |
Amrane S, Rebora K, Zniber I, Dupuy D, Mackereth
CD |
(2014) "Backbone-Independent
Nucleic Acid Binding by Splicing Factor Sup-12 Reveals
Key Aspects of Molecular Recognition."
Nat.Commun., 5, 4595. doi:
10.1038/NCOMMS5595.
|
Rrm domain from c. elegans sup-12 bound to ggtgtgc DNA
. SNAP output
|
|
4chu
|
transcription |
X-ray (2.489 Å) |
Santos JA, Alonso-Garcia N, Macedo-Ribeiro S, Pereira
PJB |
(2014) "The
Unique Regulation of Iron-Sulfur Cluster Biogenesis in
a Gram-Positive Bacterium."
Proc.Natl.Acad.Sci.USA, 111,
E2251. doi: 10.1073/PNAS.1322728111.
|
E. coli iscr-DNA complex . SNAP output
|
|
4cis
|
hydrolase |
X-ray (2.05 Å) |
Sadeghian K, Flaig D, Blank ID, Schneider S, Strasser
R, Stathis D, Winnacker M, Carell T, Ochsenfeld C |
(2014) "Ribose-protonated
DNA base excision repair: a combined theoretical and
experimental study." Angew. Chem. Int. Ed.
Engl., 53, 10044-10048. doi:
10.1002/anie.201403334.
|
Structure of mutm in complex with carbocyclic 8-oxo-g
containing DNA . SNAP
output
|
|
4cja
|
transcription |
X-ray (2.651 Å) |
Stella S, Molina R, Lopez-Mendez B, Juillerat A,
Bertonati C, Daboussi F, Campos-Olivas R, Duchateau P,
Montoya G |
(2014) "Bud, a
Helix-Loop-Helix DNA-Binding Domain for Genome
Modification." Acta Crystallogr.,Sect.D,
70, 2042. doi: 10.1107/S1399004714011183.
|
Burrh DNA-binding protein from burkholderia rhizoxinica
in complex with its target DNA . SNAP output
|
|
4cn2
|
transcription-DNA |
X-ray (2.069 Å) |
Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E,
Birck C, Davidson I, Moras D, Rochel N |
(2015) "Structural
Basis of Natural Promoter Recognition by the Retinoid X
Nuclear Receptor." Sci.Rep.,
5, 8216. doi: 10.1038/SREP08216.
|
Crystal structure of the human retinoid x receptor
DNA-binding domain bound to the human ramp2 response
element . SNAP
output
|
|
4cn3
|
transcription-DNA |
X-ray (2.35 Å) |
Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E,
Birck C, Davidson I, Moras D, Rochel N |
(2015) "Structural
Basis of Natural Promoter Recognition by the Retinoid X
Nuclear Receptor." Sci.Rep.,
5, 8216. doi: 10.1038/SREP08216.
|
Crystal structure of the human retinoid x receptor
DNA-binding domain bound to the human gde1spa response
element . SNAP
output
|
|
4cn5
|
transcription-DNA |
X-ray (2.0 Å) |
Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E,
Birck C, Davidson I, Moras D, Rochel N |
(2015) "Structural
Basis of Natural Promoter Recognition by the Retinoid X
Nuclear Receptor." Sci.Rep.,
5, 8216. doi: 10.1038/SREP08216.
|
Crystal structure of the human retinoid x receptor
DNA-binding domain bound to the human nr1d1 response
element . SNAP
output
|
|
4cn7
|
transcription-DNA |
X-ray (2.34 Å) |
Osz J, Mcewen AG, Poussin-Courmontagne P, Moutier E,
Birck C, Davidson I, Moras D, Rochel N |
(2015) "Structural
Basis of Natural Promoter Recognition by the Retinoid X
Nuclear Receptor." Sci.Rep.,
5, 8216. doi: 10.1038/SREP08216.
|
Crystal structure of the human retinoid x receptor
DNA-binding domain bound to an idealized dr1 response
element . SNAP
output
|
|
4crx
|
protein-DNA |
X-ray (2.2 Å) |
Guo F, Gopaul DN, Van Duyne GD |
(1999) "Asymmetric
DNA bending in the Cre-loxP site-specific recombination
synapse." Proc.Natl.Acad.Sci.USA,
96, 7143-7148. doi: 10.1073/pnas.96.13.7143.
|
Asymmetric DNA-bending in the cre-loxp site-specific
recombination synapse . SNAP output
|
|
4csa
|
viral protein-DNA |
X-ray (2.28 Å) |
Leyrat C, Renner M, Harlos K, Huiskonen JT, Grimes
JM |
(2014) "Drastic
Changes in Conformational Dynamics of the
Antiterminator M2-1 Regulate Transcription Efficiency
in Pneumovirinae." Elife,
3, 02674. doi: 10.7554/ELIFE.02674.
|
Crystal structure of the asymmetric human
metapneumovirus m2-1 tetramer bound to a DNA 4-mer .
SNAP output
|
|
4cyc
|
transcription |
X-ray (2.36 Å) |
Foos N, Maurel-Zaffran C, Mate MJ, Vincentelli R,
Hainaut M, Berenger H, Pradel J, Saurin AJ,
Ortiz-Lombardia M, Graba Y |
(2015) "A
Flexible Extension of the Drosophila Ultrabithorax
Homeodomain Defines a Novel Hox/Pbc Interaction
Mode." Structure, 23,
270. doi: 10.1016/J.STR.2014.12.011.
|
Crystal structure of a ubx-exd-DNA complex including
the hexapeptide and ubda motifs . SNAP output
|
|
4d1q
|
protein-DNA complex |
X-ray (3.4 Å) |
Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss A,
Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig
NL, Dyda F |
(2014) "Structural
Basis of Hat Transposon End Recognition by Hermes, an
Octameric DNA Transposase from Musca Domestica."
Cell(Cambridge,Mass.), 158,
353. doi: 10.1016/J.CELL.2014.05.037.
|
Hermes transposase bound to its terminal inverted
repeat . SNAP output
|
|
4d6n
|
hydrolase-DNA |
X-ray (2.35 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 10 days incubation in 5mm mg (state 7) .
SNAP output
|
|
4d6o
|
hydrolase-DNA |
X-ray (2.2 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 1h incubation in 5mm mg (state 2) .
SNAP output
|
|
4d8j
|
DNA binding protein |
X-ray (3.55 Å) |
Dupaigne P, Tonthat NK, Espeli O, Whitfill T, Boccard
F, Schumacher MA |
(2012) "Molecular
basis for a protein-mediated DNA-bridging mechanism
that functions in condensation of the E. coli
chromosome." Mol.Cell,
48, 560-571. doi: 10.1016/j.molcel.2012.09.009.
|
Structure of e. coli matp-mats complex . SNAP output
|
|
4da4
|
transferase-DNA |
X-ray (2.6 Å) |
Song J, Teplova M, Ishibe-Murakami S, Patel DJ |
(2012) "Structure-Based
Mechanistic Insights into DNMT1-Mediated Maintenance
DNA Methylation." Science,
335, 709-712. doi: 10.1126/science.1214453.
|
Structure of mouse dnmt1 (731-1602) bound to
hemimethylated cpg DNA . SNAP output
|
|
4dav
|
hydrolase-DNA |
X-ray (2.2 Å) |
Allen FL, Akerboom J, Bliss SJ, Blombach F,
Sedelnikova SE, van der Oost J, Baker PJ |
"The structure of SfsA and its DNA complex; A DNA/RNA
nuclease with a novel domain combination." |
The structure of pyrococcus furiosus sfsa in complex
with DNA . SNAP
output
|
|
4db4
|
RNA-binding protein-DNA,RNA |
X-ray (3.599 Å) |
Mallam AL, Del Campo M, Gilman B, Sidote DJ,
Lambowitz AM |
(2012) "Structural
basis for RNA-duplex recognition and unwinding by the
DEAD-box helicase Mss116p." Nature,
490, 121-125. doi: 10.1038/nature11402.
|
Mss116p dead-box helicase domain 2 bound to a chimaeric
RNA-DNA duplex . SNAP
output
|
|
4df4
|
transferase-DNA |
X-ray (2.2 Å) |
Bergen K, Steck AL, Strutt S, Baccaro A, Welte W,
Diederichs K, Marx A |
(2012) "Structures
of KlenTaq DNA Polymerase Caught While Incorporating
C5-Modified Pyrimidine and C7-Modified 7-Deazapurine
Nucleoside Triphosphates." J.Am.Chem.Soc.,
134, 11840-11843. doi: 10.1021/ja3017889.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with
7-(n-(10-hydroxydecanoyl)-aminopentinyl)-7-deaza-2
-datp . SNAP output
|
|
4df8
|
transferase-DNA |
X-ray (2.0 Å) |
Bergen K, Steck AL, Strutt S, Baccaro A, Welte W,
Diederichs K, Marx A |
(2012) "Structures
of KlenTaq DNA Polymerase Caught While Incorporating
C5-Modified Pyrimidine and C7-Modified 7-Deazapurine
Nucleoside Triphosphates." J.Am.Chem.Soc.,
134, 11840-11843. doi: 10.1021/ja3017889.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with aminopentinyl-7-deaza-2-datp . SNAP output
|
|
4dfj
|
transferase-DNA |
X-ray (1.9 Å) |
Bergen K, Steck AL, Strutt S, Baccaro A, Welte W,
Diederichs K, Marx A |
(2012) "Structures
of KlenTaq DNA Polymerase Caught While Incorporating
C5-Modified Pyrimidine and C7-Modified 7-Deazapurine
Nucleoside Triphosphates." J.Am.Chem.Soc.,
134, 11840-11843. doi: 10.1021/ja3017889.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with 5-(aminopentinyl)-dttp . SNAP output
|
|
4dfk
|
transferase-DNA |
X-ray (1.647 Å) |
Bergen K, Steck AL, Strutt S, Baccaro A, Welte W,
Diederichs K, Marx A |
(2012) "Structures
of KlenTaq DNA Polymerase Caught While Incorporating
C5-Modified Pyrimidine and C7-Modified 7-Deazapurine
Nucleoside Triphosphates." J.Am.Chem.Soc.,
134, 11840-11843. doi: 10.1021/ja3017889.
|
Large fragment of DNA polymerase i from thermus
aquaticus in a closed ternary complex with
5-(n-(10-hydroxydecanoyl)-aminopentinyl)-2-dutp .
SNAP output
|
|
4dfm
|
transferase-DNA |
X-ray (1.886 Å) |
Bergen K, Steck AL, Strutt S, Baccaro A, Welte W,
Diederichs K, Marx A |
(2012) "Structures
of KlenTaq DNA Polymerase Caught While Incorporating
C5-Modified Pyrimidine and C7-Modified 7-Deazapurine
Nucleoside Triphosphates." J.Am.Chem.Soc.,
134, 11840-11843. doi: 10.1021/ja3017889.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in ternary complex
with 5-(aminopentinyl)-2-dctp . SNAP output
|
|
4dfp
|
transferase-DNA |
X-ray (2.0 Å) |
Bergen K, Steck AL, Strutt S, Baccaro A, Welte W,
Diederichs K, Marx A |
(2012) "Structures
of KlenTaq DNA Polymerase Caught While Incorporating
C5-Modified Pyrimidine and C7-Modified 7-Deazapurine
Nucleoside Triphosphates." J.Am.Chem.Soc.,
134, 11840-11843. doi: 10.1021/ja3017889.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aqauticus in a ternary
complex with 7-(aminopentinyl)-7-deaza-dgtp . SNAP output
|
|
4dih
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (1.8 Å) |
Russo Krauss I, Merlino A, Randazzo A, Novellino E,
Mazzarella L, Sica F |
(2012) "High-resolution
structures of two complexes between thrombin and
thrombin-binding aptamer shed light on the role of
cations in the aptamer inhibitory activity."
Nucleic Acids Res., 40,
8119-8128. doi: 10.1093/nar/gks512.
|
X-ray structure of the complex between human alpha
thrombin and thrombin binding aptamer in the presence
of sodium ions . SNAP
output
|
|
4dii
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.05 Å) |
Russo Krauss I, Merlino A, Randazzo A, Novellino E,
Mazzarella L, Sica F |
(2012) "High-resolution
structures of two complexes between thrombin and
thrombin-binding aptamer shed light on the role of
cations in the aptamer inhibitory activity."
Nucleic Acids Res., 40,
8119-8128. doi: 10.1093/nar/gks512.
|
X-ray structure of the complex between human alpha
thrombin and thrombin binding aptamer in the presence
of potassium ions . SNAP
output
|
|
4dk9
|
hydrolase-DNA |
X-ray (2.76 Å) |
Manvilla BA, Maiti A, Begley MC, Toth EA, Drohat
AC |
(2012) "Crystal
Structure of Human Methyl-Binding Domain IV Glycosylase
Bound to Abasic DNA." J.Mol.Biol.,
420, 164-175. doi: 10.1016/j.jmb.2012.04.028.
|
Crystal structure of mbd4 catalytic domain bound to
abasic DNA . SNAP
output
|
|
4dkj
|
transferase-DNA |
X-ray (2.15 Å) |
Wojciechowski M, Czapinska H, Bochtler M |
(2013) "CpG
underrepresentation and the bacterial CpG-specific DNA
methyltransferase M.MpeI."
Proc.Natl.Acad.Sci.USA, 110,
105-110. doi: 10.1073/pnas.1207986110.
|
Cpg specific methyltransferase in complex with target
DNA . SNAP output
|
|
4dl2
|
transferase-DNA-inhibitor |
X-ray (2.15 Å) |
Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F,
Yang W |
(2012) "Structural
Basis for Chemoresistance to Cisplatin Mediated by DNA
Polymerase eta." Proc.Natl.Acad.Sci.USA,
109, 7269-7274. doi: 10.1073/pnas.1202681109.
|
Human DNA polymerase eta inserting dcmpnpp opposite cg
template (gg0a) . SNAP
output
|
|
4dl3
|
transferase-DNA-inhibitor |
X-ray (2.1 Å) |
Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F,
Yang W |
(2012) "Structural
Basis for Chemoresistance to Cisplatin Mediated by DNA
Polymerase eta." Proc.Natl.Acad.Sci.USA,
109, 7269-7274. doi: 10.1073/pnas.1202681109.
|
Human DNA polymerase eta inserting dcmpnpp opposite gg
template (gg0b). . SNAP
output
|
|
4dl4
|
transferase-DNA-inhibitor |
X-ray (2.0 Å) |
Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F,
Yang W |
(2012) "Structural
Basis for Chemoresistance to Cisplatin Mediated by DNA
Polymerase eta." Proc.Natl.Acad.Sci.USA,
109, 7269-7274. doi: 10.1073/pnas.1202681109.
|
Human DNA polymerase eta inserting dcmpnpp opposite the
3'g of cisplatin crosslinked gs (pt-gg1). . SNAP output
|
|
4dl5
|
transferase-DNA-inhibitor |
X-ray (2.92 Å) |
Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F,
Yang W |
(2012) "Structural
Basis for Chemoresistance to Cisplatin Mediated by DNA
Polymerase eta." Proc.Natl.Acad.Sci.USA,
109, 7269-7274. doi: 10.1073/pnas.1202681109.
|
Human DNA polymerase eta inserting dcmpnpp opposite the
5'g of cisplatin crosslinked gs (pt-gg2). . SNAP output
|
|
4dl6
|
transferase-DNA-inhibitor |
X-ray (2.5 Å) |
Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F,
Yang W |
(2012) "Structural
Basis for Chemoresistance to Cisplatin Mediated by DNA
Polymerase eta." Proc.Natl.Acad.Sci.USA,
109, 7269-7274. doi: 10.1073/pnas.1202681109.
|
Human DNA polymerase eta extending primer immediately
after cisplatin crosslink (pt-gg3). . SNAP output
|
|
4dl7
|
transferase-DNA-inhibitor |
X-ray (1.97 Å) |
Zhao Y, Biertumpfel C, Gregory MT, Hua YJ, Hanaoka F,
Yang W |
(2012) "Structural
Basis for Chemoresistance to Cisplatin Mediated by DNA
Polymerase eta." Proc.Natl.Acad.Sci.USA,
109, 7269-7274. doi: 10.1073/pnas.1202681109.
|
Human DNA polymerase eta fails to extend primer 2
nucleotide after cisplatin crosslink (pt-gg4). .
SNAP output
|
|
4dle
|
transferase-DNA |
X-ray (2.44 Å) |
Holzberger B, Obeid S, Welte W, Diederichs K, Marx
A |
(2012) "Structural insights into the potential of
4-fluoroproline to modulate biophysical properties of
protein." Chem Sci, 3,
2924-2931. doi: 10.1039/C2SC20545A.
|
Ternary structure of the large fragment of taq DNA
polymerase: 4-fluoroproline variant . SNAP output
|
|
4dlg
|
transferase-DNA |
X-ray (1.89 Å) |
Holzberger B, Obeid S, Welte W, Diederichs K, Marx
A |
(2012) "Structural insights into the potential of
4-fluoroproline to modulate biophysical properties of
protein." Chem Sci, 3,
2924-2931. doi: 10.1039/C2SC20545A.
|
Ternary structure of the large fragment of taq DNA
polymerase . SNAP
output
|
|
4dm0
|
hydrolase-DNA |
X-ray (2.5 Å) |
Lovell S, Goryshin IY, Reznikoff WR, Rayment I |
(2002) "Two-metal
active site binding of a TN5 transposase synaptic
complex." Nat.Struct.Biol.,
9, 278-281.
|
Tn5 transposase: 20mer outside end 2 mn complex .
SNAP output
|
|
4do9
|
transferase-DNA |
X-ray (2.05 Å) |
Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra
VK, Wilson SH, McKenna CE |
(2012) "Beta,gamma-CHF-
and beta,gamma-CHCl-dGTP Diastereomers: Synthesis,
Discrete (31)P NMR Signatures, and Absolute
Configurations of New Stereochemical Probes for DNA
Polymerases." J.Am.Chem.Soc.,
134, 8734-8737. doi: 10.1021/ja300218x.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monofluoromethylene triphosphate: stereoselective
binding of r-isomer . SNAP output
|
|
4doa
|
transferase-DNA |
X-ray (2.051 Å) |
Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra
VK, Wilson SH, McKenna CE |
(2012) "Beta,gamma-CHF-
and beta,gamma-CHCl-dGTP Diastereomers: Synthesis,
Discrete (31)P NMR Signatures, and Absolute
Configurations of New Stereochemical Probes for DNA
Polymerases." J.Am.Chem.Soc.,
134, 8734-8737. doi: 10.1021/ja300218x.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monofluoromethylene triphosphate: non-interactive
binding of s-isomer . SNAP output
|
|
4dob
|
transferase-DNA |
X-ray (2.05 Å) |
Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra
VK, Wilson SH, McKenna CE |
(2012) "Beta,Gamma-CHF-
and beta,gamma-CHCl-dGTP Diastereomers: Synthesis,
Discrete (31)P NMR Signatures, and Absolute
Configurations of New Stereochemical Probes for DNA
Polymerases." J.Am.Chem.Soc.,
134, 8734-8737. doi: 10.1021/ja300218x.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monochlororomethylene triphosphate:
stereoselective binding of r-isomer . SNAP output
|
|
4doc
|
transferase-DNA |
X-ray (1.949 Å) |
Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra
VK, Wilson SH, McKenna CE |
(2012) "Beta,gamma-CHF-
and beta,gamma-CHCl-dGTP Diastereomers: Synthesis,
Discrete (31)P NMR Signatures, and Absolute
Configurations of New Stereochemical Probes for DNA
Polymerases." J.Am.Chem.Soc.,
134, 8734-8737. doi: 10.1021/ja300218x.
|
Ternary complex of DNA polymerase beta with a dideoxy
terminated primer and 2'-deoxyguanosine 5'-beta,
gamma-monochlororomethylene triphosphate:binding of
s-isomer . SNAP
output
|
|
4dpv
|
virus-DNA |
X-ray (2.9 Å) |
Xie Q, Chapman MS |
(1996) "Canine
parvovirus capsid structure, analyzed at 2.9 A
resolution." J.Mol.Biol.,
264, 497-520. doi: 10.1006/jmbi.1996.0657.
|
Parvovirus-DNA complex . SNAP output
|
|
4dqi
|
transferase-DNA |
X-ray (1.69 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment, DNA duplex, and dctp (paired with dg of
template) . SNAP
output
|
|
4dqp
|
transferase-DNA |
X-ray (1.74 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment, DNA duplex, and ddctp (paired with dg of
template) . SNAP
output
|
|
4dqq
|
transferase-DNA |
X-ray (1.595 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment e658a, DNA duplex, and rctp (paired with dg of
template) in presence of mg2+ . SNAP output
|
|
4dqr
|
transferase-DNA |
X-ray (1.95 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment e658a, DNA duplex, and rctp (paired with dg of
template) in presence of mn2+ . SNAP output
|
|
4dqs
|
transferase-DNA |
X-ray (1.66 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Binary complex of bacillus DNA polymerase i large
fragment and duplex DNA with rc in primer terminus
paired with dg of template . SNAP output
|
|
4dqy
|
transferase-DNA |
X-ray (3.25 Å) |
Langelier MF, Planck JL, Roy S, Pascal JM |
(2012) "Structural
basis for DNA damage-dependent poly(ADP-ribosyl)ation
by human PARP-1." Science,
336, 728-732. doi: 10.1126/science.1216338.
|
Structure of human parp-1 bound to a DNA double strand
break . SNAP output
|
|
4ds4
|
transferase-DNA |
X-ray (1.681 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment, DNA duplex, and rctp in presence of mn2+ .
SNAP output
|
|
4ds5
|
transferase-DNA |
X-ray (1.68 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment, DNA duplex, and rctp in presence of mg2+ .
SNAP output
|
|
4dse
|
transferase-DNA |
X-ray (1.67 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment f710y, DNA duplex, and rctp (paired with dg of
template) in presence of mg2+ . SNAP output
|
|
4dsf
|
transferase-DNA |
X-ray (1.661 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Ternary complex of bacillus DNA polymerase i large
fragment f710y, DNA duplex, and rctp (paired with dg of
template) in presence of mn2+ . SNAP output
|
|
4dsi
|
transferase-DNA |
X-ray (2.05 Å) |
Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J,
Soares AS, Huang Z |
"Biochemical and structural insights into the
fidelity of bacillus stearothermophilus DNA
polymerase." |
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus with duplex DNA, se-dgtp
and calcium . SNAP
output
|
|
4dsj
|
transferase-DNA |
X-ray (2.86 Å) |
Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J,
Soares AS, Huang Z |
"Biochemical and structural insights into the
fidelity of bacillus stearothermophilus DNA
polymerase." |
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus with duplex DNA, dgtp and
calcium . SNAP
output
|
|
4dsk
|
transferase-DNA |
X-ray (2.18 Å) |
Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J,
Soares AS, Huang Z |
"Biochemical and structural insights into the
fidelity of bacillus stearothermophilus DNA
polymerase." |
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus with duplex DNA, ppi and
calcium . SNAP
output
|
|
4dsl
|
transferase-DNA |
X-ray (2.45 Å) |
Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J,
Soares AS, Huang Z |
"Biochemical and structural insights into the
fidelity of bacillus stearothermophilus DNA
polymerase." |
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus with duplex DNA and calcium
. SNAP output
|
|
4dtj
|
transferase-DNA |
X-ray (1.9 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dttp opposite
an abasic site and ddt-da as the penultimate base-pair
. SNAP output
|
|
4dtm
|
transferase-DNA |
X-ray (1.95 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dctp opposite
an abasic site and ddg-dc as the penultimate base-pair
. SNAP output
|
|
4dtn
|
transferase-DNA |
X-ray (1.96 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with datp opposite
an abasic site and dda-dt as the penultimate base-pair
. SNAP output
|
|
4dto
|
transferase-DNA |
X-ray (2.05 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dctp opposite
an abasic site and dda-dt as the penultimate base-pair
. SNAP output
|
|
4dtp
|
transferase-DNA |
X-ray (2.05 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dgtp opposite
an abasic site and dda-dt as the penultimate base-pair
. SNAP output
|
|
4dtr
|
transferase-DNA |
X-ray (2.04 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with datp opposite
an abasic site and ddc-dg as the penultimate base-pair
. SNAP output
|
|
4dts
|
transferase-DNA |
X-ray (1.96 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dctp opposite
an abasic site and ddc-dg as the penultimate base-pair
. SNAP output
|
|
4dtu
|
transferase-DNA |
X-ray (1.86 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dgtp opposite
an abasic site and ddc-dg as the penultimate base-pair
. SNAP output
|
|
4dtx
|
transferase-DNA |
X-ray (1.84 Å) |
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J,
Konigsberg WH |
(2012) "Contribution
of Partial Charge Interactions and Base Stacking to the
Efficiency of Primer Extension at and beyond Abasic
Sites in DNA." Biochemistry,
51, 4922-4931. doi: 10.1021/bi300296q.
|
Rb69 DNA polymerase ternary complex with dttp opposite
an abasic site and ddc-dg as the penultimate base-pair
. SNAP output
|
|
4du1
|
transferase-DNA |
X-ray (2.15 Å) |
Xia S, Christian TD, Wang J, Konigsberg WH |
(2012) "Probing
minor groove hydrogen bonding interactions between RB69
DNA polymerase and DNA." Biochemistry,
51, 4343-4353. doi: 10.1021/bi300416z.
|
Rb69 DNA polymerase ternary complex with datp opposite
dt . SNAP output
|
|
4du3
|
transferase-DNA |
X-ray (2.02 Å) |
Xia S, Christian TD, Wang J, Konigsberg WH |
(2012) "Probing
minor groove hydrogen bonding interactions between RB69
DNA polymerase and DNA." Biochemistry,
51, 4343-4353. doi: 10.1021/bi300416z.
|
Rb69 DNA polymerase ternary complex with ddtp opposite
dt with 3-deaza-adenine at the n-1 position of template
strand . SNAP output
|
|
4du4
|
transferase-DNA |
X-ray (2.28 Å) |
Xia S, Christian TD, Wang J, Konigsberg WH |
(2012) "Probing
minor groove hydrogen bonding interactions between RB69
DNA polymerase and DNA." Biochemistry,
51, 4343-4353. doi: 10.1021/bi300416z.
|
Rb69 DNA polymerase ternary complex with datp opposite
dt with 3-deaza-adenine at the n-3 position of primer
strand . SNAP output
|
|
4dwi
|
transferase-DNA |
X-ray (1.85 Å) |
Gan JH, Abdur R, Liu HH, Sheng J, Caton-Willians J,
Soares AS, Huang Z |
"Biochemical and structural insights into the
fidelity of bacillus stearothermophilus DNA
polymerase." |
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus with self complementary
DNA, se-dgtp and calcium . SNAP output
|
|
4dwp
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Semet protelomerase tela covalently complexed with
substrate DNA . SNAP
output
|
|
4e0d
|
transferase-DNA |
X-ray (1.58 Å) |
Wang W, Wu EY, Hellinga HW, Beese LS |
(2012) "Structural
factors that determine selectivity of a high fidelity
DNA polymerase for deoxy-, dideoxy-, and
ribonucleotides." J.Biol.Chem.,
287, 28215-28226. doi: 10.1074/jbc.M112.366609.
|
Binary complex of bacillus DNA polymerase i large
fragment e658a and duplex DNA . SNAP output
|
|
4e0g
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Protelomerase tela-DNA hairpin product-vanadate complex
. SNAP output
|
|
4e0j
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Protelomerase tela r255a mutant complexed with DNA
hairpin product . SNAP
output
|
|
4e0p
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Protelomerase tela covalently complexed with substrate
DNA . SNAP output
|
|
4e0y
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Protelomerase tela covalently complexed with mutated
substrate DNA . SNAP
output
|
|
4e0z
|
DNA binding protein-DNA |
X-ray (2.42 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Protelomerase tela r205a covalently complexed with
substrate DNA . SNAP
output
|
|
4e10
|
DNA binding protein-DNA |
X-ray (2.506 Å) |
Shi K, Huang WM, Aihara H |
(2013) "An
enzyme-catalyzed multistep DNA refolding mechanism in
hairpin telomere formation." Plos Biol.,
11, e1001472. doi: 10.1371/journal.pbio.1001472.
|
Protelomerase tela y201a covalently complexed with
substrate DNA . SNAP
output
|
|
4e3s
|
transferase-DNA |
X-ray (2.04 Å) |
Xia S, Christian TD, Wang J, Konigsberg WH |
(2012) "Probing
minor groove hydrogen bonding interactions between RB69
DNA polymerase and DNA." Biochemistry,
51, 4343-4353. doi: 10.1021/bi300416z.
|
Rb69 DNA polymerase ternary complex with dqtp opposite
dt . SNAP output
|
|
4e54
|
DNA binding protein-DNA |
X-ray (2.85 Å) |
Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H,
Shi H, Hsieh CL, Conway JF, Van Houten B, Rapic-Otrin
V |
(2012) "Damaged
DNA induced UV-damaged DNA-binding protein (UV-DDB)
dimerization and its roles in chromatinized DNA
repair." Proc.Natl.Acad.Sci.USA,
109, E2737-E2746. doi: 10.1073/pnas.1110067109.
|
Damaged DNA induced uv-damaged DNA-binding protein
(uv-ddb) dimerization and its roles in chromatinized
DNA repair . SNAP
output
|
|
4e5z
|
DNA binding protein-DNA |
X-ray (3.22 Å) |
Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H,
Shi H, Hsieh CL, Conway JF, Van Houten B, Rapic-Otrin
V |
(2012) "Damaged
DNA induced UV-damaged DNA-binding protein (UV-DDB)
dimerization and its roles in chromatinized DNA
repair." Proc.Natl.Acad.Sci.USA,
109, E2737-E2746. doi: 10.1073/pnas.1110067109.
|
Damaged DNA induced uv-damaged DNA-binding protein
(uv-ddb) dimerization and its roles in chromatinized
DNA repair . SNAP
output
|
|
4e68
|
transcription-DNA |
X-ray (2.585 Å) |
Nkansah E, Shah R, Collie GW, Parkinson GN, Palmer J,
Rahman KM, Bui TT, Drake AF, Husby J, Neidle S, Zinzalla
G, Thurston DE, Wilderspin AF |
(2013) "Observation
of unphosphorylated STAT3 core protein binding to
target dsDNA by PEMSA and X-ray crystallography."
Febs Lett., 587, 833-839.
doi: 10.1016/j.febslet.2013.01.065.
|
Unphosphorylated stat3b core protein binding to dsDNA .
SNAP output
|
|
4e7h
|
recombination-DNA |
X-ray (2.57 Å) |
Hare S, Maertens GN, Cherepanov P |
(2012) "3'-Processing
and strand transfer catalysed by retroviral integrase
in crystallo." Embo J.,
31, 3020-3028. doi: 10.1038/emboj.2012.118.
|
Pfv intasome prior to 3'-processing, apo form (ui-apo)
. SNAP output
|
|
4e7i
|
recombination-DNA |
X-ray (2.53 Å) |
Hare S, Maertens GN, Cherepanov P |
(2012) "3'-Processing
and strand transfer catalysed by retroviral integrase
in crystallo." Embo J.,
31, 3020-3028. doi: 10.1038/emboj.2012.118.
|
Pfv intasome freeze-trapped prior to 3'-processing,
mn-bound form (ui-mn) . SNAP output
|
|
4e7j
|
recombination-DNA |
X-ray (3.15 Å) |
Hare S, Maertens GN, Cherepanov P |
(2012) "3'-Processing
and strand transfer catalysed by retroviral integrase
in crystallo." Embo J.,
468, 326-329. doi: 10.1038/emboj.2012.118.
|
Pfv integrase target capture complex, apo form
(tcc-apo), at 3.15 Å resolution . SNAP output
|
|
4e7k
|
recombination-DNA |
X-ray (3.02 Å) |
Hare S, Maertens GN, Cherepanov P |
(2012) "3'-Processing
and strand transfer catalysed by retroviral integrase
in crystallo." Embo J.,
31, 3020-3028. doi: 10.1038/emboj.2012.118.
|
Pfv integrase target capture complex (tcc-mn),
freeze-trapped prior to strand transfer, at 3.0 Å
resolution . SNAP
output
|
|
4e7l
|
recombination-DNA |
X-ray (3.0 Å) |
Hare S, Maertens GN, Cherepanov P |
(2012) "3'-Processing
and strand transfer catalysed by retroviral integrase
in crystallo." Embo J.,
31, 3020-3028. doi: 10.1038/emboj.2012.118.
|
Pfv integrase strand transfer complex (stc-mn*)
following reaction in crystallo, at 3.0 Å resolution. .
SNAP output
|
|
4e9f
|
hydrolase-DNA |
X-ray (1.79 Å) |
Morera S, Grin I, Vigouroux A, Couve S, Henriot V,
Saparbaev M, Ishchenko AA |
(2012) "Biochemical
and structural characterization of the glycosylase
domain of MBD4 bound to thymine and
5-hydroxymethyuracil-containing DNA." Nucleic
Acids Res., 40, 9917-9926. doi:
10.1093/nar/gks714.
|
Structure of the glycosylase domain of mbd4 bound to ap
site containing DNA . SNAP output
|
|
4e9g
|
hydrolase-DNA |
X-ray (2.35 Å) |
Morera S, Grin I, Vigouroux A, Couve S, Henriot V,
Saparbaev M, Ishchenko AA |
(2012) "Biochemical
and structural characterization of the glycosylase
domain of MBD4 bound to thymine and
5-hydroxymethyuracil-containing DNA." Nucleic
Acids Res., 40, 9917-9926. doi:
10.1093/nar/gks714.
|
Structure of the glycosylase domain of mbd4 bound to
thymine containing DNA . SNAP output
|
|
4e9h
|
hydrolase-DNA |
X-ray (3.0 Å) |
Morera S, Grin I, Vigouroux A, Couve S, Henriot V,
Saparbaev M, Ishchenko AA |
(2012) "Biochemical
and structural characterization of the glycosylase
domain of MBD4 bound to thymine and
5-hydroxymethyuracil-containing DNA." Nucleic
Acids Res., 40, 9917-9926. doi:
10.1093/nar/gks714.
|
Structure of glycosylase domain of mbd4 bound to 5hmu
containing DNA . SNAP
output
|
|
4ea4
|
hydrolase-DNA |
X-ray (2.0 Å) |
Morera S, Grin I, Vigouroux A, Couve S, Henriot V,
Saparbaev M, Ishchenko AA |
(2012) "Biochemical
and structural characterization of the glycosylase
domain of MBD4 bound to thymine and
5-hydroxymethyuracil-containing DNA." Nucleic
Acids Res., 40, 9917-9926. doi:
10.1093/nar/gks714.
|
Structure of the glycosylase domain of mbd4 bound to
5hmu-containing DNA . SNAP output
|
|
4ea5
|
hydrolase-DNA |
X-ray (2.14 Å) |
Morera S, Grin I, Vigouroux A, Couve S, Henriot V,
Saparbaev M, Ishchenko AA |
(2012) "Biochemical
and structural characterization of the glycosylase
domain of MBD4 bound to thymine and
5-hydroxymethyuracil-containing DNA." Nucleic
Acids Res., 40, 9917-9926. doi:
10.1093/nar/gks714.
|
Structure of the glycoslyase domain of mbd4 bound to a
5hmu containing DNA . SNAP output
|
|
4ebc
|
transferase-DNA |
X-ray (2.901 Å) |
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M,
Eoff RL |
(2012) "A
Nucleotide-Analogue-Induced Gain of Function Corrects
the Error-Prone Nature of Human DNA Polymerase
iota." J.Am.Chem.Soc.,
134, 10698-10705. doi: 10.1021/ja304176q.
|
Conformationally restrained
north-methanocarba-2'-deoxyadenosine corrects the
error-prone nature of human DNA polymerase iota .
SNAP output
|
|
4ebd
|
transferase-DNA |
X-ray (2.571 Å) |
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M,
Eoff RL |
(2012) "A
Nucleotide-Analogue-Induced Gain of Function Corrects
the Error-Prone Nature of Human DNA Polymerase
iota." J.Am.Chem.Soc.,
134, 10698-10705. doi: 10.1021/ja304176q.
|
Conformationally restrained
north-methanocarba-2'-deoxyadenosine corrects the
error-prone nature of human DNA polymerase iota .
SNAP output
|
|
4ebe
|
transferase-DNA |
X-ray (2.1 Å) |
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M,
Eoff RL |
(2012) "A
Nucleotide-Analogue-Induced Gain of Function Corrects
the Error-Prone Nature of Human DNA Polymerase
iota." J.Am.Chem.Soc.,
134, 10698-10705. doi: 10.1021/ja304176q.
|
Conformationally restrained
north-methanocarba-2'-deoxyadenosine corrects the
error-prone nature of human DNA polymerase iota .
SNAP output
|
|
4ecq
|
transferase-DNA |
X-ray (1.5 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta- DNA ternary complex: at
crystal at ph6.8(k+ mes) with 1 ca2+ ion . SNAP output
|
|
4ecr
|
transferase-DNA |
X-ray (1.892 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 40 sec .
SNAP output
|
|
4ecs
|
transferase-DNA |
X-ray (1.951 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 80 sec .
SNAP output
|
|
4ect
|
transferase-DNA |
X-ray (1.795 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 140 sec .
SNAP output
|
|
4ecu
|
transferase-DNA |
X-ray (1.949 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 200 sec .
SNAP output
|
|
4ecv
|
transferase-DNA |
X-ray (1.521 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 230 sec .
SNAP output
|
|
4ecw
|
transferase-DNA |
X-ray (1.896 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 250 sec .
SNAP output
|
|
4ecx
|
transferase-DNA |
X-ray (1.744 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 7.0 for 300 sec .
SNAP output
|
|
4ecy
|
transferase-DNA |
X-ray (1.943 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: at
crystal at ph 6.0 (na+ mes) with 1 ca2+ ion . SNAP output
|
|
4ecz
|
transferase-DNA |
X-ray (1.834 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: at
crystal at ph 6.5 (na+ mes) with 1 ca2+ ion . SNAP output
|
|
4ed0
|
transferase-DNA |
X-ray (1.653 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: at
crystal at ph 6.8 (na+ mes) with 1 ca2+ ion . SNAP output
|
|
4ed1
|
transferase-DNA |
X-ray (1.806 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: at
crystal at ph 7.0 (na+ mes) with 1 ca2+ ion . SNAP output
|
|
4ed2
|
transferase-DNA |
X-ray (1.711 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: at
crystal at ph 7.2 (na+ hepes) with 1 ca2+ ion .
SNAP output
|
|
4ed3
|
transferase-DNA |
X-ray (1.791 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: at
crystal at ph 7.5 (na+ hepes) with 1 ca2+ ion .
SNAP output
|
|
4ed5
|
RNA binding protein-RNA |
X-ray (2.0 Å) |
Wang H, Zeng F, Liu Q, Liu H, Liu Z, Niu L, Teng M,
Li X |
(2013) "The
structure of the ARE-binding domains of Hu antigen R
(HuR) undergoes conformational changes during RNA
binding." Acta Crystallogr.,Sect.D,
69, 373-380. doi: 10.1107/S0907444912047828.
|
Crystal structure of the two n-terminal rrm domains of
hur complexed with RNA . SNAP output
|
|
4ed6
|
transferase-DNA |
X-ray (2.211 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the at crystal at ph 6.7 for 15 hr, sideway
translocation . SNAP
output
|
|
4ed7
|
transferase-DNA |
X-ray (1.717 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex: tg
crystal at ph 7.0 (k+ mes) with 1 ca2+ ion . SNAP output
|
|
4ed8
|
transferase-DNA |
X-ray (1.521 Å) |
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W |
(2012) "Watching
DNA polymerase eta make a phosphodiester bond."
Nature, 487, 196-201. doi:
10.1038/nature11181.
|
Human DNA polymerase eta - DNA ternary complex:
reaction in the tg crystal at ph 7.0, normal
translocation . SNAP
output
|
|
4eey
|
transferase-DNA |
X-ray (2.32 Å) |
Ummat A, Rechkoblit O, Jain R, Roy Choudhury J,
Johnson RE, Silverstein TD, Buku A, Lone S, Prakash L,
Prakash S, Aggarwal AK |
(2012) "Structural
basis for cisplatin DNA damage tolerance by human
polymerase {eta} during cancer chemotherapy."
Nat.Struct.Mol.Biol., 19,
628-632. doi: 10.1038/nsmb.2295.
|
Crystal structure of human DNA polymerase eta in
ternary complex with a cisplatin DNA adduct . SNAP output
|
|
4efj
|
hydrolase-DNA |
X-ray (2.8 Å) |
Kulshina N |
"Crystal structure of I-GzeMII LAGLIDADG homing
endonuclease in complex with DNA target site." |
Crystal structure of i-gzeii laglidadg homing
endonuclease in complex with DNA target site . SNAP output
|
|
4egy
|
transcription-DNA |
X-ray (2.301 Å) |
Jain D, Nair DT |
(2013) "Spacing
between core recognition motifs determines relative
orientation of AraR monomers on bipartite
operators." Nucleic Acids Res.,
41, 639-647. doi: 10.1093/nar/gks962.
|
Crystal structure of arar(dbd) in complex with operator
ora1 . SNAP output
|
|
4egz
|
transcription-DNA |
X-ray (2.3 Å) |
Jain D, Nair DT |
(2013) "Spacing
between core recognition motifs determines relative
orientation of AraR monomers on bipartite
operators." Nucleic Acids Res.,
41, 639-647. doi: 10.1093/nar/gks962.
|
Crystal structure of arar(dbd) in complex with operator
orr3 . SNAP output
|
|
4ejy
|
hydrolase-DNA |
X-ray (2.0 Å) |
Yu HJ, Yang MZ, Zhang XE, Bi LJ, Jiang T |
(2013) "Crystal
structures of MBOgg1 in complex with two abasic DNA
ligands." J.Struct.Biol.,
181, 252-263. doi: 10.1016/j.jsb.2012.12.003.
|
Structure of mbogg1 in complex with high affinity DNA
ligand . SNAP output
|
|
4ejz
|
hydrolase-DNA |
X-ray (3.05 Å) |
Yu HJ, Yang MZ, Zhang XE, Bi LJ, Jiang T |
(2013) "Crystal
structures of MBOgg1 in complex with two abasic DNA
ligands." J.Struct.Biol.,
181, 252-263. doi: 10.1016/j.jsb.2012.12.003.
|
Structure of mbogg1 in complex with low affinity DNA
ligand . SNAP output
|
|
4elt
|
transferase-DNA |
X-ray (2.2 Å) |
Obeid S, Busskamp H, Welte W, Diederichs K, Marx
A |
(2012) "Interactions
of non-polar and "Click-able" nucleotides in the
confines of a DNA polymerase active site."
Chem.Commun.(Camb.), 48,
8320-8322. doi: 10.1039/c2cc34181f.
|
Snapshot of the large fragment of DNA polymerase i from
thermus aquaticus processing modified pyrimidines .
SNAP output
|
|
4elu
|
transferase-DNA |
X-ray (1.8 Å) |
Obeid S, Busskamp H, Welte W, Diederichs K, Marx
A |
(2012) "Interactions
of non-polar and "Click-able" nucleotides in the
confines of a DNA polymerase active site."
Chem.Commun.(Camb.), 48,
8320-8322. doi: 10.1039/c2cc34181f.
|
Snapshot of the large fragment of DNA polymerase i from
thermus aquaticus processing modified pyrimidines .
SNAP output
|
|
4elv
|
transferase-DNA |
X-ray (1.9 Å) |
Obeid S, Bu kamp H, Welte W, Diederichs K, Marx
A |
"Snapshot of the large fragment of DNA polymerase I
from Thermus Aquaticus processing modified
pyrimidines." |
Snapshot of the large fragment of DNA polymerase i from
thermus aquaticus processing modified pyrimidines .
SNAP output
|
|
4enj
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown
G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai
AS, Millington CL, Povey AC, Williams DM,
Santibanez-Koref MF, Tainer JA, Margison GP |
(2012) "Atl1
Regulates Choice between Global Genome and
Transcription-Coupled Repair of
O(6)-Alkylguanines." Mol.Cell,
47, 50-60. doi: 10.1016/j.molcel.2012.04.028.
|
Crystal structure of s. pombe atl1 in complex with
damaged DNA containing o6-hydroxyethylguanine .
SNAP output
|
|
4enk
|
DNA binding protein-DNA |
X-ray (3.04 Å) |
Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown
G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai
AS, Millington CL, Povey AC, Williams DM,
Santibanez-Koref MF, Tainer JA, Margison GP |
(2012) "Atl1
Regulates Choice between Global Genome and
Transcription-Coupled Repair of
O(6)-Alkylguanines." Mol.Cell,
47, 50-60. doi: 10.1016/j.molcel.2012.04.028.
|
Crystal structure of s. pombe atl1 in complex with
damaged DNA containing o6-propylguanine . SNAP output
|
|
4enm
|
DNA binding protein-DNA |
X-ray (2.84 Å) |
Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown
G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai
AS, Millington CL, Povey AC, Williams DM,
Santibanez-Koref MF, Tainer JA, Margison GP |
(2012) "Atl1
Regulates Choice between Global Genome and
Transcription-Coupled Repair of
O(6)-Alkylguanines." Mol.Cell,
47, 50-60. doi: 10.1016/j.molcel.2012.04.028.
|
Crystal structure of s. pombe atl1 in complex with
damaged DNA containing o6-benzylguanine . SNAP output
|
|
4enn
|
DNA binding protein-DNA |
X-ray (2.84 Å) |
Latypov VF, Tubbs JL, Watson AJ, Marriott AS, McGown
G, Thorncroft M, Wilkinson OJ, Senthong P, Butt A, Arvai
AS, Millington CL, Povey AC, Williams DM,
Santibanez-Koref MF, Tainer JA, Margison GP |
(2012) "Atl1
Regulates Choice between Global Genome and
Transcription-Coupled Repair of
O(6)-Alkylguanines." Mol.Cell,
47, 50-60. doi: 10.1016/j.molcel.2012.04.028.
|
Crystal structure of s. pombe atl1 in complex with
damaged DNA containing o6-carboxymethylguanine .
SNAP output
|
|
4eot
|
transcription-DNA |
X-ray (2.855 Å) |
Lu X, Guanga GP, Wan C, Rose RB |
(2012) "A Novel
DNA Binding Mechanism for maf Basic Region-Leucine
Zipper Factors Inferred from a MafA-DNA Complex
Structure and Binding Specificities."
Biochemistry, 51, 9706-9717.
doi: 10.1021/bi301248j.
|
Crystal structure of the mafa homodimer bound to the
consensus mare . SNAP
output
|
|
4er8
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Messing SA, Ton-Hoang B, Hickman AB, McCubbin AJ,
Peaslee GF, Ghirlando R, Chandler M, Dyda F |
(2012) "The
processing of repetitive extragenic palindromes: the
structure of a repetitive extragenic palindrome bound
to its associated nuclease." Nucleic Acids
Res., 40, 9964-9979. doi:
10.1093/nar/gks741.
|
Structure of the rep associates tyrosine transposase
bound to a rep hairpin . SNAP output
|
|
4esj
|
hydrolase-DNA |
X-ray (2.05 Å) |
Siwek W, Czapinska H, Bochtler M, Bujnicki JM,
Skowronek K |
(2012) "Crystal
structure and mechanism of action of the
N6-methyladenine-dependent type IIM restriction
endonuclease R.DpnI." Nucleic Acids Res.,
40, 7563-7572. doi: 10.1093/nar/gks428.
|
Restriction endonuclease dpni in complex with target
DNA . SNAP output
|
|
4esv
|
hydrolase-DNA |
X-ray (3.2 Å) |
Itsathitphaisarn O, Wing RA, Eliason WK, Wang J,
Steitz TA |
(2012) "The
Hexameric Helicase DnaB Adopts a Nonplanar Conformation
during Translocation."
Cell(Cambridge,Mass.), 151,
267-277. doi: 10.1016/j.cell.2012.09.014.
|
A new twist on the translocation mechanism of helicases
from the structure of dnab with its substrates .
SNAP output
|
|
4euw
|
transcription-DNA |
X-ray (2.77 Å) |
Joint Center for Structural Genomics (JCSG),
Partnership for Stem Cell Biology |
"Crystal structure of a HMG domain of transcription
factor SOX-9 bound to DNA (SOX-9/DNA) from Homo sapiens
at 2.77 A resolution." |
Crystal structure of a hmg domain of transcription
factor sox-9 bound to DNA (sox-9-DNA) from homo sapiens
at 2.77 Å resolution . SNAP output
|
|
4evv
|
hydrolase-DNA |
X-ray (2.39 Å) |
Hashimoto H, Zhang X, Cheng X |
(2012) "Excision
of thymine and 5-hydroxymethyluracil by the MBD4 DNA
glycosylase domain: structural basis and implications
for active DNA demethylation." Nucleic Acids
Res., 40, 8276-8284. doi:
10.1093/nar/gks628.
|
Mouse mbd4 glycosylase domain in complex with a g:t
mismatch . SNAP
output
|
|
4ew0
|
hydrolase-DNA |
X-ray (2.39 Å) |
Hashimoto H, Zhang X, Cheng X |
(2012) "Excision
of thymine and 5-hydroxymethyluracil by the MBD4 DNA
glycosylase domain: structural basis and implications
for active DNA demethylation." Nucleic Acids
Res., 40, 8276-8284. doi:
10.1093/nar/gks628.
|
Mouse mbd4 glycosylase domain in complex with a g:5hmu
(5-hydroxymethyluracil) mismatch . SNAP output
|
|
4ew4
|
hydrolase-DNA |
X-ray (2.791 Å) |
Hashimoto H, Zhang X, Cheng X |
(2012) "Excision
of thymine and 5-hydroxymethyluracil by the MBD4 DNA
glycosylase domain: structural basis and implications
for active DNA demethylation." Nucleic Acids
Res., 40, 8276-8284. doi:
10.1093/nar/gks628.
|
Mouse mbd4 glycosylase domain in complex with DNA
containing a ribose sugar . SNAP output
|
|
4eyh
|
transferase-DNA |
X-ray (2.9 Å) |
Kirouac KN, Basu AK, Ling H |
(2013) "Replication
of a carcinogenic nitropyrene DNA lesion by human
Y-family DNA polymerase." Nucleic Acids
Res., 41, 2060-2071. doi:
10.1093/nar/gks1296.
|
Human DNA polymerase iota incorporating dctp opposite
n-(deoxyguanosin-8-yl)-1-aminopyrene lesion . SNAP output
|
|
4eyi
|
transferase-DNA |
X-ray (2.9 Å) |
Kirouac KN, Basu AK, Ling H |
(2013) "Replication
of a carcinogenic nitropyrene DNA lesion by human
Y-family DNA polymerase." Nucleic Acids
Res., 41, 2060-2071. doi:
10.1093/nar/gks1296.
|
Human DNA polymerase iota incorporating datp opposite
n-(deoxyguanosin-8-yl)-1-aminopyrene lesion . SNAP output
|
|
4ez6
|
transferase-DNA |
X-ray (1.64 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
Bacillus DNA polymerase i large fragment complex 1 .
SNAP output
|
|
4ez9
|
transferase-DNA |
X-ray (1.64 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
Bacillus DNA polymerase i large fragment complex 2 .
SNAP output
|
|
4f1h
|
hydrolase-DNA |
X-ray (1.662 Å) |
Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA,
Pommier Y, Aihara H |
(2012) "Structural
basis for recognition of 5'-phosphotyrosine adducts by
Tdp2." Nat.Struct.Mol.Biol.,
19, 1372-1377. doi: 10.1038/nsmb.2423.
|
Crystal structure of tdp2 from danio rerio complexed
with a single strand DNA . SNAP output
|
|
4f2j
|
metal binding protein-DNA |
X-ray (2.64 Å) |
Vandevenne MS, Jacques DA, Artuz C, Nguyen CD, Kwan
AH, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay
JP |
(2013) "New
insights into DNA recognition by zinc fingers revealed
by structural analysis of the oncoprotein ZNF217."
J.Biol.Chem., 288,
10616-10627. doi: 10.1074/jbc.M112.441451.
|
Crystal structure of znf217 bound to DNA, p6522 crystal
form . SNAP output
|
|
4f2r
|
transferase-DNA |
X-ray (1.63 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
DNA polymerase i large fragment complex 3 . SNAP output
|
|
4f2s
|
transferase-DNA |
X-ray (1.651 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
DNA polymerase i large fragment complex 4 . SNAP output
|
|
4f3o
|
transferase-DNA |
X-ray (1.57 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
DNA polymerase i large fragment complex 5 . SNAP output
|
|
4f41
|
recombination-DNA |
X-ray (2.5 Å) |
Huang WM, Dagloria J, Fox H, Ruan Q, Tillou J, Shi K,
Aihara H, Aron J, Casjens S |
(2012) "Linear
Chromosome-generating System of Agrobacterium
tumefaciens C58: PROTELOMERASE GENERATES AND PROTECTS
HAIRPIN ENDS." J.Biol.Chem.,
287, 25551-25563. doi: 10.1074/jbc.M112.369488.
|
Protelomerase tela mutant r255a complexed with cttg
hairpin DNA . SNAP
output
|
|
4f43
|
recombination-DNA |
X-ray (2.354 Å) |
Huang WM, Dagloria J, Fox H, Ruan Q, Tillou J, Shi K,
Aihara H, Aron J, Casjens S |
(2012) "Linear
Chromosome-generating System of Agrobacterium
tumefaciens C58: PROTELOMERASE GENERATES AND PROTECTS
HAIRPIN ENDS." J.Biol.Chem.,
287, 25551-25563. doi: 10.1074/jbc.M112.369488.
|
Protelomerase tela mutant r255a complexed with caag
hairpin DNA . SNAP
output
|
|
4f4k
|
transferase-DNA |
X-ray (1.6 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
DNA polymerase i large fragment complex 6 . SNAP output
|
|
4f4w
|
transferase-DNA |
X-ray (1.898 Å) |
Wilson RC, Jackson MA, Pata JD |
(2013) "Y-family
polymerase conformation is a major determinant of
fidelity and translesion specificity."
Structure, 21, 20-31. doi:
10.1016/j.str.2012.11.005.
|
Y-family DNA polymerase chimera dbh-dpo4-dpo4 #1 .
SNAP output
|
|
4f4x
|
transferase-DNA |
X-ray (2.049 Å) |
Wilson RC, Jackson MA, Pata JD |
(2013) "Y-family
polymerase conformation is a major determinant of
fidelity and translesion specificity."
Structure, 21, 20-31. doi:
10.1016/j.str.2012.11.005.
|
Y-family DNA polymerase chimera dbh-dpo4-dpo4 #2 .
SNAP output
|
|
4f4y
|
transferase-DNA |
X-ray (2.338 Å) |
Wilson RC, Jackson MA, Pata JD |
(2013) "Y-family
polymerase conformation is a major determinant of
fidelity and translesion specificity."
Structure, 21, 20-31. doi:
10.1016/j.str.2012.11.005.
|
Y-family DNA polymerase chimera dbh-dpo4-dbh . SNAP output
|
|
4f4z
|
transferase-DNA |
X-ray (2.305 Å) |
Wilson RC, Jackson MA, Pata JD |
(2013) "Y-family
polymerase conformation is a major determinant of
fidelity and translesion specificity."
Structure, 21, 20-31. doi:
10.1016/j.str.2012.11.005.
|
Y-family DNA polymerase chimera dpo4-dpo4-dbh .
SNAP output
|
|
4f50
|
transferase-DNA |
X-ray (2.215 Å) |
Wilson RC, Jackson MA, Pata JD |
(2013) "Y-family
polymerase conformation is a major determinant of
fidelity and translesion specificity."
Structure, 21, 20-31. doi:
10.1016/j.str.2012.11.005.
|
Y-family DNA polymerase chimera dbh-dbh-dpo4 . SNAP output
|
|
4f5n
|
transferase, lyase-DNA |
X-ray (1.8 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2012) "Structures
of dNTP Intermediate States during DNA Polymerase
Active Site Assembly." Structure,
20, 1829-1837. doi: 10.1016/j.str.2012.08.008.
|
Open ternary complex of r283k DNA polymerase beta with
a metal free dctp analog . SNAP output
|
|
4f5o
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2012) "Structures
of dNTP Intermediate States during DNA Polymerase
Active Site Assembly." Structure,
20, 1829-1837. doi: 10.1016/j.str.2012.08.008.
|
Open ternary complex of r283k DNA polymerase beta with
a one metal bound dctp analog . SNAP output
|
|
4f5p
|
transferase, lyase-DNA |
X-ray (1.85 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2012) "Structures
of dNTP Intermediate States during DNA Polymerase
Active Site Assembly." Structure,
20, 1829-1837. doi: 10.1016/j.str.2012.08.008.
|
Open ternary mismatch complex of r283k DNA polymerase
beta with a datp analog . SNAP output
|
|
4f5q
|
transferase, lyase-DNA |
X-ray (2.25 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2012) "Structures
of dNTP Intermediate States during DNA Polymerase
Active Site Assembly." Structure,
20, 1829-1837. doi: 10.1016/j.str.2012.08.008.
|
Closed ternary complex of r283k DNA polymerase beta .
SNAP output
|
|
4f5r
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2012) "Structures
of dNTP Intermediate States during DNA Polymerase
Active Site Assembly." Structure,
20, 1829-1837. doi: 10.1016/j.str.2012.08.008.
|
Open and closed ternary complex of r283k DNA polymerase
beta with a dctp analog in the same asymmetric unit .
SNAP output
|
|
4f6m
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Buck-Koehntop BA, Stanfield RL, Ekiert DC,
Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE |
(2012) "Molecular
basis for recognition of methylated and specific DNA
sequences by the zinc finger protein Kaiso."
Proc.Natl.Acad.Sci.USA, 109,
15229-15234. doi: 10.1073/pnas.1213726109.
|
Crystal structure of kaiso zinc finger DNA binding
domain in complex with kaiso binding site DNA .
SNAP output
|
|
4f6n
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Buck-Koehntop BA, Stanfield RL, Ekiert DC,
Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE |
(2012) "Molecular
basis for recognition of methylated and specific DNA
sequences by the zinc finger protein Kaiso."
Proc.Natl.Acad.Sci.USA, 109,
15229-15234. doi: 10.1073/pnas.1213726109.
|
Crystal structure of kaiso zinc finger DNA binding
protein in complex with methylated cpg site DNA .
SNAP output
|
|
4f8r
|
transferase-DNA |
X-ray (1.64 Å) |
Wang W, Hellinga HW, Beese LS |
"Structures of a High-fidelity DNA Polymerase." |
Bacillus DNA polymerase i large fragment complex 7 .
SNAP output
|
|
4fb3
|
DNA binding protein-DNA |
X-ray (3.79 Å) |
Harrison C, Jiang T, Banerjee P, Meinke G, D'Abramo
CM, Schaffhausen B, Bohm A |
(2013) "Polyomavirus
large T antigen binds symmetrical repeats at the viral
origin in an asymmetrical manner."
J.Virol., 87, 13751-13759.
doi: 10.1128/JVI.01740-13.
|
Polyomavirus t-ag binds symmetrical repeats at the
viral origin in an asymmetrical manner . SNAP output
|
|
4fbt
|
transferase-DNA |
X-ray (2.0 Å) |
Kirouac KN, Basu AK, Ling H |
(2013) "Structural
mechanism of replication stalling on a bulky
amino-polycyclic aromatic hydrocarbon DNA adduct by a y
family DNA polymerase." J.Mol.Biol.,
425, 4167-4176. doi: 10.1016/j.jmb.2013.07.020.
|
Dpo4 post-insertion complex with the
n-(deoxyguanosin-8-yl)-1-aminopyrene lesion . SNAP output
|
|
4fbu
|
transferase-DNA |
X-ray (2.6 Å) |
Kirouac KN, Basu AK, Ling H |
(2013) "Structural
mechanism of replication stalling on a bulky
amino-polycyclic aromatic hydrocarbon DNA adduct by a y
family DNA polymerase." J.Mol.Biol.,
425, 4167-4176. doi: 10.1016/j.jmb.2013.07.020.
|
Dpo4 polymerase pre-insertion binary complex with the
n-(deoxyguanosin-8-yl)-1-aminopyrene lesion . SNAP output
|
|
4fcy
|
DNA binding protein-DNA |
X-ray (3.706 Å) |
Montano SP, Pigli YZ, Rice PA |
(2012) "The Mu
transpososome structure sheds light on DDE recombinase
evolution." Nature, 491,
413-417. doi: 10.1038/nature11602.
|
Crystal structure of the bacteriophage mu transpososome
. SNAP output
|
|
4ff1
|
transferase-DNA |
X-ray (2.47 Å) |
Basu RS, Murakami KS |
(2013) "Watching
the Bacteriophage N4 RNA Polymerase Transcription by
Time-dependent Soak-trigger-freeze X-ray
Crystallography." J.Biol.Chem.,
288, 3305-3311. doi: 10.1074/jbc.M112.387712.
|
N4 mini-vrnap transcription initiation complex, 1 min
after soaking gtp, atp and mn . SNAP output
|
|
4ff2
|
transferase-DNA |
X-ray (2.0 Å) |
Basu RS, Murakami KS |
(2013) "Watching
the Bacteriophage N4 RNA Polymerase Transcription by
Time-dependent Soak-trigger-freeze X-ray
Crystallography." J.Biol.Chem.,
288, 3305-3311. doi: 10.1074/jbc.M112.387712.
|
N4 mini-vrnap transcription initiation complex, 2 min
after soaking gtp, atp and mn . SNAP output
|
|
4ff3
|
transferase-DNA |
X-ray (1.997 Å) |
Basu RS, Murakami KS |
(2013) "Watching
the Bacteriophage N4 RNA Polymerase Transcription by
Time-dependent Soak-trigger-freeze X-ray
Crystallography." J.Biol.Chem.,
288, 3305-3311. doi: 10.1074/jbc.M112.387712.
|
N4 mini-vrnap transcription initiation complex, 3 min
after soaking gtp, atp and mn . SNAP output
|
|
4ff4
|
transferase-DNA |
X-ray (2.026 Å) |
Basu RS, Murakami KS |
(2013) "Watching
the Bacteriophage N4 RNA Polymerase Transcription by
Time-dependent Soak-trigger-freeze X-ray
Crystallography." J.Biol.Chem.,
288, 3305-3311. doi: 10.1074/jbc.M112.387712.
|
N4 mini-vrnap transcription initiation complex, 4 min
after soaking gtp, atp and mn . SNAP output
|
|
4fgn
|
DNA binding protein-DNA |
X-ray (3.2 Å) |
Meinke G, Phelan PJ, Harrison CJ, Bullock PA |
(2013) "Analysis
of the Costructure of the Simian Virus 40 T-Antigen
Origin Binding Domain with Site I Reveals a Correlation
between GAGGC Spacing and Spiral Assembly."
J.Virol., 87, 2923-2934. doi:
10.1128/JVI.02549-12.
|
Crystal structure of the sv40 large t-antigen origin
bining domain bound to site i DNA . SNAP output
|
|
4fj5
|
transferase-DNA |
X-ray (2.05 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with datp-dt .
SNAP output
|
|
4fj7
|
transferase-DNA |
X-ray (1.9 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dgtp-dt .
SNAP output
|
|
4fj8
|
transferase-DNA |
X-ray (2.19 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dctp-dt .
SNAP output
|
|
4fj9
|
transferase-DNA |
X-ray (1.97 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dttp-dt .
SNAP output
|
|
4fjg
|
transferase-DNA |
X-ray (2.02 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with datp-dc .
SNAP output
|
|
4fjh
|
transferase-DNA |
X-ray (2.11 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dgtp-dc .
SNAP output
|
|
4fji
|
transferase-DNA |
X-ray (2.2 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dctp-dc .
SNAP output
|
|
4fjj
|
transferase-DNA |
X-ray (1.99 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dttp-dc .
SNAP output
|
|
4fjk
|
transferase-DNA |
X-ray (2.0 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with datp-da .
SNAP output
|
|
4fjl
|
transferase-DNA |
X-ray (1.87 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dgtp-da .
SNAP output
|
|
4fjm
|
transferase-DNA |
X-ray (2.02 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dctp-da .
SNAP output
|
|
4fjn
|
transferase-DNA |
X-ray (1.98 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dttp-da .
SNAP output
|
|
4fjx
|
transferase-DNA |
X-ray (2.11 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with datp-dg .
SNAP output
|
|
4fk0
|
transferase-DNA |
X-ray (2.18 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dctp-dg .
SNAP output
|
|
4fk2
|
transferase-DNA |
X-ray (1.98 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dttp-dg .
SNAP output
|
|
4fk4
|
transferase-DNA |
X-ray (1.9 Å) |
Xia S, Wang J, Konigsberg WH |
(2013) "DNA
mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase."
J.Am.Chem.Soc., 135, 193-202.
doi: 10.1021/ja3079048.
|
Rb69 DNA polymerase ternary complex with dgtp-dg .
SNAP output
|
|
4flt
|
transferase-DNA |
X-ray (2.9 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4flu
|
transferase-DNA |
X-ray (3.1 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4flv
|
transferase-DNA |
X-ray (2.7 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4flw
|
transferase-DNA |
X-ray (2.15 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4flx
|
transferase-DNA |
X-ray (2.9 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4fly
|
transferase-DNA |
X-ray (2.3 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4flz
|
transferase-DNA |
X-ray (3.2 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4fm0
|
transferase-DNA |
X-ray (3.12 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4fm1
|
transferase-DNA |
X-ray (3.0 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase bound to a
dsDNA, in edition mode . SNAP output
|
|
4fm2
|
transferase-DNA |
X-ray (2.9 Å) |
Gouge J, Ralec C, Henneke G, Delarue M |
(2012) "Molecular
Recognition of Canonical and Deaminated Bases by P.
abyssi Family B DNA Polymerase."
J.Mol.Biol., 423, 315-336.
doi: 10.1016/j.jmb.2012.07.025.
|
Pyrococcus abyssi b family DNA polymerase (triple
mutant) bound to a dsDNA, in edition mode . SNAP output
|
|
4fm9
|
isomerase-DNA |
X-ray (2.901 Å) |
Wendorff TJ, Schmidt BH, Heslop P, Austin CA, Berger
JM |
(2012) "The
Structure of DNA-Bound Human Topoisomerase II Alpha:
Conformational Mechanisms for Coordinating
Inter-Subunit Interactions with DNA Cleavage."
J.Mol.Biol., 424, 109-124.
doi: 10.1016/j.jmb.2012.07.014.
|
Human topoisomerase ii alpha bound to DNA . SNAP output
|
|
4fnc
|
hydrolase-DNA |
X-ray (2.493 Å) |
Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng
X |
(2012) "Excision
of 5-hydroxymethyluracil and 5-carboxylcytosine by the
thymine DNA glycosylase domain: its structural basis
and implications for active DNA demethylation."
Nucleic Acids Res., 40,
10203-10214. doi: 10.1093/nar/gks845.
|
Human tdg in a post-reactive complex with
5-hydroxymethyluracil (5hmu) . SNAP output
|
|
4fo6
|
transferase, lyase-DNA |
X-ray (2.007 Å) |
Gosavi RA, Moon AF, Kunkel TA, Pedersen LC, Bebenek
K |
(2012) "The
catalytic cycle for ribonucleotide incorporation by
human DNA Pol lambda." Nucleic Acids Res.,
40, 1-10. doi: 10.1093/nar/gks413.
|
Crystal structure of the pre-catalytic ternary complex
of polymerase lambda with a datp analog opposite a
templating t and an rcmp at the primer terminus. .
SNAP output
|
|
4fpv
|
hydrolase-DNA |
X-ray (1.73 Å) |
Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA,
Pommier Y, Aihara H |
(2012) "Structural
basis for recognition of 5'-phosphotyrosine adducts by
Tdp2." Nat.Struct.Mol.Biol.,
19, 1372-1377. doi: 10.1038/nsmb.2423.
|
Crystal structure of d. rerio tdp2 complexed with
single strand DNA product . SNAP output
|
|
4fs1
|
transferase-DNA |
X-ray (2.5 Å) |
Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY,
Rizzo CJ, Egli M, Guengerich FP |
(2012) "Basis of
Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human
Y-family DNA Polymerases." J.Biol.Chem.,
287, 35516-35526. doi: 10.1074/jbc.M112.403253.
|
Base pairing mechanism of n2,3-ethenoguanine with dttp
by human polymerase iota . SNAP output
|
|
4fs2
|
transferase-DNA |
X-ray (2.05 Å) |
Zhao L, Pence MG, Christov PP, Wawrzak Z, Choi JY,
Rizzo CJ, Egli M, Guengerich FP |
(2012) "Basis of
Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human
Y-family DNA Polymerases." J.Biol.Chem.,
287, 35516-35526. doi: 10.1074/jbc.M112.403253.
|
Base pairing mechanism of n2,3-ethenoguanine with dctp
by human polymerase iota . SNAP output
|
|
4fth
|
transcription regulator-DNA |
X-ray (3.004 Å) |
Vidangos NK, Heideker J, Lyubimov A, Lamers M, Huo Y,
Pelton JG, Ton J, Gralla J, Berger J, Wemmer DE |
(2014) "DNA
Recognition by a sigma (54) Transcriptional Activator
from Aquifex aeolicus." J.Mol.Biol.,
426, 3553-3568. doi: 10.1016/j.jmb.2014.08.009.
|
Crystal structure of ntrc4 DNA-binding domain bound to
double-stranded DNA . SNAP output
|
|
4fx4
|
transcription regulator-DNA |
X-ray (3.1 Å) |
Brugarolas P, Movahedzadeh F, Wang Y, Zhang N, Bartek
IL, Gao YN, Voskuil MI, Franzblau SG, He C |
(2012) "The
Oxidation-sensing Regulator (MosR) Is a New
Redox-dependent Transcription Factor in Mycobacterium
tuberculosis." J.Biol.Chem.,
287, 37703-37712. doi: 10.1074/jbc.M112.388611.
|
Crystal structure of m. tuberculosis transcriptional
regulator mosr (rv1049) in compex with DNA . SNAP output
|
|
4fxd
|
transferase-DNA-RNA |
X-ray (3.0 Å) |
Perera RL, Torella R, Klinge S, Kilkenny ML, Maman
JD, Pellegrini L |
(2013) "Mechanism
for priming DNA synthesis by yeast DNA Polymerase
alpha." eLife, 2, e00482.
doi: 10.7554/eLife.00482.
|
Crystal structure of yeast DNA polymerase alpha bound
to DNA-RNA . SNAP
output
|
|
4fyd
|
transferase-DNA |
X-ray (3.1 Å) |
Perera RL, Torella R, Klinge S, Kilkenny ML, Maman
JD, Pellegrini L |
(2013) "Mechanism
for priming DNA synthesis by yeast DNA Polymerase
alpha." eLife, 2, e00482.
doi: 10.7554/eLife.00482.
|
Crystal structure of yeast DNA polymerase alpha bound
to DNA-RNA and dgtp . SNAP output
|
|
4fzx
|
hydrolase-DNA |
X-ray (2.3 Å) |
Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T |
(2013) "Recognition
and processing of double-stranded DNA by ExoX, a
distributive 3'-5' exonuclease." Nucleic Acids
Res., 41, 7556-7565. doi:
10.1093/nar/gkt495.
|
Exonuclease x in complex with 3' overhanging duplex DNA
. SNAP output
|
|
4fzy
|
hydrolase-DNA |
X-ray (2.5 Å) |
Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T |
(2013) "Recognition
and processing of double-stranded DNA by ExoX, a
distributive 3'-5' exonuclease." Nucleic Acids
Res., 41, 7556-7565. doi:
10.1093/nar/gkt495.
|
Exonuclease x in complex with 12bp blunt-ended dsDNA .
SNAP output
|
|
4fzz
|
hydrolase-DNA |
X-ray (2.8 Å) |
Wang T, Sun HL, Cheng F, Zhang XE, Bi L, Jiang T |
(2013) "Recognition
and processing of double-stranded DNA by ExoX, a
distributive 3'-5' exonuclease." Nucleic Acids
Res., 41, 7556-7565. doi:
10.1093/nar/gkt495.
|
Exonuclease x in complex with 5' overhanging duplex DNA
. SNAP output
|
|
4g0r
|
virus-DNA |
X-ray (2.7 Å) |
Halder S, Nam HJ, Govindasamy L, Vogel M, Dinsart C,
Salome N, McKenna R, Agbandje-McKenna M |
(2013) "Structural
characterization of h-1 parvovirus: comparison of
infectious virions to empty capsids."
J.Virol., 87, 5128-5140. doi:
10.1128/JVI.03416-12.
|
Structural characterization of h-1 parvovirus:
comparison of infectious virions to replication
defective particles . SNAP output
|
|
4g0u
|
isomerase-DNA-isomerase inhibitor |
X-ray (2.7 Å) |
Wu CC, Li YC, Wang YR, Li TK, Chan NL |
(2013) "On the
structural basis and design guidelines for type II
topoisomerase-targeting anticancer drugs."
Nucleic Acids Res., 41,
10630-10640. doi: 10.1093/nar/gkt828.
|
Human topoisomerase iibeta in complex with DNA and
amsacrine . SNAP
output
|
|
4g0v
|
isomerase-DNA-isomerase inhibitor |
X-ray (2.548 Å) |
Wu CC, Li YC, Wang YR, Li TK, Chan NL |
(2013) "On the
structural basis and design guidelines for type II
topoisomerase-targeting anticancer drugs."
Nucleic Acids Res., 41,
10630-10640. doi: 10.1093/nar/gkt828.
|
Human topoisomerase iibeta in complex with DNA and
mitoxantrone . SNAP
output
|
|
4g0w
|
isomerase-DNA-isomerase inhibitor |
X-ray (2.696 Å) |
Wu CC, Li YC, Wang YR, Li TK, Chan NL |
(2013) "On the
structural basis and design guidelines for type II
topoisomerase-targeting anticancer drugs."
Nucleic Acids Res., 41,
10630-10640. doi: 10.1093/nar/gkt828.
|
Human topoisomerase iibeta in complex with DNA and
ametantrone . SNAP
output
|
|
4g3i
|
transferase-DNA |
X-ray (2.5 Å) |
Yan YY, Gan JH, Huang Z |
"Crystal structure of Dpo4 in complex with DNA
duplex." |
Crystal structure of dpo4 in complex with DNA duplex .
SNAP output
|
|
4g4n
|
hydrolase-DNA |
X-ray (1.85 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2013) "Structural
and Biochemical Analysis of DNA Helix Invasion by the
Bacterial 8-Oxoguanine DNA Glycosylase MutM."
J.Biol.Chem., 288,
10012-10023. doi: 10.1074/jbc.M112.415612.
|
Mutm containing m77a mutation bound to undamaged DNA .
SNAP output
|
|
4g4o
|
hydrolase-DNA |
X-ray (1.95 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2013) "Structural
and Biochemical Analysis of DNA Helix Invasion by the
Bacterial 8-Oxoguanine DNA Glycosylase MutM."
J.Biol.Chem., 288,
10012-10023. doi: 10.1074/jbc.M112.415612.
|
Mutm containing m77a mutation bound to oxog-containing
DNA . SNAP output
|
|
4g4q
|
hydrolase-DNA |
X-ray (1.86 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2013) "Structural
and Biochemical Analysis of DNA Helix Invasion by the
Bacterial 8-Oxoguanine DNA Glycosylase MutM."
J.Biol.Chem., 288,
10012-10023. doi: 10.1074/jbc.M112.415612.
|
Mutm containing f114a mutation bound to undamaged DNA .
SNAP output
|
|
4g4r
|
hydrolase-DNA |
X-ray (1.95 Å) |
Sung RJ, Zhang M, Qi Y, Verdine GL |
(2013) "Structural
and Biochemical Analysis of DNA Helix Invasion by the
Bacterial 8-Oxoguanine DNA Glycosylase MutM."
J.Biol.Chem., 288,
10012-10023. doi: 10.1074/jbc.M112.415612.
|
Mutm containing f114a mutation bound to oxog-containing
DNA . SNAP output
|
|
4g7h
|
transcription, transferase-DNA |
X-ray (2.9 Å) |
Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold
E, Ebright RH |
(2012) "Structural
basis of transcription initiation."
Science, 338, 1076-1080. doi:
10.1126/science.1227786.
|
Crystal structure of thermus thermophilus transcription
initiation complex . SNAP output
|
|
4g7o
|
transcription, transferase-DNA |
X-ray (2.993 Å) |
Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold
E, Ebright RH |
(2012) "Structural
basis of transcription initiation."
Science, 338, 1076-1080. doi:
10.1126/science.1227786.
|
Crystal structure of thermus thermophilus transcription
initiation complex containing 2 nt of RNA . SNAP output
|
|
4g7z
|
transcription, transferase-DNA |
X-ray (3.815 Å) |
Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX, Arnold
E, Ebright RH |
(2012) "Structural
basis of transcription initiation."
Science, 338, 1076-1080. doi:
10.1126/science.1227786.
|
Crystal structure of thermus thermophilus transcription
initiation complex containing 5-bru at template-strand
position +1 . SNAP
output
|
|
4g82
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Ethayathulla AS, Viadiu H |
(2013) "Crystal Structure of p73 DNA-Binding Domain
Tetramer bound to a Full Response-Element."
J.Biol.Chem. |
Crystal structure of p73 DNA-binding domain tetramer
bound to a full response-element . SNAP output
|
|
4g83
|
DNA binding protein-DNA |
X-ray (4.0 Å) |
Ethayathulla AS, Viadiu H |
(2013) "Crystal Structure of p73 DNA-Binding Domain
Tetramer bound to a Full Response-Element."
J.Biol.Chem. |
Crystal structure of p73 DNA-binding domain tetramer
bound to a full response-element . SNAP output
|
|
4g92
|
transcription-DNA |
X-ray (1.8 Å) |
Huber EM, Scharf DH, Hortschansky P, Groll M,
Brakhage AA |
(2012) "DNA
Minor Groove Sensing and Widening by the CCAAT-Binding
Complex." Structure, 20,
1757-1768. doi: 10.1016/j.str.2012.07.012.
|
Ccaat-binding complex from aspergillus nidulans with
DNA . SNAP output
|
|
4gat
|
transcription-DNA |
NMR |
Starich MR, Wikstrom M, Arst Jr HN, Clore GM,
Gronenborn AM |
(1998) "The
solution structure of a fungal AREA protein-DNA
complex: an alternative binding mode for the basic
carboxyl tail of GATA factors."
J.Mol.Biol., 277, 605-620.
doi: 10.1006/jmbi.1998.1625.
|
Solution NMR structure of the wild type DNA binding
domain of area complexed to a 13bp DNA containing a
cgata site, regularized mean structure . SNAP output
|
|
4gc6
|
transferase-DNA |
X-ray (2.895 Å) |
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M,
Eoff RL |
(2012) "Differential
furanose selection in the active sites of archaeal DNA
polymerases probed by fixed-conformation nucleotide
analogues." Biochemistry,
51, 9234-9244. doi: 10.1021/bi301043k.
|
Crystal structure of dpo4 in complex with n-mc-damp
opposite dt . SNAP
output
|
|
4gc7
|
transferase-RNA |
X-ray (2.89 Å) |
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M,
Eoff RL |
(2012) "Differential
furanose selection in the active sites of archaeal DNA
polymerases probed by fixed-conformation nucleotide
analogues." Biochemistry,
51, 9234-9244. doi: 10.1021/bi301043k.
|
Crystal structure of dpo4 in complex with s-mc-dadp
opposite dt . SNAP
output
|
|
4gck
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin
W, Schumacher MA |
(2013) "SlmA
forms a higher-order structure on DNA that inhibits
cytokinetic Z-ring formation over the nucleoid."
Proc.Natl.Acad.Sci.USA, 110,
10586-10591. doi: 10.1073/pnas.1221036110.
|
Structure of no-DNA complex . SNAP output
|
|
4gcl
|
DNA binding protein-DNA |
X-ray (2.65 Å) |
Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin
W, Schumacher MA |
(2013) "SlmA
forms a higher-order structure on DNA that inhibits
cytokinetic Z-ring formation over the nucleoid."
Proc.Natl.Acad.Sci.USA, 110,
10586-10591. doi: 10.1073/pnas.1221036110.
|
Structure of no-DNA factor . SNAP output
|
|
4gct
|
DNA binding protein-DNA |
X-ray (2.45 Å) |
Tonthat NK, Milam SL, Chinnam N, Whitfill T, Margolin
W, Schumacher MA |
(2013) "SlmA
forms a higher-order structure on DNA that inhibits
cytokinetic Z-ring formation over the nucleoid."
Proc.Natl.Acad.Sci.USA, 110,
10586-10591. doi: 10.1073/pnas.1221036110.
|
Structure of no factor protein-DNA complex . SNAP output
|
|
4gdf
|
hydrolase-DNA |
X-ray (2.8 Å) |
Chang YP, Xu M, Machado AC, Yu XJ, Rohs R, Chen
XS |
(2013) "Mechanism
of Origin DNA Recognition and Assembly of an
Initiator-Helicase Complex by SV40 Large Tumor
Antigen." Cell Rep, 3,
1117-1127. doi: 10.1016/j.celrep.2013.03.002.
|
A crystal structure of sv40 large t antigen . SNAP output
|
|
4gfb
|
transcription-DNA |
X-ray (2.99 Å) |
Le Bihan YV, Matot B, Pietrement O, Giraud-Panis MJ,
Gasparini S, Le Cam E, Gilson E, Sclavi B, Miron S, Le Du
MH |
(2013) "Effect
of Rap1 binding on DNA distortion and potassium
permanganate hypersensitivity." Acta
Crystallogr.,Sect.D, 69, 409-419.
doi: 10.1107/S0907444912049311.
|
Rap1-DNA complex . SNAP
output
|
|
4gfh
|
isomerase-DNA |
X-ray (4.408 Å) |
Schmidt BH, Osheroff N, Berger JM |
(2012) "Structure
of a topoisomerase II-DNA-nucleotide complex reveals a
new control mechanism for ATPase activity."
Nat.Struct.Mol.Biol., 19,
1147-1154. doi: 10.1038/nsmb.2388.
|
Topoisomerase ii-DNA-amppnp complex . SNAP output
|
|
4gg4
|
DNA binding protein-DNA-RNA |
X-ray (2.501 Å) |
Yin P, Deng D, Yan C, Pan XJ, Xi JJ, Yan N, Shi
Y |
(2012) "Specific
DNA-RNA hybrid recognition by TAL effectors."
Cell Rep, 2, 707-713. doi:
10.1016/j.celrep.2012.09.001.
|
Crystal structure of the tal effector dhax3 bound to
specific DNA-RNA hybrid . SNAP output
|
|
4gjp
|
transcription-DNA |
X-ray (1.94 Å) |
Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG |
"Crystal structure of a protein complex." |
Crystal structure of the tal effector dhax3 bound to
dsDNA containing repetitive methyl-cpg . SNAP output
|
|
4gjr
|
transcription-DNA |
X-ray (1.85 Å) |
Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG |
"Crystal structure of a protein complex." |
Crystal structure of the tal effector dhax3 bound to
methylated dsDNA . SNAP
output
|
|
4gle
|
hydrolase-DNA |
X-ray (2.7 Å) |
Meulenbroek EM, Peron Cane C, Jala I, Iwai S,
Moolenaar GF, Goosen N, Pannu NS |
(2013) "UV
damage endonuclease employs a novel dual-dinucleotide
flipping mechanism to recognize different DNA
lesions." Nucleic Acids Res.,
41, 1363-1371. doi: 10.1093/nar/gks1127.
|
Sacuvde in complex with 6-4pp-containing DNA . SNAP output
|
|
4glx
|
ligase-ligase inhibitor-DNA |
X-ray (1.9 Å) |
Surivet JP, Lange R, Hubschwerlen C, Keck W, Specklin
JL, Ritz D, Bur D, Locher H, Seiler P, Strasser DS, Prade
L, Kohl C, Schmitt C, Chapoux G, Ilhan E, Ekambaram N,
Athanasiou A, Knezevic A, Sabato D, Chambovey A, Gaertner
M, Enderlin M, Boehme M, Sippel V, Wyss P |
(2012) "Structure-guided
design, synthesis and biological evaluation of novel
DNA ligase inhibitors with in vitro and in vivo
anti-staphylococcal activity."
Bioorg.Med.Chem.Lett., 22,
6705-6711. doi: 10.1016/j.bmcl.2012.08.094.
|
DNA ligase a in complex with inhibitor . SNAP output
|
|
4gnx
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Pavletich NP, Fan J |
"Structure of." |
Structure of u. maydis replication protein a bound to
ssDNA . SNAP output
|
|
4gop
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Fan J, Pavletich NP |
(2012) "Structure
and conformational change of a replication protein A
heterotrimer bound to ssDNA." Genes Dev.,
26, 2337-2347. doi: 10.1101/gad.194787.112.
|
Structure and conformational change of a replication
protein a heterotrimer bound to ssDNA . SNAP output
|
|
4guo
|
transcription-DNA |
X-ray (3.19 Å) |
S Ethayathulla A, Viadiu H |
"structure of p73 DNA binding domain complex with 12
bp DNA." |
Structure of p73 DNA binding domain complex with 12 bp
DNA . SNAP output
|
|
4guq
|
transcription-DNA |
X-ray (3.7 Å) |
Ciribilli Y, Monti P, Bisio A, Nguyen HT,
Ethayathulla AS, Ramos A, Foggetti G, Menichini P,
Menendez D, Resnick MA, Viadiu H, Fronza G, Inga A |
(2013) "Transactivation
specificity is conserved among p53 family proteins and
depends on a response element sequence code."
Nucleic Acids Res., 41,
8637-8653. doi: 10.1093/nar/gkt657.
|
Structure of muts139f p73 DNA binding domain complexed
with 20bp DNA response element . SNAP output
|
|
4gxi
|
transferase-DNA |
X-ray (1.949 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2013) "DNA
polymerase minor groove interactions modulate mutagenic
bypass of a templating 8-oxoguanine lesion."
Nucleic Acids Res., 41,
1848-1858. doi: 10.1093/nar/gks1276.
|
R283k DNA polymerase beta binary complex with a
templating 8og . SNAP
output
|
|
4gxj
|
transferase-DNA |
X-ray (2.2 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2013) "DNA
polymerase minor groove interactions modulate mutagenic
bypass of a templating 8-oxoguanine lesion."
Nucleic Acids Res., 41,
1848-1858. doi: 10.1093/nar/gks1276.
|
R283k DNA polymerase beta ternary complex with a
templating 8og and incoming dctp analog . SNAP output
|
|
4gxk
|
transferase-DNA |
X-ray (1.998 Å) |
Freudenthal BD, Beard WA, Wilson SH |
(2013) "DNA
polymerase minor groove interactions modulate mutagenic
bypass of a templating 8-oxoguanine lesion."
Nucleic Acids Res., 41,
1848-1858. doi: 10.1093/nar/gks1276.
|
R283k DNA polymerase beta ternary complex with a
templating 8og and incoming datp analog . SNAP output
|
|
4gz0
|
hydrolase-DNA |
X-ray (2.113 Å) |
Schellenberg MJ, Appel CD, Adhikari S, Robertson PD,
Ramsden DA, Williams RS |
(2012) "Mechanism
of repair of 5'-topoisomerase II-DNA adducts by
mammalian tyrosyl-DNA phosphodiesterase 2."
Nat.Struct.Mol.Biol., 19,
1363-1371. doi: 10.1038/nsmb.2418.
|
Mus musculus tdp2-DNA substrate analog
(5'-6-aminohexanol) complex . SNAP output
|
|
4gz1
|
hydrolase-DNA |
X-ray (1.5 Å) |
Schellenberg MJ, Appel CD, Adhikari S, Robertson PD,
Ramsden DA, Williams RS |
(2012) "Mechanism
of repair of 5'-topoisomerase II-DNA adducts by
mammalian tyrosyl-DNA phosphodiesterase 2."
Nat.Struct.Mol.Biol., 19,
1363-1371. doi: 10.1038/nsmb.2418.
|
Mus musculus tdp2 reaction product (5'-phosphorylated
DNA)-mg2+ complex at 1.5 angstroms resolution .
SNAP output
|
|
4gz2
|
hydrolase-DNA |
X-ray (1.85 Å) |
Schellenberg MJ, Appel CD, Adhikari S, Robertson PD,
Ramsden DA, Williams RS |
(2012) "Mechanism
of repair of 5'-topoisomerase II-DNA adducts by
mammalian tyrosyl-DNA phosphodiesterase 2."
Nat.Struct.Mol.Biol., 19,
1363-1371. doi: 10.1038/nsmb.2418.
|
Mus musculus tdp2 excluded ssDNA complex . SNAP output
|
|
4gzn
|
transcription-DNA |
X-ray (0.99 Å) |
Liu Y, Toh H, Sasaki H, Zhang X, Cheng X |
(2012) "An
atomic model of Zfp57 recognition of CpG methylation
within a specific DNA sequence." Genes
Dev., 26, 2374-2379. doi:
10.1101/gad.202200.112.
|
Mouse zfp57 zinc fingers in complex with methylated DNA
. SNAP output
|
|
4gzy
|
transcription-DNA-RNA |
X-ray (3.51 Å) |
Weixlbaumer A, Leon K, Landick R, Darst SA |
(2013) "Structural
basis of transcriptional pausing in bacteria."
Cell(Cambridge,Mass.), 152,
431-441. doi: 10.1016/j.cell.2012.12.020.
|
Crystal structures of bacterial RNA polymerase paused
elongation complexes . SNAP output
|
|
4gzz
|
transcription-DNA-RNA hybrid |
X-ray (4.29 Å) |
Weixlbaumer A, Leon K, Landick R, Darst SA |
(2013) "Structural
basis of transcriptional pausing in bacteria."
Cell(Cambridge,Mass.), 152,
431-441. doi: 10.1016/j.cell.2012.12.020.
|
Crystal structures of bacterial RNA polymerase paused
elongation complexes . SNAP output
|
|
4h0e
|
transcription-DNA |
X-ray (1.973 Å) |
Jain D, Nair DT |
(2013) "Spacing
between core recognition motifs determines relative
orientation of AraR monomers on bipartite
operators." Nucleic Acids Res.,
41, 639-647. doi: 10.1093/nar/gks962.
|
Crystal structure of mutant orr3 in complex with ntd of
arar . SNAP output
|
|
4h10
|
transcription-DNA |
X-ray (2.402 Å) |
Wang Z, Wu Y, Li L, Su XD |
(2013) "Intermolecular
recognition revealed by the complex structure of human
CLOCK-BMAL1 basic helix-loop-helix domains with E-box
DNA." Cell Res., 23,
213-224. doi: 10.1038/cr.2012.170.
|
Intermolecular recognition revealed by the complex
structure of human clock-bmal1 basic helix-loop-helix
domains with e-box DNA . SNAP output
|
|
4h5q
|
viral protein-DNA |
X-ray (2.7 Å) |
Raymond DD, Piper ME, Gerrard SR, Skiniotis G, Smith
JL |
(2012) "Phleboviruses
encapsidate their genomes by sequestering RNA
bases." Proc.Natl.Acad.Sci.USA,
109, 19208-19213. doi: 10.1073/pnas.1213553109.
|
Crystal structure of rift valley fever virus
nucleocapsid protein hexamer bound to single-stranded
DNA . SNAP output
|
|
4h8k
|
hydrolase-DNA-RNA |
X-ray (2.3 Å) |
Nguyen TN, You DJ, Matsumoto H, Kanaya E, Koga Y,
Kanaya S |
(2013) "Crystal
structure of metagenome-derived LC11-RNase H1 in
complex with RNA/DNA hybrid."
J.Struct.Biol., 182, 144-154.
doi: 10.1016/j.jsb.2013.02.018.
|
Crystal structure of lc11-rnase h1 in complex with
RNA-DNA hybrid . SNAP
output
|
|
4hc7
|
transcription-DNA |
X-ray (2.65 Å) |
Chen Y, Bates DL, Dey R, Chen PH, Machado AC,
Laird-Offringa IA, Rohs R, Chen L |
(2012) "DNA
Binding by GATA Transcription Factor Suggests
Mechanisms of DNA Looping and Long-Range Gene
Regulation." Cell Rep, 2,
1197-1206. doi: 10.1016/j.celrep.2012.10.012.
|
Crystal structure of the full DNA binding domain of
gata3-complex 2 . SNAP
output
|
|
4hc9
|
transcription-DNA |
X-ray (1.6 Å) |
Chen Y, Bates DL, Dey R, Chen PH, Machado AC,
Laird-Offringa IA, Rohs R, Chen L |
(2012) "DNA
Binding by GATA Transcription Factor Suggests
Mechanisms of DNA Looping and Long-Range Gene
Regulation." Cell Rep, 2,
1197-1206. doi: 10.1016/j.celrep.2012.10.012.
|
DNA binding by gata transcription factor-complex 3 .
SNAP output
|
|
4hca
|
transcription-DNA |
X-ray (2.8 Å) |
Chen Y, Bates DL, Dey R, Chen PH, Machado AC,
Laird-Offringa IA, Rohs R, Chen L |
(2012) "DNA
Binding by GATA Transcription Factor Suggests
Mechanisms of DNA Looping and Long-Range Gene
Regulation." Cell Rep, 2,
1197-1206. doi: 10.1016/j.celrep.2012.10.012.
|
DNA binding by gata transcription factor-complex 1 .
SNAP output
|
|
4hcb
|
hydrolase-DNA |
X-ray (2.0 Å) |
Qiu R, Lou T, Wei J, Liu M, Gu S, Tang R, Ji C, Gong
W |
"The structures of Escherichia coli exonuclease I in
complex with the single strand DNA." |
The metal-free form of crystal structure of e.coli
exoi-ssDNA complex . SNAP output
|
|
4hcc
|
hydrolase-DNA |
X-ray (2.96 Å) |
Qiu R, Lou T, Wei J, Liu M, Gu S, Tang R, Ji C, Gong
W |
"The structures of Escherichia coli exonuclease I in
complex with the single strand DNA." |
The zinc ion bound form of crystal structure of e.coli
exoi-ssDNA complex . SNAP output
|
|
4hdu
|
DNA binding protein-DNA |
X-ray (2.848 Å) |
Wilkinson OJ, Latypov V, Tubbs JL, Millington CL,
Morita R, Blackburn H, Marriott A, McGown G, Thorncroft
M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA,
Tainer JA, Margison GP, Williams DM |
(2012) "Alkyltransferase-like
protein (Atl1) distinguishes alkylated guanines for DNA
repair using cation-{pi} interactions."
Proc.Natl.Acad.Sci.USA, 109,
18755-18760. doi: 10.1073/pnas.1209451109.
|
Crystal structure of s. pombe atl1 in complex with
damaged DNA containing 2-aminopurine . SNAP output
|
|
4hdv
|
DNA binding protein-DNA |
X-ray (2.702 Å) |
Wilkinson OJ, Latypov V, Tubbs JL, Millington CL,
Morita R, Blackburn H, Marriott A, McGown G, Thorncroft
M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA,
Tainer JA, Margison GP, Williams DM |
(2012) "Alkyltransferase-like
protein (Atl1) distinguishes alkylated guanines for DNA
repair using cation-{pi} interactions."
Proc.Natl.Acad.Sci.USA, 109,
18755-18760. doi: 10.1073/pnas.1209451109.
|
Crystal structure of s. pombe atl1 in complex with
damaged DNA containing 2,6-diaminopurine . SNAP output
|
|
4hf1
|
transcription-DNA |
X-ray (2.222 Å) |
Rajagopalan S, Teter SJ, Zwart PH, Brennan RG,
Phillips KJ, Kiley PJ |
(2013) "Studies
of IscR reveal a unique mechanism for metal-dependent
regulation of DNA binding specificity."
Nat.Struct.Mol.Biol., 20,
740-747. doi: 10.1038/nsmb.2568.
|
Crystal structure of iscr bound to its promoter .
SNAP output
|
|
4hf2
|
transcription-DNA |
X-ray (2.99 Å) |
Rajagopalan S, Teter SJ, Zwart PH, Brennan RG,
Phillips KJ, Kiley PJ |
(2013) "Studies
of IscR reveal a unique mechanism for metal-dependent
regulation of DNA binding specificity."
Nat.Struct.Mol.Biol., 20,
740-747. doi: 10.1038/nsmb.2568.
|
Crystal structure of e43a iscr mutant bound to its
promoter . SNAP
output
|
|
4hht
|
hydrolase-DNA |
X-ray (3.1 Å) |
Chon H, Sparks JL, Rychlik M, Nowotny M, Burgers PM,
Crouch RJ, Cerritelli SM |
(2013) "RNase H2
roles in genome integrity revealed by unlinking its
activities." Nucleic Acids Res.,
41, 3130-3143. doi: 10.1093/nar/gkt027.
|
T. maritima rnase h2 g21s in complex with nucleic acid
substrate and calcium ions . SNAP output
|
|
4hid
|
DNA binding protein |
X-ray (1.822 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (gcttacggt) . SNAP output
|
|
4hik
|
DNA binding protein |
X-ray (1.636 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (ggttacggt) . SNAP output
|
|
4him
|
DNA binding protein |
X-ray (1.75 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (ggatacggt) . SNAP output
|
|
4hio
|
DNA binding protein |
X-ray (1.753 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (ggtaacggt) . SNAP output
|
|
4hiv
|
DNA-antibiotic |
X-ray (2.6 Å) |
Lo YS, Tseng WH, Chuang CY, Hou MH |
(2013) "The
structural basis of actinomycin D-binding induces
nucleotide flipping out, a sharp bend and a left-handed
twist in CGG triplet repeats." Nucleic Acids
Res., 41, 4284-4294. doi:
10.1093/nar/gkt084.
|
Structure of actinomycin d d(atgcggcat) complex .
SNAP output
|
|
4hj5
|
DNA binding protein |
X-ray (2.04 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (ggtttcggt) . SNAP output
|
|
4hj7
|
DNA binding protein |
X-ray (1.783 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (ggttagggt) . SNAP output
|
|
4hj8
|
DNA binding protein |
X-ray (2.043 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (ggttacgct) . SNAP output
|
|
4hj9
|
DNA binding protein |
X-ray (1.85 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (cggttacggt) . SNAP output
|
|
4hja
|
DNA binding protein |
X-ray (2.1 Å) |
Dickey TH, McKercher MA, Wuttke DS |
(2013) "Nonspecific
Recognition Is Achieved in Pot1pC through the Use of
Multiple Binding Modes." Structure,
21, 121-132. doi: 10.1016/j.str.2012.10.015.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssDNA (acggttacggt) . SNAP output
|
|
4hje
|
transcription-DNA |
X-ray (1.907 Å) |
Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z,
Qin PZ, Rohs R, Chen L |
(2013) "Structure
of p53 binding to the BAX response element reveals DNA
unwinding and compression to accommodate base-pair
insertion." Nucleic Acids Res.,
41, 8368-8376. doi: 10.1093/nar/gkt584.
|
Crystal structure of p53 core domain in complex with
DNA . SNAP output
|
|
4hkq
|
transcription-RNA-DNA |
X-ray (3.04 Å) |
Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona
MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M |
(2013) "Structural
analysis of monomeric retroviral reverse transcriptase
in complex with an RNA/DNA hybrid." Nucleic
Acids Res., 41, 3874-3887. doi:
10.1093/nar/gkt053.
|
Xmrv reverse transcriptase in complex with RNA-DNA
hybrid . SNAP output
|
|
4hly
|
DNA binding protein-DNA |
X-ray (1.48 Å) |
Hew K, Dahlroth SL, Venkatachalam R, Nasertorabi F,
Lim BT, Cornvik T, Nordlund P |
(2013) "The
crystal structure of the DNA-binding domain of vIRF-1
from the oncogenic KSHV reveals a conserved fold for
DNA binding and reinforces its role as a transcription
factor." Nucleic Acids Res.,
41, 4295-4306. doi: 10.1093/nar/gkt082.
|
The complex crystal structure of the DNA binding domain
of virf-1 from the oncogenic kshv with DNA . SNAP output
|
|
4hn5
|
transcription-DNA |
X-ray (1.902 Å) |
Hudson WH, Youn C, Ortlund EA |
(2013) "The
structural basis of direct glucocorticoid-mediated
transrepression." Nat.Struct.Mol.Biol.,
20, 53-58. doi: 10.1038/nsmb.2456.
|
Gr DNA binding domain - tslp ngre complex . SNAP output
|
|
4hn6
|
transcription-DNA |
X-ray (2.549 Å) |
Hudson WH, Youn C, Ortlund EA |
(2013) "The
structural basis of direct glucocorticoid-mediated
transrepression." Nat.Struct.Mol.Biol.,
20, 53-58. doi: 10.1038/nsmb.2456.
|
Gr DNA binding domain r460d-d462r - tslp ngre complex .
SNAP output
|
|
4hp1
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y,
Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q,
Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB,
Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG |
(2012) "Tet3
CXXC Domain and Dioxygenase Activity Cooperatively
Regulate Key Genes for Xenopus Eye and Neural
Development." Cell(Cambridge,Mass.),
151, 1200-1213. doi: 10.1016/j.cell.2012.11.014.
|
Crystal structure of tet3 in complex with a non-cpg
dsDNA . SNAP output
|
|
4hp3
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y,
Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q,
Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB,
Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG |
(2012) "Tet3
CXXC Domain and Dioxygenase Activity Cooperatively
Regulate Key Genes for Xenopus Eye and Neural
Development." Cell(Cambridge,Mass.),
151, 1200-1213. doi: 10.1016/j.cell.2012.11.014.
|
Crystal structure of tet3 in complex with a cpg dsDNA .
SNAP output
|
|
4hqb
|
DNA binding protein-DNA |
X-ray (2.301 Å) |
Sugiman-Marangos SN, Peel JK, Weiss YM, Ghirlando R,
Junop MS |
(2013) "Crystal
structure of the DdrB/ssDNA complex from Deinococcus
radiodurans reveals a DNA binding surface involving
higher-order oligomeric states." Nucleic Acids
Res., 41, 9934-9944. doi:
10.1093/nar/gkt759.
|
Crystal structure of ddrb from deinococcus radiodurans
bound to ssDNA . SNAP
output
|
|
4hqe
|
transcription-DNA |
X-ray (2.299 Å) |
Ji Q, Zhang L, Jones MB, Sun F, Deng X, Liang H, Cho
H, Brugarolas P, Gao YN, Peterson SN, Lan L, Bae T, He
C |
(2013) "Molecular
mechanism of quinone signaling mediated through
S-quinonization of a YodB family repressor QsrR."
Proc.Natl.Acad.Sci.USA, 110,
5010-5015. doi: 10.1073/pnas.1219446110.
|
The crystal structure of qsrr-DNA complex . SNAP output
|
|
4hqu
|
hormone-DNA |
X-ray (2.2 Å) |
Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter
JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin
AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis
TC |
(2012) "Unique
motifs and hydrophobic interactions shape the binding
of modified DNA ligands to protein targets."
Proc.Natl.Acad.Sci.USA, 109,
19971-19976. doi: 10.1073/pnas.1213933109.
|
Crystal structure of human pdgf-bb in complex with a
modified nucleotide aptamer (somamer sl5) . SNAP output
|
|
4hqx
|
hormone-DNA |
X-ray (2.3 Å) |
Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter
JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin
AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis
TC |
(2012) "Unique
motifs and hydrophobic interactions shape the binding
of modified DNA ligands to protein targets."
Proc.Natl.Acad.Sci.USA, 109,
19971-19976. doi: 10.1073/pnas.1213933109.
|
Crystal structure of human pdgf-bb in complex with a
modified nucleotide aptamer (somamer sl4) . SNAP output
|
|
4hri
|
transcription-DNA |
X-ray (2.954 Å) |
Hu HX, Jiang YL, Zhao MX, Zhu PF, Yang XY, Wen B,
Zhang Z, Wu Q, Chen Y, Zhang CC, Zhou CZ |
"Structural and biochemical analyses of Anabaena HetR
reveal insights into its binding to DNA targets and the
inhibitory hexapeptide ERGSGR." |
Crystal structure of hetr in complex with a 21-bp
palindromic DNA at the upstream of the hetp promoter
from anabaena . SNAP
output
|
|
4hsb
|
hydrolase-DNA |
X-ray (1.9 Å) |
Adhikary S, Cato MC, McGary KL, Rokas A, Eichman
BF |
(2013) "Non-productive
DNA damage binding by DNA glycosylase-like protein Mag2
from Schizosaccharomyces pombe." Dna
Repair, 12, 196-204. doi:
10.1016/j.dnarep.2012.12.001.
|
S. pombe 3-methyladenine DNA glycosylase-like protein
mag2 bound to damaged DNA . SNAP output
|
|
4ht4
|
hydrolase-DNA |
X-ray (2.907 Å) |
Edwards JS, Betts L, Frazier ML, Pollet RM, Kwong SM,
Walton WG, Ballentine WK, Huang JJ, Habibi S, Del Campo
M, Meier JL, Dervan PB, Firth N, Redinbo MR |
(2013) "Molecular
basis of antibiotic multiresistance transfer in
Staphylococcus aureus."
Proc.Natl.Acad.Sci.USA, 110,
2804-2809. doi: 10.1073/pnas.1219701110.
|
Molecular basis of vancomycin resistance transfer in
staphylococcus aureus . SNAP output
|
|
4htu
|
hydrolase-DNA |
X-ray (1.489 Å) |
Patra A, Harp J, Pallan PS, Zhao L, Abramov M,
Herdewijn P, Egli M |
(2013) "Structure,
stability and function of 5-chlorouracil modified A:U
and G:U base pairs." Nucleic Acids Res.,
41, 2689-2697. doi: 10.1093/nar/gks1316.
|
Structure of 5-chlorouracil modified a:u base pair .
SNAP output
|
|
4hue
|
hydrolase-DNA |
X-ray (1.561 Å) |
Patra A, Harp J, Pallan PS, Zhao L, Abramov M,
Herdewijn P, Egli M |
(2013) "Structure,
stability and function of 5-chlorouracil modified A:U
and G:U base pairs." Nucleic Acids Res.,
41, 2689-2697. doi: 10.1093/nar/gks1316.
|
Structure of 5-chlorouracil modified g:u base pair .
SNAP output
|
|
4huf
|
hydrolase-DNA |
X-ray (1.69 Å) |
Patra A, Harp J, Pallan PS, Zhao L, Abramov M,
Herdewijn P, Egli M |
(2013) "Structure,
stability and function of 5-chlorouracil modified A:U
and G:U base pairs." Nucleic Acids Res.,
41, 2689-2697. doi: 10.1093/nar/gks1316.
|
Structure of 5-chlorouracil modified a:u base pair .
SNAP output
|
|
4hug
|
hydrolase-DNA |
X-ray (1.64 Å) |
Patra A, Harp J, Pallan PS, Zhao L, Abramov M,
Herdewijn P, Egli M |
(2013) "Structure,
stability and function of 5-chlorouracil modified A:U
and G:U base pairs." Nucleic Acids Res.,
41, 2689-2697. doi: 10.1093/nar/gks1316.
|
Structure of 5-chlorouracil modified a:u base pairs .
SNAP output
|
|
4hyk
|
transferase-DNA |
X-ray (2.802 Å) |
Wilson RC, Jackson MA, Pata JD |
(2013) "Y-family
polymerase conformation is a major determinant of
fidelity and translesion specificity."
Structure, 21, 20-31. doi:
10.1016/j.str.2012.11.005.
|
Dbh ternary complex (substrates partially disordered) .
SNAP output
|
|
4i27
|
transferase-DNA |
X-ray (2.6 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Ternary complex of mouse tdt with ssDNA and incoming
nucleotide . SNAP
output
|
|
4i28
|
transferase-DNA |
X-ray (2.15 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Binary complex of mouse tdt with ssDNA and zn++ .
SNAP output
|
|
4i29
|
transferase-DNA |
X-ray (2.2 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Binary complex of mouse tdt with ssDNA and mn++ .
SNAP output
|
|
4i2a
|
transferase-DNA |
X-ray (1.9 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Binary complex of mouse tdt with ssDNA in absence of
divalent transition metal ion . SNAP output
|
|
4i2b
|
transferase-DNA |
X-ray (2.2 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Ternary complex of mouse tdt with ssDNA and ampcpp .
SNAP output
|
|
4i2c
|
transferase-DNA |
X-ray (2.1 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Ternary complex of mouse tdt with ssDNA and ampcpp .
SNAP output
|
|
4i2e
|
transferase-DNA |
X-ray (2.0 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Ternary complex of mouse tdt with ssDNA and ampcpp .
SNAP output
|
|
4i2f
|
transferase-DNA |
X-ray (2.1 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Binary complex of mouse tdt with ssDNA . SNAP output
|
|
4i2g
|
transferase-DNA |
X-ray (2.5 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Binary complex of mouse tdt with ssDNA . SNAP output
|
|
4i2h
|
transferase-DNA |
X-ray (2.75 Å) |
Gouge J, Rosario S, Romain F, Beguin P, Delarue
M |
(2013) "Structures
of Intermediates along the Catalytic Cycle of Terminal
Deoxynucleotidyltransferase: Dynamical Aspects of the
Two-Metal Ion Mechanism." J.Mol.Biol.,
425, 4334-4352. doi: 10.1016/j.jmb.2013.07.009.
|
Ternary complex of mouse tdt with ssDNA and ampcpp .
SNAP output
|
|
4i2o
|
transcription regulator-DNA |
X-ray (1.77 Å) |
Bonnet M, Kurz M, Mesa S, Briand C, Hennecke H,
Grutter MG |
(2013) "The
Structure of Bradyrhizobium japonicum Transcription
Factor FixK2 Unveils Sites of DNA Binding and
Oxidation." J.Biol.Chem.,
288, 14238-14246. doi: 10.1074/jbc.M113.465484.
|
The structure of fixk2 from bradyrhizobium japonicum .
SNAP output
|
|
4i3h
|
isomerase-DNA |
X-ray (3.7 Å) |
Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher
LM, Sanderson MR |
(2013) "Structure
of an 'open' clamp type II topoisomerase-DNA complex
provides a mechanism for DNA capture and
transport." Nucleic Acids Res.,
41, 9911-9923. doi: 10.1093/nar/gkt749.
|
A three-gate structure of topoisomerase iv from
streptococcus pneumoniae . SNAP output
|
|
4i6z
|
transcription regulator-DNA |
X-ray (3.2 Å) |
Koclega KD, Chruszcz M, Cooper DR, Petkowski JJ,
Tkaczuk KL, Joachimiak A, Minor W |
"Crystal structure of the transcriptional regulator
TM1030 with 24bp DNA oligonucleotide." |
Crystal structure of the transcriptional regulator
tm1030 with 24bp DNA oligonucleotide . SNAP output
|
|
4i7y
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.4 Å) |
Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica
F |
(2013) "Duplex-quadruplex
motifs in a peculiar structural organization
cooperatively contribute to thrombin binding of a DNA
aptamer." Acta Crystallogr.,Sect.D,
69, 2403-2411. doi: 10.1107/S0907444913022269.
|
Crystal structure of human alpha thrombin in complex
with a 27-mer aptamer bound to exosite ii . SNAP output
|
|
4i8t
|
transcription-DNA |
X-ray (3.0 Å) |
Martin RN, McGeehan JE, Ball NJ, Streeter SD, Thresh
SJ, Kneale GG |
(2013) "Structural
analysis of DNA-protein complexes regulating the
restriction-modification system Esp1396I." Acta
Crystallogr.,Sect.F, 69, 962-966.
doi: 10.1107/S174430911302126X.
|
C.esp1396i bound to a 19 base pair DNA duplex .
SNAP output
|
|
4i9q
|
transferase-DNA |
X-ray (2.3 Å) |
Jacewicz A, Trzemecka A, Guja KE, Plochocka D,
Yakubovskaya E, Bebenek A, Garcia-Diaz M |
(2013) "A Remote
Palm Domain Residue of RB69 DNA Polymerase Is Critical
for Enzyme Activity and Influences the Conformation of
the Active Site." Plos One,
8, e76700. doi: 10.1371/journal.pone.0076700.
|
Crystal structure of the ternary complex of the d714a
mutant of rb69 DNA polymerase . SNAP output
|
|
4ibu
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R,
Shakked Z |
(2013) "Structural
studies of p53 inactivation by DNA-contact mutations
and its rescue by suppressor mutations via alternative
protein-DNA interactions." Nucleic Acids
Res., 41, 8748-8759. doi:
10.1093/nar/gkt630.
|
Human p53 core domain with hot spot mutation r273c and
second-site suppressor mutation t284r in
sequence-specific complex with DNA . SNAP output
|
|
4ibv
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R,
Shakked Z |
(2013) "Structural
studies of p53 inactivation by DNA-contact mutations
and its rescue by suppressor mutations via alternative
protein-DNA interactions." Nucleic Acids
Res., 41, 8748-8759. doi:
10.1093/nar/gkt630.
|
Human p53 core domain with hot spot mutation r273c and
second-site suppressor mutation s240r in
sequence-specific complex with DNA . SNAP output
|
|
4ibw
|
DNA binding protein-DNA |
X-ray (1.791 Å) |
Eldar A, Rozenberg H, Diskin-Posner Y, Rohs R,
Shakked Z |
(2013) "Structural
studies of p53 inactivation by DNA-contact mutations
and its rescue by suppressor mutations via alternative
protein-DNA interactions." Nucleic Acids
Res., 41, 8748-8759. doi:
10.1093/nar/gkt630.
|
Human p53 core domain with hot spot mutation r273h and
second-site suppressor mutation t284r in
sequence-specific complex with DNA . SNAP output
|
|
4iem
|
hydrolase, lyase-DNA |
X-ray (2.39 Å) |
Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS,
Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B,
Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S,
Tainer JA |
(2013) "Conserved
Structural Chemistry for Incision Activity in
Structurally Non-homologous Apurinic/Apyrimidinic
Endonuclease APE1 and Endonuclease IV DNA Repair
Enzymes." J.Biol.Chem.,
288, 8445-8455. doi: 10.1074/jbc.M112.422774.
|
Human apurinic-apyrimidinic endonuclease (ape1) with
product DNA and mg2+ . SNAP output
|
|
4ihs
|
transcription-DNA |
X-ray (3.1 Å) |
Alanazi AM, Neidle EL, Momany C |
(2013) "The
DNA-binding domain of BenM reveals the structural basis
for the recognition of a T-N11-A sequence motif by
LysR-type transcriptional regulators." Acta
Crystallogr.,Sect.D, 69,
1995-2007. doi: 10.1107/S0907444913017320.
|
Crystal structure of benm_dbd-catb site 1 DNA complex .
SNAP output
|
|
4iht
|
transcription-DNA |
X-ray (3.0 Å) |
Alanazi AM, Neidle EL, Momany C |
(2013) "The
DNA-binding domain of BenM reveals the structural basis
for the recognition of a T-N11-A sequence motif by
LysR-type transcriptional regulators." Acta
Crystallogr.,Sect.D, 69,
1995-2007. doi: 10.1107/S0907444913017320.
|
Crystal structure of benm_dbd-bena site 1 DNA complex .
SNAP output
|
|
4ihv
|
transcription-DNA |
X-ray (2.716 Å) |
Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R,
Johnson RC |
(2013) "Control
of DNA minor groove width and Fis protein binding by
the purine 2-amino group." Nucleic Acids
Res., 41, 6750-6760. doi:
10.1093/nar/gkt357.
|
Crystal structure of fis bound to 27 bp sequence DNA
f28 (aaatttgtttgagcgttgagcaaattt) . SNAP output
|
|
4ihw
|
transcription-DNA |
X-ray (2.7 Å) |
Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R,
Johnson RC |
(2013) "Control
of DNA minor groove width and Fis protein binding by
the purine 2-amino group." Nucleic Acids
Res., 41, 6750-6760. doi:
10.1093/nar/gkt357.
|
Crystal structure of fis bound to 27 bp inosine
substituted DNA f28-di (aaatttgtttgaicittgagcaaattt) .
SNAP output
|
|
4ihx
|
transcription-DNA |
X-ray (2.8 Å) |
Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R,
Johnson RC |
(2013) "Control
of DNA minor groove width and Fis protein binding by
the purine 2-amino group." Nucleic Acids
Res., 41, 6750-6760. doi:
10.1093/nar/gkt357.
|
Crystal structure of fis bound to 27 bp 2-aminopurine
substituted DNA f28-2ap (aaatttgtttga2t2ttgagcaaattt) .
SNAP output
|
|
4ihy
|
transcription-DNA |
X-ray (2.9 Å) |
Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R,
Johnson RC |
(2013) "Control
of DNA minor groove width and Fis protein binding by
the purine 2-amino group." Nucleic Acids
Res., 41, 6750-6760. doi:
10.1093/nar/gkt357.
|
Crystal structure of fis bound to 27bp inosine
substituted DNA f29-di (aaatttgtttgiicictgagcaaattt) .
SNAP output
|
|
4ikf
|
viral protein-DNA-inhibitor |
X-ray (3.4 Å) |
Desimmie BA, Demeulemeester J, Suchaud V, Taltynov O,
Billamboz M, Lion C, Bailly F, Strelkov SV, Debyser Z,
Cotelle P, Christ F |
(2013) "2-Hydroxyisoquinoline-1,3(2H,4H)-diones
(HIDs), novel inhibitors of HIV integrase with a high
barrier to resistance." Acs Chem.Biol.,
8, 1187-1194. doi: 10.1021/cb4000426.
|
Pfv intasome with inhibitor mb-76 . SNAP output
|
|
4iqj
|
transferase-DNA |
X-ray (3.2 Å) |
Liu B, Lin J, Steitz TA |
(2013) "Structure
of PolIIIalpha-Tauc-DNA complex suggests an atomic
model of the replisome." Structure,
21, 658-664. doi: 10.1016/j.str.2013.02.002.
|
Structure of poliiialpha-tauc-DNA complex suggests an
atomic model of the replisome . SNAP output
|
|
4iqr
|
transcription-DNA |
X-ray (2.9 Å) |
Chandra V, Huang P, Potluri N, Wu D, Kim Y,
Rastinejad F |
(2013) "Multidomain
integration in the structure of the HNF-4 alpha nuclear
receptor complex." Nature,
495, 394-398. doi: 10.1038/nature11966.
|
Multi-domain organization of the hnf4alpha nuclear
receptor complex on DNA . SNAP output
|
|
4iqv
|
transferase-transferase inhibitor-DNA |
X-ray (2.9 Å) |
Costi R, Cuzzucoli Crucitti G, Pescatori L, Messore
A, Scipione L, Tortorella S, Amoroso A, Crespan E,
Campiglia P, Maresca B, Porta A, Granata I, Novellino E,
Gouge J, Delarue M, Maga G, Di Santo R |
(2013) "New
nucleotide-competitive non-nucleoside inhibitors of
terminal deoxynucleotidyl transferase: discovery,
characterization, and crystal structure in complex with
the target." J.Med.Chem.,
56, 7431-7441. doi: 10.1021/jm4010187.
|
Tdt core in complex with inhibitor
6-[4-(3-fluorobenzoyl)-1h-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic
acid and ssDNA . SNAP
output
|
|
4iqw
|
transferase-transferase inhibitor-DNA |
X-ray (2.6 Å) |
Costi R, Cuzzucoli Crucitti G, Pescatori L, Messore
A, Scipione L, Tortorella S, Amoroso A, Crespan E,
Campiglia P, Maresca B, Porta A, Granata I, Novellino E,
Gouge J, Delarue M, Maga G, Di Santo R |
(2013) "New
nucleotide-competitive non-nucleoside inhibitors of
terminal deoxynucleotidyl transferase: discovery,
characterization, and crystal structure in complex with
the target." J.Med.Chem.,
56, 7431-7441. doi: 10.1021/jm4010187.
|
Tdt core in complex with inhibitor
(2z,5e)-6-[4-(4-fluorobenzoyl)-1h-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic
acid and ssDNA . SNAP
output
|
|
4ir1
|
transferase-DNA |
X-ray (2.38 Å) |
Sharma A, Kottur J, Narayanan N, Nair DT |
(2013) "A
strategically located serine residue is critical for
the mutator activity of DNA polymerase IV from
Escherichia coli." Nucleic Acids Res.,
41, 5104-5114. doi: 10.1093/nar/gkt146.
|
Polymerase-DNA complex . SNAP output
|
|
4ir9
|
transferase-DNA |
X-ray (2.33 Å) |
Sharma A, Kottur J, Narayanan N, Nair DT |
(2013) "A
strategically located serine residue is critical for
the mutator activity of DNA polymerase IV from
Escherichia coli." Nucleic Acids Res.,
41, 5104-5114. doi: 10.1093/nar/gkt146.
|
Polymerase-DNA complex . SNAP output
|
|
4irc
|
transferase-DNA |
X-ray (2.67 Å) |
Sharma A, Kottur J, Narayanan N, Nair DT |
(2013) "A
strategically located serine residue is critical for
the mutator activity of DNA polymerase IV from
Escherichia coli." Nucleic Acids Res.,
41, 5104-5114. doi: 10.1093/nar/gkt146.
|
Polymerase-DNA complex . SNAP output
|
|
4ird
|
transferase-DNA |
X-ray (2.48 Å) |
Sharma A, Kottur J, Narayanan N, Nair DT |
(2013) "A
strategically located serine residue is critical for
the mutator activity of DNA polymerase IV from
Escherichia coli." Nucleic Acids Res.,
41, 5104-5114. doi: 10.1093/nar/gkt146.
|
Structure of polymerase-DNA complex . SNAP output
|
|
4iri
|
DNA binding protein-DNA |
X-ray (2.77 Å) |
Regan MC, Horanyi PS, Pryor EE, Sarver JL, Cafiso DS,
Bushweller JH |
(2013) "Structural
and dynamic studies of the transcription factor ERG
reveal DNA binding is allosterically
autoinhibited." Proc.Natl.Acad.Sci.USA,
110, 13374-13379. doi: 10.1073/pnas.1301726110.
|
Auto-inhibited erg ets domain-DNA complex . SNAP output
|
|
4irk
|
transferase-DNA |
X-ray (2.32 Å) |
Sharma A, Kottur J, Narayanan N, Nair DT |
(2013) "A
strategically located serine residue is critical for
the mutator activity of DNA polymerase IV from
Escherichia coli." Nucleic Acids Res.,
41, 5104-5114. doi: 10.1093/nar/gkt146.
|
Structure of polymerase-DNA complex, DNA . SNAP output
|
|
4is1
|
metal binding protein-DNA |
X-ray (2.1 Å) |
Vandevenne M, Jacques DA, Artuz C, Nguyen CD, Kwan
AH, Segal DJ, Matthews JM, Crossley M, Guss JM, Mackay
JP |
(2013) "New
insights into DNA recognition by zinc fingers revealed
by structural analysis of the oncoprotein ZNF217."
J.Biol.Chem., 288,
10616-10627. doi: 10.1074/jbc.M112.441451.
|
Crystal structure of znf217 bound to DNA . SNAP output
|
|
4itq
|
gene regulation, structural protein-DNA |
X-ray (2.7 Å) |
Swiercz JP, Nanji T, Gloyd M, Guarne A, Elliot
MA |
(2013) "A novel
nucleoid-associated protein specific to the
actinobacteria." Nucleic Acids Res.,
41, 4171-4184. doi: 10.1093/nar/gkt095.
|
Crystal structure of hypothetical protein sco1480 bound
to DNA . SNAP output
|
|
4iuf
|
transcription regulator-DNA |
X-ray (2.752 Å) |
Kuo PH, Chiang CH, Wang YT, Doudeva LG, Yuan HS |
(2014) "The
crystal structure of TDP-43 RRM1-DNA complex reveals
the specific recognition for UG- and TG-rich nucleic
acids." Nucleic Acids Res.,
42, 4712-4722. doi: 10.1093/nar/gkt1407.
|
Crystal structure of human tdp-43 rrm1 domain in
complex with a single-stranded DNA . SNAP output
|
|
4ivz
|
transcription-DNA |
X-ray (3.1 Å) |
Martin RN, McGeehan JE, Kneale G |
(2014) "Structural
and Mutagenic Analysis of the RM Controller Protein
C.Esp1396I." Plos One, 9,
e98365. doi: 10.1371/journal.pone.0098365.
|
A y37f mutant of c.esp1396i bound to its highest
affinity operator site om . SNAP output
|
|
4iwr
|
transcription-DNA |
X-ray (2.4 Å) |
Martin RN, McGeehan JE, Ball NJ, Streeter SD, Thresh
SJ, Kneale GG |
(2013) "Structural
analysis of DNA-protein complexes regulating the
restriction-modification system Esp1396I." Acta
Crystallogr.,Sect.F, 69, 962-966.
doi: 10.1107/S174430911302126X.
|
C.esp1396i bound to a 25 base pair operator site .
SNAP output
|
|
4ix7
|
DNA binding protein-DNA |
X-ray (1.581 Å) |
Dai Q, Ren A, Westholm JO, Serganov AA, Patel DJ, Lai
EC |
(2013) "The BEN
domain is a novel sequence-specific DNA-binding domain
conserved in neural transcriptional repressors."
Genes Dev., 27, 602-614. doi:
10.1101/gad.213314.113.
|
Crystal structure of the insv-ben domain complexed to
its DNA target site . SNAP output
|
|
4izz
|
transcription-DNA |
X-ray (2.502 Å) |
Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K,
Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak
A |
(2013) "Structures
of complexes comprised of Fischerella transcription
factor HetR with Anabaena DNA targets."
Proc.Natl.Acad.Sci.USA, 110,
E1716-E1723. doi: 10.1073/pnas.1305971110.
|
Crystal structure of fischerella transcription factor
hetr complexed with 21mer DNA target . SNAP output
|
|
4j00
|
transcription-DNA |
X-ray (3.004 Å) |
Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K,
Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak
A |
(2013) "Structures
of complexes comprised of Fischerella transcription
factor HetR with Anabaena DNA targets."
Proc.Natl.Acad.Sci.USA, 110,
E1716-E1723. doi: 10.1073/pnas.1305971110.
|
Crystal structure of fischerella transcription factor
hetr complexed with 24mer DNA target . SNAP output
|
|
4j01
|
transcription-DNA |
X-ray (3.246 Å) |
Kim Y, Ye Z, Joachimiak G, Videau P, Young J, Hurd K,
Callahan SM, Gornicki P, Zhao J, Haselkorn R, Joachimiak
A |
(2013) "Structures
of complexes comprised of Fischerella transcription
factor HetR with Anabaena DNA targets."
Proc.Natl.Acad.Sci.USA, 110,
E1716-E1723. doi: 10.1073/pnas.1305971110.
|
Crystal structure of fischerella transcription factor
hetr complexed with 29mer DNA target . SNAP output
|
|
4j19
|
transcription-DNA |
X-ray (2.9 Å) |
Kappei D, Butter F, Benda C, Scheibe M, Draskovic I,
Stevense M, Novo CL, Basquin C, Araki M, Araki K, Krastev
DB, Kittler R, Jessberger R, Londono-Vallejo JA, Mann M,
Buchholz F |
(2013) "HOT1 is
a mammalian direct telomere repeat-binding protein
contributing to telomerase recruitment." Embo
J., 32, 1681-1701. doi: 10.1038/emboj.2013.105.
|
Structure of a novel telomere repeat binding protein
bound to DNA . SNAP
output
|
|
4j1j
|
viral protein-DNA |
X-ray (2.65 Å) |
Niu F, Shaw N, Wang YE, Jiao L, Ding W, Li X, Zhu P,
Upur H, Ouyang S, Cheng G, Liu ZJ |
(2013) "Structure
of the Leanyer orthobunyavirus nucleoprotein-RNA
complex reveals unique architecture for RNA
encapsidation." Proc.Natl.Acad.Sci.USA,
110, 9054-9059. doi: 10.1073/pnas.1300035110.
|
Leanyer orthobunyavirus nucleoprotein-ssDNA complex .
SNAP output
|
|
4j2a
|
transferase-DNA |
X-ray (1.8 Å) |
Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg
WH |
(2013) "Alteration
in the cavity size adjacent to the active site of RB69
DNA polymerase changes its conformational
dynamics." Nucleic Acids Res.,
41, 9077-9089. doi: 10.1093/nar/gkt674.
|
Rb69 DNA polymerase l415a ternary complex . SNAP output
|
|
4j2b
|
transferase-DNA |
X-ray (2.04 Å) |
Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg
WH |
(2013) "Alteration
in the cavity size adjacent to the active site of RB69
DNA polymerase changes its conformational
dynamics." Nucleic Acids Res.,
41, 9077-9089. doi: 10.1093/nar/gkt674.
|
Rb69 DNA polymerase l415g ternary complex . SNAP output
|
|
4j2d
|
transferase-DNA |
X-ray (1.76 Å) |
Xia S, Wang J, Konigsberg WH |
"Role of L415 in the Replication of RB69 DNA
Polymerase." |
Rb69 DNA polymerase l415k ternary complex . SNAP output
|
|
4j2e
|
transferase-DNA |
X-ray (2.02 Å) |
Xia S, Wood M, Bradley MJ, De La Cruz EM, Konigsberg
WH |
(2013) "Alteration
in the cavity size adjacent to the active site of RB69
DNA polymerase changes its conformational
dynamics." Nucleic Acids Res.,
41, 9077-9089. doi: 10.1093/nar/gkt674.
|
Rb69 DNA polymerase l415m ternary complex . SNAP output
|
|
4j2x
|
transcription-DNA binding protein-DNA |
X-ray (2.85 Å) |
Collins KJ, Yuan Z, Kovall RA |
(2014) "Structure
and Function of the CSL-KyoT2 Corepressor Complex: A
Negative Regulator of Notch Signaling."
Structure, 22, 70-81. doi:
10.1016/j.str.2013.10.010.
|
Csl (rbp-jk) with corepressor kyot2 bound to DNA .
SNAP output
|
|
4j3n
|
isomerase-DNA |
X-ray (2.3 Å) |
Wu CC, Li YC, Wang YR, Li TK, Chan NL |
(2013) "On the
structural basis and design guidelines for type II
topoisomerase-targeting anticancer drugs."
Nucleic Acids Res., 41,
10630-10640. doi: 10.1093/nar/gkt828.
|
Human topoisomerase iibeta in complex with DNA .
SNAP output
|
|
4j8u
|
structural protein-DNA |
X-ray (2.38 Å) |
Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M,
Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK,
Hartinger CG |
(2013) "Novel metal(II) arene
2-pyridinecarbothioamides: a rationale to orally active
organometallic anticancer agents." CHEM SCI,
4, 1837-1846. doi: 10.1039/C3SC22294B.
|
X-ray structure of ncp145 with
chlorido(eta-6-p-cymene)(n-phenyl-2-pyridinecarbothioamide)osmium(ii)
. SNAP output
|
|
4j8v
|
structural protein-DNA |
X-ray (2.58 Å) |
Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M,
Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK,
Hartinger CG |
(2013) "Novel metal(II) arene
2-pyridinecarbothioamides: a rationale to orally active
organometallic anticancer agents." CHEM SCI,
4, 1837-1846. doi: 10.1039/C3SC22294B.
|
X-ray structure of ncp145 with bound
chlorido(eta-6-p-cymene)(n-phenyl-2-pyridinecarbothioamide)ruthenium(ii)
. SNAP output
|
|
4j8w
|
structural protein-DNA |
X-ray (2.41 Å) |
Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M,
Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK,
Hartinger CG |
(2013) "Novel metal(II) arene
2-pyridinecarbothioamides: a rationale to orally active
organometallic anticancer agents." CHEM SCI,
4, 1837-1846. doi: 10.1039/C3SC22294B.
|
X-ray structure of ncp145 with
chlorido(eta-6-p-cymene)(n-fluorophenyl-2-pyridinecarbothioamide)osmium(ii)
. SNAP output
|
|
4j8x
|
structural protein-DNA |
X-ray (2.87 Å) |
Meier SM, Hanif M, Adhireksan Z, Pichler V, Novak M,
Jirkovsky E, Jakupec MA, Arion VB, Davey CA, Keppler BK,
Hartinger CG |
(2013) "Novel metal(II) arene
2-pyridinecarbothioamides: a rationale to orally active
organometallic anticancer agents." CHEM SCI,
4, 1837-1846. doi: 10.1039/C3SC22294B.
|
X-ray structure of ncp145 with bound
chlorido(eta-6-p-cymene)(n-fluorophenyl-2-pyridinecarbothioamide)ruthenium(ii)
. SNAP output
|
|
4j9k
|
transferase-DNA |
X-ray (2.03 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA ternary complex:
misincorporation g opposite t after a t at the primer
3' end (ta-g) . SNAP
output
|
|
4j9l
|
transferase-DNA |
X-ray (1.85 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA ternary complex:
misincorporation g opposite t after a c at the primer
3' end (ca-g) . SNAP
output
|
|
4j9m
|
transferase-DNA |
X-ray (2.25 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA ternary complex:
misincorporation g opposite t after an a at the primer
3' end (aa-g) . SNAP
output
|
|
4j9n
|
transferase-DNA |
X-ray (1.956 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA ternary complex:
misincorporation g opposite t after a g at the primer
3' end (ga-g) . SNAP
output
|
|
4j9o
|
transferase-DNA |
X-ray (2.597 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA ternary complex: primer
extension after a t:g mispair . SNAP output
|
|
4j9p
|
transferase-DNA |
X-ray (2.3 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA postinsertion binary
complex with ta base pair . SNAP output
|
|
4j9q
|
transferase-DNA |
X-ray (1.96 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA postinsertion binary
complex with tg mispair . SNAP output
|
|
4j9r
|
transferase-DNA |
X-ray (2.35 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA translocated binary
complex with tg mispair . SNAP output
|
|
4j9s
|
transferase-DNA |
X-ray (1.95 Å) |
Zhao Y, Gregory MT, Biertumpfel C, Hua YJ, Hanaoka F,
Yang W |
(2013) "Mechanism
of somatic hypermutation at the WA motif by human DNA
polymerase eta." Proc.Natl.Acad.Sci.USA,
110, 8146-8151. doi: 10.1073/pnas.1303126110.
|
Human DNA polymerase eta-DNA translocated binary
complex: with ta base pair . SNAP output
|
|
4jbk
|
DNA binding protein-DNA |
X-ray (2.963 Å) |
Ru H, Ni X, Zhao L, Crowley C, Ding W, Hung L-W, Shaw
N, Cheng G, Liu Z-J |
(2013) "Structural
basis for termination of AIM2-mediated signaling by
p202." Cell Res., 23,
855-858. doi: 10.1038/cr.2013.52.
|
Molecular basis for abrogation of activation of
pro-inflammatory cytokines . SNAP output
|
|
4jbm
|
DNA binding protein-DNA |
X-ray (2.218 Å) |
Ru H, Ni X, Zhao L, Crowley C, Ding W, Hung L-W, Shaw
N, Cheng G, Liu Z-J |
(2013) "Structural
basis for termination of AIM2-mediated signaling by
p202." Cell Res., 23,
855-858. doi: 10.1038/cr.2013.52.
|
Structure of murine DNA binding protein bound with ds
DNA . SNAP output
|
|
4jcx
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A,
McGeehan JE, Kneale GG |
(2015) "Structural
analysis of DNA binding by C.Csp231I, a member of a
novel class of R-M controller proteins regulating gene
expression." Acta Crystallogr.,Sect.D,
71, 398-407. doi: 10.1107/S139900471402690X.
|
Crystal structure of the restriction-modification
controller protein c.csp231i ol operator complex .
SNAP output
|
|
4jcy
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A,
McGeehan JE, Kneale GG |
(2015) "Structural
analysis of DNA binding by C.Csp231I, a member of a
novel class of R-M controller proteins regulating gene
expression." Acta Crystallogr.,Sect.D,
71, 398-407. doi: 10.1107/S139900471402690X.
|
Crystal structure of the restriction-modification
controller protein c.csp231i or operator complex .
SNAP output
|
|
4jgc
|
hydrolase-DNA |
X-ray (2.582 Å) |
Hashimoto H, Zhang X, Cheng X |
(2013) "Activity
and crystal structure of human thymine DNA glycosylase
mutant N140A with 5-carboxylcytosine DNA at low
pH." Dna Repair, 12,
535-540. doi: 10.1016/j.dnarep.2013.04.003.
|
Human tdg n140a mutant in a complex with
5-carboxylcytosine (5cac) . SNAP output
|
|
4jjn
|
DNA binding protein-DNA |
X-ray (3.09 Å) |
Wang F, Li G, Altaf M, Lu C, Currie MA, Johnson A,
Moazed D |
(2013) "Heterochromatin
protein Sir3 induces contacts between the amino
terminus of histone H4 and nucleosomal DNA."
Proc.Natl.Acad.Sci.USA, 110,
8495-8500. doi: 10.1073/pnas.1300126110.
|
Crystal structure of heterochromatin protein sir3 in
complex with a silenced yeast nucleosome . SNAP output
|
|
4jl3
|
transcription-DNA |
X-ray (2.5 Å) |
Yang S, Gao Z, Li T, Yang M, Zhang T, Dong Y, He
ZG |
(2013) "Structural
basis for interaction between Mycobacterium smegmatis
Ms6564, a TetR family master regulator, and its target
DNA." J.Biol.Chem., 288,
23687-23695. doi: 10.1074/jbc.M113.468694.
|
Crystal structure of ms6564-DNA complex . SNAP output
|
|
4jqd
|
transcription-DNA |
X-ray (2.75 Å) |
Shevtsov MB, Streeter SD, Thresh SJ, Swiderska A,
McGeehan JE, Kneale GG |
(2015) "Structural
analysis of DNA binding by C.Csp231I, a member of a
novel class of R-M controller proteins regulating gene
expression." Acta Crystallogr.,Sect.D,
71, 398-407. doi: 10.1107/S139900471402690X.
|
Crystal structure of the restriction-modification
controller protein c.csp231i ol operator complex .
SNAP output
|
|
4jrp
|
hydrolase-DNA |
X-ray (1.95 Å) |
Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA,
Bell CE |
(2013) "Crystal
structures of Escherichia coli exonuclease I in complex
with single-stranded DNA provide insights into the
mechanism of processive digestion." Nucleic
Acids Res., 41, 5887-5897. doi:
10.1093/nar/gkt278.
|
Structure of e. coli exonuclease i in complex with a
5cy-dt13 oligonucleotide . SNAP output
|
|
4jrq
|
hydrolase-DNA |
X-ray (3.0 Å) |
Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA,
Bell CE |
(2013) "Crystal
structures of Escherichia coli exonuclease I in complex
with single-stranded DNA provide insights into the
mechanism of processive digestion." Nucleic
Acids Res., 41, 5887-5897. doi:
10.1093/nar/gkt278.
|
Crystal structure of e. coli exonuclease i in complex
with a 5cy-da13 oligonucleotide . SNAP output
|
|
4js4
|
hydrolase-DNA |
X-ray (3.1 Å) |
Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA,
Bell CE |
(2013) "Crystal
structures of Escherichia coli exonuclease I in complex
with single-stranded DNA provide insights into the
mechanism of processive digestion." Nucleic
Acids Res., 41, 5887-5897. doi:
10.1093/nar/gkt278.
|
Crystal structure of e. coli exonuclease i in complex
with a da16 oligonucleotide . SNAP output
|
|
4js5
|
hydrolase-DNA |
X-ray (3.5 Å) |
Korada SK, Johns TD, Smith CE, Jones ND, McCabe KA,
Bell CE |
(2013) "Crystal
structures of Escherichia coli exonuclease I in complex
with single-stranded DNA provide insights into the
mechanism of processive digestion." Nucleic
Acids Res., 41, 5887-5897. doi:
10.1093/nar/gkt278.
|
Crystal structure of e. coli exonuclease i in complex
with a dt13 oligonucleotide . SNAP output
|
|
4juo
|
isomerase-DNA |
X-ray (6.53 Å) |
Laponogov I, Veselkov DA, Crevel IM, Pan XS, Fisher
LM, Sanderson MR |
(2013) "Structure
of an 'open' clamp type II topoisomerase-DNA complex
provides a mechanism for DNA capture and
transport." Nucleic Acids Res.,
41, 9911-9923. doi: 10.1093/nar/gkt749.
|
A low-resolution three-gate structure of topoisomerase
iv from streptococcus pneumoniae in space group h32 .
SNAP output
|
|
4juz
|
transferase-DNA |
X-ray (2.65 Å) |
Shanmugam G, Minko IG, Banerjee S, Christov PP,
Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP |
(2013) "Ring-Opening
of the gamma-OH-PdG Adduct Promotes Error-Free Bypass
by the Sulfolobus solfataricus DNA Polymerase
Dpo4." Chem.Res.Toxicol.,
26, 1348-1360. doi: 10.1021/tx400200b.
|
Ternary complex of gamma-ohpdg adduct modified DNA
(zero primer) with DNA polymerase iv and incoming dgtp
. SNAP output
|
|
4jv0
|
transferase-DNA |
X-ray (2.95 Å) |
Shanmugam G, Minko IG, Banerjee S, Christov PP,
Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP |
(2013) "Ring-Opening
of the gamma-OH-PdG Adduct Promotes Error-Free Bypass
by the Sulfolobus solfataricus DNA Polymerase
Dpo4." Chem.Res.Toxicol.,
26, 1348-1360. doi: 10.1021/tx400200b.
|
Ring-opening of the -oh-pdg adduct in ternary complexes
with the sulfolobus solfataricus DNA polymerase dpo4 .
SNAP output
|
|
4jv1
|
transferase-DNA |
X-ray (2.3 Å) |
Shanmugam G, Minko IG, Banerjee S, Christov PP,
Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP |
(2013) "Ring-Opening
of the gamma-OH-PdG Adduct Promotes Error-Free Bypass
by the Sulfolobus solfataricus DNA Polymerase
Dpo4." Chem.Res.Toxicol.,
26, 1348-1360. doi: 10.1021/tx400200b.
|
Ternary complex of gamma-ohpdg adduct modified DNA with
DNA (-1 primer) polymerase iv and incoming dgtp .
SNAP output
|
|
4jv2
|
transferase-DNA |
X-ray (2.74 Å) |
Shanmugam G, Minko IG, Banerjee S, Christov PP,
Kozekov ID, Rizzo CJ, Lloyd RS, Egli M, Stone MP |
(2013) "Ring-Opening
of the gamma-OH-PdG Adduct Promotes Error-Free Bypass
by the Sulfolobus solfataricus DNA Polymerase
Dpo4." Chem.Res.Toxicol.,
26, 1348-1360. doi: 10.1021/tx400200b.
|
Ternary complex of gamma-ohpdg adduct modified DNA with
DNA (-1 primer) polymerase iv and incoming datp .
SNAP output
|
|
4jwm
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Perera L, Lin P, Shock DD, Beard WA,
Pedersen LC, Pedersen LG, Wilson SH |
(2013) "Amino
Acid Substitution in the Active Site of DNA Polymerase
beta Explains the Energy Barrier of the Nucleotidyl
Transfer Reaction." J.Am.Chem.Soc.,
135, 8078-8088. doi: 10.1021/ja403842j.
|
Ternary complex of d256e mutant of DNA polymerase beta
. SNAP output
|
|
4jwn
|
transferase-DNA |
X-ray (2.39 Å) |
Batra VK, Perera L, Lin P, Shock DD, Beard WA,
Pedersen LC, Pedersen LG, Wilson SH |
(2013) "Amino
Acid Substitution in the Active Site of DNA Polymerase
beta Explains the Energy Barrier of the Nucleotidyl
Transfer Reaction." J.Am.Chem.Soc.,
135, 8078-8088. doi: 10.1021/ja403842j.
|
Ternary complex of d256a mutant of DNA polymerase beta
. SNAP output
|
|
4jzu
|
hydrolase-RNA |
X-ray (1.7 Å) |
Piton J, Larue V, Thillier Y, Dorleans A, Pellegrini
O, Li de la Sierra-Gallay I, Vasseur JJ, Debart F, Tisne
C, Condon C |
(2013) "Bacillus
subtilis RNA deprotection enzyme RppH recognizes
guanosine in the second position of its
substrates." Proc.Natl.Acad.Sci.USA,
110, 8858-8863. doi: 10.1073/pnas.1221510110.
|
Crystal structure of the bacillus subtilis
pyrophosphohydrolase bsrpph bound to a non-hydrolysable
triphosphorylated dinucleotide RNA (pcp-pgpg) - first
guanosine residue in guanosine binding pocket .
SNAP output
|
|
4k1g
|
hydrolase-DNA |
X-ray (1.9 Å) |
Mazouzi A, Vigouroux A, Aikeshev B, Brooks PJ,
Saparbaev MK, Morera S, Ishchenko AA |
(2013) "Insight
into mechanisms of 3'-5' exonuclease activity and
removal of bulky 8,5'-cyclopurine adducts by
apurinic/apyrimidinic endonucleases."
Proc.Natl.Acad.Sci.USA, 110,
E3071-E3080. doi: 10.1073/pnas.1305281110.
|
Structure of e. coli nfo(endo iv)-h69a mutant bound to
a cleaved DNA duplex containing a alphada:t basepair .
SNAP output
|
|
4k4g
|
transferase-DNA |
X-ray (2.15 Å) |
Vyas R, Zahurancik WJ, Suo Z |
(2014) "Structural
basis for the binding and incorporation of nucleotide
analogs with L-stereochemistry by human DNA polymerase
lambda." Proc.Natl.Acad.Sci.USA,
111, E3033-E3042. doi: 10.1073/pnas.1401286111.
|
Ternary crystal structures of human DNA polymerase
lambda in complex with DNA and l-dctp. . SNAP output
|
|
4k4h
|
transferase-DNA |
X-ray (2.1 Å) |
Vyas R, Zahurancik WJ, Suo Z |
(2014) "Structural
basis for the binding and incorporation of nucleotide
analogs with L-stereochemistry by human DNA polymerase
lambda." Proc.Natl.Acad.Sci.USA,
111, E3033-E3042. doi: 10.1073/pnas.1401286111.
|
Ternary crystal structures of a human DNA polymerase
lambda in complex with DNA and (-)3tc-tp. . SNAP output
|
|
4k4i
|
transferase-DNA |
X-ray (2.25 Å) |
Vyas R, Zahurancik WJ, Suo Z |
(2014) "Structural
basis for the binding and incorporation of nucleotide
analogs with L-stereochemistry by human DNA polymerase
lambda." Proc.Natl.Acad.Sci.USA,
111, E3033-E3042. doi: 10.1073/pnas.1401286111.
|
Ternary crystal structures of a human DNA polymerase
lambda in complex with DNA and (-)ftc-tp. . SNAP output
|
|
4k8x
|
transferase-DNA |
X-ray (2.28 Å) |
Bergen K, Betz K, Welte W, Diederichs K, Marx A |
(2013) "Structures
of KOD and 9N DNA Polymerases Complexed with Primer
Template Duplex." Chembiochem,
14, 1058-1062. doi: 10.1002/cbic.201300175.
|
Binary complex of 9n DNA polymerase in the replicative
state . SNAP output
|
|
4k8z
|
transferase-DNA |
X-ray (2.29 Å) |
Bergen K, Betz K, Welte W, Diederichs K, Marx A |
(2013) "Structures
of KOD and 9N DNA Polymerases Complexed with Primer
Template Duplex." Chembiochem,
14, 1058-1062. doi: 10.1002/cbic.201300175.
|
Kod polymerase in binary complex with dsDNA . SNAP output
|
|
4k96
|
transferase-DNA |
X-ray (2.084 Å) |
Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL,
Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G,
Tuschl T, Patel DJ |
(2013) "Cyclic
[G(2',5')pA(3',5')p] is the metazoan second messenger
produced by DNA-activated cyclic GMP-AMP synthase."
Cell(Cambridge,Mass.), 153,
1094-1107. doi: 10.1016/j.cell.2013.04.046.
|
Structure of binary complex of cgas with bound dsDNA .
SNAP output
|
|
4k97
|
transferase-DNA |
X-ray (2.41 Å) |
Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL,
Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G,
Tuschl T, Patel DJ |
(2013) "Cyclic
[G(2',5')pA(3',5')p] is the metazoan second messenger
produced by DNA-activated cyclic GMP-AMP synthase."
Cell(Cambridge,Mass.), 153,
1094-1107. doi: 10.1016/j.cell.2013.04.046.
|
Structure of ternary complex of cgas with dsDNA and
bound atp . SNAP
output
|
|
4k98
|
transferase-DNA |
X-ray (1.94 Å) |
Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL,
Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G,
Tuschl T, Patel DJ |
(2013) "Cyclic
[G(2',5')pA(3',5')p] is the metazoan second messenger
produced by DNA-activated cyclic GMP-AMP synthase."
Cell(Cambridge,Mass.), 153,
1094-1107. doi: 10.1016/j.cell.2013.04.046.
|
Structure of ternary complex of cgas with dsDNA and
bound 5 -pppg(2 ,5 )pg . SNAP output
|
|
4k99
|
transferase-DNA |
X-ray (1.95 Å) |
Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL,
Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G,
Tuschl T, Patel DJ |
(2013) "Cyclic
[G(2',5')pA(3',5')p] is the metazoan second messenger
produced by DNA-activated cyclic GMP-AMP synthase."
Cell(Cambridge,Mass.), 153,
1094-1107. doi: 10.1016/j.cell.2013.04.046.
|
Structure of ternary complex of cgas with dsDNA and
bound 5 -pppdg(2 ,5 )pdg . SNAP output
|
|
4k9a
|
transferase-DNA |
X-ray (2.264 Å) |
Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL,
Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G,
Tuschl T, Patel DJ |
(2013) "Cyclic
[G(2',5')pA(3',5')p] is the metazoan second messenger
produced by DNA-activated cyclic GMP-AMP synthase."
Cell(Cambridge,Mass.), 153,
1094-1107. doi: 10.1016/j.cell.2013.04.046.
|
Structure of ternary complex of cgas with dsDNA and
bound 5 -pg(2 ,5 )pa . SNAP output
|
|
4k9b
|
transferase-DNA |
X-ray (2.26 Å) |
Gao P, Ascano M, Wu Y, Barchet W, Gaffney BL,
Zillinger T, Serganov AA, Liu Y, Jones RA, Hartmann G,
Tuschl T, Patel DJ |
(2013) "Cyclic
[G(2',5')pA(3',5')p] is the metazoan second messenger
produced by DNA-activated cyclic GMP-AMP synthase."
Cell(Cambridge,Mass.), 153,
1094-1107. doi: 10.1016/j.cell.2013.04.046.
|
Structure of ternary complex of cgas with dsDNA and
bound c[g(2 ,5 )pa(3 ,5 )p] . SNAP output
|
|
4ka4
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Athanasiadis A, de Rosa M, De Sanctis D |
"Crystal structure of a proteolytically defined Zbeta
domain of human DAI (ZBP1, DLM-1)." |
Crystal structure of a proteolytically defined zbeta
domain of human dai (zbp1, dlm-1) . SNAP output
|
|
4kaz
|
hydrolase-DNA |
X-ray (1.9 Å) |
Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS |
(2014) "Structural
insights into DNA repair by RNase T--an exonuclease
processing 3' end of structured DNA in repair
pathways." Plos Biol.,
12, e1001803. doi: 10.1371/journal.pbio.1001803.
|
Crystal structure of rnase t in complex with a y
structured DNA . SNAP
output
|
|
4kb0
|
hydrolase-DNA |
X-ray (2.004 Å) |
Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS |
(2014) "Structural
insights into DNA repair by RNase T--an exonuclease
processing 3' end of structured DNA in repair
pathways." Plos Biol.,
12, e1001803. doi: 10.1371/journal.pbio.1001803.
|
Crystal structure of rnase t in complex with a bluge
DNA (two nucleotide insertion cc ) . SNAP output
|
|
4kb1
|
hydrolase-DNA |
X-ray (1.8 Å) |
Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS |
(2014) "Structural
insights into DNA repair by RNase T--an exonuclease
processing 3' end of structured DNA in repair
pathways." Plos Biol.,
12, e1001803. doi: 10.1371/journal.pbio.1001803.
|
Crystal structure of rnase t in complex with a bluge
DNA (two nucleotide insertion ct ) . SNAP output
|
|
4kb6
|
transferase-DNA |
X-ray (3.08 Å) |
Civril F, Deimling T, de Oliveira Mann CC, Ablasser
A, Moldt M, Witte G, Hornung V, Hopfner KP |
(2013) "Structural
mechanism of cytosolic DNA sensing by cGAS."
Nature, 498, 332-337. doi:
10.1038/nature12305.
|
Structure of porcine cyclic gmp amp synthase (cgas) in
complex with DNA, atp and gtp . SNAP output
|
|
4kdp
|
transcription-DNA |
X-ray (3.6 Å) |
Chang YM, Ho CH, Chen CK, Maestre-Reyna M,
Chang-Chien MW, Wang AH |
(2014) "TcaR-ssDNA
complex crystal structure reveals new DNA binding
mechanism of the MarR family proteins." Nucleic
Acids Res., 42, 5314-5321. doi:
10.1093/nar/gku128.
|
Tcar-ssDNA complex crystal structure reveals the novel
ssDNA binding mechanism of the marr family proteins .
SNAP output
|
|
4kfc
|
transcription regulator-DNA |
X-ray (2.53 Å) |
Narayanan A, Kumar S, Evrard AN, Paul LN, Yernool
DA |
(2014) "An
asymmetric heterodomain interface stabilizes a response
regulator-DNA complex." Nat Commun,
5, 3282. doi: 10.1038/ncomms4282.
|
Crystal structure of a hyperactive mutant of response
regulator kdpe complexed to its promoter DNA . SNAP output
|
|
4kgc
|
structural protein-DNA |
X-ray (2.69 Å) |
Adhireksan Z, Davey GE, Campomanes P, Groessl M,
Clavel CM, Yu H, Nazarov AA, Yeo CH, Ang WH, Droge P,
Rothlisberger U, Dyson PJ, Davey CA |
(2014) "Ligand
substitutions between ruthenium-cymene compounds can
control protein versus DNA targeting and anticancer
activity." Nat Commun, 5,
3462. doi: 10.1038/ncomms4462.
|
Nucleosome core particle containing (eta6-p-cymene)-(1,
2-ethylenediamine)-ruthenium . SNAP output
|
|
4khn
|
hydrolase, transferase-DNA |
X-ray (2.55 Å) |
Jacewicz A, Trzemecka A, Guja KE, Plochocka D,
Yakubovskaya E, Bebenek A, Garcia-Diaz M |
(2013) "A Remote
Palm Domain Residue of RB69 DNA Polymerase Is Critical
for Enzyme Activity and Influences the Conformation of
the Active Site." Plos One,
8, e76700. doi: 10.1371/journal.pone.0076700.
|
Crystal structure of the ternary complex of the d714a
mutant of rb69 DNA polymerase . SNAP output
|
|
4khq
|
transferase-DNA |
X-ray (2.186 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f wit dumpnpp .
SNAP output
|
|
4khs
|
transferase-DNA |
X-ray (2.12 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f with a
ribonucleotide at 0 position . SNAP output
|
|
4khu
|
transferase-DNA |
X-ray (2.05 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f with a
ribonucleotide at -1 position . SNAP output
|
|
4khw
|
transferase-DNA |
X-ray (2.371 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f with
ribonucleotide at -2 position . SNAP output
|
|
4khy
|
transferase-DNA |
X-ray (2.25 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f with
ribonucleotide at -3 position . SNAP output
|
|
4ki2
|
transcription-DNA |
X-ray (3.3 Å) |
Feklistov A, Darst SA |
(2013) "Crystallographic
analysis of an RNA polymerase sigma-subunit fragment
complexed with -10 promoter element ssDNA: quadruplex
formation as a possible tool for engineering crystal
contacts in protein-ssDNA complexes." Acta
Crystallogr.,Sect.F, 69, 950-955.
doi: 10.1107/S1744309113020368.
|
Crystallographic analysis of an RNA-polymerase
sigma-subunit fragment complexed with -10 promoter
element ssDNA . SNAP
output
|
|
4ki4
|
transferase-DNA |
X-ray (2.45 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f with
ribonucleotides at 0 and -1 position . SNAP output
|
|
4ki6
|
transferase-DNA |
X-ray (2.55 Å) |
Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel
TA |
(2013) "Structure-function
analysis of ribonucleotide bypass by B family DNA
replicases." Proc.Natl.Acad.Sci.USA,
110, 16802-16807. doi: 10.1073/pnas.1309119110.
|
Ternary complex of rb69 mutant l415f with
ribonucleotides at -1 and -2 position . SNAP output
|
|
4kis
|
recombination-DNA |
X-ray (3.2 Å) |
Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne
GD |
(2013) "Attachment
site recognition and regulation of directionality by
the serine integrases." Nucleic Acids
Res., 41, 8341-8356. doi:
10.1093/nar/gkt580.
|
Crystal structure of a lsr-DNA complex . SNAP output
|
|
4kld
|
transferase, lyase-DNA |
X-ray (1.916 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched substrate complex with
ca2+, 0 s . SNAP
output
|
|
4kle
|
transferase, lyase-DNA |
X-ray (1.97 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched reactant complex with mg2+,
10 s . SNAP output
|
|
4klf
|
transferase, lyase-DNA |
X-ray (1.85 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched reactant complex with mg2+,
20 s . SNAP output
|
|
4klg
|
transferase, lyase-DNA |
X-ray (1.701 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched product complex with mg2+,
40 s . SNAP output
|
|
4klh
|
transferase, lyase-DNA |
X-ray (1.876 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched product complex with mn2+,
40 s . SNAP output
|
|
4kli
|
transferase, lyase-DNA |
X-ray (1.597 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched product complex with mg2+,
90 s . SNAP output
|
|
4klj
|
transferase, lyase-DNA |
X-ray (1.799 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched product complex with mg2+,
5 min . SNAP output
|
|
4kll
|
transferase, lyase-DNA |
X-ray (1.841 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched product complex with mg2+,
45 min . SNAP output
|
|
4klm
|
transferase, lyase-DNA |
X-ray (1.747 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched product complex with mg2+,
11 h . SNAP output
|
|
4klo
|
transferase, lyase-DNA |
X-ray (1.845 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta matched nick complex with mg2+ and
ppi, 30 min . SNAP
output
|
|
4klq
|
transferase, lyase-DNA |
X-ray (1.999 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
Observing a DNA polymerase choose right from wrong. .
SNAP output
|
|
4kls
|
transferase, lyase-DNA |
X-ray (1.978 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta mismatched reactant complex with
mn2+, 10 min . SNAP
output
|
|
4klt
|
transferase, lyase-DNA |
X-ray (1.979 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta mismatched product complex with
mn2+, 30 min . SNAP
output
|
|
4klu
|
transferase, lyase-DNA |
X-ray (1.97 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta mismatched product complex with
mn2+, 15 h . SNAP
output
|
|
4kmf
|
transferase-DNA |
X-ray (1.7 Å) |
Kim D, Hur J, Park K, Bae S, Shin D, Ha SC, Hwang HY,
Hohng S, Lee JH, Lee S, Kim YG, Kim KK |
(2014) "Distinct
Z-DNA binding mode of a PKR-like protein kinase
containing a Z-DNA binding domain (PKZ)."
Nucleic Acids Res., 42,
5937-5948. doi: 10.1093/nar/gku189.
|
Crystal structure of zalpha domain from carassius
auratus pkz in complex with z-DNA . SNAP output
|
|
4kny
|
transcription regulator-DNA |
X-ray (2.945 Å) |
Narayanan A, Kumar S, Evrard AN, Paul LN, Yernool
DA |
(2014) "An
asymmetric heterodomain interface stabilizes a response
regulator-DNA complex." Nat Commun,
5, 3282. doi: 10.1038/ncomms4282.
|
Crystal structure of the response regulator kdpe
complexed to DNA in an active-like conformation .
SNAP output
|
|
4koe
|
isomerase-DNA-inhibitor |
X-ray (3.02 Å) |
Laponogov I, Pan X-S, Veselkov DA, Fisher LM,
Sanderson MR |
"Inhibitor-stabilised cleavage complexes of
topoisomerase IIa: structural analysis of drug-dependent
inter- and intramolecular interactions." |
Quinolone(trovafloxacin)-DNA cleavage complex of type
iv topoisomerase from s. pneumoniae . SNAP output
|
|
4kpe
|
isomerase-DNA-inhibitor |
X-ray (3.43 Å) |
Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A,
Moser HE, Fisher LM, Sanderson MR |
(2016) "Exploring
the active site of the Streptococcus pneumoniae
topoisomerase IV-DNA cleavage complex with novel
7,8-bridged fluoroquinolones." Open Biol,
6. doi: 10.1098/rsob.160157.
|
Novel fluoroquinolones in complex with topoisomerase iv
from s. pneumoniae and e-site g-gate . SNAP output
|
|
4kpf
|
isomerase-DNA-inhibitor |
X-ray (3.24 Å) |
Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A,
Moser HE, Fisher LM, Sanderson MR |
(2016) "Exploring
the active site of the Streptococcus pneumoniae
topoisomerase IV-DNA cleavage complex with novel
7,8-bridged fluoroquinolones." Open Biol,
6. doi: 10.1098/rsob.160157.
|
Novel fluoroquinolones in complex with topoisomerase iv
from s. pneumoniae and e-site g-gate . SNAP output
|
|
4kpy
|
DNA binding protein-DNA |
X-ray (2.406 Å) |
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC,
van der Oost J, Patel DJ, Wang Y |
(2014) "Structure-based
cleavage mechanism of Thermus thermophilus Argonaute
DNA guide strand-mediated DNA target cleavage."
Proc.Natl.Acad.Sci.USA, 111,
652-657. doi: 10.1073/pnas.1321032111.
|
DNA binding protein and DNA complex structure .
SNAP output
|
|
4ktq
|
transferase-DNA |
X-ray (2.5 Å) |
Li Y, Korolev S, Waksman G |
(1998) "Crystal
structures of open and closed forms of binary and
ternary complexes of the large fragment of Thermus
aquaticus DNA polymerase I: structural basis for
nucleotide incorporation." EMBO J.,
17, 7514-7525. doi: 10.1093/emboj/17.24.7514.
|
Binary complex of the large fragment of DNA polymerase
i from t. aquaticus bound to a primer-template DNA .
SNAP output
|
|
4kud
|
structural protein-transcription-DNA |
X-ray (3.203 Å) |
Yang D, Fang Q, Wang M, Ren R, Wang H, He M, Sun Y,
Yang N, Xu RM |
(2013) "N
alpha-acetylated Sir3 stabilizes the conformation of a
nucleosome-binding loop in the BAH domain."
Nat.Struct.Mol.Biol., 20,
1116-1118. doi: 10.1038/nsmb.2637.
|
Crystal structure of n-terminal acetylated sir3 bah
domain d205n mutant in complex with yeast nucleosome
core particle . SNAP
output
|
|
4kxt
|
hydrolase-RNA |
X-ray (2.294 Å) |
Nakanishi K, Ascano M, Gogakos T, Ishibe-Murakami S,
Serganov AA, Briskin D, Morozov P, Tuschl T, Patel
DJ |
(2013) "Eukaryote-Specific
Insertion Elements Control Human ARGONAUTE Slicer
Activity." Cell Rep, 3,
1893-1900. doi: 10.1016/j.celrep.2013.06.010.
|
Structure of human argonaute1 in complex with guide RNA
. SNAP output
|
|
4kyw
|
hydrolase-DNA |
X-ray (2.35 Å) |
Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M,
Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler
M |
(2014) "Structural
basis of the methylation specificity of R.DpnI."
Nucleic Acids Res., 42,
8745-8754. doi: 10.1093/nar/gku546.
|
Restriction endonuclease dpni in complex with two DNA
molecules . SNAP
output
|
|
4kzx
|
ribosome |
X-ray (7.809 Å) |
Lomakin IB, Steitz TA |
(2013) "The
initiation of mammalian protein synthesis and mRNA
scanning mechanism." Nature,
500, 307-311. doi: 10.1038/nature12355.
|
Rabbit 40s ribosomal subunit in complex with eif1. .
SNAP output
|
|
4kzy
|
ribosome |
X-ray (7.01 Å) |
Lomakin IB, Steitz TA |
(2013) "The
initiation of mammalian protein synthesis and mRNA
scanning mechanism." Nature,
500, 307-311. doi: 10.1038/nature12355.
|
Rabbit 40s ribosomal subunit in complex with eif1 and
eif1a. . SNAP output
|
|
4kzz
|
ribosome |
X-ray (7.03 Å) |
Lomakin IB, Steitz TA |
(2013) "The
initiation of mammalian protein synthesis and mRNA
scanning mechanism." Nature,
500, 307-311. doi: 10.1038/nature12355.
|
Rabbit 40s ribosomal subunit in complex with mrna,
initiator trna and eif1a . SNAP output
|
|
4l0y
|
transcription-DNA |
X-ray (2.5 Å) |
Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI,
Rizzino A, Tahirov TH |
(2014) "Structural
basis of Ets1 activation by Runx1."
Leukemia, 28, 2040-2048. doi:
10.1038/leu.2014.111.
|
Crystal structure of runx1 and ets1 bound to tcr alpha
promoter (crystal form 1) . SNAP output
|
|
4l0z
|
transcription-DNA |
X-ray (2.7 Å) |
Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI,
Rizzino A, Tahirov TH |
(2014) "Structural
basis of Ets1 activation by Runx1."
Leukemia, 28, 2040-2048. doi:
10.1038/leu.2014.111.
|
Crystal structure of runx1 and ets1 bound to tcr alpha
promoter (crystal form 2) . SNAP output
|
|
4l18
|
transcription-DNA |
X-ray (2.3 Å) |
Shrivastava T, Mino K, Babayeva ND, Baranovskaya OI,
Rizzino A, Tahirov TH |
(2014) "Structural
basis of Ets1 activation by Runx1."
Leukemia, 28, 2040-2048. doi:
10.1038/leu.2014.111.
|
Crystal structure of runx1 and ets1 bound to tcr alpha
promoter (crystal form 3) . SNAP output
|
|
4l5r
|
DNA binding protein-DNA |
X-ray (1.873 Å) |
Yin Q, Sester DP, Tian Y, Hsiao YS, Lu A, Cridland
JA, Sagulenko V, Thygesen SJ, Choubey D, Hornung V, Walz
T, Stacey KJ, Wu H |
(2013) "Molecular
Mechanism for p202-Mediated Specific Inhibition of AIM2
Inflammasome Activation." Cell Rep,
4, 327-339. doi: 10.1016/j.celrep.2013.06.024.
|
Crystal structure of p202 hin1 in complex with 20-mer
dsDNA . SNAP output
|
|
4l5s
|
DNA binding protein-DNA |
X-ray (2.94 Å) |
Yin Q, Sester DP, Tian Y, Hsiao YS, Lu A, Cridland
JA, Sagulenko V, Thygesen SJ, Choubey D, Hornung V, Walz
T, Stacey KJ, Wu H |
(2013) "Molecular
Mechanism for p202-Mediated Specific Inhibition of AIM2
Inflammasome Activation." Cell Rep,
4, 327-339. doi: 10.1016/j.celrep.2013.06.024.
|
P202 hin1 in complex with 12-mer dsDNA . SNAP output
|
|
4l62
|
transcription-DNA |
X-ray (2.9 Å) |
Kim Y, Kang Y, Choe J |
(2013) "Crystal
structure of Pseudomonas aeruginosa transcriptional
regulator PA2196 bound to its operator DNA."
Biochem.Biophys.Res.Commun.,
440, 317-321. doi: 10.1016/j.bbrc.2013.09.074.
|
Crystal structure of pseudomonas aeruginosa
transcriptional regulator pa2196 bound to its operator
DNA . SNAP output
|
|
4lb5
|
transferase-DNA |
X-ray (2.0 Å) |
de Rosa M, Zacarias S, Athanasiadis A |
(2013) "Structural
basis for Z-DNA binding and stabilization by the
zebrafish Z-DNA dependent protein kinase PKZ."
Nucleic Acids Res., 41,
9924-9933. doi: 10.1093/nar/gkt743.
|
Crystal structure of pkz zalpha in complex with ds(cg)6
(hexagonal form) . SNAP
output
|
|
4lb6
|
transferase-DNA |
X-ray (1.8 Å) |
de Rosa M, Zacarias S, Athanasiadis A |
(2013) "Structural
basis for Z-DNA binding and stabilization by the
zebrafish Z-DNA dependent protein kinase PKZ."
Nucleic Acids Res., 41,
9924-9933. doi: 10.1093/nar/gkt743.
|
Crystal structure of pkz zalpha in complex with ds(cg)6
(tetragonal form) . SNAP
output
|
|
4ld0
|
hydrolase-DNA |
X-ray (3.75 Å) |
Gorecka KM, Komorowska W, Nowotny M |
(2013) "Crystal
structure of RuvC resolvase in complex with Holliday
junction substrate." Nucleic Acids Res.,
41, 9945-9955. doi: 10.1093/nar/gkt769.
|
T. thermophilus ruvc in complex with holliday junction
substrate . SNAP
output
|
|
4ld9
|
nuclear protein-transcription-DNA |
X-ray (3.306 Å) |
Arnaudo N, Fernandez IS, McLaughlin SH, Peak-Chew SY,
Rhodes D, Martino F |
(2013) "The
N-terminal acetylation of Sir3 stabilizes its binding
to the nucleosome core particle."
Nat.Struct.Mol.Biol., 20,
1119-1121. doi: 10.1038/nsmb.2641.
|
Crystal structure of the n-terminally acetylated bah
domain of sir3 bound to the nucleosome core particle .
SNAP output
|
|
4ldx
|
transcription-DNA |
X-ray (2.9 Å) |
Boer DR, Freire-Rios A, van den Berg WA, Saaki T,
Manfield IW, Kepinski S, Lopez-Vidrieo I, Franco-Zorrilla
JM, de Vries SC, Solano R, Weijers D, Coll M |
(2014) "Structural
Basis for DNA Binding Specificity by the
Auxin-Dependent ARF Transcription Factors."
Cell(Cambridge,Mass.), 156,
577-589. doi: 10.1016/j.cell.2013.12.027.
|
Crystal structure of the DNA binding domain of
arabidopsis thaliana auxin response factor 1 (arf1) in
complex with protomor-like sequence er7 . SNAP output
|
|
4ley
|
transferase-DNA |
X-ray (2.5 Å) |
Li X, Shu C, Yi G, Chaton CT, Shelton CL, Diao J, Zuo
X, Kao CC, Herr AB, Li P |
(2013) "Cyclic
GMP-AMP Synthase Is Activated by Double-Stranded
DNA-Induced Oligomerization." Immunity,
39, 1019-1031. doi: 10.1016/j.immuni.2013.10.019.
|
Structure of mouse cgas bound to 18 bp DNA . SNAP output
|
|
4lez
|
transferase-DNA |
X-ray (2.36 Å) |
Li X, Shu C, Yi G, Chaton CT, Shelton CL, Diao J, Zuo
X, Kao CC, Herr AB, Li P |
(2013) "Cyclic
GMP-AMP Synthase Is Activated by Double-Stranded
DNA-Induced Oligomerization." Immunity,
39, 1019-1031. doi: 10.1016/j.immuni.2013.10.019.
|
Structure of mouse cgas bound to an 18bp DNA and cgas
product . SNAP
output
|
|
4lg0
|
transcription-DNA |
X-ray (2.19 Å) |
Birrane G, Choy WC, Datta D, Geiger CA, Grant MA |
"Structure of a ternary FOXO1-ETS1 DNA complex." |
Structure of a ternary foxo1-ets1 DNA complex .
SNAP output
|
|
4lg7
|
hydrolase-DNA |
X-ray (2.5 Å) |
Xu C, Tempel W, Wernimont AK, Bountra C, Arrowsmith
CH, Edwards AM, Min J |
"Crystal structure MBD4 MBD domain in complex with
methylated CpG DNA." |
Crystal structure mbd4 mbd domain in complex with
methylated cpg DNA . SNAP output
|
|
4ljr
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Wang W, Ding J, Zhang Y, Hu Y, Wang DC |
(2014) "Structural
insights into the unique single-stranded DNA-binding
mode of Helicobacter pylori DprA." Nucleic
Acids Res., 42, 3478-3491. doi:
10.1093/nar/gkt1334.
|
Structural insights into the unique single-stranded DNA
binding mode of DNA processing protein a from
helicobacter pylori . SNAP output
|
|
4lll
|
transcription-DNA |
X-ray (3.036 Å) |
Birukou I, Seo SM, Schindler BD, Kaatz GW, Brennan
RG |
(2014) "Structural
mechanism of transcription regulation of the
Staphylococcus aureus multidrug efflux operon mepRA by
the MarR family repressor MepR." Nucleic Acids
Res., 42, 2774-2788. doi:
10.1093/nar/gkt1215.
|
Crystal structure of s. aureus mepr-DNA complex .
SNAP output
|
|
4lln
|
transcription-DNA |
X-ray (2.842 Å) |
Birukou I, Seo SM, Schindler BD, Kaatz GW, Brennan
RG |
(2014) "Structural
mechanism of transcription regulation of the
Staphylococcus aureus multidrug efflux operon mepRA by
the MarR family repressor MepR." Nucleic Acids
Res., 42, 2774-2788. doi:
10.1093/nar/gkt1215.
|
Crystal structure of s. aureus mepr-DNA complex .
SNAP output
|
|
4lmg
|
transcription activator-DNA |
X-ray (2.2 Å) |
Poor CB, Wegner SV, Li H, Dlouhy AC, Schuermann JP,
Sanishvili R, Hinshaw JR, Riggs-Gelasco PJ, Outten CE, He
C |
(2014) "Molecular
mechanism and structure of the Saccharomyces cerevisiae
iron regulator Aft2."
Proc.Natl.Acad.Sci.USA, 111,
4043-4048. doi: 10.1073/pnas.1318869111.
|
Crystal structure of aft2 in complex with DNA .
SNAP output
|
|
4lnq
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Li H, Wang J, Wang J, Cao LS, Wang ZX, Wu JW |
(2014) "Structural
mechanism of DNA recognition by the p202 HINa domain:
insights into the inhibition of Aim2-mediated
inflammatory signalling." Acta Crystallogr F
Struct Biol Commun, 70, 21-29.
doi: 10.1107/S2053230X1303135X.
|
Crystal structure of ifi202 hina domain in complex with
20bp dsDNA . SNAP
output
|
|
4lox
|
hydrolase-DNA |
X-ray (1.98 Å) |
Chik J, Shen B, Stoddard B |
"Crystal structure of a LAGLIDADG endonuclease from
the Sordaria Macrospore." |
Crystal structure of the i-smami laglidadg homing
endonuclease bound to cleaved DNA . SNAP output
|
|
4lq0
|
hydrolase-DNA |
X-ray (2.68 Å) |
Chik J, Shen B, Stoddard B |
"Structural Comparisons of LAGLIDADG Homing
Endonucleases." |
Crystal structure of the i-ltrwi laglidadg homing
endonuclease bound to target DNA. . SNAP output
|
|
4lt5
|
oxidoreductase-DNA |
X-ray (2.893 Å) |
Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N,
Correa IR, Zheng Y, Cheng X |
(2014) "Structure
of a Naegleria Tet-like dioxygenase in complex with
5-methylcytosine DNA." Nature,
506, 391-395. doi: 10.1038/nature12905.
|
Structure of a naegleria tet-like dioxygenase in
complex with 5-methylcytosine DNA . SNAP output
|
|
4lup
|
transcription-DNA |
X-ray (1.2 Å) |
Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain
FH |
(2014) "Structural
basis for -10 promoter element melting by
environmentally induced sigma factors."
Nat.Struct.Mol.Biol., 21,
269-276. doi: 10.1038/nsmb.2777.
|
Crystal structure of the complex formed by region of e.
coli sigmae bound to its -10 element non template
strand . SNAP output
|
|
4lvi
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H,
Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M,
Coll M |
(2017) "Structural
basis of a histidine-DNA nicking/joining mechanism for
gene transfer and promiscuous spread of antibiotic
resistance." Proc. Natl. Acad. Sci.
U.S.A., 114, E6526-E6535. doi:
10.1073/pnas.1702971114.
|
Mobm relaxase domain (mobv; mob_pre) bound to plasmid
pmv158 orit DNA (22nt). mn-bound crystal structure at
ph 4.6 . SNAP output
|
|
4lvj
|
DNA binding protein-DNA |
X-ray (2.17 Å) |
Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H,
Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M,
Coll M |
(2017) "Structural
basis of a histidine-DNA nicking/joining mechanism for
gene transfer and promiscuous spread of antibiotic
resistance." Proc. Natl. Acad. Sci.
U.S.A., 114, E6526-E6535. doi:
10.1073/pnas.1702971114.
|
Mobm relaxase domain (mobv; mob_pre) bound to plasmid
pmv158 orit DNA (22nt). mn-bound crystal structure at
ph 5.5 . SNAP output
|
|
4lvk
|
DNA binding protein-DNA |
X-ray (2.37 Å) |
Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H,
Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M,
Coll M |
(2017) "Structural
basis of a histidine-DNA nicking/joining mechanism for
gene transfer and promiscuous spread of antibiotic
resistance." Proc. Natl. Acad. Sci.
U.S.A., 114, E6526-E6535. doi:
10.1073/pnas.1702971114.
|
Mobm relaxase domain (mobv; mob_pre) bound to plasmid
pmv158 orit DNA (22nt+3'phosphate). mn-bound crystal
structure at ph 4.6 . SNAP output
|
|
4lvl
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H,
Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M,
Coll M |
(2017) "Structural
basis of a histidine-DNA nicking/joining mechanism for
gene transfer and promiscuous spread of antibiotic
resistance." Proc. Natl. Acad. Sci.
U.S.A., 114, E6526-E6535. doi:
10.1073/pnas.1702971114.
|
Mobm relaxase domain (mobv; mob_pre) bound to plasmid
pmv158 orit DNA (22nt+3'thiophosphate). mn-bound
crystal structure at ph 6.8 . SNAP output
|
|
4lvm
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H,
Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M,
Coll M |
(2017) "Structural
basis of a histidine-DNA nicking/joining mechanism for
gene transfer and promiscuous spread of antibiotic
resistance." Proc. Natl. Acad. Sci.
U.S.A., 114, E6526-E6535. doi:
10.1073/pnas.1702971114.
|
Mobm relaxase domain (mobv; mob_pre) bound to plasmid
pmv158 orit DNA (23nt). mn-bound crystal structure at
ph 6.5 . SNAP output
|
|
4lvs
|
transferase, lyase-DNA |
X-ray (2.002 Å) |
Freudenthal BD, Beard WA, Shock DD, Wilson SH |
(2013) "Observing
a DNA polymerase choose right from wrong."
Cell(Cambridge,Mass.), 154,
157-168. doi: 10.1016/j.cell.2013.05.048.
|
DNA polymerase beta mismatched substrate complex with
mn2+, 2.5 min . SNAP
output
|
|
4lz1
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (1.65 Å) |
Pica A, Russo Krauss I, Merlino A, Nagatoishi S,
Sugimoto N, Sica F |
(2013) "Dissecting
the contribution of thrombin exosite I in the
recognition of thrombin binding aptamer." Febs
J., 280, 6581-6588. doi: 10.1111/febs.12561.
|
X-ray structure of the complex between human thrombin
and the tba deletion mutant lacking thymine 12
nucleobase . SNAP
output
|
|
4lz4
|
hydrolase-hydrolase inhibitor-DNA |
X-ray (2.56 Å) |
Pica A, Russo Krauss I, Merlino A, Nagatoishi S,
Sugimoto N, Sica F |
(2013) "Dissecting
the contribution of thrombin exosite I in the
recognition of thrombin binding aptamer." Febs
J., 280, 6581-6588. doi: 10.1111/febs.12561.
|
X-ray structure of the complex between human thrombin
and the tba deletion mutant lacking thymine 3
nucleobase . SNAP
output
|
|
4lzg
|
transferase-DNA |
X-ray (1.599 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2014) "Sustained
active site rigidity during synthesis by human DNA
polymerase mu." Nat.Struct.Mol.Biol.,
21, 253-260. doi: 10.1038/nsmb.2766.
|
Binary complex of human DNA polymerase mu with DNA .
SNAP output
|
|
4m04
|
transferase-DNA |
X-ray (1.898 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2014) "Sustained
active site rigidity during synthesis by human DNA
polymerase mu." Nat.Struct.Mol.Biol.,
21, 253-260. doi: 10.1038/nsmb.2766.
|
Human DNA polymerase mu ternary complex . SNAP output
|
|
4m0a
|
transferase-DNA |
X-ray (1.85 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2014) "Sustained
active site rigidity during synthesis by human DNA
polymerase mu." Nat.Struct.Mol.Biol.,
21, 253-260. doi: 10.1038/nsmb.2766.
|
Human DNA polymerase mu post-catalytic complex .
SNAP output
|
|
4m2y
|
transferase-DNA |
X-ray (2.27 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase beta complexed with
8-brg as the template base in a 1-nucleotide gapped DNA
. SNAP output
|
|
4m3r
|
hydrolase-DNA |
X-ray (2.07 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dt-dg at
position n-1 of primer-template duplex . SNAP output
|
|
4m3t
|
hydrolase-DNA |
X-ray (1.9 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dt-dg at
position n-2 of primer-template duplex . SNAP output
|
|
4m3u
|
hydrolase-DNA |
X-ray (2.07 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dt-dg at
position n-3 of primer-template duplex . SNAP output
|
|
4m3w
|
hydrolase-DNA |
X-ray (2.1 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dt-dg at
position n-4 of primer-template duplex . SNAP output
|
|
4m3x
|
hydrolase-DNA |
X-ray (2.2 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dt-dg at
position n-5 of primer-template duplex . SNAP output
|
|
4m3y
|
hydrolase-DNA |
X-ray (1.86 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dg-dt at
position n-1 of primer-template duplex . SNAP output
|
|
4m3z
|
hydrolase-DNA |
X-ray (1.84 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dg-dt at
position n-2 of primer-template duplex . SNAP output
|
|
4m41
|
hydrolase-DNA |
X-ray (2.15 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dg-dt at
position n-3 of primer-template duplex . SNAP output
|
|
4m42
|
hydrolase-DNA |
X-ray (2.04 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dg-dt at
position n-4 of primer-template duplex . SNAP output
|
|
4m45
|
hydrolase-DNA |
X-ray (1.89 Å) |
Xia S, Konigsberg WH |
(2014) "Mispairs
with Watson-Crick base-pair geometry observed in
ternary complexes of an RB69 DNA polymerase
variant." Protein Sci.,
23, 508-513. doi: 10.1002/pro.2434.
|
Rb69 DNA polymerase ternary complex with dg-dt at
position n-5 of primer-template duplex . SNAP output
|
|
4m47
|
transferase-DNA |
X-ray (2.37 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase complexed with 8-brg
in the template base paired with incoming
non-hydrolyzable gtp . SNAP output
|
|
4m6f
|
hydrolase-DNA |
X-ray (4.99 Å) |
Ritacco CJ, Steitz TA, Wang J |
(2014) "Exploiting
large non-isomorphous differences for phase
determination of a G-segment invertase-DNA
complex." Acta Crystallogr.,Sect.D,
70, 685-693. doi: 10.1107/S1399004713032392.
|
Dimer of the g-segment invertase bound to a DNA
substrate . SNAP
output
|
|
4m8b
|
transcription-DNA |
X-ray (2.61 Å) |
Lohse MB, Rosenberg OS, Cox JS, Stroud RM,
Finer-Moore JS, Johnson AD |
(2014) "Structure
of a new DNA-binding domain which regulates
pathogenesis in a wide variety of fungi."
Proc.Natl.Acad.Sci.USA, 111,
10404-10410. doi: 10.1073/pnas.1410110111.
|
Fungal protein . SNAP
output
|
|
4m8o
|
transferase-DNA |
X-ray (2.2 Å) |
Hogg M, Osterman P, Bylund GO, Ganai RA, Lundstrom
EB, Sauer-Eriksson AE, Johansson E |
(2014) "Structural
basis for processive DNA synthesis by yeast DNA
polymerase epsilon." Nat.Struct.Mol.Biol.,
21, 49-55. doi: 10.1038/nsmb.2712.
|
Ternary complex of DNA polymerase epsilon with an
incoming datp . SNAP
output
|
|
4m94
|
transferase-DNA |
X-ray (2.14 Å) |
Singh I, Lian Y, Li L, Georgiadis MM |
(2014) "The
structure of an authentic spore photoproduct lesion in
DNA suggests a basis for recognition." Acta
Crystallogr.,Sect.D, 70, 752-759.
doi: 10.1107/S1399004713032987.
|
D(atccgttataacggat) complexed with moloney murine
leukemia virus reverse transcriptase catalytic fragment
. SNAP output
|
|
4m95
|
transferase-DNA |
X-ray (1.72 Å) |
Singh I, Lian Y, Li L, Georgiadis MM |
(2014) "The
structure of an authentic spore photoproduct lesion in
DNA suggests a basis for recognition." Acta
Crystallogr.,Sect.D, 70, 752-759.
doi: 10.1107/S1399004713032987.
|
D(atccgttataacggat)complexed with moloney murine
leukemia virus reverse transcriptase catalytic fragment
. SNAP output
|
|
4m9e
|
transcription-DNA |
X-ray (1.851 Å) |
Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H,
Blumenthal RM, Zhang X, Cheng X |
(2014) "Structural
basis for Klf4 recognition of methylated DNA."
Nucleic Acids Res., 42,
4859-4867. doi: 10.1093/nar/gku134.
|
Structure of klf4 zinc finger DNA binding domain in
complex with methylated DNA . SNAP output
|
|
4m9g
|
transferase-DNA |
X-ray (2.01 Å) |
Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie
S |
(2013) "The
E295K Cancer Variant of Human Polymerase beta Favors
the Mismatch Conformational Pathway during Nucleotide
Selection." J.Biol.Chem.,
288, 34850-34860. doi: 10.1074/jbc.M113.510891.
|
DNA polymerase beta e295k binary complex . SNAP output
|
|
4m9h
|
transferase-DNA |
X-ray (2.394 Å) |
Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie
S |
(2013) "The
E295K Cancer Variant of Human Polymerase beta Favors
the Mismatch Conformational Pathway during Nucleotide
Selection." J.Biol.Chem.,
288, 34850-34860. doi: 10.1074/jbc.M113.510891.
|
DNA polymerase beta e295k soaked with dttp . SNAP output
|
|
4m9j
|
transferase-DNA |
X-ray (2.038 Å) |
Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie
S |
(2013) "The
E295K Cancer Variant of Human Polymerase beta Favors
the Mismatch Conformational Pathway during Nucleotide
Selection." J.Biol.Chem.,
288, 34850-34860. doi: 10.1074/jbc.M113.510891.
|
DNA polymerase beta e295k soaked with dumpnpp .
SNAP output
|
|
4m9l
|
transferase-DNA |
X-ray (2.091 Å) |
Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie
S |
(2013) "The
E295K Cancer Variant of Human Polymerase beta Favors
the Mismatch Conformational Pathway during Nucleotide
Selection." J.Biol.Chem.,
288, 34850-34860. doi: 10.1074/jbc.M113.510891.
|
DNA polymerase beta e295k soaked with dctp . SNAP output
|
|
4m9n
|
transferase-DNA |
X-ray (2.275 Å) |
Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie
S |
(2013) "The
E295K Cancer Variant of Human Polymerase beta Favors
the Mismatch Conformational Pathway during Nucleotide
Selection." J.Biol.Chem.,
288, 34850-34860. doi: 10.1074/jbc.M113.510891.
|
DNA polymerase beta e295k soaked with datp . SNAP output
|
|
4m9v
|
transcription-DNA |
X-ray (0.969 Å) |
Liu Y, Olanrewaju YO, Zhang X, Cheng X |
(2013) "DNA
recognition of 5-carboxylcytosine by a zfp57 mutant at
an atomic resolution of 0.97 angstrom."
Biochemistry, 52, 9310-9317.
doi: 10.1021/bi401360n.
|
Zfp57 mutant (e182q) in complex with 5-carboxylcytosine
DNA . SNAP output
|
|
4mde
|
transferase-DNA |
X-ray (1.8 Å) |
Das U, Wang LK, Smith P, Jacewicz A, Shuman S |
(2014) "Structures
of bacterial polynucleotide kinase in a Michaelis
complex with GTP*Mg2+ and 5'-OH oligonucleotide and a
product complex with GDP*Mg2+ and 5'-PO4
oligonucleotide reveal a mechanism of general acid-base
catalysis and the determinants of phosphoacceptor
recognition." Nucleic Acids Res.,
42, 1152-1161. doi: 10.1093/nar/gkt936.
|
Structure of bacterial polynucleotide kinase product
complex bound to gdp and DNA . SNAP output
|
|
4mdf
|
transferase-DNA |
X-ray (1.727 Å) |
Das U, Wang LK, Smith P, Jacewicz A, Shuman S |
(2014) "Structures
of bacterial polynucleotide kinase in a Michaelis
complex with GTP*Mg2+ and 5'-OH oligonucleotide and a
product complex with GDP*Mg2+ and 5'-PO4
oligonucleotide reveal a mechanism of general acid-base
catalysis and the determinants of phosphoacceptor
recognition." Nucleic Acids Res.,
42, 1152-1161. doi: 10.1093/nar/gkt936.
|
Structure of bacterial polynucleotide kinase michaelis
complex bound to gtp and DNA . SNAP output
|
|
4mf2
|
transferase-DNA |
X-ray (2.4 Å) |
Koag MC, Lee S |
(2014) "Metal-dependent
conformational activation explains highly promutagenic
replication across O6-methylguanine by human DNA
polymerase beta." J.Am.Chem.Soc.,
136, 5709-5721. doi: 10.1021/ja500172d.
|
Structure of human DNA polymerase beta complexed with
o6mg as the template base in a 1-nucleotide gapped DNA
. SNAP output
|
|
4mf8
|
transferase-DNA |
X-ray (2.32 Å) |
Koag MC, Min K, Monzingo AF, Lee S |
"Structures of human DNA polymerase beta inserting
bases opposite templating O6MG." |
Structure of human DNA polymerase beta complexed with
nicked DNA containing a mismatched template o6mg and
incoming ctp . SNAP
output
|
|
4mfa
|
transferase-DNA |
X-ray (2.27 Å) |
Koag MC, Min K, Monzingo AF, Lee S |
"Structures of human DNA polymerase beta inserting
bases opposite templating O6MG." |
Structure of human DNA polymerase beta complexed with
nicked DNA containing a mismatched template o6mg and
incoming ttp . SNAP
output
|
|
4mfc
|
transferase-DNA |
X-ray (2.13 Å) |
Koag MC, Lee S |
(2014) "Metal-dependent
conformational activation explains highly promutagenic
replication across O6-methylguanine by human DNA
polymerase beta." J.Am.Chem.Soc.,
136, 5709-5721. doi: 10.1021/ja500172d.
|
Structure of human DNA polymerase beta complexed with
o6mg in the template base paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
4mff
|
transferase-DNA |
X-ray (2.55 Å) |
Koag MC, Lee S |
(2014) "Metal-dependent
conformational activation explains highly promutagenic
replication across O6-methylguanine by human DNA
polymerase beta." J.Am.Chem.Soc.,
136, 5709-5721. doi: 10.1021/ja500172d.
|
Structure of human DNA polymerase beta complexed with
o6mg in the template base paired with incoming
non-hydrolyzable ttp . SNAP output
|
|
4mg2
|
oxidoreductase-DNA |
X-ray (2.3 Å) |
Chen B, Gan J, Yang CG |
(2014) "The complex structures of ALKBH2 mutants
cross-linked to dsDNA reveal the conformational swing
of β-hairpin." Sci China Chem,
57, 307-313. doi: 10.1007/s11426-013-5029-z.
|
Alkbh2 f102a cross-linked to undamaged dsDNA . SNAP output
|
|
4mgt
|
oxidoreductase-DNA |
X-ray (2.6 Å) |
Chen B, Gan J, Yang CG |
(2014) "The complex structures of ALKBH2 mutants
cross-linked to dsDNA reveal the conformational swing
of β-hairpin." Sci China Chem,
57, 307-313. doi: 10.1007/s11426-013-5029-z.
|
Alkbh2 r110a cross-linked to undamaged dsDNA . SNAP output
|
|
4mgu
|
virus-DNA |
X-ray (3.5 Å) |
Meng G, Zhang X, Plevka P, Yu Q, Tijssen P, Rossmann
MG |
(2013) "The
structure and host entry of an invertebrate
parvovirus." J.Virol.,
87, 12523-12530. doi: 10.1128/JVI.01822-13.
|
Crystal structure of acheta domesticus densovirus .
SNAP output
|
|
4mhg
|
transcription-DNA |
X-ray (2.199 Å) |
De S, Chan AC, Coyne HJ, Bhachech N, Hermsdorf U,
Okon M, Murphy ME, Graves BJ, McIntosh LP |
(2014) "Steric
Mechanism of Auto-Inhibitory Regulation of Specific and
Non-Specific DNA Binding by the ETS Transcriptional
Repressor ETV6." J.Mol.Biol.,
426, 1390-1406. doi: 10.1016/j.jmb.2013.11.031.
|
Crystal structure of etv6 bound to a specific DNA
sequence . SNAP
output
|
|
4mht
|
transferase-DNA |
X-ray (2.7 Å) |
O'Gara M, Klimasauskas S, Roberts RJ, Cheng X |
(1996) "Enzymatic
C5-cytosine methylation of DNA: mechanistic
implications of new crystal structures for HhaL
methyltransferase-DNA-AdoHcy complexes."
J.Mol.Biol., 261, 634-645.
doi: 10.1006/jmbi.1996.0489.
|
Ternary structure of hhai methyltransferase with native
DNA and adohcy . SNAP
output
|
|
4mky
|
transferase-DNA |
X-ray (2.4 Å) |
Brissett NC, Martin MJ, Bartlett EJ, Bianchi J,
Blanco L, Doherty AJ |
(2013) "Molecular
Basis for DNA Double-Strand Break Annealing and Primer
Extension by an NHEJ DNA Polymerase." Cell
Rep, 5, 1108-1120. doi: 10.1016/j.celrep.2013.10.016.
|
Polymerase domain from mycobacterium tuberculosis
ligase d in complex with an annealed double-strand DNA
break. . SNAP output
|
|
4mtd
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Gilston BA, Wang S, Marcus MD, Canalizo-Hernandez MA,
Swindell EP, Xue Y, Mondragon A, O'Halloran TV |
(2014) "Structural
and Mechanistic Basis of Zinc Regulation Across the E.
coli Zur Regulon." Plos Biol.,
12, e1001987. doi: 10.1371/journal.pbio.1001987.
|
Zinc uptake regulator complexed with zinc and DNA .
SNAP output
|
|
4mte
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Gilston BA, Wang S, Marcus MD, Canalizo-Hernandez MA,
Swindell EP, Xue Y, Mondragon A, O'Halloran TV |
(2014) "Structural
and Mechanistic Basis of Zinc Regulation Across the E.
coli Zur Regulon." Plos Biol.,
12, e1001987. doi: 10.1371/journal.pbio.1001987.
|
Zinc uptake regulator complexed with zinc and DNA .
SNAP output
|
|
4mzr
|
transcription-DNA |
X-ray (2.9 Å) |
Emamzadah S, Tropia L, Vincenti I, Falquet B,
Halazonetis TD |
(2014) "Reversal
of the DNA-Binding-Induced Loop L1 Conformational
Switch in an Engineered Human p53 Protein."
J.Mol.Biol., 426, 936-944.
doi: 10.1016/j.jmb.2013.12.020.
|
Crystal structure of a polypeptide p53 mutant bound to
DNA . SNAP output
|
|
4n0o
|
hydrolase-DNA |
X-ray (2.65 Å) |
Deng Z, Lehmann KC, Li X, Feng C, Wang G, Zhang Q, Qi
X, Yu L, Zhang X, Feng W, Wu W, Gong P, Tao Y, Posthuma
CC, Snijder EJ, Gorbalenya AE, Chen Z |
(2014) "Structural
basis for the regulatory function of a complex
zinc-binding domain in a replicative arterivirus
helicase resembling a nonsense-mediated mRNA decay
helicase." Nucleic Acids Res.,
42, 3464-3477. doi: 10.1093/nar/gkt1310.
|
Complex structure of arterivirus nonstructural protein
10 (helicase) with DNA . SNAP output
|
|
4n41
|
nuclear protein-DNA |
X-ray (2.248 Å) |
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC,
van der Oost J, Patel DJ, Wang Y |
(2014) "Structure-based
cleavage mechanism of Thermus thermophilus Argonaute
DNA guide strand-mediated DNA target cleavage."
Proc.Natl.Acad.Sci.USA, 111,
652-657. doi: 10.1073/pnas.1321032111.
|
Structure of thermus thermophilus argonaute bound to
guide DNA and 15-mer target DNA . SNAP output
|
|
4n47
|
nuclear protein-DNA |
X-ray (2.823 Å) |
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC,
van der Oost J, Patel DJ, Wang Y |
(2014) "Structure-based
cleavage mechanism of Thermus thermophilus Argonaute
DNA guide strand-mediated DNA target cleavage."
Proc.Natl.Acad.Sci.USA, 111,
652-657. doi: 10.1073/pnas.1321032111.
|
Structure of thermus thermophilus argonaute bound to
guide DNA and 12-mer target DNA . SNAP output
|
|
4n56
|
transferase-DNA |
X-ray (2.2 Å) |
Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B,
Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM,
Kermekchiev MB |
(2015) "A
Conservative Isoleucine to Leucine Mutation Causes
Major Rearrangements and Cold Sensitivity in KlenTaq1
DNA Polymerase." Biochemistry,
54, 881-889. doi: 10.1021/bi501198f.
|
Binary complex structure of klenow fragment of taq DNA
polymerase i707l mutant (cs3c klentaq) with DNA .
SNAP output
|
|
4n5s
|
transferase-DNA |
X-ray (1.67 Å) |
Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B,
Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM,
Kermekchiev MB |
(2015) "A
Conservative Isoleucine to Leucine Mutation Causes
Major Rearrangements and Cold Sensitivity in KlenTaq1
DNA Polymerase." Biochemistry,
54, 881-889. doi: 10.1021/bi501198f.
|
Ternary complex structure of klenow fragment of taq DNA
polymerase i707l mutant (cs3c klentaq) with DNA and
ddctp . SNAP output
|
|
4n76
|
nuclear protein-DNA |
X-ray (2.89 Å) |
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC,
van der Oost J, Patel DJ, Wang Y |
(2014) "Structure-based
cleavage mechanism of Thermus thermophilus Argonaute
DNA guide strand-mediated DNA target cleavage."
Proc.Natl.Acad.Sci.USA, 111,
652-657. doi: 10.1073/pnas.1321032111.
|
Structure of thermus thermophilus argonaute bound to
guide DNA and cleaved target DNA with mn2+ . SNAP output
|
|
4nca
|
nuclear protein-DNA |
X-ray (2.489 Å) |
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC,
van der Oost J, Patel DJ, Wang Y |
(2014) "Structure-based
cleavage mechanism of Thermus thermophilus Argonaute
DNA guide strand-mediated DNA target cleavage."
Proc.Natl.Acad.Sci.USA, 111,
652-657. doi: 10.1073/pnas.1321032111.
|
Structure of thermus thermophilus argonaute bound to
guide DNA 19-mer and target DNA in the presence of mg2+
. SNAP output
|
|
4ncb
|
nuclear protein-DNA |
X-ray (2.189 Å) |
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC,
van der Oost J, Patel DJ, Wang Y |
(2014) "Structure-based
cleavage mechanism of Thermus thermophilus Argonaute
DNA guide strand-mediated DNA target cleavage."
Proc.Natl.Acad.Sci.USA, 111,
652-657. doi: 10.1073/pnas.1321032111.
|
Structure of thermus thermophilus argonaute bound to
guide DNA and 19-mer target DNA with mg2+ . SNAP output
|
|
4ndf
|
DNA binding protein-RNA-DNA |
X-ray (1.944 Å) |
Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA,
Williams RS |
(2013) "Aprataxin
resolves adenylated RNA-DNA junctions to maintain
genome integrity." Nature,
506, 111-115. doi: 10.1038/nature12824.
|
Human aprataxin (aptx) bound to RNA-DNA, amp, and zn -
product complex . SNAP
output
|
|
4ndg
|
DNA binding protein-RNA-DNA |
X-ray (2.541 Å) |
Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA,
Williams RS |
(2013) "Aprataxin
resolves adenylated RNA-DNA junctions to maintain
genome integrity." Nature,
506, 111-115. doi: 10.1038/nature12824.
|
Human aprataxin (aptx) bound to RNA-DNA and zn -
adenosine vanadate transition state mimic complex .
SNAP output
|
|
4ndh
|
DNA binding protein-DNA |
X-ray (1.848 Å) |
Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA,
Williams RS |
(2013) "Aprataxin
resolves adenylated RNA-DNA junctions to maintain
genome integrity." Nature,
506, 111-115. doi: 10.1038/nature12824.
|
Human aprataxin (aptx) bound to DNA, amp, and zn -
product complex . SNAP
output
|
|
4ndi
|
DNA binding protein-RNA-DNA |
X-ray (1.9 Å) |
Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA,
Williams RS |
(2013) "Aprataxin
resolves adenylated RNA-DNA junctions to maintain
genome integrity." Nature,
506, 111-115. doi: 10.1038/nature12824.
|
Human aprataxin (aptx) aoa1 variant k197q bound to
RNA-DNA, amp, and zn - product complex . SNAP output
|
|
4ndy
|
DNA binding protein-DNA |
X-ray (6.999 Å) |
Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman
D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei
AR, Sung P, Xiong Y |
(2014) "The MHF
complex senses branched DNA by binding a pair of
crossover DNA duplexes." Nat Commun,
5, 2987. doi: 10.1038/ncomms3987.
|
Human mhf1-mhf2 DNA complex . SNAP output
|
|
4ne1
|
DNA binding protein-DNA |
X-ray (6.499 Å) |
Zhao Q, Saro D, Sachpatzidis A, Singh TR, Schlingman
D, Zheng XF, Mack A, Tsai MS, Mochrie S, Regan L, Meetei
AR, Sung P, Xiong Y |
(2014) "The MHF
complex senses branched DNA by binding a pair of
crossover DNA duplexes." Nat Commun,
5, 2987. doi: 10.1038/ncomms3987.
|
Human mhf1 mhf2 DNA complexes . SNAP output
|
|
4nhj
|
transcription regulator-DNA |
X-ray (2.701 Å) |
Li YC, Chang CK, Chang CF, Cheng YH, Fang PJ, Yu T,
Chen SC, Li YC, Hsiao CD, Huang TH |
(2014) "Structural
dynamics of the two-component response regulator RstA
in recognition of promoter DNA element."
Nucleic Acids Res., 42,
8777-8788. doi: 10.1093/nar/gku572.
|
Crystal structure of klebsiella pneumoniae rsta
DNA-binding domain in complex with rsta box . SNAP output
|
|
4ni7
|
cytokine-DNA |
X-ray (2.4 Å) |
Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter
JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y,
Jarvis TC, Janjic N |
(2014) "Crystal
structure of interleukin-6 in complex with a modified
nucleic Acid ligand." J.Biol.Chem.,
289, 8720-8734. doi: 10.1074/jbc.M113.532697.
|
Crystal structure of human interleukin 6 in complex
with a modified nucleotide aptamer (somamer sl1025) .
SNAP output
|
|
4ni9
|
cytokine-DNA |
X-ray (2.55 Å) |
Gelinas AD, Davies DR, Edwards TE, Rohloff JC, Carter
JD, Zhang C, Gupta S, Ishikawa Y, Hirota M, Nakaishi Y,
Jarvis TC, Janjic N |
(2014) "Crystal
structure of interleukin-6 in complex with a modified
nucleic Acid ligand." J.Biol.Chem.,
289, 8720-8734. doi: 10.1074/jbc.M113.532697.
|
Crystal structure of human interleukin 6 in complex
with a modified nucleotide aptamer (somamer sl1025),
form 2 . SNAP output
|
|
4nia
|
virus-RNA |
X-ray (1.82 Å) |
Larson SB, Day JS, McPherson A |
(2014) "Satellite
tobacco mosaic virus refined to 1.4 angstrom
resolution." Acta Crystallogr.,Sect.D,
70, 2316-2330. doi: 10.1107/S1399004714013789.
|
Satellite tobacco mosaic virus refined at room
temperature to 1.8 Å resolution using ncs restraints .
SNAP output
|
|
4nid
|
oxidoreductase-DNA |
X-ray (1.58 Å) |
Zhu C, Yi C |
(2014) "Switching
Demethylation Activities between AlkB Family RNA/DNA
Demethylases through Exchange of Active-Site
Residues." Angew.Chem.Int.Ed.Engl.,
53, 3659-3662. doi: 10.1002/anie.201310050.
|
Crystal structure of alkb protein with cofactors bound
to dsDNA containing m6a . SNAP output
|
|
4nig
|
oxidoreductase-DNA |
X-ray (1.52 Å) |
Zhu C, Yi C |
(2014) "Switching
Demethylation Activities between AlkB Family RNA/DNA
Demethylases through Exchange of Active-Site
Residues." Angew.Chem.Int.Ed.Engl.,
53, 3659-3662. doi: 10.1002/anie.201310050.
|
Crystal structure of alkb d135i-e136h mutant protein
with cofactors bound to dsDNA containing m6a-a .
SNAP output
|
|
4nih
|
oxidoreductase-DNA |
X-ray (1.374 Å) |
Zhu C, Yi C |
(2014) "Switching
Demethylation Activities between AlkB Family RNA/DNA
Demethylases through Exchange of Active-Site
Residues." Angew.Chem.Int.Ed.Engl.,
53, 3659-3662. doi: 10.1002/anie.201310050.
|
Crystal structure of alkb e136l mutant protein with
cofactors bound to dsDNA containing m6a-a . SNAP output
|
|
4nii
|
oxidoreductase-DNA |
X-ray (1.622 Å) |
Zhu C, Yi C |
(2014) "Switching
Demethylation Activities between AlkB Family RNA/DNA
Demethylases through Exchange of Active-Site
Residues." Angew.Chem.Int.Ed.Engl.,
53, 3659-3662. doi: 10.1002/anie.201310050.
|
Crystal structure of alkb d135i mutant protein with
cofactors bound to dsDNA containing m6a-a . SNAP output
|
|
4nlg
|
transferase-DNA |
X-ray (2.4 Å) |
Mukherjee P, Wilson RC, Lahiri I, Pata JD |
(2014) "Three
Residues of the Interdomain Linker Determine the
Conformation and Single-base Deletion Fidelity of
Y-family Translesion Polymerases."
J.Biol.Chem., 289, 6323-6331.
doi: 10.1074/jbc.M113.537860.
|
Y-family DNA polymerase chimera dbh-dpo4(243-245)-dbh .
SNAP output
|
|
4nlk
|
transferase, lyase-DNA |
X-ray (2.494 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase beta complexed with
8brg in the template base-paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
4nln
|
transferase, lyase-DNA |
X-ray (2.261 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase beta complexed with
nicked DNA containing a template 8brg and incoming ctp
. SNAP output
|
|
4nlz
|
transferase, lyase-DNA |
X-ray (2.683 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase beta complexed with
nicked DNA containing a mismatched template 8brg and
incoming gtp . SNAP
output
|
|
4nm1
|
transferase, lyase-DNA |
X-ray (2.415 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase beta complexed with a
nicked DNA containing a 8brg-c at n-1 position and g-c
at n position . SNAP
output
|
|
4nm2
|
transferase, lyase-DNA |
X-ray (2.524 Å) |
Koag MC, Min K, Lee S |
(2014) "Structural
basis for promutagenicity of 8-halogenated
Guanine." J.Biol.Chem.,
289, 6289-6298. doi: 10.1074/jbc.M113.537803.
|
Structure of human DNA polymerase beta complexed with a
nicked DNA containing a 8brg-g at n-1 position and g-c
at n position . SNAP
output
|
|
4nm6
|
oxidoreductase-DNA |
X-ray (2.026 Å) |
Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG,
Zhu J, Wang P, Xu Y |
(2013) "Crystal
Structure of TET2-DNA Complex: Insight into
TET-Mediated 5mC Oxidation."
Cell(Cambridge,Mass.), 155,
1545-1555. doi: 10.1016/j.cell.2013.11.020.
|
Crystal structure of tet2-DNA complex . SNAP output
|
|
4nnu
|
transcription-DNA |
X-ray (2.81 Å) |
Ngo HB, Lovely GA, Phillips R, Chan DC |
(2014) "Distinct
structural features of TFAM drive mitochondrial DNA
packaging versus transcriptional activation."
Nat Commun, 5, 3077. doi:
10.1038/ncomms4077.
|
Distinct structural features of tfam drive
mitochondrial DNA packaging versus transcriptional
activation . SNAP
output
|
|
4nod
|
transcription regulator-DNA |
X-ray (2.897 Å) |
Ngo HB, Lovely GA, Phillips R, Chan DC |
(2014) "Distinct
structural features of TFAM drive mitochondrial DNA
packaging versus transcriptional activation."
Nat Commun, 5, 3077. doi:
10.1038/ncomms4077.
|
Distinct structural features of tfam drive
mitochondrial DNA packaging versus transcriptional
activation . SNAP
output
|
|
4noe
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Sugiman-Marangos SN, Weiss YM, Junop MS |
(2016) "Mechanism
for accurate, protein-assisted DNA annealing by
Deinococcus radiodurans DdrB."
Proc.Natl.Acad.Sci.USA, 113,
4308-4313. doi: 10.1073/pnas.1520847113.
|
Crystal structure of ddrb bound to 30b ssDNA . SNAP output
|
|
4nqa
|
transcription regulator-DNA |
X-ray (3.102 Å) |
Lou X, Toresson G, Benod C, Suh JH, Philips KJ, Webb
P, Gustafsson JA |
(2014) "Structure
of the retinoid X receptor alpha-liver X receptor beta
(RXR alpha-LXR beta ) heterodimer on DNA."
Nat.Struct.Mol.Biol., 21,
277-281. doi: 10.1038/nsmb.2778.
|
Crystal structure of liganded hrxr-alpha-hlxr-beta
heterodimer on DNA . SNAP output
|
|
4nrw
|
hydrolase, lyase-DNA |
X-ray (2.845 Å) |
Prakash A, Carroll BL, Sweasy JB, Wallace SS, Doublie
S |
(2014) "Genome
and cancer single nucleotide polymorphisms of the human
NEIL1 DNA glycosylase: Activity, structure, and the
effect of editing." Dna Repair,
14, 17-26. doi: 10.1016/j.dnarep.2013.12.003.
|
Mvnei1-g86d . SNAP
output
|
|
4nw3
|
DNA binding protein-DNA |
X-ray (2.82 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Crystal structure of mll cxxc domain in complex with a
cpg DNA . SNAP
output
|
|
4nxz
|
transferase, lyase-DNA |
X-ray (2.557 Å) |
Koag MC, Lee S |
(2014) "Metal-dependent
conformational activation explains highly promutagenic
replication across O6-methylguanine by human DNA
polymerase beta." J.Am.Chem.Soc.,
136, 5709-5721. doi: 10.1021/ja500172d.
|
DNA polymerase beta with o6mg in the template base
opposite to incoming non-hydrolyzable ttp with
manganese in the active site . SNAP output
|
|
4ny8
|
transferase, lyase-DNA |
X-ray (2.246 Å) |
Koag MC, Lee S |
(2014) "Metal-dependent
conformational activation explains highly promutagenic
replication across O6-methylguanine by human DNA
polymerase beta." J.Am.Chem.Soc.,
136, 5709-5721. doi: 10.1021/ja500172d.
|
DNA polymerase beta with o6mg in the template base
opposite to incoming non-hydrolyzable ctp with
manganese in the active site . SNAP output
|
|
4o0i
|
transferase-DNA |
X-ray (2.203 Å) |
Jiang S, Gan J, Sun H, Huang Z |
"Crystal structure of fragment DNA polymerase I from
Bacillus stearothermophilus with
2'-MeSe-arabino-guanosine derivatized DNA." |
Crystal structure of fragment DNA polymerase i from
bacillus stearothermophilus with
2'-mese-arabino-guanosine derivatized DNA . SNAP output
|
|
4o3m
|
hydrolase-DNA |
X-ray (2.3 Å) |
Swan MK, Legris V, Tanner A, Reaper PM, Vial S,
Bordas R, Pollard JR, Charlton PA, Golec JM, Bertrand
JA |
(2014) "Structure
of human Bloom's syndrome helicase in complex with ADP
and duplex DNA." Acta Crystallogr.,Sect.D,
70, 1465-1475. doi: 10.1107/S139900471400501X.
|
Ternary complex of bloom's syndrome helicase . SNAP output
|
|
4o3n
|
transferase-DNA |
X-ray (1.579 Å) |
Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich
FP, Egli M |
(2014) "Kinetics,
Structure, and Mechanism of
8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA
Polymerase eta." J.Biol.Chem.,
289, 16867-16882. doi: 10.1074/jbc.M114.551820.
|
Crystal structure of human DNA polymerase eta in
ternary complex with native DNA and incoming nucleotide
(dcp) . SNAP output
|
|
4o3o
|
transferase-DNA |
X-ray (1.698 Å) |
Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich
FP, Egli M |
(2014) "Kinetics,
Structure, and Mechanism of
8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA
Polymerase eta." J.Biol.Chem.,
289, 16867-16882. doi: 10.1074/jbc.M114.551820.
|
Crystal structure of human polymerase eta inserting
datp opposite an 8-oxog containing DNA template .
SNAP output
|
|
4o3p
|
transferase-DNA |
X-ray (1.72 Å) |
Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich
FP, Egli M |
(2014) "Kinetics,
Structure, and Mechanism of
8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA
Polymerase eta." J.Biol.Chem.,
289, 16867-16882. doi: 10.1074/jbc.M114.551820.
|
Crystal structure of human polymerase eta inserting
dctp opposite an 8-oxog containing DNA template .
SNAP output
|
|
4o3q
|
transferase-DNA |
X-ray (1.72 Å) |
Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich
FP, Egli M |
(2014) "Kinetics,
Structure, and Mechanism of
8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA
Polymerase eta." J.Biol.Chem.,
289, 16867-16882. doi: 10.1074/jbc.M114.551820.
|
Crystal structure of human polymerase eta inserting
dgtp opposite an 8-oxog containing DNA template .
SNAP output
|
|
4o3r
|
transferase-DNA |
X-ray (1.62 Å) |
Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich
FP, Egli M |
(2014) "Kinetics,
Structure, and Mechanism of
8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA
Polymerase eta." J.Biol.Chem.,
289, 16867-16882. doi: 10.1074/jbc.M114.551820.
|
Crystal structure of human polymerase eta extending an
8-oxog DNA lesion: post insertion of 8-oxog-da pair .
SNAP output
|
|
4o3s
|
transferase-DNA |
X-ray (1.717 Å) |
Patra A, Nagy LD, Zhang Q, Su Y, Muller L, Guengerich
FP, Egli M |
(2014) "Kinetics,
Structure, and Mechanism of
8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA
Polymerase eta." J.Biol.Chem.,
289, 16867-16882. doi: 10.1074/jbc.M114.551820.
|
Crystal structure of human polymerase eta extending an
8-oxog DNA lesion: post insertion of 8-oxog-dc pair .
SNAP output
|
|
4o5c
|
transferase, lyase-DNA |
X-ray (2.363 Å) |
Koag MC, Kou Y, Ouzon-Shubeita H, Lee S |
(2014) "Transition-state
destabilization reveals how human DNA polymerase beta
proceeds across the chemically unstable lesion
N7-methylguanine." Nucleic Acids Res.,
42, 8755-8766. doi: 10.1093/nar/gku554.
|
Structure of human DNA polymerase complexed with n7-mg
as the template base in a 1-nucleotide gapped DNA .
SNAP output
|
|
4o5e
|
transferase, lyase-DNA |
X-ray (2.532 Å) |
Koag MC, Kou Y, Ouzon-Shubeita H, Lee S |
(2014) "Transition-state
destabilization reveals how human DNA polymerase beta
proceeds across the chemically unstable lesion
N7-methylguanine." Nucleic Acids Res.,
42, 8755-8766. doi: 10.1093/nar/gku554.
|
Structure of human DNA polymerase complexed with n7mg
in the template base paired with incoming
non-hydrolyzable ttp . SNAP output
|
|
4o5k
|
transferase, lyase-DNA |
X-ray (2.058 Å) |
Koag MC, Kou Y, Ouzon-Shubeita H, Lee S |
(2014) "Transition-state
destabilization reveals how human DNA polymerase beta
proceeds across the chemically unstable lesion
N7-methylguanine." Nucleic Acids Res.,
42, 8755-8766. doi: 10.1093/nar/gku554.
|
Structure of human DNA polymerase complexed with n7mg
in the template base paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
4o6a
|
transferase-DNA |
X-ray (1.859 Å) |
Zhang X, Wu J, Du F, Xu H, Sun L, Chen Z, Brautigam
CA, Zhang X, Chen ZJ |
(2014) "The
Cytosolic DNA Sensor cGAS Forms an Oligomeric Complex
with DNA and Undergoes Switch-like Conformational
Changes in the Activation Loop." Cell Rep,
6, 421-430. doi: 10.1016/j.celrep.2014.01.003.
|
Mouse cyclic gmp-amp synthase (cgas) in complex with
DNA . SNAP output
|
|
4o9m
|
transferase-DNA |
X-ray (2.295 Å) |
Caglayan M, Batra VK, Sassa A, Prasad R, Wilson
SH |
(2014) "Role of
polymerase beta in complementing aprataxin deficiency
during abasic-site base excision repair."
Nat.Struct.Mol.Biol., 21,
497-499. doi: 10.1038/nsmb.2818.
|
Human DNA polymerase beta complexed with adenylated
tetrahydrofuran (abasic site) containing DNA . SNAP output
|
|
4ofa
|
hydrolase-DNA |
X-ray (1.55 Å) |
Ouzon-Shubeita H, Lin Y-L, Lee S |
"Structure of MBD4 bound to G:T mispair DNA." |
Structural basis for thymine glycosylase activity on
t:o6-methylg mismatch by methyl-cpg binding domain
protein 4: implications for roles of arg468 in mismatch
recognition and catalysis . SNAP output
|
|
4ofe
|
hydrolase-DNA |
X-ray (2.15 Å) |
Ouzon-Shubeita H, Lin Y-L, Lee S |
"Structure of R468K/D560N MBD4 bound to G:T mispair
DNA." |
Structural basis for thymine glycosylase activity on
t:o6-methylg mismatch by methyl-cpg binding domain
protein 4: implications for roles of arg468 in mismatch
recognition and catalysis . SNAP output
|
|
4ofh
|
hydrolase-DNA |
X-ray (2.22 Å) |
Ouzon-Shubeita H, Lin Y-L, Lee S |
"Structure of MBD4 bound to O6MeG:T mispair
DNA." |
Structural basis for thymine glycosylase activity on
t:o6-methylg mismatch by methyl-cpg binding domain
protein 4: implications for roles of arg468 in mismatch
recognition and catalysis . SNAP output
|
|
4oi7
|
transport protein,signaling protein-DNA |
X-ray (3.104 Å) |
Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura
H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L,
Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury
PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS,
Latz E |
(2013) "RAGE is
a nucleic acid receptor that promotes inflammatory
responses to DNA." J.Exp.Med.,
210, 2447-2463. doi: 10.1084/jem.20120201.
|
Rage recognizes nucleic acids and promotes inflammatory
responses to DNA . SNAP
output
|
|
4oi8
|
transport protein,signaling protein-DNA |
X-ray (3.101 Å) |
Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura
H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L,
Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury
PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS,
Latz E |
(2013) "RAGE is
a nucleic acid receptor that promotes inflammatory
responses to DNA." J.Exp.Med.,
210, 2447-2463. doi: 10.1084/jem.20120201.
|
Rage is a nucleic acid receptor that promotes
inflammatory responses to DNA. . SNAP output
|
|
4oin
|
transcription, transferase-antibiotic |
X-ray (2.8 Å) |
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY,
Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R,
Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S,
Arnold E, Ebright RH |
(2014) "GE23077
binds to the RNA polymerase 'i' and 'i+1' sites and
prevents the binding of initiating nucleotides."
Elife, 3, e02450.
|
Crystal structure of thermus thermophilus transcription
initiation complex soaked with ge23077 . SNAP output
|
|
4oio
|
transcription, transferase |
X-ray (3.1 Å) |
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY,
Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R,
Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S,
Arnold E, Ebright RH |
(2014) "GE23077
binds to the RNA polymerase 'i' and 'i+1' sites and
prevents the binding of initiating nucleotides."
Elife, 3, e02450.
|
Crystal structure of thermus thermophilus pre-insertion
substrate complex for de novo transcription initiation
. SNAP output
|
|
4oip
|
transcription, transferase-antibiotic |
X-ray (3.4 Å) |
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY,
Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R,
Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S,
Arnold E, Ebright RH |
(2014) "GE23077
binds to the RNA polymerase 'i' and 'i+1' sites and
prevents the binding of initiating nucleotides."
Elife, 3, e02450.
|
Crystal structure of thermus thermophilus transcription
initiation complex soaked with ge23077, atp, and cmpcpp
. SNAP output
|
|
4oiq
|
transcription, transferase-antibiotic |
X-ray (3.624 Å) |
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY,
Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R,
Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S,
Arnold E, Ebright RH |
(2014) "GE23077
binds to the RNA polymerase 'i' and 'i+1' sites and
prevents the binding of initiating nucleotides."
Elife, 3, e02450.
|
Crystal structure of thermus thermophilus transcription
initiation complex soaked with ge23077 and rifampicin .
SNAP output
|
|
4oir
|
transcription, transferase-antibiotic |
X-ray (3.105 Å) |
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY,
Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R,
Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S,
Arnold E, Ebright RH |
(2014) "GE23077
binds to the RNA polymerase 'i' and 'i+1' sites and
prevents the binding of initiating nucleotides."
Elife, 3, e02450.
|
Crystal structure of thermus thermophilus RNA
polymerase transcription initiation complex soaked with
ge23077 and rifamycin sv . SNAP output
|
|
4ol8
|
transferase, hydrolase-RNA-DNA |
X-ray (3.1 Å) |
Nowak E, Miller JT, Bona MK, Studnicka J,
Szczepanowski RH, Jurkowski J, Le Grice SF, Nowotny
M |
(2014) "Ty3
reverse transcriptase complexed with an RNA-DNA hybrid
shows structural and functional asymmetry."
Nat.Struct.Mol.Biol., 21,
389-396. doi: 10.1038/nsmb.2785.
|
Ty3 reverse transcriptase bound to DNA-RNA . SNAP output
|
|
4oln
|
transcription-DNA |
X-ray (1.7 Å) |
McKeown AN, Bridgham JT, Anderson DW, Murphy MN,
Ortlund EA, Thornton JW |
(2014) "Evolution
of DNA specificity in a transcription factor family
produced a new gene regulatory module."
Cell(Cambridge,Mass.), 159,
58-68. doi: 10.1016/j.cell.2014.09.003.
|
Ancestral steroid receptor 1 in complex with estrogen
response element DNA . SNAP output
|
|
4omy
|
transcription-DNA |
X-ray (3.062 Å) |
Lee SG, Krishnan HB, Jez JM |
(2014) "Structural
basis for regulation of rhizobial nodulation and
symbiosis gene expression by the regulatory protein
NolR." Proc.Natl.Acad.Sci.USA,
111, 6509-6514. doi: 10.1073/pnas.1402243111.
|
Crystal structure of semet nolr from sinorhizobium
fredii in complex with oligo at DNA . SNAP output
|
|
4on0
|
transcription-DNA |
X-ray (3.0 Å) |
Lee SG, Krishnan HB, Jez JM |
(2014) "Structural
basis for regulation of rhizobial nodulation and
symbiosis gene expression by the regulatory protein
NolR." Proc.Natl.Acad.Sci.USA,
111, 6509-6514. doi: 10.1073/pnas.1402243111.
|
Crystal structure of nolr from sinorhizobium fredii in
complex with oligo aa DNA . SNAP output
|
|
4ond
|
transcription-DNA |
X-ray (2.253 Å) |
McKeown AN, Bridgham JT, Anderson DW, Murphy MN,
Ortlund EA, Thornton JW |
(2014) "Evolution
of DNA specificity in a transcription factor family
produced a new gene regulatory module."
Cell(Cambridge,Mass.), 159,
58-68. doi: 10.1016/j.cell.2014.09.003.
|
Ancestral steroid receptor 2 dbd helix mutant - ere DNA
complex . SNAP
output
|
|
4oo8
|
hydrolase-DNA-RNA |
X-ray (2.5 Å) |
Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI,
Dohmae N, Ishitani R, Zhang F, Nureki O |
(2014) "Crystal
structure of Cas9 in complex with guide RNA and target
DNA." Cell(Cambridge,Mass.),
156, 935-949. doi: 10.1016/j.cell.2014.02.001.
|
Crystal structure of streptococcus pyogenes cas9 in
complex with guide RNA and target DNA . SNAP output
|
|
4oor
|
transcription-DNA |
X-ray (2.701 Å) |
McKeown AN, Bridgham JT, Anderson DW, Murphy MN,
Ortlund EA, Thornton JW |
(2014) "Evolution
of DNA specificity in a transcription factor family
produced a new gene regulatory module."
Cell(Cambridge,Mass.), 159,
58-68. doi: 10.1016/j.cell.2014.09.003.
|
Ancestral steroid receptor 2 DNA binding domain in
complex with a steroid response element . SNAP output
|
|
4opj
|
hydrolase-DNA |
X-ray (1.541 Å) |
Egli M, Pallan PS |
"Generating
Crystallographic Models of DNA Dodecamers from
Structures of RNase H:DNA Complexes." Methods
Mol.Biol., 1320, 111-126. doi:
10.1007/978-1-4939-2763-0_8.
|
Bh-rnaseh:tcda-DNA complex . SNAP output
|
|
4opk
|
hydrolase-DNA |
X-ray (1.539 Å) |
Egli M, Pallan PS |
"Generating
Crystallographic Models of DNA Dodecamers from
Structures of RNase H:DNA Complexes." Methods
Mol.Biol., 1320, 111-126. doi:
10.1007/978-1-4939-2763-0_8.
|
Bh-rnaseh:2'-sme-DNA complex . SNAP output
|
|
4opx
|
transferase-DNA-transferase inhibitor |
X-ray (3.314 Å) |
Patel MR, Bhatt A, Steffen JD, Chergui A, Murai J,
Pommier Y, Pascal JM, Trombetta LD, Fronczek FR, Talele
TT |
(2014) "Discovery
and Structure-Activity Relationship of Novel
2,3-Dihydrobenzofuran-7-carboxamide and
2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide
Derivatives as Poly(ADP-ribose)polymerase-1
Inhibitors." J.Med.Chem.,
57, 5579-5601. doi: 10.1021/jm5002502.
|
Structure of human parp-1 bound to a DNA double strand
break in complex with
(2r)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide
. SNAP output
|
|
4oq9
|
virus-RNA |
X-ray (1.45 Å) |
Larson SB, Day JS, McPherson A |
(2014) "Satellite
tobacco mosaic virus refined to 1.4 angstrom
resolution." Acta Crystallogr.,Sect.D,
70, 2316-2330. doi: 10.1107/S1399004714013789.
|
Satellite tobacco mosaic virus refined to 1.4 Å
resolution using non-crystallographic symmetry
restraints . SNAP
output
|
|
4oqa
|
transferase-DNA-transferase inhibitor |
X-ray (3.65 Å) |
Patel MR, Bhatt A, Steffen JD, Chergui A, Murai J,
Pommier Y, Pascal JM, Trombetta LD, Fronczek FR, Talele
TT |
(2014) "Discovery
and Structure-Activity Relationship of Novel
2,3-Dihydrobenzofuran-7-carboxamide and
2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide
Derivatives as Poly(ADP-ribose)polymerase-1
Inhibitors." J.Med.Chem.,
57, 5579-5601. doi: 10.1021/jm5002502.
|
Structure of human parp-1 bound to a DNA double strand
break in complex with
(2z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide
. SNAP output
|
|
4oqb
|
transferase-DNA-transferase inhibitor |
X-ray (3.362 Å) |
Patel MR, Bhatt A, Steffen JD, Chergui A, Murai J,
Pommier Y, Pascal JM, Trombetta LD, Fronczek FR, Talele
TT |
(2014) "Discovery
and Structure-Activity Relationship of Novel
2,3-Dihydrobenzofuran-7-carboxamide and
2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide
Derivatives as Poly(ADP-ribose)polymerase-1
Inhibitors." J.Med.Chem.,
57, 5579-5601. doi: 10.1021/jm5002502.
|
Structure of human parp-1 bound to a DNA double strand
break in complex with
(2z)-2-{4-[2-(morpholin-4-yl)ethoxy]benzylidene}-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide
. SNAP output
|
|
4osh
|
DNA binding protein-DNA |
X-ray (2.201 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the tal effector dhax3 with ni rvd
at 2.2 angstrom resolution . SNAP output
|
|
4osi
|
DNA binding protein-DNA |
X-ray (2.849 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the tal effector dhax3 with ni rvd
at 2.8 angstrom resolution . SNAP output
|
|
4osj
|
DNA binding protein-DNA |
X-ray (2.79 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of tal effector reveals the
recognition between asparagine and adenine . SNAP output
|
|
4osk
|
DNA binding protein-DNA |
X-ray (2.398 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of tal effector reveals the
recognition between asparagine and guanine . SNAP output
|
|
4osl
|
DNA binding protein-DNA |
X-ray (2.447 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of tal effector reveals the
recognition between histidine and guanine . SNAP output
|
|
4osm
|
DNA binding protein-DNA |
X-ray (2.454 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505h mutant of tal effector
dhax3 . SNAP output
|
|
4osq
|
DNA binding protein-DNA |
X-ray (2.256 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505r mutant of tal effector
dhax3 . SNAP output
|
|
4osr
|
DNA binding protein-DNA |
X-ray (1.944 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505k mutant of tal effector
dhax3 . SNAP output
|
|
4oss
|
DNA binding protein-DNA |
X-ray (2.397 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505q mutant of tal effector
dhax3 . SNAP output
|
|
4ost
|
DNA binding protein-DNA |
X-ray (1.996 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505c mutant of tal effector
dhax3 . SNAP output
|
|
4osv
|
DNA binding protein-DNA |
X-ray (1.996 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505m mutant of tal effector
dhax3 . SNAP output
|
|
4osw
|
DNA binding protein-DNA |
X-ray (2.302 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505e mutant of tal effector
dhax3 . SNAP output
|
|
4osz
|
DNA binding protein-DNA |
X-ray (2.614 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505p mutant of tal effector
dhax3 . SNAP output
|
|
4ot0
|
DNA binding protein-DNA |
X-ray (2.491 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505t mutant of tal effector
dhax3 . SNAP output
|
|
4ot3
|
DNA binding protein-DNA |
X-ray (1.944 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505l mutant of tal effector
dhax3 . SNAP output
|
|
4oto
|
DNA binding protein-DNA |
X-ray (2.588 Å) |
Deng D, Yan CY, Wu JP, Pan XJ, Yan N |
(2014) "Revisiting
the TALE repeat." Protein Cell,
5, 297-306. doi: 10.1007/s13238-014-0035-2.
|
Crystal structure of the s505w mutant of tal effector
dhax3 . SNAP output
|
|
4ou6
|
replication-DNA |
X-ray (1.96 Å) |
Liu Z, Chen P, Wang X, Cai G, Niu L, Teng M, Li
X |
(2014) "Crystal
structure of DnaT84-153-dT10 ssDNA complex reveals a
novel single-stranded DNA binding mode."
Nucleic Acids Res., 42,
9470-9483. doi: 10.1093/nar/gku633.
|
Crystal structure of dnat84-153-dt10 ssDNA complex form
1 . SNAP output
|
|
4ou7
|
replication-DNA |
X-ray (2.83 Å) |
Liu Z, Chen P, Wang X, Cai G, Niu L, Teng M, Li
X |
(2014) "Crystal
structure of DnaT84-153-dT10 ssDNA complex reveals a
novel single-stranded DNA binding mode."
Nucleic Acids Res., 42,
9470-9483. doi: 10.1093/nar/gku633.
|
Crystal structure of dnat84-153-dt10 ssDNA complex
reveals a novel single-stranded DNA binding mode .
SNAP output
|
|
4ov7
|
transcription-DNA |
X-ray (2.701 Å) |
McKeown AN, Bridgham JT, Anderson DW, Murphy MN,
Ortlund EA, Thornton JW |
(2014) "Evolution
of DNA specificity in a transcription factor family
produced a new gene regulatory module."
Cell(Cambridge,Mass.), 159,
58-68. doi: 10.1016/j.cell.2014.09.003.
|
Ancestral steroid receptor 2 dbd helix mutant - sre DNA
complex . SNAP
output
|
|
4oww
|
DNA binding protein |
X-ray (2.3 Å) |
Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song
H |
(2014) "Structural
Basis of SOSS1 Complex Assembly and Recognition of
ssDNA." Cell Rep, 6,
982-991. doi: 10.1016/j.celrep.2014.02.020.
|
Structural basis of soss1 in complex with a 35nt ssDNA
. SNAP output
|
|
4owx
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song
H |
(2014) "Structural
Basis of SOSS1 Complex Assembly and Recognition of
ssDNA." Cell Rep, 6,
982-991. doi: 10.1016/j.celrep.2014.02.020.
|
Structural basis of soss1 in complex with a 12nt ssDNA
. SNAP output
|
|
4p0p
|
hydrolase-DNA |
X-ray (2.8 Å) |
Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y,
Cho Y |
(2014) "Crystal
structures of the structure-selective nuclease
Mus81-Eme1 bound to flap DNA substrates." Embo
J., 33, 1061-1072. doi: 10.1002/embj.201487820.
|
Crystal structure of human mus81-eme1 in complex with
5'-flap DNA, and mg2+ . SNAP output
|
|
4p0q
|
hydrolase-DNA |
X-ray (2.851 Å) |
Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y,
Cho Y |
(2014) "Crystal
structures of the structure-selective nuclease
Mus81-Eme1 bound to flap DNA substrates." Embo
J., 33, 1061-1072. doi: 10.1002/embj.201487820.
|
Crystal structure of human mus81-eme1 in complex with
5'-flap DNA . SNAP
output
|
|
4p0r
|
hydrolase-DNA |
X-ray (6.501 Å) |
Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y,
Cho Y |
(2014) "Crystal
structures of the structure-selective nuclease
Mus81-Eme1 bound to flap DNA substrates." Embo
J., 33, 1061-1072. doi: 10.1002/embj.201487820.
|
Human mus81-eme1-3'flap DNA complex . SNAP output
|
|
4p0s
|
hydrolase-DNA |
X-ray (6.0 Å) |
Gwon GH, Jo A, Baek K, Jin KS, Fu Y, Lee JB, Kim Y,
Cho Y |
(2014) "Crystal
structures of the structure-selective nuclease
Mus81-Eme1 bound to flap DNA substrates." Embo
J., 33, 1061-1072. doi: 10.1002/embj.201487820.
|
Human mus81-eme1-3'flap DNA complex . SNAP output
|
|
4p2h
|
transferase-DNA |
X-ray (1.987 Å) |
Koag MC, Kou Y, Ouzon-Shubeita H, Lee S |
(2014) "Transition-state
destabilization reveals how human DNA polymerase beta
proceeds across the chemically unstable lesion
N7-methylguanine." Nucleic Acids Res.,
42, 8755-8766. doi: 10.1093/nar/gku554.
|
Structure of human DNA polymerase complexed with n7mg
in the template opposite to incoming non-hydrolyzable
ttp with manganese in the active site . SNAP output
|
|
4p4m
|
transferase-DNA |
X-ray (1.92 Å) |
Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA,
Bebenek K, Garcia-Diaz M |
(2014) "Structures
of the Leishmania infantum polymerase beta."
DNA Repair (Amst.), 18, 1-9.
doi: 10.1016/j.dnarep.2014.03.001.
|
Crystal structure of leishmania infantum polymerase
beta: ternary p-t complex . SNAP output
|
|
4p4o
|
transferase-DNA |
X-ray (2.3 Å) |
Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA,
Bebenek K, Garcia-Diaz M |
(2014) "Structures
of the Leishmania infantum polymerase beta."
DNA Repair (Amst.), 18, 1-9.
doi: 10.1016/j.dnarep.2014.03.001.
|
Crystal structure of leishmania infantum polymerase
beta: ternary gap complex . SNAP output
|
|
4p4p
|
transferase-DNA |
X-ray (2.3 Å) |
Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA,
Bebenek K, Garcia-Diaz M |
(2014) "Structures
of the Leishmania infantum polymerase beta."
DNA Repair (Amst.), 18, 1-9.
doi: 10.1016/j.dnarep.2014.03.001.
|
Crystal structure of leishmania infantum polymerase
beta: nick complex . SNAP output
|
|
4p9u
|
transcription regulator-DNA |
X-ray (3.208 Å) |
Shi W, Kovacikova G, Lin W, Taylor RK, Skorupski K,
Kull FJ |
(2015) "The
40-residue insertion in Vibrio cholerae FadR
facilitates binding of an additional fatty acyl-CoA
ligand." Nat Commun, 6,
6032. doi: 10.1038/ncomms7032.
|
Fadr, fatty acid responsive transcription factor from
vibrio cholerae, in complex with DNA . SNAP output
|
|
4par
|
DNA binding protein-DNA |
X-ray (2.89 Å) |
Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S,
Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X |
(2014) "Structure
of 5-hydroxymethylcytosine-specific restriction enzyme,
AbaSI, in complex with DNA." Nucleic Acids
Res., 42, 7947-7959. doi:
10.1093/nar/gku497.
|
The 5-hydroxymethylcytosine-specific restriction enzyme
abasi in a complex with product-like DNA . SNAP output
|
|
4pba
|
DNA binding protein-DNA |
X-ray (3.301 Å) |
Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S,
Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X |
(2014) "Structure
of 5-hydroxymethylcytosine-specific restriction enzyme,
AbaSI, in complex with DNA." Nucleic Acids
Res., 42, 7947-7959. doi:
10.1093/nar/gku497.
|
The 5-hydroxymethylcytosine-specific restriction enzyme
abasi in a complex with substrate-like DNA . SNAP output
|
|
4pcb
|
transferase-DNA |
X-ray (2.5 Å) |
Carballeira JD, Gonzalez-Perez B, Moncalian G, la
Cruz Fd |
(2014) "A high
security double lock and key mechanism in HUH relaxases
controls oriT-processing for plasmid conjugation."
Nucleic Acids Res., 42,
10632-10643. doi: 10.1093/nar/gku741.
|
Conjugative relaxase trwc in complex with mutant orit
DNA . SNAP output
|
|
4pcz
|
hydrolase-DNA |
X-ray (1.7 Å) |
Biela A, Coste F, Culard F, Guerin M, Goffinont S,
Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z,
Gasparutto D, Carell T, Tudek B, Castaing B |
(2014) "Zinc
finger oxidation of Fpg/Nei DNA glycosylases by
2-thioxanthine: biochemical and X-ray structural
characterization." Nucleic Acids Res.,
42, 10748-10761. doi: 10.1093/nar/gku613.
|
Crystal structure of a complex between r247g llfpg
mutant and a thf containing DNA . SNAP output
|
|
4pd2
|
hydrolase-DNA |
X-ray (1.65 Å) |
Biela A, Coste F, Culard F, Guerin M, Goffinont S,
Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z,
Gasparutto D, Carell T, Tudek B, Castaing B |
(2014) "Zinc
finger oxidation of Fpg/Nei DNA glycosylases by
2-thioxanthine: biochemical and X-ray structural
characterization." Nucleic Acids Res.,
42, 10748-10761. doi: 10.1093/nar/gku613.
|
Crystal structure of a complex between a c248gh llfpg
mutant and a thf containing DNA . SNAP output
|
|
4pdg
|
hydrolase-DNA |
X-ray (2.4 Å) |
Biela A, Coste F, Culard F, Guerin M, Goffinont S,
Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z,
Gasparutto D, Carell T, Tudek B, Castaing B |
(2014) "Zinc
finger oxidation of Fpg/Nei DNA glycosylases by
2-thioxanthine: biochemical and X-ray structural
characterization." Nucleic Acids Res.,
42, 10748-10761. doi: 10.1093/nar/gku613.
|
Crystal structure of a complex between an inhibited
llfpg and a thf containing DNA . SNAP output
|
|
4pdi
|
hydrolase-DNA |
X-ray (2.1 Å) |
Biela A, Coste F, Culard F, Guerin M, Goffinont S,
Gasteiger K, Ciesla J, Winczura A, Kazimierczuk Z,
Gasparutto D, Carell T, Tudek B, Castaing B |
(2014) "Zinc
finger oxidation of Fpg/Nei DNA glycosylases by
2-thioxanthine: biochemical and X-ray structural
characterization." Nucleic Acids Res.,
42, 10748-10761. doi: 10.1093/nar/gku613.
|
Crystal structure of a complex between an inhibited
llfpg and a n7-benzyl-fapy-dg containing DNA . SNAP output
|
|
4pe8
|
hydrolase-DNA |
X-ray (2.894 Å) |
Chen YC, Li CL, Hsiao YY, Duh Y, Yuan HS |
(2014) "Structure
and function of TatD exonuclease in DNA repair."
Nucleic Acids Res., 42,
10776-10785. doi: 10.1093/nar/gku732.
|
Crystal structure of tatd in complex with trinucleotide
DNA . SNAP output
|
|
4peh
|
hydrolase-RNA |
X-ray (2.1 Å) |
Montemayor EJ, Katolik A, Clark NE, Taylor AB,
Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens
SW, Damha MJ, Hart PJ |
(2014) "Structural
basis of lariat RNA recognition by the intron
debranching enzyme Dbr1." Nucleic Acids
Res., 42, 10845-10855. doi:
10.1093/nar/gku725.
|
Dbr1 in complex with synthetic linear RNA . SNAP output
|
|
4pei
|
hydrolase-RNA |
X-ray (1.95 Å) |
Montemayor EJ, Katolik A, Clark NE, Taylor AB,
Schuermann JP, Combs DJ, Johnsson R, Holloway SP, Stevens
SW, Damha MJ, Hart PJ |
(2014) "Structural
basis of lariat RNA recognition by the intron
debranching enzyme Dbr1." Nucleic Acids
Res., 42, 10845-10855. doi:
10.1093/nar/gku725.
|
Dbr1 in complex with synthetic branched RNA analog .
SNAP output
|
|
4pgq
|
transferase,lyase-DNA |
X-ray (2.3 Å) |
Koag MC, Nam K, Lee S |
(2015) "The
spontaneous replication error and the mismatch
discrimination mechanisms of human DNA polymerase
beta." Nucleic Acids Res.,
42, 11233-11245. doi: 10.1093/nar/gku789.
|
Structure of human DNA polymerase beta complexed with g
in the template base paired with incoming
non-hydrolyzable ttp . SNAP output
|
|
4pgx
|
transferase,lyase-DNA |
X-ray (2.077 Å) |
Koag MC, Nam K, Lee S |
(2015) "The
spontaneous replication error and the mismatch
discrimination mechanisms of human DNA polymerase
beta." Nucleic Acids Res.,
42, 11233-11245. doi: 10.1093/nar/gku789.
|
Structure of human DNA polymerase beta complexed with g
in the template base paired with incoming
non-hydrolyzable ttp and manganese . SNAP output
|
|
4pgy
|
transferase,lyase-DNA |
X-ray (2.26 Å) |
Koag MC, Lee S |
"The spontaneous base substitution mechanisms of
human DNA polymerase beta." |
Structure of human DNA polymerase beta complexed with a
nicked DNA containing a gt at n-1 position and gc at n
position . SNAP
output
|
|
4ph5
|
transferase,lyase-DNA |
X-ray (2.55 Å) |
Koag MC, Lee S |
"The spontaneous base substitution mechanisms of
human DNA polymerase beta." |
Structure of human DNA polymerase beta complexed with a
nicked DNA containing a ac at n-1 position and gc at n
position . SNAP
output
|
|
4pha
|
transferase,lyase-DNA |
X-ray (2.52 Å) |
Koag MC, Nam K, Lee S |
(2015) "The
spontaneous replication error and the mismatch
discrimination mechanisms of human DNA polymerase
beta." Nucleic Acids Res.,
42, 11233-11245. doi: 10.1093/nar/gku789.
|
Structure of human DNA polymerase beta complexed with a
in the template base paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
4phd
|
transferase,lyase-DNA |
X-ray (2.21 Å) |
Koag MC, Nam K, Lee S |
(2015) "The
spontaneous replication error and the mismatch
discrimination mechanisms of human DNA polymerase
beta." Nucleic Acids Res.,
42, 11233-11245. doi: 10.1093/nar/gku789.
|
Structure of human DNA polymerase beta complexed with a
in the template base paired with incoming
non-hydrolyzable ctp and manganese . SNAP output
|
|
4phe
|
transferase,lyase-DNA |
X-ray (2.15 Å) |
Koag MC, Lee S |
"The spontaneous base substitution mechanisms of
human DNA polymerase beta." |
Structure of human DNA polymerase beta complexed with t
in the template base paired with incoming
non-hydrolyzable gtp . SNAP output
|
|
4php
|
transferase,lyase-DNA |
X-ray (2.6 Å) |
Koag MC, Lee S |
"The spontaneous base substitution mechanisms of
human DNA polymerase beta." |
Structure of human DNA polymerase beta complexed with t
in the template base paired with incoming
non-hydrolyzable gtp and manganese . SNAP output
|
|
4plb
|
isomerase-isomerase inhibitor-DNA |
X-ray (2.69 Å) |
Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke
PT, Olsen D, Lagrutta A, Bradley P, Lu J, Patel S,
Rickert KW, Smith RF, Soisson S, Wei C, Fukuda H, Kishii
R, Takei M, Fukuda Y |
(2014) "Oxabicyclooctane-linked
novel bacterial topoisomerase inhibitors as broad
spectrum antibacterial agents." Acs
Med.Chem.Lett., 5, 609-614. doi:
10.1021/ml500069w.
|
Crystal structure of s.a. gyrase-am8191 complex .
SNAP output
|
|
4pog
|
replication, DNA binding protein-DNA |
X-ray (3.203 Å) |
Froelich CA, Kang S, Epling LB, Bell SP, Enemark
EJ |
(2014) "A
conserved MCM single-stranded DNA binding element is
essential for replication initiation."
Elife, 3, e01993. doi:
10.7554/eLife.01993.
|
Mcm-ssDNA co-crystal structure . SNAP output
|
|
4ppx
|
transferase, lyase-DNA |
X-ray (2.08 Å) |
Eckenroth BE, Fleming AM, Sweasy JB, Burrows CJ,
Doublie S |
(2014) "Crystal
Structure of DNA Polymerase beta with DNA Containing
the Base Lesion Spiroiminodihydantoin in a Templating
Position." Biochemistry,
53, 2075-2077. doi: 10.1021/bi500270e.
|
DNA polymerase beta e295k with spiroiminodihydantoin in
templating position . SNAP output
|
|
4pqu
|
transferase, hydrolase-DNA-RNA |
X-ray (2.508 Å) |
Das K, Martinez SE, Bandwar RP, Arnold E |
(2014) "Structures
of HIV-1 RT-RNA/DNA ternary complexes with dATP and
nevirapine reveal conformational flexibility of
RNA/DNA: insights into requirements for RNase H
cleavage." Nucleic Acids Res.,
42, 8125-8137. doi: 10.1093/nar/gku487.
|
Crystal structure of hiv-1 reverse transcriptase in
complex with RNA-DNA and datp . SNAP output
|
|
4pso
|
DNA binding protein |
X-ray (2.9 Å) |
Ghalei H, Moeller Hv, Eppers D, Sohmen D, Wilson DN,
Loll B, Wahl MC |
(2014) "Entrapment
of DNA in an intersubunit tunnel system of a
single-stranded DNA-binding protein." Nucleic
Acids Res., 42, 6698-6708. doi:
10.1093/nar/gku259.
|
Crystal structure of apethermo-dbp-rp2 bound to ssDNA
dt10 . SNAP output
|
|
4ptf
|
transferase-DNA |
X-ray (2.809 Å) |
Jain R, Rajashankar KR, Buku A, Johnson RE, Prakash
L, Prakash S, Aggarwal AK |
(2014) "Crystal
Structure of Yeast DNA Polymerase epsilon Catalytic
Domain." Plos One, 9,
e94835. doi: 10.1371/journal.pone.0094835.
|
Ternary crystal structure of yeast DNA polymerase
epsilon with template g . SNAP output
|
|
4pu3
|
toxin-antitoxin-DNA |
X-ray (3.39 Å) |
Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B,
Devreese B, Savvides SN |
(2014) "The
bacterial antitoxin HipB establishes a ternary complex
with operator DNA and phosphorylated toxin HipA to
regulate bacterial persistence." Nucleic Acids
Res., 42, 10134-10147. doi:
10.1093/nar/gku665.
|
Shewanella oneidensis mr-1 toxin antitoxin system hipa,
hipb and its operator DNA complex (space group p212121)
. SNAP output
|
|
4pu4
|
toxin-antitoxin-DNA |
X-ray (3.786 Å) |
Wen Y, Behiels E, Felix J, Elegheert J, Vergauwen B,
Devreese B, Savvides SN |
(2014) "The
bacterial antitoxin HipB establishes a ternary complex
with operator DNA and phosphorylated toxin HipA to
regulate bacterial persistence." Nucleic Acids
Res., 42, 10134-10147. doi:
10.1093/nar/gku665.
|
Shewanella oneidensis mr-1 toxin antitoxin system hipa,
hipb and its operator DNA complex (space group p21) .
SNAP output
|
|
4puo
|
transferase, hydrolase-DNA-RNA-inhibitor |
X-ray (2.901 Å) |
Das K, Martinez SE, Bandwar RP, Arnold E |
(2014) "Structures
of HIV-1 RT-RNA/DNA ternary complexes with dATP and
nevirapine reveal conformational flexibility of
RNA/DNA: insights into requirements for RNase H
cleavage." Nucleic Acids Res.,
42, 8125-8137. doi: 10.1093/nar/gku487.
|
Crystal structure of hiv-1 reverse transcriptase in
complex with RNA-DNA and nevirapine . SNAP output
|
|
4puq
|
hydrolase-DNA-RNA |
X-ray (1.6 Å) |
Gao R, Schellenberg MJ, Huang SY, Abdelmalak M,
Marchand C, Nitiss KC, Nitiss JL, Williams RS, Pommier
Y |
(2014) "Proteolytic
Degradation of Topoisomerase II (Top2) Enables the
Processing of Top2DNA and Top2RNA Covalent Complexes by
Tyrosyl-DNA-Phosphodiesterase 2 (TDP2)."
J.Biol.Chem., 289,
17960-17969. doi: 10.1074/jbc.M114.565374.
|
Mus musculus tdp2 reaction product complex with
5'-phosphorylated RNA-DNA, glycerol, and mg2+ .
SNAP output
|
|
4pw5
|
ligase-DNA |
X-ray (2.204 Å) |
Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu
RM |
(2014) "Structural
Basis for Hydroxymethylcytosine Recognition by the SRA
Domain of UHRF2." Mol.Cell,
54, 879-886. doi: 10.1016/j.molcel.2014.04.003.
|
Structure of uhrf2-sra in complex with a
5hmc-containing DNA, complex i . SNAP output
|
|
4pw6
|
ligase-DNA |
X-ray (3.789 Å) |
Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu
RM |
(2014) "Structural
Basis for Hydroxymethylcytosine Recognition by the SRA
Domain of UHRF2." Mol.Cell,
54, 879-886. doi: 10.1016/j.molcel.2014.04.003.
|
Structure of uhrf2-sra in complex with a
5hmc-containing DNA, complex ii . SNAP output
|
|
4pw7
|
ligase-DNA |
X-ray (2.001 Å) |
Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu
RM |
(2014) "Structural
Basis for Hydroxymethylcytosine Recognition by the SRA
Domain of UHRF2." Mol.Cell,
54, 879-886. doi: 10.1016/j.molcel.2014.04.003.
|
Structure of uhrf2-sra in complex with a 5mc-containing
DNA . SNAP output
|
|
4pwd
|
transferase, hydrolase-DNA-RNA-inhibitor |
X-ray (3.0 Å) |
Das K, Martinez SE, Bandwar RP, Arnold E |
(2014) "Structures
of HIV-1 RT-RNA/DNA ternary complexes with dATP and
nevirapine reveal conformational flexibility of
RNA/DNA: insights into requirements for RNase H
cleavage." Nucleic Acids Res.,
42, 8125-8137. doi: 10.1093/nar/gku487.
|
Crystal structure of hiv-1 reverse transcriptase in
complex with bulge-RNA-DNA and nevirapine . SNAP output
|
|
4pxi
|
transcription-DNA |
X-ray (3.2 Å) |
Bhukya H, Bhujbalrao R, Bitra A, Anand R |
(2014) "Structural
and functional basis of transcriptional regulation by
TetR family protein CprB from S. coelicolor A3(2)."
Nucleic Acids Res., 42,
10122-10133. doi: 10.1093/nar/gku587.
|
Elucidation of the structural and functional mechanism
of action of the tetr family protein, cprb from s.
coelicolor a3(2) . SNAP
output
|
|
4py5
|
hydrolase-DNA-RNA |
X-ray (2.1 Å) |
Figiel M, Nowotny M |
(2014) "Crystal
structure of RNase H3-substrate complex reveals
parallel evolution of RNA/DNA hybrid recognition."
Nucleic Acids Res., 42,
9285-9294. doi: 10.1093/nar/gku615.
|
Thermovibrio ammonificans rnase h3 in complex with
19-mer RNA-DNA . SNAP
output
|
|
4pzi
|
transcription-DNA |
X-ray (2.15 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Zinc finger region of mll2 in complex with cpg DNA .
SNAP output
|
|
4q0b
|
transferase, hydrolase-RNA-DNA-inhibitor |
X-ray (3.3 Å) |
Das K, Martinez SE, Bandwar RP, Arnold E |
(2014) "Structures
of HIV-1 RT-RNA/DNA ternary complexes with dATP and
nevirapine reveal conformational flexibility of
RNA/DNA: insights into requirements for RNase H
cleavage." Nucleic Acids Res.,
42, 8125-8137. doi: 10.1093/nar/gku487.
|
Crystal structure of hiv-1 reverse transcriptase in
complex with gap-RNA-DNA and nevirapine . SNAP output
|
|
4q0r
|
hydrolase-DNA |
X-ray (2.75 Å) |
Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J,
Nowotny M |
(2014) "Crystal
structure of the catalytic core of Rad2: insights into
the mechanism of substrate binding." Nucleic
Acids Res., 42, 10762-10775. doi:
10.1093/nar/gku729.
|
The catalytic core of rad2 (complex i) . SNAP output
|
|
4q0w
|
hydrolase-DNA |
X-ray (2.1 Å) |
Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J,
Nowotny M |
(2014) "Crystal
structure of the catalytic core of Rad2: insights into
the mechanism of substrate binding." Nucleic
Acids Res., 42, 10762-10775. doi:
10.1093/nar/gku729.
|
He catalytic core of rad2 in complex with DNA substrate
(complex ii) . SNAP
output
|
|
4q0z
|
hydrolase-DNA |
X-ray (2.398 Å) |
Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J,
Nowotny M |
(2014) "Crystal
structure of the catalytic core of Rad2: insights into
the mechanism of substrate binding." Nucleic
Acids Res., 42, 10762-10775. doi:
10.1093/nar/gku729.
|
The catalytic core of rad2 in complex with DNA
substrate (complex iii) . SNAP output
|
|
4q10
|
hydrolase-DNA |
X-ray (2.7 Å) |
Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J,
Nowotny M |
(2014) "Crystal
structure of the catalytic core of Rad2: insights into
the mechanism of substrate binding." Nucleic
Acids Res., 42, 10762-10775. doi:
10.1093/nar/gku729.
|
The catalytic core of rad2 in complex with DNA
substrate (complex iv) . SNAP output
|
|
4q43
|
transferase-DNA |
X-ray (2.45 Å) |
Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B,
Pradeepkumar PI, Nair DT |
(2015) "Unique
structural features in DNA polymerase IV enable
efficient bypass of the N2 adduct induced by the
nitrofurazone antibiotic." Structure,
23, 56-67. doi: 10.1016/j.str.2014.10.019.
|
Polymerase-damaged DNA complex . SNAP output
|
|
4q44
|
transferase-DNA |
X-ray (2.71 Å) |
Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B,
Pradeepkumar PI, Nair DT |
(2015) "Unique
structural features in DNA polymerase IV enable
efficient bypass of the N2 adduct induced by the
nitrofurazone antibiotic." Structure,
23, 56-67. doi: 10.1016/j.str.2014.10.019.
|
Polymerase-damaged DNA complex . SNAP output
|
|
4q45
|
transferase-DNA |
X-ray (2.176 Å) |
Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B,
Pradeepkumar PI, Nair DT |
(2015) "Unique
structural features in DNA polymerase IV enable
efficient bypass of the N2 adduct induced by the
nitrofurazone antibiotic." Structure,
23, 56-67. doi: 10.1016/j.str.2014.10.019.
|
DNA polymerase- damaged DNA complex . SNAP output
|
|
4q4z
|
transcription-DNA |
X-ray (2.9 Å) |
Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D,
Fernandez-Tornero C, Kulbachinskiy A, Murakami KS |
(2014) "Structural
basis of transcription initiation by bacterial RNA
polymerase holoenzyme." J.Biol.Chem.,
289, 24549-24559. doi: 10.1074/jbc.M114.584037.
|
Thermus thermophilus RNA polymerase de novo
transcription initiation complex . SNAP output
|
|
4q5s
|
transcription-DNA-RNA |
X-ray (3.0 Å) |
Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D,
Fernandez-Tornero C, Kulbachinskiy A, Murakami KS |
(2014) "Structural
basis of transcription initiation by bacterial RNA
polymerase holoenzyme." J.Biol.Chem.,
289, 24549-24559. doi: 10.1074/jbc.M114.584037.
|
Thermus thermophilus RNA polymerase initially
transcribing complex containing 6-mer RNA . SNAP output
|
|
4q5v
|
transferase-DNA-RNA |
X-ray (2.52 Å) |
Baranovskiy AG, Babayeva ND, Suwa Y, Gu J, Pavlov YI,
Tahirov TH |
(2014) "Structural
basis for inhibition of DNA replication by
aphidicolin." Nucleic Acids Res.,
42, 14013-14021. doi: 10.1093/nar/gku1209.
|
Crystal structure of the catalytic core of human DNA
polymerase alpha in ternary complex with an RNA-primed
DNA template and aphidicolin . SNAP output
|
|
4q8e
|
transferase-DNA |
X-ray (1.549 Å) |
Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W,
Lippard SJ |
(2014) "Structural
and mechanistic studies of polymerase eta bypass of
phenanthriplatin DNA damage."
Proc.Natl.Acad.Sci.USA, 111,
9133-9138. doi: 10.1073/pnas.1405739111.
|
Human DNA polymerase eta inserting dcmpnpp opposite a
phenanthriplatin adducted g . SNAP output
|
|
4q8f
|
transferase-DNA |
X-ray (2.797 Å) |
Gregory MT, Park GY, Johnstone TC, Lee YS, Yang W,
Lippard SJ |
(2014) "Structural
and mechanistic studies of polymerase eta bypass of
phenanthriplatin DNA damage."
Proc.Natl.Acad.Sci.USA, 111,
9133-9138. doi: 10.1073/pnas.1405739111.
|
Human DNA polymerase eta extending primer immediately
after a phenanthriplatin adducted g . SNAP output
|
|
4qcb
|
hydrolase-DNA |
X-ray (2.89 Å) |
Schormann N, Banerjee S, Ricciardi R, Chattopadhyay
D |
(2015) "Binding
of undamaged double stranded DNA to vaccinia virus
uracil-DNA Glycosylase." BMC Struct.
Biol., 15, 10. doi: 10.1186/s12900-015-0037-1.
|
Protein-DNA complex of vaccinia virus d4 with
double-stranded non-specific DNA . SNAP output
|
|
4qcl
|
transferase-DNA-RNA |
X-ray (2.2 Å) |
Baranovskiy AG, Duong V, Babayeva ND, Zhang Y, Pavlov
Y, Anderson K, Tahirov TH |
(2018) "Activity and fidelity of human DNA polymerase
alpha depend on primer structure."
J.Biol.Chem. |
Crystal structure of the catalytic core of human DNA
polymerase alpha in ternary complex with an RNA-primed
DNA template and dctp . SNAP output
|
|
4qen
|
transcription-DNA |
X-ray (2.002 Å) |
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S,
Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel
DJ, Jacobsen SE |
(2014) "Mechanism
of DNA Methylation-Directed Histone Methylation by
KRYPTONITE." Mol.Cell,
55, 495-504. doi: 10.1016/j.molcel.2014.06.009.
|
Crystal structure of kryptonite in complex with mchh
DNA and sah . SNAP
output
|
|
4qeo
|
transcription-DNA |
X-ray (2.0 Å) |
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S,
Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel
DJ, Jacobsen SE |
(2014) "Mechanism
of DNA Methylation-Directed Histone Methylation by
KRYPTONITE." Mol.Cell,
55, 495-504. doi: 10.1016/j.molcel.2014.06.009.
|
Crystal structure of kryptonite in complex with mchh
DNA, h3(1-15) peptide and sah . SNAP output
|
|
4qep
|
transcription-DNA |
X-ray (3.1 Å) |
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S,
Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel
DJ, Jacobsen SE |
(2014) "Mechanism
of DNA Methylation-Directed Histone Methylation by
KRYPTONITE." Mol.Cell,
55, 495-504. doi: 10.1016/j.molcel.2014.06.009.
|
Crystal structure of kryptonite in complex with mchg
DNA and sah . SNAP
output
|
|
4qgu
|
transcription-DNA |
X-ray (2.545 Å) |
Ni X, Ru H, Ma F, Zhao L, Shaw N, Feng Y, Ding W,
Gong W, Wang Q, Ouyang S, Cheng G, Liu ZJ |
(2016) "New
insights into the structural basis of DNA recognition
by HINa and HINb domains of IFI16." J Mol Cell
Biol, 8, 51-61. doi: 10.1093/jmcb/mjv053.
|
Protein domain complex with ssDNA . SNAP output
|
|
4qju
|
DNA binding protein-DNA |
X-ray (2.16 Å) |
Kim D-H, Im H, Jee J-G, Jang S-B, Yoon H-J, Kwon A-R,
Kang S-M, Lee B-J |
(2014) "beta-Arm
flexibility of HU from Staphylococcus aureus dictates
the DNA-binding and recognition mechanism."
Acta Crystallogr.,Sect.D, 70,
3273-3289. doi: 10.1107/S1399004714023931.
|
Crystal structure of DNA-bound nucleoid associated
protein, sav1473 . SNAP
output
|
|
4qlc
|
chromatin binding protein-DNA |
X-ray (3.503 Å) |
Zhou BR, Jiang J, Feng H, Ghirlando R, Xiao TS, Bai
Y |
(2015) "Structural
Mechanisms of Nucleosome Recognition by Linker
Histones." Mol.Cell, 33 Suppl
1, 2-3. doi: 10.1016/j.molcel.2015.06.025.
|
Crystal structure of chromatosome at 3.5 angstrom
resolution . SNAP
output
|
|
4qm7
|
transferase-DNA |
X-ray (1.8 Å) |
Das U, Wang LK, Smith P, Munir A, Shuman S |
(2014) "Structures
of bacterial polynucleotide kinase in a michaelis
complex with nucleoside triphosphate (NTP)-Mg2+ and
5'-OH RNA and a mixed substrate-product complex with
NTP-Mg2+ and a 5'-phosphorylated oligonucleotide."
J.Bacteriol., 196, 4285-4292.
doi: 10.1128/JB.02197-14.
|
Structure of bacterial polynucleotide kinase bound to
gtp and pDNA . SNAP
output
|
|
4qpq
|
transcription-DNA |
X-ray (3.106 Å) |
Peng Y, Lu J, Wong JJ, Edwards RA, Frost LS, Mark
Glover JN |
(2014) "Mechanistic
Basis of Plasmid-Specific DNA Binding of the F Plasmid
Regulatory Protein, TraM." J.Mol.Biol.,
426, 3783-3795. doi: 10.1016/j.jmb.2014.09.018.
|
Mechanistic basis of plasmid-specific DNA binding of
the f plasmid regulatory protein, tram . SNAP output
|
|
4qqw
|
hydrolase-DNA |
X-ray (2.664 Å) |
Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione
MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A |
(2014) "Structures
of CRISPR Cas3 offer mechanistic insights into
Cascade-activated DNA unwinding and degradation."
Nat.Struct.Mol.Biol., 21,
771-777. doi: 10.1038/nsmb.2875.
|
Crystal structure of t. fusca cas3 . SNAP output
|
|
4qqx
|
hydrolase-DNA |
X-ray (3.34 Å) |
Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione
MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A |
(2014) "Structures
of CRISPR Cas3 offer mechanistic insights into
Cascade-activated DNA unwinding and degradation."
Nat.Struct.Mol.Biol., 21,
771-777. doi: 10.1038/nsmb.2875.
|
Crystal structure of t. fusca cas3-atp . SNAP output
|
|
4qqy
|
hydrolase-DNA |
X-ray (3.12 Å) |
Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione
MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A |
(2014) "Structures
of CRISPR Cas3 offer mechanistic insights into
Cascade-activated DNA unwinding and degradation."
Nat.Struct.Mol.Biol., 21,
771-777. doi: 10.1038/nsmb.2875.
|
Crystal structure of t. fusca cas3-adp . SNAP output
|
|
4qqz
|
hydrolase-DNA |
X-ray (2.93 Å) |
Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione
MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A |
(2014) "Structures
of CRISPR Cas3 offer mechanistic insights into
Cascade-activated DNA unwinding and degradation."
Nat.Struct.Mol.Biol., 21,
771-777. doi: 10.1038/nsmb.2875.
|
Crystal structure of t. fusca cas3-amppnp . SNAP output
|
|
4qr9
|
DNA binding protein |
X-ray (2.0 Å) |
Sanchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS,
Saperas N, Churchill ME, Campos JL |
(2015) "Two
high-mobility group box domains act together to
underwind and kink DNA." Acta
Crystallogr.,Sect.D, 71,
1423-1432. doi: 10.1107/S1399004715007452.
|
Crystal structure of two hmgb1 box a domains
cooperating to underwind and kink a DNA . SNAP output
|
|
4qtj
|
transcription-DNA |
X-ray (2.1 Å) |
Zhang S, Zhang T, Yan M, Ding J, Chen J |
(2014) "Crystal
structure of the WOPR-DNA complex and implications for
Wor1 function in white-opaque switching of Candida
albicans." Cell Res., 24,
1108-1120. doi: 10.1038/cr.2014.102.
|
Complex of wopr domain of wor1 in candida albicans with
the 13bp dsDNA . SNAP
output
|
|
4qtk
|
transcription-DNA |
X-ray (2.99 Å) |
Zhang S, Zhang T, Yan M, Ding J, Chen J |
(2014) "Crystal
structure of the WOPR-DNA complex and implications for
Wor1 function in white-opaque switching of Candida
albicans." Cell Res., 24,
1108-1120. doi: 10.1038/cr.2014.102.
|
Complex of wopr domain of wor1 in candida albicans with
the 17bp dsDNA . SNAP
output
|
|
4qtr
|
de novo design-DNA |
X-ray (3.2 Å) |
Mou Y, Yu JY, Wannier TM, Guo CL, Mayo SL |
(2015) "Computational
design of co-assembling protein-DNA nanowires."
Nature, 525, 230-233. doi:
10.1038/nature14874.
|
Computational design of co-assembling protein-DNA
nanowires . SNAP
output
|
|
4qw8
|
transferase-DNA |
X-ray (2.29 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Ternary crystal structures of a y-family DNA polymerase
dpo4 from sulfolobus solfataricus in complex with DNA
and d-dctp . SNAP
output
|
|
4qw9
|
transferase-DNA |
X-ray (2.4 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Ternary crystal structures of a y-family DNA polymerase
dpo4 from sulfolobus solfataricus in complex with DNA
and (-)ftc-ppnp . SNAP
output
|
|
4qwa
|
transferase-DNA |
X-ray (2.2 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Ternary crystal structures of a y-family DNA polymerase
dpo4 from sulfolobus solfataricus in complex with DNA
and (-)3tc-dp . SNAP
output
|
|
4qwb
|
transferase-DNA |
X-ray (1.8 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Crystal structure of dpo4 linker region p236a mutant
with an incoming d-dcdp . SNAP output
|
|
4qwc
|
transferase-DNA |
X-ray (2.4 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Ternary crystal structures of a y-family DNA polymerase
dpo4 from sulfobus solfataricus in comples with DNA and
l-dcdp . SNAP output
|
|
4qwd
|
transferase-DNA |
X-ray (2.05 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Ternary crystal structures of a y-family DNA polymerase
dpo4 from sulfolobus solfataricus in complex with DNA
and (-)3tc-ppnp . SNAP
output
|
|
4qwe
|
transferase-DNA |
X-ray (2.2 Å) |
Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY,
Suo Z |
(2014) "Structural
and kinetic insights into binding and incorporation of
L-nucleotide analogs by a Y-family DNA polymerase."
Nucleic Acids Res., 42,
9984-9995. doi: 10.1093/nar/gku709.
|
Ternary crystal structures of a y-family DNA polymerase
dpo4 from sulfolobus solfataricus in complex with DNA
and (-)ftc-dp . SNAP
output
|
|
4qyz
|
immune system-DNA-RNA |
X-ray (3.03 Å) |
Mulepati S, Heroux A, Bailey S |
(2014) "Structural
biology. Crystal structure of a CRISPR RNA-guided
surveillance complex bound to a ssDNA target."
Science, 345, 1479-1484. doi:
10.1126/science.1256996.
|
Crystal structure of a crispr RNA-guided surveillance
complex, cascade, bound to a ssDNA target . SNAP output
|
|
4qz8
|
transferase-DNA |
X-ray (2.7 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt in complex with a dsb substrate, c-g base
pair . SNAP output
|
|
4qz9
|
transferase-DNA |
X-ray (2.05 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt in complex with a dsb substrate, c-a base
pair . SNAP output
|
|
4qza
|
transferase-DNA |
X-ray (2.15 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt in complex with a dsb substrate, c-c base
pair . SNAP output
|
|
4qzb
|
transferase-DNA |
X-ray (2.15 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt in complex with a dsb substrate, c-t base
pair . SNAP output
|
|
4qzc
|
transferase-DNA |
X-ray (2.75 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f405a mutant, in complex with a dsb
substrate, c-g base pair . SNAP output
|
|
4qzd
|
transferase-DNA |
X-ray (2.7 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f405a mutant, in complex with a dsb
substrate, c-c base pair . SNAP output
|
|
4qze
|
transferase-DNA |
X-ray (2.25 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f401a mutant, in complex with a dsb
substrate, c-g base pair . SNAP output
|
|
4qzf
|
transferase-DNA |
X-ray (2.6 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f401a mutant, in complex with a dsb
substrate, c-a base pair . SNAP output
|
|
4qzg
|
transferase-DNA |
X-ray (2.75 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f401a mutant, in complex with a dsb
substrate, c-c base pair . SNAP output
|
|
4qzh
|
transferase-DNA |
X-ray (2.6 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f401a mutant, in complex with a dsb
substrate, c-t base pair . SNAP output
|
|
4qzi
|
transferase-DNA |
X-ray (2.65 Å) |
Gouge J, Rosario S, Romain F, Poitevin F, Beguin P,
Delarue M |
(2015) "Structural
basis for a novel mechanism of DNA bridging and
alignment in eukaryotic DSB DNA repair." Embo
J., 34, 1126-1142. doi: 10.15252/embj.201489643.
|
Mouse tdt, f401a mutant, in complex with a dsb
substrate and zn2+ . SNAP output
|
|
4r22
|
transcription-DNA |
X-ray (2.6 Å) |
Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK,
Whitfill T |
(2015) "Structures
of regulatory machinery reveal novel molecular
mechanisms controlling B. subtilis nitrogen
homeostasis." Genes Dev.,
29, 451-464. doi: 10.1101/gad.254714.114.
|
Tnra-DNA complex . SNAP
output
|
|
4r24
|
transcrption-DNA |
X-ray (2.25 Å) |
Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK,
Whitfill T |
(2015) "Structures
of regulatory machinery reveal novel molecular
mechanisms controlling B. subtilis nitrogen
homeostasis." Genes Dev.,
29, 451-464. doi: 10.1101/gad.254714.114.
|
Complete dissection of b. subtilis nitrogen homeostatic
circuitry . SNAP
output
|
|
4r28
|
hydrolase-DNA |
X-ray (3.055 Å) |
Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ,
Zheng Y, Wilson GG, Cheng X |
(2014) "Modification-dependent
restriction endonuclease, MspJI, flips 5-methylcytosine
out of the DNA helix." Nucleic Acids Res.,
42, 12092-12101. doi: 10.1093/nar/gku871.
|
Mspji restriction endonuclease in complex with 27-mer
oligonucleotide . SNAP
output
|
|
4r2a
|
DNA binding protein-DNA |
X-ray (1.591 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Egr1-zif268 zinc fingers in complex with methylated DNA
. SNAP output
|
|
4r2c
|
DNA binding protein-DNA |
X-ray (1.89 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Egr1-zif268 zinc fingers in complex with
hydroxymethylated DNA . SNAP output
|
|
4r2d
|
DNA binding protein-DNA |
X-ray (2.088 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Egr1-zif268 zinc fingers in complex with formylated DNA
. SNAP output
|
|
4r2e
|
DNA binding protein-DNA |
X-ray (1.84 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) zinc fingers in complex with
methylated DNA . SNAP
output
|
|
4r2p
|
DNA binding protein-DNA |
X-ray (1.788 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) zinc fingers in complex with
hydroxymethylated DNA . SNAP output
|
|
4r2q
|
DNA binding protein-DNA |
X-ray (1.54 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) zinc fingers in complex with
formylated DNA . SNAP
output
|
|
4r2r
|
DNA binding protein-DNA |
X-ray (2.089 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) zinc fingers in complex with
carboxylated DNA . SNAP
output
|
|
4r2s
|
DNA binding protein-DNA |
X-ray (2.489 Å) |
Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang
X, Cheng X |
(2014) "Wilms
tumor protein recognizes 5-carboxylcytosine within a
specific DNA sequence." Genes Dev.,
28, 2304-2313. doi: 10.1101/gad.250746.114.
|
Wilms tumor protein (wt1) q369p zinc fingers in complex
with methylated DNA . SNAP output
|
|
4r4e
|
transcription regulator-DNA |
X-ray (2.57 Å) |
Schumacher MA, Chinnam NB, Cuthbert B, Tonthat NK,
Whitfill T |
(2015) "Structures
of regulatory machinery reveal novel molecular
mechanisms controlling B. subtilis nitrogen
homeostasis." Genes Dev.,
29, 451-464. doi: 10.1101/gad.254714.114.
|
Structure of glnr-DNA complex . SNAP output
|
|
4r55
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Zhang ZF, Gong Y, Chen YY, Li HB, Huang L |
(2015) "Insights
into the interaction between Cren7 and DNA: the role of
loop beta 3-beta 4." Extremophiles,
19, 395-406. doi: 10.1007/s00792-014-0725-y.
|
The crystal structure of a cren7 mutant protein gr and
dsDNA complex . SNAP
output
|
|
4r56
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Zhang ZF, Gong Y, Chen YY, Li HB, Huang L |
(2015) "Insights
into the interaction between Cren7 and DNA: the role of
loop beta 3-beta 4." Extremophiles,
19, 395-406. doi: 10.1007/s00792-014-0725-y.
|
Crystal structure of sulfolobus cren7-dsDNA(gtgatcac)
complex . SNAP
output
|
|
4r5p
|
transferase, hydrolase-DNA-inhibitor |
X-ray (2.894 Å) |
Balzarini J, Das K, Bernatchez JA, Martinez SE, Ngure
M, Keane S, Ford A, Maguire N, Mullins N, John J, Kim Y,
Dehaen W, Vande Voorde J, Liekens S, Naesens L, Gotte M,
Maguire AR, Arnold E |
(2015) "Alpha-carboxy
nucleoside phosphonates as universal nucleoside
triphosphate mimics."
Proc.Natl.Acad.Sci.USA, 112,
3475-3480. doi: 10.1073/pnas.1420233112.
|
Crystal structure of hiv-1 reverse transcriptase (rt)
with DNA and a nucleoside triphosphate mimic
alpha-carboxy nucleoside phosphonate inhibitor .
SNAP output
|
|
4r63
|
transferase-DNA |
X-ray (1.85 Å) |
Beard WA, Shock DD, Batra VK, Prasad R, Wilson
SH |
(2014) "Substrate-induced
DNA Polymerase beta Activation."
J.Biol.Chem., 289,
31411-31422. doi: 10.1074/jbc.M114.607432.
|
Binary complex crystal structure of r258a mutant of DNA
polymerase beta . SNAP
output
|
|
4r64
|
transferase-DNA |
X-ray (2.2 Å) |
Beard WA, Shock DD, Batra VK, Prasad R, Wilson
SH |
(2014) "Substrate-induced
DNA Polymerase beta Activation."
J.Biol.Chem., 289,
31411-31422. doi: 10.1074/jbc.M114.607432.
|
Binary complex crystal structure of e295k mutant of DNA
polymerase beta . SNAP
output
|
|
4r65
|
transferase-DNA |
X-ray (1.95 Å) |
Beard WA, Shock DD, Batra VK, Prasad R, Wilson
SH |
(2014) "Substrate-induced
DNA Polymerase beta Activation."
J.Biol.Chem., 289,
31411-31422. doi: 10.1074/jbc.M114.607432.
|
Ternary complex crystal structure of r258a mutant of
DNA polymerase beta . SNAP output
|
|
4r66
|
transferase-DNA |
X-ray (2.25 Å) |
Beard WA, Shock DD, Batra VK, Prasad R, Wilson
SH |
(2014) "Substrate-induced
DNA Polymerase beta Activation."
J.Biol.Chem., 289,
31411-31422. doi: 10.1074/jbc.M114.607432.
|
Ternary complex crystal structure of e295k mutant of
DNA polymerase beta . SNAP output
|
|
4r79
|
recombination-DNA |
X-ray (3.1 Å) |
Trubitsyna M, Grey H, Houston DR, Finnegan DJ,
Richardson JM |
(2015) "Structural
Basis for the Inverted Repeat Preferences of mariner
Transposases." J.Biol.Chem.,
290, 13531-13540. doi: 10.1074/jbc.M115.636704.
|
Mos1 transposase paired-end complex with left
transposon end . SNAP
output
|
|
4r89
|
hydrolase-DNA |
X-ray (4.002 Å) |
Gwon GH, Kim YR, Liu Y, Watson AT, Jo A, Etheridge
TJ, Yuan F, Zhang Y, Kim YC, Carr AM, Cho Y |
(2014) "Crystal
structure of a Fanconi anemia-associated nuclease
homolog bound to 5' flap DNA: basis of interstrand
cross-link repair by FAN1." Genes Dev.,
28, 2276-2290. doi: 10.1101/gad.248492.114.
|
Crystal structure of pafan1 - 5' flap DNA complex with
manganase . SNAP
output
|
|
4r8a
|
hydrolase-DNA |
X-ray (3.2 Å) |
Gwon GH, Kim YR, Liu Y, Watson AT, Jo A, Etheridge
TJ, Yuan F, Zhang Y, Kim YC, Carr AM, Cho Y |
(2014) "Crystal
structure of a Fanconi anemia-associated nuclease
homolog bound to 5' flap DNA: basis of interstrand
cross-link repair by FAN1." Genes Dev.,
28, 2276-2290. doi: 10.1101/gad.248492.114.
|
Crystal structure of pafan1 - 5' flap DNA complex .
SNAP output
|
|
4r8p
|
structural protein-DNA |
X-ray (3.28 Å) |
McGinty RK, Henrici RC, Tan S |
(2014) "Crystal
structure of the PRC1 ubiquitylation module bound to
the nucleosome." Nature,
514, 591-596. doi: 10.1038/nature13890.
|
Crystal structure of the ring1b-bmi1-ubch5c prc1
ubiquitylation module bound to the nucleosome core
particle . SNAP
output
|
|
4r8u
|
transferase-DNA |
X-ray (2.3 Å) |
Weinert T, Olieric V, Waltersperger S, Panepucci E,
Chen L, Zhang H, Zhou D, Rose J, Ebihara A, Kuramitsu S,
Li D, Howe N, Schnapp G, Pautsch A, Bargsten K, Prota AE,
Surana P, Kottur J, Nair DT, Basilico F, Cecatiello V,
Pasqualato S, Boland A, Weichenrieder O, Wang BC,
Steinmetz MO, Caffrey M, Wang M |
(2015) "Fast
native-SAD phasing for routine macromolecular structure
determination." Nat.Methods,
12, 131-133. doi: 10.1038/nmeth.3211.
|
S-sad structure of dinb-DNA complex . SNAP output
|
|
4rb1
|
metal binding protein-DNA |
X-ray (2.75 Å) |
Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP,
Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi
X, Li X, Wu W, Rohs R, Li Y, Chen Z |
"Mechanistic
insights into metal ion activation and operator
recognition by the ferric uptake regulator."
Nat Commun, 6, 7642. doi:
10.1038/ncomms8642.
|
Crystal structure of magnetospirillum gryphiswaldense
msr-1 fur-mn2+-e. coli fur box . SNAP output
|
|
4rb2
|
metal binding protein-DNA |
X-ray (2.82 Å) |
Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP,
Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi
X, Li X, Wu W, Rohs R, Li Y, Chen Z |
"Mechanistic
insights into metal ion activation and operator
recognition by the ferric uptake regulator."
Nat Commun, 6, 7642. doi:
10.1038/ncomms8642.
|
Crystal structure of magnetospirillum gryphiswaldense
msr-1 semet-fur-mn2+-feoab1 operator . SNAP output
|
|
4rb3
|
metal binding protein-DNA |
X-ray (2.6 Å) |
Deng Z, Wang Q, Liu Z, Zhang M, Machado AC, Chiu TP,
Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi
X, Li X, Wu W, Rohs R, Li Y, Chen Z |
"Mechanistic
insights into metal ion activation and operator
recognition by the ferric uptake regulator."
Nat Commun, 6, 7642. doi:
10.1038/ncomms8642.
|
Crystal structure of magnetospirillum gryphiswaldense
msr-1 fur-mn2+-feoab1 operator . SNAP output
|
|
4rbo
|
DNA binding protein, transcription-DNA |
X-ray (3.3 Å) |
Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T,
Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD,
Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K,
Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ |
(2015) "Structure-based
discovery of NANOG variant with enhanced properties to
promote self-renewal and reprogramming of pluripotent
stem cells." Proc.Natl.Acad.Sci.USA,
112, 4666-4671. doi: 10.1073/pnas.1502855112.
|
Crystal structure of a nanog homeobox (nanog) from homo
sapiens at 3.30 Å resolution . SNAP output
|
|
4rd5
|
hydrolase-DNA |
X-ray (2.7 Å) |
Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M,
Siksnys V |
(2014) "Crystal
structure of the R-protein of the multisubunit
ATP-dependent restriction endonuclease NgoAVII."
Nucleic Acids Res., 42,
14022-14030. doi: 10.1093/nar/gku1237.
|
Crystal structure of r.ngoavii restriction endonuclease
b3 domain with cognate DNA . SNAP output
|
|
4rdm
|
hydrolase-DNA |
X-ray (2.7 Å) |
Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M,
Siksnys V |
(2014) "Crystal
structure of the R-protein of the multisubunit
ATP-dependent restriction endonuclease NgoAVII."
Nucleic Acids Res., 42,
14022-14030. doi: 10.1093/nar/gku1237.
|
Crystal structure of r.ngoavii restriction endonuclease
b3 domain with cognate DNA . SNAP output
|
|
4rdu
|
transcription-DNA |
X-ray (1.85 Å) |
Joint Center for Structural Genomics (JCSG),
Partnership for Stem Cell Biology (STEMCELL) |
"Crystal structure of a distal-less homeobox protein
5 (Dlx5) from Homo sapiens at 1.85 A resolution." |
Crystal structure of a distal-less homeobox protein 5
(dlx5) from homo sapiens at 1.85 Å resolution .
SNAP output
|
|
4rea
|
hydrolase-DNA |
X-ray (3.81 Å) |
Zhao Q, Xue X, Longerich S, Sung P, Xiong Y |
(2014) "Structural
insights into 5' flap DNA unwinding and incision by the
human FAN1 dimer." Nat Commun,
5, 5726. doi: 10.1038/ncomms6726.
|
A nuclease DNA complex . SNAP output
|
|
4reb
|
hydrolase-DNA |
X-ray (4.2 Å) |
Zhao Q, Xue X, Longerich S, Sung P, Xiong Y |
(2014) "Structural
insights into 5' flap DNA unwinding and incision by the
human FAN1 dimer." Nat Commun,
5, 5726. doi: 10.1038/ncomms6726.
|
Structural insights into 5' flap DNA unwinding and
incision by the human fan1 dimer . SNAP output
|
|
4rec
|
hydrolase-DNA |
X-ray (2.2 Å) |
Zhao Q, Xue X, Longerich S, Sung P, Xiong Y |
(2014) "Structural
insights into 5' flap DNA unwinding and incision by the
human FAN1 dimer." Nat Commun,
5, 5726. doi: 10.1038/ncomms6726.
|
A nuclease-DNA complex form 3 . SNAP output
|
|
4ri8
|
hydrolase-DNA |
X-ray (2.9 Å) |
Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska
A, Elledge SJ, Pavletich NP |
(2014) "DNA
repair. Mechanism of DNA interstrand cross-link
processing by repair nuclease FAN1."
Science, 346, 1127-1130. doi:
10.1126/science.1258973.
|
Fan1 nuclease bound to 5' phosphorylated
p(dg)-3'(dt-dt-dt-dt) double flap DNA . SNAP output
|
|
4ri9
|
hydrolase-DNA |
X-ray (2.9 Å) |
Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska
A, Elledge SJ, Pavletich NP |
(2014) "DNA
repair. Mechanism of DNA interstrand cross-link
processing by repair nuclease FAN1."
Science, 346, 1127-1130. doi:
10.1126/science.1258973.
|
Fan1 nuclease bound to 5' phosphorylated
p(dt)-3'(dt-dt-dt-dt-dt-dt-dt-dt) double flap DNA .
SNAP output
|
|
4ria
|
hydrolase-DNA |
X-ray (3.0 Å) |
Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska
A, Elledge SJ, Pavletich NP |
(2014) "DNA
repair. Mechanism of DNA interstrand cross-link
processing by repair nuclease FAN1."
Science, 346, 1127-1130. doi:
10.1126/science.1258973.
|
Fan1 nuclease bound to 5' phosphorylated nicked DNA .
SNAP output
|
|
4rib
|
hydrolase-DNA |
X-ray (3.25 Å) |
Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska
A, Elledge SJ, Pavletich NP |
(2014) "DNA
repair. Mechanism of DNA interstrand cross-link
processing by repair nuclease FAN1."
Science, 346, 1127-1130. doi:
10.1126/science.1258973.
|
Fan1 nuclease bound to 5' phosphorylated p(dt) single
flap DNA . SNAP
output
|
|
4ric
|
hydrolase-DNA |
X-ray (2.8 Å) |
Wang R, Persky NS, Yoo B, Ouerfelli O, Smogorzewska
A, Elledge SJ, Pavletich NP |
(2014) "DNA
repair. Mechanism of DNA interstrand cross-link
processing by repair nuclease FAN1."
Science, 346, 1127-1130. doi:
10.1126/science.1258973.
|
Fan1 nuclease bound to 5' hydroxyl (dt-dt) single flap
DNA . SNAP output
|
|
4rkg
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Zheng S, Villa R, Wang J, Feng Y, Wang J, Becker PB,
Ye K |
(2014) "Structural
basis of X chromosome DNA recognition by the MSL2 CXC
domain during Drosophila dosage compensation."
Genes Dev., 28, 2652-2662.
doi: 10.1101/gad.250936.114.
|
Structure of the msl2 cxc domain bound with a
non-specific (gc)6 DNA . SNAP output
|
|
4rkh
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Zheng S, Villa R, Wang J, Feng Y, Wang J, Becker PB,
Ye K |
(2014) "Structural
basis of X chromosome DNA recognition by the MSL2 CXC
domain during Drosophila dosage compensation."
Genes Dev., 28, 2652-2662.
doi: 10.1101/gad.250936.114.
|
Structure of the msl2 cxc domain bound with a specific
mre sequence . SNAP
output
|
|
4rnm
|
transferase-DNA |
X-ray (2.144 Å) |
Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich
FP |
(2015) "Structural
and Kinetic Analysis of Nucleoside Triphosphate
Incorporation Opposite an Abasic Site by Human
Translesion DNA Polymerase eta."
J.Biol.Chem., 290, 8028-8038.
doi: 10.1074/jbc.M115.637561.
|
Crystal structure of human polymerase eta inserting
dampnpp opposite DNA template containing an abasic site
. SNAP output
|
|
4rnn
|
transferase-DNA |
X-ray (1.808 Å) |
Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich
FP |
(2015) "Structural
and Kinetic Analysis of Nucleoside Triphosphate
Incorporation Opposite an Abasic Site by Human
Translesion DNA Polymerase eta."
J.Biol.Chem., 290, 8028-8038.
doi: 10.1074/jbc.M115.637561.
|
Crystal structure of human polymerase eta inserting
dgmpnpp opposite DNA template containing an abasic site
. SNAP output
|
|
4rno
|
transferase-DNA |
X-ray (2.82 Å) |
Patra A, Zhang Q, Lei L, Su Y, Egli M, Guengerich
FP |
(2015) "Structural
and Kinetic Analysis of Nucleoside Triphosphate
Incorporation Opposite an Abasic Site by Human
Translesion DNA Polymerase eta."
J.Biol.Chem., 290, 8028-8038.
doi: 10.1074/jbc.M115.637561.
|
Crystal structure of human polymerase eta extending an
abasic site-da pair by inserting dctp opposite template
g . SNAP output
|
|
4roc
|
transcription |
X-ray (1.9 Å) |
Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ,
Cousin P, Dergai O, Hernandez N, Vannini A |
(2015) "Redox
Signaling by the RNA Polymerase III TFIIB-Related
Factor Brf2." Cell(Cambridge,Mass.),
163, 1375-1387. doi: 10.1016/j.cell.2015.11.005.
|
Human tfiib-related factor 2 (brf2) and tbp bound to
u6#2 promoter . SNAP
output
|
|
4rod
|
transcription |
X-ray (2.7 Å) |
Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ,
Cousin P, Dergai O, Hernandez N, Vannini A |
(2015) "Redox
Signaling by the RNA Polymerase III TFIIB-Related
Factor Brf2." Cell(Cambridge,Mass.),
163, 1375-1387. doi: 10.1016/j.cell.2015.11.005.
|
Human tfiib-related factor 2 (brf2) and tbp bound to
trnau1 promoter . SNAP
output
|
|
4roe
|
transcription |
X-ray (2.2 Å) |
Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ,
Cousin P, Dergai O, Hernandez N, Vannini A |
(2015) "Redox
Signaling by the RNA Polymerase III TFIIB-Related
Factor Brf2." Cell(Cambridge,Mass.),
163, 1375-1387. doi: 10.1016/j.cell.2015.11.005.
|
Human tfiib-related factor 2 (brf2) and tbp bound to
rpph1 promoter . SNAP
output
|
|
4rpx
|
transferase-DNA |
X-ray (1.9 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Precatalytic ternary complex of human DNA polymerase
beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog) and dctp in the
presence of cacl2 . SNAP
output
|
|
4rpy
|
transferase-DNA |
X-ray (1.9 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine(8-oxog) and dctp soaked with
mgcl2 for 30 s . SNAP
output
|
|
4rpz
|
transferase-DNA |
X-ray (2.19 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog)and dctp soaked with
mgcl2 for 60 s . SNAP
output
|
|
4rq0
|
transferase-DNA |
X-ray (2.2 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog)and dctp soaked with
mgcl2 for 80 s . SNAP
output
|
|
4rq1
|
transferase-DNA |
X-ray (2.7 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine(8-oxog) and dctp soaked with
mgcl2 for 1hr . SNAP
output
|
|
4rq2
|
transferase-DNA |
X-ray (2.2 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog)and dctp soaked with
mncl2 for 35 s . SNAP
output
|
|
4rq3
|
transferase-DNA |
X-ray (2.0 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Precatalytic ternary complex of human DNA polymerase
beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog) and datp in the
presence of cacl2 . SNAP
output
|
|
4rq4
|
transferase-DNA |
X-ray (2.1 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine(8-oxog) and datp soaked with
mgcl2 for 30 s . SNAP
output
|
|
4rq5
|
transferase-DNA |
X-ray (2.32 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog)and datp soaked with
mgcl2 for 60 s . SNAP
output
|
|
4rq6
|
transferase-DNA |
X-ray (2.25 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine(8-oxog) and datp soaked with
mgcl2 for 80 s . SNAP
output
|
|
4rq7
|
transferase-DNA |
X-ray (2.0 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine (8-oxog)and datp soaked with
mgcl2 for 1hr . SNAP
output
|
|
4rq8
|
transferase-DNA |
X-ray (2.0 Å) |
Vyas R, Reed AJ, Tokarsky EJ, Suo Z |
(2015) "Viewing
Human DNA Polymerase beta Faithfully and Unfaithfully
Bypass an Oxidative Lesion by Time-Dependent
Crystallography." J.Am.Chem.Soc.,
137, 5225-5230. doi: 10.1021/jacs.5b02109.
|
Human DNA polymerase beta with gapped DNA containing an
8-oxo-7,8-dihydro-guanine(8-oxog) and datp soaked with
mncl2 for 35 s . SNAP
output
|
|
4rt2
|
transferase-DNA |
X-ray (1.92 Å) |
Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson
SH, Goodman MF, McKenna CE |
(2015) "Two
Scaffolds from Two Flips: (alpha, beta)/(beta, gamma)
CH2/NH "Met-Im" Analogues of dTTP."
Org.Lett., 17, 2586-2589.
doi: 10.1021/acs.orglett.5b00799.
|
Ternary complex crystal structure of DNA polymerase
beta with (alpha,beta)-ch2-(beta,gamma)-nh-dttp .
SNAP output
|
|
4rt3
|
transferase-DNA |
X-ray (1.92 Å) |
Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson
SH, Goodman MF, McKenna CE |
(2015) "Two
Scaffolds from Two Flips: (alpha, beta)/(beta, gamma)
CH2/NH "Met-Im" Analogues of dTTP."
Org.Lett., 17, 2586-2589.
doi: 10.1021/acs.orglett.5b00799.
|
Ternary complex crystal structure of DNA polymerase
beta with (alpha, beta)-nh-(beta,gamma)-ch2-dttp .
SNAP output
|
|
4rtj
|
transferase-DNA |
X-ray (1.99 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
A non-cognate complex of escherichia coli DNA adenine
methyltransferase (dam) with DNA and sinefungin .
SNAP output
|
|
4rtk
|
transferase-DNA |
X-ray (1.96 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with sah and with DNA
containing distal pap regulon sequence . SNAP output
|
|
4rtl
|
transferase-DNA |
X-ray (2.193 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with sinefungin and with DNA
containing distal pap regulon sequence . SNAP output
|
|
4rtm
|
transferase-DNA |
X-ray (2.5 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with adomet and with DNA
containing distal pap regulon sequence . SNAP output
|
|
4rtn
|
transferase-DNA |
X-ray (2.59 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with adohcy and with DNA
containing proximal pap regulon sequence . SNAP output
|
|
4rto
|
transferase-DNA |
X-ray (2.69 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with sinefungin and with DNA
containing proximal pap regulon sequence . SNAP output
|
|
4rtp
|
transferase-DNA |
X-ray (2.39 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with adomet and with DNA
containing proximal pap regulon sequence . SNAP output
|
|
4rtq
|
transferase-DNA |
X-ray (1.997 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with adohcy and a 5-bp
non-canonical site (gttta ) . SNAP output
|
|
4rtr
|
transferase-DNA |
X-ray (2.393 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with adomet and a 5-bp
non-canonical site (gttta ) . SNAP output
|
|
4rts
|
transferase-DNA |
X-ray (2.49 Å) |
Horton JR, Zhang X, Blumenthal RM, Cheng X |
(2015) "Structures
of Escherichia coli DNA adenine methyltransferase (Dam)
in complex with a non-GATC sequence: potential
implications for methylation-independent
transcriptional repression." Nucleic Acids
Res., 43, 4296-4308. doi:
10.1093/nar/gkv251.
|
Complex of escherichia coli DNA adenine
methyltransferase (dam) with adomet and a 5-bp
non-canonical site (gtcta) . SNAP output
|
|
4ru9
|
transferase-DNA |
X-ray (2.65 Å) |
Patra A, Banerjee S, Johnson Salyard TL, Malik CK,
Christov PP, Rizzo CJ, Stone MP, Egli M |
(2015) "Structural
Basis for Error-Free Bypass of the
5-N-Methylformamidopyrimidine-dG Lesion by Human DNA
Polymerase eta and Sulfolobus solfataricus P2
Polymerase IV." J.Am.Chem.Soc.,
137, 7011-7014. doi: 10.1021/jacs.5b02701.
|
Crystal structure of human DNA polymerase eta inserting
dcmpnpp opposite a mefapy-dg adducted DNA template .
SNAP output
|
|
4rua
|
transferase-DNA |
X-ray (3.07 Å) |
Patra A, Banerjee S, Johnson Salyard TL, Malik CK,
Christov PP, Rizzo CJ, Stone MP, Egli M |
(2015) "Structural
Basis for Error-Free Bypass of the
5-N-Methylformamidopyrimidine-dG Lesion by Human DNA
Polymerase eta and Sulfolobus solfataricus P2
Polymerase IV." J.Am.Chem.Soc.,
137, 7011-7014. doi: 10.1021/jacs.5b02701.
|
Crystal structure of y-family DNA polymerase dpo4
bypassing a mefapy-dg adduct . SNAP output
|
|
4ruc
|
transferase-DNA |
X-ray (2.9 Å) |
Patra A, Banerjee S, Johnson Salyard TL, Malik CK,
Christov PP, Rizzo CJ, Stone MP, Egli M |
(2015) "Structural
Basis for Error-Free Bypass of the
5-N-Methylformamidopyrimidine-dG Lesion by Human DNA
Polymerase eta and Sulfolobus solfataricus P2
Polymerase IV." J.Am.Chem.Soc.,
137, 7011-7014. doi: 10.1021/jacs.5b02701.
|
Crystal structure of y-family DNA polymerase dpo4
extending from a mefapy-dg:dc pair . SNAP output
|
|
4rul
|
isomerase-DNA |
X-ray (2.9 Å) |
Tan K, Zhou Q, Cheng B, Zhang Z, Joachimiak A,
Tse-Dinh YC |
(2015) "Structural
basis for suppression of hypernegative DNA supercoiling
by E. coli topoisomerase I." Nucleic Acids
Res., 43, 11031-11046. doi:
10.1093/nar/gkv1073.
|
Crystal structure of full-length e.coli topoisomerase i
in complex with ssDNA . SNAP output
|
|
4rve
|
hydrolase-DNA |
X-ray (3.0 Å) |
Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown
RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson
KS |
(1993) "The
crystal structure of EcoRV endonuclease and of its
complexes with cognate and non-cognate DNA
fragments." EMBO J., 12,
1781-1795.
|
The crystal structure of ecorv endonuclease and of its
complexes with cognate and non-cognate DNA segments .
SNAP output
|
|
4rzr
|
transferase-DNA |
X-ray (2.2 Å) |
Vyas R, Efthimiopoulos G, Tokarsky EJ, Malik CK, Basu
AK, Suo Z |
(2015) "Mechanistic
Basis for the Bypass of a Bulky DNA Adduct Catalyzed by
a Y-Family DNA Polymerase."
J.Am.Chem.Soc., 137,
12131-12142. doi: 10.1021/jacs.5b08027.
|
Bypass of a bulky adduct dg1,8 by dpo4 . SNAP output
|
|
4s04
|
transcription-DNA |
X-ray (3.2 Å) |
Lou YC, Weng TH, Li YC, Kao YF, Lin WF, Peng HL, Chou
SH, Hsiao CD, Chen C |
(2015) "Structure
and dynamics of polymyxin-resistance-associated
response regulator PmrA in complex with promoter
DNA." Nat Commun, 6,
8838. doi: 10.1038/ncomms9838.
|
Crystal structure of klebsiella pneumoniae pmra in
complex with pmra box DNA . SNAP output
|
|
4s05
|
transcription-DNA |
X-ray (3.8 Å) |
Lou YC, Weng TH, Li YC, Kao YF, Lin WF, Peng HL, Chou
SH, Hsiao CD, Chen C |
(2015) "Structure
and dynamics of polymyxin-resistance-associated
response regulator PmrA in complex with promoter
DNA." Nat Commun, 6,
8838. doi: 10.1038/ncomms9838.
|
Crystal structure of klebsiella pneumoniae pmra in
complex with pmra box DNA . SNAP output
|
|
4s0h
|
transcription-DNA |
X-ray (2.817 Å) |
Pradhan L, Gopal S, Li S, Ashur S, Suryanarayanan S,
Kasahara H, Nam HJ |
(2016) "Intermolecular
Interactions of Cardiac Transcription Factors NKX2.5
and TBX5." Biochemistry,
55, 1702-1710. doi: 10.1021/acs.biochem.6b00171.
|
Tbx5 db, nkx2.5 hd, anf DNA complex . SNAP output
|
|
4s0n
|
DNA binding protein-DNA |
X-ray (1.501 Å) |
Kile AC, Chavez DA, Bacal J, Eldirany S, Korzhnev DM,
Bezsonova I, Eichman BF, Cimprich KA |
(2015) "HLTF's
Ancient HIRAN Domain Binds 3' DNA Ends to Drive
Replication Fork Reversal." Mol.Cell,
58, 1090-1100. doi: 10.1016/j.molcel.2015.05.013.
|
Crystal structure of hltf hiran domain bound to DNA .
SNAP output
|
|
4s20
|
transferase-DNA-RNA |
X-ray (4.7 Å) |
Liu B, Zuo Y, Steitz TA |
(2015) "Structural
basis for transcription reactivation by RapA."
Proc.Natl.Acad.Sci.USA, 112,
2006-2010. doi: 10.1073/pnas.1417152112.
|
Structural basis for transcription reactivation by rapa
. SNAP output
|
|
4s2q
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Vivekanandan S, Moovarkumudalvan B, Lescar J,
Kolatkar PR |
"Crystal Structure of HMG domain of the
chondrogenesis master regulator, Sox9 in complex with
ChIP-Seq identified DNA element." |
Crystal structure of hmg domain of the chondrogenesis
master regulator, sox9 in complex with chip-seq
identified DNA element . SNAP output
|
|
4skn
|
hydrolase-DNA |
X-ray (2.9 Å) |
Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE,
Tainer JA |
(1996) "A
nucleotide-flipping mechanism from the structure of
human uracil-DNA glycosylase bound to DNA."
Nature, 384, 87-92. doi:
10.1038/384087a0.
|
A nucleotide-flipping mechanism from the structure of
human uracil-DNA glycosylase bound to DNA . SNAP output
|
|
4tmu
|
hydrolase-DNA |
X-ray (2.4 Å) |
Manthei KA, Hill MC, Burke JE, Butcher SE, Keck
JL |
(2015) "Structural
mechanisms of DNA binding and unwinding in bacterial
RecQ helicases." Proc.Natl.Acad.Sci.USA,
112, 4292-4297. doi: 10.1073/pnas.1416746112.
|
Crystal structure of recq catalytic core from c.
sakazakii bound to DNA . SNAP output
|
|
4tnt
|
DNA binding protein-DNA |
X-ray (2.39 Å) |
Hudson WH, Youn C, Ortlund EA |
(2014) "Crystal
structure of the mineralocorticoid receptor DNA binding
domain in complex with DNA." Plos One,
9, e107000. doi: 10.1371/journal.pone.0107000.
|
Structure of the human mineralocorticoid receptor in
complex with DNA . SNAP
output
|
|
4tqr
|
transferase-DNA |
X-ray (1.58 Å) |
Xu W, Ouellette AM, Wawrzak Z, Shriver SJ, Anderson
SM, Zhao L |
(2015) "Kinetic
and Structural Mechanisms of
(5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA
Replication Stalling." Biochemistry,
54, 639-651. doi: 10.1021/bi5014936.
|
Ternary complex of y-family DNA polymerase dpo4 with
(5's)-8,5'-cyclo-2'-deoxyguanosine and dttp . SNAP output
|
|
4tqs
|
transferase-DNA |
X-ray (2.06 Å) |
Xu W, Ouellette AM, Wawrzak Z, Shriver SJ, Anderson
SM, Zhao L |
(2015) "Kinetic
and Structural Mechanisms of
(5'S)-8,5'-Cyclo-2'-deoxyguanosine-Induced DNA
Replication Stalling." Biochemistry,
54, 639-651. doi: 10.1021/bi5014936.
|
Ternary complex of y-family DNA polymerase dpo4 with
(5's)-8,5'-cyclo-2'-deoxyguanosine and dctp . SNAP output
|
|
4tu7
|
RNA binding protein-DNA |
X-ray (2.087 Å) |
Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf
CL |
(2014) "Structure-guided
U2AF65 variant improves recognition and splicing of a
defective pre-mRNA."
Proc.Natl.Acad.Sci.USA, 111,
17420-17425. doi: 10.1073/pnas.1412743111.
|
Structure of u2af65 d231v variant with bru5 DNA .
SNAP output
|
|
4tu8
|
RNA binding protein-DNA |
X-ray (1.918 Å) |
Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf
CL |
(2014) "Structure-guided
U2AF65 variant improves recognition and splicing of a
defective pre-mRNA."
Proc.Natl.Acad.Sci.USA, 111,
17420-17425. doi: 10.1073/pnas.1412743111.
|
Structure of u2af65 variant with bru5a6 DNA . SNAP output
|
|
4tu9
|
RNA binding protein-DNA |
X-ray (1.992 Å) |
Agrawal AA, McLaughlin KJ, Jenkins JL, Kielkopf
CL |
(2014) "Structure-guided
U2AF65 variant improves recognition and splicing of a
defective pre-mRNA."
Proc.Natl.Acad.Sci.USA, 111,
17420-17425. doi: 10.1073/pnas.1412743111.
|
Structure of u2af65 variant with bru5g6 DNA . SNAP output
|
|
4tug
|
DNA binding protein-DNA |
X-ray (3.55 Å) |
Sung S, Li F, Park YB, Kim JS, Kim AK, Song OK, Kim
J, Che J, Lee SE, Cho Y |
(2014) "DNA end
recognition by the Mre11 nuclease dimer: insights into
resection and repair of damaged DNA." Embo
J., 33, 2422-2435. doi: 10.15252/embj.201488299.
|
Crystal structure of mjmre11-dna2 complex . SNAP output
|
|
4tui
|
DNA binding protein-DNA |
X-ray (3.59 Å) |
Sung S, Li F, Park YB, Kim JS, Kim AK, Song OK, Kim
J, Che J, Lee SE, Cho Y |
(2014) "DNA end
recognition by the Mre11 nuclease dimer: insights into
resection and repair of damaged DNA." Embo
J., 33, 2422-2435. doi: 10.15252/embj.201488299.
|
Crystal structure of mjmre11-dna1 complex . SNAP output
|
|
4tup
|
transferase,lyase-DNA |
X-ray (1.8 Å) |
Koag MC, Lai L, Lee S |
(2014) "Structural
Basis for the Inefficient Nucleotide Incorporation
Opposite Cisplatin-DNA Lesion by Human DNA Polymerase
beta." J.Biol.Chem., 289,
31341-31348. doi: 10.1074/jbc.M114.605451.
|
Structure of human DNA polymerase beta complexed with
gg as the template (gg0b) in a 1-nucleotide gapped DNA
. SNAP output
|
|
4tuq
|
transferase,lyase-DNA |
X-ray (2.367 Å) |
Koag MC, Lai L, Lee S |
(2014) "Structural
Basis for the Inefficient Nucleotide Incorporation
Opposite Cisplatin-DNA Lesion by Human DNA Polymerase
beta." J.Biol.Chem., 289,
31341-31348. doi: 10.1074/jbc.M114.605451.
|
Human DNA polymerase beta inserting dcmpnpp opposite gg
template (gg0b). . SNAP
output
|
|
4tur
|
transferase,lyase-DNA |
X-ray (2.169 Å) |
Koag MC, Lai L, Lee S |
(2014) "Structural
Basis for the Inefficient Nucleotide Incorporation
Opposite Cisplatin-DNA Lesion by Human DNA Polymerase
beta." J.Biol.Chem., 289,
31341-31348. doi: 10.1074/jbc.M114.605451.
|
Human DNA polymerase beta inserting dcmpnpp opposite
the 5'g of cisplatin crosslinked gs (pt-gg2) . SNAP output
|
|
4tus
|
transferase,lyase-DNA |
X-ray (2.42 Å) |
Koag MC, Lai L, Lee S |
(2014) "Structural
Basis for the Inefficient Nucleotide Incorporation
Opposite Cisplatin-DNA Lesion by Human DNA Polymerase
beta." J.Biol.Chem., 289,
31341-31348. doi: 10.1074/jbc.M114.605451.
|
Human DNA polymerase beta inserting dcmpnpp opposite
the 5'g of cisplatin crosslinked gs (pt-gg2) with
manganese in the active site. . SNAP output
|
|
4tyn
|
hydrolase-DNA |
X-ray (2.959 Å) |
Mallam AL, Sidote DJ, Lambowitz AM |
(2014) "Molecular
insights into RNA and DNA helicase evolution from the
determinants of specificity for a DEAD-box RNA
helicase." Elife, 3,
e04630. doi: 10.7554/eLife.04630.
|
Dead-box helicase mss116 bound to ssDNA and adp-bef .
SNAP output
|
|
4tzd
|
carbohydrate binding protein-DNA |
X-ray (3.2 Å) |
Vieira DBHA, Delatorre P, Cavada BS, Nobrega RB,
Teixeira CS, Silva-Filho JC, Lima EM, Rocha BAM |
"Crystal structure of Canavalia maritima lectin
(ConM) complexed with interleukin 1 - beta primer." |
Crystal structure of canavalia maritima lectin (conm)
complexed with interleukin - 1 beta primer . SNAP output
|
|
4u0y
|
transcription |
X-ray (1.91 Å) |
Fillenberg SB, Grau FC, Seidel G, Muller YA |
(2015) "Structural
insight into operator dre-sites recognition and
effector binding in the GntR/HutC transcription
regulator NagR." Nucleic Acids Res.,
43, 1283-1296. doi: 10.1093/nar/gku1374.
|
Crystal structure of the DNA-binding domains of yvoa in
complex with palindromic operator DNA . SNAP output
|
|
4u6p
|
transferase-DNA |
X-ray (2.593 Å) |
Jha V, Bian C, Xing G, Ling H |
(2016) "Structure
and mechanism of error-free replication past the major
benzo[a]pyrene adduct by human DNA polymerase
kappa." Nucleic Acids Res.,
44, 4957-4967. doi: 10.1093/nar/gkw204.
|
Structural mechanism of error-free bypass of major
benzo[a]pyrene adduct by human polymerase kappa .
SNAP output
|
|
4u7b
|
hydrolase-DNA |
X-ray (3.09 Å) |
Dornan J, Grey H, Richardson JM |
(2015) "Structural
role of the flanking DNA in mariner transposon
excision." Nucleic Acids Res.,
43, 2424-2432. doi: 10.1093/nar/gkv096.
|
Crystal structure of a pre-cleavage mos1 transpososome
. SNAP output
|
|
4u7c
|
transferase-DNA |
X-ray (2.8 Å) |
Jha V, Bian C, Xing G, Ling H |
(2016) "Structure
and mechanism of error-free replication past the major
benzo[a]pyrene adduct by human DNA polymerase
kappa." Nucleic Acids Res.,
44, 4957-4967. doi: 10.1093/nar/gkw204.
|
Structure of DNA polymerase kappa in complex with
benzopyrene adducted DNA . SNAP output
|
|
4u7d
|
hydrolase-DNA |
X-ray (3.4 Å) |
Pike AC, Gomathinayagam S, Swuec P, Berti M, Zhang Y,
Schnecke C, Marino F, von Delft F, Renault L, Costa A,
Gileadi O, Vindigni A |
(2015) "Human
RECQ1 helicase-driven DNA unwinding, annealing, and
branch migration: Insights from DNA complex
structures." Proc.Natl.Acad.Sci.USA,
112, 4286-4291. doi: 10.1073/pnas.1417594112.
|
Structure of human recq-like helicase in complex with
an oligonucleotide . SNAP output
|
|
4uaw
|
transferase, lyase-DNA |
X-ray (1.9 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta substrate complex with a templating
adenine and incoming 8-oxodgtp, 0 s . SNAP output
|
|
4uay
|
transferase, lyase-DNA |
X-ray (1.984 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta product complex with a templating
adenine and inserted 8-oxodgmp, 40 s . SNAP output
|
|
4uaz
|
transferase, lyase-DNA |
X-ray (1.88 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta reactant complex with a templating
adenine and incoming 8-oxodgtp, 20 s . SNAP output
|
|
4ub1
|
transferase, lyase-DNA |
X-ray (2.341 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta product complex with a templating
adenine and 8-oxodgmp, 90 s . SNAP output
|
|
4ub2
|
transferase, lyase-DNA |
X-ray (2.51 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta product complex with a templating
cytosine and 8-oxodgmp, 120 s . SNAP output
|
|
4ub3
|
transferase, lyase-DNA |
X-ray (2.06 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta closed product complex with a
templating cytosine and 8-oxodgmp, 60 s . SNAP output
|
|
4ub4
|
transferase, lyase-DNA |
X-ray (1.954 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta substrate complex with a templating
cytosine and incoming dgtp, 0 s . SNAP output
|
|
4ub5
|
transferase, lyase-DNA |
X-ray (2.15 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta substrate complex with a templating
cytosine, incoming 8-oxodgtp, and mn2+, 5 s . SNAP output
|
|
4ubb
|
transferase, lyase-DNA |
X-ray (1.9 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta reactant complex with a templating
cytosine and incoming 8-oxodgtp, 40 s . SNAP output
|
|
4ubc
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Freudenthal BD, Beard WA, Perera L, Shock DD, Kim T,
Schlick T, Wilson SH |
(2015) "Uncovering
the polymerase-induced cytotoxicity of an oxidized
nucleotide." Nature, 517,
635-639. doi: 10.1038/nature13886.
|
DNA polymerase beta substrate complex with a templating
cytosine and incoming 8-oxodgtp, 0 s . SNAP output
|
|
4ug0
|
ribosome |
cryo-EM (3.6 Å) |
Khatter K, Mysanikov AG, Natchiar SK, Klaholz BP |
(2015) "Structure
of the human 80S ribosome." NATURE,
520, 640-645. doi: 10.1038/nature14427.
|
Structure of the human 80s ribosome . SNAP output
|
|
4umk
|
DNA binding protein-DNA |
X-ray (3.096 Å) |
Chen BW, Lin MH, Chu CH, Hsu CE, Sun YJ |
(2015) "Insights
into ParB spreading from the complex structure of Spo0J
and parS." Proc. Natl. Acad. Sci. U.S.A.,
112, 6613-6618. doi: 10.1073/pnas.1421927112.
|
The complex of spo0j and pars DNA in chromosomal
partition system . SNAP
output
|
|
4umm
|
nuclear receptor |
cryo-EM (11.6 Å) |
Maletta M, Orlov I, Moras D, Billas IML, Klaholz
BP |
(2014) "The
Palindromic DNA-Bound Usp-Ecr Nuclear Receptor Adopts
an Asymmetric Organization with Allosteric Domain
Positioning." Nat.Commun.,
5, 4139. doi: 10.1038/NCOMMS5139.
|
The cryo-EM structure of the palindromic DNA-bound
usp-ecr nuclear receptor reveals an asymmetric
organization with allosteric domain positioning .
SNAP output
|
|
4un3
|
hydrolase-DNA-RNA |
X-ray (2.593 Å) |
Anders C, Niewoehner O, Duerst A, Jinek M |
(2014) "Structural
Basis of Pam-Dependent Target DNA Recognition by the
Cas9 Endonuclease." Nature,
513, 569. doi: 10.1038/NATURE13579.
|
Crystal structure of cas9 bound to pam-containing DNA
target . SNAP output
|
|
4un4
|
hydrolase-DNA-RNA |
X-ray (2.371 Å) |
Anders C, Niewoehner O, Duerst A, Jinek M |
(2014) "Structural
Basis of Pam-Dependent Target DNA Recognition by the
Cas9 Endonuclease." Nature,
513, 569. doi: 10.1038/NATURE13579.
|
Crystal structure of cas9 bound to pam-containing DNA
target with mismatches at positions 1-2 . SNAP output
|
|
4un5
|
hydrolase-DNA-RNA |
X-ray (2.4 Å) |
Anders C, Niewoehner O, Duerst A, Jinek M |
(2014) "Structural
Basis of Pam-Dependent Target DNA Recognition by the
Cas9 Endonuclease." Nature,
513, 569. doi: 10.1038/NATURE13579.
|
Crystal structure of cas9 bound to pam-containing DNA
target containing mismatches at positions 1-3 .
SNAP output
|
|
4un7
|
hydrolase-DNA |
X-ray (2.7 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA before incubation in 5mm mn (state 1) .
SNAP output
|
|
4un8
|
hydrolase-DNA |
X-ray (2.6 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 1h incubation in 5mm mn (state 2) .
SNAP output
|
|
4un9
|
hydrolase-DNA |
X-ray (2.734 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 8h incubation in 5mm mn (state 3) .
SNAP output
|
|
4una
|
hydrolase-DNA |
X-ray (2.3 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 2 days incubation in 5mm mn (state 4) .
SNAP output
|
|
4unb
|
hydrolase-DNA |
X-ray (2.55 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 6 days incubation in 5mm mn (state 5) .
SNAP output
|
|
4unc
|
hydrolase-DNA |
X-ray (2.3 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 8 days incubation in 5mm mn (state 6) .
SNAP output
|
|
4uno
|
DNA binding protein |
X-ray (1.95 Å) |
Cooper CDO, Newman JA, Aitkenhead H, Allerston CK,
Gileadi O |
(2015) "Structures
of the Ets Domains of Transcription Factors Etv1, Etv4,
Etv5 and Fev: Determinants of DNA Binding and Redox
Regulation by Disulfide Bond Formation."
J.Biol.Chem., 290, 13692.
doi: 10.1074/JBC.M115.646737.
|
Crystal structure of the ets domain of human etv5 in
complex with DNA . SNAP
output
|
|
4uqg
|
transferase-DNA |
X-ray (2.0 Å) |
Tomas-Gamasa M, Serdjukow S, Su M, Muller M, Carell
T |
(2015) ""Post-it"
type connected DNA created with a reversible covalent
cross-link." Angew. Chem. Int. Ed. Engl.,
54, 796-800. doi: 10.1002/anie.201407854.
|
A new bio-isosteric base pair based on reversible
bonding . SNAP
output
|
|
4uqm
|
hydrolase-DNA |
X-ray (1.35 Å) |
Pedersen HL, Johnson KA, McVey CE, Leiros I, Moe
E |
(2015) "Structure
determination of uracil-DNA N-glycosylase from
Deinococcus radiodurans in complex with DNA."
Acta Crystallogr. D Biol. Crystallogr.,
71, 2137-2149. doi: 10.1107/S1399004715014157.
|
Crystal structure determination of uracil-DNA
n-glycosylase (ung) from deinococcus radiodurans in
complex with DNA - new insights into the role of the
leucine-loop for damage recognition and repair .
SNAP output
|
|
4usg
|
transcription |
X-ray (1.973 Å) |
Huang J, Zhao Y, Liu H, Huang D, Cheng X, Zhao W,
Taylor IA, Liu J, Peng YL |
(2015) "Substitution
of Tryptophan 89 with Tyrosine Switches the DNA Binding
Mode of Pc4." Sci.Rep.,
5, 8789. doi: 10.1038/SREP08789.
|
Crystal structure of pc4 w89y mutant complex with DNA .
SNAP output
|
|
4ut0
|
hydrolase-DNA |
X-ray (2.4 Å) |
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ,
Orozco M, Prieto J, Montoya G |
(2015) "Visualizing
Phosphodiester-Bond Hydrolysis by an Endonuclease."
Nat.Struct.Mol.Biol., 22, 65.
doi: 10.1038/NSMB.2932.
|
The crystal structure of i-dmoi in complex with its
target DNA at 10 days incubation in 5mm mn (state 7) .
SNAP output
|
|
4uus
|
transcription |
X-ray (2.55 Å) |
Foos N, Maurel-Zaffran C, Mate MJ, Vincentelli R,
Hainaut M, Berenger H, Pradel J, Saurin AJ,
Ortiz-Lombardia M, Graba Y |
(2015) "A
Flexible Extension of the Drosophila Ultrabithorax
Homeodomain Defines a Novel Hox/Pbc Interaction
Mode." Structure, 23,
270. doi: 10.1016/J.STR.2014.12.011.
|
Crystal structure of a ubx-exd-DNA complex including
the ubda motif . SNAP
output
|
|
4uuv
|
transcription |
X-ray (2.8 Å) |
Cooper CDO, Newman JA, Aitkenhead H, Allerston CK,
Gileadi O |
(2015) "Structures
of the Ets Domains of Transcription Factors Etv1, Etv4,
Etv5 and Fev: Determinants of DNA Binding and Redox
Regulation by Disulfide Bond Formation."
J.Biol.Chem., 290, 13692.
doi: 10.1074/JBC.M115.646737.
|
Structure of the DNA binding ets domain of human etv4
in complex with DNA . SNAP output
|
|
4ux5
|
transcription |
X-ray (2.4 Å) |
Liu J, Huang J, Zhao Y, Liu H, Wang D, Yang J, Zhao
W, Taylor IA, Peng Y |
(2015) "Structural
Basis of DNA Recognition by Pcg2 Reveals a Novel DNA
Binding Mode for Winged Helix-Turn-Helix Domains."
Nucleic Acids Res., 43, 1231.
doi: 10.1093/NAR/GKU1351.
|
Structure of DNA complex of pcg2 . SNAP output
|
|
4uzb
|
viral protein-DNA |
X-ray (2.865 Å) |
Hellert J, Weidner-Glunde M, Krausze J, Lunsdorf H,
Ritter C, Schulz TF, Luhrs T |
(2015) "The 3D
Structure of Kaposi Sarcoma Herpesvirus Lana C-Terminal
Domain Bound to DNA."
Proc.Natl.Acad.Sci.USA, 112,
6694. doi: 10.1073/PNAS.1421804112.
|
Kshv lana (orf73) c-terminal domain mutant bound to
lbs1 DNA (r1039q, r1040q, k1055e, k1109a, d1110a,
a1121e, k1138s, k1140d, k1141d) . SNAP output
|
|
4v1m
|
transcription |
cryo-EM (6.6 Å) |
Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann
M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W,
Herzog F, Villa E, Cramer P |
(2015) "Architecture
of the RNA Polymerase II-Mediator Core Initiation
Complex." Nature, 518,
376. doi: 10.1038/NATURE14229.
|
Architecture of the RNA polymerase ii-mediator core
transcription initiation complex . SNAP output
|
|
4v1n
|
transcription |
cryo-EM (7.8 Å) |
Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann
M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W,
Herzog F, Villa E, Cramer P |
(2015) "Architecture
of the RNA Polymerase II-Mediator Core Initiation
Complex." Nature, 518,
376. doi: 10.1038/NATURE14229.
|
Architecture of the RNA polymerase ii-mediator core
transcription initiation complex . SNAP output
|
|
4v1o
|
transcription |
cryo-EM (9.7 Å) |
Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann
M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W,
Herzog F, Villa E, Cramer P |
(2015) "Architecture
of the RNA Polymerase II-Mediator Core Initiation
Complex." Nature, 518,
376. doi: 10.1038/NATURE14229.
|
Architecture of the RNA polymerase ii-mediator core
transcription initiation complex . SNAP output
|
|
4v3p
|
ribosome |
cryo-EM (34.0 Å) |
Myasnikov AG, Afonina ZA, Menetret JF, Shirokov VA,
Spirin AS, Klaholz BP |
(2014) "The
molecular structure of the left-handed supra-molecular
helix of eukaryotic polyribosomes." Nat
Commun, 5, 5294. doi: 10.1038/ncomms6294.
|
The molecular structure of the left-handed
supra-molecular helix of eukaryotic polyribosomes .
SNAP output
|
|
4v4b
|
ribosome |
cryo-EM (11.7 Å) |
Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jorgensen
R, Andersen GR, Beckmann R, Penczek PA, Ballesta JP,
Frank J |
(2004) "Domain
movements of elongation factor eEF2 and the eukaryotic
80S ribosome facilitate tRNA translocation."
Embo J., 23, 1008-1019. doi:
10.1038/sj.emboj.7600102.
|
Structure of the ribosomal 80s-eef2-sordarin complex
from yeast obtained by docking atomic models for RNA
and protein components into a 11.7 a cryo-EM map. .
SNAP output
|
|
4v4r
|
ribosome |
X-ray (5.9 Å) |
Petry S, Brodersen DE, Murphy IV FV, Dunham CM,
Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V |
(2005) "Crystal
Structures of the Ribosome in Complex with Release
Factors RF1 and RF2 Bound to a Cognate Stop Codon."
Cell(Cambridge,Mass.), 123,
1255-1266. doi: 10.1016/j.cell.2005.09.039.
|
Crystal structure of the whole ribosomal complex. .
SNAP output
|
|
4v4s
|
ribosome |
X-ray (6.76 Å) |
Petry S, Brodersen DE, Murphy IV FV, Dunham CM,
Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V |
(2005) "Crystal
Structures of the Ribosome in Complex with Release
Factors RF1 and RF2 Bound to a Cognate Stop Codon."
Cell(Cambridge,Mass.), 123,
1255-1266. doi: 10.1016/j.cell.2005.09.039.
|
Crystal structure of the whole ribosomal complex. .
SNAP output
|
|
4v4t
|
ribosome |
X-ray (6.46 Å) |
Petry S, Brodersen DE, Murphy IV FV, Dunham CM,
Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V |
(2005) "Crystal
Structures of the Ribosome in Complex with Release
Factors RF1 and RF2 Bound to a Cognate Stop Codon."
Cell(Cambridge,Mass.), 123,
1255-1266. doi: 10.1016/j.cell.2005.09.039.
|
Crystal structure of the whole ribosomal complex with a
stop codon in the a-site. . SNAP output
|
|
4v6i
|
ribosome |
cryo-EM (8.8 Å) |
Armache JP, Jarasch A, Anger AM, Villa E, Becker T,
Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg
S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix
B, Soding J, Westhof E, Wilson DN, Beckmann R |
(2010) "Cryo-EM
structure and rRNA model of a translating eukaryotic
80S ribosome at 5.5-A resolution."
Proc.Natl.Acad.Sci.USA, 107,
19748-19753. doi: 10.1073/pnas.1009999107.
|
Localization of the small subunit ribosomal proteins
into a 6.1 a cryo-EM map of saccharomyces cerevisiae
translating 80s ribosome . SNAP output
|
|
4v6w
|
ribosome |
cryo-EM (6.0 Å) |
Anger AM, Armache J-P, Berninghausen O, Habeck M,
Subklewe M, Wilson DN, Beckmann R |
(2013) "Structures
of the human and Drosophila 80S ribosome."
Nature, 497, 80-85. doi:
10.1038/nature12104.
|
Structure of the d. melanogaster 80s ribosome .
SNAP output
|
|
4v6x
|
ribosome |
cryo-EM (5.0 Å) |
Anger AM, Armache J-P, Berninghausen O, Habeck M,
Subklewe M, Wilson DN, Beckmann R |
(2013) "Structures
of the human and Drosophila 80S ribosome."
Nature, 497, 80-85. doi:
10.1038/nature12104.
|
Structure of the human 80s ribosome . SNAP output
|
|
4v7h
|
ribosome |
cryo-EM (8.9 Å) |
Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E,
Sali A, Harvey SC, Frank J |
(2009) "Comprehensive
molecular structure of the eukaryotic ribosome."
Structure, 17, 1591-1604.
doi: 10.1016/j.str.2009.09.015.
|
Structure of the 80s rrna and proteins and p-e trna for
eukaryotic ribosome based on cryo-EM map of thermomyces
lanuginosus ribosome at 8.9a resolution . SNAP output
|
|
4v8s
|
transferase-DNA |
X-ray (4.323 Å) |
Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia
NGA |
(2012) "Structural
and Functional Analyses of the Interaction of Archaeal
RNA Polymerase with DNA." Nucleic Acids
Res., 40, 9941. doi: 10.1093/NAR/GKS692.
|
Archaeal rnap-DNA binary complex at 4.32ang . SNAP output
|
|
4v8t
|
ribosome |
cryo-EM (8.1 Å) |
Greber BJ, Boehringer D, Montellese C, Ban N |
(2012) "Cryo-Em
Structures of Arx1 and Maturation Factors Rei1 and Jjj1
Bound to the 60S Ribosomal Subunit."
Nat.Struct.Mol.Biol., 19,
1228. doi: 10.1038/NSMB.2425.
|
cryo-EM structure of the 60s ribosomal subunit in
complex with arx1 and rei1 . SNAP output
|
|
4v9r
|
ribosome-antibiotic |
X-ray (3.0 Å) |
Bulkley D, Brandi L, Polikanov YS, Fabbretti A,
O'Connor M, Gualerzi CO, Steitz TA |
(2014) "The
antibiotics dityromycin and GE82832 bind protein S12
and block EF-G-catalyzed translocation." Cell
Rep, 6, 357-365. doi: 10.1016/j.celrep.2013.12.024.
|
Crystal structure of antibiotic dityromycin bound to
70s ribosome . SNAP
output
|
|
4v9s
|
ribosome-antibiotic |
X-ray (3.1 Å) |
Bulkley D, Brandi L, Polikanov YS, Fabbretti A,
O'Connor M, Gualerzi CO, Steitz TA |
(2014) "The
antibiotics dityromycin and GE82832 bind protein S12
and block EF-G-catalyzed translocation." Cell
Rep, 6, 357-365. doi: 10.1016/j.celrep.2013.12.024.
|
Crystal structure of antibiotic ge82832 bound to 70s
ribosome . SNAP
output
|
|
4w9m
|
hydrolase |
X-ray (2.7 Å) |
Rojowska A, Lammens K, Seifert FU, Direnberger C,
Feldmann H, Hopfner KP |
(2014) "Structure
of the Rad50 DNA double-strand break repair protein in
complex with DNA." Embo J.,
33, 2847-2859. doi: 10.15252/embj.201488889.
|
Amppnp bound rad50 in complex with dsDNA . SNAP output
|
|
4wal
|
protein binding-RNA |
X-ray (2.2 Å) |
Jacewicz A, Chico L, Smith P, Schwer B, Shuman S |
(2015) "Structural
basis for recognition of intron branchpoint RNA by
yeast Msl5 and selective effects of interfacial
mutations on splicing of yeast pre-mRNAs."
Rna, 21, 401-414. doi:
10.1261/rna.048942.114.
|
Crystal structure of selenomethionine msl5 protein in
complex with RNA at 2.2 a . SNAP output
|
|
4wan
|
protein binding-RNA |
X-ray (1.8 Å) |
Jacewicz A, Chico L, Smith P, Schwer B, Shuman S |
(2015) "Structural
basis for recognition of intron branchpoint RNA by
yeast Msl5 and selective effects of interfacial
mutations on splicing of yeast pre-mRNAs."
Rna, 21, 401-414. doi:
10.1261/rna.048942.114.
|
Crystal structure of msl5 protein in complex with RNA
at 1.8 a . SNAP
output
|
|
4wb2
|
DNA-RNA hybrid |
X-ray (1.8 Å) |
Yatime L, Maasch C, Hoehlig K, Klussmann S, Andersen
GR, Vater A |
(2015) "Structural
basis for the targeting of complement anaphylatoxin C5a
using a mixed L-RNA/L-DNA aptamer." Nat
Commun, 6, 6481. doi: 10.1038/ncomms7481.
|
Crystal structure of the mirror-image l-RNA-l-DNA
aptamer nox-d20 in complex with mouse c5a complement
anaphylatoxin . SNAP
output
|
|
4wb3
|
DNA-RNA hybrid |
X-ray (2.0 Å) |
Yatime L, Maasch C, Hoehlig K, Klussmann S, Andersen
GR, Vater A |
(2015) "Structural
basis for the targeting of complement anaphylatoxin C5a
using a mixed L-RNA/L-DNA aptamer." Nat
Commun, 6, 6481. doi: 10.1038/ncomms7481.
|
Crystal structure of the mirror-image l-RNA-l-DNA
aptamer nox-d20 in complex with mouse c5a-desarg
complement anaphylatoxin . SNAP output
|
|
4wcg
|
DNA binding protein |
X-ray (1.5 Å) |
Kus K, Rakus K, Boutier M, Tsigkri T, Gabriel L,
Vanderplasschen A, Athanasiadis A |
(2015) "The
Structure of the Cyprinid herpesvirus 3 ORF112-Z alpha
Z-DNA Complex Reveals a Mechanism of Nucleic Acids
Recognition Conserved with E3L, a Poxvirus Inhibitor of
Interferon Response." J.Biol.Chem.,
290, 30713-30725. doi: 10.1074/jbc.M115.679407.
|
The binding mode of cyprinid herpesvirus3 orf112-zalpha
to z-DNA . SNAP
output
|
|
4wk8
|
transcription-DNA |
X-ray (3.4 Å) |
Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza
CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen
L |
(2015) "DNA
binding by FOXP3 domain-swapped dimer suggests
mechanisms of long-range chromosomal interactions."
Nucleic Acids Res., 43,
1268-1282. doi: 10.1093/nar/gku1373.
|
Foxp3 forms a domain-swapped dimer to bridge DNA .
SNAP output
|
|
4wkr
|
RNA binding protein |
X-ray (3.2 Å) |
Uchikawa E, Natchiar KS, Han X, Proux F, Roblin P,
Zhang E, Durand A, Klaholz BP, Dock-Bregeon AC |
(2015) "Structural
insight into the mechanism of stabilization of the 7SK
small nuclear RNA by LARP7." Nucleic Acids
Res., 43, 3373-3388. doi:
10.1093/nar/gkv173.
|
Larp7 wrapping up the 3' hairpin of 7sk non-coding RNA
(302-332) . SNAP
output
|
|
4wls
|
transcription regulator-DNA |
X-ray (2.105 Å) |
Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz
GC, Mondragon A, O'Halloran TV |
(2015) "Allosteric
transcriptional regulation via changes in the overall
topology of the core promoter." Science,
349, 877-881. doi: 10.1126/science.aaa9809.
|
Crystal structure of the metal-free (repressor) form of
e. coli cuer, a copper efflux regulator, bound to copa
promoter DNA . SNAP
output
|
|
4wlw
|
transcription-DNA |
X-ray (2.8 Å) |
Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz
GC, Mondragon A, O'Halloran TV |
(2015) "TRANSCRIPTION.
Allosteric transcriptional regulation via changes in
the overall topology of the core promoter."
Science, 349, 877-881. doi:
10.1126/science.aaa9809.
|
Crystal structure of the ag(i) (activator) form of e.
coli cuer, a copper efflux regulator, bound to copa
promoter DNA . SNAP
output
|
|
4wqs
|
transferase-DNA-RNA |
X-ray (4.306 Å) |
Sekine SI, Murayama Y, Svetlov V, Nudler E, Yokoyama
S |
(2015) "The
Ratcheted and Ratchetable Structural States of RNA
Polymerase Underlie Multiple Transcriptional
Functions." Mol.Cell, 57,
408-421. doi: 10.1016/j.molcel.2014.12.014.
|
Thermus thermophilus RNA polymerase backtracked complex
. SNAP output
|
|
4wt8
|
ribosome |
X-ray (3.4 Å) |
Amunts A, Fiedorczuk K, Truong TT, Chandler J, Peter
Greenberg E, Ramakrishnan V |
(2015) "Bactobolin
A Binds to a Site on the 70S Ribosome Distinct from
Previously Seen Antibiotics." J.Mol.Biol.,
427, 753-755. doi: 10.1016/j.jmb.2014.12.018.
|
Crystal structure of bactobolin a bound to 70s
ribosome-trna complex . SNAP output
|
|
4wtg
|
transferase-RNA |
X-ray (2.9 Å) |
Appleby TC, Perry JK, Murakami E, Barauskas O, Feng
J, Cho A, Fox D, Wetmore DR, McGrath ME, Ray AS, Sofia
MJ, Swaminathan S, Edwards TE |
(2015) "Structural
basis for RNA replication by the hepatitis C virus
polymerase." Science,
347, 771-775. doi: 10.1126/science.1259210.
|
Crystal structure of hcv ns5b genotype 2a jfh-1 isolate
with s15g e86q e87q c223h v321i mutations and delta8
beta hairpin loop deletion in complex with sofosbuvir
diphosphate gs-607596, mn2+ and symmetrical primer
template 5'-caaaauuu . SNAP output
|
|
4wu4
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR,
Arias CA, Ladbury JE, Shamoo Y |
(2015) "A
variable DNA recognition site organization establishes
the LiaR-mediated cell envelope stress response of
enterococci to daptomycin." Nucleic Acids
Res., 43, 4758-4773. doi:
10.1093/nar/gkv321.
|
Crystal structure of e. faecalis DNA binding domain
liard191n complexed with 22bp DNA . SNAP output
|
|
4wu8
|
structural protein-DNA |
X-ray (2.45 Å) |
Chua EY, Davey GE, Chin CF, Droge P, Ang WH, Davey
CA |
(2015) "Stereochemical
control of nucleosome targeting by
platinum-intercalator antitumor agents."
Nucleic Acids Res., 43,
5284-5296. doi: 10.1093/nar/gkv356.
|
Structure of trptnap-ncp145 . SNAP output
|
|
4wu9
|
structural protein-DNA |
X-ray (2.6 Å) |
Chua EY, Davey GE, Chin CF, Droge P, Ang WH, Davey
CA |
(2015) "Stereochemical
control of nucleosome targeting by
platinum-intercalator antitumor agents."
Nucleic Acids Res., 43,
5284-5296. doi: 10.1093/nar/gkv356.
|
Structure of cisptnap-ncp145 . SNAP output
|
|
4wuh
|
DNA binding protein-DNA |
X-ray (2.294 Å) |
Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR,
Arias CA, Ladbury JE, Shamoo Y |
(2015) "A
variable DNA recognition site organization establishes
the LiaR-mediated cell envelope stress response of
enterococci to daptomycin." Nucleic Acids
Res., 43, 4758-4773. doi:
10.1093/nar/gkv321.
|
Crystal structure of e. faecalis DNA binding domain
liar wild type complexed with 22bp DNA . SNAP output
|
|
4wul
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Davlieva M, Shi Y, Leonard PG, Johnson TA, Zianni MR,
Arias CA, Ladbury JE, Shamoo Y |
(2015) "A
variable DNA recognition site organization establishes
the LiaR-mediated cell envelope stress response of
enterococci to daptomycin." Nucleic Acids
Res., 43, 4758-4773. doi:
10.1093/nar/gkv321.
|
Crystal structure of e. faecalis DNA binding domain
liard191n complexed with 26bp DNA . SNAP output
|
|
4wuz
|
hydrolase-DNA |
X-ray (2.38 Å) |
Zhang J, Pan X, Bell CE |
(2014) "Crystal
Structure of lambda Exonuclease in Complex with DNA and
Ca(2+)." Biochemistry,
53, 7415-7425. doi: 10.1021/bi501155q.
|
Crystal structure of lambda exonuclease in complex with
DNA and ca2+ . SNAP
output
|
|
4wwc
|
transcription |
X-ray (2.903 Å) |
Fillenberg SB, Grau FC, Seidel G, Muller YA |
(2015) "Structural
insight into operator dre-sites recognition and
effector binding in the GntR/HutC transcription
regulator NagR." Nucleic Acids Res.,
43, 1283-1296. doi: 10.1093/nar/gku1374.
|
Crystal structure of full length yvoa in complex with
palindromic operator DNA . SNAP output
|
|
4wx9
|
transferase |
X-ray (3.0 Å) |
Miggiano R, Perugino G, Ciaramella M, Serpe M, Rejman
D, Pav O, Pohl R, Garavaglia S, Lahiri S, Rizzi M, Rossi
F |
(2016) "Crystal
structure of Mycobacterium tuberculosis
O6-methylguanine-DNA methyltransferase protein clusters
assembled on to damaged DNA." Biochem.J.,
473, 123-133. doi: 10.1042/BJ20150833.
|
Crystal structure of mycobacterium tuberculosis ogt in
complex with DNA . SNAP
output
|
|
4wzs
|
transcription |
X-ray (3.78 Å) |
Butryn A, Schuller JM, Stoehr G, Runge-Wollmann P,
Forster F, Auble DT, Hopfner KP |
(2015) "Structural
basis for recognition and remodeling of the TBP:DNA:NC2
complex by Mot1." Elife,
4. doi: 10.7554/eLife.07432.
|
Crystal structure of the mot1 n-terminal domain in
complex with tbp and nc2 bound to a promoter DNA
fragment . SNAP
output
|
|
4wzw
|
DNA binding protein, RNA binding protein-DNA |
X-ray (2.95 Å) |
Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TM |
(2014) "A
divergent Pumilio repeat protein family for pre-rRNA
processing and mRNA localization."
Proc.Natl.Acad.Sci.USA, 111,
18554-18559. doi: 10.1073/pnas.1407634112.
|
Crystal structure of human puf-a in complex with DNA .
SNAP output
|
|
4x0g
|
DNA binding protein-DNA |
X-ray (3.21 Å) |
Dai Q, Ren A, Westholm JO, Duan H, Patel DJ, Lai
EC |
(2015) "Common
and distinct DNA-binding and regulatory activities of
the BEN-solo transcription factor family."
Genes Dev., 29, 48-62. doi:
10.1101/gad.252122.114.
|
Structure of bsg25a binding with DNA . SNAP output
|
|
4x0p
|
transferase-DNA |
X-ray (3.911 Å) |
Zahn KE, Averill AM, Aller P, Wood RD, Doublie S |
(2015) "Human
DNA polymerase theta grasps the primer terminus to
mediate DNA repair." Nat.Struct.Mol.Biol.,
22, 304-311. doi: 10.1038/nsmb.2993.
|
Ternary complex of human DNA polymerase theta
c-terminal domain binding ddatp opposite a
tetrahydrofuran ap site analog . SNAP output
|
|
4x0q
|
transferase-DNA |
X-ray (3.9 Å) |
Zahn KE, Averill AM, Aller P, Wood RD, Doublie S |
(2015) "Human
DNA polymerase theta grasps the primer terminus to
mediate DNA repair." Nat.Struct.Mol.Biol.,
22, 304-311. doi: 10.1038/nsmb.2993.
|
Ternary complex of human DNA polymerase theta
c-terminal domain binding ddgtp opposite dcmp .
SNAP output
|
|
4x23
|
structural protein-DNA |
X-ray (3.5 Å) |
Kato H, Jiang JS, Zhou BR, Rozendaal M, Feng H,
Ghirlando R, Xiao TS, Straight AF, Bai Y |
(2013) "A
conserved mechanism for centromeric nucleosome
recognition by centromere protein CENP-C."
Science, 340, 1110-1113. doi:
10.1126/science.1235532.
|
Crystal structure of cenp-c in complex with the
nucleosome core particle . SNAP output
|
|
4x4b
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 2.1 mgy . SNAP output
|
|
4x4c
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 6.2 mgy . SNAP output
|
|
4x4d
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 10.3 mgy . SNAP output
|
|
4x4e
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 14.4 mgy . SNAP output
|
|
4x4f
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 20.6 mgy . SNAP output
|
|
4x4g
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 26.8 mgy . SNAP output
|
|
4x4h
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 35.7 mgy . SNAP output
|
|
4x4i
|
gene regulation |
X-ray (2.8 Å) |
Bury C, Garman EF, Ginn HM, Ravelli RB, Carmichael I,
Kneale G, McGeehan JE |
(2015) "Radiation
damage to nucleoprotein complexes in macromolecular
crystallography." J.Synchrotron Radiat.,
22, 213-224. doi: 10.1107/S1600577514026289.
|
Radiation damage to the nucleoprotein complex
c.esp1396i: dose (dwd) 44.6 mgy . SNAP output
|
|
4x5v
|
transferase-DNA |
X-ray (2.15 Å) |
Burak MJ, Guja KE, Garcia-Diaz M |
(2015) "Nucleotide
binding interactions modulate dNTP selectivity and
facilitate 8-oxo-dGTP incorporation by DNA polymerase
lambda." Nucleic Acids Res.,
43, 8089-8099. doi: 10.1093/nar/gkv760.
|
Crystal structure of the post-catalytic nick complex of
DNA polymerase lambda with a templating a and
incorporated 8-oxo-dgmp . SNAP output
|
|
4x67
|
transcription-DNA |
X-ray (4.1 Å) |
Walmacq C, Wang L, Chong J, Scibelli K, Lubkowska L,
Gnatt A, Brooks PJ, Wang D, Kashlev M |
(2015) "Mechanism
of RNA polymerase II bypass of oxidative cyclopurine
DNA lesions." Proc.Natl.Acad.Sci.USA,
112, E410-E419. doi: 10.1073/pnas.1415186112.
|
Crystal structure of elongating yeast RNA polymerase ii
stalled at oxidative cyclopurine DNA lesions. .
SNAP output
|
|
4x6a
|
transcription-DNA |
X-ray (3.96 Å) |
Walmacq C, Wang L, Chong J, Scibelli K, Lubkowska L,
Gnatt A, Brooks PJ, Wang D, Kashlev M |
(2015) "Mechanism
of RNA polymerase II bypass of oxidative cyclopurine
DNA lesions." Proc.Natl.Acad.Sci.USA,
112, E410-E419. doi: 10.1073/pnas.1415186112.
|
Crystal structure of yeast RNA polymerase ii
encountering oxidative cyclopurine DNA lesions .
SNAP output
|
|
4x9e
|
hydrolase-DNA |
X-ray (3.1 Å) |
Singh D, Gawel D, Itsko M, Hochkoeppler A, Krahn JM,
London RE, Schaaper RM |
(2015) "Structure
of Escherichia coli dGTP Triphosphohydrolase: A
HEXAMERIC ENZYME WITH DNA EFFECTOR MOLECULES."
J.Biol.Chem., 290,
10418-10429. doi: 10.1074/jbc.M115.636936.
|
Deoxyguanosinetriphosphate triphosphohydrolase from
escherichia coli with two DNA effector molecules .
SNAP output
|
|
4x9j
|
transcription regulator-DNA |
X-ray (1.412 Å) |
Zandarashvili L, White MA, Esadze A, Iwahara J |
(2015) "Structural
impact of complete CpG methylation within target DNA on
specific complex formation of the inducible
transcription factor Egr-1." Febs Lett.,
589, 1748-1753. doi: 10.1016/j.febslet.2015.05.022.
|
Egr-1 with doubly methylated DNA . SNAP output
|
|
4xa5
|
transferase-DNA |
X-ray (1.9 Å) |
Burak MJ, Guja KE, Garcia-Diaz M |
(2015) "Nucleotide
binding interactions modulate dNTP selectivity and
facilitate 8-oxo-dGTP incorporation by DNA polymerase
lambda." Nucleic Acids Res.,
43, 8089-8099. doi: 10.1093/nar/gkv760.
|
Crystal structure of the pre-catalytic ternary complex
of DNA polymerase lambda with a templating a and an
incoming 8-oxo-dgtp . SNAP output
|
|
4xeg
|
hydrolase-DNA |
X-ray (1.72 Å) |
Malik SS, Coey CT, Varney KM, Pozharski E, Drohat
AC |
(2015) "Thymine
DNA glycosylase exhibits negligible affinity for
nucleobases that it removes from DNA." Nucleic
Acids Res., 43, 9541-9552. doi:
10.1093/nar/gkv890.
|
Structure of the enzyme-product complex resulting from
tdg action on a g-hmu mismatch . SNAP output
|
|
4xic
|
transcription regulator-DNA |
X-ray (2.69 Å) |
Zandarashvili L, Nguyen D, Anderson KM, White MA,
Gorenstein DG, Iwahara J |
(2015) "Entropic
Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur
Substitution in DNA Phosphate."
Biophys.J., 109, 1026-1037.
doi: 10.1016/j.bpj.2015.07.032.
|
Antphd with 15bp di-thioate modified DNA duplex .
SNAP output
|
|
4xid
|
transcription regulator-DNA |
X-ray (2.701 Å) |
Zandarashvili L, Nguyen D, Anderson KM, White MA,
Gorenstein DG, Iwahara J |
(2015) "Entropic
Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur
Substitution in DNA Phosphate."
Biophys.J., 109, 1026-1037.
doi: 10.1016/j.bpj.2015.07.032.
|
Antphd with 15bp DNA duplex . SNAP output
|
|
4xiu
|
transferase-DNA |
X-ray (2.5 Å) |
Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B,
Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM,
Kermekchiev MB |
(2015) "A
Conservative Isoleucine to Leucine Mutation Causes
Major Rearrangements and Cold Sensitivity in KlenTaq1
DNA Polymerase." Biochemistry,
54, 881-889. doi: 10.1021/bi501198f.
|
Binary complex structure of klenow fragment of taq DNA
polymerase i707l mutant with DNA containing ttt
overhang . SNAP
output
|
|
4xln
|
transcription-DNA-RNA |
X-ray (4.0 Å) |
Bae B, Feklistov A, Lass-Napiorkowska A, Landick R,
Darst SA |
(2015) "Structure
of a bacterial RNA polymerase holoenzyme open promoter
complex." Elife, 4. doi:
10.7554/eLife.08504.
|
Crystal structure of t. aquaticus transcription
initiation complex containing bubble promoter and RNA .
SNAP output
|
|
4xlp
|
transcription-DNA |
X-ray (4.0 Å) |
Bae B, Feklistov A, Lass-Napiorkowska A, Landick R,
Darst SA |
(2015) "Structure
of a bacterial RNA polymerase holoenzyme open promoter
complex." Elife, 4. doi:
10.7554/eLife.08504.
|
Crystal structure of t.aquaticus transcription
initiation complex containing upstream fork promoter .
SNAP output
|
|
4xlq
|
transcription-DNA |
X-ray (4.6 Å) |
Bae B, Feklistov A, Lass-Napiorkowska A, Landick R,
Darst SA |
(2015) "Structure
of a bacterial RNA polymerase holoenzyme open promoter
complex." Elife, 4. doi:
10.7554/eLife.08504.
|
Crystal structure of t.aquaticus transcription
initiation complex containing upstream fork (-11
base-paired) promoter . SNAP output
|
|
4xlr
|
transcription-DNA |
X-ray (4.3 Å) |
Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell
EA |
(2015) "CarD
uses a minor groove wedge mechanism to stabilize the
RNA polymerase open promoter complex."
Elife, 4. doi: 10.7554/eLife.08505.
|
Crystal structure of t.aquaticus transcription
initiation complex with card containing bubble promoter
and RNA . SNAP
output
|
|
4xls
|
transcription |
X-ray (4.01 Å) |
Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell
EA |
(2015) "CarD
uses a minor groove wedge mechanism to stabilize the
RNA polymerase open promoter complex."
Elife, 4. doi: 10.7554/eLife.08505.
|
Crystal structure of t. aquaticus transcription
initiation complex with card containing upstream fork
promoter. . SNAP
output
|
|
4xo0
|
transferase-DNA |
X-ray (1.7 Å) |
Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner
SA, Richards NG |
(2015) "Structural
basis for a six nucleotide genetic alphabet."
J. Am. Chem. Soc., 137,
6947-6955. doi: 10.1021/jacs.5b03482.
|
Crystal structure of 5'-cttatpptazzataag in a
host-guest complex . SNAP output
|
|
4xpc
|
transferase-DNA |
X-ray (1.68 Å) |
Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner
SA, Richards NG |
(2015) "Structural
basis for a six nucleotide genetic alphabet."
J. Am. Chem. Soc., 137,
6947-6955. doi: 10.1021/jacs.5b03482.
|
Crystal structure of 5'- cttataaatttataag in a
host-guest complex . SNAP output
|
|
4xpe
|
transferase-DNA |
X-ray (1.78 Å) |
Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner
SA, Richards NG |
(2015) "Structural
basis for a six nucleotide genetic alphabet."
J. Am. Chem. Soc., 137,
6947-6955. doi: 10.1021/jacs.5b03482.
|
Crystal structure of 5'-cttatgggcccataag in a
host-guest complex . SNAP output
|
|
4xq8
|
transferase-DNA |
X-ray (2.798 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda- mgdatp binary complex and
complex with 6 paired DNA . SNAP output
|
|
4xqj
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Rajasree K, Fasim A, Gopal B |
(2016) "Conformational
features of theStaphylococcus aureusAgrA-promoter
interactions rationalize quorum-sensing triggered gene
expression." Biochem Biophys Rep,
6, 124-134. doi: 10.1016/j.bbrep.2016.03.012.
|
Crystal structure of agra lyttr domain in complex with
promoters . SNAP
output
|
|
4xqk
|
hydrolase-DNA |
X-ray (2.7 Å) |
Chand MK, Nirwan N, Diffin FM, Aelst KV, Kulkarni M,
Pernstich C, Szczelkun MD, Saikrishnan K |
(2015) "Translocation-coupled
DNA cleavage by the Type ISP restriction-modification
enzymes." Nat.Chem.Biol.,
11, 870-877. doi: 10.1038/nchembio.1926.
|
Atp-dependent type isp restriction-modification enzyme
llabiii bound to DNA . SNAP output
|
|
4xqn
|
DNA-DNA binding protein |
X-ray (2.3 Å) |
Rajasree K, Fasim A, Gopal B |
(2016) "Conformational
features of theStaphylococcus aureusAgrA-promoter
interactions rationalize quorum-sensing triggered gene
expression." Biochem Biophys Rep,
6, 124-134. doi: 10.1016/j.bbrep.2016.03.012.
|
Crystal structure of agra lyttr domain in complex with
promoters . SNAP
output
|
|
4xqq
|
DNA binding protein-DNA |
X-ray (3.05 Å) |
Rajasree K, Fasim A, Gopal B |
(2016) "Conformational
features of theStaphylococcus aureusAgrA-promoter
interactions rationalize quorum-sensing triggered gene
expression." Biochem Biophys Rep,
6, 124-134. doi: 10.1016/j.bbrep.2016.03.012.
|
Crystal structure of agra lyttr domain in complex with
promoters . SNAP
output
|
|
4xr0
|
replication-DNA |
X-ray (2.8 Å) |
Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M,
Oakley AJ, Dixon NE, Hamdan SM |
(2015) "Replisome
speed determines the efficiency of the Tus-Ter
replication termination barrier." Nature,
525, 394-398. doi: 10.1038/nature14866.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA- g-t mismatch. . SNAP output
|
|
4xr1
|
replication-DNA |
X-ray (2.4 Å) |
Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M,
Oakley AJ, Dixon NE, Hamdan SM |
(2015) "Replisome
speed determines the efficiency of the Tus-Ter
replication termination barrier." Nature,
525, 394-398. doi: 10.1038/nature14866.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA- ag-at mismatch. . SNAP output
|
|
4xr2
|
replication-DNA |
X-ray (2.35 Å) |
Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M,
Oakley AJ, Dixon NE, Hamdan SM |
(2015) "Replisome
speed determines the efficiency of the Tus-Ter
replication termination barrier." Nature,
525, 394-398. doi: 10.1038/nature14866.
|
Escherichia coli replication terminator protein (tus)
h114a mutant complexed with DNA- tera lock. . SNAP output
|
|
4xr3
|
replication-DNA |
X-ray (2.7 Å) |
Elshenawy MM, Jergic S, Xu ZQ, Sobhy MA, Takahashi M,
Oakley AJ, Dixon NE, Hamdan SM |
(2015) "Replisome
speed determines the efficiency of the Tus-Ter
replication termination barrier." Nature,
525, 394-398. doi: 10.1038/nature14866.
|
Escherichia coli replication terminator protein (tus)
complexed with DNA- gc(6) swapped. . SNAP output
|
|
4xrh
|
transferase-DNA |
X-ray (3.0 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda- mgdttp binary and complex
with 6 paired DNA . SNAP
output
|
|
4xrm
|
transcription |
X-ray (1.6 Å) |
Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M,
Enge M, Kivioja T, Morgunova E, Taipale J |
(2015) "DNA-dependent
formation of transcription factor pairs alters their
binding specificity." Nature,
527, 384-388. doi: 10.1038/nature15518.
|
Homodimer of tale type homeobox transcription factor
meis1 complexes with specific DNA . SNAP output
|
|
4xrs
|
transcription |
X-ray (3.5 Å) |
Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M,
Enge M, Kivioja T, Morgunova E, Taipale J |
(2015) "DNA-dependent
formation of transcription factor pairs alters their
binding specificity." Nature,
527, 384-388. doi: 10.1038/nature15518.
|
Heterodimeric complex of transcription factors meis1
and dlx3 on specific DNA . SNAP output
|
|
4xuj
|
DNA-binding protein-DNA |
X-ray (3.18 Å) |
Hanif M, Meier SM, Adhireksan Z, Henke H, Martic S,
Labib M, Kandioller W, Jakupec MA, Kraatz HB, Davey CA,
Keppler BK, Hartinger CG |
"Contrasting Cytotoxicity and Reactivity of
RuII-Arene Complexes of Morpholine vs Thiomorpholine
Substituted 3-Hydroxy-2-pyridone Ligands." |
Nucleosome core particle containing adducts from
treatment with a thiomorpholine-substituted
[(eta-6-p-cymene)ru(3-hydroxy-2-pyridone)cl] compound .
SNAP output
|
|
4xus
|
transferase-DNA |
X-ray (2.4 Å) |
Burak MJ, Guja KE, Garcia-Diaz M |
(2015) "Nucleotide
binding interactions modulate dNTP selectivity and
facilitate 8-oxo-dGTP incorporation by DNA polymerase
lambda." Nucleic Acids Res.,
43, 8089-8099. doi: 10.1093/nar/gkv760.
|
Crystal structure of the pre-catalytic ternary complex
of DNA polymerase lambda with a templating a and an
incoming dttp . SNAP
output
|
|
4xvi
|
transferase-DNA |
X-ray (3.1 Å) |
Lee YS, Gao Y, Yang W |
(2015) "How a
homolog of high-fidelity replicases conducts mutagenic
DNA synthesis." Nat.Struct.Mol.Biol.,
22, 298-303. doi: 10.1038/nsmb.2985.
|
Binary complex of human polymerase nu and DNA with the
finger domain ajar . SNAP output
|
|
4xvk
|
transferase-DNA |
X-ray (2.95 Å) |
Lee YS, Gao Y, Yang W |
(2015) "How a
homolog of high-fidelity replicases conducts mutagenic
DNA synthesis." Nat.Struct.Mol.Biol.,
22, 298-303. doi: 10.1038/nsmb.2985.
|
Binary complex of human polymerase nu and DNA with the
finger domain closed . SNAP output
|
|
4xvl
|
transferase-DNA |
X-ray (3.301 Å) |
Lee YS, Gao Y, Yang W |
(2015) "How a
homolog of high-fidelity replicases conducts mutagenic
DNA synthesis." Nat.Struct.Mol.Biol.,
22, 298-303. doi: 10.1038/nsmb.2985.
|
Binary complex of human polymerase nu and DNA with the
finger domain open . SNAP output
|
|
4xvm
|
transferase-DNA |
X-ray (3.2 Å) |
Lee YS, Gao Y, Yang W |
(2015) "How a
homolog of high-fidelity replicases conducts mutagenic
DNA synthesis." Nat.Struct.Mol.Biol.,
22, 298-303. doi: 10.1038/nsmb.2985.
|
Binary complex of human polymerase nu and DNA with the
finger domain closed and thumb domain rotated out .
SNAP output
|
|
4xxe
|
transcription-DNA |
X-ray (3.2 Å) |
Rajasree K, Fasim A, Gopal B |
(2016) "Conformational
features of theStaphylococcus aureusAgrA-promoter
interactions rationalize quorum-sensing triggered gene
expression." Biochem Biophys Rep,
6, 124-134. doi: 10.1016/j.bbrep.2016.03.012.
|
Structure of agra lyttr domain in complex with
promoters . SNAP
output
|
|
4xyq
|
DNA-DNA binding protein |
X-ray (2.4 Å) |
Rajasree K, Fasim A, Gopal B |
(2016) "Conformational
features of theStaphylococcus aureusAgrA-promoter
interactions rationalize quorum-sensing triggered gene
expression." Biochem Biophys Rep,
6, 124-134. doi: 10.1016/j.bbrep.2016.03.012.
|
Structure of agra lyttr domain in complex with
promoters . SNAP
output
|
|
4xzf
|
DNA binding protein-DNA |
X-ray (1.38 Å) |
Hishiki A, Hara K, Ikegaya Y, Yokoyama H, Shimizu T,
Sato M, Hashimoto H |
(2015) "Structure
of a Novel DNA-binding Domain of Helicase-like
Transcription Factor (HLTF) and Its Functional
Implication in DNA Damage Tolerance."
J.Biol.Chem., 290,
13215-13223. doi: 10.1074/jbc.M115.643643.
|
Crystal structure of hiran domain of human hltf in
complex with DNA . SNAP
output
|
|
4xzq
|
structural protein-DNA |
X-ray (2.4 Å) |
Chatterjee N, North JA, Dechassa ML, Manohar M,
Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew
B |
(2015) "Histone
Acetylation near the Nucleosome Dyad Axis Enhances
Nucleosome Disassembly by RSC and SWI/SNF."
Mol.Cell.Biol., 35,
4083-4092. doi: 10.1128/MCB.00441-15.
|
Nucleosome disassembly by rsc and swi-snf is enhanced
by h3 acetylation near the nucleosome dyad axis .
SNAP output
|
|
4y00
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Chiang CH, Grauffel C, Wu LS, Kuo PH, Doudeva LG, Lim
C, Shen CK, Yuan HS |
(2016) "Structural
analysis of disease-related TDP-43 D169G mutation:
linking enhanced stability and caspase cleavage
efficiency to protein accumulation." Sci
Rep, 6, 21581. doi: 10.1038/srep21581.
|
Crystal structure of human tdp-43 rrm1 domain with
d169g mutation in complex with an unmodified
single-stranded DNA . SNAP output
|
|
4y0f
|
DNA binding protein-DNA |
X-ray (2.648 Å) |
Chiang CH, Grauffel C, Wu LS, Kuo PH, Doudeva LG, Lim
C, Shen CK, Yuan HS |
(2016) "Structural
analysis of disease-related TDP-43 D169G mutation:
linking enhanced stability and caspase cleavage
efficiency to protein accumulation." Sci
Rep, 6, 21581. doi: 10.1038/srep21581.
|
Crystal structure of human tdp-43 rrm1 domain in
complex with an unmodified single-stranded DNA .
SNAP output
|
|
4y52
|
transcription-DNA-RNA |
X-ray (3.5 Å) |
Wang L, Zhou Y, Xu L, Xiao R, Lu X, Chen L, Chong J,
Li H, He C, Fu XD, Wang D |
(2015) "Molecular
basis for 5-carboxycytosine recognition by RNA
polymerase II elongation complex." Nature,
523, 621-625. doi: 10.1038/nature14482.
|
Crystal structure of 5-carboxycytosine recognition by
RNA polymerase ii during transcription elongation. .
SNAP output
|
|
4y5w
|
transcription-DNA |
X-ray (3.104 Å) |
Li J, Rodriguez JP, Niu F, Pu M, Wang J, Hung LW,
Shao Q, Zhu Y, Ding W, Liu Y, Da Y, Yao Z, Yang J, Zhao
Y, Wei GH, Cheng G, Liu ZJ, Ouyang S |
(2016) "Structural
basis for DNA recognition by STAT6."
Proc.Natl.Acad.Sci.USA, 113,
13015-13020. doi: 10.1073/pnas.1611228113.
|
Transcription factor-DNA complex . SNAP output
|
|
4y60
|
transcription-DNA |
X-ray (1.75 Å) |
Klaus M, Prokoph N, Girbig M, Wang X, Huang YH,
Srivastava Y, Hou L, Narasimhan K, Kolatkar PR, Francois
M, Jauch R |
(2016) "Structure
and decoy-mediated inhibition of the SOX18/Prox1-DNA
interaction." Nucleic Acids Res.,
44, 3922-3935. doi: 10.1093/nar/gkw130.
|
Structure of sox18-hmg-prox1-DNA . SNAP output
|
|
4y7n
|
transcription-DNA-RNA |
X-ray (3.3 Å) |
Wang L, Zhou Y, Xu L, Xiao R, Lu X, Chen L, Chong J,
Li H, He C, Fu XD, Wang D |
(2015) "Molecular
basis for 5-carboxycytosine recognition by RNA
polymerase II elongation complex." Nature,
523, 621-625. doi: 10.1038/nature14482.
|
The structure insight into 5-carboxycytosine
recognition by RNA polymerase ii during transcription
elongation. . SNAP
output
|
|
4ycp
|
oxidoreductase-RNA |
X-ray (2.55 Å) |
Byrne RT, Jenkins HT, Peters DT, Whelan F, Stowell J,
Aziz N, Kasatsky P, Rodnina MV, Koonin EV, Konevega AL,
Antson AA |
(2015) "Major
reorientation of tRNA substrates defines specificity of
dihydrouridine synthases."
Proc.Natl.Acad.Sci.USA, 112,
6033-6037. doi: 10.1073/pnas.1500161112.
|
E. coli dihydrouridine synthase c (dusc) in complex
with trnatrp . SNAP
output
|
|
4ycx
|
transferase-DNA |
X-ray (2.1 Å) |
Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek
K |
(2015) "Creative
template-dependent synthesis by human polymerase
mu." Proc.Natl.Acad.Sci.USA,
112, E4530-E4536. doi: 10.1073/pnas.1505798112.
|
Binary complex of human DNA polymerase mu with 2-nt
gapped DNA substrate . SNAP output
|
|
4yd1
|
transferase-DNA |
X-ray (1.75 Å) |
Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek
K |
(2015) "Creative
template-dependent synthesis by human polymerase
mu." Proc.Natl.Acad.Sci.USA,
112, E4530-E4536. doi: 10.1073/pnas.1505798112.
|
Ternary complex of human DNA polymerase mu with 2-nt
gapped DNA substrate and an incoming nonhydrolyzable
dumpnpp . SNAP
output
|
|
4yd2
|
transferase-DNA |
X-ray (2.471 Å) |
Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek
K |
(2015) "Creative
template-dependent synthesis by human polymerase
mu." Proc.Natl.Acad.Sci.USA,
112, E4530-E4536. doi: 10.1073/pnas.1505798112.
|
Nicked complex of human DNA polymerase mu with 2-nt
gapped DNA substrate . SNAP output
|
|
4yew
|
DNA binding protein-DNA |
X-ray (2.683 Å) |
Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R,
Tang HY, Larabell CA, Tainer JA, Adhya S |
(2016) "HU
multimerization shift controls nucleoid
compaction." Sci Adv, 2,
e1600650. doi: 10.1126/sciadv.1600650.
|
Huab-19bp . SNAP
output
|
|
4yex
|
DNA binding protein-DNA |
X-ray (3.2 Å) |
Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R,
Tang HY, Larabell CA, Tainer JA, Adhya S |
(2016) "HU
multimerization shift controls nucleoid
compaction." Sci Adv, 2,
e1600650. doi: 10.1126/sciadv.1600650.
|
Huaa-19bp . SNAP
output
|
|
4yey
|
DNA binding protein-DNA |
X-ray (3.354 Å) |
Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R,
Tang HY, Larabell CA, Tainer JA, Adhya S |
(2016) "HU
multimerization shift controls nucleoid
compaction." Sci Adv, 2,
e1600650. doi: 10.1126/sciadv.1600650.
|
Huaa-20bp . SNAP
output
|
|
4yf0
|
DNA binding protein-DNA |
X-ray (2.79 Å) |
Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R,
Tang HY, Larabell CA, Tainer JA, Adhya S |
(2016) "HU
multimerization shift controls nucleoid
compaction." Sci Adv, 2,
e1600650. doi: 10.1126/sciadv.1600650.
|
Hu38-19bp . SNAP
output
|
|
4yfh
|
DNA binding protein-DNA |
X-ray (3.49 Å) |
Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R,
Tang HY, Larabell CA, Tainer JA, Adhya S |
(2016) "HU
multimerization shift controls nucleoid
compaction." Sci Adv, 2,
e1600650. doi: 10.1126/sciadv.1600650.
|
Hu38-20bp . SNAP
output
|
|
4yft
|
DNA binding protein-DNA |
X-ray (2.914 Å) |
Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R,
Tang HY, Larabell CA, Tainer JA, Adhya S |
(2016) "HU
multimerization shift controls nucleoid
compaction." Sci Adv, 2,
e1600650. doi: 10.1126/sciadv.1600650.
|
Huab-20bp . SNAP
output
|
|
4yfu
|
transferase-DNA |
X-ray (1.5 Å) |
Miller BR, Beese LS, Parish CA, Wu EY |
(2015) "The
Closing Mechanism of DNA Polymerase I at Atomic
Resolution." Structure,
23, 1609-1620. doi: 10.1016/j.str.2015.06.016.
|
Crystal structure of open bacillus fragment DNA
polymerase bound to DNA and dttp . SNAP output
|
|
4yg1
|
transcription-DNA |
X-ray (3.25 Å) |
Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S,
Vulic M, Lewis K, Brennan RG |
(2015) "HipBA-promoter
structures reveal the basis of heritable multidrug
tolerance." Nature, 524,
59-64. doi: 10.1038/nature14662.
|
Hipb-o1-o2 complex-p21212 crystal form . SNAP output
|
|
4yg4
|
transcription-DNA |
X-ray (3.5 Å) |
Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S,
Vulic M, Lewis K, Brennan RG |
(2015) "HipBA-promoter
structures reveal the basis of heritable multidrug
tolerance." Nature, 524,
59-64. doi: 10.1038/nature14662.
|
Hipb-o1-o1* complex . SNAP output
|
|
4yg7
|
transcription, transferase-DNA |
X-ray (3.77 Å) |
Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S,
Vulic M, Lewis K, Brennan RG |
(2015) "HipBA-promoter
structures reveal the basis of heritable multidrug
tolerance." Nature, 524,
59-64. doi: 10.1038/nature14662.
|
Structure of fl autorepression promoter complex .
SNAP output
|
|
4ygi
|
transferase-DNA |
X-ray (2.6 Å) |
Rajakumara E, Nakarakanti NK, Nivya MA, Satish M |
(2016) "Mechanistic
insights into the recognition of 5-methylcytosine
oxidation derivatives by the SUVH5 SRA domain."
Sci Rep, 6, 20161. doi:
10.1038/srep20161.
|
Crystal structure of suvh5 sra bound to fully
hydroxymethylated cg DNA . SNAP output
|
|
4yhx
|
hydrolase-DNA |
X-ray (2.15 Å) |
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM,
Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K,
Scharenberg AM, Stoddard BL |
(2016) "Indirect
DNA Sequence Recognition and Its Impact on Nuclease
Cleavage Activity." Structure,
24, 862-873. doi: 10.1016/j.str.2016.03.024.
|
Crystal structure of laglidadg meganuclease i-gpemi
bound to uncleaved DNA . SNAP output
|
|
4yig
|
hydrolase |
X-ray (2.7 Å) |
Burmeister WP, Tarbouriech N, Fender P,
Contesto-Richefeu C, Peyrefitte CN, Iseni F |
(2015) "Crystal
Structure of the Vaccinia Virus Uracil-DNA Glycosylase
in Complex with DNA." J.Biol.Chem.,
290, 17923-17934. doi: 10.1074/jbc.M115.648352.
|
Vaccinia virus d4-a20(1-50) in complex with dsDNA
containing an abasic site and free uracyl . SNAP output
|
|
4yir
|
DNA binding protein-DNA |
X-ray (3.05 Å) |
Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y,
Liu L, Van Houten B, He C, Ansari A, Min JH |
(2015) "Kinetic
gating mechanism of DNA damage recognition by
Rad4/XPC." Nat Commun, 6,
5849. doi: 10.1038/ncomms6849.
|
Crystal structure of rad4-rad23 crosslinked to an
undamaged DNA . SNAP
output
|
|
4yis
|
hydrolase-DNA |
X-ray (2.89 Å) |
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM,
Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K,
Scharenberg AM, Stoddard BL |
(2016) "Indirect
DNA Sequence Recognition and Its Impact on Nuclease
Cleavage Activity." Structure,
24, 862-873. doi: 10.1016/j.str.2016.03.024.
|
Crystal structure of laglidadg meganuclease i-cpami
bound to uncleaved DNA . SNAP output
|
|
4yit
|
hydrolase-DNA |
X-ray (3.24 Å) |
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM,
Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K,
Scharenberg AM, Stoddard BL |
(2016) "Indirect
DNA Sequence Recognition and Its Impact on Nuclease
Cleavage Activity." Structure,
24, 862-873. doi: 10.1016/j.str.2016.03.024.
|
Crystal structure of laglidadg meganuclease i-aabmi
bound to uncleaved DNA . SNAP output
|
|
4yj0
|
transcription |
X-ray (3.814 Å) |
Murphy MW, Lee JK, Rojo S, Gearhart MD, Kurahashi K,
Banerjee S, Loeuille GA, Bashamboo A, McElreavey K,
Zarkower D, Aihara H, Bardwell VJ |
(2015) "An
ancient protein-DNA interaction underlying metazoan sex
determination." Nat.Struct.Mol.Biol.,
22, 442-451. doi: 10.1038/nsmb.3032.
|
Crystal structure of the dm domain of human dmrt1 bound
to 25mer target DNA . SNAP output
|
|
4ykl
|
hydrolase-DNA |
X-ray (2.25 Å) |
Chauleau M, Jacewicz A, Shuman S |
(2015) "DNA3'pp5'G
de-capping activity of aprataxin: effect of cap
nucleoside analogs and structural basis for guanosine
recognition." Nucleic Acids Res.,
43, 6075-6083. doi: 10.1093/nar/gkv501.
|
Hnt3 in complex with DNA and guanosine . SNAP output
|
|
4yln
|
transcription-DNA-RNA |
X-ray (5.5 Å) |
Zuo Y, Steitz TA |
(2015) "Crystal
Structures of the E. coli Transcription Initiation
Complexes with a Complete Bubble."
Mol.Cell, 58, 534-540. doi:
10.1016/j.molcel.2015.03.010.
|
E. coli transcription initiation complex - 17-bp spacer
and 4-nt RNA . SNAP
output
|
|
4ylo
|
transcription-DNA-RNA |
X-ray (6.0 Å) |
Zuo Y, Steitz TA |
(2015) "Crystal
Structures of the E. coli Transcription Initiation
Complexes with a Complete Bubble."
Mol.Cell, 58, 534-540. doi:
10.1016/j.molcel.2015.03.010.
|
E. coli transcription initiation complex - 16-bp spacer
and 4-nt RNA . SNAP
output
|
|
4ylp
|
transcription-DNA-RNA |
X-ray (5.5 Å) |
Zuo Y, Steitz TA |
(2015) "Crystal
Structures of the E. coli Transcription Initiation
Complexes with a Complete Bubble."
Mol.Cell, 58, 534-540. doi:
10.1016/j.molcel.2015.03.010.
|
E. coli transcription initiation complex - 16-bp spacer
and 5-nt RNA . SNAP
output
|
|
4ym5
|
structural protein-DNA |
X-ray (4.005 Å) |
Osakabe A, Tachiwana H, Kagawa W, Horikoshi N,
Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J,
Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka
H |
(2015) "Structural
basis of pyrimidine-pyrimidone (6-4) photoproduct
recognition by UV-DDB in the nucleosome." Sci
Rep, 5, 16330. doi: 10.1038/srep16330.
|
Crystal structure of the human nucleosome containing
6-4pp (inside) . SNAP
output
|
|
4ym6
|
structural protein-DNA |
X-ray (3.514 Å) |
Osakabe A, Tachiwana H, Kagawa W, Horikoshi N,
Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J,
Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka
H |
(2015) "Structural
basis of pyrimidine-pyrimidone (6-4) photoproduct
recognition by UV-DDB in the nucleosome." Sci
Rep, 5, 16330. doi: 10.1038/srep16330.
|
Crystal structure of the human nucleosome containing
6-4pp (outside) . SNAP
output
|
|
4ymm
|
transferase-DNA |
X-ray (2.199 Å) |
Lee S, Koag M-C |
"Structure of human DNA polymerase beta complexed
with 7BG as the template base in a 1-nucleotide gapped
DNA." |
Structure of human DNA polymerase beta complexed with
7bg as the template base in a 1-nucleotide gapped DNA .
SNAP output
|
|
4ymn
|
transferase-DNA |
X-ray (2.591 Å) |
Kou Y, Koag MC, Lee S |
(2018) "Structural
and kinetic studies of the effect of guanine-N7
alkylation and metal cofactors on DNA replication."
Biochemistry. doi: 10.1021/acs.biochem.8b00331.
|
Structure of human DNA polymerase beta complexed with
n7bg in the template base paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
4ymo
|
transferase-DNA |
X-ray (2.148 Å) |
Kou Y, Koag MC, Lee S |
(2018) "Structural
and kinetic studies of the effect of guanine-N7
alkylation and metal cofactors on DNA replication."
Biochemistry. doi: 10.1021/acs.biochem.8b00331.
|
Structure of human DNA polymerase beta complexed with
n7bg in the template opposite to incoming
non-hydrolyzable ctp with manganese in the active site
. SNAP output
|
|
4yn4
|
transferase-DNA |
X-ray (2.243 Å) |
Kou Y, Koag MC, Lee S |
(2018) "Structural
and kinetic studies of the effect of guanine-N7
alkylation and metal cofactors on DNA replication."
Biochemistry. doi: 10.1021/acs.biochem.8b00331.
|
Structure of human DNA polymerase beta complexed with
n7bg in the template opposite to incoming
non-hydrolyzable dttp with manganese in the active site
. SNAP output
|
|
4ynq
|
hydrolase-DNA |
X-ray (2.8 Å) |
Grieves JL, Fye JM, Harvey S, Grayson JM, Hollis T,
Perrino FW |
(2015) "Exonuclease
TREX1 degrades double-stranded DNA to prevent
spontaneous lupus-like inflammatory disease."
Proc.Natl.Acad.Sci.USA, 112,
5117-5122. doi: 10.1073/pnas.1423804112.
|
Trex1-dsDNA complex . SNAP output
|
|
4yo2
|
transcription |
X-ray (3.073 Å) |
Morgunova E, Yin Y, Jolma A, Dave K, Schmierer B,
Popov A, Eremina N, Nilsson L, Taipale J |
(2015) "Structural
insights into the DNA-binding specificity of E2F family
transcription factors." Nat Commun,
6, 10050. doi: 10.1038/ncomms10050.
|
Structure of e2f8, an atypical member of e2f family of
transcription factors . SNAP output
|
|
4yoq
|
hydrolase-DNA |
X-ray (2.21 Å) |
Wang L, Lee SJ, Verdine GL |
(2015) "Structural
Basis for Avoidance of Promutagenic DNA Repair by MutY
Adenine DNA Glycosylase." J.Biol.Chem.,
290, 17096-17105. doi: 10.1074/jbc.M115.657866.
|
Crystal structure of muty bound to its anti-substrate .
SNAP output
|
|
4yov
|
hydrolase-DNA |
X-ray (2.05 Å) |
Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y,
Tanokura M |
(2015) "Structural
basis for substrate recognition and processive cleavage
mechanisms of the trimeric exonuclease PhoExo I."
Nucleic Acids Res., 43,
7122-7136. doi: 10.1093/nar/gkv654.
|
Crystal structure of a trimeric exonuclease phoexo i
from pyrococcus horikoshii ot3 in complex with poly-da
. SNAP output
|
|
4yow
|
hydrolase-DNA |
X-ray (2.5 Å) |
Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y,
Tanokura M |
(2015) "Structural
basis for substrate recognition and processive cleavage
mechanisms of the trimeric exonuclease PhoExo I."
Nucleic Acids Res., 43,
7122-7136. doi: 10.1093/nar/gkv654.
|
Crystal structure of a trimeric exonuclease phoexo i
from pyrococcus horikoshii ot3 in complex with poly-dc
. SNAP output
|
|
4yox
|
hydrolase-DNA |
X-ray (2.05 Å) |
Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y,
Tanokura M |
(2015) "Structural
basis for substrate recognition and processive cleavage
mechanisms of the trimeric exonuclease PhoExo I."
Nucleic Acids Res., 43,
7122-7136. doi: 10.1093/nar/gkv654.
|
Crystal structure of a trimeric exonuclease phoexo i
from pyrococcus horikoshii ot3 in complex with poly-dt
. SNAP output
|
|
4yoy
|
hydrolase-DNA |
X-ray (1.95 Å) |
Miyazono K, Ishino S, Tsutsumi K, Ito T, Ishino Y,
Tanokura M |
(2015) "Structural
basis for substrate recognition and processive cleavage
mechanisms of the trimeric exonuclease PhoExo I."
Nucleic Acids Res., 43,
7122-7136. doi: 10.1093/nar/gkv654.
|
Crystal structure of a trimeric exonuclease phoexo i
from pyrococcus horikoshii ot3 in complex with poly-dt
and mg2+ ion . SNAP
output
|
|
4yp3
|
transferase-DNA |
X-ray (1.89 Å) |
Su Y, Patra A, Harp JM, Egli M, Guengerich FP |
(2015) "Roles of
Residues Arg-61 and Gln-38 of Human DNA Polymerase eta
in Bypass of Deoxyguanosine and
7,8-Dihydro-8-oxo-2'-deoxyguanosine."
J.Biol.Chem., 290,
15921-15933. doi: 10.1074/jbc.M115.653691.
|
Mutant human DNA polymerase eta q38a-r61a inserting
dctp opposite an 8-oxoguanine lesion . SNAP output
|
|
4yph
|
hydrolase-DNA |
X-ray (2.32 Å) |
Wang L, Lee SJ, Verdine GL |
(2015) "Structural
Basis for Avoidance of Promutagenic DNA Repair by MutY
Adenine DNA Glycosylase." J.Biol.Chem.,
290, 17096-17105. doi: 10.1074/jbc.M115.657866.
|
Crystal structure of muty bound to its anti-substrate
with the disulfide cross-linker reduced . SNAP output
|
|
4ypr
|
hydrolase-DNA |
X-ray (2.59 Å) |
Wang L, Lee SJ, Verdine GL |
(2015) "Structural
Basis for Avoidance of Promutagenic DNA Repair by MutY
Adenine DNA Glycosylase." J.Biol.Chem.,
290, 17096-17105. doi: 10.1074/jbc.M115.657866.
|
Crystal structure of d144n muty bound to its
anti-substrate . SNAP
output
|
|
4yqw
|
transferase-DNA |
X-ray (2.064 Å) |
Su Y, Patra A, Harp JM, Egli M, Guengerich FP |
(2015) "Roles of
Residues Arg-61 and Gln-38 of Human DNA Polymerase eta
in Bypass of Deoxyguanosine and
7,8-Dihydro-8-oxo-2'-deoxyguanosine."
J.Biol.Chem., 290,
15921-15933. doi: 10.1074/jbc.M115.653691.
|
Mutant human DNA polymerase eta q38a-r61a inserting
dctp opposite template g . SNAP output
|
|
4yr0
|
transferase-DNA |
X-ray (1.78 Å) |
Su Y, Patra A, Harp JM, Egli M, Guengerich FP |
(2015) "Roles of
Residues Arg-61 and Gln-38 of Human DNA Polymerase eta
in Bypass of Deoxyguanosine and
7,8-Dihydro-8-oxo-2'-deoxyguanosine."
J.Biol.Chem., 290,
15921-15933. doi: 10.1074/jbc.M115.653691.
|
Mutant human DNA polymerase eta r61m inserting dctp
opposite an 8-oxoguanine lesion . SNAP output
|
|
4yr2
|
transferase-DNA |
X-ray (1.95 Å) |
Su Y, Patra A, Harp JM, Egli M, Guengerich FP |
(2015) "Roles of
Residues Arg-61 and Gln-38 of Human DNA Polymerase eta
in Bypass of Deoxyguanosine and
7,8-Dihydro-8-oxo-2'-deoxyguanosine."
J.Biol.Chem., 290,
15921-15933. doi: 10.1074/jbc.M115.653691.
|
Mutant human DNA polymerase eta r61m inserting datp
opposite an 8-oxoguanine lesion . SNAP output
|
|
4yr3
|
transferase-DNA |
X-ray (2.0 Å) |
Su Y, Patra A, Harp JM, Egli M, Guengerich FP |
(2015) "Roles of
Residues Arg-61 and Gln-38 of Human DNA Polymerase eta
in Bypass of Deoxyguanosine and
7,8-Dihydro-8-oxo-2'-deoxyguanosine."
J.Biol.Chem., 290,
15921-15933. doi: 10.1074/jbc.M115.653691.
|
Mutant human DNA polymerase eta r61m inserting dctp
opposite template g . SNAP output
|
|
4yrv
|
transcription-DNA |
X-ray (2.8 Å) |
Hu HX, Jiang YL, Zhao MX, Cai K, Liu S, Wen B, Lv P,
Zhang Y, Peng J, Zhong H, Yu HM, Ren YM, Zhang Z, Tian C,
Wu Q, Oliveberg M, Zhang CC, Chen Y, Zhou CZ |
(2015) "Structural
insights into HetR-PatS interaction involved in
cyanobacterial pattern formation." Sci
Rep, 5, 16470. doi: 10.1038/srep16470.
|
Crystal structure of anabaena transcription factor hetr
complexed with 21-bp DNA from hetp promoter . SNAP output
|
|
4ys3
|
structural protein-DNA |
X-ray (3.0 Å) |
Chatterjee N, North JA, Dechassa ML, Manohar M,
Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew
B |
(2015) "Histone
Acetylation near the Nucleosome Dyad Axis Enhances
Nucleosome Disassembly by RSC and SWI/SNF."
Mol.Cell.Biol., 35,
4083-4092. doi: 10.1128/MCB.00441-15.
|
Nucleosome disassembly by rsc and swi-snf is enhanced
by h3 acetylation near the nucleosome dyad axis .
SNAP output
|
|
4z1x
|
hydrolase-DNA |
X-ray (2.8 Å) |
Stoddard BL, Lambert AR, Kulshina N |
"Crystal structure of LAGLIDADG homing endonuclease
I-GzeII in complex with DNA target." |
Crystal structure of laglidadg homing endonuclease
i-gzeii in complex with DNA target . SNAP output
|
|
4z1z
|
hydrolase-DNA |
X-ray (3.2 Å) |
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM,
Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K,
Scharenberg AM, Stoddard BL |
(2016) "Indirect
DNA Sequence Recognition and Its Impact on Nuclease
Cleavage Activity." Structure,
24, 862-873. doi: 10.1016/j.str.2016.03.024.
|
Crystal structure of meganuclease i-smami bound to
uncleaveable DNA with a ttct central four . SNAP output
|
|
4z20
|
hydrolase-DNA |
X-ray (3.2 Å) |
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM,
Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K,
Scharenberg AM, Stoddard BL |
(2016) "Indirect
DNA Sequence Recognition and Its Impact on Nuclease
Cleavage Activity." Structure,
24, 862-873. doi: 10.1016/j.str.2016.03.024.
|
Crystal structure of meganuclease i-smami bound to
uncleaveable DNA with a ttgt central four . SNAP output
|
|
4z2c
|
isomerase |
X-ray (3.19 Å) |
Laponogov I, Veselkov DA, Pan X-S, Selvarajah J,
Crevel IM-T, Fisher LM, Sanderson MR |
"Structural studies of the drug-stabilized cleavage
complexes of topoisomerase IV and gyrase from
Streptococcus pneumoniae." |
Quinolone(moxifloxacin)-DNA cleavage complex of gyrase
from s. pneumoniae . SNAP output
|
|
4z2d
|
isomerase |
X-ray (3.38 Å) |
Laponogov I, Veselkov DA, Pan X-S, Selvarajah J,
Crevel IM-T, Fisher LM, Sanderson MR |
"Structural studies of the drug-stabilized cleavage
complexes of topoisomerase IV and gyrase from
Streptococcus pneumoniae." |
Quinolone(levofloxacin)-DNA cleavage complex of gyrase
from s. pneumoniae . SNAP output
|
|
4z2e
|
isomerase |
X-ray (3.46 Å) |
Laponogov I, Veselkov DA, Pan X-S, Selvarajah J,
Crevel IM-T, Fisher LM, Sanderson MR |
"Structural studies of the drug-stabilized cleavage
complexes of topoisomerase IV and gyrase from
Streptococcus pneumoniae." |
Quinolone(trovafloxacin)-DNA cleavage complex of gyrase
from s. pneumoniae . SNAP output
|
|
4z3a
|
hydrolase-DNA |
X-ray (1.72 Å) |
Malik SS, Coey CT, Varney KM, Pozharski E, Drohat
AC |
(2015) "Thymine
DNA glycosylase exhibits negligible affinity for
nucleobases that it removes from DNA." Nucleic
Acids Res., 43, 9541-9552. doi:
10.1093/nar/gkv890.
|
Acetate-free structure of the enzyme-product complex
resulting from tdg action on a gu mismatch . SNAP output
|
|
4z3c
|
DNA binding protein-DNA |
X-ray (1.57 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2017) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure. doi:
10.1016/j.str.2017.11.022.
|
Zinc finger region of human tet3 in complex with cpg
DNA . SNAP output
|
|
4z3o
|
isomerase |
X-ray (3.44 Å) |
Laponogov I, Veselkov DA, Pan X-S, Selvarajah J,
Crevel IM-T, Fisher LM, Sanderson MR |
"Structural studies of the drug-stabilized cleavage
complexes of topoisomerase IV and gyrase from
Streptococcus pneumoniae." |
Quinolone(moxifloxacin)-DNA cleavage complex of
topoisomerase iv from s. pneumoniae . SNAP output
|
|
4z47
|
DNA binding protein-DNA |
X-ray (1.45 Å) |
Malik SS, Coey CT, Varney KM, Pozharski E, Drohat
AC |
(2015) "Thymine
DNA glycosylase exhibits negligible affinity for
nucleobases that it removes from DNA." Nucleic
Acids Res., 43, 9541-9552. doi:
10.1093/nar/gkv890.
|
Structure of the enzyme-product complex resulting from
tdg action on a gu mismatch in the presence of excess
base . SNAP output
|
|
4z4q
|
isomerase |
X-ray (3.04 Å) |
Laponogov I, Veselkov DA, Pan X-S, Selvarajah J,
Crevel IM-T, Fisher LM, Sanderson MR |
"Structural studies of the drug-stabilized cleavage
complexes of topoisomerase IV and gyrase from
Streptococcus pneumoniae." |
Quinazolinedione(pd 0305970)-DNA cleavage complex of
topoisomerase iv from s. pneumoniae . SNAP output
|
|
4z53
|
isomerase |
X-ray (3.26 Å) |
Laponogov I, Veselkov DA, Pan X-S, Selvarajah J,
Crevel IM-T, Fisher LM, Sanderson MR |
"Structural studies of the drug-stabilized cleavage
complexes of topoisomerase IV and gyrase from
Streptococcus pneumoniae." |
Quinolone(trovafloxacin)-DNA cleavage complex of
topoisomerase iv from s. pneumoniae . SNAP output
|
|
4z58
|
transcription-DNA |
X-ray (2.5 Å) |
Min J, Wang A, Brennan RG, Schumacher MA |
"Molecular mechanism on hipBA gene regulation." |
Hipb-o3 20mer complex . SNAP output
|
|
4z59
|
transcription-DNA |
X-ray (2.3 Å) |
Min J, Wang A, Brennan RG, Schumacher MA |
"Molecular mechanism on hipBA gene regulation." |
Hipb-o4 20mer complex . SNAP output
|
|
4z5c
|
transcription-DNA |
X-ray (2.5 Å) |
Min J, Wang A, Brennan RG, Schumacher MA |
"Molecular mechanism on hipBA gene regulation." |
Hipb-o3 21mer complex . SNAP output
|
|
4z5d
|
transcription-DNA |
X-ray (2.15 Å) |
Min J, Wang A, Brennan RG, Schumacher MA |
"Molecular mechanism on hipBA gene regulation." |
Hipb-o4 21mer complex . SNAP output
|
|
4z5h
|
transcription-DNA |
X-ray (2.1 Å) |
Min J, Wang A, Brennan RG, Schumacher MA |
"Molecular mechanism on hipBA gene regulation." |
Hipb(s29a)-o2 20mer complex . SNAP output
|
|
4z5t
|
structural protein-DNA |
X-ray (2.8 Å) |
Urahama T, Harada A, Maehara K, Horikoshi N, Sato K,
Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H,
Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H |
(2016) "Histone
H3.5 forms an unstable nucleosome and accumulates
around transcription start sites in human testis."
Epigenetics Chromatin, 9, 2.
doi: 10.1186/s13072-016-0051-y.
|
The nucleosome containing human h3.5 . SNAP output
|
|
4z66
|
structural protein-DNA |
X-ray (2.5 Å) |
Chatterjee N, North JA, Dechassa ML, Manohar M,
Prasad R, Luger K, Ottesen JJ, Poirier MG, Bartholomew
B |
(2015) "Histone
Acetylation near the Nucleosome Dyad Axis Enhances
Nucleosome Disassembly by RSC and SWI/SNF."
Mol.Cell.Biol., 35,
4083-4092. doi: 10.1128/MCB.00441-15.
|
Nucleosome disassembly by rsc and swi-snf is enhanced
by h3 acetylation near the nucleosome dyad axis .
SNAP output
|
|
4z6c
|
transferase-DNA |
X-ray (2.677 Å) |
Koag MC, Lee S |
(2018) "Insights
into the effect of minor groove interactions and metal
cofactors on mutagenic replication by human DNA
polymerase beta." Biochem. J.,
475, 571-585. doi: 10.1042/BCJ20170787.
|
Structure of human DNA polymerase beta 279na mutant
complexed with g in the template base paired with
incoming non-hydrolyzable ctp . SNAP output
|
|
4z6d
|
transferase-DNA |
X-ray (2.51 Å) |
Koag MC, Lee S |
(2018) "Insights
into the effect of minor groove interactions and metal
cofactors on mutagenic replication by human DNA
polymerase beta." Biochem. J.,
475, 571-585. doi: 10.1042/BCJ20170787.
|
Structure of human DNA polymerase beta 279na mutant
complexed with g in the template base paired with
incoming non-hydrolyzable ttp . SNAP output
|
|
4z6e
|
transferase-DNA |
X-ray (2.752 Å) |
Koag MC, Lee S |
(2018) "Insights
into the effect of minor groove interactions and metal
cofactors on mutagenic replication by human DNA
polymerase beta." Biochem. J.,
475, 571-585. doi: 10.1042/BCJ20170787.
|
Structure of human DNA polymerase beta 279na mutant
complexed with g in the template base paired with
incoming non-hydrolyzable ttp and manganese . SNAP output
|
|
4z6f
|
transferase-DNA |
X-ray (2.444 Å) |
Koag MC, Lee S |
(2018) "Insights
into the effect of minor groove interactions and metal
cofactors on mutagenic replication by human DNA
polymerase beta." Biochem. J.,
475, 571-585. doi: 10.1042/BCJ20170787.
|
Structure of human DNA polymerase beta 279na mutant
complexed with g in the template base paired with
incoming non-hydrolyzable ttp and manganese . SNAP output
|
|
4z7b
|
hydrolase-DNA |
X-ray (2.02 Å) |
Malik SS, Coey CT, Varney KM, Pozharski E, Drohat
AC |
(2015) "Thymine
DNA glycosylase exhibits negligible affinity for
nucleobases that it removes from DNA." Nucleic
Acids Res., 43, 9541-9552. doi:
10.1093/nar/gkv890.
|
Structure of the enzyme-product complex resulting from
tdg action on a gfc mismatch . SNAP output
|
|
4z7z
|
hydrolase-DNA |
X-ray (1.83 Å) |
Malik SS, Coey CT, Varney KM, Pozharski E, Drohat
AC |
(2015) "Thymine
DNA glycosylase exhibits negligible affinity for
nucleobases that it removes from DNA." Nucleic
Acids Res., 43, 9541-9552. doi:
10.1093/nar/gkv890.
|
Structure of the enzyme-product complex resulting from
tdg action on a gt mismatch in the presence of excess
base . SNAP output
|
|
4z8f
|
immune system-DNA |
X-ray (1.75 Å) |
Haji-Ghassemi O, Muller-Loennies S, Rodriguez T,
Brade L, Kosma P, Brade H, Evans SV |
(2015) "Structural
Basis for Antibody Recognition of Lipid A: INSIGHTS TO
POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA."
J.Biol.Chem., 290,
19629-19640. doi: 10.1074/jbc.M115.657874.
|
Fab structure of antibody s1-15 in complex with ssDNA
DNA, 5'-p5(dt)p-3' . SNAP output
|
|
4zbn
|
immune system-DNA |
X-ray (2.447 Å) |
Jarvis TC, Davies DR, Hisaminato A, Resnicow DI,
Gupta S, Waugh SM, Nagabukuro A, Wadatsu T, Hishigaki H,
Gawande B, Zhang C, Wolk SK, Mayfield WS, Nakaishi Y,
Burgin AB, Stewart LJ, Edwards TE, Gelinas AD, Schneider
DJ, Janjic N |
(2015) "Non-helical
DNA Triplex Forms a Unique Aptamer Scaffold for High
Affinity Recognition of Nerve Growth Factor."
Structure, 23, 1293-1304.
doi: 10.1016/j.str.2015.03.027.
|
Non-helical DNA triplex forms a unique aptamer scaffold
for high affinity recognition of nerve growth factor .
SNAP output
|
|
4zcf
|
hydrolase-DNA complex |
X-ray (2.6 Å) |
Gupta YK, Chan SH, Xu SY, Aggarwal AK |
(2015) "Structural
basis of asymmetric DNA methylation and ATP-triggered
long-range diffusion by EcoP15I." Nat
Commun, 6, 7363. doi: 10.1038/ncomms8363.
|
Structural basis of asymmetric DNA methylation and
atp-triggered long-range diffusion by ecop15i .
SNAP output
|
|
4zhn
|
oxidoreductase-DNA |
X-ray (1.333 Å) |
Hall ML, Ergel B, Miller EB, Yu B, Rinaldo D, Hunt
JF, Friesner R |
"DFT Studies of the Rate-Limiting Step in the
Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related
Experimental Studies." |
Crystal structure of alkb t208a mutant protein in
complex with co(ii), 2-oxoglutarate, and methylated
trinucleotide t-mea-t . SNAP output
|
|
4zm0
|
transcription |
X-ray (3.17 Å) |
Garcia-Pino A, De Gieter S, Talavera A, De Greve H,
Efremov RG, Loris R |
(2016) "An
intrinsically disordered entropic switch determines
allostery in Phd-Doc regulation."
Nat.Chem.Biol., 12, 490-496.
doi: 10.1038/nchembio.2078.
|
Antitoxin phd from phage p1 in complex with its
operator DNA inverted repeat . SNAP output
|
|
4zm2
|
transcription |
X-ray (3.88 Å) |
Garcia-Pino A, De Gieter S, Talavera A, De Greve H,
Efremov RG, Loris R |
(2016) "An
intrinsically disordered entropic switch determines
allostery in Phd-Doc regulation."
Nat.Chem.Biol., 12, 490-496.
doi: 10.1038/nchembio.2078.
|
Antitoxin phd from phage p1 in complex with its
operator DNA inverted repeat in a monoclinic space
group . SNAP output
|
|
4zpk
|
protein transport-transcription-DNA |
X-ray (3.6 Å) |
Wu D, Potluri N, Lu J, Kim Y, Rastinejad F |
(2015) "Structural
integration in hypoxia-inducible factors."
Nature, 524, 303-308. doi:
10.1038/nature14883.
|
Crystal structure of the heterodimeric hif-2a:arnt
complex with hre DNA . SNAP output
|
|
4zpr
|
protein transport-transcription-DNA |
X-ray (3.902 Å) |
Wu D, Potluri N, Lu J, Kim Y, Rastinejad F |
(2015) "Structural
integration in hypoxia-inducible factors."
Nature, 524, 303-308. doi:
10.1038/nature14883.
|
Crystal structure of the heterodimeric hif-1a:arnt
complex with hre DNA . SNAP output
|
|
4zq9
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Musayev FN, Zarate-Perez F, Bishop C, Burgner JW,
Escalante CR |
(2015) "Structural
Insights into the Assembly of the Adeno-associated
Virus Type 2 Rep68 Protein on the Integration Site
AAVS1." J.Biol.Chem.,
290, 27487-27499. doi: 10.1074/jbc.M115.669960.
|
X-ray structure of aav-2 obd bound to aavs1 site 3:1 .
SNAP output
|
|
4zsf
|
protein-DNA |
X-ray (1.8 Å) |
Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S,
Tamulaitiene G, Siksnys V |
(2015) "Functional
significance of protein assemblies predicted by the
crystal structure of the restriction endonuclease
BsaWI." Nucleic Acids Res.,
43, 8100-8110. doi: 10.1093/nar/gkv768.
|
Crystal structure of pre-specific restriction
endonuclease bsawi-DNA complex . SNAP output
|
|
4ztf
|
transferase-DNA-inhibitor |
X-ray (2.7 Å) |
Raheem IT, Walji AM, Klein D, Sanders JM, Powell DA,
Abeywickrema P, Barbe G, Bennet A, Clas SD, Dubost D,
Embrey M, Grobler J, Hafey MJ, Hartingh TJ, Hazuda DJ,
Miller MD, Moore KP, Pajkovic N, Patel S, Rada V, Rearden
P, Schreier JD, Sisko J, Steele TG, Truchon JF, Wai J, Xu
M, Coleman PJ |
(2015) "Discovery
of 2-Pyridinone Aminals: A Prodrug Strategy to Advance
a Second Generation of HIV-1 Integrase Strand Transfer
Inhibitors." J.Med.Chem.,
58, 8154-8165. doi: 10.1021/acs.jmedchem.5b01037.
|
Crystal structure of the prototype foamy virus intasome
with a 2-pyridinone aminal inhibitor . SNAP output
|
|
4ztj
|
transferase-DNA-inhibitor |
X-ray (2.67 Å) |
Raheem IT, Walji AM, Klein D, Sanders JM, Powell DA,
Abeywickrema P, Barbe G, Bennet A, Clas SD, Dubost D,
Embrey M, Grobler J, Hafey MJ, Hartingh TJ, Hazuda DJ,
Miller MD, Moore KP, Pajkovic N, Patel S, Rada V, Rearden
P, Schreier JD, Sisko J, Steele TG, Truchon JF, Wai J, Xu
M, Coleman PJ |
(2015) "Discovery
of 2-Pyridinone Aminals: A Prodrug Strategy to Advance
a Second Generation of HIV-1 Integrase Strand Transfer
Inhibitors." J.Med.Chem.,
58, 8154-8165. doi: 10.1021/acs.jmedchem.5b01037.
|
Crystal structure of the prototype foamy virus intasome
with a 2-pyridinone aminal inhibitor . SNAP output
|
|
4ztu
|
DNA binding protein-DNA |
X-ray (3.299 Å) |
Szymanski MR, Kuznestov VB, Shumate CK, Meng Q, Lee
Y-S, Patel G, Patel SS, Yin YW |
(2015) "Structural
basis for processivity and antiviral drug toxicity in
human mitochondrial DNA replicase." EMBO
J., 34, 1959. doi: 10.15252/embj.201591520.
|
Structural basis for processivity and antiviral drug
toxicity in human mitochondrial DNA replicase .
SNAP output
|
|
4ztz
|
DNA binding protein-DNA |
X-ray (3.442 Å) |
Szymanski MR, Kuznestov VB, Shumate CK, Meng Q, Lee
Y-S, Patel G, Patel SS, Yin YW |
(2015) "Structural
basis for processivity and antiviral drug toxicity in
human mitochondrial DNA replicase." EMBO
J., 34, 1959. doi: 10.15252/embj.201591520.
|
Structural basis for processivity and antiviral drug
toxicity in human mitochondrial DNA replicase .
SNAP output
|
|
4zux
|
hydrolase-DNA |
X-ray (3.82 Å) |
Morgan MT, Haj-Yahya M, Ringel AE, Bandi P, Brik A,
Wolberger C |
(2016) "Structural
basis for histone H2B deubiquitination by the SAGA DUB
module." Science, 351,
725-728. doi: 10.1126/science.aac5681.
|
Saga dub module ubp8-sgf11-sus1-sgf73 bound to
ubiqitinated nucleosome . SNAP output
|
|
4zyd
|
transferase |
X-ray (2.682 Å) |
Perugino G, Miggiano R, Serpe M, Vettone A, Valenti
A, Lahiri S, Rossi F, Rossi M, Rizzi M, Ciaramella M |
(2015) "Structure-function
relationships governing activity and stability of a DNA
alkylation damage repair thermostable protein."
Nucleic Acids Res., 43,
8801-8816. doi: 10.1093/nar/gkv774.
|
Crystal structure of sulfolobus solfataricus
o6-methylguanine methyltransferase in complex with
modified DNA . SNAP
output
|
|
5a0m
|
hydrolase-DNA |
X-ray (2.9 Å) |
Prieto J, Redondo P, Merino N, Villate M, Montoya G,
Blanco FJ, Molina R |
(2016) "Structure
of the I-Scei Nuclease Complexed with its DsDNA Target
and Three Catalytic Metal Ions." Acta
Crystallogr.,Sect.F, 72, 473.
doi: 10.1107/S2053230X16007512.
|
The crystal structure of i-scei in complex with its
target DNA in the presence of mn . SNAP output
|
|
5a0v
|
hydrolase-RNA |
X-ray (2.8 Å) |
Pei XY, Bralley P, Jones GH, Luisi BF |
(2015) "Linkage
of Catalysis and 5' End Recognition in Ribonuclease
Rnase J." Nucleic Acids Res.,
43, 8066. doi: 10.1093/NAR/GKV732.
|
Catalysis and 5' end sensing by ribonuclease rnase j of
the metallo- beta-lactamase family . SNAP output
|
|
5a0w
|
hydrolase-DNA |
X-ray (2.2 Å) |
Molina R, Besker N, Prieto J, Montoya G, D'Abramo
M |
"Structural and Dynamical Characterization of the I-
Dmo Catalytic Activity." |
The crystal structure of i-dmoi e117a in complex with
its target DNA and in the presence of 2mm mn . SNAP output
|
|
5a39
|
replication |
X-ray (2.8 Å) |
Koch SC, Kuper J, Gasteiger KL, Simon N, Strasser R,
Eisen D, Geiger S, Schneider S, Kisker C, Carell T |
(2015) "Structural
Insights Into the Recognition of Cisplatin and Aaf-Dg
Lesion by Rad14 (Xpa)."
Proc.Natl.Acad.Sci.USA, 112,
8272. doi: 10.1073/PNAS.1508509112.
|
Structure of rad14 in complex with cisplatin containing
DNA . SNAP output
|
|
5a3d
|
DNA binding protein |
X-ray (1.8 Å) |
Koch SC, Kuper J, Gasteiger KL, Simon N, Strasser R,
Eisen D, Geiger S, Schneider S, Kisker C, Carell T |
(2015) "Structural
Insights Into the Recognition of Cisplatin and Aaf-Dg
Lesion by Rad14 (Xpa)."
Proc.Natl.Acad.Sci.USA, 112,
8272. doi: 10.1073/PNAS.1508509112.
|
Structural insights into the recognition of cisplatin
and aaf-dg lesions by rad14 (xpa) . SNAP output
|
|
5a72
|
hydrolase-DNA |
X-ray (2.6 Å) |
Molina R, Redondo P, Lopez-Mendez B, Villate M,
Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P,
Prieto J, Montoya G |
(2015) "Crystal
Structure of the Homing Endonuclease I-Cvui Provides a
New Template for Genome Modification."
J.Biol.Chem., 290, 28727.
doi: 10.1074/JBC.M115.678342.
|
Crystal structure of the homing endonuclease i-cvui in
complex with its target (sro1.3) in the presence of 2
mm ca . SNAP output
|
|
5a74
|
hydrolase-DNA |
X-ray (2.5 Å) |
Molina R, Redondo P, Lopez-Mendez B, Villate M,
Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P,
Prieto J, Montoya G |
(2015) "Crystal
Structure of the Homing Endonuclease I-Cvui Provides a
New Template for Genome Modification."
J.Biol.Chem., 290, 28727.
doi: 10.1074/JBC.M115.678342.
|
Crystal structure of the homing endonuclease i-cvui in
complex with its target (sro1.3) in the presence of 2
mm mn . SNAP output
|
|
5a77
|
hydrolase-DNA |
X-ray (2.5 Å) |
Molina R, Redondo P, Lopez-Mendez B, Villate M,
Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P,
Prieto J, Montoya G |
(2015) "Crystal
Structure of the Homing Endonuclease I-Cvui Provides a
New Template for Genome Modification."
J.Biol.Chem., 290, 28727.
doi: 10.1074/JBC.M115.678342.
|
Crystal structure of the homing endonuclease i-cvui in
complex with i- crei target (c1221) in the presence of
2 mm mg revealing DNA cleaved . SNAP output
|
|
5a78
|
hydrolase-DNA |
X-ray (2.5 Å) |
Molina R, Redondo P, Lopez-Mendez B, Villate M,
Merino N, Blanco FJ, Valton J, Grizot S, Duchateau P,
Prieto J, Montoya G |
(2015) "Crystal
Structure of the Homing Endonuclease I-Cvui Provides a
New Template for Genome Modification."
J.Biol.Chem., 290, 28727.
doi: 10.1074/JBC.M115.678342.
|
Crystal structure of the homing endonuclease i-cvui in
complex with i- crei target (c1221) in the presence of
2 mm mg revealing DNA not cleaved . SNAP output
|
|
5ak9
|
hydrolase |
X-ray (2.601 Å) |
Molina R, Marcaida MJ, Redondo P, Marenchino M,
Duchateau P, D'Abramo M, Montoya G, Prieto J |
(2015) "Engineering
a Nickase on the Homing Endonuclease I-Dmoi
Scaffold." J.Biol.Chem.,
290, 18534. doi: 10.1074/JBC.M115.658666.
|
The crystal structure of i-dmoi q42ak120m in complex
with its target DNA in the presence of 2mm mn .
SNAP output
|
|
5akf
|
hydrolase |
X-ray (2.45 Å) |
Molina R, Marcaida MJ, Redondo P, Marenchino M,
Duchateau P, D'Abramo M, Montoya G, Prieto J |
(2015) "Engineering
a Nickase on the Homing Endonuclease I-Dmoi
Scaffold." J.Biol.Chem.,
290, 18534. doi: 10.1074/JBC.M115.658666.
|
The crystal structure of i-dmoi q42ak120m in complex
with its target DNA nicked in the coding strand a and
in the presence of 2mm mn . SNAP output
|
|
5akm
|
hydrolase |
X-ray (2.4 Å) |
Molina R, Marcaida MJ, Redondo P, Marenchino M,
Duchateau P, D'Abramo M, Montoya G, Prieto J |
(2015) "Engineering
a Nickase on the Homing Endonuclease I-Dmoi
Scaffold." J.Biol.Chem.,
290, 18534. doi: 10.1074/JBC.M115.658666.
|
The crystal structure of i-dmoi g20s in complex with
its target DNA in the presence of 2mm mg . SNAP output
|
|
5akn
|
hydrolase-DNA |
X-ray (2.75 Å) |
Molina R, Marcaida MJ, Redondo P, Marenchino M,
Duchateau P, D'Abramo M, Montoya G, Prieto J |
(2015) "Engineering
a Nickase on the Homing Endonuclease I-Dmoi
Scaffold." J.Biol.Chem.,
290, 18534. doi: 10.1074/JBC.M115.658666.
|
The crystal structure of i-dmoi q42ak120m in complex
with its target DNA nicked in the non-coding strand b
and in the presence of 2mm mn . SNAP output
|
|
5aox
|
translation |
X-ray (2.04 Å) |
Ahl V, Keller H, Schmidt S, Weichenrieder O |
(2015) "Retrotransposition
and Crystal Structure of an Alu Rnp in the
Ribosome-Stalling Conformation." Mol.Cell,
60, 715. doi: 10.1016/J.MOLCEL.2015.10.003.
|
Human alu RNA retrotransposition complex in the
ribosome-stalling conformation . SNAP output
|
|
5av5
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K,
Umehara T, Yokoyama S |
(2015) "Intra-
and inter-nucleosomal interactions of the histone H4
tail revealed with a human nucleosome core particle
with genetically-incorporated H4
tetra-acetylation." Sci Rep,
5, 17204. doi: 10.1038/srep17204.
|
Human nucleosome core particle . SNAP output
|
|
5av6
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K,
Umehara T, Yokoyama S |
(2015) "Intra-
and inter-nucleosomal interactions of the histone H4
tail revealed with a human nucleosome core particle
with genetically-incorporated H4
tetra-acetylation." Sci Rep,
5, 17204. doi: 10.1038/srep17204.
|
Human nucleosome core particle . SNAP output
|
|
5av8
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K,
Umehara T, Yokoyama S |
(2015) "Intra-
and inter-nucleosomal interactions of the histone H4
tail revealed with a human nucleosome core particle
with genetically-incorporated H4
tetra-acetylation." Sci Rep,
5, 17204. doi: 10.1038/srep17204.
|
Human nucleosome core particle . SNAP output
|
|
5av9
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K,
Umehara T, Yokoyama S |
(2015) "Intra-
and inter-nucleosomal interactions of the histone H4
tail revealed with a human nucleosome core particle
with genetically-incorporated H4
tetra-acetylation." Sci Rep,
5, 17204. doi: 10.1038/srep17204.
|
Human nucleosome core particle . SNAP output
|
|
5avb
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K,
Umehara T, Yokoyama S |
(2015) "Intra-
and inter-nucleosomal interactions of the histone H4
tail revealed with a human nucleosome core particle
with genetically-incorporated H4
tetra-acetylation." Sci Rep,
5, 17204. doi: 10.1038/srep17204.
|
Human nucleosome core particle . SNAP output
|
|
5avc
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K,
Umehara T, Yokoyama S |
(2015) "Intra-
and inter-nucleosomal interactions of the histone H4
tail revealed with a human nucleosome core particle
with genetically-incorporated H4
tetra-acetylation." Sci Rep,
5, 17204. doi: 10.1038/srep17204.
|
Human nucleosome core particle . SNAP output
|
|
5awh
|
RNA binding protein-DNA-RNA |
X-ray (2.0 Å) |
Miyoshi T, Ito K, Murakami R, Uchiumi T |
(2016) "Structural
basis for the recognition of guide RNA and target DNA
heteroduplex by Argonaute." Nat Commun,
7, 11846. doi: 10.1038/ncomms11846.
|
Rhodobacter sphaeroides argonaute in complex with guide
RNA-target DNA heteroduplex . SNAP output
|
|
5axw
|
hydrolase-RNA-DNA |
X-ray (2.7 Å) |
Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y,
Kurabayashi A, Ishitani R, Zhang F, Nureki O |
(2015) "Crystal
Structure of Staphylococcus aureus Cas9."
Cell, 162, 1113-1126. doi:
10.1016/j.cell.2015.08.007.
|
Crystal structure of staphylococcus aureus cas9 in
complex with sgrna and target DNA (ttgggt pam) .
SNAP output
|
|
5ay8
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S,
Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H |
(2016) "Structure
and function of human histone H3.Y nucleosome."
Nucleic Acids Res., 44,
6127-6141. doi: 10.1093/nar/gkw202.
|
Crystal structure of human nucleosome containing h3.y .
SNAP output
|
|
5b0y
|
DNA binding protein |
X-ray (2.557 Å) |
Suzuki Y, Horikoshi N, Kato D, Kurumizaka H |
(2016) "Crystal
structure of the nucleosome containing histone H3 with
crotonylated lysine 122."
Biochem.Biophys.Res.Commun.,
469, 483-489. doi: 10.1016/j.bbrc.2015.12.041.
|
Crystal structure of the nucleosome containing histone
h3 with the crotonylated lysine 122 . SNAP output
|
|
5b0z
|
DNA binding protein |
X-ray (1.987 Å) |
Suzuki Y, Horikoshi N, Kato D, Kurumizaka H |
(2016) "Crystal
structure of the nucleosome containing histone H3 with
crotonylated lysine 122."
Biochem.Biophys.Res.Commun.,
469, 483-489. doi: 10.1016/j.bbrc.2015.12.041.
|
The crystal structure of the nucleosome containing
h3.2, at 1.98 Å resolution . SNAP output
|
|
5b1l
|
structural protein-DNA |
X-ray (2.35 Å) |
Ueda J, Harada A, Urahama T, Machida S, Maehara K,
Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A,
Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M,
Iwamoto T, Isotani A, Ikawa M, Tachibana T, Okada Y,
Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K |
(2017) "Testis-Specific
Histone Variant H3t Gene Is Essential for Entry into
Spermatogenesis." Cell Rep,
18, 593-600. doi: 10.1016/j.celrep.2016.12.065.
|
The mouse nucleosome structure containing h3t .
SNAP output
|
|
5b1m
|
structural protein-DNA |
X-ray (2.34 Å) |
Ueda J, Harada A, Urahama T, Machida S, Maehara K,
Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A,
Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M,
Iwamoto T, Isotani A, Ikawa M, Tachibana T, Okada Y,
Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K |
(2017) "Testis-Specific
Histone Variant H3t Gene Is Essential for Entry into
Spermatogenesis." Cell Rep,
18, 593-600. doi: 10.1016/j.celrep.2016.12.065.
|
The mouse nucleosome structure containing h3.1 .
SNAP output
|
|
5b24
|
structural protein-DNA |
X-ray (3.6 Å) |
Horikoshi N, Tachiwana H, Kagawa W, Osakabe A,
Matsumoto S, Iwai S, Sugasawa K, Kurumizaka H |
(2016) "Crystal
structure of the nucleosome containing ultraviolet
light-induced cyclobutane pyrimidine dimer."
Biochem.Biophys.Res.Commun.,
471, 117-122. doi: 10.1016/j.bbrc.2016.01.170.
|
The crystal structure of the nucleosome containing
cyclobutane pyrimidine dimer . SNAP output
|
|
5b2i
|
transcription-DNA |
X-ray (3.0 Å) |
Fujii Y, Wakamori M, Umehara T, Yokoyama S |
(2016) "Crystal
structure of human nucleosome core particle containing
enzymatically introduced CpG methylation." Febs
Open Bio, 6, 498-514. doi:
10.1002/2211-5463.12064.
|
Human nucleosome containing cpg unmethylated DNA .
SNAP output
|
|
5b2j
|
transcription-DNA |
X-ray (2.6 Å) |
Fujii Y, Wakamori M, Umehara T, Yokoyama S |
(2016) "Crystal
structure of human nucleosome core particle containing
enzymatically introduced CpG methylation." Febs
Open Bio, 6, 498-514. doi:
10.1002/2211-5463.12064.
|
Human nucleosome containing cpg methylated DNA .
SNAP output
|
|
5b2o
|
hydrolase-RNA-DNA |
X-ray (1.7 Å) |
Hirano H, Gootenberg JS, Horii T, Abudayyeh OO,
Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang
F, Nishimasu H, Nureki O |
(2016) "Structure
and Engineering of Francisella novicida Cas9."
Cell, 164, 950-961. doi:
10.1016/j.cell.2016.01.039.
|
Crystal structure of francisella novicida cas9 in
complex with sgrna and target DNA (tgg pam) . SNAP output
|
|
5b2p
|
hydrolase-RNA-DNA |
X-ray (1.7 Å) |
Hirano H, Gootenberg JS, Horii T, Abudayyeh OO,
Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang
F, Nishimasu H, Nureki O |
(2016) "Structure
and Engineering of Francisella novicida Cas9."
Cell, 164, 950-961. doi:
10.1016/j.cell.2016.01.039.
|
Crystal structure of francisella novicida cas9 in
complex with sgrna and target DNA (tga pam) . SNAP output
|
|
5b2q
|
hydrolase-RNA-DNA |
X-ray (1.7 Å) |
Hirano H, Gootenberg JS, Horii T, Abudayyeh OO,
Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang
F, Nishimasu H, Nureki O |
(2016) "Structure
and Engineering of Francisella novicida Cas9."
Cell, 164, 950-961. doi:
10.1016/j.cell.2016.01.039.
|
Crystal structure of francisella novicida cas9 rha in
complex with sgrna and target DNA (tgg pam) . SNAP output
|
|
5b2r
|
hydrolase-RNA-DNA |
X-ray (2.0 Å) |
Hirano S, Nishimasu H, Ishitani R, Nureki O |
(2016) "Structural
Basis for the Altered PAM Specificities of Engineered
CRISPR-Cas9." Mol.Cell,
61, 886-894. doi: 10.1016/j.molcel.2016.02.018.
|
Crystal structure of the streptococcus pyogenes cas9
vqr variant in complex with sgrna and target DNA (tga
pam) . SNAP output
|
|
5b2s
|
hydrolase-RNA-DNA |
X-ray (2.2 Å) |
Hirano S, Nishimasu H, Ishitani R, Nureki O |
(2016) "Structural
Basis for the Altered PAM Specificities of Engineered
CRISPR-Cas9." Mol.Cell,
61, 886-894. doi: 10.1016/j.molcel.2016.02.018.
|
Crystal structure of the streptococcus pyogenes cas9
eqr variant in complex with sgrna and target DNA (tgag
pam) . SNAP output
|
|
5b2t
|
hydrolase-RNA-DNA |
X-ray (2.2 Å) |
Hirano S, Nishimasu H, Ishitani R, Nureki O |
(2016) "Structural
Basis for the Altered PAM Specificities of Engineered
CRISPR-Cas9." Mol.Cell,
61, 886-894. doi: 10.1016/j.molcel.2016.02.018.
|
Crystal structure of the streptococcus pyogenes cas9
vrer variant in complex with sgrna and target DNA (tgcg
pam) . SNAP output
|
|
5b31
|
DNA binding protein |
X-ray (2.2 Å) |
Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H |
(2016) "Crystal
structures of heterotypic nucleosomes containing
histones H2A.Z and H2A." Open Biology,
6. doi: 10.1098/rsob.160127.
|
The crystal structure of the heterotypic h2az-h2a
nucleosome with h3.1. . SNAP output
|
|
5b32
|
DNA binding protein |
X-ray (2.35 Å) |
Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H |
(2016) "Crystal
structures of heterotypic nucleosomes containing
histones H2A.Z and H2A." Open Biology,
6. doi: 10.1098/rsob.160127.
|
The crystal structure of the heterotypic h2az-h2a
nucleosome with h3.3. . SNAP output
|
|
5b33
|
DNA binding protein |
X-ray (2.925 Å) |
Horikoshi N, Arimura Y, Taguchi H, Kurumizaka H |
(2016) "Crystal
structures of heterotypic nucleosomes containing
histones H2A.Z and H2A." Open Biology,
6. doi: 10.1098/rsob.160127.
|
The crystal structure of the h2az nucleosome with h3.3.
. SNAP output
|
|
5b40
|
structural protein-DNA |
X-ray (3.33 Å) |
Machida S, Sekine S, Nishiyama Y, Horikoshi N,
Kurumizaka H |
"Monoubiquitination of histones H2B and H4 changes
the nucleosome stability without affecting the nucleosome
structure." |
The nucleosome structure containing h2b-k120 and h4-k31
monoubiquitinations . SNAP output
|
|
5b43
|
hydrolase-RNA-DNA |
X-ray (2.8 Å) |
Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker
IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV,
Ishitani R, Zhang F, Nureki O |
(2016) "Crystal
Structure of Cpf1 in Complex with Guide RNA and Target
DNA." Cell, 165, 949-962.
doi: 10.1016/j.cell.2016.04.003.
|
Crystal structure of acidaminococcus sp. cpf1 in
complex with crrna and target DNA . SNAP output
|
|
5b7j
|
DNA binding protein-DNA |
NMR |
Guan L, He P, Yang F, Zhang Y, Hu Y, Ding J, Hua Y,
Zhang Y, Ye Q, Hu J, Wang T, Jin C, Kong D |
(2017) "Sap1 is
a replication-initiation factor essential for the
assembly of pre-replicative complex in the fission
yeast Schizosaccharomyces pombe." J. Biol.
Chem., 292, 6056-6075. doi:
10.1074/jbc.M116.767806.
|
Structure model of sap1-DNA complex . SNAP output
|
|
5bk4
|
hydrolase-DNA |
cryo-EM (3.9 Å) |
Noguchi Y, Yuan Z, Bai L, Schneider S, Zhao G,
Stillman B, Speck C, Li H |
(2017) "Cryo-EM
structure of Mcm2-7 double hexamer on DNA suggests a
lagging-strand DNA extrusion model." Proc.
Natl. Acad. Sci. U.S.A., 114,
E9529-E9538. doi: 10.1073/pnas.1712537114.
|
cryo-EM structure of mcm2-7 double hexamer on dsDNA .
SNAP output
|
|
5bmz
|
transcription |
X-ray (3.001 Å) |
Kim Y, Joachimiak G, Biglow L, Cobb G, Joachimiak
A |
"Crystal Structure of Putative MarR Family
Transcriptional Regulator HcaR from Acinetobacter sp. ADP
complexed with 24mer DNA." |
Crystal structure of putative marr family
transcriptional regulator hcar from acinetobacter sp.
adp complexed with 24mer DNA. . SNAP output
|
|
5bng
|
protein-DNA |
X-ray (3.5 Å) |
Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M,
Enge M, Kivioja T, Morgunova E, Taipale J |
(2015) "DNA-dependent
formation of transcription factor pairs alters their
binding specificity." Nature,
527, 384-388. doi: 10.1038/nature15518.
|
Monomer of tale type homeobox transcription factor
meis1 complexes with specific DNA . SNAP output
|
|
5bnh
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Neculai D, Walker JR, Weigelt J, Bountra C, Edwards
AM, Arrowsmith CH, Dhe-Paganon S |
"Co-crystal structure of the HLTF HIRAN domain with a
ssDNA fragment." |
Crystal structure of the hltf hiran domain with a ssDNA
fragment . SNAP
output
|
|
5bol
|
transferase-DNA |
X-ray (1.981 Å) |
Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC,
Li D, Delaney JC, Wilson SH, Essigmann JM |
(2015) "Intrinsic
mutagenic properties of 5-chlorocytosine: A mechanistic
connection between chronic inflammation and
cancer." Proc.Natl.Acad.Sci.USA,
112, E4571-E4580. doi: 10.1073/pnas.1507709112.
|
DNA polymerase beta ternary complex with a templating
5clc and incoming dgtp analog . SNAP output
|
|
5bom
|
transferase, lyase-DNA |
X-ray (2.0 Å) |
Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC,
Li D, Delaney JC, Wilson SH, Essigmann JM |
(2015) "Intrinsic
mutagenic properties of 5-chlorocytosine: A mechanistic
connection between chronic inflammation and
cancer." Proc.Natl.Acad.Sci.USA,
112, E4571-E4580. doi: 10.1073/pnas.1507709112.
|
DNA polymerase beta binary complex with a templating
5clc . SNAP output
|
|
5box
|
DNA binding protein |
X-ray (2.5 Å) |
Ahmad MU, Waege I, Hausner W, Thomm M, Boos W,
Diederichs K, Welte W |
(2015) "Structural
Insights into Nonspecific Binding of DNA by TrmBL2, an
Archaeal Chromatin Protein." J.Mol.Biol.,
427, 3216-3229. doi: 10.1016/j.jmb.2015.08.012.
|
Structure of trmbl2, an archaeal chromatin protein,
shows a novel mode of DNA binding. . SNAP output
|
|
5bpc
|
transferase, ligase-DNA |
X-ray (2.0 Å) |
Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC,
Li D, Delaney JC, Wilson SH, Essigmann JM |
(2015) "Intrinsic
mutagenic properties of 5-chlorocytosine: A mechanistic
connection between chronic inflammation and
cancer." Proc.Natl.Acad.Sci.USA,
112, E4571-E4580. doi: 10.1073/pnas.1507709112.
|
DNA polymerase beta ternary complex with a templating
5clc and incoming datp analog . SNAP output
|
|
5bpd
|
DNA binding protein |
X-ray (2.4 Å) |
Ahmad MU, Waege I, Hausner W, Thomm M, Boos W,
Diederichs K, Welte W |
(2015) "Structural
Insights into Nonspecific Binding of DNA by TrmBL2, an
Archaeal Chromatin Protein." J.Mol.Biol.,
427, 3216-3229. doi: 10.1016/j.jmb.2015.08.012.
|
Structure of trmbl2, an archaeal chromatin protein,
shows a novel mode of DNA binding. . SNAP output
|
|
5bpi
|
DNA binding protein |
X-ray (3.198 Å) |
Ahmad MU, Waege I, Hausner W, Thomm M, Boos W,
Diederichs K, Welte W |
(2015) "Structural
Insights into Nonspecific Binding of DNA by TrmBL2, an
Archaeal Chromatin Protein." J.Mol.Biol.,
427, 3216-3229. doi: 10.1016/j.jmb.2015.08.012.
|
Structure of trmbl2, an archaeal chromatin protein,
shows a novel mode of DNA binding. . SNAP output
|
|
5bs3
|
isomerase-DNA-RNA |
X-ray (2.65 Å) |
Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Black T,
Nargund R, Meinke PT, Olsen DB, Lagrutta A, Lu J, Patel
S, Rickert KW, Smith RF, Soisson S, Sherer E, Joyce LA,
Wei C, Peng X, Wang X, Fukuda H, Kishii R, Takei M,
Takano H, Shibasaki M, Yajima M, Nishimura A, Shibata T,
Fukuda Y |
(2015) "Tricyclic
1,5-naphthyridinone oxabicyclooctane-linked novel
bacterial topoisomerase inhibitors as broad-spectrum
antibacterial agents-SAR of left-hand-side moiety
(Part-2)." Bioorg.Med.Chem.Lett.,
25, 1831-1835. doi: 10.1016/j.bmcl.2015.03.044.
|
Crystal structure of s.a. gyrase in complex with
compound 7 . SNAP
output
|
|
5bs8
|
isomerase-DNA |
X-ray (2.399 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5bt2
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Chia JY, Tan WS, Ng CL, Hu NJ, Foo HL, Ho KL |
(2016) "A/T Run
Geometry of B-form DNA Is Independent of Bound
Methyl-CpG Binding Domain, Cytosine Methylation and
Flanking Sequence." Sci Rep,
6, 31210. doi: 10.1038/srep31210.
|
Mecp2 mbd domain (a140v) in complex with methylated DNA
. SNAP output
|
|
5bta
|
isomerase-DNA |
X-ray (2.55 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5btc
|
isomerase-DNA |
X-ray (2.55 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5btd
|
isomerase-DNA |
X-ray (2.497 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5btf
|
isomerase-DNA |
X-ray (2.61 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5btg
|
isomerase-DNA |
X-ray (2.5 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5bti
|
isomerase-DNA |
X-ray (2.501 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5btl
|
isomerase-DNA |
X-ray (2.5 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5btn
|
isomerase-DNA |
X-ray (2.5 Å) |
Blower TR, Williamson BH, Kerns RJ, Berger JM |
(2016) "Crystal
structure and stability of gyrase-fluoroquinolone
cleaved complexes from Mycobacterium tuberculosis."
Proc.Natl.Acad.Sci.USA, 113,
1706-1713. doi: 10.1073/pnas.1525047113.
|
Crystal structure of a topoisomerase ii complex .
SNAP output
|
|
5bua
|
transcription |
X-ray (1.812 Å) |
Vainer R, Cohen S, Shahar A, Zarivach R, Arbely
E |
(2016) "Structural
Basis for p53 Lys120-Acetylation-Dependent DNA-Binding
Mode." J.Mol.Biol., 428,
3013-3025. doi: 10.1016/j.jmb.2016.06.009.
|
Lysine 120-acetylated p53 DNA binding domain in a
complex with DNA. . SNAP
output
|
|
5byg
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Musayev FN, Zarate-Perez F, Bishop C, Burgner JW,
Escalante CR |
(2015) "Structural
Insights into the Assembly of the Adeno-associated
Virus Type 2 Rep68 Protein on the Integration Site
AAVS1." J.Biol.Chem.,
290, 27487-27499. doi: 10.1074/jbc.M115.669960.
|
X-ray structure of aav2 obd-aavs1 complex 2:1 .
SNAP output
|
|
5c0y
|
hydrolase |
X-ray (2.1 Å) |
Makino DL, Schuch B, Stegmann E, Baumgartner M,
Basquin C, Conti E |
(2015) "RNA
degradation paths in a 12-subunit nuclear exosome
complex." Nature, 524,
54-58. doi: 10.1038/nature14865.
|
Crystal structure of the rrp6 catalytic domain bound to
poly(u) RNA . SNAP
output
|
|
5c3e
|
transferase-DNA-RNA |
X-ray (3.7 Å) |
Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin
G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA,
Kaplan CD, Calero G |
(2015) "Crystal
Structure of a Transcribing RNA Polymerase II Complex
Reveals a Complete Transcription Bubble."
Mol.Cell, 59, 258-269. doi:
10.1016/j.molcel.2015.06.034.
|
Crystal structure of a transcribing RNA polymerase ii
complex reveals a complete transcription bubble .
SNAP output
|
|
5c44
|
transferase-DNA-RNA |
X-ray (3.95 Å) |
Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin
G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA,
Kaplan CD, Calero G |
(2015) "Crystal
Structure of a Transcribing RNA Polymerase II Complex
Reveals a Complete Transcription Bubble."
Mol.Cell, 59, 258-269. doi:
10.1016/j.molcel.2015.06.034.
|
Crystal structure of a transcribing RNA polymerase ii
complex reveals a complete transcription bubble .
SNAP output
|
|
5c4a
|
transferase-RNA-DNA |
X-ray (4.2 Å) |
Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin
G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA,
Kaplan CD, Calero G |
(2015) "Crystal
Structure of a Transcribing RNA Polymerase II Complex
Reveals a Complete Transcription Bubble."
Mol.Cell, 59, 258-269. doi:
10.1016/j.molcel.2015.06.034.
|
Crystal structure of a transcribing RNA polymerase ii
complex reveals a complete transcription bubble .
SNAP output
|
|
5c4j
|
transferase-DNA-RNA |
X-ray (4.0 Å) |
Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin
G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA,
Kaplan CD, Calero G |
(2015) "Crystal
Structure of a Transcribing RNA Polymerase II Complex
Reveals a Complete Transcription Bubble."
Mol.Cell, 59, 258-269. doi:
10.1016/j.molcel.2015.06.034.
|
Crystal structure of a transcribing RNA polymerase ii
complex reveals a complete transcription bubble .
SNAP output
|
|
5c4x
|
transferase-RNA-DNA |
X-ray (4.0 Å) |
Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin
G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA,
Kaplan CD, Calero G |
(2015) "Crystal
Structure of a Transcribing RNA Polymerase II Complex
Reveals a Complete Transcription Bubble."
Mol.Cell, 59, 258-269. doi:
10.1016/j.molcel.2015.06.034.
|
Crystal structure of a transcribing RNA polymerase ii
complex reveals a complete transcription bubble .
SNAP output
|
|
5c51
|
transferase-DNA |
X-ray (3.426 Å) |
Sohl CD, Szymanski MR, Mislak AC, Shumate CK,
Amiralaei S, Schinazi RF, Anderson KS, Yin YW |
(2015) "Probing
the structural and molecular basis of nucleotide
selectivity by human mitochondrial DNA polymerase
gamma." Proc.Natl.Acad.Sci.USA,
112, 8596-8601. doi: 10.1073/pnas.1421733112.
|
Probing the structural and molecular basis of
nucleotide selectivity by human mitochondrial DNA
polymerase gamma . SNAP
output
|
|
5c52
|
transferase-DNA |
X-ray (3.637 Å) |
Sohl CD, Szymanski MR, Mislak AC, Shumate CK,
Amiralaei S, Schinazi RF, Anderson KS, Yin YW |
(2015) "Probing
the structural and molecular basis of nucleotide
selectivity by human mitochondrial DNA polymerase
gamma." Proc.Natl.Acad.Sci.USA,
112, 8596-8601. doi: 10.1073/pnas.1421733112.
|
Probing the structural and molecular basis of
nucleotide selectivity by human mitochondrial DNA
polymerase gamma . SNAP
output
|
|
5c53
|
transferase-DNA |
X-ray (3.567 Å) |
Sohl CD, Szymanski MR, Mislak AC, Shumate CK,
Amiralaei S, Schinazi RF, Anderson KS, Yin YW |
(2015) "Probing
the structural and molecular basis of nucleotide
selectivity by human mitochondrial DNA polymerase
gamma." Proc.Natl.Acad.Sci.USA,
112, 8596-8601. doi: 10.1073/pnas.1421733112.
|
Probing the structural and molecular basis of
nucleotide selectivity by human mitochondrial DNA
polymerase gamma . SNAP
output
|
|
5c5j
|
transferase-DNA |
X-ray (2.1 Å) |
Kottur J, Nair DT |
(2016) "Reactive
Oxygen Species Play an Important Role in the
Bactericidal Activity of Quinolone Antibiotics."
Angew.Chem.Int.Ed.Engl., 55,
2397-2400. doi: 10.1002/anie.201509340.
|
Poymerase nucleotide complex . SNAP output
|
|
5c8e
|
transcription regulator-DNA |
X-ray (3.89 Å) |
Jost M, Fernandez-Zapata J, Polanco MC,
Ortiz-Guerrero JM, Chen PY, Kang G, Padmanabhan S,
Elias-Arnanz M, Drennan CL |
(2015) "Structural
basis for gene regulation by a B12-dependent
photoreceptor." Nature,
526, 536-541. doi: 10.1038/nature14950.
|
Crystal structure of thermus thermophilus carh bound to
adenosylcobalamin and a 26-bp DNA segment . SNAP output
|
|
5ca7
|
transferase-DNA |
X-ray (2.522 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda- mgdgtp binary and complex
with 6 paired DNA . SNAP
output
|
|
5cbx
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum
ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund
EA |
(2016) "Distal
substitutions drive divergent DNA specificity among
paralogous transcription factors through subdivision of
conformational space."
Proc.Natl.Acad.Sci.USA, 113,
326-331. doi: 10.1073/pnas.1518960113.
|
Ancgr DNA binding domain - (+)gre complex . SNAP output
|
|
5cby
|
DNA binding protein-DNA |
X-ray (1.997 Å) |
Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum
ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund
EA |
(2016) "Distal
substitutions drive divergent DNA specificity among
paralogous transcription factors through subdivision of
conformational space."
Proc.Natl.Acad.Sci.USA, 113,
326-331. doi: 10.1073/pnas.1518960113.
|
Ancgr2 DNA binding domain - (+)gre complex . SNAP output
|
|
5cbz
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum
ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund
EA |
(2016) "Distal
substitutions drive divergent DNA specificity among
paralogous transcription factors through subdivision of
conformational space."
Proc.Natl.Acad.Sci.USA, 113,
326-331. doi: 10.1073/pnas.1518960113.
|
Ancmr DNA binding domain - (+)gre complex . SNAP output
|
|
5cc0
|
DNA binding protein-DNA |
X-ray (2.405 Å) |
Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum
ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund
EA |
(2016) "Distal
substitutions drive divergent DNA specificity among
paralogous transcription factors through subdivision of
conformational space."
Proc.Natl.Acad.Sci.USA, 113,
326-331. doi: 10.1073/pnas.1518960113.
|
Ancsr2 - tslp ngre complex . SNAP output
|
|
5cc1
|
DNA binding protein-DNA |
X-ray (2.302 Å) |
Hudson WH, Kossmann BR, de Vera IM, Chuo SW, Weikum
ER, Eick GN, Thornton JW, Ivanov IN, Kojetin DJ, Ortlund
EA |
(2016) "Distal
substitutions drive divergent DNA specificity among
paralogous transcription factors through subdivision of
conformational space."
Proc.Natl.Acad.Sci.USA, 113,
326-331. doi: 10.1073/pnas.1518960113.
|
S425g glucocorticoid receptor DNA binding domain -
(+)gre complex . SNAP
output
|
|
5cdm
|
isomerase |
X-ray (2.5 Å) |
Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry
AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo
J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R,
Theobald AJ, Stavenger RA, Bax BD, Gwynn MN |
(2015) "Structural
basis of DNA gyrase inhibition by antibacterial QPT-1,
anticancer drug etoposide and moxifloxacin."
Nat Commun, 6, 10048. doi:
10.1038/ncomms10048.
|
2.5a structure of qpt-1 with s.aureus DNA gyrase and
DNA . SNAP output
|
|
5cdn
|
isomerase |
X-ray (2.79 Å) |
Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry
AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo
J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R,
Theobald AJ, Stavenger RA, Bax BD, Gwynn MN |
(2015) "Structural
basis of DNA gyrase inhibition by antibacterial QPT-1,
anticancer drug etoposide and moxifloxacin."
Nat Commun, 6, 10048. doi:
10.1038/ncomms10048.
|
2.8a structure of etoposide with s.aureus DNA gyrase
and DNA . SNAP
output
|
|
5cdo
|
isomerase |
X-ray (3.15 Å) |
Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry
AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo
J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R,
Theobald AJ, Stavenger RA, Bax BD, Gwynn MN |
(2015) "Structural
basis of DNA gyrase inhibition by antibacterial QPT-1,
anticancer drug etoposide and moxifloxacin."
Nat Commun, 6, 10048. doi:
10.1038/ncomms10048.
|
3.15a structure of qpt-1 with s.aureus DNA gyrase and
DNA . SNAP output
|
|
5cdp
|
isomerase |
X-ray (2.45 Å) |
Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry
AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo
J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R,
Theobald AJ, Stavenger RA, Bax BD, Gwynn MN |
(2015) "Structural
basis of DNA gyrase inhibition by antibacterial QPT-1,
anticancer drug etoposide and moxifloxacin."
Nat Commun, 6, 10048. doi:
10.1038/ncomms10048.
|
2.45a structure of etoposide with s.aureus DNA gyrase
and DNA . SNAP
output
|
|
5cdq
|
hydrolase |
X-ray (2.95 Å) |
Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry
AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo
J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R,
Theobald AJ, Stavenger RA, Bax BD, Gwynn MN |
(2015) "Structural
basis of DNA gyrase inhibition by antibacterial QPT-1,
anticancer drug etoposide and moxifloxacin."
Nat Commun, 6, 10048. doi:
10.1038/ncomms10048.
|
2.95a structure of moxifloxacin with s.aureus DNA
gyrase and DNA . SNAP
output
|
|
5cdr
|
isomerase |
X-ray (2.65 Å) |
Chan PF, Srikannathasan V, Huang J, Cui H, Fosberry
AP, Gu M, Hann MM, Hibbs M, Homes P, Ingraham K, Pizzollo
J, Shen C, Shillings AJ, Spitzfaden CE, Tanner R,
Theobald AJ, Stavenger RA, Bax BD, Gwynn MN |
(2015) "Structural
basis of DNA gyrase inhibition by antibacterial QPT-1,
anticancer drug etoposide and moxifloxacin."
Nat Commun, 6, 10048. doi:
10.1038/ncomms10048.
|
2.65 structure of s.aureus DNA gyrase and artificially
nicked DNA . SNAP
output
|
|
5cg8
|
oxidoreductase-DNA |
X-ray (2.702 Å) |
Hashimoto H, Pais JE, Dai N, Correa IR, Zhang X,
Zheng Y, Cheng X |
(2015) "Structure
of Naegleria Tet-like dioxygenase (NgTet1) in complexes
with a reaction intermediate 5-hydroxymethylcytosine
DNA." Nucleic Acids Res.,
43, 10713-10721. doi: 10.1093/nar/gkv870.
|
Ngtet1 in complex with 5hmc DNA . SNAP output
|
|
5cg9
|
oxidoreductase-DNA |
X-ray (2.693 Å) |
Hashimoto H, Pais JE, Dai N, Correa IR, Zhang X,
Zheng Y, Cheng X |
(2015) "Structure
of Naegleria Tet-like dioxygenase (NgTet1) in complexes
with a reaction intermediate 5-hydroxymethylcytosine
DNA." Nucleic Acids Res.,
43, 10713-10721. doi: 10.1093/nar/gkv870.
|
Ngtet1 in complex with 5mc DNA in space group p3221 .
SNAP output
|
|
5chg
|
transferase-DNA |
X-ray (2.9 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda l431a mutant- mgdgtp binary
and complex with 6 paired DNA . SNAP output
|
|
5chi
|
hydrolase-DNA |
X-ray (2.472 Å) |
Kim JS, Sambalkhundev GD, Kim SH, Han A, Ko SM, Hwang
KY, Lee WC |
"Structural basis of two-nucleotide removal of ssDNA
by a cryptic RNase H fold 3'-5' exonuclease PF2046 from
Pyrococcus furiosus." |
Crystal structure of pf2046 in complex with ssDNA .
SNAP output
|
|
5chz
|
hydrolase-DNA |
X-ray (1.83 Å) |
Ouzon-Shubeita H, Lin Y-L, Lee S |
"Structure of wild-type human MBD4 bound to a G:T
mismatch." |
Structure of wild-type human mbd4 bound to a g:t
mismatch . SNAP
output
|
|
5ciy
|
transferase-DNA |
X-ray (1.594 Å) |
Rondelet G, Dal Maso T, Willems L, Wouters J |
(2016) "Structural
basis for recognition of histone H3K36me3 nucleosome by
human de novo DNA methyltransferases 3A and 3B."
J.Struct.Biol., 194, 357-367.
doi: 10.1016/j.jsb.2016.03.013.
|
Structural basis of the recognition of h3k36me3 by
dnmt3b pwwp domain . SNAP output
|
|
5ciz
|
gene regulation-DNA |
X-ray (5.01 Å) |
Lara-Gonzalez S, Machado ACD, Rao S, Napoli AA,
Birktoft J, Di Felice R, Rohs R, Lawson CL |
(2020) "The RNA Polymerase alpha Subunit Recognizes the
DNA Shape of the Upstream Promoter Element."
Biochemistry. doi: 10.1021/acs.biochem.0c00571.
|
E. coli RNA polymerase alpha subunit ctd in complex
with cap and DNA: a(5)-tract binding site for alpha ctd
. SNAP output
|
|
5cj7
|
transferase-DNA |
X-ray (2.901 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda l431a mutant- mgdttp binary
and complex with 6 paired DNA . SNAP output
|
|
5cky
|
transcription-DNA |
X-ray (2.62 Å) |
Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C,
Garcia-Diaz M |
(2016) "Base
Flipping by MTERF1 Can Accommodate Multiple
Conformations and Occurs in a Stepwise Fashion."
J.Mol.Biol., 428, 2542-2556.
doi: 10.1016/j.jmb.2015.10.021.
|
Crystal structure of the mterf1 r162a substitution
bound to the termination sequence. . SNAP output
|
|
5cl3
|
hydrolase-DNA |
X-ray (1.971 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog (100% substrate at
4 hours) . SNAP
output
|
|
5cl4
|
hydrolase-DNA |
X-ray (1.866 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog or DNA containing
an abasic site and a free nucleobase (71% substrate-29%
product at 24 hours) . SNAP output
|
|
5cl5
|
hydrolase-DNA |
X-ray (1.569 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog or DNA containing
an abasic site and a free nucleobase (51% substrate-49%
product at 48 hours) . SNAP output
|
|
5cl6
|
hydrolase-DNA |
X-ray (1.541 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog or DNA containing
an abasic site and a free nucleobase (33% substrate-67%
product at 72 hours) . SNAP output
|
|
5cl7
|
hydrolase-DNA |
X-ray (1.44 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog or DNA containing
an abasic site and a free nucleobase (18% substrate-82%
product at 96 hours) . SNAP output
|
|
5cl8
|
hydrolase-DNA |
X-ray (1.38 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing an abasic site and a free nucleobase (100%
product at 144 hours) . SNAP output
|
|
5cl9
|
hydrolase-DNA |
X-ray (1.538 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing an abasic site and a free nucleobase (100%
product at 240 hours) . SNAP output
|
|
5cla
|
hydrolase-DNA |
X-ray (1.541 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing an abasic site and a free nucleobase (100%
product at 360 hours) . SNAP output
|
|
5clb
|
hydrolase-DNA |
X-ray (1.766 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog (9-mer a) .
SNAP output
|
|
5clc
|
hydrolase-DNA |
X-ray (1.729 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing a 3-methyladenine analog (9-mer b) .
SNAP output
|
|
5cld
|
hydrolase-DNA |
X-ray (1.541 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing an oxocarbenium-intermediate analog and a
free 3-methyladenine nucleobase . SNAP output
|
|
5cle
|
hydrolase-DNA |
X-ray (1.73 Å) |
Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS,
Igarashi Y, Eichman BF |
(2015) "The DNA
glycosylase AlkD uses a non-base-flipping mechanism to
excise bulky lesions." Nature,
527, 254-258. doi: 10.1038/nature15728.
|
Alkylpurine DNA glycosylase alkd bound to DNA
containing an abasic-site analog and a free
3-methyladenine nucleobase . SNAP output
|
|
5clv
|
transcription |
X-ray (2.5 Å) |
Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris
SA, Bingle LE, Roessle M, Thomas CM, Hyde EI, White
SA |
(2016) "Flexibility
of KorA, a plasmid-encoded, global transcription
regulator, in the presence and the absence of its
operator." Nucleic Acids Res.,
44, 4947-4956. doi: 10.1093/nar/gkw191.
|
Crystal structure of kora-operator DNA complex
(kora-oa) . SNAP
output
|
|
5cm3
|
transcription |
X-ray (2.302 Å) |
Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris
SA, Bingle LE, Roessle M, Thomas CM, Hyde EI, White
SA |
(2016) "Flexibility
of KorA, a plasmid-encoded, global transcription
regulator, in the presence and the absence of its
operator." Nucleic Acids Res.,
44, 4947-4956. doi: 10.1093/nar/gkw191.
|
Crystal structure of kora, a plasmid-encoded, global
transcription regulator . SNAP output
|
|
5cmx
|
hydrolase |
X-ray (2.98 Å) |
Russo Krauss I, Spiridonova V, Pica A, Napolitano V,
Sica F |
(2016) "Different
duplex/quadruplex junctions determine the properties of
anti-thrombin aptamers with mixed folding."
Nucleic Acids Res., 44,
983-991. doi: 10.1093/nar/gkv1384.
|
X-ray structure of the complex between human alpha
thrombin and a duplex-quadruplex 31-mer DNA aptamer .
SNAP output
|
|
5cnq
|
replication |
X-ray (2.602 Å) |
Liu Y, Freeman AD, Declais AC, Wilson TJ, Gartner A,
Lilley DM |
(2015) "Crystal
Structure of a Eukaryotic GEN1 Resolving Enzyme Bound
to DNA." Cell Rep, 13,
2565-2575. doi: 10.1016/j.celrep.2015.11.042.
|
Crystal structure of the holliday junction-resolving
enzyme gen1 (wt) in complex with product DNA, mg2+ and
mn2+ ions . SNAP
output
|
|
5co0
|
transcription-DNA |
X-ray (2.65 Å) |
Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C,
Garcia-Diaz M |
(2016) "Base
Flipping by MTERF1 Can Accommodate Multiple
Conformations and Occurs in a Stepwise Fashion."
J.Mol.Biol., 428, 2542-2556.
doi: 10.1016/j.jmb.2015.10.021.
|
Crystal structure of the mterf1 y288a substitution
bound to the termination sequence. . SNAP output
|
|
5co8
|
hydrolase |
X-ray (2.4 Å) |
Liu Y, Freeman AD, Declais AC, Wilson TJ, Gartner A,
Lilley DM |
(2015) "Crystal
Structure of a Eukaryotic GEN1 Resolving Enzyme Bound
to DNA." Cell Rep, 13,
2565-2575. doi: 10.1016/j.celrep.2015.11.042.
|
Crystal structure of the holliday junction-resolving
enzyme gen1 (wt) in complex with product DNA and mg2+
ion . SNAP output
|
|
5cp2
|
transferase-DNA |
X-ray (2.36 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda l431a mutant- apoenzyme and
complex with 6 paired DNA . SNAP output
|
|
5cp6
|
structural protein-DNA |
X-ray (2.6 Å) |
Ma Z, Palermo G, Adhireksan Z, Murray BS, von Erlach
T, Dyson PJ, Rothlisberger U, Davey CA |
(2016) "An
Organometallic Compound which Exhibits a DNA
Topology-Dependent One-Stranded Intercalation
Mode." Angew.Chem.Int.Ed.Engl.,
55, 7441-7444. doi: 10.1002/anie.201602145.
|
Nucleosome core particle with adducts from the
anticancer compound,
[(eta6-5,8,9,10-tetrahydroanthracene)ru(ethylenediamine)cl][pf6]
. SNAP output
|
|
5cpi
|
structural protein-DNA |
X-ray (2.902 Å) |
Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y,
Kurumizaka H |
(2015) "Influence
of DNA methylation on positioning and DNA flexibility
of nucleosomes with pericentric satellite DNA."
Open Biology, 5. doi:
10.1098/rsob.150128.
|
Nucleosome containing unmethylated sat2r DNA . SNAP output
|
|
5cpj
|
"structural protein-DNA |
X-ray (3.15 Å) |
Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y,
Kurumizaka H |
(2015) "Influence
of DNA methylation on positioning and DNA flexibility
of nucleosomes with pericentric satellite DNA."
Open Biology, 5. doi:
10.1098/rsob.150128.
|
Nucleosome containing methylated sat2r DNA . SNAP output
|
|
5cpk
|
structural protein-DNA |
X-ray (2.632 Å) |
Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y,
Kurumizaka H |
(2015) "Influence
of DNA methylation on positioning and DNA flexibility
of nucleosomes with pericentric satellite DNA."
Open Biology, 5. doi:
10.1098/rsob.150128.
|
Nucleosome containing methylated sat2l DNA . SNAP output
|
|
5cqq
|
transcription-DNA |
X-ray (3.1 Å) |
Gao GN, Wang M, Yang N, Huang Y, Xu RM |
(2015) "Structure
of Zeste-DNA Complex Reveals a New Modality of DNA
Recognition by Homeodomain-Like Proteins."
J.Mol.Biol., 427, 3824-3833.
doi: 10.1016/j.jmb.2015.10.008.
|
Crystal structure of the drosophila zeste DNA binding
domain in complex with DNA . SNAP output
|
|
5cr0
|
transferase-DNA |
X-ray (2.75 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda l431a mutant- mgdctp binary
and complex with 6 paired DNA . SNAP output
|
|
5cr2
|
hydrolase |
X-ray (2.9 Å) |
Zorzini V, Mernik A, Lah J, Sterckx YG, De Jonge N,
Garcia-Pino A, De Greve H, Versees W, Loris R |
(2016) "Substrate
Recognition and Activity Regulation of the Escherichia
coli mRNA Endonuclease MazF."
J.Biol.Chem., 291,
10950-10960. doi: 10.1074/jbc.M116.715912.
|
E. coli mazf in complex with single strand DNA
substrate analog . SNAP
output
|
|
5crj
|
transcription-DNA |
X-ray (2.59 Å) |
Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C,
Garcia-Diaz M |
(2016) "Base
Flipping by MTERF1 Can Accommodate Multiple
Conformations and Occurs in a Stepwise Fashion."
J.Mol.Biol., 428, 2542-2556.
doi: 10.1016/j.jmb.2015.10.021.
|
Crystal structure of the mterf1 f322a substitution
bound to the termination sequence. . SNAP output
|
|
5crk
|
transcription-DNA |
X-ray (2.48 Å) |
Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C,
Garcia-Diaz M |
(2016) "Base
Flipping by MTERF1 Can Accommodate Multiple
Conformations and Occurs in a Stepwise Fashion."
J.Mol.Biol., 428, 2542-2556.
doi: 10.1016/j.jmb.2015.10.021.
|
Crystal structure of the mterf1 f243a substitution
bound to the termination sequence. . SNAP output
|
|
5crx
|
protein-DNA |
X-ray (2.7 Å) |
Guo F, Gopaul DN, Van Duyne GD |
(1999) "Asymmetric
DNA bending in the Cre-loxP site-specific recombination
synapse." Proc.Natl.Acad.Sci.USA,
96, 7143-7148. doi: 10.1073/pnas.96.13.7143.
|
Asymmetric DNA-bending in the cre-loxp site-specific
recombination synapse . SNAP output
|
|
5cwr
|
transferase-DNA |
X-ray (2.5 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Crystal structure of human DNA polymerase lambda l431a
mutant in complex with a one nucleotide DNA gap and
dctp . SNAP output
|
|
5cy1
|
hydrolase, ligase-DNA |
X-ray (3.4 Å) |
Montano SP, Rice PA |
"Tn3 resolvase - accessory site complexes: DNA
geometry dictates complex geometry." |
Tn3 resolvase - site iii complex crystal form i .
SNAP output
|
|
5cy2
|
recombination-DNA |
X-ray (4.0 Å) |
Montano SP, Rice PA |
"Structures of resolvase - accessory site
complexes." |
Tn3 resolvase - site iii complex crystal form ii .
SNAP output
|
|
5cys
|
hydrolase-DNA |
X-ray (2.45 Å) |
Malik SS, Varney KM, Pozharski E, Drohat AC |
(2015) "Characterizing the enzyme-product complexes
of thymine DNA glycosylase using crystallography and
NMR." Nucleic Acids Res. |
Structure of the enzyme-product complex resulting from
tdg action on a gcac mismatch . SNAP output
|
|
5czz
|
hydrolase-RNA-DNA |
X-ray (2.6 Å) |
Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y,
Kurabayashi A, Ishitani R, Zhang F, Nureki O |
(2015) "Crystal
Structure of Staphylococcus aureus Cas9."
Cell, 162, 1113-1126. doi:
10.1016/j.cell.2015.08.007.
|
Crystal structure of staphylococcus aureus cas9 in
complex with sgrna and target DNA (ttgaat pam) .
SNAP output
|
|
5d23
|
transcription-DNA |
X-ray (1.95 Å) |
Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X,
Wu Q, Chen Y, Zhou CZ |
(2016) "Structures
of an all-alpha protein running along the DNA major
groove." Nucleic Acids Res. doi: 10.1093/nar/gkw133.
|
The crystal structure of stpr from bombyx mori in
complex with 13-bp DNA derived from the +290 site of
fibroin gene . SNAP
output
|
|
5d2q
|
transcription-DNA |
X-ray (2.4 Å) |
Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X,
Wu Q, Chen Y, Zhou CZ |
(2016) "Structures
of an all-alpha protein running along the DNA major
groove." Nucleic Acids Res. doi: 10.1093/nar/gkw133.
|
Crystal structure of stpr from bombyx mori in complex
with 20-bp DNA derived from +290 site of the fibroin
gene . SNAP output
|
|
5d2s
|
transcription-DNA |
X-ray (2.2 Å) |
Yu LY, Cheng W, Zhou K, Li WF, Yu HM, Gao X, Shen X,
Wu Q, Chen Y, Zhou CZ |
(2016) "Structures
of an all-alpha protein running along the DNA major
groove." Nucleic Acids Res. doi: 10.1093/nar/gkw133.
|
Crystal structure of stpr from bombyx mori in complex
with 18-bp DNA containing four repetitive units of atac
. SNAP output
|
|
5d39
|
transcription-DNA |
X-ray (3.2 Å) |
Li J, Rodriguez JP, Niu F, Pu M, Wang J, Hung LW,
Shao Q, Zhu Y, Ding W, Liu Y, Da Y, Yao Z, Yang J, Zhao
Y, Wei GH, Cheng G, Liu ZJ, Ouyang S |
(2016) "Structural
basis for DNA recognition by STAT6."
Proc.Natl.Acad.Sci.USA, 113,
13015-13020. doi: 10.1073/pnas.1611228113.
|
Transcription factor-DNA complex . SNAP output
|
|
5d3g
|
transferase |
X-ray (2.3 Å) |
Miller MT, Tuske S, Das K, DeStefano JJ, Arnold
E |
(2016) "Structure
of HIV-1 reverse transcriptase bound to a novel 38-mer
hairpin template-primer DNA aptamer." Protein
Sci., 25, 46-55. doi: 10.1002/pro.2776.
|
Structure of hiv-1 reverse transcriptase bound to a
novel 38-mer hairpin template-primer DNA aptamer .
SNAP output
|
|
5d46
|
transferase |
X-ray (2.8 Å) |
Loc'h J, Rosario S, Delarue M |
(2016) "Structural
Basis for a New Templated Activity by Terminal
Deoxynucleotidyl Transferase: Implications for V(D)J
Recombination." Structure,
24, 1452-1463. doi: 10.1016/j.str.2016.06.014.
|
Structural basis for a new templated activity by
terminal deoxynucleotidyl transferase: implications for
v(d)j recombination . SNAP output
|
|
5d49
|
transferase |
X-ray (1.99 Å) |
Loc'h J, Rosario S, Delarue M |
(2016) "Structural
Basis for a New Templated Activity by Terminal
Deoxynucleotidyl Transferase: Implications for V(D)J
Recombination." Structure,
24, 1452-1463. doi: 10.1016/j.str.2016.06.014.
|
Structural basis for a new templated activity by
terminal deoxynucleotidyl transferase: implications for
v(d)j recombination . SNAP output
|
|
5d4b
|
transferase |
X-ray (2.66 Å) |
Loc'h J, Rosario S, Delarue M |
(2016) "Structural
Basis for a New Templated Activity by Terminal
Deoxynucleotidyl Transferase: Implications for V(D)J
Recombination." Structure,
24, 1452-1463. doi: 10.1016/j.str.2016.06.014.
|
Structural basis for a new templated activity by
terminal deoxynucleotidyl transferase: implications for
v(d)j recombination . SNAP output
|
|
5d4c
|
transcription-DNA |
X-ray (3.28 Å) |
Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene
L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright
RH, Nickels BE |
(2016) "The
mechanism of RNA 5' capping with NAD(+), NADH and
desphospho-CoA." Nature,
535, 444-447. doi: 10.1038/nature18622.
|
Crystal structure of thermus thermophilus product
complex for transcription initiation with atp and ctp .
SNAP output
|
|
5d4d
|
transcription-DNA |
X-ray (3.0 Å) |
Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene
L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright
RH, Nickels BE |
(2016) "The
mechanism of RNA 5' capping with NAD(+), NADH and
desphospho-CoA." Nature,
535, 444-447. doi: 10.1038/nature18622.
|
Crystal structure of thermus thermophilus product
complex for transcription initiation with nad and ctp .
SNAP output
|
|
5d4e
|
transcription-DNA |
X-ray (3.08 Å) |
Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene
L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright
RH, Nickels BE |
(2016) "The
mechanism of RNA 5' capping with NAD(+), NADH and
desphospho-CoA." Nature,
535, 444-447. doi: 10.1038/nature18622.
|
Crystal structure of thermus thermophilus product
complex for transcription initiation with
3'-dephosphate-coa and ctp . SNAP output
|
|
5d4r
|
transcription-DNA |
X-ray (2.07 Å) |
Jain D, Narayanan N, Nair DT |
(2016) "Plasticity
in Repressor-DNA Interactions Neutralizes Loss of
Symmetry in Bipartite Operators."
J.Biol.Chem., 291, 1235-1242.
doi: 10.1074/jbc.M115.689695.
|
Crystal structure of arar(dbd) in complex with operator
ore1 . SNAP output
|
|
5d4s
|
transcription-DNA |
X-ray (1.972 Å) |
Jain D, Narayanan N, Nair DT |
(2016) "Plasticity
in Repressor-DNA Interactions Neutralizes Loss of
Symmetry in Bipartite Operators."
J.Biol.Chem., 291, 1235-1242.
doi: 10.1074/jbc.M115.689695.
|
Crystal structure of arar(dbd) in complex with operator
orx1 . SNAP output
|
|
5d5u
|
transcription-DNA |
X-ray (2.91 Å) |
Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU,
Bracher A |
(2016) "Structure
of human heat-shock transcription factor 1 in complex
with DNA." Nat.Struct.Mol.Biol.,
23, 140-146. doi: 10.1038/nsmb.3149.
|
Crystal structure of human hsf1 with hse DNA . SNAP output
|
|
5d5v
|
transcription-DNA |
X-ray (2.55 Å) |
Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU,
Bracher A |
(2016) "Structure
of human heat-shock transcription factor 1 in complex
with DNA." Nat.Struct.Mol.Biol.,
23, 140-146. doi: 10.1038/nsmb.3149.
|
Crystal structure of human hsf1 with satellite iii
repeat DNA . SNAP
output
|
|
5d5w
|
transcription |
X-ray (2.35 Å) |
Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU,
Bracher A |
(2016) "Structure
of human heat-shock transcription factor 1 in complex
with DNA." Nat.Struct.Mol.Biol.,
23, 140-146. doi: 10.1038/nsmb.3149.
|
Crystal structure of chaetomium thermophilum skn7 with
hse DNA . SNAP
output
|
|
5d5x
|
transcription |
X-ray (2.4 Å) |
Neudegger T, Verghese J, Hayer-Hartl M, Hartl FU,
Bracher A |
(2016) "Structure
of human heat-shock transcription factor 1 in complex
with DNA." Nat.Struct.Mol.Biol.,
23, 140-146. doi: 10.1038/nsmb.3149.
|
Crystal structure of chaetomium thermophilum skn7 with
ssre DNA . SNAP
output
|
|
5d8c
|
transcription-DNA |
X-ray (2.25 Å) |
Counago RM, Chen NH, Chang CW, Djoko KY, McEwan AG,
Kobe B |
(2016) "Structural
basis of thiol-based regulation of formaldehyde
detoxification in H. influenzae by a MerR regulator
with no sensor region." Nucleic Acids
Res., 44, 6981-6993. doi:
10.1093/nar/gkw543.
|
Crystal structure of hinmlr, a merr family regulator
lacking the sensor domain, bound to promoter DNA .
SNAP output
|
|
5d8f
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Li YH, Gao ZQ, Dong YH |
"crystal structure of SSB and ssDNA complex from homo
sapiens." |
Crystal structure of ssb and ssDNA complex from homo
sapiens . SNAP
output
|
|
5d8k
|
transcription-DNA |
X-ray (1.728 Å) |
Jaeger AM, Pemble CW, Sistonen L, Thiele DJ |
(2016) "Structures
of HSF2 reveal mechanisms for differential regulation
of human heat-shock factors."
Nat.Struct.Mol.Biol., 23,
147-154. doi: 10.1038/nsmb.3150.
|
Human hsf2 DNA-binding domain bound to 2-site hse DNA
at 1.73 angstroms resolution . SNAP output
|
|
5d8l
|
transcription-DNA |
X-ray (2.069 Å) |
Jaeger AM, Pemble CW, Sistonen L, Thiele DJ |
(2016) "Structures
of HSF2 reveal mechanisms for differential regulation
of human heat-shock factors."
Nat.Struct.Mol.Biol., 23,
147-154. doi: 10.1038/nsmb.3150.
|
Human hsf2 DNA binding domain in complex with 3-site
hse DNA at 2.1 angstroms resolution . SNAP output
|
|
5d9i
|
replication-DNA |
X-ray (1.7 Å) |
Meinke G, Phelan PJ, Fradet-Turcotte A, Bohm A,
Archambault J, Bullock PA |
(2011) "Structure-based
analysis of the interaction between the simian virus 40
T-antigen origin binding domain and single-stranded
DNA." J. Virol., 85,
818-827. doi: 10.1128/JVI.01738-10.
|
Sv40 large t antigen origin binding domain bound to
artificial DNA fork . SNAP output
|
|
5d9y
|
oxidoreductase-DNA |
X-ray (1.971 Å) |
Hu L, Lu J, Cheng J, Rao Q, Li Z, Hou H, Lou Z, Zhang
L, Li W, Gong W, Liu M, Sun C, Yin X, Li J, Tan X, Wang
P, Wang Y, Fang D, Cui Q, Yang P, He C, Jiang H, Luo C,
Xu Y |
(2015) "Structural
insight into substrate preference for TET-mediated
oxidation." Nature, 527,
118-122. doi: 10.1038/nature15713.
|
Crystal structure of tet2-5fc complex . SNAP output
|
|
5dac
|
hydrolase |
X-ray (2.503 Å) |
Seifert FU, Lammens K, Stoehr G, Kessler B, Hopfner
KP |
(2016) "Structural
mechanism of ATP-dependent DNA binding and DNA end
bridging by eukaryotic Rad50." Embo J.,
35, 759-772. doi: 10.15252/embj.201592934.
|
Atp-gamma-s bound rad50 from chaetomium thermophilum in
complex with DNA . SNAP
output
|
|
5db6
|
transferase-DNA |
X-ray (2.83 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the n7mg base paired with a dc . SNAP output
|
|
5db7
|
transferase-DNA |
X-ray (2.209 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the n7mg base paired with a dt . SNAP output
|
|
5db8
|
transferase-DNA |
X-ray (2.547 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the n7mg base paired with a da . SNAP output
|
|
5db9
|
transferase-DNA |
X-ray (2.45 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the n7mg base paired with a dg . SNAP output
|
|
5dba
|
transferase-DNA |
X-ray (1.965 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the dg base paired with a dt . SNAP output
|
|
5dbb
|
transferase-DNA |
X-ray (2.25 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the dg base paired with a da . SNAP output
|
|
5dbc
|
transferase-DNA |
X-ray (2.402 Å) |
Kou Y, Koag MC, Lee S |
(2015) "N7
Methylation Alters Hydrogen-Bonding Patterns of Guanine
in Duplex DNA." J.Am.Chem.Soc.,
137, 14067-14070. doi: 10.1021/jacs.5b10172.
|
Structure of human DNA polymerase beta host-guest
complex with the dg base paired with a dg . SNAP output
|
|
5ddg
|
transcription regulator-DNA |
X-ray (3.06 Å) |
Chang C, Tesar C, Li X, Kim Y, Rodionov DA,
Joachimiak A |
(2015) "A novel
transcriptional regulator of L-arabinose utilization in
human gut bacteria." Nucleic Acids Res.,
43, 10546-10559. doi: 10.1093/nar/gkv1005.
|
The structure of transcriptional factor arar from
bacteroides thetaiotaomicron vpi in complex with target
double strand DNA . SNAP
output
|
|
5ddm
|
transferase-DNA |
X-ray (2.802 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Human DNA polymerase lambda- apoenzyme and complex with
6 paired DNA . SNAP
output
|
|
5deu
|
oxidoreductase-DNA |
X-ray (1.801 Å) |
Hu L, Lu J, Cheng J, Rao Q, Li Z, Hou H, Lou Z, Zhang
L, Li W, Gong W, Liu M, Sun C, Yin X, Li J, Tan X, Wang
P, Wang Y, Fang D, Cui Q, Yang P, He C, Jiang H, Luo C,
Xu Y |
(2015) "Structural
insight into substrate preference for TET-mediated
oxidation." Nature, 527,
118-122. doi: 10.1038/nature15713.
|
Crystal structure of tet2-5hmc complex . SNAP output
|
|
5dff
|
lyase-DNA |
X-ray (1.57 Å) |
Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS,
Wilson SH |
(2015) "Capturing
snapshots of APE1 processing DNA damage."
Nat.Struct.Mol.Biol., 22,
924-931. doi: 10.1038/nsmb.3105.
|
Human ape1 product complex . SNAP output
|
|
5dfh
|
lyase-DNA |
X-ray (1.949 Å) |
Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS,
Wilson SH |
(2015) "Capturing
snapshots of APE1 processing DNA damage."
Nat.Struct.Mol.Biol., 22,
924-931. doi: 10.1038/nsmb.3105.
|
Human ape1 mismatch product complex . SNAP output
|
|
5dfi
|
lyase-DNA |
X-ray (1.63 Å) |
Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS,
Wilson SH |
(2015) "Capturing
snapshots of APE1 processing DNA damage."
Nat.Struct.Mol.Biol., 22,
924-931. doi: 10.1038/nsmb.3105.
|
Human ape1 phosphorothioate substrate complex .
SNAP output
|
|
5dfj
|
lyase-DNA |
X-ray (1.85 Å) |
Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS,
Wilson SH |
(2015) "Capturing
snapshots of APE1 processing DNA damage."
Nat.Struct.Mol.Biol., 22,
924-931. doi: 10.1038/nsmb.3105.
|
Human ape1 e96q-d210n mismatch substrate complex .
SNAP output
|
|
5dg0
|
hydrolase,lyase-DNA |
X-ray (1.8 Å) |
Freudenthal BD, Beard WA, Cuneo MJ, Dyrkheeva NS,
Wilson SH |
(2015) "Capturing
snapshots of APE1 processing DNA damage."
Nat.Struct.Mol.Biol., 22,
924-931. doi: 10.1038/nsmb.3105.
|
Human ape1 phosphorothioate substrate complex with mn2+
. SNAP output
|
|
5dg7
|
transferase-DNA |
X-ray (2.26 Å) |
Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP,
Egli M |
(2016) "Structural
and Kinetic Analysis of Miscoding Opposite the DNA
Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion
DNA Polymerase eta." J.Biol.Chem.,
291, 14134-14145. doi: 10.1074/jbc.M116.732487.
|
Crystal structure of human DNA polymerase eta inserting
dttp across a DNA template containing
1,n6-ethenodeoxyadenosine lesion . SNAP output
|
|
5dg8
|
transferase-DNA |
X-ray (2.12 Å) |
Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP,
Egli M |
(2016) "Structural
and Kinetic Analysis of Miscoding Opposite the DNA
Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion
DNA Polymerase eta." J.Biol.Chem.,
291, 14134-14145. doi: 10.1074/jbc.M116.732487.
|
Crystal structure of human DNA polymerase eta inserting
dampnpp across a DNA template containing
1,n6-ethenodeoxyadenosine lesion . SNAP output
|
|
5dg9
|
transferase-DNA |
X-ray (2.15 Å) |
Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP,
Egli M |
(2016) "Structural
and Kinetic Analysis of Miscoding Opposite the DNA
Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion
DNA Polymerase eta." J.Biol.Chem.,
291, 14134-14145. doi: 10.1074/jbc.M116.732487.
|
Crystal structure of human DNA polymerase eta inserting
dgmpnpp across a DNA template containing
1,n6-ethenodeoxyadenosine lesion . SNAP output
|
|
5dga
|
transferase-DNA |
X-ray (2.3 Å) |
Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP,
Egli M |
(2016) "Structural
and Kinetic Analysis of Miscoding Opposite the DNA
Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion
DNA Polymerase eta." J.Biol.Chem.,
291, 14134-14145. doi: 10.1074/jbc.M116.732487.
|
Crystal structure of human DNA polymerase eta extending
an 1,n6-ethenodeoxyadenosine : dt pair by inserting
dtmpnpp opposite template da . SNAP output
|
|
5dgb
|
transferase-DNA |
X-ray (1.79 Å) |
Patra A, Su Y, Zhang Q, Johnson KM, Guengerich FP,
Egli M |
(2016) "Structural
and Kinetic Analysis of Miscoding Opposite the DNA
Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion
DNA Polymerase eta." J.Biol.Chem.,
291, 14134-14145. doi: 10.1074/jbc.M116.732487.
|
Crystal structure of human DNA polymerase eta extending
an 1,n6-ethenodeoxyadenosine : da pair by inserting
dtmpnpp opposite template da . SNAP output
|
|
5dkw
|
transferase-DNA |
X-ray (2.689 Å) |
Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD |
(2016) "Structural
Mechanism for the Fidelity Modulation of DNA Polymerase
lambda." J.Am.Chem.Soc.,
138, 2389-2398. doi: 10.1021/jacs.5b13368.
|
Ternary crystal structure of polymerase lambda with a
ga mispair at the primer terminus with ca2+ in the
active . SNAP output
|
|
5dlf
|
transferase-DNA |
X-ray (1.97 Å) |
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M,
Wilds CJ |
(2016) "Lesion
Orientation ofO4-Alkylthymidine Influences Replication
by Human DNA Polymeraseeta." Chem Sci,
7, 4896-4904. doi: 10.1039/C6SC00666C.
|
Crystal structure of human DNA polymerase eta inserting
datp opposite o4-methylhymidine . SNAP output
|
|
5dlg
|
transferase-DNA |
X-ray (2.351 Å) |
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M,
Wilds CJ |
(2016) "Lesion
Orientation ofO4-Alkylthymidine Influences Replication
by Human DNA Polymeraseeta." Chem Sci,
7, 4896-4904. doi: 10.1039/C6SC00666C.
|
Crystal structure of human DNA polymerase eta inserting
dgmpnpp opposite o4-methylhymidine . SNAP output
|
|
5dlj
|
hydrolase-DNA |
X-ray (2.6 Å) |
Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang
Y |
(2015) "Structural
and Mechanistic Basis of PAM-Dependent Spacer
Acquisition in CRISPR-Cas Systems." Cell,
163, 840-853. doi: 10.1016/j.cell.2015.10.008.
|
Crystal structure of cas-DNA-n1 complex . SNAP output
|
|
5dlo
|
hydrolase |
X-ray (1.401 Å) |
Zorzini V, Loris R |
"Substrate recognition, regulation mechanism and
activity regulation of MazF mRNA interferase." |
S. aureus mazf in complex with substrate analogue .
SNAP output
|
|
5dnm
|
structural protein-DNA |
X-ray (2.81 Å) |
Adhireksan Z, Palermo G, Riedel T, Ma Z, Muhammad R,
Rothlisberger U, Dyson PJ, Davey CA |
(2017) "Allosteric
cross-talk in chromatin can mediate drug-drug
synergy." Nat Commun, 8,
14860. doi: 10.1038/ncomms14860.
|
Nucleosome core particle containing adducts of
ruthenium(ii)-toluene pta complex . SNAP output
|
|
5dnn
|
structural protein-DNA |
X-ray (2.8 Å) |
Adhireksan Z, Palermo G, Riedel T, Ma Z, Muhammad R,
Rothlisberger U, Dyson PJ, Davey CA |
(2017) "Allosteric
cross-talk in chromatin can mediate drug-drug
synergy." Nat Commun, 8,
14860. doi: 10.1038/ncomms14860.
|
Nucleosome core particle containing adducts of
gold(i)-triethylphosphane and ruthenium(ii)-toluene pta
complexes . SNAP
output
|
|
5dny
|
recombination-DNA |
X-ray (3.11 Å) |
Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim
T, Song OK, Lee SE, Cho Y |
(2016) "ATP-dependent
DNA binding, unwinding, and resection by the
Mre11/Rad50 complex." Embo J.,
35, 743-758. doi: 10.15252/embj.201592462.
|
Structure of the atprs-mre11-rad50-DNA complex .
SNAP output
|
|
5doy
|
ribosome-antibiotic |
X-ray (2.6 Å) |
Polikanov YS, Starosta AL, Juette MF, Altman RB,
Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds KA,
Blanchard SC, Steitz TA, Wilson DN |
(2015) "Distinct
tRNA Accommodation Intermediates Observed on the
Ribosome with the Antibiotics Hygromycin A and
A201A." Mol.Cell, 58,
832-844. doi: 10.1016/j.molcel.2015.04.014.
|
Crystal structure of the thermus thermophilus 70s
ribosome in complex with antibiotic hygromycin a, mrna
and three trnas in the a, p and e sites at 2.6a
resolution . SNAP
output
|
|
5dqg
|
transferase-DNA |
X-ray (2.29 Å) |
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M,
Wilds CJ |
(2016) "Lesion
Orientation ofO4-Alkylthymidine Influences Replication
by Human DNA Polymeraseeta." Chem Sci,
7, 4896-4904. doi: 10.1039/C6SC00666C.
|
Crystal structure of human DNA polymerase eta inserting
dampnpp opposite o4-ethylthymidine . SNAP output
|
|
5dqh
|
transferase-DNA |
X-ray (1.99 Å) |
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M,
Wilds CJ |
(2016) "Lesion
Orientation ofO4-Alkylthymidine Influences Replication
by Human DNA Polymeraseeta." Chem Sci,
7, 4896-4904. doi: 10.1039/C6SC00666C.
|
Crystal structure of human DNA polymerase eta inserting
dgmpnpp opposite o4-ethylthymidine . SNAP output
|
|
5dqi
|
transferase-DNA |
X-ray (2.3 Å) |
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M,
Wilds CJ |
(2016) "Lesion
Orientation ofO4-Alkylthymidine Influences Replication
by Human DNA Polymeraseeta." Chem Sci,
7, 4896-4904. doi: 10.1039/C6SC00666C.
|
Crystal structure of human DNA polymerase eta extending
an o4-ethylthymidine : da pair by inserting dctp
opposite dg . SNAP
output
|
|
5dqt
|
hydrolase-DNA |
X-ray (3.1 Å) |
Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang
Y |
(2015) "Structural
and Mechanistic Basis of PAM-Dependent Spacer
Acquisition in CRISPR-Cas Systems." Cell,
163, 840-853. doi: 10.1016/j.cell.2015.10.008.
|
Crystal structure of cas-DNA-22 complex . SNAP output
|
|
5dqu
|
hydrolase-DNA |
X-ray (4.5 Å) |
Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang
Y |
(2015) "Structural
and Mechanistic Basis of PAM-Dependent Spacer
Acquisition in CRISPR-Cas Systems." Cell,
163, 840-853. doi: 10.1016/j.cell.2015.10.008.
|
Crystal structure of cas-DNA-10 complex . SNAP output
|
|
5dqz
|
hydrolase-DNA |
X-ray (2.7 Å) |
Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang
Y |
(2015) "Structural
and Mechanistic Basis of PAM-Dependent Spacer
Acquisition in CRISPR-Cas Systems." Cell,
163, 840-853. doi: 10.1016/j.cell.2015.10.008.
|
Crystal structure of cas-DNA-pam complex . SNAP output
|
|
5ds4
|
hydrolase-DNA |
X-ray (3.2 Å) |
Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN,
Doudna JA |
(2015) "Foreign
DNA capture during CRISPR-Cas adaptive immunity."
Nature, 527, 535-538. doi:
10.1038/nature15760.
|
Crystal structure the escherichia coli cas1-cas2
complex bound to protospacer DNA . SNAP output
|
|
5ds5
|
hydrolase-DNA |
X-ray (2.951 Å) |
Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN,
Doudna JA |
(2015) "Foreign
DNA capture during CRISPR-Cas adaptive immunity."
Nature, 527, 535-538. doi:
10.1038/nature15760.
|
Crystal structure the escherichia coli cas1-cas2
complex bound to protospacer DNA and mg . SNAP output
|
|
5ds6
|
hydrolase-DNA |
X-ray (3.352 Å) |
Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN,
Doudna JA |
(2015) "Foreign
DNA capture during CRISPR-Cas adaptive immunity."
Nature, 527, 535-538. doi:
10.1038/nature15760.
|
Crystal structure the escherichia coli cas1-cas2
complex bound to protospacer DNA with splayed ends .
SNAP output
|
|
5ds9
|
DNA binding protein-DNA |
X-ray (2.561 Å) |
Hancock SP, Stella S, Cascio D, Johnson RC |
(2016) "DNA
Sequence Determinants Controlling Affinity, Stability
and Shape of DNA Complexes Bound by the Nucleoid
Protein Fis." Plos One,
11, e0150189. doi: 10.1371/journal.pone.0150189.
|
Crystal structure of fis bound to 27bp DNA f1-8a
(aaattagtttgaattttgagctaattt) . SNAP output
|
|
5dtd
|
DNA binding protein-DNA |
X-ray (2.642 Å) |
Hancock SP, Stella S, Cascio D, Johnson RC |
(2016) "DNA
Sequence Determinants Controlling Affinity, Stability
and Shape of DNA Complexes Bound by the Nucleoid
Protein Fis." Plos One,
11, e0150189. doi: 10.1371/journal.pone.0150189.
|
Crystal structure of fis bound to 27bp DNA f1-8c
(aaattcgtttgaattttgagcgaattt) . SNAP output
|
|
5dui
|
transcription-DNA |
X-ray (2.306 Å) |
Singh P, Han EH, Endrizzi JA, O'Brien RM, Chi YI |
(2017) "Crystal
structures reveal a new and novel FoxO1 binding site
within the human glucose-6-phosphatase catalytic
subunit 1 gene promoter." J. Struct.
Biol., 198, 54-64. doi: 10.1016/j.jsb.2017.02.006.
|
Identification of a new foxo1 binding site that
precludes creb binding at the glucose-6-phosphatase
catalytic subunit gene promoter . SNAP output
|
|
5dwa
|
hydrolase |
X-ray (1.5 Å) |
Tamulaitiene G, Jovaisaite V, Tamulaitis G,
Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY,
Siksnys V |
(2017) "Restriction
endonuclease AgeI is a monomer which dimerizes to
cleave DNA." Nucleic Acids Res.,
45, 3547-3558. doi: 10.1093/nar/gkw1310.
|
Crystal structure of pre-specific restriction
endonuclease agei-DNA complex . SNAP output
|
|
5dwb
|
hydrolase |
X-ray (2.4 Å) |
Tamulaitiene G, Jovaisaite V, Tamulaitis G,
Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY,
Siksnys V |
(2017) "Restriction
endonuclease AgeI is a monomer which dimerizes to
cleave DNA." Nucleic Acids Res.,
45, 3547-3558. doi: 10.1093/nar/gkw1310.
|
Crystal structure of specific restriction endonuclease
agei-DNA complex . SNAP
output
|
|
5dy0
|
DNA binding protein |
X-ray (3.0 Å) |
Palanca C, Rubio V |
(2016) "Structure
of AmtR, the global nitrogen regulator of
Corynebacterium glutamicum, in free and DNA-bound
forms." Febs J., 283,
1039-1059. doi: 10.1111/febs.13643.
|
Crystal of amtr from corynebacterium glutamicum in
complex with DNA . SNAP
output
|
|
5e01
|
transcription |
X-ray (2.3 Å) |
Counago RM, Chen NH, Chang CW, Djoko KY, McEwan AG,
Kobe B |
(2016) "Structural
basis of thiol-based regulation of formaldehyde
detoxification in H. influenzae by a MerR regulator
with no sensor region." Nucleic Acids
Res., 44, 6981-6993. doi:
10.1093/nar/gkw543.
|
Crystal structure of hinmlr, a merr family regulator
lacking the sensor domain, bound to palyndromic
promoter DNA . SNAP
output
|
|
5e17
|
transcription-DNA-RNA |
X-ray (3.2 Å) |
Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird
JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE |
(2016) "Multiplexed
protein-DNA cross-linking: Scrunching in transcription
start site selection." Science,
351, 1090-1093. doi: 10.1126/science.aad6881.
|
T. thermophilus transcription initiation complex having
a rrr discriminator sequence and a nontemplate-strand
length corresponding to tss selection at position 7
(rpo-ggg-7) . SNAP
output
|
|
5e18
|
transcription-DNA-RNA |
X-ray (3.3 Å) |
Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird
JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE |
(2016) "Multiplexed
protein-DNA cross-linking: Scrunching in transcription
start site selection." Science,
351, 1090-1093. doi: 10.1126/science.aad6881.
|
T. thermophilus transcription initiation complex having
a yyy discriminator sequence and a nontemplate-strand
length corresponding to tss selection at position 8
(rpo-ccc-8) . SNAP
output
|
|
5e24
|
transport-DNA binding-DNA |
X-ray (2.14 Å) |
Yuan Z, Praxenthaler H, Tabaja N, Torella R, Preiss
A, Maier D, Kovall RA |
(2016) "Structure
and Function of the Su(H)-Hairless Repressor Complex,
the Major Antagonist of Notch Signaling in Drosophila
melanogaster." Plos Biol.,
14, e1002509. doi: 10.1371/journal.pbio.1002509.
|
Structure of the su(h)-hairless-DNA repressor complex .
SNAP output
|
|
5e3l
|
DNA binding protein-DNA |
X-ray (2.66 Å) |
Hancock SP, Stella S, Cascio D, Johnson RC |
(2016) "DNA
Sequence Determinants Controlling Affinity, Stability
and Shape of DNA Complexes Bound by the Nucleoid
Protein Fis." Plos One,
11, e0150189. doi: 10.1371/journal.pone.0150189.
|
Crystal structure of fis bound to 27bp DNA f1-8g
(aaattggtttgaattttgagccaattt) . SNAP output
|
|
5e3m
|
DNA binding protein-DNA |
X-ray (2.886 Å) |
Hancock SP, Stella S, Cascio D, Johnson RC |
(2016) "DNA
Sequence Determinants Controlling Affinity, Stability
and Shape of DNA Complexes Bound by the Nucleoid
Protein Fis." Plos One,
11, e0150189. doi: 10.1371/journal.pone.0150189.
|
Crystal structure of fis bound to 27bp DNA f35
(aaattagtttgaatctcgagctaattt) . SNAP output
|
|
5e3n
|
DNA binding protein-DNA |
X-ray (2.66 Å) |
Hancock SP, Stella S, Cascio D, Johnson RC |
(2016) "DNA
Sequence Determinants Controlling Affinity, Stability
and Shape of DNA Complexes Bound by the Nucleoid
Protein Fis." Plos One,
11, e0150189. doi: 10.1371/journal.pone.0150189.
|
Crystal structure of fis bound to 27bp DNA f31
(aaatttgtaggaattttctgcaaattt) . SNAP output
|
|
5e3o
|
DNA binding protein-DNA |
X-ray (2.78 Å) |
Hancock SP, Stella S, Cascio D, Johnson RC |
(2016) "DNA
Sequence Determinants Controlling Affinity, Stability
and Shape of DNA Complexes Bound by the Nucleoid
Protein Fis." Plos One,
11, e0150189. doi: 10.1371/journal.pone.0150189.
|
Crystal structure of fis bound to 27bp DNA f32
(aaatttggaggaattttctccaaattt) . SNAP output
|
|
5e41
|
transferase |
X-ray (1.8 Å) |
Hottin A, Betz K, Diederichs K, Marx A |
(2017) "Structural
Basis for the KlenTaq DNA Polymerase Catalysed
Incorporation of Alkene- versus Alkyne-Modified
Nucleotides." Chemistry,
23, 2109-2118. doi: 10.1002/chem.201604515.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with
5-(n-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate
. SNAP output
|
|
5e5a
|
protein binding-viral protein-DNA |
X-ray (2.809 Å) |
Fang Q, Chen P, Wang M, Fang J, Yang N, Li G, Xu
RM |
(2016) "Human
cytomegalovirus IE1 protein alters the higher-order
chromatin structure by targeting the acidic patch of
the nucleosome." Elife,
5. doi: 10.7554/eLife.11911.
|
Crystal structure of the chromatin-tethering domain of
human cytomegalovirus ie1 protein bound to the
nucleosome core particle . SNAP output
|
|
5e5o
|
hydrolase-DNA |
X-ray (2.36 Å) |
Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser
BK |
(2016) "The
Structural Basis of Asymmetry in DNA Binding and
Cleavage as Exhibited by the I-SmaMI LAGLIDADG
Meganuclease." J.Mol.Biol.,
428, 206-220. doi: 10.1016/j.jmb.2015.12.005.
|
I-smami bound to uncleaved DNA target in the presence
of calcium ions . SNAP
output
|
|
5e5s
|
hydrolase-DNA |
X-ray (2.29 Å) |
Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser
BK |
(2016) "The
Structural Basis of Asymmetry in DNA Binding and
Cleavage as Exhibited by the I-SmaMI LAGLIDADG
Meganuclease." J.Mol.Biol.,
428, 206-220. doi: 10.1016/j.jmb.2015.12.005.
|
I-smami k103a mutant . SNAP output
|
|
5e63
|
hydrolase-DNA |
X-ray (2.6 Å) |
Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser
BK |
(2016) "The
Structural Basis of Asymmetry in DNA Binding and
Cleavage as Exhibited by the I-SmaMI LAGLIDADG
Meganuclease." J.Mol.Biol.,
428, 206-220. doi: 10.1016/j.jmb.2015.12.005.
|
K262a mutant of i-smami . SNAP output
|
|
5e67
|
hydrolase-DNA |
X-ray (2.2 Å) |
Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser
BK |
(2016) "The
Structural Basis of Asymmetry in DNA Binding and
Cleavage as Exhibited by the I-SmaMI LAGLIDADG
Meganuclease." J.Mol.Biol.,
428, 206-220. doi: 10.1016/j.jmb.2015.12.005.
|
K103a-k262a double mutant of i-smami . SNAP output
|
|
5e69
|
DNA binding protein-DNA |
X-ray (1.85 Å) |
Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst
AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund
EA |
(2018) "Cryptic
glucocorticoid receptor-binding sites pervade genomic
NF-kappa B response elements." Nat Commun,
9, 1337. doi: 10.1038/s41467-018-03780-1.
|
Glucocorticoid receptor DNA binding domain - il8 nf-kb
response element complex . SNAP output
|
|
5e6a
|
DNA binding protein-DNA |
X-ray (2.197 Å) |
Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst
AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund
EA |
(2018) "Cryptic
glucocorticoid receptor-binding sites pervade genomic
NF-kappa B response elements." Nat Commun,
9, 1337. doi: 10.1038/s41467-018-03780-1.
|
Glucocorticoid receptor DNA binding domain - plau nf-kb
response element complex . SNAP output
|
|
5e6b
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst
AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund
EA |
(2018) "Cryptic
glucocorticoid receptor-binding sites pervade genomic
NF-kappa B response elements." Nat Commun,
9, 1337. doi: 10.1038/s41467-018-03780-1.
|
Glucocorticoid receptor DNA binding domain - relb nf-kb
response element complex . SNAP output
|
|
5e6c
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst
AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund
EA |
(2018) "Cryptic
glucocorticoid receptor-binding sites pervade genomic
NF-kappa B response elements." Nat Commun,
9, 1337. doi: 10.1038/s41467-018-03780-1.
|
Glucocorticoid receptor DNA binding domain - ccl2 nf-kb
response element complex . SNAP output
|
|
5e6d
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Hudson WH, Vera IMS, Nwachukwu JC, Weikum ER, Herbst
AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund
EA |
(2018) "Cryptic
glucocorticoid receptor-binding sites pervade genomic
NF-kappa B response elements." Nat Commun,
9, 1337. doi: 10.1038/s41467-018-03780-1.
|
Glucocorticoid receptor DNA binding domain - icam1
nf-kb response element complex . SNAP output
|
|
5e8i
|
DNA binding protein-DNA |
X-ray (3.45 Å) |
Hou C, Tsodikov OV |
(2015) "Structural
Basis for Dimerization and DNA Binding of Transcription
Factor FLI1." Biochemistry,
54, 7365-7374. doi: 10.1021/acs.biochem.5b01121.
|
Crystal structure of the DNA binding domain of human
transcription factor fli1 in complex with a 10-mer DNA
accggaagtg . SNAP
output
|
|
5ean
|
hydrolase-DNA |
X-ray (2.36 Å) |
Zhou C, Pourmal S, Pavletich NP |
(2015) "Dna2
nuclease-helicase structure, mechanism and regulation
by Rpa." Elife, 4. doi:
10.7554/eLife.09832.
|
Crystal structure of dna2 in complex with a 5' overhang
DNA . SNAP output
|
|
5eax
|
hydrolase-DNA |
X-ray (3.05 Å) |
Zhou C, Pourmal S, Pavletich NP |
(2015) "Dna2
nuclease-helicase structure, mechanism and regulation
by Rpa." Elife, 4. doi:
10.7554/eLife.09832.
|
Crystal structure of dna2 in complex with an ssDNA .
SNAP output
|
|
5ed4
|
transcription-DNA |
X-ray (2.4 Å) |
He X, Wang L, Wang S |
(2016) "Structural
basis of DNA sequence recognition by the response
regulator PhoP in Mycobacterium tuberculosis."
Sci Rep, 6, 24442. doi:
10.1038/srep24442.
|
Structure of a phop-DNA complex . SNAP output
|
|
5edn
|
transcription |
X-ray (3.2 Å) |
Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A,
Xu Y, Nilsson L, Taipale J |
(2018) "Two
distinct DNA sequences recognized by transcription
factors represent enthalpy and entropy optima."
Elife, 7. doi: 10.7554/eLife.32963.
|
Structure of hoxb13-DNA(tcg) complex . SNAP output
|
|
5edw
|
transferase-DNA |
X-ray (2.62 Å) |
Koag M-C, Lee S |
"Structure of Dpo4 DNA polymerase replicating across
the genotoxic N7-methylguanine lesion." |
Ternary structure of dpo4 bound to g in the template
base paired with incoming dttp . SNAP output
|
|
5eea
|
transcription |
X-ray (2.195 Å) |
Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A,
Xu Y, Nilsson L, Taipale J |
(2018) "Two
distinct DNA sequences recognized by transcription
factors represent enthalpy and entropy optima."
Elife, 7. doi: 10.7554/eLife.32963.
|
Structure of hoxb13-DNA(caa) complex . SNAP output
|
|
5ef6
|
transcription |
X-ray (3.0 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Structure of hoxb13 complex with methylated DNA .
SNAP output
|
|
5eg0
|
transcription |
X-ray (3.101 Å) |
Xie Z, Sokolov I, Osmala M, Yue X, Bower G, Pett JP,
Chen Y, Wang K, Cavga AD, Popov A, Teichmann SA,
Morgunova E, Kvon EZ, Yin Y, Taipale J |
(2025) "DNA-guided
transcription factor interactions extend human gene
regulatory code." Nature. doi: 10.1038/s41586-025-08844-z.
|
Hoxb13-meis1 heterodimer bound to DNA . SNAP output
|
|
5eg6
|
transcription-DNA binding protein-DNA |
X-ray (2.094 Å) |
Tabaja NH, Kovall RA |
"CSL-RITA complex bound to DNA." |
Csl-rita complex bound to DNA . SNAP output
|
|
5egb
|
transcription-DNA |
X-ray (1.977 Å) |
Patel A, Horton JR, Wilson GG, Zhang X, Cheng X |
(2016) "Structural
basis for human PRDM9 action at recombination hot
spots." Genes Dev., 30,
257-265. doi: 10.1101/gad.274928.115.
|
Human prdm9 allele-a znf domain with associated
recombination hotspot DNA sequence ii . SNAP output
|
|
5ego
|
transcription |
X-ray (2.54 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Hoxb13-meis1 heterodimer bound to methylated DNA .
SNAP output
|
|
5eh2
|
transcription-DNA |
X-ray (2.05 Å) |
Patel A, Horton JR, Wilson GG, Zhang X, Cheng X |
(2016) "Structural
basis for human PRDM9 action at recombination hot
spots." Genes Dev., 30,
257-265. doi: 10.1101/gad.274928.115.
|
Human prdm9 allele-a znf domain with associated
recombination hotspot DNA sequence iii . SNAP output
|
|
5ei9
|
transcription-DNA |
X-ray (1.921 Å) |
Patel A, Horton JR, Wilson GG, Zhang X, Cheng X |
(2016) "Structural
basis for human PRDM9 action at recombination hot
spots." Genes Dev., 30,
257-265. doi: 10.1101/gad.274928.115.
|
Human prdm9 allele-a znf domain with associated
recombination hotspot DNA sequence i . SNAP output
|
|
5eix
|
isomerase-DNA |
X-ray (3.35 Å) |
Veselkov DA, Laponogov I, Pan XS, Selvarajah J,
Skamrova GB, Branstrom A, Narasimhan J, Prasad JV, Fisher
LM, Sanderson MR |
(2016) "Structure
of a quinolone-stabilized cleavage complex of
topoisomerase IV from Klebsiella pneumoniae and
comparison with a related Streptococcus pneumoniae
complex." Acta Crystallogr D Struct Biol,
72, 488-496. doi: 10.1107/S2059798316001212.
|
Quinolone-stabilized cleavage complex of topoisomerase
iv from klebsiella pneumoniae . SNAP output
|
|
5ejk
|
transferase-DNA |
X-ray (3.8 Å) |
Yin Z, Shi K, Banerjee S, Pandey KK, Bera S,
Grandgenett DP, Aihara H |
(2016) "Crystal
structure of the Rous sarcoma virus intasome."
Nature, 530, 362-366. doi:
10.1038/nature16950.
|
Crystal structure of the rous sarcoma virus intasome .
SNAP output
|
|
5elk
|
RNA binding protein-RNA |
X-ray (2.3 Å) |
Murn J, Teplova M, Zarnack K, Shi Y, Patel DJ |
(2016) "Recognition
of distinct RNA motifs by the clustered CCCH zinc
fingers of neuronal protein Unkempt."
Nat.Struct.Mol.Biol., 23,
16-23. doi: 10.1038/nsmb.3140.
|
Crystal structure of mouse unkempt zinc fingers 4-6
(znf4-6), bound to RNA . SNAP output
|
|
5emc
|
transcription-DNA |
X-ray (2.3 Å) |
Jin J, Lian T, SU XD |
"The effects of cytosine methylation on general
transcription factors." |
Transcription factor grdbd and smgre complex . SNAP output
|
|
5emp
|
transcription-DNA |
X-ray (2.3 Å) |
Lian T, Jin J, Su X |
"The effects of cytosine methylation on general
transcription factors." |
Transcription factor grdbd and mmgre complex . SNAP output
|
|
5emq
|
transcription-DNA |
X-ray (2.3 Å) |
Lian T, Jin J, Su X |
"The effects of cytosine methylation on general
transcription factors." |
Transcription factor grdbd and gre complex . SNAP output
|
|
5eoz
|
transferase-DNA |
X-ray (2.088 Å) |
Kou Y, Koag MC, Lee S |
(2018) "Structural
and kinetic studies of the effect of guanine-N7
alkylation and metal cofactors on DNA replication."
Biochemistry. doi: 10.1021/acs.biochem.8b00331.
|
Mutagenicity of 7-benzyl guanine lesion and replication
by human DNA polymerase beta . SNAP output
|
|
5esp
|
hydrolase-DNA |
X-ray (2.995 Å) |
Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM,
Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K,
Scharenberg AM, Stoddard BL |
(2016) "Indirect
DNA Sequence Recognition and Its Impact on Nuclease
Cleavage Activity." Structure,
24, 862-873. doi: 10.1016/j.str.2016.03.024.
|
Crystal structure of laglidadg meganuclease i-panmi
with coordinated calcium ions . SNAP output
|
|
5ev1
|
RNA binding protein-RNA |
X-ray (2.037 Å) |
Agrawal AA, Salsi E, Chatrikhi R, Henderson S,
Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL |
(2016) "An
extended U2AF(65)-RNA-binding domain recognizes the 3'
splice site signal." Nat Commun,
7, 10950. doi: 10.1038/ncomms10950.
|
Structure i of intact u2af65 recognizing a 3' splice
site signal . SNAP
output
|
|
5ev2
|
RNA binding protein-RNA |
X-ray (1.86 Å) |
Agrawal AA, Salsi E, Chatrikhi R, Henderson S,
Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL |
(2016) "An
extended U2AF(65)-RNA-binding domain recognizes the 3'
splice site signal." Nat Commun,
7, 10950. doi: 10.1038/ncomms10950.
|
Structure ii of intact u2af65 recognizing the 3' splice
site signal . SNAP
output
|
|
5ev3
|
RNA binding protein-RNA |
X-ray (1.5 Å) |
Agrawal AA, Salsi E, Chatrikhi R, Henderson S,
Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL |
(2016) "An
extended U2AF(65)-RNA-binding domain recognizes the 3'
splice site signal." Nat Commun,
7, 10950. doi: 10.1038/ncomms10950.
|
Structure iii of intact u2af65 recognizing the 3'
splice site signal . SNAP output
|
|
5ev4
|
RNA binding protein-RNA |
X-ray (1.57 Å) |
Agrawal AA, Salsi E, Chatrikhi R, Henderson S,
Jenkins JL, Green MR, Ermolenko DN, Kielkopf CL |
(2016) "An
extended U2AF(65)-RNA-binding domain recognizes the 3'
splice site signal." Nat Commun,
7, 10950. doi: 10.1038/ncomms10950.
|
Structure iv of intact u2af65 recognizing the 3' splice
site signal . SNAP
output
|
|
5ew1
|
protein-DNA |
X-ray (2.95 Å) |
Pica A, Russo Krauss I, Parente V, Tateishi-Karimata
H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F |
(2017) "Through-bond
effects in the ternary complexes of thrombin sandwiched
by two DNA aptamers." Nucleic Acids Res.,
45, 461-469. doi: 10.1093/nar/gkw1113.
|
Human thrombin sandwiched between two DNA aptamers:
hd22 and hd1-deltat3 . SNAP output
|
|
5ew2
|
protein-DNA |
X-ray (3.59 Å) |
Pica A, Russo Krauss I, Parente V, Tateishi-Karimata
H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F |
(2017) "Through-bond
effects in the ternary complexes of thrombin sandwiched
by two DNA aptamers." Nucleic Acids Res.,
45, 461-469. doi: 10.1093/nar/gkw1113.
|
Human thrombin sandwiched between two DNA aptamers:
hd22 and hd1-deltat12 . SNAP output
|
|
5ewe
|
transferase-DNA |
X-ray (1.66 Å) |
Su Y, Egli M, Guengerich FP |
(2016) "Mechanism
of Ribonucleotide Incorporation by Human DNA Polymerase
eta." J.Biol.Chem., 291,
3747-3756. doi: 10.1074/jbc.M115.706226.
|
Ternary complex of human DNA polymerase eta inserting
rctp opposite template g . SNAP output
|
|
5ewf
|
transferase-DNA |
X-ray (1.782 Å) |
Su Y, Egli M, Guengerich FP |
(2016) "Mechanism
of Ribonucleotide Incorporation by Human DNA Polymerase
eta." J.Biol.Chem., 291,
3747-3756. doi: 10.1074/jbc.M115.706226.
|
Ternary complex of human DNA polymerase eta inserting
rctp opposite an 8-oxodeoxyguanosine lesion . SNAP output
|
|
5ewg
|
transferase-DNA |
X-ray (1.75 Å) |
Su Y, Egli M, Guengerich FP |
(2016) "Mechanism
of Ribonucleotide Incorporation by Human DNA Polymerase
eta." J.Biol.Chem., 291,
3747-3756. doi: 10.1074/jbc.M115.706226.
|
Ternary complex of human DNA polymerase eta inserting
ratp opposite an 8-oxodeoxyguanosine lesion . SNAP output
|
|
5exh
|
oxidoreductase-DNA |
X-ray (1.3 Å) |
Jin SG, Zhang ZM, Dunwell TL, Harter MR, Wu X,
Johnson J, Li Z, Liu J, Szabo PE, Lu Q, Xu GL, Song J,
Pfeifer GP |
(2016) "Tet3
Reads 5-Carboxylcytosine through Its CXXC Domain and Is
a Potential Guardian against Neurodegeneration."
Cell Rep, 14, 493-505. doi:
10.1016/j.celrep.2015.12.044.
|
Crystal structure of mtet3-cxxc domain in complex with
5-carboxylcytosine DNA at 1.3 angstroms resolution. .
SNAP output
|
|
5eyb
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Jaiswal R, Choudhury M, Zaman S, Singh S, Santosh V,
Bastia D, Escalante CR |
(2016) "Functional
architecture of the Reb1-Ter complex of
Schizosaccharomyces pombe."
Proc.Natl.Acad.Sci.USA, 113,
E2267-E2276. doi: 10.1073/pnas.1525465113.
|
X-ray structure of reb1-ter complex . SNAP output
|
|
5eyo
|
transcription-DNA |
X-ray (2.39 Å) |
Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S,
Boise LH, Vertino PM, Cheng X |
(2017) "MAX is
an epigenetic sensor of 5-carboxylcytosine and is
altered in multiple myeloma." Nucleic Acids
Res., 45, 2396-2407. doi:
10.1093/nar/gkw1184.
|
The crystal structure of the max bhlh domain in complex
with 5-carboxyl cytosine DNA . SNAP output
|
|
5f0q
|
tranferase-DNA-RNA |
X-ray (2.21 Å) |
Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y,
Pavlov YI, Tahirov TH |
(2016) "Mechanism
of Concerted RNA-DNA Primer Synthesis by the Human
Primosome." J.Biol.Chem.,
291, 10006-10020. doi: 10.1074/jbc.M116.717405.
|
Crystal structure of c-terminal domain of the human DNA
primase large subunit with bound DNA template-RNA
primer . SNAP output
|
|
5f0s
|
replication-DNA-RNA |
X-ray (3.0 Å) |
Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y,
Pavlov YI, Tahirov TH |
(2016) "Mechanism
of Concerted RNA-DNA Primer Synthesis by the Human
Primosome." J.Biol.Chem.,
291, 10006-10020. doi: 10.1074/jbc.M116.717405.
|
Crystal structure of c-terminal domain of the human DNA
primase large subunit with bound DNA template-RNA
primer and manganese ion . SNAP output
|
|
5f3w
|
DNA binding protein-hydrolase-DNA |
X-ray (3.11 Å) |
Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim
T, Song OK, Lee SE, Cho Y |
(2016) "ATP-dependent
DNA binding, unwinding, and resection by the
Mre11/Rad50 complex." Embo J.,
35, 743-758. doi: 10.15252/embj.201592462.
|
Structure of the atprs-mre11-rad50-DNA complex .
SNAP output
|
|
5f55
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua
Y |
(2016) "Structural
basis for DNA 5 -end resection by RecJ."
Elife, 5, e14294. doi:
10.7554/eLife.14294.
|
Structure of recj complexed with DNA . SNAP output
|
|
5f56
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua
Y |
(2016) "Structural
basis for DNA 5 -end resection by RecJ."
Elife, 5, e14294. doi:
10.7554/eLife.14294.
|
Structure of recj complexed with DNA and ssb-ct .
SNAP output
|
|
5f7q
|
transcription-DNA |
X-ray (2.4 Å) |
Light SH, Cahoon LA, Halavaty AS, Freitag NE,
Anderson WF |
(2016) "Structure
to function of an alpha-glucan metabolic pathway that
promotes Listeria monocytogenes pathogenesis."
Nat Microbiol, 2, 16202. doi:
10.1038/nmicrobiol.2016.202.
|
Rok repressor lmo0178 from listeria monocytogenes bound
to operator . SNAP
output
|
|
5f8a
|
hydrolase-DNA |
X-ray (1.76 Å) |
Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson
L |
(2016) "Metal
Ion Binding at the Catalytic Site Induces Widely
Distributed Changes in a Sequence Specific Protein-DNA
Complex." Biochemistry,
55, 6115-6132. doi: 10.1021/acs.biochem.6b00919.
|
Crystal structure of the ternary ecorv-DNA-lu complex
with uncleaved DNA substrate. lanthanide binding to
ecorv-DNA complex inhibits cleavage. . SNAP output
|
|
5f99
|
DNA binding protein |
X-ray (2.63 Å) |
Frouws TD, Duda SC, Richmond TJ |
(2016) "X-ray
structure of the MMTV-A nucleosome core."
Proc.Natl.Acad.Sci.USA, 113,
1214-1219. doi: 10.1073/pnas.1524607113.
|
X-ray structure of the mmtv-a nucleosome core particle
. SNAP output
|
|
5f9l
|
transferase-DNA |
X-ray (2.592 Å) |
Patra A, Egli M |
"Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by
Human DNA Polymerase Eta." |
Crystal structure of human DNA polymerase eta inserting
dampnpp across a DNA template containing
1,n2-ethenodeoxyguanosine lesion . SNAP output
|
|
5f9n
|
transferase-DNA |
X-ray (2.23 Å) |
Patra A, Egli M |
"Bypass of the 1, N2-Ethenodeoxyguanosine Lesion by
Human DNA Polymerase Eta." |
Crystal structure of human DNA polymerase eta inserting
dcmpnpp across a DNA template containing
1,n2-ethenodeoxyguanosine lesion . SNAP output
|
|
5f9r
|
hydrolase-DNA-RNA |
X-ray (3.4 Å) |
Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K,
Thompson AJ, Nogales E, Doudna JA |
(2016) "Structures
of a CRISPR-Cas9 R-loop complex primed for DNA
cleavage." Science, 351,
867-871. doi: 10.1126/science.aad8282.
|
Crystal structure of catalytically-active streptococcus
pyogenes crispr-cas9 in complex with single-guided RNA
and double-stranded DNA primed for target DNA cleavage
. SNAP output
|
|
5fb2
|
transcription-DNA |
X-ray (1.8 Å) |
Birukou I, Newman CE, Brennan RG |
"S. aureus MepR F27L Mutant bound to
oligodeoxyribonucleotide." |
S. aureus mepr f27l mutant bound to
oligodeoxyribonucleotide . SNAP output
|
|
5fd3
|
transcription-DNA |
X-ray (2.42 Å) |
Marceau AH, Felthousen JG, Goetsch PD, Iness AN, Lee
HW, Tripathi SM, Strome S, Litovchick L, Rubin SM |
(2016) "Structural
basis for LIN54 recognition of CHR elements in cell
cycle-regulated promoters." Nat Commun,
7, 12301. doi: 10.1038/ncomms12301.
|
Structure of lin54 tesmin domain bound to DNA .
SNAP output
|
|
5fdk
|
hydrolase |
X-ray (3.208 Å) |
Khavnekar S, Dantu SC, Sedelnikova S, Ayora S,
Rafferty J, Kale A |
(2017) "Structural
insights into dynamics of RecU-HJ complex formation
elucidates key role of NTR and stalk region toward
formation of reactive state." Nucleic Acids
Res., 45, 975-986. doi: 10.1093/nar/gkw1165.
|
Crystal structure of recu(d88n) in complex with
palindromic DNA duplex . SNAP output
|
|
5ff8
|
hydrolase-DNA |
X-ray (1.7 Å) |
Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E,
Drohat AC |
(2016) "Structural
basis of damage recognition by thymine DNA glycosylase:
Key roles for N-terminal residues." Nucleic
Acids Res., 44, 10248-10258. doi:
10.1093/nar/gkw768.
|
Tdg enzyme-product complex . SNAP output
|
|
5ffj
|
DNA binding protein-DNA |
X-ray (2.84 Å) |
Kulkarni M, Nirwan N, van Aelst K, Szczelkun MD,
Saikrishnan K |
(2016) "Structural
insights into DNA sequence recognition by Type ISP
restriction-modification enzymes." Nucleic
Acids Res., 44, 4396-4408. doi:
10.1093/nar/gkw154.
|
Structure of a nuclease-deletion mutant of the type isp
restriction-modification enzyme llagi in complex with a
DNA substrate mimic . SNAP output
|
|
5fgp
|
DNA binding protein |
X-ray (2.0 Å) |
Weber J, Bao H, Hartlmuller C, Wang Z, Windhager A,
Janowski R, Madl T, Jin P, Niessing D |
(2016) "Structural
basis of nucleic-acid recognition and double-strand
unwinding by the essential neuronal protein
Pur-alpha." Elife, 5.
doi: 10.7554/eLife.11297.
|
Crystal structure of d. melanogaster pur-alpha repeat
i-ii in complex with DNA. . SNAP output
|
|
5fhd
|
hydrolase-DNA |
X-ray (2.0 Å) |
Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu
Z, Li D, Song H |
(2016) "Structural
and Functional Insights into the Unwinding Mechanism of
Bacteroides sp Pif1." Cell Rep,
14, 2030-2039. doi: 10.1016/j.celrep.2016.02.008.
|
Structure of bacteroides sp pif1 complexed with tailed
dsDNA resulting in ssDNA bound complex . SNAP output
|
|
5fhe
|
hydrolase-DNA |
X-ray (2.9 Å) |
Zhou X, Ren W, Bharath SR, Tang X, He Y, Chen C, Liu
Z, Li D, Song H |
(2016) "Structural
and Functional Insights into the Unwinding Mechanism of
Bacteroides sp Pif1." Cell Rep,
14, 2030-2039. doi: 10.1016/j.celrep.2016.02.008.
|
Crystal structure of bacteroides pif1 bound to ssDNA .
SNAP output
|
|
5fj8
|
transcription |
cryo-EM (3.9 Å) |
Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S,
Kosinski J, Hagen WJH, Sachse C, Muller CW |
(2015) "Molecular
Structures of Unbound and Transcribing RNA Polymerase
III." Nature, 528, 231.
doi: 10.1038/NATURE16143.
|
cryo-EM structure of yeast RNA polymerase iii
elongation complex at 3. 9 a . SNAP output
|
|
5fkv
|
transferase |
cryo-EM (8.04 Å) |
Fernandez-Leiro R, Conrad J, Scheres SH, Lamers
MH |
(2015) "cryo-EM
structures of theE. colireplicative DNA polymerase
reveal its dynamic interactions with the DNA sliding
clamp, exonuclease andtau." Elife,
4. doi: 10.7554/eLife.11134.
|
cryo-EM structure of the e. coli replicative DNA
polymerase complex bound to DNA (DNA polymerase iii
alpha, beta, epsilon, tau complex) . SNAP output
|
|
5fkw
|
transferase |
cryo-EM (7.3 Å) |
Fernandez-Leiro R, Conrad J, Scheres SH, Lamers
MH |
(2015) "cryo-EM
structures of theE. colireplicative DNA polymerase
reveal its dynamic interactions with the DNA sliding
clamp, exonuclease andtau." Elife,
4. doi: 10.7554/eLife.11134.
|
cryo-EM structure of the e. coli replicative DNA
polymerase complex bound to DNA (DNA polymerase iii
alpha, beta, epsilon) . SNAP output
|
|
5flm
|
transcription |
cryo-EM (3.4 Å) |
Bernecky C, Herzog F, Baumeister W, Plitzko JM,
Cramer P |
(2016) "Structure
of Transcribing Mammalian RNA Polymerase II."
Nature, 529, 551. doi:
10.1038/NATURE16482.
|
Structure of transcribing mammalian RNA polymerase ii .
SNAP output
|
|
5flv
|
transcription |
X-ray (3.005 Å) |
Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL,
Thomas S, Baudin F, Samee MAH, He D, Small EM,
Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Muller
CW, Bruneau BG |
(2016) "Complex
Interdependence Regulates Heterotypic Transcription
Factor Distribution and Coordinates Cardiogenesis."
Cell(Cambridge,Mass.), 164,
999. doi: 10.1016/J.CELL.2016.01.004.
|
Crystal structure of nkx2-5 and tbx5 bound to the nppa
promoter region . SNAP
output
|
|
5fmf
|
transcription |
cryo-EM (6.0 Å) |
Murakami K, Tsai K, Kalisman N, Bushnell DA, Asturias
FJ, Kornberg RD |
(2015) "Structure
of an RNA Polymerase II Pre-Initiation Complex."
Proc.Natl.Acad.Sci.USA, 112,
13543. doi: 10.1073/PNAS.1518255112.
|
The p-lobe of RNA polymerase ii pre-initiation complex
. SNAP output
|
|
5fmp
|
DNA binding protein |
X-ray (2.26 Å) |
Podust LM, Ouellet H |
"Kstr, Transcriptional Repressor of Cholesterol
Degradation in Mycobacterium Tuberculosis." |
Kstr, transcriptional repressor of cholesterol
degradation in mycobacterium tuberculosis, bound to the
DNA operator . SNAP
output
|
|
5fq5
|
hydrolase-DNA |
X-ray (2.136 Å) |
Olieric V, Weinert T, Finke AD, Anders C, Li D,
Olieric N, Borca CN, Steinmetz MO, Caffrey M, Jinek M,
Wang M |
(2016) "Data-Collection
Strategy for Challenging Native Sad Phasing."
Acta Crystallogr.,Sect.D, 72,
421. doi: 10.1107/S2059798315024110.
|
Crystal structure of cas9-sgrna-DNA complex solved by
native sad phasing . SNAP output
|
|
5frm
|
recombination |
X-ray (2.58 Å) |
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE,
Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH,
Burke TRJ |
(2016) "HIV-1
Integrase Strand Transfer Inhibitors with Reduced
Susceptibility to Drug Resistant Mutant
Integrases." Acs Chem.Biol.,
11, 1074. doi: 10.1021/ACSCHEMBIO.5B00948.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti xz384
(compound 4a) . SNAP
output
|
|
5frn
|
transferase |
X-ray (2.85 Å) |
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE,
Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH,
Burke TRJ |
(2016) "HIV-1
Integrase Strand Transfer Inhibitors with Reduced
Susceptibility to Drug Resistant Mutant
Integrases." Acs Chem.Biol.,
11, 1074. doi: 10.1021/ACSCHEMBIO.5B00948.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti xz419
(compound 4c) . SNAP
output
|
|
5fro
|
transferase |
X-ray (2.67 Å) |
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE,
Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH,
Burke TRJ |
(2016) "HIV-1
Integrase Strand Transfer Inhibitors with Reduced
Susceptibility to Drug Resistant Mutant
Integrases." Acs Chem.Biol.,
11, 1074. doi: 10.1021/ACSCHEMBIO.5B00948.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti xz446
(compound 4f) . SNAP
output
|
|
5fte
|
hydrolase |
X-ray (3.19 Å) |
Chen W-F, Dai Y-X, Duan X-L, Liu N-N, Shi W, Li N, Li
M, Dou S-X, Dong Y-H, Rety S, Xi X-G |
(2016) "Crystal
Structures of the Bspif1 Helicase Reveal that a Major
Movement of the 2B SH3 Domain is Required for DNA
Unwinding." Nucleic Acids Res.,
44, 2949. doi: 10.1093/NAR/GKW033.
|
Crystal structure of pif1 helicase from bacteroides in
complex with adp-alf3 and ssDNA . SNAP output
|
|
5fur
|
transcription |
cryo-EM (8.5 Å) |
Louder RK, He Y, Lopez-Blanco JR, Fang J, Chacon P,
Nogales E |
(2016) "Structure
of Promoter-Bound TFIID and Model of Human
Pre-Initiation Complex Assembly." Nature,
531, 604. doi: 10.1038/NATURE17394.
|
Structure of human tfiid-iia bound to core promoter DNA
. SNAP output
|
|
5fw1
|
hydrolase-DNA |
X-ray (2.499 Å) |
Anders C, Bargsten K, Jinek M |
(2016) "Structural
Plasticity of Pam Recognition by Engineered Variants of
the RNA-Guided Endonuclease Cas9."
Mol.Cell, 61, 895. doi:
10.1016/J.MOLCEL.2016.02.020.
|
Crystal structure of spycas9 variant vqr bound to sgrna
and tgag pam target DNA . SNAP output
|
|
5fw2
|
hydrolase-DNA-RNA |
X-ray (2.676 Å) |
Anders C, Bargsten K, Jinek M |
(2016) "Structural
Plasticity of Pam Recognition by Engineered Variants of
the RNA-Guided Endonuclease Cas9."
Mol.Cell, 61, 895. doi:
10.1016/J.MOLCEL.2016.02.020.
|
Crystal structure of spcas9 variant eqr bound to sgrna
and tgag pam target DNA . SNAP output
|
|
5fw3
|
hydrolase-DNA-RNA |
X-ray (2.7 Å) |
Anders C, Bargsten K, Jinek M |
(2016) "Structural
Plasticity of Pam Recognition by Engineered Variants of
the RNA-Guided Endonuclease Cas9."
Mol.Cell, 61, 895. doi:
10.1016/J.MOLCEL.2016.02.020.
|
Crystal structure of spcas9 variant vrer bound to sgrna
and tgcg pam target DNA . SNAP output
|
|
5fyw
|
transcription |
cryo-EM (4.35 Å) |
Plaschka C, Hantsche M, Dienemann C, Burzinski C,
Plitzko J, Cramer P |
(2016) "Transcription
Initiation Complex Structures Elucidate DNA
Opening." Nature, 533,
353. doi: 10.1038/NATURE17990.
|
Transcription initiation complex structures elucidate
DNA opening (oc) . SNAP
output
|
|
5fz5
|
transcription |
cryo-EM (8.8 Å) |
Plaschka C, Hantsche M, Dienemann C, Burzinski C,
Plitzko J, Cramer P |
(2016) "Transcription
Initiation Complex Structures Elucidate DNA
Opening." Nature, 533,
353. doi: 10.1038/NATURE17990.
|
Transcription initiation complex structures elucidate
DNA opening (cc) . SNAP
output
|
|
5g32
|
cell cycle |
X-ray (2.2 Å) |
Schneider S, Simon N, Ebert C |
(2016) "Structural
Basis for Bulky Adduct DNA Lesion Recognition by the
Nucleotide Excision Repair Protein Rad14."
Chemistry, 22, 10782. doi:
10.1002/CHEM.201602438.
|
Structure of rad14 in complex with
acetylaminophenyl-guanine containing DNA . SNAP output
|
|
5g33
|
cell cycle |
X-ray (2.4 Å) |
Schneider S, Simon N, Ebert C |
(2016) "Structural
Basis for Bulky Adduct DNA Lesion Recognition by the
Nucleotide Excision Repair Protein Rad14."
Chemistry, 22, 10782. doi:
10.1002/CHEM.201602438.
|
Structure of rad14 in complex with
acetylnaphtyl-guanine containing DNA . SNAP output
|
|
5g34
|
cell cycle |
X-ray (1.9 Å) |
Schneider S, Simon N, Ebert C |
(2016) "Structural
Basis for Bulky Adduct DNA Lesion Recognition by the
Nucleotide Excision Repair Protein Rad14."
Chemistry, 22, 10782. doi:
10.1002/CHEM.201602438.
|
Structure of rad14 in complex with
acetylaminoanthracene-c8-guanine containing DNA .
SNAP output
|
|
5g35
|
cell cycle |
X-ray (2.0 Å) |
Schneider S, Simon N, Ebert C |
(2016) "Structural
Basis for Bulky Adduct DNA Lesion Recognition by the
Nucleotide Excision Repair Protein Rad14."
Chemistry, 22, 10782. doi:
10.1002/CHEM.201602438.
|
Structure of rad14 in complex with
acetylaminopyren-c8-guanine containing DNA . SNAP output
|
|
5g5t
|
hydrolase-DNA |
X-ray (2.85 Å) |
Willkomm S, Oellig CA, Zander A, Restle T, Keegan R,
Grohmann D, Schneider S |
(2017) "Structural
and mechanistic insights into an archaeal DNA-guided
Argonaute protein." Nat Microbiol,
2, 17035. doi: 10.1038/nmicrobiol.2017.35.
|
Structure of the argonaute protein from
methanocaldcoccus janaschii in complex with guide DNA .
SNAP output
|
|
5gat
|
transcription-DNA |
NMR |
Starich MR, Wikstrom M, Arst Jr HN, Clore GM,
Gronenborn AM |
(1998) "The
solution structure of a fungal AREA protein-DNA
complex: an alternative binding mode for the basic
carboxyl tail of GATA factors."
J.Mol.Biol., 277, 605-620.
doi: 10.1006/jmbi.1998.1625.
|
Solution NMR structure of the wild type DNA binding
domain of area complexed to a 13bp DNA containing a
cgata site, 35 structures . SNAP output
|
|
5gke
|
hydrolase-DNA |
X-ray (2.4 Å) |
Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI,
Mayanagi K, Ishino S, Ishino Y, Shirai T |
(2016) "Structure
of the EndoMS-DNA Complex as Mismatch Restriction
Endonuclease." Structure,
24, 1960-1971. doi: 10.1016/j.str.2016.09.005.
|
Structure of endoms-dsdna1 complex . SNAP output
|
|
5gkf
|
hydrolase-DNA |
X-ray (2.8 Å) |
Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI,
Mayanagi K, Ishino S, Ishino Y, Shirai T |
(2016) "Structure
of the EndoMS-DNA Complex as Mismatch Restriction
Endonuclease." Structure,
24, 1960-1971. doi: 10.1016/j.str.2016.09.005.
|
Structure of endoms-dsdna1' complex . SNAP output
|
|
5gkg
|
hydrolase-DNA |
X-ray (2.6 Å) |
Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI,
Mayanagi K, Ishino S, Ishino Y, Shirai T |
(2016) "Structure
of the EndoMS-DNA Complex as Mismatch Restriction
Endonuclease." Structure,
24, 1960-1971. doi: 10.1016/j.str.2016.09.005.
|
Structure of endoms-dsdna1'' complex . SNAP output
|
|
5gkh
|
hydrolase-DNA |
X-ray (2.9 Å) |
Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI,
Mayanagi K, Ishino S, Ishino Y, Shirai T |
(2016) "Structure
of the EndoMS-DNA Complex as Mismatch Restriction
Endonuclease." Structure,
24, 1960-1971. doi: 10.1016/j.str.2016.09.005.
|
Structure of endoms-dsdna2 complex . SNAP output
|
|
5gki
|
hydrolase-DNA |
X-ray (2.9 Å) |
Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI,
Mayanagi K, Ishino S, Ishino Y, Shirai T |
(2016) "Structure
of the EndoMS-DNA Complex as Mismatch Restriction
Endonuclease." Structure,
24, 1960-1971. doi: 10.1016/j.str.2016.09.005.
|
Structure of endoms-dsdna3 complex . SNAP output
|
|
5gkp
|
hydrolase-DNA |
X-ray (2.3 Å) |
Lin JL, Wu CC, Yang WZ, Yuan HS |
(2016) "Crystal
structure of endonuclease G in complex with DNA reveals
how it nonspecifically degrades DNA as a
homodimer." Nucleic Acids Res.,
44, 10480-10490. doi: 10.1093/nar/gkw931.
|
Crystal structure of the endog worm homologue cps-6
h148a-f122a in complex with DNA . SNAP output
|
|
5gkr
|
immune system-DNA |
X-ray (2.1 Å) |
Sakakibara S, Arimori T, Yamashita K, Jinzai H,
Motooka D, Nakamura S, Li S, Takeda K, Katayama J, El
Hussien MA, Narazaki M, Tanaka T, Standley DM, Takagi J,
Kikutani H |
(2017) "Clonal
evolution and antigen recognition of anti-nuclear
antibodies in acute systemic lupus erythematosus."
Sci Rep, 7, 16428. doi:
10.1038/s41598-017-16681-y.
|
Crystal structure of sle patient-derived anti-DNA
antibody in complex with oligonucleotide . SNAP output
|
|
5gnj
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Lian TF, Xu YP, Li LF, Su XD |
(2017) "Crystal
Structure of Tetrameric Arabidopsis MYC2 Reveals the
Mechanism of Enhanced Interaction with DNA."
Cell Rep, 19, 1334-1342. doi:
10.1016/j.celrep.2017.04.057.
|
Structure of a transcription factor and DNA complex .
SNAP output
|
|
5gpc
|
transcription, DNA binding protein-DNA |
X-ray (2.8 Å) |
Yeo HK, Park YW, Lee JY |
(2017) "Structural
basis of operator sites recognition and effector
binding in the TetR family transcription regulator
FadR." Nucleic Acids Res.,
45, 4244-4254. doi: 10.1093/nar/gkx009.
|
Structural analysis of fatty acid degradation regulator
fadr from bacillus halodurans . SNAP output
|
|
5gq9
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Zhao H, Sheng G, Wang Y |
"Crystal structure of Thermus thermophilus Argonaute
in complex with g1C siDNA and DNA target." |
Crystal structure of thermus thermophilus argonaute in
complex with g1c siDNA and DNA target . SNAP output
|
|
5gse
|
structural protein-DNA |
X-ray (3.14 Å) |
Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi
N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J,
Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R,
Sugiyama M, Kurumizaka H |
(2017) "Crystal
structure of the overlapping dinucleosome composed of
hexasome and octasome." Science,
356, 205-208. doi: 10.1126/science.aak9867.
|
Crystal structure of unusual nucleosome . SNAP output
|
|
5gsu
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K,
Kumasaka T, Ishii S, Kumarevel T |
(2017) "Structural
analyses of the nucleosome complexes with human
testis-specific histone variants, hTh2a and hTh2b."
Biophys. Chem., 221, 41-48.
doi: 10.1016/j.bpc.2016.11.013.
|
Crystal structure of nucleosome core particle
consisting of human testis-specific histone variants,
th2a and th2b . SNAP
output
|
|
5gt0
|
structural protein-DNA |
X-ray (2.82 Å) |
Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K,
Kumasaka T, Ishii S, Kumarevel T |
(2017) "Structural
analyses of the nucleosome complexes with human
testis-specific histone variants, hTh2a and hTh2b."
Biophys. Chem., 221, 41-48.
doi: 10.1016/j.bpc.2016.11.013.
|
Crystal structure of nucleosome complex with human
testis-specific histone variants, th2a . SNAP output
|
|
5gt3
|
structural protein-DNA |
X-ray (2.91 Å) |
Padavattan S, Thiruselvam V, Shinagawa T, Hasegawa K,
Kumasaka T, Ishii S, Kumarevel T |
(2017) "Structural
analyses of the nucleosome complexes with human
testis-specific histone variants, hTh2a and hTh2b."
Biophys. Chem., 221, 41-48.
doi: 10.1016/j.bpc.2016.11.013.
|
Crystal structure of nucleosome particle in the
presence of human testis-specific histone variant,
hth2b . SNAP output
|
|
5gtc
|
structural protein-DNA |
X-ray (2.7 Å) |
Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D,
Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA,
Yamatsugu K, Kanai M |
(2017) "Synthetic
Posttranslational Modifications: Chemical
Catalyst-Driven Regioselective Histone Acylation of
Native Chromatin." J. Am. Chem. Soc.,
139, 7568-7576. doi: 10.1021/jacs.7b02138.
|
Crystal structure of complex between dmap-sh conjugated
with a kaposi's sarcoma herpesvirus lana peptide (5-15)
and nucleosome core particle . SNAP output
|
|
5gwi
|
isomerase-DNA-isomerase inhibitor |
X-ray (2.737 Å) |
Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT,
Chen YS, Li TK, Chien TC, Chan NL |
(2017) "Producing
irreversible topoisomerase II-mediated DNA breaks by
site-specific Pt(II)-methionine coordination
chemistry." Nucleic Acids Res.,
45, 10861-10871. doi: 10.1093/nar/gkx742.
|
Structure of a human topoisomerase iibeta fragment in
complex with DNA and e7873r . SNAP output
|
|
5gwj
|
isomerase-DNA-isomerase inhibitor |
X-ray (2.566 Å) |
Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT,
Chen YS, Li TK, Chien TC, Chan NL |
(2017) "Producing
irreversible topoisomerase II-mediated DNA breaks by
site-specific Pt(II)-methionine coordination
chemistry." Nucleic Acids Res.,
45, 10861-10871. doi: 10.1093/nar/gkx742.
|
Structure of a human topoisomerase iibeta fragment in
complex with DNA and e7873s . SNAP output
|
|
5gwk
|
isomerase-DNA-isomerase inhibitor |
X-ray (3.152 Å) |
Wang YR, Chen SF, Wu CC, Liao YW, Lin TS, Liu KT,
Chen YS, Li TK, Chien TC, Chan NL |
(2017) "Producing
irreversible topoisomerase II-mediated DNA breaks by
site-specific Pt(II)-methionine coordination
chemistry." Nucleic Acids Res.,
45, 10861-10871. doi: 10.1093/nar/gkx742.
|
Human topoisomerase iialpha in complex with DNA and
etoposide . SNAP
output
|
|
5gxq
|
structural protein-DNA |
X-ray (2.85 Å) |
Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A,
Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T,
Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y,
Kurumizaka H |
(2017) "Crystal
Structure and Characterization of Novel Human Histone
H3 Variants, H3.6, H3.7, and H3.8."
Biochemistry, 56, 2184-2196.
doi: 10.1021/acs.biochem.6b01098.
|
The crystal structure of the nucleosome containing h3.6
. SNAP output
|
|
5gzb
|
transcription-DNA |
X-ray (2.704 Å) |
Shi ZB, He F, Chen M, Hua L, Wang W, Jiao S, Zhou
ZC |
(2017) "DNA-binding
mechanism of the Hippo pathway transcription factor
TEAD4." Oncogene, 36,
4362-4369. doi: 10.1038/onc.2017.24.
|
Crystal structure of transcription factor tead4 in
complex with m-cat DNA . SNAP output
|
|
5h1b
|
DNA binding protein-DNA |
cryo-EM (4.4 Å) |
Xu J, Zhao L, Xu Y, Zhao W, Sung P, Wang HW |
(2017) "Cryo-EM
structures of human RAD51 recombinase filaments during
catalysis of DNA-strand exchange." Nat. Struct.
Mol. Biol., 24, 40-46. doi:
10.1038/nsmb.3336.
|
Human rad51 presynaptic complex . SNAP output
|
|
5h1c
|
DNA binding protein-DNA |
cryo-EM (4.5 Å) |
Xu J, Zhao L, Xu Y, Zhao W, Sung P, Wang HW |
(2017) "Cryo-EM
structures of human RAD51 recombinase filaments during
catalysis of DNA-strand exchange." Nat. Struct.
Mol. Biol., 24, 40-46. doi:
10.1038/nsmb.3336.
|
Human rad51 post-synaptic complexes . SNAP output
|
|
5h3r
|
transcription-DNA |
X-ray (2.67 Å) |
Zhu R, Hao Z, Lou H, Song Y, Zhao J, Chen Y, Zhu J,
Chen PR |
(2017) "Structural
characterization of the DNA-binding mechanism
underlying the copper(II)-sensing MarR transcriptional
regulator." J. Biol. Inorg. Chem.,
22, 685-693. doi: 10.1007/s00775-017-1442-7.
|
Crystal structure of mutant marr c80s from e.coli
complexed with operator DNA . SNAP output
|
|
5h58
|
transcription-DNA |
X-ray (3.991 Å) |
Bhukya H, Jana AK, Sengupta N, Anand R |
(2017) "Structural
and dynamics studies of the TetR family protein, CprB
from Streptomyces coelicolor in complex with its
biological operator sequence." J. Struct.
Biol., 198, 134-146. doi:
10.1016/j.jsb.2017.03.006.
|
Structural and dynamics studies of the tetr family
protein, cprb from streptomyces coelicolor in complex
with its biological operator sequence . SNAP output
|
|
5h8w
|
hydrolase |
X-ray (2.2 Å) |
Constantinescu-Aruxandei D, Petrovic-Stojanovska B,
Penedo JC, White MF, Naismith JH |
(2016) "Mechanism
of DNA loading by the DNA repair helicase XPD."
Nucleic Acids Res., 44,
2806-2815. doi: 10.1093/nar/gkw102.
|
Xpd mechanism . SNAP
output
|
|
5h9e
|
immune system-RNA |
X-ray (3.21 Å) |
Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K,
Bailey S, Wiedenheft B, Ke A |
(2016) "Structural
basis for promiscuous PAM recognition in type I-E
Cascade from E. coli." Nature,
530, 499-503. doi: 10.1038/nature16995.
|
Crystal structure of e. coli cascade bound to a
pam-containing dsDNA target (32-nt spacer) at 3.20
angstrom resolution. . SNAP output
|
|
5h9f
|
immune system-RNA |
X-ray (2.45 Å) |
Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K,
Bailey S, Wiedenheft B, Ke A |
(2016) "Structural
basis for promiscuous PAM recognition in type I-E
Cascade from E. coli." Nature,
530, 499-503. doi: 10.1038/nature16995.
|
Crystal structure of e. coli cascade bound to a
pam-containing dsDNA target at 2.45 angstrom
resolution. . SNAP
output
|
|
5haw
|
cell cycle-DNA |
X-ray (1.89 Å) |
Schumacher MA, Zeng W |
(2016) "Structures
of the nucleoid occlusion protein SlmA bound to DNA and
the C-terminal domain of the cytoskeletal protein
FtsZ." Proc.Natl.Acad.Sci.USA,
113, 4988-4993. doi: 10.1073/pnas.1602327113.
|
Structures of the no factor slma bound to DNA and the
cytoskeletal cell division protein ftsz . SNAP output
|
|
5hbu
|
cell cycle-DNA |
X-ray (2.6 Å) |
Schumacher MA, Zeng W |
(2016) "Structures
of the nucleoid occlusion protein SlmA bound to DNA and
the C-terminal domain of the cytoskeletal protein
FtsZ." Proc.Natl.Acad.Sci.USA,
113, 4988-4993. doi: 10.1073/pnas.1602327113.
|
Structure of the e. coli nucleoid occlusion protein
slma bound to DNA and the c-terminal tail of the
cytoskeletal cell division protein ftsz . SNAP output
|
|
5hch
|
sugar binding protein |
X-ray (2.9 Å) |
Roethlisberger P, Istrate A, Marcaida Lopez MJ,
Visini R, Stocker A, Reymond JL, Leumann CJ |
(2016) "X-ray
structure of a lectin-bound DNA duplex containing an
unnatural phenanthrenyl pair."
Chem.Commun.(Camb.), 52,
4749-4752. doi: 10.1039/c6cc00374e.
|
X-ray structure of a lectin-bound DNA duplex containing
an unnatural phenanthrenyl pair . SNAP output
|
|
5hdn
|
transcription |
X-ray (1.68 Å) |
Feng H, Liu W, Wang DC |
"HSF1-DBD crystal structure." |
Crystal structure of heat shock factor1-dbd complex
with ds-DNA and ttt . SNAP output
|
|
5hf7
|
hydrolase-DNA |
X-ray (1.54 Å) |
Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E,
Drohat AC |
(2016) "Structural
basis of damage recognition by thymine DNA glycosylase:
Key roles for N-terminal residues." Nucleic
Acids Res., 44, 10248-10258. doi:
10.1093/nar/gkw768.
|
Tdg enzyme-substrate complex . SNAP output
|
|
5hhh
|
transferase, lyase-DNA |
X-ray (2.363 Å) |
Cheun Y, Koag MC, Naguib YW, Ouzon-Shubeita H, Cui Z,
Pakotiprapha D, Lee S |
(2018) "Synthesis,
structure, and biological evaluation of a
platinum-carbazole conjugate." Chem Biol Drug
Des, 91, 116-125. doi: 10.1111/cbdd.13062.
|
Structure of human DNA polymerase beta host-guest
complexed with the control g for n7-cbz-platination .
SNAP output
|
|
5hhi
|
transferase, lyase-DNA |
X-ray (2.517 Å) |
Cheun Y, Koag MC, Naguib YW, Ouzon-Shubeita H, Cui Z,
Pakotiprapha D, Lee S |
(2018) "Synthesis,
structure, and biological evaluation of a
platinum-carbazole conjugate." Chem Biol Drug
Des, 91, 116-125. doi: 10.1111/cbdd.13062.
|
Structure of human DNA polymerase beta host-guest
complexed with cbz-platinated n7-g . SNAP output
|
|
5hk0
|
hydrolase-RNA |
X-ray (2.25 Å) |
Yen TJ, Brennan RG |
"Crystal structure of M. tuberculosis MazF-mt3
(Rv1991c) in complex with RNA." |
Crystal structure of m. tuberculosis mazf-mt3 (rv1991c)
in complex with RNA . SNAP output
|
|
5hk3
|
hydrolase-DNA |
X-ray (1.56 Å) |
Yen TJ, Brennan RG |
"Crystal structure of M. tuberculosis MazF-mt3
T52D-F62D mutant in complex with DNA." |
Crystal structure of m. tuberculosis mazf-mt3 t52d-f62d
mutant in complex with DNA . SNAP output
|
|
5hkc
|
hydrolase-RNA |
X-ray (1.68 Å) |
Yen TJ, Brennan RG |
"Crystal structure of M. tuberculosis MazF-mt3
T52D-F62D mutant in complex with 8-mer RNA." |
Crystal structure of m. tuberculosis mazf-mt3 t52d-f62d
mutant in complex with 8-mer RNA . SNAP output
|
|
5hlf
|
transferase-inhibitor-DNA |
X-ray (2.95 Å) |
Mullins ND, Maguire NM, Ford A, Das K, Arnold E,
Balzarini J, Maguire AR |
(2016) "Exploring
the role of the alpha-carboxyphosphonate moiety in the
HIV-RT activity of alpha-carboxy nucleoside
phosphonates." Org.Biomol.Chem.,
14, 2454-2465. doi: 10.1039/c5ob02507a.
|
Structure of hiv-1 reverse transcriptase in complex
with a 38-mer hairpin template-primer DNA aptamer and
an alpha-carboxyphosphonate inhibitor . SNAP output
|
|
5hlg
|
transcription regulator-DNA |
X-ray (3.0 Å) |
Liu G, Liu X, Xu H, Liu X, Zhou H, Huang Z, Gan J,
Chen H, Lan L, Yang CG |
(2017) "Structural
Insights into the Redox-Sensing Mechanism of MarR-Type
Regulator AbfR." J. Am. Chem. Soc.,
139, 1598-1608. doi: 10.1021/jacs.6b11438.
|
Structure of reduced abfr bound to DNA . SNAP output
|
|
5hlh
|
transcription regulator-DNA |
X-ray (3.0 Å) |
Liu G, Liu X, Xu H, Liu X, Zhou H, Huang Z, Gan J,
Chen H, Lan L, Yang CG |
(2017) "Structural
Insights into the Redox-Sensing Mechanism of MarR-Type
Regulator AbfR." J. Am. Chem. Soc.,
139, 1598-1608. doi: 10.1021/jacs.6b11438.
|
Crystal structure of the overoxidized abfr bound to DNA
. SNAP output
|
|
5hlk
|
hydrolase-DNA |
X-ray (2.0 Å) |
Sinha K, Sangani SS, Kehr AD, Rule GS, Jen-Jacobson
L |
(2016) "Metal
Ion Binding at the Catalytic Site Induces Widely
Distributed Changes in a Sequence Specific Protein-DNA
Complex." Biochemistry,
55, 6115-6132. doi: 10.1021/acs.biochem.6b00919.
|
Crystal structure of the ternary ecorv-DNA-lu complex
with cleaved DNA substrate. . SNAP output
|
|
5hlt
|
hydrolase |
X-ray (2.672 Å) |
Probst M, Aeschimann W, Chau TT, Langenegger SM,
Stocker A, Haner R |
(2016) "Structural
insight into DNA-assembled oligochromophores:
crystallographic analysis of pyrene- and
phenanthrene-modified DNA in complex with BpuJI
endonuclease." Nucleic Acids Res.,
44, 7079-7089. doi: 10.1093/nar/gkw644.
|
Crystal structure of pyrene- and phenanthrene-modified
DNA in complex with the bpuj1 endonuclease binding
domain . SNAP output
|
|
5hnf
|
hydrolase |
X-ray (1.546 Å) |
Probst M, Aeschimann W, Chau TT, Langenegger SM,
Stocker A, Haner R |
(2016) "Structural
insight into DNA-assembled oligochromophores:
crystallographic analysis of pyrene- and
phenanthrene-modified DNA in complex with BpuJI
endonuclease." Nucleic Acids Res.,
44, 7079-7089. doi: 10.1093/nar/gkw644.
|
Crystal structure of pyrene- and phenanthrene-modified
DNA in complex with the bpuj1 endonuclease binding
domain . SNAP output
|
|
5hnh
|
hydrolase |
X-ray (1.876 Å) |
Probst M, Aeschimann W, Chau TT, Langenegger SM,
Stocker A, Haner R |
(2016) "Structural
insight into DNA-assembled oligochromophores:
crystallographic analysis of pyrene- and
phenanthrene-modified DNA in complex with BpuJI
endonuclease." Nucleic Acids Res.,
44, 7079-7089. doi: 10.1093/nar/gkw644.
|
Crystal structure of pyrene- and phenanthrene-modified
DNA in complex with the bpuj1 endonuclease binding
domain . SNAP output
|
|
5hnk
|
hydrolase |
X-ray (2.22 Å) |
AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova
SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ |
(2016) "Direct
observation of DNA threading in flap endonuclease
complexes." Nat.Struct.Mol.Biol.,
23, 640-646. doi: 10.1038/nsmb.3241.
|
Crystal structure of t5fen in complex intact substrate
and metal ions. . SNAP
output
|
|
5hod
|
transcription |
X-ray (2.682 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Structure of lhx4 transcription factor complexed with
DNA . SNAP output
|
|
5hoo
|
DNA |
X-ray (3.3 Å) |
Morris ER, Grey H, McKenzie G, Jones AC, Richardson
JM |
(2016) "A bend,
flip and trap mechanism for transposon
integration." Elife, 5.
doi: 10.7554/eLife.15537.
|
Crystal structure of the mos1 strand transfer complex .
SNAP output
|
|
5hp1
|
transferase-inhibitor-DNA |
X-ray (2.9 Å) |
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano
JJ, Arnold E |
(2016) "Conformational
States of HIV-1 Reverse Transcriptase for Nucleotide
Incorporation vs Pyrophosphorolysis-Binding of
Foscarnet." Acs Chem.Biol.,
11, 2158-2164. doi: 10.1021/acschembio.6b00187.
|
Structure of hiv-1 reverse transcriptase in complex
with a DNA aptamer and foscarnet, a pyrophosphate
analog . SNAP output
|
|
5hp4
|
hydrolase |
X-ray (1.86 Å) |
AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova
SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ |
(2016) "Direct
observation of DNA threading in flap endonuclease
complexes." Nat.Struct.Mol.Biol.,
23, 640-646. doi: 10.1038/nsmb.3241.
|
Crystal structure bacteriohage t5 d15 flap endonuclease
(d155k) pseudo-enzyme-product complex with DNA and
metal ions . SNAP
output
|
|
5hq2
|
transferase-DNA |
X-ray (4.5 Å) |
Girish TS, McGinty RK, Tan S |
(2016) "Multivalent
Interactions by the Set8 Histone Methyltransferase With
Its Nucleosome Substrate." J.Mol.Biol.,
428, 1531-1543. doi: 10.1016/j.jmb.2016.02.025.
|
Structural model of set8 histone h4 lys20
methyltransferase bound to nucleosome core particle .
SNAP output
|
|
5hr4
|
hydrolase-DNA |
X-ray (2.6 Å) |
Callahan SJ, Luyten YA, Gupta YK, Wilson GG, Roberts
RJ, Morgan RD, Aggarwal AK |
(2016) "Structure
of Type IIL Restriction-Modification Enzyme MmeI in
Complex with DNA Has Implications for Engineering New
Specificities." Plos Biol.,
14, e1002442. doi: 10.1371/journal.pbio.1002442.
|
Structure of type iil restriction-modification enzyme
mmei in complex with DNA has implications for
engineering of new specificities . SNAP output
|
|
5hr9
|
transferase-DNA |
X-ray (2.2 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of se-asfvpolx(l52-163m mutant)
in complex with 1nt-gap dna1 . SNAP output
|
|
5hrb
|
transferase-DNA |
X-ray (1.7 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx:dna1 binary complex .
SNAP output
|
|
5hrd
|
transferase-DNA |
X-ray (1.8 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx:dna2 binary complex .
SNAP output
|
|
5hre
|
transferase-DNA |
X-ray (1.75 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx:dna3 binary complex .
SNAP output
|
|
5hrf
|
transferase-DNA |
X-ray (2.25 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx: dna5: dgtp ternary
complex . SNAP
output
|
|
5hrg
|
transferase-DNA |
X-ray (2.0 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx(d51n mutant):dna4
binary complex . SNAP
output
|
|
5hrh
|
transferase-DNA |
X-ray (3.0 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx(h115f-r127a mutant):
1nt-gap(p) dna2:dgtp ternary complex . SNAP output
|
|
5hri
|
transferase-DNA |
X-ray (2.2 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of AsfvPolX: 1nt-gap(P) DNA1:
dGTP ternary complex." |
The crystal structure of asfvpolx:dna1 binary complex .
SNAP output
|
|
5hrk
|
transferase-DNA |
X-ray (2.9 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx(h115f mutant):
1nt-gap(p) dna2:dgtp ternary complex . SNAP output
|
|
5hrl
|
transferase-DNA |
X-ray (2.4 Å) |
Chen YQ, Zhang J, Gan JH |
"The crystal structure of Se-AsfvPolX(L52/163M
mutant) in complex with 1nt-gap DNA1." |
The crystal structure of asfvpolx: 1nt-gap(p) dna2:
dgtp ternary complex. . SNAP output
|
|
5hro
|
transferase-transferase inhibitor |
X-ray (2.75 Å) |
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano
JJ, Arnold E |
(2016) "Conformational
States of HIV-1 Reverse Transcriptase for Nucleotide
Incorporation vs Pyrophosphorolysis-Binding of
Foscarnet." Acs Chem.Biol.,
11, 2158-2164. doi: 10.1021/acschembio.6b00187.
|
Structure of hiv-1 reverse transcriptase in complex
with a DNA aptamer and an alpha-carboxy nucleoside
phosphonate inhibitor (alpha-cnp) . SNAP output
|
|
5hrt
|
hydrolase |
X-ray (1.997 Å) |
Kato K, Ikeda H, Miyakawa S, Futakawa S, Nonaka Y,
Fujiwara M, Okudaira S, Kano K, Aoki J, Morita J,
Ishitani R, Nishimasu H, Nakamura Y, Nureki O |
(2016) "Structural
basis for specific inhibition of Autotaxin by a DNA
aptamer." Nat.Struct.Mol.Biol.,
23, 395-401. doi: 10.1038/nsmb.3200.
|
Crystal structure of mouse autotaxin in complex with a
DNA aptamer . SNAP
output
|
|
5hru
|
oxidoreductase-DNA |
X-ray (1.71 Å) |
Choi SJ, Ban C |
(2016) "Crystal
structure of a DNA aptamer bound to PvLDH elucidates
novel single-stranded DNA structural elements for
folding and recognition." Sci Rep,
6, 34998. doi: 10.1038/srep34998.
|
Crystal structure of plasmodium vivax ldh in complex
with a DNA aptamer called pl1 . SNAP output
|
|
5hso
|
transcription |
X-ray (2.5 Å) |
Gao YR, Li DF, Fleming J, Zhou YF, Liu Y, Deng JY,
Zhou L, Zhou J, Zhu GF, Zhang XE, Wang DC, Bi LJ |
(2017) "Structural
analysis of the regulatory mechanism of MarR protein
Rv2887 in M. tuberculosis." Sci Rep,
7, 6471. doi: 10.1038/s41598-017-01705-4.
|
Crystal structure of mycobacterium tuberculosis marr
family protein rv2887 complex with DNA . SNAP output
|
|
5ht2
|
hydrolase-DNA |
X-ray (1.43 Å) |
Schellenberg MJ, Perera L, Strom CN, Waters CA,
Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA,
Williams RS |
(2016) "Reversal
of DNA damage induced Topoisomerase 2 DNA-protein
crosslinks by Tdp2." Nucleic Acids Res.,
44, 3829-3844. doi: 10.1093/nar/gkw228.
|
Mouse tdp2 reaction product (5'-phosphorylated
DNA)-mg2+ complex with 1-n6-etheno-adenine . SNAP output
|
|
5hto
|
oxidoreductase-DNA |
X-ray (1.9 Å) |
Choi SJ, Ban C |
(2016) "Crystal
structure of a DNA aptamer bound to PvLDH elucidates
novel single-stranded DNA structural elements for
folding and recognition." Sci Rep,
6, 34998. doi: 10.1038/srep34998.
|
Crystal structure of plasmodium vivax ldh in complex
with a DNA aptamer called pl1 (tetrameric ldh in an
asymmetric unit) . SNAP
output
|
|
5i2d
|
transcription-DNA-RNA |
X-ray (4.405 Å) |
Feng Y, Zhang Y, Ebright RH |
(2016) "Structural
basis of transcription activation."
Science, 352, 1330-1333. doi:
10.1126/science.aaf4417.
|
Crystal structure of t. thermophilus tthb099 class ii
transcription activation complex: tap-rpo . SNAP output
|
|
5i3u
|
transferase-DNA |
X-ray (3.0 Å) |
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano
JJ, Arnold E |
(2016) "Conformational
States of HIV-1 Reverse Transcriptase for Nucleotide
Incorporation vs Pyrophosphorolysis-Binding of
Foscarnet." Acs Chem.Biol.,
11, 2158-2164. doi: 10.1021/acschembio.6b00187.
|
Structure of hiv-1 reverse transcriptase n-site
complex; catalytic incorporation of aztmp to a DNA
aptamer in crystal . SNAP output
|
|
5i42
|
transferase-DNA |
X-ray (3.3 Å) |
Das K, Balzarini J, Miller MT, Maguire AR, DeStefano
JJ, Arnold E |
(2016) "Conformational
States of HIV-1 Reverse Transcriptase for Nucleotide
Incorporation vs Pyrophosphorolysis-Binding of
Foscarnet." Acs Chem.Biol.,
11, 2158-2164. doi: 10.1021/acschembio.6b00187.
|
Structure of hiv-1 reverse transcriptase in complex
with a DNA aptamer, azttp, and ca(2+) ion . SNAP output
|
|
5i44
|
DNA binding protein-DNA |
X-ray (2.621 Å) |
Schumacher MA, Lee J, Zeng W |
(2016) "Molecular
insights into DNA binding and anchoring by the Bacillus
subtilis sporulation kinetochore-like RacA
protein." Nucleic Acids Res.,
44, 5438-5449. doi: 10.1093/nar/gkw248.
|
Structure of raca-DNA complex; p21 form . SNAP output
|
|
5i4a
|
RNA binding protein-RNA |
X-ray (1.949 Å) |
Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC,
Kranzusch PJ, Doudna JA |
(2016) "A
bacterial Argonaute with noncanonical guide RNA
specificity." Proc.Natl.Acad.Sci.USA,
113, 4057-4062. doi: 10.1073/pnas.1524385113.
|
X-ray crystal structure of marinitoga piezophila
argonaute in complex with 5' oh guide RNA . SNAP output
|
|
5i50
|
transcription |
X-ray (2.701 Å) |
Jung LA, Gebhardt A, Koelmel W, Ade CP, Walz S, Kuper
J, von Eyss B, Letschert S, Redel C, d'Artista L, Biankin
A, Zender L, Sauer M, Wolf E, Evan G, Kisker C, Eilers
M |
(2017) "OmoMYC
blunts promoter invasion by oncogenic MYC to inhibit
gene expression characteristic of MYC-dependent
tumors." Oncogene, 36,
1911-1924. doi: 10.1038/onc.2016.354.
|
Structure of omomyc bound to double-stranded DNA .
SNAP output
|
|
5i9g
|
RNA binding protein-RNA |
X-ray (2.288 Å) |
Shen C, Zhang D, Guan Z, Liu Y, Yang Z, Yang Y, Wang
X, Wang Q, Zhang Q, Fan S, Zou T, Yin P |
(2016) "Structural
basis for specific single-stranded RNA recognition by
designer pentatricopeptide repeat proteins."
Nat Commun, 7, 11285. doi:
10.1038/ncomms11285.
|
Crystal structure of designed pentatricopeptide repeat
protein dppr-u8c2 in complex with its target RNA u8c2 .
SNAP output
|
|
5iff
|
hydrolase-DNA |
X-ray (1.9 Å) |
Wang D, Miyazono KI, Tanokura M |
(2016) "Tetrameric
structure of the restriction DNA glycosylase R.PabI in
complex with nonspecific double-stranded DNA."
Sci Rep, 6, 35197. doi:
10.1038/srep35197.
|
Crystal structure of r.pabi-nonspecific DNA complex .
SNAP output
|
|
5iii
|
transferase-DNA |
X-ray (1.8 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the pre-catalytic ternary complex
of DNA polymerase lambda with a templating 8-oxo-dg and
an incoming datp . SNAP
output
|
|
5iij
|
transferase-DNA |
X-ray (1.724 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the pre-catalytic ternary complex
of DNA polymerase lambda with a templating 8-oxo-dg and
an incoming dctp . SNAP
output
|
|
5iik
|
transferase-DNA |
X-ray (1.982 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the post-catalytic nick complex of
DNA polymerase lambda with a templating 8-oxo-dg and
incorporated dc . SNAP
output
|
|
5iil
|
transferase-DNA |
X-ray (1.96 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the post-catalytic nick complex of
DNA polymerase lambda with a templating 8-oxo-dg and
incorporated da . SNAP
output
|
|
5iim
|
transferase-DNA |
X-ray (1.941 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the pre-catalytic ternary
extension complex of DNA polymerase lambda with an
8-oxo-dg:da base-pair . SNAP output
|
|
5iin
|
transferase-DNA |
X-ray (2.15 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the pre-catalytic ternary
extension complex of DNA polymerase lambda with an
8-oxo-dg:dc base-pair . SNAP output
|
|
5iio
|
transferase-DNA |
X-ray (2.08 Å) |
Burak MJ, Guja KE, Hambardjieva E, Derkunt B,
Garcia-Diaz M |
(2016) "A
fidelity mechanism in DNA polymerase lambda promotes
error-free bypass of 8-oxo-dG." Embo J.,
35, 2045-2059. doi: 10.15252/embj.201694332.
|
Crystal structure of the DNA polymerase lambda binary
complex . SNAP
output
|
|
5ink
|
hydrolase-DNA |
X-ray (2.15 Å) |
Schellenberg MJ, Perera L, Strom CN, Waters CA,
Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA,
Williams RS |
(2016) "Reversal
of DNA damage induced Topoisomerase 2 DNA-protein
crosslinks by Tdp2." Nucleic Acids Res.,
44, 3829-3844. doi: 10.1093/nar/gkw228.
|
Mouse tdp2 reaction product (5'-phosphorylated
DNA)-abasic-thf-mg2+ complex . SNAP output
|
|
5inl
|
hydrolase-DNA |
X-ray (1.551 Å) |
Schellenberg MJ, Perera L, Strom CN, Waters CA,
Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA,
Williams RS |
(2016) "Reversal
of DNA damage induced Topoisomerase 2 DNA-protein
crosslinks by Tdp2." Nucleic Acids Res.,
44, 3829-3844. doi: 10.1093/nar/gkw228.
|
Mouse tdp2 reaction product (5'-phosphorylated
DNA)-mg2+ complex with deoxyadenosine . SNAP output
|
|
5ino
|
hydrolase-DNA |
X-ray (3.205 Å) |
Schellenberg MJ, Perera L, Strom CN, Waters CA,
Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA,
Williams RS |
(2016) "Reversal
of DNA damage induced Topoisomerase 2 DNA-protein
crosslinks by Tdp2." Nucleic Acids Res.,
44, 3829-3844. doi: 10.1093/nar/gkw228.
|
Human tdp2 reaction product (5'-phosphorylated
DNA)-mg2+ complex . SNAP
output
|
|
5inp
|
hydrolase-DNA |
X-ray (1.947 Å) |
Schellenberg MJ, Perera L, Strom CN, Waters CA,
Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA,
Williams RS |
(2016) "Reversal
of DNA damage induced Topoisomerase 2 DNA-protein
crosslinks by Tdp2." Nucleic Acids Res.,
44, 3829-3844. doi: 10.1093/nar/gkw228.
|
Mouse tdp2 reaction product (5'-phosphorylated
DNA)-mn2+ complex . SNAP
output
|
|
5inq
|
hydrolase-DNA |
X-ray (1.848 Å) |
Schellenberg MJ, Perera L, Strom CN, Waters CA,
Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA,
Williams RS |
(2016) "Reversal
of DNA damage induced Topoisomerase 2 DNA-protein
crosslinks by Tdp2." Nucleic Acids Res.,
44, 3829-3844. doi: 10.1093/nar/gkw228.
|
Mouse tdp2 reaction product (5'-phosphorylated
DNA)-ca2+ complex . SNAP
output
|
|
5ip3
|
viral protein-DNA |
X-ray (3.0 Å) |
Komoda K, Narita M, Yamashita K, Tanaka I, Yao M |
(2017) "Asymmetric
Trimeric Ring Structure of the Nucleocapsid Protein of
Tospovirus." J. Virol.,
91. doi: 10.1128/JVI.01002-17.
|
Tomato spotted wilt tospovirus nucleocapsid
protein-ssDNA complex . SNAP output
|
|
5ipl
|
transcription, transferase-DNA-RNA |
X-ray (3.6 Å) |
Liu B, Zuo Y, Steitz TA |
(2016) "Structures
of E. coli sigma S-transcription initiation complexes
provide new insights into polymerase mechanism."
Proc.Natl.Acad.Sci.USA, 113,
4051-4056. doi: 10.1073/pnas.1520555113.
|
Sigmas-transcription initiation complex with 4-nt
nascent RNA . SNAP
output
|
|
5ipm
|
transcription, transferase-DNA-RNA |
X-ray (4.2 Å) |
Liu B, Zuo Y, Steitz TA |
(2016) "Structures
of E. coli sigma S-transcription initiation complexes
provide new insights into polymerase mechanism."
Proc.Natl.Acad.Sci.USA, 113,
4051-4056. doi: 10.1073/pnas.1520555113.
|
Sigmas-transcription initiation complex with 4-nt
nascent RNA . SNAP
output
|
|
5ipn
|
transcription, transferase-DNA-RNA |
X-ray (4.61 Å) |
Liu B, Zuo Y, Steitz TA |
(2016) "Structures
of E. coli sigma S-transcription initiation complexes
provide new insights into polymerase mechanism."
Proc.Natl.Acad.Sci.USA, 113,
4051-4056. doi: 10.1073/pnas.1520555113.
|
Sigmas-transcription initiation complex with 4-nt
nascent RNA . SNAP
output
|
|
5it7
|
ribosome |
cryo-EM (3.6 Å) |
Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan
V, Fernandez IS |
(2016) "Structural
characterization of ribosome recruitment and
translocation by type IV IRES." Elife,
5. doi: 10.7554/eLife.13567.
|
Structure of the kluyveromyces lactis 80s ribosome in
complex with the cricket paralysis virus ires and eef2
. SNAP output
|
|
5it9
|
ribosome |
cryo-EM (3.8 Å) |
Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan
V, Fernandez IS |
(2016) "Structural
characterization of ribosome recruitment and
translocation by type IV IRES." Elife,
5. doi: 10.7554/eLife.13567.
|
Structure of the yeast kluyveromyces lactis small
ribosomal subunit in complex with the cricket paralysis
virus ires. . SNAP
output
|
|
5ith
|
RNA binding protein-DNA |
X-ray (2.31 Å) |
Waris S, Garcia-Maurino SM, Sivakumaran A, Beckham
SA, Loughlin FE, Gorospe M, Diaz-Moreno I, Wilce MCJ,
Wilce JA |
(2017) "TIA-1
RRM23 binding and recognition of target
oligonucleotides." Nucleic Acids Res.,
45, 4944-4957. doi: 10.1093/nar/gkx102.
|
Tia-1 rrm2 recognition of target oligonucleotide .
SNAP output
|
|
5itr
|
DNA binding protein-DNA |
X-ray (2.46 Å) |
Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M,
Stovicek O, Gao YQ, Yi C |
(2016) "Tautomerization-dependent
recognition and excision of oxidation damage in
base-excision DNA repair."
Proc.Natl.Acad.Sci.USA, 113,
7792-7797. doi: 10.1073/pnas.1604591113.
|
Crystal structure of human neil1(p2g) bound to duplex
DNA containing thf . SNAP output
|
|
5itt
|
DNA binding protein-DNA |
X-ray (2.53 Å) |
Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M,
Stovicek O, Gao YQ, Yi C |
(2016) "Tautomerization-dependent
recognition and excision of oxidation damage in
base-excision DNA repair."
Proc.Natl.Acad.Sci.USA, 113,
7792-7797. doi: 10.1073/pnas.1604591113.
|
Crystal structure of human neil1 bound to duplex DNA
containing thf . SNAP
output
|
|
5itu
|
DNA binding protein-DNA |
X-ray (2.41 Å) |
Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M,
Stovicek O, Gao YQ, Yi C |
(2016) "Tautomerization-dependent
recognition and excision of oxidation damage in
base-excision DNA repair."
Proc.Natl.Acad.Sci.USA, 113,
7792-7797. doi: 10.1073/pnas.1604591113.
|
Crystal structure of human neil1(242k) bound to duplex
DNA containing thf . SNAP output
|
|
5itx
|
DNA binding protein-DNA |
X-ray (2.65 Å) |
Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M,
Stovicek O, Gao YQ, Yi C |
(2016) "Tautomerization-dependent
recognition and excision of oxidation damage in
base-excision DNA repair."
Proc.Natl.Acad.Sci.USA, 113,
7792-7797. doi: 10.1073/pnas.1604591113.
|
Crystal structure of human neil1(p2g r242k) bound to
duplex DNA containing thymine glycol . SNAP output
|
|
5ity
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Zhu C, Lu L, Zhang J, Yue Z, Song J, Zong S, Liu M,
Stovicek O, Gao YQ, Yi C |
(2016) "Tautomerization-dependent
recognition and excision of oxidation damage in
base-excision DNA repair."
Proc.Natl.Acad.Sci.USA, 113,
7792-7797. doi: 10.1073/pnas.1604591113.
|
Crystal structure of human neil1(p2g) bound to duplex
DNA containing thymine glycol . SNAP output
|
|
5iud
|
transferase-DNA |
X-ray (3.3 Å) |
Coloma J, Johnson RE, Prakash L, Prakash S, Aggarwal
AK |
(2016) "Human
DNA polymerase alpha in binary complex with a DNA:DNA
template-primer." Sci Rep,
6, 23784. doi: 10.1038/srep23784.
|
Human DNA polymerase alpha in binary complex with a
DNA:DNA template-primer . SNAP output
|
|
5ivw
|
transcription-DNA |
cryo-EM (10.0 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human core tfiih bound to DNA within the pic . SNAP output
|
|
5iwi
|
isomerase |
X-ray (1.98 Å) |
Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS,
Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken
JM, Giordano I, Hoover JL, Jones GE, Kusalakumari Sukmar
SK, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN,
Pearson ND |
(2016) "Novel
tricyclics (e.g., GSK945237) as potent inhibitors of
bacterial type IIA topoisomerases."
Bioorg.Med.Chem.Lett., 26,
2464-2469. doi: 10.1016/j.bmcl.2016.03.106.
|
1.98a structure of gsk945237 with s.aureus DNA gyrase
and singly nicked DNA . SNAP output
|
|
5iwm
|
isomerase |
X-ray (2.5 Å) |
Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS,
Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken
JM, Giordano I, Hoover JL, Jones GE, Kusalakumari Sukmar
SK, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN,
Pearson ND |
(2016) "Novel
tricyclics (e.g., GSK945237) as potent inhibitors of
bacterial type IIA topoisomerases."
Bioorg.Med.Chem.Lett., 26,
2464-2469. doi: 10.1016/j.bmcl.2016.03.106.
|
2.5a structure of gsk945237 with s.aureus DNA gyrase
and DNA. . SNAP
output
|
|
5iy6
|
transcription, transferase-DNA |
cryo-EM (7.2 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human holo-pic in the closed state . SNAP output
|
|
5iy7
|
transcription, transferase-DNA |
cryo-EM (8.6 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human holo-pic in the open state . SNAP output
|
|
5iy8
|
transcription, transferase-DNA |
cryo-EM (7.9 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human holo-pic in the initial transcribing state .
SNAP output
|
|
5iy9
|
transcription, transferase-DNA-RNA |
cryo-EM (6.3 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human holo-pic in the initial transcribing state (no
iis) . SNAP output
|
|
5iya
|
transcription, transferase-DNA |
cryo-EM (5.4 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human core-pic in the closed state . SNAP output
|
|
5iyb
|
transcription, transferase-DNA |
cryo-EM (3.9 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human core-pic in the open state . SNAP output
|
|
5iyc
|
transcription, transferase-DNA |
cryo-EM (3.9 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human core-pic in the initial transcribing state .
SNAP output
|
|
5iyd
|
transcription, transferase-DNA-RNA |
cryo-EM (3.9 Å) |
He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I,
Nogales E |
(2016) "Near-atomic
resolution visualization of human transcription
promoter opening." Nature,
533, 359-365. doi: 10.1038/nature17970.
|
Human core-pic in the initial transcribing state (no
iis) . SNAP output
|
|
5j0n
|
transferase, hydrolase-DNA |
cryo-EM (11.0 Å) |
Laxmikanthan G, Xu C, Brilot AF, Warren D, Steele L,
Seah N, Tong W, Grigorieff N, Landy A, Van Duyne GD |
(2016) "Structure
of a Holliday junction complex reveals mechanisms
governing a highly regulated DNA transaction."
Elife, 5. doi: 10.7554/eLife.14313.
|
Lambda excision hj intermediate . SNAP output
|
|
5j0o
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with a:a mismatch at the primer terminus . SNAP output
|
|
5j0p
|
transferase-DNA |
X-ray (2.2 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with a:c mismatch at the primer terminus . SNAP output
|
|
5j0q
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with a:g mismatch at the primer terminus . SNAP output
|
|
5j0r
|
transferase-DNA |
X-ray (2.001 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with c:a mismatch at the primer terminus . SNAP output
|
|
5j0s
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with c:t mismatch at the primer terminus . SNAP output
|
|
5j0t
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with g:a mismatch at the primer terminus . SNAP output
|
|
5j0u
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with g:g mismatch at the primer terminus . SNAP output
|
|
5j0w
|
transferase-DNA |
X-ray (2.4 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with t:c mismatch at the primer terminus . SNAP output
|
|
5j0x
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with t:g mismatch at the primer terminus . SNAP output
|
|
5j0y
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with t:t mismatch at the primer terminus . SNAP output
|
|
5j29
|
transferase-DNA |
X-ray (2.2 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with a:a mismatch at the primer terminus .
SNAP output
|
|
5j2a
|
transferase-DNA |
X-ray (2.5 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with a:c mismatch at the primer terminus .
SNAP output
|
|
5j2b
|
transferase-DNA |
X-ray (2.5 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with a:c mismatch at the primer terminus .
SNAP output
|
|
5j2c
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with c:a mismatch at the primer terminus .
SNAP output
|
|
5j2d
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with c:c mismatch at the primer terminus .
SNAP output
|
|
5j2e
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with c:t mismatch at the primer terminus .
SNAP output
|
|
5j2f
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with g:a mismatch at the primer terminus .
SNAP output
|
|
5j2g
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with g:g mismatch at the primer terminus .
SNAP output
|
|
5j2h
|
transferase-DNA |
X-ray (2.3 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with g:t mismatch at the primer terminus .
SNAP output
|
|
5j2i
|
transferase-DNA |
X-ray (2.4 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with t:c mismatch at the primer terminus .
SNAP output
|
|
5j2j
|
transferase-DNA |
X-ray (2.2 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with t:g mismatch at the primer terminus .
SNAP output
|
|
5j2k
|
transferase-DNA |
X-ray (2.1 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Ternary complex crystal structure of DNA polymerase
beta with t:t mismatch at the primer terminus .
SNAP output
|
|
5j2m
|
transferase-DNA |
X-ray (2.432 Å) |
Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh
K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos
SG |
(2016) "Structural
basis of HIV inhibition by translocation-defective RT
inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine
(EFdA)." Proc.Natl.Acad.Sci.USA,
113, 9274-9279. doi: 10.1073/pnas.1605223113.
|
Hiv-1 reverse transcriptase in complex with DNA and
efda-triphosphate, a translocation-defective rt
inhibitor . SNAP
output
|
|
5j2n
|
transferase-DNA |
X-ray (2.896 Å) |
Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh
K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos
SG |
(2016) "Structural
basis of HIV inhibition by translocation-defective RT
inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine
(EFdA)." Proc.Natl.Acad.Sci.USA,
113, 9274-9279. doi: 10.1073/pnas.1605223113.
|
Hiv-1 reverse transcriptase in complex with DNA that
has incorporated efda-mp at the p-(post-translocation)
site and dtmp at the n-(pre-translocation) site .
SNAP output
|
|
5j2p
|
transferase-DNA |
X-ray (2.53 Å) |
Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh
K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos
SG |
(2016) "Structural
basis of HIV inhibition by translocation-defective RT
inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine
(EFdA)." Proc.Natl.Acad.Sci.USA,
113, 9274-9279. doi: 10.1073/pnas.1605223113.
|
Hiv-1 reverse transcriptase in complex with DNA that
has incorporated efda-mp at the p-(post-translocation)
site and a second efda-mp at the n-(pre-translocation)
site . SNAP output
|
|
5j2q
|
transferase-DNA |
X-ray (2.789 Å) |
Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh
K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA, Sarafianos
SG |
(2016) "Structural
basis of HIV inhibition by translocation-defective RT
inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine
(EFdA)." Proc.Natl.Acad.Sci.USA,
113, 9274-9279. doi: 10.1073/pnas.1605223113.
|
Hiv-1 reverse transcriptase in complex with DNA that
has incorporated a mismatched efda-mp at the
n-(pre-translocation) site . SNAP output
|
|
5j2y
|
gene regulation-DNA |
X-ray (2.4 Å) |
Kang H, Gan J, Zhao J, Kong W, Zhang J, Zhu M, Li F,
Song Y, Qin J, Liang H |
(2017) "Crystal
structure of Pseudomonas aeruginosa RsaL bound to
promoter DNA reaffirms its role as a global regulator
involved in quorum-sensing." Nucleic Acids
Res., 45, 699-710. doi: 10.1093/nar/gkw954.
|
Molecular insight into the regulatory mechanism of the
quorum-sensing repressor rsal in pseudomonas aeruginosa
. SNAP output
|
|
5j37
|
virus-DNA |
X-ray (2.3 Å) |
Sarker S, Terron MC, Khandokar Y, Aragao D, Hardy JM,
Radjainia M, Jimenez-Zaragoza M, de Pablo PJ, Coulibaly
F, Luque D, Raidal SR, Forwood JK |
(2016) "Structural
insights into the assembly and regulation of distinct
viral capsid complexes." Nat Commun,
7, 13014. doi: 10.1038/ncomms13014.
|
Crystal structure of 60-mer bfdv capsid protein in
complex with single stranded DNA . SNAP output
|
|
5j3e
|
nuclear protein-DNA |
X-ray (2.6 Å) |
Halabelian L, Tempel W, Li Y, Bountra C, Edwards AM,
Arrowsmith CH |
"Crystal Structure of Human THYN1 protein in complex
with 5-methylcytosine containing DNA." |
Crystal structure of human thyn1 protein in complex
with 5-methylcytosine containing DNA . SNAP output
|
|
5j5p
|
isomerase-DNA |
X-ray (1.97 Å) |
Laponogov I, Pan XS, Veselkov DA, Skamrova GB,
Umrekar TR, Fisher LM, Sanderson MR |
(2018) "Trapping
of the transport-segment DNA by the ATPase domains of a
type II topoisomerase." Nat Commun,
9, 2579. doi: 10.1038/s41467-018-05005-x.
|
Amp-pnp-stabilized atpase domain of topoisomerase iv
from streptococcus pneumoniae, complex type i .
SNAP output
|
|
5j5q
|
isomerase-DNA |
X-ray (2.83 Å) |
Laponogov I, Pan XS, Veselkov DA, Skamrova GB,
Umrekar TR, Fisher LM, Sanderson MR |
(2018) "Trapping
of the transport-segment DNA by the ATPase domains of a
type II topoisomerase." Nat Commun,
9, 2579. doi: 10.1038/s41467-018-05005-x.
|
Amp-pnp-stabilized atpase domain of topoisomerase iv
from streptococcus pneumoniae, complex type ii .
SNAP output
|
|
5j70
|
chromatin-binding protein-DNA |
X-ray (2.956 Å) |
Nodelman IM, Jenkins KR, Ren R, Horvath KC, Hauk G,
Bowman GD |
"Chd1 domains communicate across the DNA gyres of the
nucleosome." |
The chd1 DNA-binding domain in complex with 17mer DNA
duplex . SNAP output
|
|
5jgh
|
DNA binding protein |
X-ray (2.6 Å) |
Chakraborty A, Lyonnais S, Battistini F, Hospital A,
Medici G, Prohens R, Orozco M, Vilardell J, Sola M |
(2017) "DNA
structure directs positioning of the mitochondrial
genome packaging protein Abf2p." Nucleic Acids
Res., 45, 951-967. doi: 10.1093/nar/gkw1147.
|
Crystal structure of the mitochondrial DNA packaging
protein abf2p in complex with DNA at 2.6 angstrom
resolution . SNAP
output
|
|
5jh0
|
DNA binding protein |
X-ray (2.18 Å) |
Chakraborty A, Lyonnais S, Battistini F, Hospital A,
Medici G, Prohens R, Orozco M, Vilardell J, Sola M |
(2017) "DNA
structure directs positioning of the mitochondrial
genome packaging protein Abf2p." Nucleic Acids
Res., 45, 951-967. doi: 10.1093/nar/gkw1147.
|
Crystal structure of the mitochondrial DNA packaging
protein abf2p in complex with DNA at 2.18 angstrom
resolution . SNAP
output
|
|
5jjv
|
recombination |
X-ray (2.4 Å) |
Bebel A, Karaca E, Kumar B, Stark WM, Barabas O |
(2016) "Structural
snapshots of Xer recombination reveal activation by
synaptic complex remodeling and DNA bending."
Elife, 5. doi: 10.7554/eLife.19706.
|
Crystal structure of xerh site-specific recombinase
bound to palindromic difh substrate: post-cleavage
complex . SNAP
output
|
|
5jk0
|
cell cycle |
X-ray (2.1 Å) |
Bebel A, Karaca E, Kumar B, Stark WM, Barabas O |
(2016) "Structural
snapshots of Xer recombination reveal activation by
synaptic complex remodeling and DNA bending."
Elife, 5. doi: 10.7554/eLife.19706.
|
Crystal structure of xerh site-specific recombinase
bound to difh substrate: pre-cleavage complex .
SNAP output
|
|
5jlt
|
viral protein-DNA |
X-ray (2.955 Å) |
Cuypers MG, Robertson RM, Knipling L, Waddell MB,
Moon K, Hinton DM, White SW |
(2018) "The
phage T4 MotA transcription factor contains a novel DNA
binding motif that specifically recognizes modified
DNA." Nucleic Acids Res.,
46, 5308-5318. doi: 10.1093/nar/gky292.
|
The crystal structure of the bacteriophage t4 mota
c-terminal domain in complex with dsDNA reveals a novel
protein-DNA recognition motif . SNAP output
|
|
5jlw
|
transcription regulator-DNA |
X-ray (2.088 Å) |
Nguyen D, Zandarashvili L, White MA, Iwahara J |
(2016) "Stereospecific
Effects of Oxygen-to-Sulfur Substitution in DNA
Phosphate on Ion Pair Dynamics and Protein-DNA
Affinity." Chembiochem,
17, 1636-1642. doi: 10.1002/cbic.201600265.
|
Antphd with 15bp DNA duplex r-monothioated at
cytidine-8 . SNAP
output
|
|
5jlx
|
transcription regulator-DNA |
X-ray (2.748 Å) |
Nguyen D, Zandarashvili L, White MA, Iwahara J |
(2016) "Stereospecific
Effects of Oxygen-to-Sulfur Substitution in DNA
Phosphate on Ion Pair Dynamics and Protein-DNA
Affinity." Chembiochem,
17, 1636-1642. doi: 10.1002/cbic.201600265.
|
Antphd with 15bp DNA duplex s-monothioated at
cytidine-8 . SNAP
output
|
|
5jre
|
DNA binding protein |
X-ray (2.1 Å) |
Zhang J, Liu H, Yao Q, Yu X, Chen Y, Cui R, Wu B,
Zheng L, Zuo J, Huang Z, Ma J, Gan J |
(2016) "Structural
basis for single-stranded RNA recognition and cleavage
by C3PO." Nucleic Acids Res.,
44, 9494-9504. doi: 10.1093/nar/gkw776.
|
Crystal structure of nec3po in complex with ssDNA. .
SNAP output
|
|
5jrg
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Osakabe A, Arimura Y, Matsumoto S, Horikoshi N,
Sugasawa K, Kurumizaka H |
(2017) "Polymorphism
of apyrimidinic DNA structures in the nucleosome."
Sci Rep, 7, 41783. doi:
10.1038/srep41783.
|
Crystal structure of the nucleosome containing the DNA
with tetrahydrofuran (thf) . SNAP output
|
|
5jub
|
transcription |
X-ray (2.57 Å) |
Talagas A, Fontaine L, Ledesma-Garca L, Mignolet J,
Li de la Sierra-Gallay I, Lazar N, Aumont-Nicaise M,
Federle MJ, Prehna G, Hols P, Nessler S |
(2016) "Structural
Insights into Streptococcal Competence Regulation by
the Cell-to-Cell Communication System ComRS."
PLoS Pathog., 12, e1005980.
doi: 10.1371/journal.ppat.1005980.
|
Crystal structure of comr from s.thermophilus in
complex with DNA and its signalling peptide coms. .
SNAP output
|
|
5jum
|
transferase-DNA |
X-ray (2.6 Å) |
Patra A, Politica DA, Chatterjee A, Tokarsky EJ, Suo
Z, Basu AK, Stone MP, Egli M |
(2016) "Mechanism
of Error-Free Bypass of the Environmental Carcinogen
N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone Adduct by
Human DNA Polymerase eta." Chembiochem,
17, 2033-2037. doi: 10.1002/cbic.201600420.
|
Crystal structure of human DNA polymerase eta inserting
dctp opposite n-(2'-deoxyguanosin-8-
yl)-3-aminobenzanthrone (c8-dg-aba) . SNAP output
|
|
5juo
|
ribosome |
cryo-EM (4.0 Å) |
Abeyrathne PD, Koh CS, Grant T, Grigorieff N,
Korostelev AA |
(2016) "Ensemble
cryo-EM uncovers inchworm-like translocation of a viral
IRES through the ribosome." Elife,
5. doi: 10.7554/eLife.14874.
|
Saccharomyces cerevisiae 80s ribosome bound with
elongation factor eef2-gdp-sordarin and taura syndrome
virus ires, structure i (fully rotated 40s subunit) .
SNAP output
|
|
5jup
|
ribosome |
cryo-EM (3.5 Å) |
Abeyrathne PD, Koh CS, Grant T, Grigorieff N,
Korostelev AA |
(2016) "Ensemble
cryo-EM uncovers inchworm-like translocation of a viral
IRES through the ribosome." Elife,
5. doi: 10.7554/eLife.14874.
|
Saccharomyces cerevisiae 80s ribosome bound with
elongation factor eef2-gdp-sordarin and taura syndrome
virus ires, structure ii (mid-rotated 40s subunit) .
SNAP output
|
|
5jus
|
ribosome |
cryo-EM (4.2 Å) |
Abeyrathne PD, Koh CS, Grant T, Grigorieff N,
Korostelev AA |
(2016) "Ensemble
cryo-EM uncovers inchworm-like translocation of a viral
IRES through the ribosome." Elife,
5. doi: 10.7554/eLife.14874.
|
Saccharomyces cerevisiae 80s ribosome bound with
elongation factor eef2-gdp-sordarin and taura syndrome
virus ires, structure iii (mid-rotated 40s subunit) .
SNAP output
|
|
5jut
|
ribosome |
cryo-EM (4.0 Å) |
Abeyrathne PD, Koh CS, Grant T, Grigorieff N,
Korostelev AA |
(2016) "Ensemble
cryo-EM uncovers inchworm-like translocation of a viral
IRES through the ribosome." Elife,
5. doi: 10.7554/eLife.14874.
|
Saccharomyces cerevisiae 80s ribosome bound with
elongation factor eef2-gdp-sordarin and taura syndrome
virus ires, structure iv (almost non-rotated 40s
subunit) . SNAP
output
|
|
5juu
|
ribosome |
cryo-EM (4.0 Å) |
Abeyrathne PD, Koh CS, Grant T, Grigorieff N,
Korostelev AA |
(2016) "Ensemble
cryo-EM uncovers inchworm-like translocation of a viral
IRES through the ribosome." Elife,
5. doi: 10.7554/eLife.14874.
|
Saccharomyces cerevisiae 80s ribosome bound with
elongation factor eef2-gdp-sordarin and taura syndrome
virus ires, structure v (least rotated 40s subunit) .
SNAP output
|
|
5jvt
|
transcription-DNA |
X-ray (3.1 Å) |
Hou C, Weidenbach S, Cano KE, Wang Z, Mitra P, Ivanov
DN, Rohr J, Tsodikov OV |
(2016) "Structures
of mithramycin analogues bound to DNA and implications
for targeting transcription factor FLI1."
Nucleic Acids Res., 44,
8990-9004. doi: 10.1093/nar/gkw761.
|
Crystal structure of the DNA binding domain of
transcription factor fli1 in complex with an 11-mer DNA
gaccggaagtg . SNAP
output
|
|
5jxy
|
hydrolase-DNA |
X-ray (1.71 Å) |
Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E,
Drohat AC |
(2016) "Structural
basis of damage recognition by thymine DNA glycosylase:
Key roles for N-terminal residues." Nucleic
Acids Res., 44, 10248-10258. doi:
10.1093/nar/gkw768.
|
Enzyme-substrate complex of tdg catalytic domain bound
to a g-u analog . SNAP
output
|
|
5k07
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Tian L, Zhang ZF, Wang H, Zhao M, Dong Y, Gong Y |
(2016) "Sequence-Dependent
T:G Base Pair Opening in DNA Double Helix Bound by
Cren7, a Chromatin Protein Conserved among
Crenarchaea." PLoS ONE,
11, e0163361. doi: 10.1371/journal.pone.0163361.
|
Crystal structure of cren7-dsDNA (gtaattgc) complex .
SNAP output
|
|
5k17
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Tian L, Zhang ZF, Wang H, Zhao M, Dong Y, Gong Y |
(2016) "Sequence-Dependent
T:G Base Pair Opening in DNA Double Helix Bound by
Cren7, a Chromatin Protein Conserved among
Crenarchaea." PLoS ONE,
11, e0163361. doi: 10.1371/journal.pone.0163361.
|
Crystal structure of cren7-dsDNA (gtgatcgc) complex .
SNAP output
|
|
5k1y
|
transcription-DNA |
X-ray (2.97 Å) |
Schumacher M |
"Detailed structural analysis of AspA-DNA
contacts." |
P2(1) structure of pnob8 aspa-DNA complex . SNAP output
|
|
5k58
|
DNA binding protein-DNA |
X-ray (2.772 Å) |
Schumacher MA, Zeng W |
(2016) "Structures
of the nucleoid occlusion protein SlmA bound to DNA and
the C-terminal domain of the cytoskeletal protein
FtsZ." Proc. Natl. Acad. Sci. U.S.A.,
113, 4988-4993. doi: 10.1073/pnas.1602327113.
|
Structure of the k. pneumonia slma-DNA complex bound to
the c-terminal of the cell division protein ftsz .
SNAP output
|
|
5k5h
|
transcription-DNA |
X-ray (3.108 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Homo sapiens ccctc-binding factor (ctcf) znf4-7 and DNA
complex structure . SNAP
output
|
|
5k5i
|
transcription-DNA |
X-ray (2.19 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Homo sapiens ccctc-binding factor (ctcf) znf5-8 and DNA
complex structure in space group p65 . SNAP output
|
|
5k5j
|
transcription-DNA |
X-ray (2.287 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Homo sapiens ccctc-binding factor (ctcf) znf5-8 and DNA
complex structure in space group p41212 . SNAP output
|
|
5k5l
|
transcription-DNA |
X-ray (3.125 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Homo sapiens ccctc-binding factor (ctcf) znf6-8 and h19
sequence DNA complex structure . SNAP output
|
|
5k5o
|
transcription-DNA |
X-ray (3.2 Å) |
Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda
FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT,
Shaw PL, Barilla D |
(2015) "Structures
of archaeal DNA segregation machinery reveal bacterial
and eukaryotic linkages." Science,
349, 1120-1124. doi: 10.1126/science.aaa9046.
|
Structure of aspa-26mer DNA complex . SNAP output
|
|
5k5q
|
transcription-DNA |
X-ray (2.649 Å) |
Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda
FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT,
Shaw PL, Barilla D |
(2015) "Structures
of archaeal DNA segregation machinery reveal bacterial
and eukaryotic linkages." Science,
349, 1120-1124. doi: 10.1126/science.aaa9046.
|
Structure of aspa-DNA complex: novel centromere bindng
protein-centromere complex . SNAP output
|
|
5k5r
|
transcription-DNA |
X-ray (3.09 Å) |
Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castaneda
FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT,
Shaw PL, Barilla D |
(2015) "Structures
of archaeal DNA segregation machinery reveal bacterial
and eukaryotic linkages." Science,
349, 1120-1124. doi: 10.1126/science.aaa9046.
|
Aspa-32mer DNA,crystal form 2 . SNAP output
|
|
5k77
|
hydrolase-RNA |
X-ray (2.17 Å) |
Clark NE, Katolik A, Roberts KM, Taylor AB, Holloway
SP, Schuermann JP, Montemayor EJ, Stevens SW, Fitzpatrick
PF, Damha MJ, Hart PJ |
(2016) "Metal
dependence and branched RNA cocrystal structures of the
RNA lariat debranching enzyme Dbr1." Proc.
Natl. Acad. Sci. U.S.A., 113,
14727-14732. doi: 10.1073/pnas.1612729114.
|
Dbr1 in complex with 7-mer branched RNA . SNAP output
|
|
5k78
|
hydrolase-RNA |
X-ray (2.64 Å) |
Clark NE, Katolik A, Roberts K, Taylor AB, Holloway
SP, Schuermann JP, Montemayor EJ, Stevens SW, Fitzpatrick
PF, Damha MJ, Hart PJ |
(2016) "The RNA lariat debranching enzyme Dbr1: metal
dependence and branched RNA co-crystal structures."
Proc.Natl.Acad.Sci.USA. doi: 10.1073/pnas.1612729114.
|
Dbr1 in complex with 16-mer branched RNA . SNAP output
|
|
5k7z
|
transcription |
X-ray (2.92 Å) |
Bock T, Volz C, Mueller R, Blankenfeldt W |
"Crystal structure of AibR in complex with isovaleryl
coenzyme A and operator DNA." |
Crystal structure of aibr in complex with isovaleryl
coenzyme a and operator DNA . SNAP output
|
|
5k83
|
hydrolase |
X-ray (2.39 Å) |
Xiao X, Li SX, Yang H, Chen XS |
(2016) "Crystal
structures of APOBEC3G N-domain alone and its complex
with DNA." Nat Commun, 7,
12193. doi: 10.1038/ncomms12193.
|
Crystal structure of a primate apobec3g n-domain, in
complex with ssDNA . SNAP output
|
|
5k97
|
hydrolase-DNA |
X-ray (2.102 Å) |
Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw
SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham
VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM,
Grasby JA, Tainer JA |
(2017) "Phosphate
steering by Flap Endonuclease 1 promotes 5'-flap
specificity and incision to prevent genome
instability." Nat Commun,
8, 15855. doi: 10.1038/ncomms15855.
|
Flap endonuclease 1 (fen1) d233n with cleaved product
fragment and sm3+ . SNAP
output
|
|
5k98
|
transcription-DNA |
X-ray (3.99 Å) |
Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S,
Vulic M, Lewis K, Brennan RG |
(2015) "HipBA-promoter
structures reveal the basis of heritable multidrug
tolerance." Nature, 524,
59-64. doi: 10.1038/nature14662.
|
Structure of hipa-hipb-o2-o3 complex . SNAP output
|
|
5kbd
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Nguyen HT, Huang D |
"Structural Studies of Transcription Factor p73 DNA
Binding Domain Bound to PA26 20-mer Response
Element." |
Structural studies of transcription factor p73 DNA
binding domain bound to pa26 20-mer response element .
SNAP output
|
|
5kbj
|
transcription-DNA |
X-ray (3.09 Å) |
Schumacher MA, Tonthat NK, Kwong SM, Chinnam NB, Liu
MA, Skurray RA, Firth N |
(2014) "Mechanism
of staphylococcal multiresistance plasmid replication
origin assembly by the RepA protein." Proc.
Natl. Acad. Sci. U.S.A., 111,
9121-9126. doi: 10.1073/pnas.1406065111.
|
Structure of rep-DNA complex . SNAP output
|
|
5ke6
|
transcription-DNA |
X-ray (1.99 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 znf1-3 and tpg-cpa sequence DNA complex
structure . SNAP
output
|
|
5ke7
|
transcription-DNA |
X-ray (2.06 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 znf1-3 and tpg-mpa sequence DNA complex
structure . SNAP
output
|
|
5ke8
|
transcription-DNA |
X-ray (2.45 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 e446p znf1-3 and mpg-mpg sequence DNA
complex structure . SNAP
output
|
|
5ke9
|
transcription factor-DNA |
X-ray (2.336 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 e446p znf1-3 and tpg-cpa sequence DNA
complex structure . SNAP
output
|
|
5kea
|
transcription factor-DNA |
X-ray (2.458 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 znf1-3 (e446d) and cpg-cpg sequence DNA
complex structure: form i . SNAP output
|
|
5keb
|
transcription factor-DNA |
X-ray (2.453 Å) |
Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM,
Zhang X, Cheng X |
(2016) "Distinctive
Klf4 mutants determine preference for DNA methylation
status." Nucleic Acids Res.,
44, 10177-10185. doi: 10.1093/nar/gkw774.
|
Mouse klf4 znf1-3 (e446d) and cpg-cpg sequence DNA
complex structure: form ii . SNAP output
|
|
5keg
|
hydrolase-DNA |
X-ray (2.2 Å) |
Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn
MF, Kelch BA, Royer WE, Somasundaran M, Kurt Yilmaz N,
Matsuo H, Schiffer CA |
(2017) "Crystal
structure of APOBEC3A bound to single-stranded DNA
reveals structural basis for cytidine deamination and
specificity." Nat Commun,
8, 15024. doi: 10.1038/ncomms15024.
|
Crystal structure of apobec3a in complex with a
single-stranded DNA . SNAP output
|
|
5kfa
|
replication, transferase-DNA |
X-ray (1.51 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: ground
state at ph7.0 (k+ mes) with 1 ca2+ ion . SNAP output
|
|
5kfb
|
replication, transferase-DNA |
X-ray (1.55 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 1 mm mn2+ for 90s . SNAP output
|
|
5kfc
|
replication, transferase-DNA |
X-ray (1.5 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 1 mm mn2+ for 180s . SNAP output
|
|
5kfd
|
replication, transferase-DNA |
X-ray (1.65 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 1 mm mn2+ for 300s . SNAP output
|
|
5kfe
|
replication, transferase-DNA |
X-ray (1.55 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 1 mm mn2+ for 600s . SNAP output
|
|
5kff
|
replication, transferase-DNA |
X-ray (1.7 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 1 mm mn2+ for 1800s . SNAP output
|
|
5kfg
|
replication, transferase-DNA |
X-ray (1.55 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 30s . SNAP output
|
|
5kfh
|
replication, transferase-DNA |
X-ray (1.72 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 90s . SNAP output
|
|
5kfi
|
replication, transferase-DNA |
X-ray (1.65 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 120s . SNAP output
|
|
5kfj
|
replication, transferase-DNA |
X-ray (1.7 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 180s . SNAP output
|
|
5kfk
|
replication, transferase-DNA |
X-ray (1.7 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 300s . SNAP output
|
|
5kfl
|
replication, transferase-DNA |
X-ray (1.65 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 600s . SNAP output
|
|
5kfm
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex with
sp-datp-alpha-s: ground state at ph7.0 (k+ mes) with 1
ca2+ ion . SNAP
output
|
|
5kfn
|
replication, transferase-DNA |
X-ray (1.45 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex with
sp-datp-alpha-s: reaction with 1 mm mg2+ for 1800s .
SNAP output
|
|
5kfo
|
replication, transferase-DNA |
X-ray (1.52 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex with
sp-datp-alpha-s: reaction with 1 mm mn2+ for 1800s .
SNAP output
|
|
5kfp
|
replication, transferase-DNA |
X-ray (1.7 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex with
sp-datp-alpha-s: reaction with 20 mm mg2+ for 600s .
SNAP output
|
|
5kfq
|
replication, transferase-DNA |
X-ray (1.55 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex with
sp-datp-alpha-s: reaction with 10 mm mn2+ for 600s .
SNAP output
|
|
5kfr
|
replication, transferase-DNA |
X-ray (1.75 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex with
sp-datp-alpha-s: reaction with 20 mm mn2+ for 600s .
SNAP output
|
|
5kfs
|
replication, transferase-DNA |
X-ray (1.46 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta r61a-DNA ternary complex:
ground state at ph7.0 (k+ mes) with 1 ca2+ ion .
SNAP output
|
|
5kft
|
replication, transferase-DNA |
X-ray (1.52 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta r61a-DNA ternary complex:
reaction with 1 mm mg2+ for 40s . SNAP output
|
|
5kfu
|
replication, transferase-DNA |
X-ray (1.55 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta r61a-DNA ternary complex:
reaction with 1 mm mg2+ for 80s . SNAP output
|
|
5kfv
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta r61a-DNA ternary complex:
reaction with 1 mm mg2+ for 140s . SNAP output
|
|
5kfw
|
replication, transferase-DNA |
X-ray (1.62 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta r61a-DNA ternary complex:
reaction with 1 mm mg2+ for 200s . SNAP output
|
|
5kfx
|
replication, transferase-DNA |
X-ray (1.52 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta r61a-DNA ternary complex:
reaction with 1 mm mg2+ for 300s . SNAP output
|
|
5kfy
|
replication, transferase-DNA |
X-ray (1.7 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for
60s at 4 degree . SNAP
output
|
|
5kfz
|
replication, transferase-DNA |
X-ray (1.44 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for
60s at 14 degree . SNAP
output
|
|
5kg0
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for
60s at 22 degree . SNAP
output
|
|
5kg1
|
replication, transferase-DNA |
X-ray (1.62 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for
60s at 30 degree . SNAP
output
|
|
5kg2
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 5 mm mn2+ for
60s at 37 degree . SNAP
output
|
|
5kg3
|
replication, transferase-DNA |
X-ray (1.7 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 10 mm mn2+ for
60s . SNAP output
|
|
5kg4
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 10 mm mg2+ for
60s . SNAP output
|
|
5kg5
|
replication, transferase-DNA |
X-ray (1.6 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 10 mm cd2+ for
60s . SNAP output
|
|
5kg6
|
replication, transferase-DNA |
X-ray (1.55 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 10 mm ca2+ for
60s . SNAP output
|
|
5kg7
|
replication, transferase-DNA |
X-ray (1.75 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
first with 1 mm mn2+ for 1800s then with 10 mm zn2+ for
60s . SNAP output
|
|
5kgf
|
structural protein-DNA |
cryo-EM (4.54 Å) |
Wilson MD, Benlekbir S, Fradet-Turcotte A, Sherker A,
Julien JP, McEwan A, Noordermeer SM, Sicheri F,
Rubinstein JL, Durocher D |
(2016) "The
structural basis of modified nucleosome recognition by
53BP1." Nature, 536,
100-103. doi: 10.1038/nature18951.
|
Structural model of 53bp1 bound to a ubiquitylated and
methylated nucleosome, at 4.5 Å resolution . SNAP output
|
|
5kk1
|
transcription-DNA |
X-ray (3.38 Å) |
Schumacher M |
"to be published." |
Structure of pnob8 aspa-DNA complex. . SNAP output
|
|
5kk5
|
hydrolase-DNA-RNA |
X-ray (3.289 Å) |
Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ |
(2016) "Type V
CRISPR-Cas Cpf1 endonuclease employs a unique mechanism
for crRNA-mediated target DNA recognition."
Cell Res., 26, 901-913. doi:
10.1038/cr.2016.88.
|
Ascpf1(e993a)-crrna-DNA ternary complex . SNAP output
|
|
5kkq
|
transcription-DNA |
X-ray (1.744 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Homo sapiens ccctc-binding factor (ctcf) znf3-7 and DNA
complex structure . SNAP
output
|
|
5kl2
|
transcription-DNA |
X-ray (1.692 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4 in complex with DNA .
SNAP output
|
|
5kl3
|
transcription-DNA |
X-ray (1.449 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4 q369h in complex with
DNA . SNAP output
|
|
5kl4
|
transcription-DNA |
X-ray (1.783 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4 q369h in complex with
formylated DNA . SNAP
output
|
|
5kl5
|
transcription-DNA |
X-ray (2.289 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4 q369h in complex with
carboxylated DNA . SNAP
output
|
|
5kl6
|
transcription-DNA |
X-ray (1.641 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) q369r znf2-4 in complex with
DNA . SNAP output
|
|
5kl7
|
transcription-DNA |
X-ray (1.579 Å) |
Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng
X |
(2016) "Denys-Drash
syndrome associated WT1 glutamine 369 mutants have
altered sequence-preferences and altered responses to
epigenetic modifications." Nucleic Acids
Res., 44, 10165-10176. doi:
10.1093/nar/gkw766.
|
Wilms tumor protein (wt1) znf2-4q369r in complex with
carboxylated DNA . SNAP
output
|
|
5kn8
|
hydrolase-DNA |
X-ray (1.81 Å) |
Wang L, Chakravarthy S, Verdine GL |
(2017) "Structural
Basis for the Lesion-scanning Mechanism of the MutY DNA
Glycosylase." J. Biol. Chem.,
292, 5007-5017. doi: 10.1074/jbc.M116.757039.
|
Muty n-terminal domain in complex with undamaged DNA .
SNAP output
|
|
5kn9
|
hydrolase-DNA |
X-ray (1.93 Å) |
Wang L, Chakravarthy S, Verdine GL |
(2017) "Structural
Basis for the Lesion-scanning Mechanism of the MutY DNA
Glycosylase." J. Biol. Chem.,
292, 5007-5017. doi: 10.1074/jbc.M116.757039.
|
Muty n-terminal domain in complex with DNA containing
an intrahelical oxog:a base-pair . SNAP output
|
|
5krb
|
transcription-DNA |
X-ray (2.101 Å) |
Weikum ER, Tuntland ML, Murphy MN, Ortlund EA |
(2016) "A
Structural Investigation into Oct4 Regulation by Orphan
Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and
Liver Receptor Homolog-1 (LRH-1)." J. Mol.
Biol., 428, 4981-4992. doi:
10.1016/j.jmb.2016.10.025.
|
Gcnf DNA binding domain - oct4 dr0 complex . SNAP output
|
|
5kse
|
hydrolase-DNA |
X-ray (2.105 Å) |
Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw
SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham
VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM,
Grasby JA, Tainer JA |
(2017) "Phosphate
steering by Flap Endonuclease 1 promotes 5'-flap
specificity and incision to prevent genome
instability." Nat Commun,
8, 15855. doi: 10.1038/ncomms15855.
|
Flap endonuclease 1 (fen1) r100a with 5'-flap substrate
DNA and sm3+ . SNAP
output
|
|
5kt2
|
transferase |
X-ray (2.488 Å) |
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M,
Guengerich FP |
(2016) "Kinetic
and Structural Impact of Metal Ions and Genetic
Variations on Human DNA Polymerase iota."
J.Biol.Chem., 291,
21063-21073. doi: 10.1074/jbc.M116.748285.
|
Teranry complex of human DNA polymerase iota(26-445)
inserting dcmpnpp opposite template g in the presence
of mg2+ . SNAP
output
|
|
5kt3
|
transferase |
X-ray (2.64 Å) |
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M,
Guengerich FP |
(2016) "Kinetic
and Structural Impact of Metal Ions and Genetic
Variations on Human DNA Polymerase iota."
J.Biol.Chem., 291,
21063-21073. doi: 10.1074/jbc.M116.748285.
|
Teranry complex of human DNA polymerase iota(26-445)
inserting dcmpnpp opposite template g in the presence
of mn2+ . SNAP
output
|
|
5kt4
|
transferase |
X-ray (2.78 Å) |
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M,
Guengerich FP |
(2016) "Kinetic
and Structural Impact of Metal Ions and Genetic
Variations on Human DNA Polymerase iota."
J.Biol.Chem., 291,
21063-21073. doi: 10.1074/jbc.M116.748285.
|
Teranry complex of human DNA polymerase iota r96g
inserting dcmpnpp opposite template g in the presence
of mg2+ . SNAP
output
|
|
5kt5
|
transferase |
X-ray (2.798 Å) |
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M,
Guengerich FP |
(2016) "Kinetic
and Structural Impact of Metal Ions and Genetic
Variations on Human DNA Polymerase iota."
J.Biol.Chem., 291,
21063-21073. doi: 10.1074/jbc.M116.748285.
|
Teranry complex of human DNA polymerase iota r96g
inserting dcmpnpp opposite template g in the presence
of mn2+ . SNAP
output
|
|
5kt6
|
transferase |
X-ray (3.54 Å) |
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M,
Guengerich FP |
(2016) "Kinetic
and Structural Impact of Metal Ions and Genetic
Variations on Human DNA Polymerase iota."
J.Biol.Chem., 291,
21063-21073. doi: 10.1074/jbc.M116.748285.
|
Teranry complex of human DNA polymerase iota(1-445)
inserting dcmpnpp opposite template g in the presence
of mg2+ . SNAP
output
|
|
5kt7
|
transferase |
X-ray (3.151 Å) |
Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M,
Guengerich FP |
(2016) "Kinetic
and Structural Impact of Metal Ions and Genetic
Variations on Human DNA Polymerase iota."
J.Biol.Chem., 291,
21063-21073. doi: 10.1074/jbc.M116.748285.
|
Teranry complex of human DNA polymerase iota(1-445)
inserting dcmpnpp opposite template g in the presence
of mn2+ . SNAP
output
|
|
5kub
|
hydrolase-DNA |
X-ray (1.73 Å) |
Parsons ZD, Bland JM, Mullins EA, Eichman BF |
(2016) "A
Catalytic Role for C-H/ pi Interactions in Base
Excision Repair by Bacillus cereus DNA Glycosylase
AlkD." J.Am.Chem.Soc.,
138, 11485-11488. doi: 10.1021/jacs.6b07399.
|
Bacillus cereus DNA glycosylase alkd bound to
7-methylguanine nucleobase and DNA containing an
oxocarbenium-intermediate analog . SNAP output
|
|
5kvy
|
splicing-DNA |
X-ray (1.95 Å) |
Hsiao HT, Crichlow GV, Murphy JW, Folta-Stogniew EJ,
Lolis EJ, Braddock DT |
(2020) "Unraveling
the mechanism of recognition of the 3' splice site of
the adenovirus major late promoter intron by the
alternative splicing factor PUF60." Plos
One, 15, e0242725. doi: 10.1371/journal.pone.0242725.
|
Crystal structure of the two tandem rrm domains of
puf60 bound to a portion of an adml pre-mrna 3' splice
site analog . SNAP
output
|
|
5kw1
|
splicing-DNA |
X-ray (2.1 Å) |
Hsiao HT, Crichlow GV, Murphy JW, Folta-Stogniew EJ,
Lolis EJ, Braddock DT |
(2020) "Unraveling
the mechanism of recognition of the 3' splice site of
the adenovirus major late promoter intron by the
alternative splicing factor PUF60." Plos
One, 15, e0242725. doi: 10.1371/journal.pone.0242725.
|
Crystal structure of the two tandem rrm domains of
puf60 bound to a modified adml pre-mrna 3' splice site
analogue . SNAP
output
|
|
5kw6
|
splicing-DNA |
X-ray (1.91 Å) |
Hsiao HT, Crichlow GV, Murphy JW, Folta-Stogniew EJ,
Lolis EJ, Braddock DT |
(2020) "Unraveling
the mechanism of recognition of the 3' splice site of
the adenovirus major late promoter intron by the
alternative splicing factor PUF60." Plos
One, 15, e0242725. doi: 10.1371/journal.pone.0242725.
|
Two tandem rrm domains of puf60 bound to an adml
pre-mrna 3' splice site analogue with a modified
binding-site nucleic acid base . SNAP output
|
|
5l0m
|
transcription-DNA |
X-ray (2.197 Å) |
Weikum ER, Tuntland ML, Murphy MN, Ortlund EA |
(2016) "A
Structural Investigation into Oct4 Regulation by Orphan
Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and
Liver Receptor Homolog-1 (LRH-1)." J. Mol.
Biol., 428, 4981-4992. doi:
10.1016/j.jmb.2016.10.025.
|
Hlrh-1 DNA binding domain - 12bp oct4 promoter complex
. SNAP output
|
|
5l1i
|
transferase-DNA |
X-ray (2.78 Å) |
Patra A, Zhang Q, Guengerich FP, Egli M |
(2016) "Mechanisms
of Insertion of dCTP and dTTP Opposite the DNA Lesion
O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase
eta." J.Biol.Chem., 291,
24304-24313. doi: 10.1074/jbc.M116.755462.
|
Crystal structure of human DNA polymerase eta inserting
dctp opposite o6-methyl-2'-deoxyguanosine . SNAP output
|
|
5l1j
|
transferase-DNA |
X-ray (1.94 Å) |
Patra A, Zhang Q, Guengerich FP, Egli M |
(2016) "Mechanisms
of Insertion of dCTP and dTTP Opposite the DNA Lesion
O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase
eta." J.Biol.Chem., 291,
24304-24313. doi: 10.1074/jbc.M116.755462.
|
Crystal structure of human DNA polymerase eta inserting
dtmpnpp opposite o6-methyl-2'-deoxyguanosine . SNAP output
|
|
5l1k
|
transferase-DNA |
X-ray (1.82 Å) |
Patra A, Zhang Q, Guengerich FP, Egli M |
(2016) "Mechanisms
of Insertion of dCTP and dTTP Opposite the DNA Lesion
O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase
eta." J.Biol.Chem., 291,
24304-24313. doi: 10.1074/jbc.M116.755462.
|
Postinsertion complex of human DNA polymerase eta
bypassing an o6-methyl-2'-deoxyguanosine : dc site .
SNAP output
|
|
5l1l
|
transferase-DNA |
X-ray (1.62 Å) |
Patra A, Zhang Q, Guengerich FP, Egli M |
(2016) "Mechanisms
of Insertion of dCTP and dTTP Opposite the DNA Lesion
O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase
eta." J.Biol.Chem., 291,
24304-24313. doi: 10.1074/jbc.M116.755462.
|
Postinsertion complex of human DNA polymerase eta
bypassing an o6-methyl-2'-deoxyguanosine : dt site .
SNAP output
|
|
5l2x
|
transferase-DNA |
X-ray (2.2 Å) |
Rechkoblit O, Gupta YK, Malik R, Rajashankar KR,
Johnson RE, Prakash L, Prakash S, Aggarwal AK |
(2016) "Structure
and mechanism of human PrimPol, a DNA polymerase with
primase activity." Sci Adv,
2, e1601317. doi: 10.1126/sciadv.1601317.
|
Crystal structure of human primpol ternary complex .
SNAP output
|
|
5l6l
|
hydrolase |
X-ray (2.7 Å) |
Bendtsen KL, Xu K, Luckmann M, Winther KS, Shah SA,
Pedersen CNS, Brodersen DE |
(2017) "Toxin
inhibition in C. crescentus VapBC1 is mediated by a
flexible pseudo-palindromic protein motif and modulated
by DNA binding." Nucleic Acids Res.,
45, 2875-2886. doi: 10.1093/nar/gkw1266.
|
Structure of caulobacter crescentus vapbc1 bound to
operator DNA . SNAP
output
|
|
5l9x
|
transferase |
X-ray (1.9 Å) |
Gao Y, Yang W |
(2016) "Capture
of a third Mg2+ is essential for catalyzing DNA
synthesis." Science, 352,
1334-1337. doi: 10.1126/science.aad9633.
|
Human DNA polymerase eta-DNA ternary complex: reaction
with 10 mm mn2+ for 60s . SNAP output
|
|
5lcl
|
DNA binding protein |
X-ray (2.2 Å) |
Ebert C, Simon N, Schneider S, Carell T |
(2017) "Structural
Insights into the Recognition of N(2) -Aryl- and
C8-Aryl DNA Lesions by the Repair Protein
XPA/Rad14." Chembiochem,
18, 1379-1382. doi: 10.1002/cbic.201700169.
|
Structure of the rad14 DNA-binding domain in complex
with c8-aminofluorene- guanine containing DNA .
SNAP output
|
|
5lcm
|
DNA binding protein |
X-ray (1.9 Å) |
Ebert C, Simon N, Schneider S, Carell T |
(2017) "Structural
Insights into the Recognition of N(2) -Aryl- and
C8-Aryl DNA Lesions by the Repair Protein
XPA/Rad14." Chembiochem,
18, 1379-1382. doi: 10.1002/cbic.201700169.
|
Structure of the rad14 DNA-binding domain in complex
with n2-acetylaminonaphtyl- guanine containing DNA .
SNAP output
|
|
5ld2
|
hydrolase |
cryo-EM (3.83 Å) |
Wilkinson M, Chaban Y, Wigley DB |
(2016) "Mechanism
for nuclease regulation in RecBCD." Elife,
5. doi: 10.7554/eLife.18227.
|
cryo-EM structure of recbcd+DNA complex revealing
activated nuclease domain . SNAP output
|
|
5lej
|
transcription |
X-ray (2.7 Å) |
Hall M, Grundstrom C, Begum A, Lindberg MJ, Sauer UH,
Almqvist F, Johansson J, Sauer-Eriksson AE |
(2016) "Structural
basis for glutathione-mediated activation of the
virulence regulatory protein PrfA in Listeria."
Proc. Natl. Acad. Sci. U.S.A.,
113, 14733-14738. doi: 10.1073/pnas.1614028114.
|
The transcriptional regulator prfa from listeria
monocytogenes in complex with a 30-bp operator prfa-box
motif . SNAP output
|
|
5lek
|
transcription |
X-ray (2.8 Å) |
Hall M, Grundstrom C, Begum A, Lindberg MJ, Sauer UH,
Almqvist F, Johansson J, Sauer-Eriksson AE |
(2016) "Structural
basis for glutathione-mediated activation of the
virulence regulatory protein PrfA in Listeria."
Proc. Natl. Acad. Sci. U.S.A.,
113, 14733-14738. doi: 10.1073/pnas.1614028114.
|
The transcriptional regulator prfa-g145s mutant from
listeria monocytogenes in complex with a 30-bp operator
prfa-box motif . SNAP
output
|
|
5lgy
|
transcription |
X-ray (2.92 Å) |
Vainer R, Cohen S, Shahar A, Zarivach R, Arbely
E |
(2016) "Structural
Basis for p53 Lys120-Acetylation-Dependent DNA-Binding
Mode." J.Mol.Biol., 428,
3013-3025. doi: 10.1016/j.jmb.2016.06.009.
|
Lysine 120-acetylated p53 DNA binding domain in a
complex with the bax response element. . SNAP output
|
|
5lks
|
ribosome |
cryo-EM (3.6 Å) |
Myasnikov AG, Kundhavai Natchiar S, Nebout M,
Hazemann I, Imbert V, Khatter H, Peyron JF, Klaholz
BP |
(2016) "Structure-function
insights reveal the human ribosome as a cancer target
for antibiotics." Nat Commun,
7, 12856. doi: 10.1038/ncomms12856.
|
Structure-function insights reveal the human ribosome
as a cancer target for antibiotics . SNAP output
|
|
5lrs
|
transcription |
X-ray (2.9 Å) |
Hall M, Grundstrom C, Begum A, Lindberg MJ, Sauer UH,
Almqvist F, Johansson J, Sauer-Eriksson AE |
(2016) "Structural
basis for glutathione-mediated activation of the
virulence regulatory protein PrfA in Listeria."
Proc. Natl. Acad. Sci. U.S.A.,
113, 14733-14738. doi: 10.1073/pnas.1614028114.
|
The transcriptional regulator prfa from listeria
monocytogenes in complex with glutathione and a 30-bp
operator prfa-box motif . SNAP output
|
|
5lty
|
transcription |
X-ray (2.66 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Homeobox transcription factor cdx2 bound to methylated
DNA . SNAP output
|
|
5lux
|
transcription |
X-ray (3.23 Å) |
Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B,
Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta
KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J,
Schubeler D, Vinson C, Taipale J |
(2017) "Impact
of cytosine methylation on DNA binding specificities of
human transcription factors." Science,
356. doi: 10.1126/science.aaj2239.
|
Homeobox transcription factor cdx1 bound to methylated
DNA . SNAP output
|
|
5lxu
|
DNA binding protein |
X-ray (2.14 Å) |
Zubieta C, Silva CS, Lai X, Wigge P, Nanao MH, Nayak
A |
"Structure of the DNA-binding domain of LUX
ARRHYTHMO." |
Structure of the DNA-binding domain of lux arrhythmo .
SNAP output
|
|
5m0r
|
hydrolase |
cryo-EM (8.2 Å) |
Ballandras-Colas A, Maskell DP, Serrao E, Locke J,
Swuec P, Jonsson SR, Kotecha A, Cook NJ, Pye VE, Taylor
IA, Andresdottir V, Engelman AN, Costa A, Cherepanov
P |
(2017) "A
supramolecular assembly mediates lentiviral DNA
integration." Science,
355, 93-95. doi: 10.1126/science.aah7002.
|
cryo-EM reconstruction of the maedi-visna virus (mvv)
strand transfer complex . SNAP output
|
|
5m1s
|
DNA binding protein |
cryo-EM (6.7 Å) |
Fernandez-Leiro R, Conrad J, Yang JC, Freund SM,
Scheres SH, Lamers MH |
(2017) "Self-correcting
mismatches during high-fidelity DNA replication."
Nat. Struct. Mol. Biol., 24,
140-143. doi: 10.1038/nsmb.3348.
|
cryo-EM structure of the e. coli replicative DNA
polymerase-clamp-exonuclase-theta complex bound to DNA
in the editing mode . SNAP output
|
|
5m3f
|
transcription |
cryo-EM (3.8 Å) |
Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau VV,
Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis
AS |
(2016) "Structure
of RNA polymerase I transcribing ribosomal DNA
genes." Nature, 540,
607-610. doi: 10.1038/nature20561.
|
Yeast RNA polymerase i elongation complex at 3.8a .
SNAP output
|
|
5m5w
|
transcription |
cryo-EM (3.8 Å) |
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R,
Hagen WJ, Sachse C, Muller CW |
(2016) "Molecular
Structures of Transcribing RNA Polymerase I."
Mol. Cell, 64, 1135-1143.
doi: 10.1016/j.molcel.2016.11.013.
|
RNA polymerase i open complex . SNAP output
|
|
5m5x
|
transcription |
cryo-EM (4.0 Å) |
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R,
Hagen WJ, Sachse C, Muller CW |
(2016) "Molecular
Structures of Transcribing RNA Polymerase I."
Mol. Cell, 64, 1135-1143.
doi: 10.1016/j.molcel.2016.11.013.
|
RNA polymerase i elongation complex 1 . SNAP output
|
|
5m5y
|
transcription |
cryo-EM (4.0 Å) |
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R,
Hagen WJ, Sachse C, Muller CW |
(2016) "Molecular
Structures of Transcribing RNA Polymerase I."
Mol. Cell, 64, 1135-1143.
doi: 10.1016/j.molcel.2016.11.013.
|
RNA polymerase i elongation complex 2 . SNAP output
|
|
5m64
|
transcription |
cryo-EM (4.6 Å) |
Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ, Wetzel R,
Hagen WJ, Sachse C, Muller CW |
(2016) "Molecular
Structures of Transcribing RNA Polymerase I."
Mol. Cell, 64, 1135-1143.
doi: 10.1016/j.molcel.2016.11.013.
|
RNA polymerase i elongation complex with a49 tandem
winged helix domain . SNAP output
|
|
5mct
|
transcription |
X-ray (1.446 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-lhg1) .
SNAP output
|
|
5mcu
|
transcription |
X-ray (1.7 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-lhg2) .
SNAP output
|
|
5mcv
|
transcription |
X-ray (1.6 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-lwc1) .
SNAP output
|
|
5mcw
|
transcription |
X-ray (1.897 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-lwc2) .
SNAP output
|
|
5mey
|
transcription |
X-ray (2.05 Å) |
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R,
Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A,
Marquez JA, Massague J, Macias MJ |
(2017) "Structural
basis for genome wide recognition of 5-bp GC motifs by
SMAD transcription factors." Nat Commun,
8, 2070. doi: 10.1038/s41467-017-02054-6.
|
Crystal structure of smad4-mh1 bound to the ggcgc site.
. SNAP output
|
|
5mez
|
transcription |
X-ray (2.98 Å) |
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R,
Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A,
Marquez JA, Massague J, Macias MJ |
(2017) "Structural
basis for genome wide recognition of 5-bp GC motifs by
SMAD transcription factors." Nat Commun,
8, 2070. doi: 10.1038/s41467-017-02054-6.
|
Crystal structure of smad4-mh1 bound to the ggct site.
. SNAP output
|
|
5mf0
|
transcription |
X-ray (3.03 Å) |
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R,
Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A,
Marquez JA, Massague J, Macias MJ |
(2017) "Structural
basis for genome wide recognition of 5-bp GC motifs by
SMAD transcription factors." Nat Commun,
8, 2070. doi: 10.1038/s41467-017-02054-6.
|
Crystal structure of smad4-mh1 bound to the ggccg site.
. SNAP output
|
|
5mf7
|
transcription |
X-ray (1.59 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-gadd45) .
SNAP output
|
|
5mg7
|
transcription |
X-ray (1.45 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-p53r2) .
SNAP output
|
|
5mga
|
hydrolase |
X-ray (3.0 Å) |
Stella S, Alcon P, Montoya G |
(2017) "Structure
of the Cpf1 endonuclease R-loop complex after target
DNA cleavage." Nature,
546, 559-563. doi: 10.1038/nature22398.
|
Structure of the cpf1 endonuclease r-loop complex after
DNA cleavage . SNAP
output
|
|
5mhj
|
transcription |
X-ray (2.117 Å) |
Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP,
Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov
AP |
(2017) "The
herpes viral transcription factor ICP4 forms a novel
DNA recognition complex." Nucleic Acids
Res., 45, 8064-8078. doi:
10.1093/nar/gkx419.
|
Icp4 DNA-binding domain, lacking intrinsically
disordered region, in complex with 12mer DNA duplex
from its own promoter . SNAP output
|
|
5mhk
|
transcription |
X-ray (2.28 Å) |
Tunnicliffe RB, Lockhart-Cairns MP, Levy C, Mould AP,
Jowitt TA, Sito H, Baldock C, Sandri-Goldin RM, Golovanov
AP |
(2017) "The
herpes viral transcription factor ICP4 forms a novel
DNA recognition complex." Nucleic Acids
Res., 45, 8064-8078. doi:
10.1093/nar/gkx419.
|
Icp4 DNA-binding domain in complex with 19mer DNA
duplex from its own promoter . SNAP output
|
|
5mht
|
transferase-DNA |
X-ray (2.7 Å) |
O'Gara M, Roberts RJ, Cheng X |
(1996) "A
structural basis for the preferential binding of
hemimethylated DNA by HhaI DNA methyltransferase."
J.Mol.Biol., 263, 597-606.
doi: 10.1006/jmbi.1996.0601.
|
Ternary structure of hhai methyltransferase with
hemimethylated DNA and adohcy . SNAP output
|
|
5mlu
|
DNA binding protein |
X-ray (2.8 Å) |
Lesbats P, Serrao E, Maskell DP, Pye VE, O'Reilly N,
Lindemann D, Engelman AN, Cherepanov P |
(2017) "Structural
basis for spumavirus GAG tethering to chromatin."
Proc. Natl. Acad. Sci. U.S.A.,
114, 5509-5514. doi: 10.1073/pnas.1621159114.
|
Crystal structure of the pfv gag cbs bound to a
mononucleosome . SNAP
output
|
|
5mma
|
viral protein |
X-ray (2.55 Å) |
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE,
Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH,
Burke TR |
(2017) "Structure-Guided
Optimization of HIV Integrase Strand Transfer
Inhibitors." J. Med. Chem.,
60, 7315-7332. doi: 10.1021/acs.jmedchem.7b00596.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti xz379
(compound 5'g) . SNAP
output
|
|
5mmb
|
viral protein |
X-ray (2.77 Å) |
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE,
Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH,
Burke TR |
(2017) "Structure-Guided
Optimization of HIV Integrase Strand Transfer
Inhibitors." J. Med. Chem.,
60, 7315-7332. doi: 10.1021/acs.jmedchem.7b00596.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti xz434
(compound 6p) . SNAP
output
|
|
5mpf
|
transcription |
X-ray (2.918 Å) |
Ming Q, Roske Y, Schuetz A, Walentin K, Ibraimi I,
Schmidt-Ott KM, Heinemann U |
(2018) "Structural
basis of gene regulation by the Grainyhead/CP2
transcription factor family." Nucleic Acids
Res., 46, 2082-2095. doi:
10.1093/nar/gkx1299.
|
Structural basis of gene regulation by the grainyhead
transcription factor superfamily . SNAP output
|
|
5ms0
|
transcription-DNA-RNA |
cryo-EM (9.8 Å) |
Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O,
Huang YH, Lee CT, Loll B, Behrmann E, Burger J, Mielke T,
Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC |
(2017) "Structural
basis for lambda N-dependent processive transcription
antitermination." Nat Microbiol,
2, 17062. doi: 10.1038/nmicrobiol.2017.62.
|
Pseudo-atomic model of the RNA polymerase lambda-based
antitermination complex solved by cryo-EM . SNAP output
|
|
5n2q
|
DNA binding protein |
X-ray (2.0 Å) |
Pluta R, Boer DR, Lorenzo-Diaz F, Russi S, Gomez H,
Fernandez-Lopez C, Perez-Luque R, Orozco M, Espinosa M,
Coll M |
(2017) "Structural
basis of a histidine-DNA nicking/joining mechanism for
gene transfer and promiscuous spread of antibiotic
resistance." Proc. Natl. Acad. Sci.
U.S.A., 114, E6526-E6535. doi:
10.1073/pnas.1702971114.
|
Mobm relaxase domain (mobv; mob_pre) bound to 26nt
pmv158 orit DNA . SNAP
output
|
|
5n61
|
transferase |
cryo-EM (3.4 Å) |
Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C,
Baejen C, Bernecky C, Cramer P |
(2017) "Structural
Basis of RNA Polymerase I Transcription
Initiation." Cell, 169,
120-131.e22. doi: 10.1016/j.cell.2017.03.003.
|
RNA polymerase i initially transcribing complex .
SNAP output
|
|
5n6i
|
transferase |
X-ray (3.6 Å) |
Andreeva L, Hiller B, Kostrewa D, Lassig C, de
Oliveira Mann CC, Jan Drexler D, Maiser A, Gaidt M,
Leonhardt H, Hornung V, Hopfner KP |
(2017) "cGAS
senses long and HMGB/TFAM-bound U-turn DNA by forming
protein-DNA ladders." Nature,
549, 394-398. doi: 10.1038/nature23890.
|
Crystal structure of mouse cgas in complex with 39 bp
DNA . SNAP output
|
|
5n8o
|
transferase |
cryo-EM (3.9 Å) |
Ilangovan A, Kay CWM, Roier S, El Mkami H, Salvadori
E, Zechner EL, Zanetti G, Waksman G |
(2017) "Cryo-EM
Structure of a Relaxase Reveals the Molecular Basis of
DNA Unwinding during Bacterial Conjugation."
Cell, 169, 708-721.e12. doi:
10.1016/j.cell.2017.04.010.
|
Cryo em structure of the conjugative relaxase trai of
the f-r1 plasmid system . SNAP output
|
|
5n8r
|
hydrolase |
X-ray (2.2 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophilia dhx36 helicase in
complex with gagcactgc . SNAP output
|
|
5n8s
|
hydrolase |
X-ray (2.88 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophila dhx36 helicase in
complex with polyt . SNAP output
|
|
5n8u
|
hydrolase |
X-ray (2.62 Å) |
Chen W-F, Rety S, Guo H-L, Wu W-Q, Liu N-N, Liu Q-W,
Dai Y-X, Xi X-G |
"Structural and mechanistic insights into
DHX36-mediated innate immunity and G-quadruplex
unfolding." |
Crystal structure of drosophila dhx36 helicase in
complex with ctctcct . SNAP output
|
|
5n8z
|
hydrolase |
X-ray (3.477 Å) |
Chen W-F, Rety S, Guo H-L, Wu W-Q, Liu N-N, Liu Q-W,
Dai Y-X, Xi X-G |
"Structural and mechanistic insights into
DHX36-mediated innate immunity and G-quadruplex
unfolding." |
Crystal structure of drosophila dhx36 helicase in
complex with ctctccctt . SNAP output
|
|
5n90
|
hydrolase |
X-ray (3.069 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophila dhx36 helicase in
complex with ttgtggtgt . SNAP output
|
|
5n96
|
hydrolase |
X-ray (2.716 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophila dhx36 helicase in
complex with agggtttttt . SNAP output
|
|
5n98
|
hydrolase |
X-ray (2.756 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophila dhx36 helicase in
complex with tagggtttt . SNAP output
|
|
5n9a
|
hydrolase |
X-ray (3.036 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophila dhx36 helicase in
complex with gttagggtt . SNAP output
|
|
5n9d
|
hydrolase |
X-ray (2.71 Å) |
Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN,
Auguin D, Liu QW, Hou XM, Dou SX, Xi XG |
(2018) "Molecular
Mechanistic Insights into Drosophila DHX36-Mediated
G-Quadruplex Unfolding: A Structure-Based Model."
Structure, 26, 403-415.e4.
doi: 10.1016/j.str.2018.01.008.
|
Crystal structure of drosophila dhx36 helicase in
complex with gggttagggt . SNAP output
|
|
5n9e
|
hydrolase |
X-ray (3.007 Å) |
Chen W-F, Rety S, Hai-Lei Guo H-L, Wu W-Q, Liu N-N,
Liu Q-W, Dai Y-X, Xi X-G |
"Structural and mechanistic insights into
DHX36-mediated innate immunity and G-quadruplex
unfolding." |
Crystal structure of drosophila dhx36 helicase in
complex with tggggattt . SNAP output
|
|
5n9f
|
hydrolase |
X-ray (2.969 Å) |
Chen W-F, Rety S, Hai-Lei Guo H-L, Wu W-Q, Liu N-N,
Liu Q-W, Dai Y-X, Xi X-G |
"Structural and mechanistic insights into
DHX36-mediated innate immunity and G-quadruplex
unfolding." |
Crystal structure of drosophila dhx36 helicase in
complex with ssDNA cpg_a . SNAP output
|
|
5n9g
|
transcription |
X-ray (2.7 Å) |
Gouge J, Guthertz N, Kramm K, Dergai O,
Abascal-Palacios G, Satia K, Cousin P, Hernandez N,
Grohmann D, Vannini A |
(2017) "Molecular
mechanisms of Bdp1 in TFIIIB assembly and RNA
polymerase III transcription initiation." Nat
Commun, 8, 130. doi: 10.1038/s41467-017-00126-1.
|
Tfiiib -tbp-brf2-DNA and sant domain of bdp1- .
SNAP output
|
|
5nfv
|
hydrolase |
X-ray (2.501 Å) |
Swarts DC, van der Oost J, Jinek M |
(2017) "Structural
Basis for Guide RNA Processing and Seed-Dependent DNA
Targeting by CRISPR-Cas12a." Mol. Cell,
66, 221-233.e4. doi: 10.1016/j.molcel.2017.03.016.
|
Crystal structure of catalytically inactive fncas12
mutant bound to an r-loop structure containing a
pre-crrna mimic and full-length DNA target . SNAP output
|
|
5nj8
|
transcription |
X-ray (3.3 Å) |
Schulte KW, Green E, Wilz A, Platten M, Daumke O |
(2017) "Structural
Basis for Aryl Hydrocarbon Receptor-Mediated Gene
Activation." Structure,
25, 1025-1033.e3. doi: 10.1016/j.str.2017.05.008.
|
Structural basis for aryl hydrocarbon receptor mediated
gene activation . SNAP
output
|
|
5nkl
|
transferase |
X-ray (1.7 Å) |
Betz K, Kimoto M, Diederichs K, Hirao I, Marx A |
(2017) "Structural
Basis for Expansion of the Genetic Alphabet with an
Artificial Nucleobase Pair." Angew. Chem. Int.
Ed. Engl., 56, 12000-12003. doi:
10.1002/anie.201704190.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with the artificial base pair dds-dpxtp .
SNAP output
|
|
5nl0
|
chromatin binding protein - DNA |
X-ray (5.4 Å) |
Bednar J, Garcia-Saez I, Boopathi R, Cutter AR, Papai
G, Reymer A, Syed SH, Lone IN, Tonchev O, Crucifix C,
Menoni H, Papin C, Skoufias DA, Kurumizaka H, Lavery R,
Hamiche A, Hayes JJ, Schultz P, Angelov D, Petosa C,
Dimitrov S |
(2017) "Structure
and Dynamics of a 197 bp Nucleosome in Complex with
Linker Histone H1." Mol. Cell,
66, 384-397.e8. doi: 10.1016/j.molcel.2017.04.012.
|
Crystal structure of a 197-bp palindromic 601l
nucleosome in complex with linker histone h1 . SNAP output
|
|
5nm9
|
transcription |
X-ray (2.43 Å) |
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R,
Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A,
Marquez JA, Massague J, Macias MJ |
(2017) "Structural
basis for genome wide recognition of 5-bp GC motifs by
SMAD transcription factors." Nat Commun,
8, 2070. doi: 10.1038/s41467-017-02054-6.
|
Crystal structure of the placozoa trichoplax adhaerens
smad4-mh1 bound to the ggcgc site. . SNAP output
|
|
5nnu
|
hydrolase |
X-ray (2.97 Å) |
Earl C, Bagneris C, Zeman K, Cole A, Barrett T, Savva
R |
(2018) "A
structurally conserved motif in gamma-herpesvirus
uracil-DNA glycosylases elicits duplex
nucleotide-flipping." Nucleic Acids Res.,
46, 4286-4300. doi: 10.1093/nar/gky217.
|
Kshv uracil-DNA glycosylase, product complex with dsDNA
exhibiting duplex nucleotide flipping . SNAP output
|
|
5nnx
|
transcription |
X-ray (3.29 Å) |
Morgunova E, Jolma A, Yin Y, Popov A, Taipale J |
"TEAD1 bound to DNA." |
Tead1 bound to DNA . SNAP output
|
|
5no1
|
viral protein |
X-ray (2.6 Å) |
Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE,
Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH,
Burke TR |
(2017) "Structure-Guided
Optimization of HIV Integrase Strand Transfer
Inhibitors." J. Med. Chem.,
60, 7315-7332. doi: 10.1021/acs.jmedchem.7b00596.
|
Crystal structure of the prototype foamy virus (pfv)
intasome in complex with magnesium and the insti xz407
(compound 5g) . SNAP
output
|
|
5no6
|
transcription |
X-ray (2.88 Å) |
Xie Z, Sokolov I, Osmala M, Yue X, Bower G, Pett JP,
Chen Y, Wang K, Cavga AD, Popov A, Teichmann SA,
Morgunova E, Kvon EZ, Yin Y, Taipale J |
(2025) "DNA-guided
transcription factor interactions extend human gene
regulatory code." Nature. doi: 10.1038/s41586-025-08844-z.
|
Tead4-hoxb13 complex bound to DNA . SNAP output
|
|
5npk
|
isomerase |
X-ray (1.98 Å) |
Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacque
E, Checchia A, Chen D, Cui H, Ding X, Ingraham K,
McCloskey L, Raha K, Srikannathasan V, Maxwell A,
Stavenger RA |
(2017) "Thiophene
antibacterials that allosterically stabilize
DNA-cleavage complexes with DNA gyrase." Proc.
Natl. Acad. Sci. U.S.A., 114,
E4492-E4500. doi: 10.1073/pnas.1700721114.
|
1.98a structure of thiophene1 with s.aureus DNA gyrase
and DNA . SNAP
output
|
|
5npp
|
isomerase |
X-ray (2.22 Å) |
Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacque
E, Checchia A, Chen D, Cui H, Ding X, Ingraham K,
McCloskey L, Raha K, Srikannathasan V, Maxwell A,
Stavenger RA |
(2017) "Thiophene
antibacterials that allosterically stabilize
DNA-cleavage complexes with DNA gyrase." Proc.
Natl. Acad. Sci. U.S.A., 114,
E4492-E4500. doi: 10.1073/pnas.1700721114.
|
2.22a structure of thiophene2 and gsk945237 with
s.aureus DNA gyrase and DNA . SNAP output
|
|
5nsr
|
transcription |
cryo-EM (3.8 Å) |
Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang
X |
(2017) "Structures
of RNA Polymerase Closed and Intermediate Complexes
Reveal Mechanisms of DNA Opening and Transcription
Initiation." Mol. Cell,
67, 106-116.e4. doi: 10.1016/j.molcel.2017.05.010.
|
cryo-EM structure of RNA polymerase-sigma54 holo enzyme
with promoter DNA closed complex . SNAP output
|
|
5nss
|
transcription |
cryo-EM (5.8 Å) |
Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang
X |
(2017) "Structures
of RNA Polymerase Closed and Intermediate Complexes
Reveal Mechanisms of DNA Opening and Transcription
Initiation." Mol. Cell,
67, 106-116.e4. doi: 10.1016/j.molcel.2017.05.010.
|
cryo-EM structure of RNA polymerase-sigma54 holoenzyme
with promoter DNA and transcription activator pspf
intermedate complex . SNAP output
|
|
5nw5
|
DNA binding protein |
X-ray (6.502 Å) |
Mattarocci S, Reinert JK, Bunker RD, Fontana GA, Shi
T, Klein D, Cavadini S, Faty M, Shyian M, Hafner L, Shore
D, Thoma NH, Rass U |
(2017) "Rif1
maintains telomeres and mediates DNA repair by encasing
DNA ends." Nat. Struct. Mol. Biol.,
24, 588-595. doi: 10.1038/nsmb.3420.
|
Crystal structure of the rif1 n-terminal domain
(rif1-ntd) from saccharomyces cerevisiae in complex
with DNA . SNAP
output
|
|
5nw9
|
hydrolase |
X-ray (2.04 Å) |
Flett FJ, Ruksenaite E, Armstrong LA, Bharati S,
Carloni R, Morris ER, Mackay CL, Interthal H, Richardson
JM |
(2018) "Structural
basis for DNA 3'-end processing by human tyrosyl-DNA
phosphodiesterase 1." Nat Commun,
9, 24. doi: 10.1038/s41467-017-02530-z.
|
Crystal structure of the complex of tdp1 with duplex
DNA . SNAP output
|
|
5nwa
|
hydrolase |
X-ray (3.2 Å) |
Flett FJ, Ruksenaite E, Armstrong LA, Bharati S,
Carloni R, Morris ER, Mackay CL, Interthal H, Richardson
JM |
(2018) "Structural
basis for DNA 3'-end processing by human tyrosyl-DNA
phosphodiesterase 1." Nat Commun,
9, 24. doi: 10.1038/s41467-017-02530-z.
|
Crystal structure of the complex of tdp1 with duplex
DNA . SNAP output
|
|
5o20
|
transcription |
X-ray (3.53 Å) |
Franco-Echevarria E, Gonzalez-Polo N, Zorrilla S,
Martinez-Lumbreras S, Santiveri CM, Campos-Olivas R,
Sanchez M, Calvo O, Gonzalez B, Perez-Canadillas JM |
(2017) "The
structure of transcription termination factor Nrd1
reveals an original mode for GUAA recognition."
Nucleic Acids Res., 45,
10293-10305. doi: 10.1093/nar/gkx685.
|
Structure of nrd1 RNA binding domain in complex with
RNA (uuaguaaucc) . SNAP
output
|
|
5o63
|
hydrolase |
X-ray (1.6 Å) |
Sasnauskas G, Tamulaitiene G, Tamulaitis G, Calyseva
J, Laime M, Rimseliene R, Lubys A, Siksnys V |
(2017) "UbaLAI
is a monomeric Type IIE restriction enzyme."
Nucleic Acids Res., 45,
9583-9594. doi: 10.1093/nar/gkx634.
|
Crystal structure of ubalai restriction endonuclease b3
domain domain (mutant l24m l53m l95m) with cognate DNA
. SNAP output
|
|
5o6b
|
hydrolase |
X-ray (2.029 Å) |
Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D,
Ma HY, Dou SX, Xi XG |
(2018) "Insights
into the structural and mechanistic basis of
multifunctional S. cerevisiae Pif1p helicase."
Nucleic Acids Res., 46,
1486-1500. doi: 10.1093/nar/gkx1217.
|
Structure of scpif1 in complex with gggtttt and
adp-alf4 . SNAP
output
|
|
5o6d
|
hydrolase |
X-ray (3.283 Å) |
Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D,
Ma HY, Dou SX, Xi XG |
(2018) "Insights
into the structural and mechanistic basis of
multifunctional S. cerevisiae Pif1p helicase."
Nucleic Acids Res., 46,
1486-1500. doi: 10.1093/nar/gkx1217.
|
Structure of scpif1 in complex with polydt and atpgs .
SNAP output
|
|
5o6e
|
hydrolase |
X-ray (3.345 Å) |
Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D,
Ma HY, Dou SX, Xi XG |
(2018) "Insights
into the structural and mechanistic basis of
multifunctional S. cerevisiae Pif1p helicase."
Nucleic Acids Res., 46,
1486-1500. doi: 10.1093/nar/gkx1217.
|
Structure of scpif1 in complex with tttgggtt and
adp-alf4 . SNAP
output
|
|
5o6g
|
DNA binding protein |
X-ray (2.75 Å) |
Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R,
D'Abramo M |
(2017) "Structure
and dynamics of mesophilic variants from the homing
endonuclease I-DmoI." J. Comput. Aided Mol.
Des., 31, 1063-1072. doi:
10.1007/s10822-017-0087-5.
|
Structures and dynamics of mesophilic variants from the
homing endonuclease i-dmoi . SNAP output
|
|
5o6i
|
DNA binding protein |
X-ray (2.25 Å) |
Alba J, Marcaida MJ, Prieto J, Montoya G, Molina R,
D'Abramo M |
(2017) "Structure
and dynamics of mesophilic variants from the homing
endonuclease I-DmoI." J. Comput. Aided Mol.
Des., 31, 1063-1072. doi:
10.1007/s10822-017-0087-5.
|
Structures and dynamics of mesophilic variants from the
homing endonuclease i-dmoi . SNAP output
|
|
5o6u
|
antiviral protein |
X-ray (3.25 Å) |
Pausch P, Muller-Esparza H, Gleditzsch D, Altegoer F,
Randau L, Bange G |
(2017) "Structural
Variation of Type I-F CRISPR RNA Guided DNA
Surveillance." Mol. Cell,
67, 622-632.e4. doi: 10.1016/j.molcel.2017.06.036.
|
Structure of the cascade-i-fv r-loop complex from
shewanella putrefaciens . SNAP output
|
|
5o7t
|
transferase |
X-ray (1.8 Å) |
Betz K, Nilforoushan A, Wyss LA, Diederichs K, Sturla
SJ, Marx A |
(2017) "Structural
basis for the selective incorporation of an artificial
nucleotide opposite a DNA adduct by a DNA
polymerase." Chem. Commun. (Camb.),
53, 12704-12707. doi: 10.1039/c7cc07173f.
|
Crystal structure of klentaq mutant m747k in a closed
ternary complex with a dg:dctp base pair . SNAP output
|
|
5o9g
|
DNA binding protein |
cryo-EM (4.8 Å) |
Farnung L, Vos SM, Wigge C, Cramer P |
(2017) "Nucleosome-Chd1
structure and implications for chromatin
remodelling." Nature,
550, 539-542. doi: 10.1038/nature24046.
|
Structure of nucleosome-chd1 complex . SNAP output
|
|
5oa1
|
transcription |
cryo-EM (4.4 Å) |
Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R,
Buczak K, Hagen WJ, Beck M, Sachse C, Muller CW |
(2017) "Structural
insights into transcription initiation by yeast RNA
polymerase I." EMBO J.,
36, 2698-2709. doi: 10.15252/embj.201796958.
|
RNA polymerase i pre-initiation complex . SNAP output
|
|
5od6
|
transcription |
X-ray (2.0 Å) |
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R,
Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A,
Marquez JA, Massague J, Macias MJ |
(2017) "Structural
basis for genome wide recognition of 5-bp GC motifs by
SMAD transcription factors." Nat Commun,
8, 2070. doi: 10.1038/s41467-017-02054-6.
|
Crystal structure of smad3-mh1 bound to the ggcgc site.
. SNAP output
|
|
5odg
|
transcription |
X-ray (2.12 Å) |
Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R,
Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A,
Marquez JA, Massague J, Macias MJ |
(2017) "Structural
basis for genome wide recognition of 5-bp GC motifs by
SMAD transcription factors." Nat Commun,
8, 2070. doi: 10.1038/s41467-017-02054-6.
|
Crystal structure of smad3-mh1 bound to the ggct site.
. SNAP output
|
|
5odl
|
DNA binding protein |
X-ray (1.56 Å) |
Cernooka E, Rumnieks J, Tars K, Kazaks A |
(2017) "Structural
Basis for DNA Recognition of a Single-stranded
DNA-binding Protein from Enterobacter Phage Enc34."
Sci Rep, 7, 15529. doi:
10.1038/s41598-017-15774-y.
|
Single-stranded DNA-binding protein from bacteriophage
enc34 in complex with ssDNA . SNAP output
|
|
5odn
|
DNA binding protein |
X-ray (2.598 Å) |
Pierechod M, Rothweiler U |
"Salinibacter ruber Single-Strand Binding
protein." |
Salinibacter ruber single-strand binding protein .
SNAP output
|
|
5odp
|
DNA binding protein |
X-ray (2.535 Å) |
Pierechod M, Rothweiler U |
"Salinibacter ruber Single-Strand Binding protein
D17K D71K mutant." |
Salinibacter ruber single-strand binding protein d17k
d71k mutant . SNAP
output
|
|
5oik
|
transcription |
cryo-EM (3.7 Å) |
Bernecky C, Plitzko JM, Cramer P |
(2017) "Structure
of a transcribing RNA polymerase II-DSIF complex
reveals a multidentate DNA-RNA clamp." Nat.
Struct. Mol. Biol., 24, 809-815.
doi: 10.1038/nsmb.3465.
|
Structure of an RNA polymerase ii-dsif transcription
elongation complex . SNAP output
|
|
5ola
|
transcription |
X-ray (3.904 Å) |
Hillen HS, Parshin AV, Agaronyan K, Morozov YI,
Graber JJ, Chernev A, Schwinghammer K, Urlaub H, Anikin
M, Cramer P, Temiakov D |
(2017) "Mechanism
of Transcription Anti-termination in Human
Mitochondria." Cell, 171,
1082-1093.e13. doi: 10.1016/j.cell.2017.09.035.
|
Structure of mitochondrial transcription elongation
complex in complex with elongation factor tefm .
SNAP output
|
|
5omf
|
DNA binding protein |
X-ray (2.092 Å) |
Kropp HM, Betz K, Wirth J, Diederichs K, Marx A |
(2017) "Crystal
structures of ternary complexes of archaeal B-family
DNA polymerases." PLoS ONE,
12, e0188005. doi: 10.1371/journal.pone.0188005.
|
Closed, ternary structure of kod DNA polymerase .
SNAP output
|
|
5omq
|
transferase |
X-ray (2.199 Å) |
Kropp HM, Betz K, Wirth J, Diederichs K, Marx A |
(2017) "Crystal
structures of ternary complexes of archaeal B-family
DNA polymerases." PLoS ONE,
12, e0188005. doi: 10.1371/journal.pone.0188005.
|
Ternary complex of 9n DNA polymerase in the replicative
state with three metal ions in the active site .
SNAP output
|
|
5omv
|
transferase |
X-ray (2.003 Å) |
Kropp HM, Betz K, Wirth J, Diederichs K, Marx A |
(2017) "Crystal
structures of ternary complexes of archaeal B-family
DNA polymerases." PLoS ONE,
12, e0188005. doi: 10.1371/journal.pone.0188005.
|
Ternary complex of 9n DNA polymerase in the replicative
state with two metal ions in the active site . SNAP output
|
|
5omx
|
DNA binding protein |
X-ray (2.32 Å) |
Frouws TD, Barth PD, Richmond TJ |
(2018) "Site-Specific
Disulfide Crosslinked Nucleosomes with Enhanced
Stability." J. Mol. Biol.,
430, 45-57. doi: 10.1016/j.jmb.2017.10.029.
|
X-ray structure of the h2a-n38c nucleosome core
particle . SNAP
output
|
|
5ond
|
transcription |
X-ray (2.1 Å) |
Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z,
Nedialkov Y, Schweimer K, Rosch P, Knauer SH |
(2018) "The
universally-conserved transcription factor RfaH is
recruited to a hairpin structure of the non-template
DNA strand." Elife, 7.
doi: 10.7554/eLife.36349.
|
Rfah from escherichia coli in complex with ops DNA .
SNAP output
|
|
5ong
|
DNA binding protein |
X-ray (2.797 Å) |
Frouws TD, Barth PD, Richmond TJ |
(2018) "Site-Specific
Disulfide Crosslinked Nucleosomes with Enhanced
Stability." J. Mol. Biol.,
430, 45-57. doi: 10.1016/j.jmb.2017.10.029.
|
X-ray crystal structure of a nucleosome core particle
with its DNA site-specifically crosslinked to the
histone octamer . SNAP
output
|
|
5onw
|
DNA binding protein |
X-ray (2.8 Å) |
Frouws TD, Barth PD, Richmond TJ |
(2018) "Site-Specific
Disulfide Crosslinked Nucleosomes with Enhanced
Stability." J. Mol. Biol.,
430, 45-57. doi: 10.1016/j.jmb.2017.10.029.
|
X-ray crystal structure of a nucleosome core particle
with its DNA site-specifically crosslinked to the
histone octamer and the two h2a-h2b dimers crosslinked
via h2a n38c . SNAP
output
|
|
5oqj
|
transcription |
cryo-EM (4.7 Å) |
Schilbach S, Hantsche M, Tegunov D, Dienemann C,
Wigge C, Urlaub H, Cramer P |
(2017) "Structures
of transcription pre-initiation complex with TFIIH and
Mediator." Nature, 551,
204-209. doi: 10.1038/nature24282.
|
Structure of yeast transcription pre-initiation complex
with tfiih . SNAP
output
|
|
5oqm
|
transcription |
cryo-EM (5.8 Å) |
Schilbach S, Hantsche M, Tegunov D, Dienemann C,
Wigge C, Urlaub H, Cramer P |
(2017) "Structures
of transcription pre-initiation complex with TFIIH and
Mediator." Nature, 551,
204-209. doi: 10.1038/nature24282.
|
Structure of yeast transcription pre-initiation complex
with tfiih and core mediator . SNAP output
|
|
5oqn
|
cell cycle |
X-ray (3.15 Å) |
Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V,
Hassler M, Haering CH |
(2017) "Structural
Basis for a Safety-Belt Mechanism That Anchors
Condensin to Chromosomes." Cell,
171, 588-600.e24. doi: 10.1016/j.cell.2017.09.008.
|
Crystal structure of the s. cerevisiae condensin
ycg1-brn1 subcomplex bound to DNA (short kleisin loop)
. SNAP output
|
|
5oqo
|
cell cycle |
X-ray (3.25 Å) |
Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V,
Hassler M, Haering CH |
(2017) "Structural
Basis for a Safety-Belt Mechanism That Anchors
Condensin to Chromosomes." Cell,
171, 588-600.e24. doi: 10.1016/j.cell.2017.09.008.
|
Crystal structure of the s. cerevisiae condensin
ycg1-brn1 subcomplex bound to DNA (crystal form ii) .
SNAP output
|
|
5oqp
|
cell cycle |
X-ray (2.98 Å) |
Kschonsak M, Merkel F, Bisht S, Metz J, Rybin V,
Hassler M, Haering CH |
(2017) "Structural
Basis for a Safety-Belt Mechanism That Anchors
Condensin to Chromosomes." Cell,
171, 588-600.e24. doi: 10.1016/j.cell.2017.09.008.
|
Crystal structure of the s. cerevisiae condensin
ycg1-brn1 subcomplex bound to DNA (crystal form i) .
SNAP output
|
|
5or5
|
transcription |
NMR |
Campagne S, Vorholt JA, Allain FH |
"Engineered promoter selectivity of an ECF sigma
factor." Not published. |
NMR structure of the complex formed by an engineered
region 2 of sigmae in complex with gtaaaa . SNAP output
|
|
5orq
|
de novo protein |
X-ray (1.95 Å) |
Spahr H, Chia T, Lingford JP, Siira SJ, Cohen SB,
Filipovska A, Rackham O |
(2018) "Modular
ssDNA binding and inhibition of telomerase activity by
designer PPR proteins." Nat Commun,
9, 2212. doi: 10.1038/s41467-018-04388-1.
|
Crystal structure of designed cppr-telo1 in complex
with ssDNA . SNAP
output
|
|
5ot2
|
transcription |
X-ray (3.2 Å) |
Malvezzi S, Farnung L, Aloisi CMN, Angelov T, Cramer
P, Sturla SJ |
(2017) "Mechanism
of RNA polymerase II stalling by DNA alkylation."
Proc. Natl. Acad. Sci. U.S.A.,
114, 12172-12177. doi: 10.1073/pnas.1706592114.
|
RNA polymerase ii elongation complex in the presence of
3d-napht-a . SNAP
output
|
|
5oxj
|
transferase |
X-ray (2.0 Å) |
Betz K, Nilforoushan A, Wyss LA, Diederichs K, Sturla
SJ, Marx A |
(2017) "Structural
basis for the selective incorporation of an artificial
nucleotide opposite a DNA adduct by a DNA
polymerase." Chem. Commun. (Camb.),
53, 12704-12707. doi: 10.1039/c7cc07173f.
|
Crystal structure of klentaq mutant m747k in a closed
ternary complex with a o6-meg:benzitp base pair .
SNAP output
|
|
5oxv
|
gene regulation |
X-ray (6.721 Å) |
Ekundayo B, Richmond TJ, Schalch T |
(2017) "Capturing
Structural Heterogeneity in Chromatin Fibers."
J. Mol. Biol., 429,
3031-3042. doi: 10.1016/j.jmb.2017.09.002.
|
Structure of the 4_601_157 tetranucleosome (c2 form) .
SNAP output
|
|
5oy7
|
gene regulation |
X-ray (5.774 Å) |
Ekundayo B, Richmond TJ, Schalch T |
(2017) "Capturing
Structural Heterogeneity in Chromatin Fibers."
J. Mol. Biol., 429,
3031-3042. doi: 10.1016/j.jmb.2017.09.002.
|
Structure of the 4_601_157 tetranucleosome (p1 form) .
SNAP output
|
|
5sva
|
transcription, transferase-DNA |
cryo-EM (15.3 Å) |
Robinson PJ, Trnka MJ, Bushnell DA, Davis RE, Mattei
PJ, Burlingame AL, Kornberg RD |
(2016) "Structure
of a Complete Mediator-RNA Polymerase II Pre-Initiation
Complex." Cell, 166,
1411-1422.e16. doi: 10.1016/j.cell.2016.08.050.
|
Mediator-RNA polymerase ii pre-initiation complex .
SNAP output
|
|
5swm
|
hydrolase-RNA-DNA |
X-ray (1.5 Å) |
Pallan PS, Prakash TP, de Leon AR, Egli M |
(2016) "Limits
of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of
Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA
Hybrid." Biochemistry,
55, 5321-5325. doi: 10.1021/acs.biochem.6b00849.
|
Bacillus halodurans rnase h mutant d132n in complex
with 12-mer frna-DNA hybrid . SNAP output
|
|
5sww
|
hydrolase-DNA |
X-ray (3.151 Å) |
Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi
K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir
O, Amaro RE, Harki DA, Harris RS, Aihara H |
(2017) "Structural
basis for targeted DNA cytosine deamination and
mutagenesis by APOBEC3A and APOBEC3B." Nat.
Struct. Mol. Biol., 24, 131-139.
doi: 10.1038/nsmb.3344.
|
Crystal structure of human apobec3a complexed with
ssDNA . SNAP output
|
|
5sy7
|
transcription-DNA |
X-ray (4.2 Å) |
Wu D, Su X, Potluri N, Kim Y, Rastinejad F |
(2016) "NPAS1-ARNT
and NPAS3-ARNT crystal structures implicate the
bHLH-PAS family as multi-ligand binding transcription
factors." Elife, 5. doi:
10.7554/eLife.18790.
|
Crystal structure of the heterodimeric npas3-arnt
complex with hre DNA . SNAP output
|
|
5szt
|
transferase |
X-ray (1.8 Å) |
Hottin A, Betz K, Diederichs K, Marx A |
(2017) "Structural
Basis for the KlenTaq DNA Polymerase Catalysed
Incorporation of Alkene- versus Alkyne-Modified
Nucleotides." Chemistry,
23, 2109-2118. doi: 10.1002/chem.201604515.
|
Crystal structure of the large fragment of DNA
polymerase i from thermus aquaticus in a closed ternary
complex with
7-(n-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-datp
. SNAP output
|
|
5szx
|
transcription regulator-DNA |
X-ray (2.251 Å) |
Hong S, Wang D, Horton JR, Zhang X, Speck SH,
Blumenthal RM, Cheng X |
(2017) "Methyl-dependent
and spatial-specific DNA recognition by the orthologous
transcription factors human AP-1 and Epstein-Barr virus
Zta." Nucleic Acids Res.,
45, 2503-2515. doi: 10.1093/nar/gkx057.
|
Epstein-barr virus zta DNA binding domain homodimer in
complex with methylated DNA . SNAP output
|
|
5t00
|
transcription regulator-DNA |
X-ray (2.19 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Human ctcf znf3-7 and methylated DNA complex . SNAP output
|
|
5t01
|
transcription regulator-DNA |
X-ray (1.89 Å) |
Hong S, Wang D, Horton JR, Zhang X, Speck SH,
Blumenthal RM, Cheng X |
(2017) "Methyl-dependent
and spatial-specific DNA recognition by the orthologous
transcription factors human AP-1 and Epstein-Barr virus
Zta." Nucleic Acids Res.,
45, 2503-2515. doi: 10.1093/nar/gkx057.
|
Human c-jun DNA binding domain homodimer in complex
with methylated DNA . SNAP output
|
|
5t0u
|
transcription regulator-DNA |
X-ray (3.199 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Ctcf znf2-7 and DNA complex structure . SNAP output
|
|
5t14
|
transferase-DNA |
X-ray (3.0 Å) |
Jha V, Ling H |
(2017) "Structural
basis of accurate replication beyond a bulky major
benzo[a]pyrene adduct by human DNA polymerase
kappa." DNA Repair (Amst.),
49, 43-50. doi: 10.1016/j.dnarep.2016.11.001.
|
DNA polymerase kappa extending beyond a bulky major
benzo[a]pyrene adduct . SNAP output
|
|
5t1j
|
transcription-DNA |
X-ray (2.947 Å) |
Liu CF, Brandt GS, Hoang QQ, Naumova N, Lazarevic V,
Hwang ES, Dekker J, Glimcher LH, Ringe D, Petsko GA |
(2016) "Crystal
structure of the DNA binding domain of the
transcription factor T-bet suggests simultaneous
recognition of distant genome sites."
Proc.Natl.Acad.Sci.USA, 113,
E6572-E6581. doi: 10.1073/pnas.1613914113.
|
Crystal structure of the tbox DNA binding domain of the
transcription factor t-bet . SNAP output
|
|
5t2c
|
ribosome |
cryo-EM (3.6 Å) |
Zhang X, Lai M, Chang W, Yu I, Ding K, Mrazek J, Ng
HL, Yang OO, Maslov DA, Zhou ZH |
(2016) "Structures
and stabilization of kinetoplastid-specific split rRNAs
revealed by comparing leishmanial and human
ribosomes." Nat Commun,
7, 13223. doi: 10.1038/ncomms13223.
|
Cryoem structure of the human ribosome at 3.6 angstrom
resolution . SNAP
output
|
|
5t2h
|
hydrolase-DNA |
X-ray (2.517 Å) |
Werther R, Hallinan JP, Lambert AR, Havens K, Pogson
M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan
T, Stoddard BL |
(2017) "Crystallographic
analyses illustrate significant plasticity and
efficient recoding of meganuclease target
specificity." Nucleic Acids Res.,
45, 8621-8634. doi: 10.1093/nar/gkx544.
|
Engineered variant of i-onui meganuclease targeting the
human tcra gene; harbors 43 point mutations relative to
wild-type i-onui . SNAP
output
|
|
5t2n
|
hydrolase-DNA |
X-ray (2.079 Å) |
Werther R, Hallinan JP, Lambert AR, Havens K, Pogson
M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan
T, Stoddard BL |
(2017) "Crystallographic
analyses illustrate significant plasticity and
efficient recoding of meganuclease target
specificity." Nucleic Acids Res.,
45, 8621-8634. doi: 10.1093/nar/gkx544.
|
Engineered variant of i-onui meganuclease targeting the
anopheles agap007280 gene; harbors 38 point mutations
relative to wild-type i-onui . SNAP output
|
|
5t2o
|
hydrolase-DNA |
X-ray (2.801 Å) |
Werther R, Hallinan JP, Lambert AR, Havens K, Pogson
M, Jarjour J, Galizi R, Windbichler N, Crisanti A, Nolan
T, Stoddard BL |
(2017) "Crystallographic
analyses illustrate significant plasticity and
efficient recoding of meganuclease target
specificity." Nucleic Acids Res.,
45, 8621-8634. doi: 10.1093/nar/gkx544.
|
Engineered variant of i-onui meganuclease targeting the
anopheles agap011377 gene; harbors 53 point mutations
relative to wild-type i-onui . SNAP output
|
|
5t2w
|
hydrolase-DNA |
X-ray (2.2 Å) |
Pidugu LS, Flowers JW, Coey CT, Pozharski E,
Greenberg MM, Drohat AC |
(2016) "Structural
Basis for Excision of 5-Formylcytosine by Thymine DNA
Glycosylase." Biochemistry,
55, 6205-6208. doi: 10.1021/acs.biochem.6b00982.
|
Structure of thymine DNA glycosylase bound to substrate
analog 2'-f-5-formyl-dc . SNAP output
|
|
5t4i
|
hydrolase-DNA |
X-ray (2.389 Å) |
Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ,
Lee JC, Yin YW |
(2017) "A domain
in human EXOG converts apoptotic endonuclease to
DNA-repair exonuclease." Nat Commun,
8, 14959. doi: 10.1038/ncomms14959.
|
A novel domain in human exog converts apoptotic
endonuclease to DNA-repair enzyme . SNAP output
|
|
5t5c
|
hydrolase-DNA |
X-ray (1.851 Å) |
Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ,
Lee JC, Yin YW |
(2017) "A domain
in human EXOG converts apoptotic endonuclease to
DNA-repair exonuclease." Nat Commun,
8, 14959. doi: 10.1038/ncomms14959.
|
A novel domain in human exog converts apoptotic
endonuclease to DNA-repair enzyme . SNAP output
|
|
5t5k
|
DNA binding protein-DNA |
X-ray (4.0 Å) |
Mattiroli F, Bhattacharyya S, Dyer PN, White AE,
Sandman K, Burkhart BW, Byrne KR, Lee T, Ahn NG,
Santangelo TJ, Reeve JN, Luger K |
(2017) "Structure
of histone-based chromatin in Archaea."
Science, 357, 609-612. doi:
10.1126/science.aaj1849.
|
Structure of histone-based chromatin in archaea .
SNAP output
|
|
5t7x
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Dheekollu J, Malecka K, Wiedmer A, Delecluse HJ,
Chiang AK, Altieri DC, Messick TE, Lieberman PM |
(2017) "Carcinoma-risk
variant of EBNA1 deregulates Epstein-Barr Virus
episomal latency." Oncotarget,
8, 7248-7264. doi: 10.18632/oncotarget.14540.
|
Crystal structure of hhv-4 ebna1 DNA binding domain
(patient-derived, nasopharyngeal carcinoma) bound to
DNA . SNAP output
|
|
5t8d
|
hydrolase-DNA |
X-ray (2.15 Å) |
Niyonzima N, Lambert AR, Werther R, De Silva Feelixge
H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL,
Jerome KR |
(2017) "Tuning
DNA binding affinity and cleavage specificity of an
engineered gene-targeting nuclease via surface display,
flow cytometry and cellular analyses." Protein
Eng.Des.Sel., 30, 503-522. doi:
10.1093/protein/gzx037.
|
Engineered variant of i-onui meganuclease targeting the
hiv integrase gene; harbors 47 point mutations relative
to wild-type i-onui . SNAP output
|
|
5t9j
|
hydrolase |
X-ray (3.0 Å) |
Lee SH, Princz LN, Klugel MF, Habermann B, Pfander B,
Biertumpfel C |
(2015) "Human
Holliday junction resolvase GEN1 uses a chromodomain
for efficient DNA recognition and cleavage."
Elife, 4. doi: 10.7554/eLife.12256.
|
Crystal structure of human gen1 in complex with
holliday junction DNA in the upper interface . SNAP output
|
|
5tb8
|
transferase-DNA |
X-ray (2.0 Å) |
Reed AJ, Vyas R, Raper AT, Suo Z |
(2017) "Structural
Insights into the Post-Chemistry Steps of Nucleotide
Incorporation Catalyzed by a DNA Polymerase."
J. Am. Chem. Soc., 139,
465-471. doi: 10.1021/jacs.6b11258.
|
Precatalytic ternary complex of human DNA polymerase
beta in closed conformation with gapped DNA substrate
incoming (-)3tc-tp and mn2+. . SNAP output
|
|
5tb9
|
transferase-DNA |
X-ray (2.49 Å) |
Reed AJ, Vyas R, Raper AT, Suo Z |
(2017) "Structural
Insights into the Post-Chemistry Steps of Nucleotide
Incorporation Catalyzed by a DNA Polymerase."
J. Am. Chem. Soc., 139,
465-471. doi: 10.1021/jacs.6b11258.
|
Precatalytic ternary complex of human DNA polymerase
beta in closed conformation with gapped DNA substrate
incoming (-)ftc-tp and mn2+. . SNAP output
|
|
5tba
|
transferase-DNA |
X-ray (2.49 Å) |
Reed AJ, Vyas R, Raper AT, Suo Z |
(2017) "Structural
Insights into the Post-Chemistry Steps of Nucleotide
Incorporation Catalyzed by a DNA Polymerase."
J. Am. Chem. Soc., 139,
465-471. doi: 10.1021/jacs.6b11258.
|
Postcatalytic ternary complex of human DNA polymerase
beta with gapped DNA substrate, incorporated (-)3tc and
ppi. . SNAP output
|
|
5tbb
|
transferase-DNA |
X-ray (2.39 Å) |
Reed AJ, Vyas R, Raper AT, Suo Z |
(2017) "Structural
Insights into the Post-Chemistry Steps of Nucleotide
Incorporation Catalyzed by a DNA Polymerase."
J. Am. Chem. Soc., 139,
465-471. doi: 10.1021/jacs.6b11258.
|
Postcatalytic ternary complex of human DNA polymerase
beta with gapped DNA substrate, incorporated (-)ftc and
ppi. . SNAP output
|
|
5tbc
|
transferase-DNA |
X-ray (1.85 Å) |
Reed AJ, Vyas R, Raper AT, Suo Z |
(2017) "Structural
Insights into the Post-Chemistry Steps of Nucleotide
Incorporation Catalyzed by a DNA Polymerase."
J. Am. Chem. Soc., 139,
465-471. doi: 10.1021/jacs.6b11258.
|
Precatalytic ternary complex of human DNA polymerase
beta with gapped DNA substrate, incorporated (-)3tc-mp
and an another incoming (-)3tc-tp nucleotide. .
SNAP output
|
|
5td5
|
hydrolase-DNA |
X-ray (1.718 Å) |
Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi
K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir
O, Amaro RE, Harki DA, Harris RS, Aihara H |
(2017) "Structural
basis for targeted DNA cytosine deamination and
mutagenesis by APOBEC3A and APOBEC3B." Nat.
Struct. Mol. Biol., 24, 131-139.
doi: 10.1038/nsmb.3344.
|
Crystal structure of human apobec3b variant complexed
with ssDNA . SNAP
output
|
|
5tgx
|
DNA binding protein |
X-ray (2.3 Å) |
Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard
BL |
(2017) "DNA
recognition by the SwaI restriction endonuclease
involves unusual distortion of an 8 base pair A:T-rich
target." Nucleic Acids Res.,
45, 1516-1528. doi: 10.1093/nar/gkw1200.
|
Restriction-modification system-type ii r-swai
complexed with partially cleaved DNA . SNAP output
|
|
5th3
|
DNA binding protein |
X-ray (2.33 Å) |
Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard
BL |
(2017) "DNA
recognition by the SwaI restriction endonuclease
involves unusual distortion of an 8 base pair A:T-rich
target." Nucleic Acids Res.,
45, 1516-1528. doi: 10.1093/nar/gkw1200.
|
Restriction-modification system-type ii r.swai cleaved
DNA complex . SNAP
output
|
|
5thg
|
hydrolase-DNA |
X-ray (3.106 Å) |
Werther R, Hallinan JP, Lambert A, Haven K, Jarjor J,
Stoddard BL |
"The structural basis of altered gene specificity
resulting from meganuclease and MegaTAL
engineering." |
Engineered variant of i-onui meganuclease targeting the
hiv ccr5 gene; harbors 43 point mutations relative to
wild-type i-onui . SNAP
output
|
|
5tjg
|
transferase-DNA |
X-ray (2.6 Å) |
Feklistov A, Bae B, Hauver J, Lass-Napiorkowska A,
Kalesse M, Glaus F, Altmann KH, Heyduk T, Landick R,
Darst SA |
(2017) "RNA
polymerase motions during promoter melting."
Science, 356, 863-866. doi:
10.1126/science.aam7858.
|
Thermus aquaticus delta1.1-sigmaa
holoenzyme-downstream-fork promoter complex with an
open clamp . SNAP
output
|
|
5tkz
|
splicing |
X-ray (1.529 Å) |
Soufari H, Mackereth CD |
(2017) "Conserved
binding of GCAC motifs by MEC-8, couch potato, and the
RBPMS protein family." RNA,
23, 308-316. doi: 10.1261/rna.059733.116.
|
Mec-8 n-terminal rrm bound to tandem gcac ligand .
SNAP output
|
|
5trd
|
transferase-DNA |
X-ray (1.85 Å) |
Vetting MW, Rodionova IA, Li X, Osterman AL, Rodionov
DA, Almo SC |
"Structure of RbkR (Riboflavin Kinase) from
Thermoplasma acidophilum determined in complex with CTP
and its cognate DNA operator." |
Structure of rbkr (riboflavin kinase) from thermoplasma
acidophilum determined in complex with ctp and its
cognate DNA operator . SNAP output
|
|
5tvp
|
hydrolase-DNA |
X-ray (2.399 Å) |
Schellenberg MJ, Lieberman JA, Herrero-Ruiz A, Butler
LR, Williams JG, Munoz-Cabello AM, Mueller GA, London RE,
Cortes-Ledesma F, Williams RS |
(2017) "ZATT
(ZNF451)-mediated resolution of topoisomerase 2
DNA-protein cross-links." Science,
357, 1412-1416. doi: 10.1126/science.aam6468.
|
Sumo2 bound to mouse tdp2 catalytic domain with a
5'-phosphorylated DNA ternary complex . SNAP output
|
|
5tw1
|
transcription activator-transferase-DNA |
X-ray (2.76 Å) |
Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman
MS, Darst SA, Campbell EA |
(2017) "Structure
and function of the mycobacterial transcription
initiation complex with the essential regulator
RbpA." Elife, 6. doi:
10.7554/eLife.22520.
|
Crystal structure of a mycobacterium smegmatis
transcription initiation complex with rbpa . SNAP output
|
|
5twp
|
transferase-DNA |
X-ray (2.001 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Pre-catalytic ternary complex of human polymerase mu
with incoming nonhydrolyzable umpnpp . SNAP output
|
|
5twq
|
transferase-DNA |
X-ray (1.8 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic nicked complex of human polymerase mu
with newly incorporated utp . SNAP output
|
|
5twr
|
transferase-DNA |
X-ray (1.9 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Pre-catalytic ternary complex of human polymerase mu
(h329a) mutant with incoming nonhydrolyzable umpnpp .
SNAP output
|
|
5tws
|
transferase-DNA |
X-ray (1.85 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (h329a)
with newly incorporated utp . SNAP output
|
|
5txl
|
transferase-DNA |
X-ray (2.501 Å) |
Das K, Martinez SE, Arnold E |
(2017) "Structural
Insights into HIV Reverse Transcriptase Mutations Q151M
and Q151M Complex That Confer Multinucleoside Drug
Resistance." Antimicrob. Agents
Chemother., 61. doi: 10.1128/AAC.00224-17.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming datp
. SNAP output
|
|
5txm
|
transferase-DNA |
X-ray (2.7 Å) |
Das K, Martinez SE, Arnold E |
(2017) "Structural
Insights into HIV Reverse Transcriptase Mutations Q151M
and Q151M Complex That Confer Multinucleoside Drug
Resistance." Antimicrob. Agents
Chemother., 61. doi: 10.1128/AAC.00224-17.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
ddatp . SNAP output
|
|
5txn
|
transferase-DNA |
X-ray (2.55 Å) |
Das K, Martinez SE, Arnold E |
(2017) "Structural
Insights into HIV Reverse Transcriptase Mutations Q151M
and Q151M Complex That Confer Multinucleoside Drug
Resistance." Antimicrob. Agents
Chemother., 61. doi: 10.1128/AAC.00224-17.
|
Structure of q151m mutant hiv-1 reverse transcriptase
(rt) ternary complex with a double stranded DNA and an
incoming datp . SNAP
output
|
|
5txo
|
transferase-DNA |
X-ray (2.546 Å) |
Das K, Martinez SE, Arnold E |
(2017) "Structural
Insights into HIV Reverse Transcriptase Mutations Q151M
and Q151M Complex That Confer Multinucleoside Drug
Resistance." Antimicrob. Agents
Chemother., 61. doi: 10.1128/AAC.00224-17.
|
Structure of q151m complex (a62v, v75i, f77l, f116y,
q151m) mutant hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming datp
. SNAP output
|
|
5txp
|
transferase-DNA |
X-ray (2.7 Å) |
Das K, Martinez SE, Arnold E |
(2017) "Structural
Insights into HIV Reverse Transcriptase Mutations Q151M
and Q151M Complex That Confer Multinucleoside Drug
Resistance." Antimicrob. Agents
Chemother., 61. doi: 10.1128/AAC.00224-17.
|
Structure of q151m complex (a62v, v75i, f77l, f116y,
q151m) mutant hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
ddatp . SNAP output
|
|
5txx
|
transferase-DNA |
X-ray (1.948 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu pre-catalytic ground state ternary
complex, ca2+ . SNAP
output
|
|
5txz
|
transferase-DNA |
X-ray (1.651 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, 100mm mg2+ (15 min)
. SNAP output
|
|
5tyb
|
transferase-DNA |
X-ray (1.848 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, 10mm mg2+ (7.5 min)
. SNAP output
|
|
5tyc
|
transferase-DNA |
X-ray (2.101 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, 10mm mg2+ (15 min)
. SNAP output
|
|
5tyd
|
transferase-DNA |
X-ray (1.899 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, 10 mm mg2+ (45 min)
. SNAP output
|
|
5tye
|
transferase-DNA |
X-ray (2.047 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu product complex, 10 mm mg2+ (60 min)
. SNAP output
|
|
5tyf
|
transferase-DNA |
X-ray (1.971 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu product complex, 10 mm mg2+ (270 min)
. SNAP output
|
|
5tyg
|
transferase-DNA |
X-ray (1.726 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu product complex, 10 mm mg2+ (960 min)
. SNAP output
|
|
5tyu
|
transferase-DNA |
X-ray (2.048 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, mn2+ (4 min) .
SNAP output
|
|
5tyv
|
transferase-DNA |
X-ray (1.93 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, mn2+ (7.5 min) .
SNAP output
|
|
5tyw
|
transferase-DNA |
X-ray (1.88 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu reactant complex, mn2+ (10 min) .
SNAP output
|
|
5tyx
|
transferase-DNA |
X-ray (1.948 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu product complex, mn2+ (15 min) .
SNAP output
|
|
5tyy
|
transferase-DNA |
X-ray (1.931 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu product complex, mn2+ (60 min) .
SNAP output
|
|
5tyz
|
transferase-DNA |
X-ray (1.977 Å) |
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF,
Krahn JM, Bebenek K, Kunkel TA, Wilson SH |
(2017) "Time-lapse
crystallography snapshots of a double-strand break
repair polymerase in action." Nat Commun,
8, 253. doi: 10.1038/s41467-017-00271-7.
|
DNA polymerase mu product complex, mn2+ (960 min) .
SNAP output
|
|
5tzv
|
transferase-DNA |
X-ray (2.0 Å) |
Batra VK, Beard WA, Pedersen LC, Wilson SH |
(2016) "Structures
of DNA Polymerase Mispaired DNA Termini Transitioning
to Pre-catalytic Complexes Support an Induced-Fit
Fidelity Mechanism." Structure,
24, 1863-1875. doi: 10.1016/j.str.2016.08.006.
|
Binary complex crystal structure of DNA polymerase beta
with g:t mismatch at the primer terminus . SNAP output
|
|
5u01
|
transcription-DNA |
X-ray (2.5 Å) |
Mulero MC, Huang DB, Nguyen HT, Wang VY, Li Y, Biswas
T, Ghosh G |
(2017) "DNA-binding
affinity and transcriptional activity of the RelA
homodimer of nuclear factor kappa B are not
correlated." J. Biol. Chem.,
292, 18821-18830. doi: 10.1074/jbc.M117.813980.
|
Cooperative DNA binding by two rela dimers . SNAP output
|
|
5u07
|
immune system |
cryo-EM (3.8 Å) |
Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M,
Ke A |
(2017) "Structure
Basis for Directional R-loop Formation and Substrate
Handover Mechanisms in Type I CRISPR-Cas System."
Cell, 170, 48-60.e11. doi:
10.1016/j.cell.2017.06.012.
|
Crispr RNA-guided surveillance complex . SNAP output
|
|
5u0a
|
immune system |
cryo-EM (3.3 Å) |
Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M,
Ke A |
(2017) "Structure
Basis for Directional R-loop Formation and Substrate
Handover Mechanisms in Type I CRISPR-Cas System."
Cell, 170, 48-60.e11. doi:
10.1016/j.cell.2017.06.012.
|
Crispr RNA-guided surveillance complex . SNAP output
|
|
5u1c
|
viral protein |
cryo-EM (3.9 Å) |
Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R,
Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis
D |
(2017) "Cryo-EM
structures and atomic model of the HIV-1 strand
transfer complex intasome." Science,
355, 89-92. doi: 10.1126/science.aah5163.
|
Structure of tetrameric hiv-1 strand transfer complex
intasome . SNAP
output
|
|
5u1j
|
DNA binding protein-DNA |
X-ray (2.95 Å) |
Zhang H, Schumacher MA |
(2017) "Structures
of partition protein ParA with nonspecific DNA and ParB
effector reveal molecular insights into principles
governing Walker-box DNA segregation." Genes
Dev., 31, 481-492. doi: 10.1101/gad.296319.117.
|
Structure of pnob8 para bound to nonspecific DNA .
SNAP output
|
|
5u2r
|
transferase-DNA |
X-ray (1.8 Å) |
Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer
PC, Suo Z |
(2017) "Structural
basis for the D-stereoselectivity of human DNA
polymerase beta." Nucleic Acids Res.,
45, 6228-6237. doi: 10.1093/nar/gkx252.
|
Precatalytic ternary complex of human DNA polymerase
beta with gapped DNA substarte, incoming l-dctp and
ca2+ . SNAP output
|
|
5u2s
|
transferase-DNA |
X-ray (2.3 Å) |
Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer
PC, Suo Z |
(2017) "Structural
basis for the D-stereoselectivity of human DNA
polymerase beta." Nucleic Acids Res.,
45, 6228-6237. doi: 10.1093/nar/gkx252.
|
Pre-catalytic ternary complex of human DNA polymerase
beta with gapped DNA substrate incoming (-)3tc-tp and
ca2+. . SNAP output
|
|
5u2t
|
transferase-DNA |
X-ray (1.79 Å) |
Vyas R, Reed AJ, Raper AT, Zahurancik WJ, Wallenmeyer
PC, Suo Z |
(2017) "Structural
basis for the D-stereoselectivity of human DNA
polymerase beta." Nucleic Acids Res.,
45, 6228-6237. doi: 10.1093/nar/gkx252.
|
Pre-catalytic ternary complex of human DNA polymerase
beta with gapped DNA substrate incoming (-)ftc-tp and
ca2+. . SNAP output
|
|
5u30
|
hydrolase-DNA |
X-ray (2.92 Å) |
Yang H, Gao P, Rajashankar KR, Patel DJ |
(2016) "PAM-Dependent
Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas
Endonuclease." Cell, 167,
1814-1828.e12. doi: 10.1016/j.cell.2016.11.053.
|
Crystal structure of aacc2c1-sgrna-extended target DNA
ternary complex . SNAP
output
|
|
5u31
|
hydrolase-DNA |
X-ray (2.89 Å) |
Yang H, Gao P, Rajashankar KR, Patel DJ |
(2016) "PAM-Dependent
Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas
Endonuclease." Cell, 167,
1814-1828.e12. doi: 10.1016/j.cell.2016.11.053.
|
Crystal structure of aacc2c1-sgrna-8mer substrate DNA
ternary complex . SNAP
output
|
|
5u33
|
hydrolase-DNA |
X-ray (3.75 Å) |
Yang H, Gao P, Rajashankar KR, Patel DJ |
(2016) "PAM-Dependent
Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas
Endonuclease." Cell, 167,
1814-1828.e12. doi: 10.1016/j.cell.2016.11.053.
|
Crystal structure of aacc2c1-sgrna-extended non-target
DNA ternary complex . SNAP output
|
|
5u8g
|
transferase,lyase-DNA |
X-ray (2.166 Å) |
Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL,
Sweasy JB, Doublie S |
(2017) "Remote
Mutations Induce Functional Changes in Active Site
Residues of Human DNA Polymerase beta."
Biochemistry, 56, 2363-2371.
doi: 10.1021/acs.biochem.6b01287.
|
DNA polymerase beta crystallized in peg 400 . SNAP output
|
|
5u8h
|
transferase,lyase-DNA |
X-ray (2.155 Å) |
Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL,
Sweasy JB, Doublie S |
(2017) "Remote
Mutations Induce Functional Changes in Active Site
Residues of Human DNA Polymerase beta."
Biochemistry, 56, 2363-2371.
doi: 10.1021/acs.biochem.6b01287.
|
DNA polymerase beta g231d crystallized in peg 400 .
SNAP output
|
|
5u8i
|
transferase,lyase-DNA |
X-ray (2.45 Å) |
Eckenroth BE, Towle-Weicksel JB, Nemec AA, Murphy DL,
Sweasy JB, Doublie S |
(2017) "Remote
Mutations Induce Functional Changes in Active Site
Residues of Human DNA Polymerase beta."
Biochemistry, 56, 2363-2371.
doi: 10.1021/acs.biochem.6b01287.
|
DNA polymerase beta s229l crystallized in peg 400 .
SNAP output
|
|
5u8s
|
replication |
cryo-EM (6.1 Å) |
Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R,
Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME |
(2017) "Structure
of eukaryotic CMG helicase at a replication fork and
implications to replisome architecture and origin
initiation." Proc. Natl. Acad. Sci.
U.S.A., 114, E697-E706. doi:
10.1073/pnas.1620500114.
|
Structure of eukaryotic cmg helicase at a replication
fork . SNAP output
|
|
5u8t
|
replication |
cryo-EM (4.9 Å) |
Georgescu R, Yuan Z, Bai L, de Luna Almeida Santos R,
Sun J, Zhang D, Yurieva O, Li H, O'Donnell ME |
(2017) "Structure
of eukaryotic CMG helicase at a replication fork and
implications to replisome architecture and origin
initiation." Proc. Natl. Acad. Sci.
U.S.A., 114, E697-E706. doi:
10.1073/pnas.1620500114.
|
Structure of eukaryotic cmg helicase at a replication
fork and implications . SNAP output
|
|
5u91
|
isomerase-DNA |
X-ray (3.104 Å) |
Meinke G, Karpinski J, Buchholz F, Bohm A |
(2017) "Crystal
structure of an engineered, HIV-specific recombinase
for removal of integrated proviral DNA."
Nucleic Acids Res., 45,
9726-9740. doi: 10.1093/nar/gkx603.
|
Crystal structure of tre-loxltr complex . SNAP output
|
|
5u9h
|
transferase-DNA |
X-ray (1.85 Å) |
Perera L, Freudenthal BD, Beard WA, Pedersen LG,
Wilson SH |
(2017) "Revealing
the role of the product metal in DNA polymerase beta
catalysis." Nucleic Acids Res.,
45, 2736-2745. doi: 10.1093/nar/gkw1363.
|
DNA polymerase beta product complex with inserted
sp-isomer of dctp-alpha-s . SNAP output
|
|
5ua1
|
transcription-DNA |
X-ray (2.9 Å) |
Ho NAT, Dawes SS, Baker EN, Lott JS |
"Crystal structure of KstR in complex with cognate
DNA operator." |
Mycobacterium tuberculosis kstr in complex with a 18-bp
DNA operator . SNAP
output
|
|
5ua2
|
transcription-DNA |
X-ray (2.9 Å) |
Ho NAT, Dawes SS, Baker EN, Lott JS |
"Crystal structure of KstR in complex with cognate
DNA operator." |
Mycobacterium tuberculosis kstr in complex with a 26-bp
DNA operator . SNAP
output
|
|
5uan
|
transcription-DNA |
X-ray (3.508 Å) |
Chandra V, Wu D, Li S, Potluri N, Kim Y, Rastinejad
F |
(2017) "The
quaternary architecture of RAR beta-RXR alpha
heterodimer facilitates domain-domain signal
transmission." Nat Commun,
8, 868. doi: 10.1038/s41467-017-00981-y.
|
Crystal structure of multi-domain rar-beta-rxr-alpha
heterodimer on DNA . SNAP output
|
|
5uc6
|
immune system-DNA |
X-ray (2.1 Å) |
Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle
AM |
(2017) "Structural
basis for IL-1 alpha recognition by a modified DNA
aptamer that specifically inhibits IL-1 alpha
signaling." Nat Commun,
8, 810. doi: 10.1038/s41467-017-00864-2.
|
Structural insights into il-1 alpha recognition by a
naphthyl-modified aptamer that mimics il-1ri domain iii
. SNAP output
|
|
5ugn
|
transferase-DNA |
X-ray (1.997 Å) |
Shock DD, Freudenthal BD, Beard WA, Wilson SH |
(2017) "Modulating
the DNA polymerase beta reaction equilibrium to dissect
the reverse reaction." Nat. Chem. Biol.,
13, 1074-1080. doi: 10.1038/nchembio.2450.
|
DNA polymerase beta imidodiphosphate reactant complex .
SNAP output
|
|
5ugo
|
transferase-DNA |
X-ray (1.897 Å) |
Shock DD, Freudenthal BD, Beard WA, Wilson SH |
(2017) "Modulating
the DNA polymerase beta reaction equilibrium to dissect
the reverse reaction." Nat. Chem. Biol.,
13, 1074-1080. doi: 10.1038/nchembio.2450.
|
DNA polymerase beta nick complex with imidodiphosphate
. SNAP output
|
|
5ugp
|
transferase-DNA |
X-ray (1.955 Å) |
Shock DD, Freudenthal BD, Beard WA, Wilson SH |
(2017) "Modulating
the DNA polymerase beta reaction equilibrium to dissect
the reverse reaction." Nat. Chem. Biol.,
13, 1074-1080. doi: 10.1038/nchembio.2450.
|
DNA polymerase beta complex with a 1nt gap and dcmppnp
. SNAP output
|
|
5uh5
|
transcription-DNA-RNA |
X-ray (3.746 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex containing 3 nt of RNA
. SNAP output
|
|
5uh6
|
transcription-DNA-RNA-antibiotic |
X-ray (3.837 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex containing 2ntrna in
complex with rifampin . SNAP output
|
|
5uh8
|
transcription-DNA-RNA |
X-ray (4.176 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex containing 4nt RNA .
SNAP output
|
|
5uh9
|
transcription-DNA-RNA |
X-ray (4.402 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex containing 2nt RNA .
SNAP output
|
|
5uha
|
transcription-DNA |
X-ray (3.906 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex . SNAP output
|
|
5uhb
|
transcription-DNA-RNA |
X-ray (4.29 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex in complex with
rifampin . SNAP
output
|
|
5uhc
|
transcription-DNA-RNA |
X-ray (3.796 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex containing 3nt RNA in
complex with rifampin . SNAP output
|
|
5uhd
|
transcription-DNA-RNA |
X-ray (4.01 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex containing 4nt RNA in
complex with rifampin . SNAP output
|
|
5uhe
|
transcription-DNA-RNA |
X-ray (4.039 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex in complex with d-aap1
. SNAP output
|
|
5uhf
|
transcription-DNA-RNA |
X-ray (4.345 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex in complex with
d-ix336 . SNAP
output
|
|
5uhg
|
transcription-DNA-RNA |
X-ray (3.971 Å) |
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S,
Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M,
Talaue M, Connell N, Das K, Arnold E, Ebright RH |
(2017) "Structural
Basis of Mycobacterium tuberculosis Transcription and
Transcription Inhibition." Mol. Cell,
66, 169-179.e8. doi: 10.1016/j.molcel.2017.03.001.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex in complex with d-aap1
and rifampin . SNAP
output
|
|
5ui5
|
transcription-DNA |
X-ray (3.4 Å) |
Campbell EA, Kamath S, Rajashankar KR, Wu M, Darst
SA |
(2017) "Crystal
structure of Aquifex aeolicus sigma (N) bound to
promoter DNA and the structure of sigma
(N)-holoenzyme." Proc. Natl. Acad. Sci.
U.S.A., 114, E1805-E1814. doi:
10.1073/pnas.1619464114.
|
Crystal structure of aquifex aeolicus sigman bound to
promoter DNA . SNAP
output
|
|
5uj2
|
immune system-RNA |
X-ray (2.9 Å) |
Kirschberg TA, Metobo S, Clarke MO, Aktoudianakis V,
Babusis D, Barauskas O, Birkus G, Butler T, Byun D, Chin
G, Doerffler E, Edwards TE, Fenaux M, Lee R, Lew W, Mish
MR, Murakami E, Park Y, Squires NH, Tirunagari N, Wang T,
Whitcomb M, Xu J, Yang H, Ye H, Zhang L, Appleby TC, Feng
JY, Ray AS, Cho A, Kim CU |
(2017) "Discovery
of a 2'-fluoro-2'-C-methyl C-nucleotide HCV polymerase
inhibitor and a phosphoramidate prodrug with favorable
properties." Bioorg. Med. Chem. Lett.,
27, 1840-1847. doi: 10.1016/j.bmcl.2017.02.037.
|
Crystal structure of hcv ns5b genotype 2a jfh-1 isolate
with s15g e86q e87q c223h v321i mutations and delta8
neta hairpoin loop deletion in complex with gs-639476
(diphsohate version of gs-9813), mn2+ and symmetrical
primer template 5'-auaaauuu . SNAP output
|
|
5uk7
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Orans J, Kovach AR, Hoff KE, Brennan RG |
"Crystal structure of Escherichia coli Hfq DNA
complex reveals multifunctional nucleic acid binding
site." |
Escherichia coli hfq bound to dsDNA . SNAP output
|
|
5ulw
|
thansferase-DNA |
X-ray (2.617 Å) |
Jain R, Choudhury JR, Buku A, Johnson RE, Prakash L,
Prakash S, Aggarwal AK |
(2017) "Mechanism
of error-free DNA synthesis across
N1-methyl-deoxyadenosine by human DNA
polymerase-iota." Sci Rep,
7, 43904. doi: 10.1038/srep43904.
|
Structure of human DNA polymerase iota bound to
template 1-methyl-deoxyadenosine . SNAP output
|
|
5ulx
|
thansferase-DNA |
X-ray (1.96 Å) |
Jain R, Choudhury JR, Buku A, Johnson RE, Prakash L,
Prakash S, Aggarwal AK |
(2017) "Mechanism
of error-free DNA synthesis across
N1-methyl-deoxyadenosine by human DNA
polymerase-iota." Sci Rep,
7, 43904. doi: 10.1038/srep43904.
|
Structure of human DNA polymerase iota bound to
template 1-methyl-deoxyadenosine crystallized in the
presence of dctp . SNAP
output
|
|
5um9
|
hydrolase-DNA |
X-ray (2.805 Å) |
Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw
SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham
VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM,
Grasby JA, Tainer JA |
(2017) "Phosphate
steering by Flap Endonuclease 1 promotes 5'-flap
specificity and incision to prevent genome
instability." Nat Commun,
8, 15855. doi: 10.1038/ncomms15855.
|
Flap endonuclease 1 (fen1) d86n with 5'-flap substrate
DNA and sm3+ . SNAP
output
|
|
5und
|
transcription-DNA |
X-ray (2.549 Å) |
Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG,
Cheng X |
(2017) "Structural
Basis for the Versatile and Methylation-Dependent
Binding of CTCF to DNA." Mol. Cell,
66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004.
|
Crystal structure of ctcf(znf 4-10) with 28-mer DNA .
SNAP output
|
|
5uop
|
transferase-DNA-inhibitor |
X-ray (2.85 Å) |
Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau
LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ,
Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N,
Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J,
Steele TG, Wai J, Walji A, Xu M, Coleman PJ |
(2017) "Discovery
and optimization of 2-pyridinone aminal integrase
strand transfer inhibitors for the treatment of
HIV." Bioorg. Med. Chem. Lett.,
27, 2038-2046. doi: 10.1016/j.bmcl.2017.02.039.
|
Crystal structure of the prototype foamy virus intasome
with a 2- pyridinone aminal inhibitor (compound 18) .
SNAP output
|
|
5uoq
|
transferase-DNA-inhibitor |
X-ray (2.61 Å) |
Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau
LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ,
Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N,
Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J,
Steele TG, Wai J, Walji A, Xu M, Coleman PJ |
(2017) "Discovery
and optimization of 2-pyridinone aminal integrase
strand transfer inhibitors for the treatment of
HIV." Bioorg. Med. Chem. Lett.,
27, 2038-2046. doi: 10.1016/j.bmcl.2017.02.039.
|
Crystal structure of the prototype foamy virus intasome
with a 2- pyridinone aminal inhibitor (compound 31) .
SNAP output
|
|
5us2
|
hydrolase - RNA - DNA |
X-ray (1.9 Å) |
Fang Z, Yang F, Huang Z |
"2-Se-T-modified-DNA and native RNA hybrid in complex
with RNase H catalytic domain D132N mutant." |
2-se-t2-DNA and native RNA hybrid in complex with rnase
h catalytic domain d132n mutant . SNAP output
|
|
5usa
|
hydrolase - RNA - DNA |
X-ray (1.8 Å) |
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z |
(2023) "Synthesis of Pyrimidine Modified Seleno-DNA as
a Novel Approach to Antisense Candidate."
Chemistryselect, 8. doi:
10.1002/slct.202302253.
|
5-se-t2-DNA and native RNA hybrid in complex with rnase
h catalytic domain d132n mutant . SNAP output
|
|
5usb
|
DNA binding protein-DNA-RNA |
X-ray (1.615 Å) |
Lloyd NR, Wuttke DS |
(2018) "Discrimination
against RNA Backbones by a ssDNA Binding Protein."
Structure, 26, 722-733.e2.
doi: 10.1016/j.str.2018.03.016.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssrna-ssDNA chimera (rggttacggt) . SNAP output
|
|
5use
|
hydrolase - RNA - DNA |
X-ray (1.73 Å) |
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z |
(2023) "Synthesis of Pyrimidine Modified Seleno-DNA as
a Novel Approach to Antisense Candidate."
Chemistryselect, 8. doi:
10.1002/slct.202302253.
|
5-se-t4-DNA and native RNA hybrid in complex with rnase
h catalytic domain d132n mutant . SNAP output
|
|
5usg
|
hydrolase - RNA - DNA |
X-ray (1.7 Å) |
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z |
(2023) "Synthesis of Pyrimidine Modified Seleno-DNA as
a Novel Approach to Antisense Candidate."
Chemistryselect, 8. doi:
10.1002/slct.202302253.
|
5-se-t2-4-DNA and native RNA hybrid in complex with
rnase h catalytic domain d132n mutant . SNAP output
|
|
5usn
|
DNA binding protein-DNA-RNA |
X-ray (1.9 Å) |
Lloyd NR, Wuttke DS |
(2018) "Discrimination
against RNA Backbones by a ssDNA Binding Protein."
Structure, 26, 722-733.e2.
doi: 10.1016/j.str.2018.03.016.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssrna-ssDNA chimera (rgrgrutacggt) . SNAP output
|
|
5uso
|
DNA binding protein-DNA-RNA |
X-ray (2.0 Å) |
Lloyd NR, Wuttke DS |
(2018) "Discrimination
against RNA Backbones by a ssDNA Binding Protein."
Structure, 26, 722-733.e2.
doi: 10.1016/j.str.2018.03.016.
|
Crystal structure of schizosaccharomyces pombe pot1pc
bound to ssrna-ssDNA chimera (ggttacrgrgru) . SNAP output
|
|
5uuf
|
hydrolase-DNA-antibiotic |
X-ray (1.612 Å) |
Mullins EA, Shi R, Eichman BF |
(2017) "Toxicity
and repair of DNA adducts produced by the natural
product yatakemycin." Nat. Chem. Biol.,
13, 1002-1008. doi: 10.1038/nchembio.2439.
|
Bacillus cereus DNA glycosylase alkd bound to a
yatakemycin-adenine nucleobase adduct and DNA
containing an abasic site (12-mer product complex) .
SNAP output
|
|
5uug
|
hydrolase-DNA-antibiotic |
X-ray (1.712 Å) |
Mullins EA, Shi R, Eichman BF |
(2017) "Toxicity
and repair of DNA adducts produced by the natural
product yatakemycin." Nat. Chem. Biol.,
13, 1002-1008. doi: 10.1038/nchembio.2439.
|
Bacillus cereus DNA glycosylase alkd bound to a
yatakemycin-adenine nucleobase adduct and DNA
containing an abasic site (9-mer product complex) .
SNAP output
|
|
5uuh
|
hydrolase-DNA-antibiotic |
X-ray (1.569 Å) |
Mullins EA, Shi R, Eichman BF |
(2017) "Toxicity
and repair of DNA adducts produced by the natural
product yatakemycin." Nat. Chem. Biol.,
13, 1002-1008. doi: 10.1038/nchembio.2439.
|
Bacillus cereus DNA glycosylase alkd bound to a
yatakemycin-adenine nucleobase adduct and DNA
containing a fluorinated abasic site (9-mer product
complex) . SNAP
output
|
|
5ux0
|
hydrolase-RNA-DNA |
X-ray (3.197 Å) |
Doxzen KW, Doudna JA |
(2017) "DNA
recognition by an RNA-guided bacterial Argonaute."
PLoS ONE, 12, e0177097. doi:
10.1371/journal.pone.0177097.
|
X-ray crystal structure of marinitoga piezophila
argonaute in complex with 5' oh guide RNA and target
DNA . SNAP output
|
|
5uzv
|
hydrolase-DNA |
X-ray (2.45 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' recessed-end DNA (ri) . SNAP output
|
|
5v04
|
hydrolase-DNA |
X-ray (2.65 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' recessed-end DNA (rii) . SNAP output
|
|
5v05
|
hydrolase-DNA |
X-ray (2.902 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' recessed-end DNA (riii) . SNAP output
|
|
5v06
|
hydrolase-DNA |
X-ray (2.75 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' recessed-end DNA (riv) . SNAP output
|
|
5v07
|
hydrolase-DNA |
X-ray (2.15 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (d173a)
in complex with 5' recessed-end DNA (rv) . SNAP output
|
|
5v08
|
hydrolase-DNA |
X-ray (2.812 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (d173a)
in complex with 5' recessed-end DNA (rvi) . SNAP output
|
|
5v09
|
hydrolase-DNA |
X-ray (2.75 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (d225a)
in complex with 5' recessed-end DNA (rvii) . SNAP output
|
|
5v0a
|
hydrolase-DNA |
X-ray (2.38 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (d225a)
in complex with 5' recessed-end DNA (rviii) . SNAP output
|
|
5v0b
|
hydrolase-DNA |
X-ray (2.63 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' recessed-end DNA (rix) . SNAP output
|
|
5v0c
|
hydrolase-DNA |
X-ray (2.58 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' flap DNA (f2i) . SNAP output
|
|
5v0d
|
hydrolase-DNA |
X-ray (2.63 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' flap DNA (f2ii) . SNAP output
|
|
5v0e
|
hydrolase-DNA |
X-ray (2.744 Å) |
Shi Y, Hellinga HW, Beese LS |
(2017) "Interplay
of catalysis, fidelity, threading, and processivity in
the exo- and endonucleolytic reactions of human
exonuclease I." Proc. Natl. Acad. Sci.
U.S.A., 114, 6010-6015. doi:
10.1073/pnas.1704845114.
|
Crystal structure of human exonuclease 1 exo1 (wt) in
complex with 5' flap DNA (f5i) . SNAP output
|
|
5v0l
|
transcription-DNA |
X-ray (4.0 Å) |
Seok SH, Lee W, Jiang L, Molugu K, Zheng A, Li Y,
Park S, Bradfield CA, Xing Y |
(2017) "Structural
hierarchy controlling dimerization and target DNA
recognition in the AHR transcriptional complex."
Proc. Natl. Acad. Sci. U.S.A.,
114, 5431-5436. doi: 10.1073/pnas.1617035114.
|
Crystal structure of the ahr-arnt heterodimer in
complex with the dre . SNAP output
|
|
5v0q
|
hydrolase-DNA |
X-ray (2.4 Å) |
Niyonzima N, Lambert AR, Werther R, De Silva Feelixge
H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL,
Jerome KR |
(2017) "Tuning
DNA binding affinity and cleavage specificity of an
engineered gene-targeting nuclease via surface display,
flow cytometry and cellular analyses." Protein
Eng. Des. Sel., 30, 503-522. doi:
10.1093/protein/gzx037.
|
Original engineered variant of i-onui meganuclease
targeting the hiv integrase gene; harbors 49 point
mutations relative to wild-type i-onui . SNAP output
|
|
5v1f
|
transferase-DNA, ligase-DNA |
X-ray (2.181 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta substrate complex with 8-oxog at
the primer terminus and incoming dctp . SNAP output
|
|
5v1g
|
transferase-DNA, ligase-DNA |
X-ray (1.798 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta binary complex with 8-oxog at the
primer terminus . SNAP
output
|
|
5v1h
|
transferase-DNA, ligase-DNA |
X-ray (1.946 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta binary complex with 8-oxog:a at the
primer terminus . SNAP
output
|
|
5v1i
|
transferase-DNA, ligase-DNA |
X-ray (2.035 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta ternary product complex with
8-oxog:c and inserted dctp . SNAP output
|
|
5v1j
|
transferase-DNA, ligase-DNA |
X-ray (2.616 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta open product complex with 8-oxog:c
and inserted dctp . SNAP
output
|
|
5v1n
|
transferase-DNA, ligase-DNA |
X-ray (2.005 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta substrate complex with 8-oxog:a at
the primer terminus and incoming dctp . SNAP output
|
|
5v1o
|
transferase-DNA, ligase-DNA |
X-ray (1.801 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta product complex with 8-oxog:a and
inserted dctp . SNAP
output
|
|
5v1p
|
transferase-DNA, ligase-DNA |
X-ray (1.991 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta substrate complex with 8-oxog:c at
the primer terminus and incoming dctp analog . SNAP output
|
|
5v1r
|
transferase-DNA, ligase-DNA |
X-ray (2.077 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta reactant complex with 8-oxog:c at
the primer terminus and incoming dctp . SNAP output
|
|
5v3g
|
transferase-DNA |
X-ray (2.416 Å) |
Patel A, Zhang X, Blumenthal RM, Cheng X |
(2017) "Structural
basis of human PR/SET domain 9 (PRDM9) allele
C-specific recognition of its cognate DNA
sequence." J. Biol. Chem.,
292, 15994-16002. doi: 10.1074/jbc.M117.805754.
|
Prdm9-allele-c znf8-13 . SNAP output
|
|
5v3j
|
transferase-DNA |
X-ray (2.064 Å) |
Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang
Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T,
Cheng X |
(2018) "DNA
Conformation Induces Adaptable Binding by Tandem Zinc
Finger Proteins." Cell,
173, 221-233.e12. doi: 10.1016/j.cell.2018.02.058.
|
Mousezfp568-znf1-10 in complex with DNA . SNAP output
|
|
5v3m
|
DNA binding protein-DNA |
X-ray (2.091 Å) |
Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang
Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T,
Cheng X |
(2018) "DNA
Conformation Induces Adaptable Binding by Tandem Zinc
Finger Proteins." Cell,
173, 221-233.e12. doi: 10.1016/j.cell.2018.02.058.
|
Mousezfp568-znf1-11 in complex with DNA . SNAP output
|
|
5v8f
|
replication |
cryo-EM (3.9 Å) |
Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C,
Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li
H |
(2017) "Structural
basis of Mcm2-7 replicative helicase loading by
ORC-Cdc6 and Cdt1." Nat. Struct. Mol.
Biol., 24, 316-324. doi: 10.1038/nsmb.3372.
|
Structural basis of mcm2-7 replicative helicase loading
by orc-cdc6 and cdt1 . SNAP output
|
|
5v9x
|
hydrolase-DNA |
X-ray (2.797 Å) |
Ejaz A, Ordonez H, Jacewicz A, Ferrao R, Shuman
S |
(2018) "Structure
of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to
a ssDNA tracking strand highlights distinctive features
of a novel family of bacterial helicases."
Nucleic Acids Res., 46,
442-455. doi: 10.1093/nar/gkx1163.
|
Structure of mycobacterium smegmatis helicase lhr bound
to ssDNA and amp-pnp . SNAP output
|
|
5va0
|
transcription-DNA |
X-ray (2.295 Å) |
Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH,
Nettles KW, Kojetin DJ, Ortlund EA |
(2017) "Tethering
not required: the glucocorticoid receptor binds
directly to activator protein-1 recognition motifs to
repress inflammatory genes." Nucleic Acids
Res., 45, 8596-8608. doi:
10.1093/nar/gkx509.
|
Glucocorticoid receptor DNA binding domain in complex
with ap-1 response element from vcam-1 promoter .
SNAP output
|
|
5va7
|
transcription-DNA |
X-ray (2.153 Å) |
Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH,
Nettles KW, Kojetin DJ, Ortlund EA |
(2017) "Tethering
not required: the glucocorticoid receptor binds
directly to activator protein-1 recognition motifs to
repress inflammatory genes." Nucleic Acids
Res., 45, 8596-8608. doi:
10.1093/nar/gkx509.
|
Glucocorticoid receptor DNA binding domain - il11 ap-1
recognition element complex . SNAP output
|
|
5vaj
|
hydrolase-RNA-DNA |
X-ray (1.95 Å) |
Mutisya D, Hardcastle T, Cheruiyot SK, Pallan PS,
Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E |
(2017) "Amide
linkages mimic phosphates in RNA interactions with
proteins and are well tolerated in the guide strand of
short interfering RNAs." Nucleic Acids
Res., 45, 8142-8155. doi:
10.1093/nar/gkx558.
|
Bhrnase h - amide-RNA-DNA complex . SNAP output
|
|
5vbs
|
transferase-DNA |
X-ray (1.749 Å) |
Singh I, Kim MJ, Molt RW, Hoshika S, Benner SA,
Georgiadis MM |
(2017) "Structure
and Biophysics for a Six Letter DNA Alphabet that
Includes
Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and
2,4-Diaminopyrimidine (K)." ACS Synth
Biol, 6, 2118-2129. doi: 10.1021/acssynbio.7b00150.
|
Structural basis for a six letter alphabet including
gatckx . SNAP output
|
|
5vc8
|
DNA binding protein |
X-ray (1.8 Å) |
Zhang M, Yang Y, Zhou M, Dong A, Yan X, Loppnau P,
Min J, Liu Y |
(2021) "Histone
and DNA binding ability studies of the NSD subfamily of
PWWP domains."
Biochem.Biophys.Res.Commun.,
569, 199-206. doi: 10.1016/j.bbrc.2021.07.017.
|
Crystal structure of the whsc1 pwwp1 domain . SNAP output
|
|
5vc9
|
DNA binding protein |
X-ray (2.1 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Zinc finger of human cxxc4 in complex with cpg DNA .
SNAP output
|
|
5vez
|
transferase-DNA, ligase-DNA |
X-ray (2.039 Å) |
Whitaker AM, Smith MR, Schaich MA, Freudenthal
BD |
(2017) "Capturing
a mammalian DNA polymerase extending from an oxidized
nucleotide." Nucleic Acids Res.,
45, 6934-6944. doi: 10.1093/nar/gkx293.
|
DNA polymerase beta substrate complex with 8-oxog:a at
the primer terminus and incoming dctp analog . SNAP output
|
|
5vfx
|
DNA binding protein-DNA |
X-ray (2.81 Å) |
Traore DAK, Wisniewski JA, Flanigan SF, Conroy PJ,
Panjikar S, Mok YF, Lao C, Griffin MDW, Adams V, Rood JI,
Whisstock JC |
(2018) "Crystal
structure of TcpK in complex with oriT DNA of the
antibiotic resistance plasmid pCW3." Nat
Commun, 9, 3732. doi: 10.1038/s41467-018-06096-2.
|
Structure of an accessory protein of the pcw3
relaxosome in complex with the origin of transfer
(orit) DNA . SNAP
output
|
|
5vhe
|
hydrolase |
X-ray (3.793 Å) |
Chen MC, Tippana R, Demeshkina NA, Murat P,
Balasubramanian S, Myong S, Ferre-D'Amare AR |
(2018) "Structural
basis of G-quadruplex unfolding by the DEAH/RHA
helicase DHX36." Nature,
558, 465-469. doi: 10.1038/s41586-018-0209-9.
|
Dhx36 in complex with the c-myc g-quadruplex . SNAP output
|
|
5vhv
|
hydrolase-DNA |
X-ray (1.799 Å) |
Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David
SS, Rokas A, Eichman BF |
(2018) "Selective
base excision repair of DNA damage by the
non-base-flipping DNA glycosylase AlkC." EMBO
J., 37, 63-74. doi: 10.15252/embj.201797833.
|
Pseudomonas fluorescens alkylpurine DNA glycosylase
alkc bound to DNA containing an
oxocarbenium-intermediate analog . SNAP output
|
|
5vi0
|
hydrolase-DNA |
X-ray (2.396 Å) |
Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David
SS, Rokas A, Eichman BF |
(2018) "Selective
base excision repair of DNA damage by the
non-base-flipping DNA glycosylase AlkC." EMBO
J., 37, 63-74. doi: 10.15252/embj.201797833.
|
Pseudomonas fluorescens alkylpurine DNA glycosylase
alkc bound to DNA containing an abasic site analog .
SNAP output
|
|
5vi5
|
transcription |
X-ray (3.196 Å) |
Hubin EA, Lilic M, Darst SA, Campbell EA |
(2017) "Structural
insights into the mycobacteria transcription initiation
complex from analysis of X-ray crystal structures."
Nat Commun, 8, 16072. doi:
10.1038/ncomms16072.
|
Structure of mycobacterium smegmatis transcription
initiation complex with a full transcription bubble .
SNAP output
|
|
5vi8
|
transcription |
X-ray (2.76 Å) |
Hubin EA, Lilic M, Darst SA, Campbell EA |
(2017) "Structural
insights into the mycobacteria transcription initiation
complex from analysis of X-ray crystal structures."
Nat Commun, 8, 16072. doi:
10.1038/ncomms16072.
|
Structure of a mycobacterium smegmatis transcription
initiation complex with an upstream-fork promoter
fragment . SNAP
output
|
|
5vl9
|
transcription-DNA |
X-ray (2.16 Å) |
Ruegg TL, Pereira JH, Chen JC, DeGiovanni A,
Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson
NJ, Simmons BA, Adams PD, Thelen MP |
(2018) "Jungle
Express is a versatile repressor system for tight
transcriptional control." Nat Commun,
9, 3617. doi: 10.1038/s41467-018-05857-3.
|
Crystal structure of eilr in complex with eilo DNA
element . SNAP
output
|
|
5vmu
|
transcription-DNA |
X-ray (2.346 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a double cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . SNAP output
|
|
5vmv
|
transcription-DNA |
X-ray (2.313 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with its double cpg-methylated DNA consensus
binding site . SNAP
output
|
|
5vmw
|
transcription-DNA |
X-ray (2.397 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a double cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . SNAP output
|
|
5vmx
|
transcription-DNA |
X-ray (2.05 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a hemi cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . SNAP output
|
|
5vmy
|
transcription-DNA |
X-ray (2.002 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a hemi cpg-methylated DNA resembling the
specific kaiso binding sequence (kbs) . SNAP output
|
|
5vmz
|
transcription-DNA |
X-ray (2.319 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2018) "CH···O
Hydrogen Bonds Mediate Highly Specific Recognition of
Methylated CpG Sites by the Zinc Finger Protein
Kaiso." Biochemistry, 57,
2109-2120. doi: 10.1021/acs.biochem.8b00065.
|
Kaiso (zbtb33) e535q mutant zinc finger DNA binding
domain in complex with a double cpg-methylated DNA
resembling the specific kaiso binding sequence (kbs) .
SNAP output
|
|
5vo8
|
transcription-DNA-RNA |
X-ray (3.3 Å) |
Murakami KS, Shin Y, Turnbough CL, Molodtsov V |
(2017) "X-ray
crystal structure of a reiterative transcription
complex reveals an atypical RNA extension pathway."
Proc. Natl. Acad. Sci. U.S.A.,
114, 8211-8216. doi: 10.1073/pnas.1702741114.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter . SNAP output
|
|
5voi
|
transcription-DNA-RNA |
X-ray (2.8 Å) |
Murakami KS, Shin Y, Turnbough CL, Molodtsov V |
(2017) "X-ray
crystal structure of a reiterative transcription
complex reveals an atypical RNA extension pathway."
Proc. Natl. Acad. Sci. U.S.A.,
114, 8211-8216. doi: 10.1073/pnas.1702741114.
|
X-ray crystal structure of bacterial RNA polymerase and
pyrg promoter complex . SNAP output
|
|
5vpe
|
transcription-DNA |
X-ray (2.053 Å) |
Yin Z, Machius M, Nestler EJ, Rudenko G |
(2017) "Activator
Protein-1: redox switch controlling structure and
DNA-binding." Nucleic Acids Res.,
45, 11425-11436. doi: 10.1093/nar/gkx795.
|
Transcription factor fosb-jund bzip domain in complex
with cognate DNA, type-i crystal . SNAP output
|
|
5vpf
|
transcription-DNA |
X-ray (2.694 Å) |
Yin Z, Machius M, Nestler EJ, Rudenko G |
(2017) "Activator
Protein-1: redox switch controlling structure and
DNA-binding." Nucleic Acids Res.,
45, 11425-11436. doi: 10.1093/nar/gkx795.
|
Transcription factor fosb-jund bzip domain in complex
with cognate DNA, type-ii crystal . SNAP output
|
|
5vrw
|
transferase, lyase-DNA |
X-ray (2.58 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta pre-catalytic 8-oxog:dc
extension complex with dttp bound in non-planar
conformation . SNAP
output
|
|
5vrx
|
transferase, lyase-DNA |
X-ray (2.2 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta pre-catalytic 8-oxog:dc
extension complex with dttp bound in watson-crick
conformation . SNAP
output
|
|
5vry
|
transferase, lyase-DNA |
X-ray (1.9 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta 8-oxog:dc extension with dttp
after 20 s . SNAP
output
|
|
5vrz
|
transferase, lyase-DNA |
X-ray (2.05 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta 8-oxog:dc extension with dttp
after 60 s . SNAP
output
|
|
5vs0
|
transferase, lyase-DNA |
X-ray (2.1 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta 8-oxog:dc extension with dttp
after 80 s . SNAP
output
|
|
5vs1
|
transferase, lyase-DNA |
X-ray (2.5 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta pre-catalytic 8-oxog:da
extension complex with dttp bound in non-planar
conformation . SNAP
output
|
|
5vs2
|
transferase, lyase-DNA |
X-ray (2.33 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta pre-catalytic 8-oxog:da
extension complex with dttp bound in watson-crick
conformation . SNAP
output
|
|
5vs3
|
transferase, lyase-DNA |
X-ray (1.7 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta 8-oxog:da extension with dttp
after 90 s . SNAP
output
|
|
5vs4
|
transferase, lyase-DNA |
X-ray (1.87 Å) |
Reed AJ, Suo Z |
(2017) "Time-Dependent
Extension from an 8-Oxoguanine Lesion by Human DNA
Polymerase Beta." J. Am. Chem. Soc.,
139, 9684-9690. doi: 10.1021/jacs.7b05048.
|
Human DNA polymerase beta 8-oxog:da extension with dttp
after 120 s . SNAP
output
|
|
5vu6
|
transferase-DNA |
X-ray (3.0 Å) |
Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC |
(2017) "Structural
basis for TNA synthesis by an engineered TNA
polymerase." Nat Commun,
8, 1810. doi: 10.1038/s41467-017-02014-0.
|
Tna polymerase binary complex with primer-template
duplex . SNAP output
|
|
5vu7
|
transferase-DNA |
X-ray (2.72 Å) |
Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC |
(2017) "Structural
basis for TNA synthesis by an engineered TNA
polymerase." Nat Commun,
8, 1810. doi: 10.1038/s41467-017-02014-0.
|
Tna polymerase, open ternary complex . SNAP output
|
|
5vu8
|
transferase-DNA |
X-ray (3.2 Å) |
Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC |
(2017) "Structural
basis for TNA synthesis by an engineered TNA
polymerase." Nat Commun,
8, 1810. doi: 10.1038/s41467-017-02014-0.
|
Tna polymerase, closed ternary complex . SNAP output
|
|
5vu9
|
transferase-DNA |
X-ray (2.05 Å) |
Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC |
(2017) "Structural
basis for TNA synthesis by an engineered TNA
polymerase." Nat Commun,
8, 1810. doi: 10.1038/s41467-017-02014-0.
|
Tna polymerase, translocated product . SNAP output
|
|
5vvj
|
hydrolase-DNA |
X-ray (3.89 Å) |
Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E,
Doudna JA |
(2017) "Structures
of the CRISPR genome integration complex."
Science, 357, 1113-1118. doi:
10.1126/science.aao0679.
|
Cas1-cas2 bound to half-site intermediate . SNAP output
|
|
5vvk
|
hydrolase-DNA |
X-ray (2.9 Å) |
Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E,
Doudna JA |
(2017) "Structures
of the CRISPR genome integration complex."
Science, 357, 1113-1118. doi:
10.1126/science.aao0679.
|
Cas1-cas2 bound to full-site mimic . SNAP output
|
|
5vvl
|
hydrolase-DNA |
X-ray (3.31 Å) |
Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E,
Doudna JA |
(2017) "Structures
of the CRISPR genome integration complex."
Science, 357, 1113-1118. doi:
10.1126/science.aao0679.
|
Cas1-cas2 bound to full-site mimic with ni . SNAP output
|
|
5vvr
|
transcription-RNA-DNA |
cryo-EM (5.8 Å) |
Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong
J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang
D |
(2017) "Structural
basis for the initiation of eukaryotic
transcription-coupled DNA repair." Nature,
551, 653-657. doi: 10.1038/nature24658.
|
Ternary complex of RNA pol ii, transcription scaffold
and rad26 . SNAP
output
|
|
5vvs
|
transcription-RNA-DNA |
cryo-EM (6.4 Å) |
Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong
J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang
D |
(2017) "Structural
basis for the initiation of eukaryotic
transcription-coupled DNA repair." Nature,
551, 653-657. doi: 10.1038/nature24658.
|
RNA pol ii elongation complex . SNAP output
|
|
5vxn
|
DNA binding protein-DNA |
X-ray (3.375 Å) |
Filippova EV, Zemaitaitis B, Aung T, Wolfe AJ,
Anderson WF |
(2018) "Structural
Basis for DNA Recognition by the Two-Component Response
Regulator RcsB." MBio, 9.
doi: 10.1128/mBio.01993-17.
|
Structure of two rcsb dimers bound to two parallel
dnas. . SNAP output
|
|
5vyc
|
ribosome |
X-ray (6.0 Å) |
Lomakin IB, Stolboushkina EA, Vaidya AT, Zhao C,
Garber MB, Dmitriev SE, Steitz TA |
(2017) "Crystal
Structure of the Human Ribosome in Complex with
DENR-MCT-1." Cell Rep,
20, 521-528. doi: 10.1016/j.celrep.2017.06.025.
|
Crystal structure of the human 40s ribosomal subunit in
complex with denr-mct-1. . SNAP output
|
|
5vz7
|
transferase-DNA |
X-ray (1.551 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Pre-catalytic ternary complex of human polymerase mu
(g433a) mutant with incoming nonhydrolyzable umpnpp .
SNAP output
|
|
5vz8
|
transferase-DNA |
X-ray (1.601 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (g433a)
mutant with incoming utp . SNAP output
|
|
5vz9
|
transferase-DNA |
X-ray (1.65 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (g433a)
mutant with incoming dttp . SNAP output
|
|
5vza
|
transferase-DNA |
X-ray (1.501 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Pre-catalytic ternary complex of human polymerase mu
(g433s) mutant with incoming nonhydrolyzable umpnpp .
SNAP output
|
|
5vzb
|
transferase-DNA |
X-ray (1.5 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (g433s)
mutant with incoming utp . SNAP output
|
|
5vzc
|
transferase-DNA |
X-ray (1.552 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (g433s)
mutant with incoming dttp . SNAP output
|
|
5vzd
|
transferase-DNA |
X-ray (1.602 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Pre-catalytic ternary complex of human polymerase mu
(w434a) mutant with incoming nonhydrolyzable umpnpp .
SNAP output
|
|
5vze
|
transferase-DNA |
X-ray (1.506 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (w434a)
mutant with incoming utp . SNAP output
|
|
5vzf
|
transferase-DNA |
X-ray (1.65 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (w434a)
mutant with incoming dttp . SNAP output
|
|
5vzg
|
transferase-DNA |
X-ray (1.85 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Pre-catalytic ternary complex of human polymerase mu
(w434h) mutant with incoming nonhydrolyzable umpnpp .
SNAP output
|
|
5vzh
|
transferase-DNA |
X-ray (1.95 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (w434h)
mutant with incoming utp . SNAP output
|
|
5vzi
|
transferase-DNA |
X-ray (1.5 Å) |
Moon AF, Pryor JM, Ramsden DA, Kunkel TA, Bebenek K,
Pedersen LC |
(2017) "Structural
accommodation of ribonucleotide incorporation by the
DNA repair enzyme polymerase Mu." Nucleic Acids
Res., 45, 9138-9148. doi:
10.1093/nar/gkx527.
|
Post-catalytic complex of human polymerase mu (w434h)
mutant with incoming dttp . SNAP output
|
|
5w0u
|
hydrolase-DNA |
X-ray (2.9 Å) |
Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H |
(2017) "AID
Recognizes Structured DNA for Class Switch
Recombination." Mol. Cell,
67, 361-373.e4. doi: 10.1016/j.molcel.2017.06.034.
|
Crystal structure of mbp fused activation-induced
cytidine deaminase (aid) in complex with dcmp .
SNAP output
|
|
5w1c
|
DNA binding protein-DNA |
X-ray (3.18 Å) |
Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H |
(2017) "AID
Recognizes Structured DNA for Class Switch
Recombination." Mol. Cell,
67, 361-373.e4. doi: 10.1016/j.molcel.2017.06.034.
|
Crystal structure of mbp fused activation-induced
cytidine deaminase (aid) in complex with cytidine .
SNAP output
|
|
5w1i
|
RNA binding protein-RNA |
X-ray (2.2 Å) |
Knott GJ, East-Seletsky A, Cofsky JC, Holton JM,
Charles E, O'Connell MR, Doudna JA |
(2017) "Guide-bound
structures of an RNA-targeting A-cleaving CRISPR-Cas13a
enzyme." Nat. Struct. Mol. Biol.,
24, 825-833. doi: 10.1038/nsmb.3466.
|
Crystal structure of lbacas13a (c2c2) bound to mature
crrna (20-nt spacer) . SNAP output
|
|
5w2a
|
replication |
X-ray (2.9 Å) |
Yockey OP, Jha V, Ghodke PP, Xu T, Xu W, Ling H,
Pradeepkumar PI, Zhao L |
(2017) "Mechanism
of Error-Free DNA Replication Past Lucidin-Derived DNA
Damage by Human DNA Polymerase kappa." Chem.
Res. Toxicol., 30, 2023-2032.
doi: 10.1021/acs.chemrestox.7b00227.
|
Structure of human DNA polymerase kappa in complex with
lucidin-derived DNA adduct and incoming dcmpnpp .
SNAP output
|
|
5w2c
|
replication |
X-ray (2.5 Å) |
Yockey OP, Jha V, Ghodke PP, Xu T, Xu W, Ling H,
Pradeepkumar PI, Zhao L |
(2017) "Mechanism
of Error-Free DNA Replication Past Lucidin-Derived DNA
Damage by Human DNA Polymerase kappa." Chem.
Res. Toxicol., 30, 2023-2032.
doi: 10.1021/acs.chemrestox.7b00227.
|
Structure of human DNA polymerase kappa in complex with
lucidin-derived DNA adduct and incoming dampnpp .
SNAP output
|
|
5w2m
|
DNA binding protein |
X-ray (3.7 Å) |
Fang Y, Xiao X, Li SX, Wolfe A, Chen XS |
(2018) "Molecular
Interactions of a DNA Modifying Enzyme APOBEC3F
Catalytic Domain with a Single-Stranded DNA."
J. Mol. Biol., 430, 87-101.
doi: 10.1016/j.jmb.2017.11.007.
|
Apobec3f catalytic domain complex with a
single-stranded DNA . SNAP output
|
|
5w34
|
transferase |
X-ray (2.95 Å) |
Hou C, Biswas T, Tsodikov OV |
(2018) "Structures
of the Catalytic Domain of Bacterial Primase DnaG in
Complexes with DNA Provide Insight into Key Priming
Events." Biochemistry,
57, 2084-2093. doi: 10.1021/acs.biochem.8b00036.
|
Crystal structure of the RNA polymerase domain (rpd) of
mycobacterium tuberculosis primase dnag in complex with
double-stranded DNA gaccggaagtgg . SNAP output
|
|
5w35
|
transferase-DNA |
X-ray (3.31 Å) |
Hou C, Biswas T, Tsodikov OV |
(2018) "Structures
of the Catalytic Domain of Bacterial Primase DnaG in
Complexes with DNA Provide Insight into Key Priming
Events." Biochemistry,
57, 2084-2093. doi: 10.1021/acs.biochem.8b00036.
|
Crystal structure of the RNA polymerase domain (rpd) of
mycobacterium tuberculosis primase dnag in complex with
a double-stranded DNA oligomer with a 1-nucleotide
overhang . SNAP
output
|
|
5w36
|
transferase |
X-ray (2.46 Å) |
Hou C, Biswas T, Tsodikov OV |
(2018) "Structures
of the Catalytic Domain of Bacterial Primase DnaG in
Complexes with DNA Provide Insight into Key Priming
Events." Biochemistry,
57, 2084-2093. doi: 10.1021/acs.biochem.8b00036.
|
Crystal structure of the RNA polymerase domain (rpd) of
mycobacterium tuberculosis primase dnag in complex with
a double-stranded DNA oligomer with a 6-nucleotide
overhang . SNAP
output
|
|
5w43
|
DNA binding protein |
X-ray (3.15 Å) |
Filippova EV, Zemaitaitis B, Aung T, Wolfe AJ,
Anderson WF |
(2018) "Structural
Basis for DNA Recognition by the Two-Component Response
Regulator RcsB." MBio, 9.
doi: 10.1128/mBio.01993-17.
|
Structure of the two-component response regulator
rcsb-DNA complex . SNAP
output
|
|
5w4u
|
DNA binding protein-RNA-DNA |
X-ray (3.6 Å) |
Wang W, Xu L, Hu L, Chong J, He C, Wang D |
(2017) "Epigenetic
DNA Modification N6-Methyladenine Causes Site-Specific
RNA Polymerase II Transcriptional Pausing."
J.Am.Chem.Soc., 139,
14436-14442. doi: 10.1021/jacs.7b06381.
|
Pol ii elongation complex with an
n6-methyladenine-containing template . SNAP output
|
|
5w51
|
DNA binding protein-RNA-DNA |
X-ray (3.404 Å) |
Wang W, Xu L, Hu L, Chong J, He C, Wang D |
(2017) "Epigenetic
DNA Modification N6-Methyladenine Causes Site-Specific
RNA Polymerase II Transcriptional Pausing."
J.Am.Chem.Soc., 139,
14436-14442. doi: 10.1021/jacs.7b06381.
|
Pol ii elongation complex with an
n6-methyladenine-containing template and a matched
umpnpp . SNAP output
|
|
5w5y
|
transcription |
cryo-EM (3.8 Å) |
Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I,
Knutson BA, He Y |
(2017) "Structural
mechanism of ATP-independent transcription initiation
by RNA polymerase I." Elife,
6. doi: 10.7554/eLife.27414.
|
RNA polymerase i initial transcribing complex .
SNAP output
|
|
5w64
|
transcription |
cryo-EM (4.2 Å) |
Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I,
Knutson BA, He Y |
(2017) "Structural
mechanism of ATP-independent transcription initiation
by RNA polymerase I." Elife,
6. doi: 10.7554/eLife.27414.
|
RNA polymerase i initial transcribing complex state 1 .
SNAP output
|
|
5w65
|
transcription |
cryo-EM (4.3 Å) |
Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I,
Knutson BA, He Y |
(2017) "Structural
mechanism of ATP-independent transcription initiation
by RNA polymerase I." Elife,
6. doi: 10.7554/eLife.27414.
|
RNA polymerase i initial transcribing complex state 2 .
SNAP output
|
|
5w66
|
transcription |
cryo-EM (3.9 Å) |
Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I,
Knutson BA, He Y |
(2017) "Structural
mechanism of ATP-independent transcription initiation
by RNA polymerase I." Elife,
6. doi: 10.7554/eLife.27414.
|
RNA polymerase i initial transcribing complex state 3 .
SNAP output
|
|
5w6k
|
DNA binding protein-DNA |
X-ray (2.339 Å) |
Singh I, Laos R, Hoshika S, Benner SA, Georgiadis
MM |
(2018) "Snapshots
of an evolved DNA polymerase pre- and
post-incorporation of an unnatural nucleotide."
Nucleic Acids Res., 46,
7977-7988. doi: 10.1093/nar/gky552.
|
Structure of mutant taq polymerase incorporating
unnatural base pairs z:p . SNAP output
|
|
5w6q
|
DNA binding protein-DNA |
X-ray (2.66 Å) |
Singh I, Laos R, Hoshika S, Benner SA, Georgiadis
MM |
(2018) "Snapshots
of an evolved DNA polymerase pre- and
post-incorporation of an unnatural nucleotide."
Nucleic Acids Res., 46,
7977-7988. doi: 10.1093/nar/gky552.
|
Structural basis for recognition of artificial DNA by
an evolved klentaq variant . SNAP output
|
|
5w7g
|
virus |
cryo-EM (4.5 Å) |
Egelman EH, Kasson PM, DiMaio F, Yu X, Lucas-Staat S,
Krupovic M, Schouten S, Prangishvili D |
(2017) "Model
for a novel membrane envelope in a filamentous
hyperthermophilic virus." Elife,
6. doi: 10.7554/eLife.26268.
|
An envelope of a filamentous hyperthermophilic virus
carries lipids in a horseshoe conformation . SNAP output
|
|
5w7n
|
hydrolase-DNA-RNA |
X-ray (1.8 Å) |
Fang Z, Yang F, Huang Z |
"2-Se-T2/4-modified-DNA and native RNA hybrid in
complex with RNase H catalytic domain D132N mutant." |
2-se-t2-4-DNA and native RNA hybrid in complex with
rnase h catalytic domain d132n mutant . SNAP output
|
|
5w7o
|
hydrolase-DNA-RNA |
X-ray (1.75 Å) |
Fang Z, Yang F, Huang Z |
"2-Se-T-modified-DNA and native RNA hybrid in complex
with RNase H catalytic domain D132N mutant." |
2-se-t4-DNA and native RNA hybrid in complex with rnase
h catalytic domain d132n mutant . SNAP output
|
|
5w9q
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Zinc finger region of mbd1 in complex with cpg DNA .
SNAP output
|
|
5w9s
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Zinc finger of human cxxc5 in complex with cpg DNA .
SNAP output
|
|
5wc9
|
DNA binding protein |
X-ray (3.15 Å) |
Agarwal S, Cho TY |
(2018) "Biochemical
and structural characterization of a novel cooperative
binding mode by Pit-1 with CATT repeats in the
macrophage migration inhibitory factor promoter."
Nucleic Acids Res., 46,
929-941. doi: 10.1093/nar/gkx1183.
|
Human pit-1 and 4xcatt DNA complex . SNAP output
|
|
5wcu
|
chromatin binding protein-DNA |
X-ray (5.53 Å) |
Zhou BR, Jiang J, Ghirlando R, Norouzi D, Sathish
Yadav KN, Feng H, Wang R, Zhang P, Zhurkin V, Bai Y |
(2018) "Revisit
of Reconstituted 30-nm Nucleosome Arrays Reveals an
Ensemble of Dynamic Structures." J. Mol.
Biol., 430, 3093-3110. doi:
10.1016/j.jmb.2018.06.020.
|
Crystal structure of 167 bp nucleosome bound to the
globular domain of linker histone h5 . SNAP output
|
|
5wfe
|
DNA binding protein-DNA |
cryo-EM (3.64 Å) |
Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E,
Doudna JA |
(2017) "Structures
of the CRISPR genome integration complex."
Science, 357, 1113-1118. doi:
10.1126/science.aao0679.
|
Cas1-cas2-ihf-DNA holo-complex . SNAP output
|
|
5wjq
|
gene regulation-DNA |
X-ray (2.794 Å) |
Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang
Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T,
Cheng X |
(2018) "DNA
Conformation Induces Adaptable Binding by Tandem Zinc
Finger Proteins." Cell,
173, 221-233.e12. doi: 10.1016/j.cell.2018.02.058.
|
Mousezfp568-znf2-11 in complex with DNA . SNAP output
|
|
5wjr
|
hydrolase |
X-ray (1.7 Å) |
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z |
(2023) "Synthesis of Pyrimidine Modified Seleno-DNA as
a Novel Approach to Antisense Candidate."
Chemistryselect, 8. doi:
10.1002/slct.202302253.
|
High resolution native hexamer DNA and RNA hybrid in
complex with rnase h catalytic domain d132n mutant .
SNAP output
|
|
5wm1
|
transferase-DNA |
X-ray (1.85 Å) |
Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE,
Aggarwal AK |
(2017) "Mechanism
of error-free replication across benzo[a]pyrene
stereoisomers by Rev1 DNA polymerase." Nat
Commun, 8, 965. doi: 10.1038/s41467-017-01013-5.
|
Structure of the 10s (+)-trans-bp-dg modified rev1
ternary complex . SNAP
output
|
|
5wm8
|
transferase-DNA |
X-ray (1.92 Å) |
Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE,
Aggarwal AK |
(2017) "Mechanism
of error-free replication across benzo[a]pyrene
stereoisomers by Rev1 DNA polymerase." Nat
Commun, 8, 965. doi: 10.1038/s41467-017-01013-5.
|
Structure of the 10r (+)-cis-bp-dg modified rev1
ternary complex . SNAP
output
|
|
5wmb
|
transferase-DNA |
X-ray (2.25 Å) |
Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE,
Aggarwal AK |
(2017) "Mechanism
of error-free replication across benzo[a]pyrene
stereoisomers by Rev1 DNA polymerase." Nat
Commun, 8, 965. doi: 10.1038/s41467-017-01013-5.
|
Structure of the 10s (-)-cis-bp-dg modified rev1
ternary complex (the bp residue is disordered) .
SNAP output
|
|
5wn0
|
hydrolase, lyase-DNA |
X-ray (2.6 Å) |
Whitaker AM, Flynn TS, Freudenthal BD |
(2018) "Molecular
snapshots of APE1 proofreading mismatches and removing
DNA damage." Nat Commun,
9, 399. doi: 10.1038/s41467-017-02175-y.
|
Ape1 exonuclease substrate complex with a c-g match .
SNAP output
|
|
5wn1
|
hydrolase, lyase-DNA |
X-ray (2.3 Å) |
Whitaker AM, Flynn TS, Freudenthal BD |
(2018) "Molecular
snapshots of APE1 proofreading mismatches and removing
DNA damage." Nat Commun,
9, 399. doi: 10.1038/s41467-017-02175-y.
|
Ape1 exonuclease product complex . SNAP output
|
|
5wn2
|
hydrolase, lyase-DNA |
X-ray (2.288 Å) |
Whitaker AM, Flynn TS, Freudenthal BD |
(2018) "Molecular
snapshots of APE1 proofreading mismatches and removing
DNA damage." Nat Commun,
9, 399. doi: 10.1038/s41467-017-02175-y.
|
Ape1 exonuclease substrate complex with
phosphoglycolate . SNAP
output
|
|
5wn3
|
hydrolase, lyase-DNA |
X-ray (2.0 Å) |
Whitaker AM, Flynn TS, Freudenthal BD |
(2018) "Molecular
snapshots of APE1 proofreading mismatches and removing
DNA damage." Nat Commun,
9, 399. doi: 10.1038/s41467-017-02175-y.
|
Ape1 f266a exonuclease substrate complex with a c-t
mismatch . SNAP
output
|
|
5wn4
|
hydrolase, lyase-DNA |
X-ray (2.1 Å) |
Whitaker AM, Flynn TS, Freudenthal BD |
(2018) "Molecular
snapshots of APE1 proofreading mismatches and removing
DNA damage." Nat Commun,
9, 399. doi: 10.1038/s41467-017-02175-y.
|
Ape1 exonuclease substrate complex with a c-t mismatch
. SNAP output
|
|
5wn5
|
hydrolase, lyase-DNA |
X-ray (2.2 Å) |
Whitaker AM, Flynn TS, Freudenthal BD |
(2018) "Molecular
snapshots of APE1 proofreading mismatches and removing
DNA damage." Nat Commun,
9, 399. doi: 10.1038/s41467-017-02175-y.
|
Ape1 exonuclease substrate complex with a c-t mismatch
and mn2+ . SNAP
output
|
|
5wnx
|
DNA ligase-DNA, transferase |
X-ray (2.55 Å) |
Schaich MA, Smith MR, Cloud AS, Holloran SM,
Freudenthal BD |
(2017) "Structures
of a DNA Polymerase Inserting Therapeutic Nucleotide
Analogues." Chem. Res. Toxicol.,
30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173.
|
DNA polymerase beta substrate complex with incoming
6-tdgtp . SNAP
output
|
|
5wny
|
DNA ligase-DNA, transferase |
X-ray (2.1 Å) |
Schaich MA, Smith MR, Cloud AS, Holloran SM,
Freudenthal BD |
(2017) "Structures
of a DNA Polymerase Inserting Therapeutic Nucleotide
Analogues." Chem. Res. Toxicol.,
30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173.
|
DNA polymerase beta substrate complex with incoming
5-fdutp . SNAP
output
|
|
5wnz
|
DNA ligase-DNA, transferase |
X-ray (2.2 Å) |
Schaich MA, Smith MR, Cloud AS, Holloran SM,
Freudenthal BD |
(2017) "Structures
of a DNA Polymerase Inserting Therapeutic Nucleotide
Analogues." Chem. Res. Toxicol.,
30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173.
|
DNA polymerase beta substrate complex with incoming
5-fodctp . SNAP
output
|
|
5wo0
|
DNA ligase-DNA, transferase |
X-ray (1.6 Å) |
Schaich MA, Smith MR, Cloud AS, Holloran SM,
Freudenthal BD |
(2017) "Structures
of a DNA Polymerase Inserting Therapeutic Nucleotide
Analogues." Chem. Res. Toxicol.,
30, 1993-2001. doi: 10.1021/acs.chemrestox.7b00173.
|
DNA polymerase beta substrate complex with incoming
5-fodutp . SNAP
output
|
|
5wti
|
hydrolase-DNA-RNA |
X-ray (2.682 Å) |
Wu D, Guan X, Zhu Y, Ren K, Huang Z |
(2017) "Structural
basis of stringent PAM recognition by CRISPR-C2c1 in
complex with sgRNA." Cell Res.,
27, 705-708. doi: 10.1038/cr.2017.46.
|
Crystal structure of the crispr-associated protein in
complex with crrna and DNA . SNAP output
|
|
5wvw
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y,
Huang L |
(2017) "Roles of
Leu28 side chain intercalation in the interaction
between Cren7 and DNA." Biochem. J.,
474, 1727-1739. doi: 10.1042/BCJ20170036.
|
The crystal structure of cren7 mutant l28a in complex
with dsDNA . SNAP
output
|
|
5wvy
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y,
Huang L |
(2017) "Roles of
Leu28 side chain intercalation in the interaction
between Cren7 and DNA." Biochem. J.,
474, 1727-1739. doi: 10.1042/BCJ20170036.
|
The crystal structure of cren7 mutant l28v in complex
with dsDNA . SNAP
output
|
|
5wvz
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y,
Huang L |
(2017) "Roles of
Leu28 side chain intercalation in the interaction
between Cren7 and DNA." Biochem. J.,
474, 1727-1739. doi: 10.1042/BCJ20170036.
|
The crystal structure of cren7 mutant l28f in complex
with dsDNA . SNAP
output
|
|
5wwc
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Zhang Z, Zhao M, Wang L, Chen Y, Dong Y, Gong Y,
Huang L |
(2017) "Roles of
Leu28 side chain intercalation in the interaction
between Cren7 and DNA." Biochem. J.,
474, 1727-1739. doi: 10.1042/BCJ20170036.
|
The crystal structure of cren7 mutant l28m in complex
with dsDNA . SNAP
output
|
|
5wx9
|
DNA binding protein-DNA |
X-ray (1.76 Å) |
Chen CY, Lin PH, Chen KH, Cheng YS |
(2020) "Structural
insights into Arabidopsis ethylene response factor 96
with an extended N-terminal binding to GCC box."
Plant Mol.Biol., 104,
483-498. doi: 10.1007/s11103-020-01052-5.
|
Crystal structure of aterf96 with gcc-box . SNAP output
|
|
5x07
|
DNA binding protein-DNA |
X-ray (2.796 Å) |
Li J, Machado ACD, Guo M, Sagendorf JM, Zhou Z, Jiang
L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen
Y |
(2017) "Structure
of the Forkhead Domain of FOXA2 Bound to a Complete DNA
Consensus Site." Biochemistry,
56, 3745-3753. doi: 10.1021/acs.biochem.7b00211.
|
Crystal structure of foxa2 DNA binding domain bound to
a full consensus DNA site . SNAP output
|
|
5x0x
|
structural protein-hydrolase-DNA |
cryo-EM (3.97 Å) |
Liu X, Li M, Xia X, Li X, Chen Z |
(2017) "Mechanism
of chromatin remodelling revealed by the
Snf2-nucleosome structure." Nature,
544, 440-445. doi: 10.1038/nature22036.
|
Complex of snf2-nucleosome complex with snf2 bound to
position +6 of the nucleosome . SNAP output
|
|
5x0y
|
structural protein-hydrolase-DNA |
cryo-EM (4.69 Å) |
Liu X, Li M, Xia X, Li X, Chen Z |
(2017) "Mechanism
of chromatin remodelling revealed by the
Snf2-nucleosome structure." Nature,
544, 440-445. doi: 10.1038/nature22036.
|
Complex of snf2-nucleosome complex with snf2 bound to
shl2 of the nucleosome . SNAP output
|
|
5x11
|
transcription-DNA |
X-ray (2.65 Å) |
Park SC, Kwak YM, Song WS, Hong M, Yoon SI |
(2017) "Structural
basis of effector and operator recognition by the
phenolic acid-responsive transcriptional regulator
PadR." Nucleic Acids Res.,
45, 13080-13093. doi: 10.1093/nar/gkx1055.
|
Crystal structure of bacillus subtilis padr in complex
with operator DNA . SNAP
output
|
|
5x21
|
transferase-DNA |
X-ray (3.323 Å) |
Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto
G, Serina S, Monciardini P, Mazzetti C, Guglierame P,
Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG,
Deho G, Donadio S, Ebright RH |
(2017) "Antibacterial
Nucleoside-Analog Inhibitor of Bacterial RNA
Polymerase." Cell, 169,
1240-1248.e23. doi: 10.1016/j.cell.2017.05.042.
|
Crystal structure of thermus thermophilus transcription
initiation complex with gpa and pseudouridimycin (pum)
. SNAP output
|
|
5x22
|
transferase-DNA |
X-ray (3.35 Å) |
Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto
G, Serina S, Monciardini P, Mazzetti C, Guglierame P,
Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG,
Deho G, Donadio S, Ebright RH |
(2017) "Antibacterial
Nucleoside-Analog Inhibitor of Bacterial RNA
Polymerase." Cell, 169,
1240-1248.e23. doi: 10.1016/j.cell.2017.05.042.
|
Crystal structure of thermus thermophilus transcription
initiation complex with gpa and cmpcpp . SNAP output
|
|
5x2g
|
hydrolase-RNA-DNA |
X-ray (2.4 Å) |
Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran
FA, Nakane T, Ishitani R, Zhang F, Nishimasu H, Nureki
O |
(2017) "Crystal
Structure of the Minimal Cas9 from Campylobacter jejuni
Reveals the Molecular Diversity in the CRISPR-Cas9
Systems." Mol. Cell, 65,
1109-1121.e3. doi: 10.1016/j.molcel.2017.02.007.
|
Crystal structure of campylobacter jejuni cas9 in
complex with sgrna and target DNA (agaaacc pam) .
SNAP output
|
|
5x2h
|
hydrolase-RNA-DNA |
X-ray (2.3 Å) |
Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran
FA, Nakane T, Ishitani R, Zhang F, Nishimasu H, Nureki
O |
(2017) "Crystal
Structure of the Minimal Cas9 from Campylobacter jejuni
Reveals the Molecular Diversity in the CRISPR-Cas9
Systems." Mol. Cell, 65,
1109-1121.e3. doi: 10.1016/j.molcel.2017.02.007.
|
Crystal structure of campylobacter jejuni cas9 in
complex with sgrna and target DNA (agaaaca pam) .
SNAP output
|
|
5x5l
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Wen Y, Ouyang Z, Yu Y, Zhou X, Pei Y, Devreese B,
Higgins PG, Zheng F |
(2017) "Mechanistic
insight into how multidrug resistant Acinetobacter
baumannii response regulator AdeR recognizes an
intercistronic region." Nucleic Acids
Res., 45, 9773-9787. doi:
10.1093/nar/gkx624.
|
Crystal structure of response regulator ader DNA
binding domain in complex with an intercistronic region
. SNAP output
|
|
5x6d
|
DNA binding proten-DNA |
X-ray (2.94 Å) |
Wang Y, Feng H, Zhu Y, Gao P |
(2017) "Structural
insights into glutathione-mediated activation of the
master regulator PrfA in Listeria monocytogenes."
Protein Cell, 8, 308-312.
doi: 10.1007/s13238-017-0390-x.
|
Crystal structure of prfa-DNA binary complex . SNAP output
|
|
5x6e
|
DNA binding protein-DNA |
X-ray (2.99 Å) |
Wang Y, Feng H, Zhu Y, Gao P |
(2017) "Structural
insights into glutathione-mediated activation of the
master regulator PrfA in Listeria monocytogenes."
Protein Cell, 8, 308-312.
doi: 10.1007/s13238-017-0390-x.
|
Crystal structure of prfa-DNA binary complex . SNAP output
|
|
5x6g
|
metal binding protein-DNA |
X-ray (3.05 Å) |
Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW |
(2015) "Structural
basis for the Smad5 MH1 domain to recognize different
DNA sequences." Nucleic Acids Res.,
43, 9051-9064. doi: 10.1093/nar/gkv848.
|
Crystal structure of smad5-mh1-palindromic sbe DNA
complex . SNAP
output
|
|
5x6h
|
metal binding protein-DNA |
X-ray (3.1 Å) |
Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW |
(2015) "Structural
basis for the Smad5 MH1 domain to recognize different
DNA sequences." Nucleic Acids Res.,
43, 9051-9064. doi: 10.1093/nar/gkv848.
|
Crystal structure of smad5-mh1-gc-bre DNA complex .
SNAP output
|
|
5x6m
|
metal binding protein-DNA |
X-ray (3.2 Å) |
Chai N, Li WX, Wang J, Wang ZX, Yang SM, Wu JW |
(2015) "Structural
basis for the Smad5 MH1 domain to recognize different
DNA sequences." Nucleic Acids Res.,
43, 9051-9064. doi: 10.1093/nar/gkv848.
|
Crystal structure of smad5-mh1 in complex with a
composite DNA sequence . SNAP output
|
|
5x7x
|
structural protein-DNA |
X-ray (2.184 Å) |
Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A,
Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T,
Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y,
Kurumizaka H |
(2017) "Crystal
Structure and Characterization of Novel Human Histone
H3 Variants, H3.6, H3.7, and H3.8."
Biochemistry, 56, 2184-2196.
doi: 10.1021/acs.biochem.6b01098.
|
The crystal structure of the nucleosome containing h3.3
at 2.18 angstrom resolution . SNAP output
|
|
5xf3
|
structural protein-DNA |
X-ray (2.6 Å) |
Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D,
Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS,
Dyson PJ, Davey CA |
(2017) "Nucleosome
acidic patch-targeting binuclear ruthenium compounds
induce aberrant chromatin condensation." Nat
Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4.
|
Nucleosome core particle with an adduct of a binuclear
rapta (ru-arene-phosphaadamantane) compound having a
1,2-diphenylethylenediamine linker (r,r-configuration)
. SNAP output
|
|
5xf4
|
structural protein-DNA |
X-ray (2.87 Å) |
Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D,
Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS,
Dyson PJ, Davey CA |
(2017) "Nucleosome
acidic patch-targeting binuclear ruthenium compounds
induce aberrant chromatin condensation." Nat
Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4.
|
Nucleosome core particle with an adduct of a binuclear
rapta (ru-arene-phosphaadamantane) compound having a
1,2-diphenylethylenediamine linker (s,s-configuration)
. SNAP output
|
|
5xf5
|
structural protein-DNA |
X-ray (2.82 Å) |
Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D,
Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS,
Dyson PJ, Davey CA |
(2017) "Nucleosome
acidic patch-targeting binuclear ruthenium compounds
induce aberrant chromatin condensation." Nat
Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4.
|
Nucleosome core particle with an adduct of a binuclear
rapta (ru-arene-phosphaadamantane) compound having a
1,2-diphenylethylenediamine linker (r,s-configuration)
. SNAP output
|
|
5xf6
|
structural protein-DNA |
X-ray (2.63 Å) |
Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D,
Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS,
Dyson PJ, Davey CA |
(2017) "Nucleosome
acidic patch-targeting binuclear ruthenium compounds
induce aberrant chromatin condensation." Nat
Commun, 8, 1575. doi: 10.1038/s41467-017-01680-4.
|
Nucleosome core particle with an adduct of a binuclear
rapta (ru-arene-phosphaadamantane) compound having an
ethylenediamine linker . SNAP output
|
|
5xfp
|
transcription-DNA |
X-ray (2.3 Å) |
Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P,
Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z |
(2017) "Polycomb-like
proteins link the PRC2 complex to CpG islands."
Nature, 549, 287-291. doi:
10.1038/nature23881.
|
Binary complex of phf1 and a double stranded DNA .
SNAP output
|
|
5xfq
|
transcription-DNA |
X-ray (2.4 Å) |
Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P,
Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z |
(2017) "Polycomb-like
proteins link the PRC2 complex to CpG islands."
Nature, 549, 287-291. doi:
10.1038/nature23881.
|
Ternary complex of phf1, a DNA duplex and a histone
peptide . SNAP
output
|
|
5xfr
|
transcription-DNA |
X-ray (2.25 Å) |
Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P,
Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z |
(2017) "Polycomb-like
proteins link the PRC2 complex to CpG islands."
Nature, 549, 287-291. doi:
10.1038/nature23881.
|
Ternary complex of mtf2, DNA and histone . SNAP output
|
|
5xh6
|
hydrolase-RNA-DNA |
X-ray (2.0 Å) |
Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R,
Nureki O |
(2017) "Structural
Basis for the Altered PAM Recognition by Engineered
CRISPR-Cpf1." Mol. Cell,
67, 139-147.e2. doi: 10.1016/j.molcel.2017.04.019.
|
Crystal structure of the acidaminococcus sp. bv3l6 cpf1
rvr variant in complex with crrna and target DNA (tata
pam) . SNAP output
|
|
5xh7
|
hydrolase-RNA-DNA |
X-ray (2.0 Å) |
Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R,
Nureki O |
(2017) "Structural
Basis for the Altered PAM Recognition by Engineered
CRISPR-Cpf1." Mol. Cell,
67, 139-147.e2. doi: 10.1016/j.molcel.2017.04.019.
|
Crystal structure of the acidaminococcus sp. bv3l6 cpf1
rr variant in complex with crrna and target DNA (tcca
pam) . SNAP output
|
|
5xm0
|
structural protein-DNA |
X-ray (2.874 Å) |
Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K,
Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S,
Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H,
Ohkawa Y |
(2018) "Histone
H3.3 sub-variant H3mm7 is required for normal skeletal
muscle regeneration." Nat Commun,
9, 1400. doi: 10.1038/s41467-018-03845-1.
|
The mouse nucleosome structure containing h2a, h2b
type3-a, h3.3, and h4 . SNAP output
|
|
5xm1
|
structural protein-DNA |
X-ray (3.45 Å) |
Harada A, Maehara K, Ono Y, Taguchi H, Yoshioka K,
Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S,
Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H,
Ohkawa Y |
(2018) "Histone
H3.3 sub-variant H3mm7 is required for normal skeletal
muscle regeneration." Nat Commun,
9, 1400. doi: 10.1038/s41467-018-03845-1.
|
The mouse nucleosome structure containing h2a, h2b
type3-a, h3mm7, and h4 . SNAP output
|
|
5xm8
|
transferase-DNA |
X-ray (2.55 Å) |
Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L,
Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J,
Huang Z, Ma J, Gan J |
(2017) "Crystal
structure of an RNA-cleaving DNAzyme." Nat
Commun, 8, 2006. doi: 10.1038/s41467-017-02203-x.
|
Crystal structure of asfvpolx in complex with DNA
enzyme and pb. . SNAP
output
|
|
5xm9
|
transferase-DNA |
X-ray (3.053 Å) |
Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L,
Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J,
Huang Z, Ma J, Gan J |
(2017) "Crystal
structure of an RNA-cleaving DNAzyme." Nat
Commun, 8, 2006. doi: 10.1038/s41467-017-02203-x.
|
Crystal structure of asfvpolx in complex with DNA
enzyme. . SNAP
output
|
|
5xma
|
transferase-DNA |
X-ray (3.8 Å) |
Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L,
Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J,
Huang Z, Ma J, Gan J |
(2017) "Crystal
structure of an RNA-cleaving DNAzyme." Nat
Commun, 8, 2006. doi: 10.1038/s41467-017-02203-x.
|
Crystal structure of asfvpolx in complex with DNA
enzyme at p43212 space group . SNAP output
|
|
5xn0
|
transferase-DNA |
X-ray (2.596 Å) |
Yasutake Y, Hattori SI, Hayashi H, Matsuda K, Tamura
N, Kohgo S, Maeda K, Mitsuya H |
(2018) "HIV-1
with HBV-associated Q151M substitution in RT becomes
highly susceptible to entecavir: structural insights
into HBV-RT inhibition by entecavir." Sci
Rep, 8, 1624. doi: 10.1038/s41598-018-19602-9.
|
Hiv-1 reverse transcriptase q151m:DNA binary complex .
SNAP output
|
|
5xn1
|
transferase-DNA |
X-ray (2.446 Å) |
Yasutake Y, Hattori SI, Hayashi H, Matsuda K, Tamura
N, Kohgo S, Maeda K, Mitsuya H |
(2018) "HIV-1
with HBV-associated Q151M substitution in RT becomes
highly susceptible to entecavir: structural insights
into HBV-RT inhibition by entecavir." Sci
Rep, 8, 1624. doi: 10.1038/s41598-018-19602-9.
|
Hiv-1 reverse transcriptase
q151m:DNA:entecavir-triphosphate ternary complex .
SNAP output
|
|
5xn2
|
transferase-DNA |
X-ray (2.381 Å) |
Yasutake Y, Hattori SI, Hayashi H, Matsuda K, Tamura
N, Kohgo S, Maeda K, Mitsuya H |
(2018) "HIV-1
with HBV-associated Q151M substitution in RT becomes
highly susceptible to entecavir: structural insights
into HBV-RT inhibition by entecavir." Sci
Rep, 8, 1624. doi: 10.1038/s41598-018-19602-9.
|
Hiv-1 reverse transcriptase q151m:DNA:dgtp ternary
complex . SNAP
output
|
|
5xog
|
transcription |
X-ray (3.0 Å) |
Ehara H, Yokoyama T, Shigematsu H, Yokoyama S,
Shirouzu M, Sekine SI |
(2017) "Structure
of the complete elongation complex of RNA polymerase II
with basal factors." Science,
357, 921-924. doi: 10.1126/science.aan8552.
|
RNA polymerase ii elongation complex bound with spt5
kow5 and elf1 . SNAP
output
|
|
5xon
|
transcription-RNA |
cryo-EM (3.83 Å) |
Ehara H, Yokoyama T, Shigematsu H, Yokoyama S,
Shirouzu M, Sekine SI |
(2017) "Structure
of the complete elongation complex of RNA polymerase II
with basal factors." Science,
357, 921-924. doi: 10.1126/science.aan8552.
|
RNA polymerase ii elongation complex bound with spt4-5
and tfiis . SNAP
output
|
|
5xou
|
DNA binding protein |
X-ray (2.63 Å) |
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A,
Juranek S, Tuschl T, Patel DJ, Wang Y |
(2017) "Structure/cleavage-based
insights into helical perturbations at bulge sites
within T. thermophilus Argonaute silencing
complexes." Nucleic Acids Res.,
45, 9149-9163. doi: 10.1093/nar/gkx547.
|
Crystal structure of t. thermophilus argonaute protein
complexed with a bulge 7t8 on the guide strand .
SNAP output
|
|
5xow
|
DNA binding protein |
X-ray (2.902 Å) |
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A,
Juranek S, Tuschl T, Patel DJ, Wang Y |
(2017) "Structure/cleavage-based
insights into helical perturbations at bulge sites
within T. thermophilus Argonaute silencing
complexes." Nucleic Acids Res.,
45, 9149-9163. doi: 10.1093/nar/gkx547.
|
Crystal structure of t. thermophilus argonaute protein
complexed with a bulge 6'a7' on the target strand .
SNAP output
|
|
5xp8
|
DNA binding protein |
X-ray (3.1 Å) |
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A,
Juranek S, Tuschl T, Patel DJ, Wang Y |
(2017) "Structure/cleavage-based
insights into helical perturbations at bulge sites
within T. thermophilus Argonaute silencing
complexes." Nucleic Acids Res.,
45, 9149-9163. doi: 10.1093/nar/gkx547.
|
Crystal structure of t. thermophilus argonaute protein
complexed with a bulge 4a5 on the guide strand .
SNAP output
|
|
5xpa
|
DNA binding protein |
X-ray (2.9 Å) |
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A,
Juranek S, Tuschl T, Patel DJ, Wang Y |
(2017) "Structure/cleavage-based
insights into helical perturbations at bulge sites
within T. thermophilus Argonaute silencing
complexes." Nucleic Acids Res.,
45, 9149-9163. doi: 10.1093/nar/gkx547.
|
Crystal structure of t. thermophilus argonaute protein
complexed with a bulge 9'u10' on the target strand .
SNAP output
|
|
5xpg
|
DNA binding protein |
X-ray (2.8 Å) |
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A,
Juranek S, Tuschl T, Patel DJ, Wang Y |
(2017) "Structure/cleavage-based
insights into helical perturbations at bulge sites
within T. thermophilus Argonaute silencing
complexes." Nucleic Acids Res.,
45, 9149-9163. doi: 10.1093/nar/gkx547.
|
Crystal structure of t. thermophilus argonaute protein
complexed with a bulge 6'u7' on the target strand .
SNAP output
|
|
5xq2
|
DNA binding protein |
X-ray (3.33 Å) |
Sheng G, Gogakos T, Wang J, Zhao H, Serganov A,
Juranek S, Tuschl T, Patel DJ, Wang Y |
(2017) "Structure/cleavage-based
insights into helical perturbations at bulge sites
within T. thermophilus Argonaute silencing
complexes." Nucleic Acids Res.,
45, 9149-9163. doi: 10.1093/nar/gkx547.
|
Crystal structure of t. thermophilus argonaute protein
complexed with a bulge 5a6 on the guide strand .
SNAP output
|
|
5xrz
|
recombination |
X-ray (3.6 Å) |
Saotome M, Saito K, Yasuda T, Ohtomo H, Sugiyama S,
Nishimura Y, Kurumizaka H, Kagawa W |
(2018) "Structural
Basis of Homology-Directed DNA Repair Mediated by
RAD52." iScience, 3,
50-62. doi: 10.1016/j.isci.2018.04.005.
|
Structure of a ssDNA bound to the inner DNA binding
site of rad52 . SNAP
output
|
|
5xs0
|
recombination |
X-ray (3.0 Å) |
Saotome M, Saito K, Yasuda T, Ohtomo H, Sugiyama S,
Nishimura Y, Kurumizaka H, Kagawa W |
(2018) "Structural
Basis of Homology-Directed DNA Repair Mediated by
RAD52." iScience, 3,
50-62. doi: 10.1016/j.isci.2018.04.005.
|
Structure of a ssDNA bound to the outer DNA binding
site of rad52 . SNAP
output
|
|
5xsk
|
hormone |
X-ray (2.84 Å) |
Chen LY, Huang YC, Hsieh YC, Lin PJ |
"Structure of PWWP-DNA complex at 2.84 Angstroms
resolution." |
Crystal structure of pwwp-DNA complex for human
hepatoma-derived growth factor . SNAP output
|
|
5xus
|
hydrolase-RNA-DNA |
X-ray (2.5 Å) |
Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu
H, Nureki O |
(2017) "Structural
Basis for the Canonical and Non-canonical PAM
Recognition by CRISPR-Cpf1." Mol. Cell,
67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035.
|
Crystal structure of lachnospiraceae bacterium nd2006
cpf1 in complex with crrna and target DNA (ttta pam) .
SNAP output
|
|
5xut
|
hydrolase-RNA-DNA |
X-ray (2.4 Å) |
Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu
H, Nureki O |
(2017) "Structural
Basis for the Canonical and Non-canonical PAM
Recognition by CRISPR-Cpf1." Mol. Cell,
67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035.
|
Crystal structure of lachnospiraceae bacterium nd2006
cpf1 in complex with crrna and target DNA (tcta pam) .
SNAP output
|
|
5xuu
|
hydrolase-RNA-DNA |
X-ray (2.5 Å) |
Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu
H, Nureki O |
(2017) "Structural
Basis for the Canonical and Non-canonical PAM
Recognition by CRISPR-Cpf1." Mol. Cell,
67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035.
|
Crystal structure of lachnospiraceae bacterium nd2006
cpf1 in complex with crrna and target DNA (tcca pam) .
SNAP output
|
|
5xuz
|
hydrolase-RNA-DNA |
X-ray (2.4 Å) |
Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu
H, Nureki O |
(2017) "Structural
Basis for the Canonical and Non-canonical PAM
Recognition by CRISPR-Cpf1." Mol. Cell,
67, 633-645.e3. doi: 10.1016/j.molcel.2017.06.035.
|
Crystal structure of lachnospiraceae bacterium nd2006
cpf1 in complex with crrna and target DNA (ccca pam) .
SNAP output
|
|
5xvn
|
immune system |
X-ray (3.25 Å) |
Xiao Y, Ng S, Hyun Nam K, Ke A |
(2017) "How type
II CRISPR-Cas establish immunity through
Cas1-Cas2-mediated spacer integration."
Nature, 550, 137-141. doi:
10.1038/nature24020.
|
E. far cas1-cas2-prespacer binary complex . SNAP output
|
|
5xvo
|
immune system |
X-ray (3.1 Å) |
Xiao Y, Ng S, Hyun Nam K, Ke A |
(2017) "How type
II CRISPR-Cas establish immunity through
Cas1-Cas2-mediated spacer integration."
Nature, 550, 137-141. doi:
10.1038/nature24020.
|
E. fae cas1-cas2-prespacer-target ternary complex
revealing DNA sampling and half-integration states .
SNAP output
|
|
5xvp
|
immune system |
X-ray (3.0 Å) |
Xiao Y, Ng S, Hyun Nam K, Ke A |
(2017) "How type
II CRISPR-Cas establish immunity through
Cas1-Cas2-mediated spacer integration."
Nature, 550, 137-141. doi:
10.1038/nature24020.
|
E. fae cas1-cas2-prespacer-target ternary complex
revealing the fully integrated states . SNAP output
|
|
5xxp
|
DNA binding protein |
X-ray (2.55 Å) |
Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda
T |
(2018) "Crystal
structure of the DNA-binding domain of the LysR-type
transcriptional regulator CbnR in complex with a DNA
fragment of the recognition-binding site in the
promoter region." FEBS J.,
285, 977-989. doi: 10.1111/febs.14380.
|
Crystal structure of cbnr_dbd-DNA complex . SNAP output
|
|
5xzb
|
immune system-inhibitor |
X-ray (2.13 Å) |
Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y,
Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T,
Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ,
Glickman JF, Ascano M |
(2017) "Small
molecule inhibition of cGAS reduces interferon
expression in primary macrophages from autoimmune
mice." Nat Commun, 8,
750. doi: 10.1038/s41467-017-00833-9.
|
Mouse cgas bound to the inhibitor ru365 . SNAP output
|
|
5xze
|
immune system-inhibitor |
X-ray (2.177 Å) |
Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y,
Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T,
Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ,
Glickman JF, Ascano M |
(2017) "Small
molecule inhibition of cGAS reduces interferon
expression in primary macrophages from autoimmune
mice." Nat Commun, 8,
750. doi: 10.1038/s41467-017-00833-9.
|
Mouse cgas bound to the inhibitor ru332 . SNAP output
|
|
5xzg
|
immune system-inhibitor |
X-ray (1.828 Å) |
Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y,
Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T,
Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ,
Glickman JF, Ascano M |
(2017) "Small
molecule inhibition of cGAS reduces interferon
expression in primary macrophages from autoimmune
mice." Nat Commun, 8,
750. doi: 10.1038/s41467-017-00833-9.
|
Mouse cgas bound to the inhibitor ru521 . SNAP output
|
|
5y0c
|
DNA binding protein-DNA |
X-ray (2.087 Å) |
Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W,
Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa
Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H |
(2018) "Cancer-associated
mutations of histones H2B, H3.1 and H2A.Z.1 affect the
structure and stability of the nucleosome."
Nucleic Acids Res., 46,
10007-10018. doi: 10.1093/nar/gky661.
|
Crystal structure of the human nucleosome at 2.09
angstrom resolution . SNAP output
|
|
5y0d
|
DNA binding protein-DNA |
X-ray (1.99 Å) |
Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W,
Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa
Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H |
(2018) "Cancer-associated
mutations of histones H2B, H3.1 and H2A.Z.1 affect the
structure and stability of the nucleosome."
Nucleic Acids Res., 46,
10007-10018. doi: 10.1093/nar/gky661.
|
Crystal structure of the human nucleosome containing
the h2b e76k mutant . SNAP output
|
|
5y36
|
hydrolase-RNA-DNA |
cryo-EM (5.2 Å) |
Huai C, Li G, Yao R, Zhang Y, Cao M, Kong L, Jia C,
Yuan H, Chen H, Lu D, Huang Q |
(2017) "Structural
insights into DNA cleavage activation of CRISPR-Cas9
system." Nat Commun, 8,
1375. doi: 10.1038/s41467-017-01496-2.
|
cryo-EM structure of spcas9-sgrna-DNA ternary complex .
SNAP output
|
|
5y3j
|
immune system |
X-ray (1.81 Å) |
Ohto U, Ishida H, Shibata T, Sato R, Miyake K,
Shimizu T |
(2018) "Toll-like
Receptor 9 Contains Two DNA Binding Sites that Function
Cooperatively to Promote Receptor Dimerization and
Activation." Immunity,
48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013.
|
Crystal structure of horse tlr9 in complex with two
dnas (cpg DNA and tcgcac DNA) . SNAP output
|
|
5y3k
|
immune system |
X-ray (2.7 Å) |
Ohto U, Ishida H, Shibata T, Sato R, Miyake K,
Shimizu T |
(2018) "Toll-like
Receptor 9 Contains Two DNA Binding Sites that Function
Cooperatively to Promote Receptor Dimerization and
Activation." Immunity,
48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013.
|
Crystal structure of horse tlr9 in complex with two
dnas (cpg DNA and gcgcac DNA) . SNAP output
|
|
5y3l
|
immune system |
X-ray (2.6 Å) |
Ohto U, Ishida H, Shibata T, Sato R, Miyake K,
Shimizu T |
(2018) "Toll-like
Receptor 9 Contains Two DNA Binding Sites that Function
Cooperatively to Promote Receptor Dimerization and
Activation." Immunity,
48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013.
|
Crystal structure of horse tlr9 in complex with two
dnas (cpg DNA and ccgcac DNA) . SNAP output
|
|
5y3m
|
immune system |
X-ray (2.5 Å) |
Ohto U, Ishida H, Shibata T, Sato R, Miyake K,
Shimizu T |
(2018) "Toll-like
Receptor 9 Contains Two DNA Binding Sites that Function
Cooperatively to Promote Receptor Dimerization and
Activation." Immunity,
48, 649-658.e4. doi: 10.1016/j.immuni.2018.03.013.
|
Crystal structure of bovine tlr9 in complex with two
dnas (cpg DNA and tcgttt DNA) . SNAP output
|
|
5y3r
|
DNA binding protein |
cryo-EM (6.6 Å) |
Yin X, Liu M, Tian Y, Wang J, Xu Y |
(2017) "Cryo-EM
structure of human DNA-PK holoenzyme." Cell
Res., 27, 1341-1350. doi:
10.1038/cr.2017.110.
|
cryo-EM structure of human DNA-pk holoenzyme . SNAP output
|
|
5y7g
|
hydrolase-DNA |
X-ray (3.4 Å) |
Jin H, Roy U, Lee G, Scharer OD, Cho Y |
(2018) "Structural
mechanism of DNA interstrand cross-link unhooking by
the bacterial FAN1 nuclease." J. Biol.
Chem., 293, 6482-6496. doi:
10.1074/jbc.RA118.002171.
|
Crystal structure of pafan1 bound to 1nt 5'flap DNA
with gap . SNAP
output
|
|
5y7q
|
hydrolase-DNA |
X-ray (2.7 Å) |
Jin H, Roy U, Lee G, Scharer OD, Cho Y |
(2018) "Structural
mechanism of DNA interstrand cross-link unhooking by
the bacterial FAN1 nuclease." J. Biol.
Chem., 293, 6482-6496. doi:
10.1074/jbc.RA118.002171.
|
Crystal structure of pafan1 bound to 2nt 5'flap DNA
with gap . SNAP
output
|
|
5ybb
|
DNA binding protein-DNA |
X-ray (3.2 Å) |
Liu YP, Tang Q, Zhang JZ, Tian LF, Gao P, Yan XX |
(2017) "Structural
basis underlying complex assembly and conformational
transition of the type I R-M system." Proc.
Natl. Acad. Sci. U.S.A., 114,
11151-11156. doi: 10.1073/pnas.1711754114.
|
Structural basis underlying complex assembly
andconformational transition of the type i r-m system .
SNAP output
|
|
5ybd
|
DNA binding protein |
X-ray (2.769 Å) |
Sharma R, Gangwar SP, Saxena AK |
(2018) "Comparative
structure analysis of the ETSi domain of ERG3 and its
complex with the E74 promoter DNA sequence."
Acta Crystallogr F Struct Biol Commun,
74, 656-663. doi: 10.1107/S2053230X1801110X.
|
X-ray structure of ets domain of ergp55 in complex with
e74DNA . SNAP output
|
|
5yef
|
DNA binding protein-DNA |
X-ray (2.807 Å) |
Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang
Y |
(2017) "Molecular
mechanism of directional CTCF recognition of a diverse
range of genomic sites." Cell Res.,
27, 1365-1377. doi: 10.1038/cr.2017.131.
|
Crystal structure of ctcf zfs2-8-hs5-1ae . SNAP output
|
|
5yeg
|
DNA binding protein |
X-ray (2.0 Å) |
Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang
Y |
(2017) "Molecular
mechanism of directional CTCF recognition of a diverse
range of genomic sites." Cell Res.,
27, 1365-1377. doi: 10.1038/cr.2017.131.
|
Crystal structure of ctcf zfs4-8-hs5-1a complex .
SNAP output
|
|
5yeh
|
DNA binding protein-DNA |
X-ray (2.328 Å) |
Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang
Y |
(2017) "Molecular
mechanism of directional CTCF recognition of a diverse
range of genomic sites." Cell Res.,
27, 1365-1377. doi: 10.1038/cr.2017.131.
|
Crystal structure of ctcf zfs4-8-ecbs . SNAP output
|
|
5yej
|
DNA binding protein-DNA |
X-ray (2.698 Å) |
Yan L, Tang Q, Guan Z, Pei K, Zou T, He J |
(2018) "Structural
insights into operator recognition by BioQ in the
Mycobacterium smegmatis biotin synthesis pathway."
Biochim Biophys Acta Gen Subj,
1862, 1843-1851. doi: 10.1016/j.bbagen.2018.05.015.
|
Crystal structure of bioq with its naturel
double-stranded DNA operator . SNAP output
|
|
5yel
|
DNA binding protein-DNA |
X-ray (2.96 Å) |
Yin M, Wang J, Wang M, Li X, Zhang M, Wu Q, Wang
Y |
(2017) "Molecular
mechanism of directional CTCF recognition of a diverse
range of genomic sites." Cell Res.,
27, 1365-1377. doi: 10.1038/cr.2017.131.
|
Crystal structure of ctcf zfs6-11-gb7cse . SNAP output
|
|
5yi2
|
metal binding protein |
X-ray (2.6 Å) |
Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen
PR |
(2017) "Allosteric
histidine switch for regulation of intracellular
zinc(II) fluctuation."
Proc.Natl.Acad.Sci.USA, 114,
13661-13666. doi: 10.1073/pnas.1708563115.
|
Structure of lactococcus lactis zitr, wild type in
complex with DNA . SNAP
output
|
|
5yi3
|
metal binding protein-DNA |
X-ray (2.9 Å) |
Zhu R, Song Y, Liu H, Yang Y, Wang S, Yi C, Chen
PR |
(2017) "Allosteric
histidine switch for regulation of intracellular
zinc(II) fluctuation."
Proc.Natl.Acad.Sci.USA, 114,
13661-13666. doi: 10.1073/pnas.1708563115.
|
Structure of lactococcus lactis zitr, c30s mutant in
complex with DNA . SNAP
output
|
|
5yiv
|
DNA binding protein-DNA |
X-ray (2.914 Å) |
Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L,
Zhuang N, Laub MT, Zhang Y |
(2018) "Structural
insights into the unique mechanism of transcription
activation by Caulobacter crescentus GcrA."
Nucleic Acids Res., 46,
3245-3256. doi: 10.1093/nar/gky161.
|
Caulobacter crescentus gcra DNA-binding domain(dbd) in
complex with methylated dsDNA(crystal form 1) .
SNAP output
|
|
5yiw
|
DNA binding protein-DNA |
X-ray (1.551 Å) |
Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L,
Zhuang N, Laub MT, Zhang Y |
(2018) "Structural
insights into the unique mechanism of transcription
activation by Caulobacter crescentus GcrA."
Nucleic Acids Res., 46,
3245-3256. doi: 10.1093/nar/gky161.
|
Caulobacter crescentus gcra DNA-binding domain (dbd) in
complex with methylated dsDNA (crystal form 2) .
SNAP output
|
|
5yj3
|
DNA binding protein-DNA |
X-ray (2.845 Å) |
Zhao Y, Zhang G, He C, Mei Y, Shi Y, Li F |
(2018) "The 11th
C2H2 zinc finger and an adjacent C-terminal arm are
responsible for TZAP recognition of telomeric DNA."
Cell Res., 28, 130-134. doi:
10.1038/cr.2017.141.
|
Crystal structure of tzap and telomeric DNA complex .
SNAP output
|
|
5ytc
|
transferase-DNA |
X-ray (2.28 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Large fragment of DNA polymerase i from thermus
aquaticus in a closed ternary complex with the
unnatural base m-fc pair with datp in the active site .
SNAP output
|
|
5ytd
|
replication-DNA |
X-ray (2.0 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Large fragment of DNA polymerase i from thermus
aquaticus in a closed ternary complex with the natural
base pair 5fc:dgtp . SNAP output
|
|
5yte
|
replication-DNA |
X-ray (2.21 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Large fragment of DNA polymerase i from thermus
aquaticus in a closed ternary complex with with natural
dt:datp base pair . SNAP
output
|
|
5ytf
|
transferase-DNA |
X-ray (1.98 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Structure of large fragment of DNA polymerase i from
thermus aquaticus host-guest complex with the unnatural
base m-fc pair with da . SNAP output
|
|
5ytg
|
transferase-DNA |
X-ray (2.07 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Structure of large fragment of DNA polymerase i from
thermus aquaticus host-guest complex with the unnatural
base i-fc pair with da . SNAP output
|
|
5yth
|
transferase-DNA |
X-ray (2.53 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Structure of large fragment of DNA polymerase i from
thermus aquaticus host-guest complex with the unnatural
base m-fc pair with dg . SNAP output
|
|
5yty
|
antibiotic-DNA |
X-ray (1.58 Å) |
Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou
MH |
(2018) "Cooperative
recognition of T:T mismatch by echinomycin causes
structural distortions in DNA duplex." Nucleic
Acids Res., 46, 7396-7404. doi:
10.1093/nar/gky345.
|
Crystal structure of echinomycin-d(acgacgt-acgtcgt)
complex . SNAP
output
|
|
5ytz
|
antibiotic-DNA |
X-ray (1.55 Å) |
Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou
MH |
(2018) "Cooperative
recognition of T:T mismatch by echinomycin causes
structural distortions in DNA duplex." Nucleic
Acids Res., 46, 7396-7404. doi:
10.1093/nar/gky345.
|
Crystal structure of echinomycin-d(acgtcgt)2 complex .
SNAP output
|
|
5yur
|
DNA binding protein-DNA |
X-ray (2.035 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 1 . SNAP output
|
|
5yus
|
DNA binding protein-DNA |
X-ray (1.94 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 2 . SNAP output
|
|
5yut
|
DNA binding protein-DNA |
X-ray (2.15 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 3 . SNAP output
|
|
5yuu
|
DNA binding protein-DNA |
X-ray (1.892 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 4 . SNAP output
|
|
5yuv
|
DNA binding protein-DNA |
X-ray (2.06 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 5 . SNAP output
|
|
5yuw
|
DNA binding protein-dan |
X-ray (2.124 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 6 . SNAP output
|
|
5yux
|
DNA binding protein-DNA |
X-ray (2.04 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 8 . SNAP output
|
|
5yuy
|
DNA binding protein-DNA |
X-ray (1.74 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 9 . SNAP output
|
|
5yuz
|
DNA binding protein-DNA |
X-ray (1.83 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 11 . SNAP output
|
|
5yv0
|
DNA binding protein-DNA |
X-ray (2.09 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 12 . SNAP output
|
|
5yv1
|
DNA binding protein-DNA |
X-ray (2.09 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 13 . SNAP output
|
|
5yv2
|
DNA binding protein |
X-ray (1.9 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 14 . SNAP output
|
|
5yv3
|
DNA binding protein-DNA |
X-ray (2.03 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 7 . SNAP output
|
|
5yws
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW,
Hsiao YY |
(2018) "Structural
basis for overhang excision and terminal unwinding of
DNA duplexes by TREX1." PLoS Biol.,
16, e2005653. doi: 10.1371/journal.pbio.2005653.
|
Crystal structure of trex1 in complex with a y
structured DNA . SNAP
output
|
|
5ywt
|
DNA binding protein |
X-ray (1.7 Å) |
Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW,
Hsiao YY |
(2018) "Structural
basis for overhang excision and terminal unwinding of
DNA duplexes by TREX1." PLoS Biol.,
16, e2005653. doi: 10.1371/journal.pbio.2005653.
|
Crystal structure of trex1 in complex with a duplex DNA
with 3' overhang . SNAP
output
|
|
5ywu
|
DNA binding protein-DNA |
X-ray (3.4 Å) |
Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW,
Hsiao YY |
(2018) "Structural
basis for overhang excision and terminal unwinding of
DNA duplexes by TREX1." PLoS Biol.,
16, e2005653. doi: 10.1371/journal.pbio.2005653.
|
Crystal structure of trex1 in complex with a inosine
contained dsDNA . SNAP
output
|
|
5ywv
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Huang KW, Liu TC, Liang RY, Chu LY, Cheng HL, Chu JW,
Hsiao YY |
(2018) "Structural
basis for overhang excision and terminal unwinding of
DNA duplexes by TREX1." PLoS Biol.,
16, e2005653. doi: 10.1371/journal.pbio.2005653.
|
Crystal structure of trex1 in complex with a inosine
contained ssDNA . SNAP
output
|
|
5yx2
|
transferase-transferase regulator-DNA |
X-ray (2.653 Å) |
Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S,
Ji D, Rothbart SB, Wang Y, Wang GG, Song J |
(2018) "Structural
basis for DNMT3A-mediated de novo DNA methylation."
Nature, 554, 387-391. doi:
10.1038/nature25477.
|
Crystal structure of dnmt3a-dnmt3l in complex with DNA
containing two cpg sites . SNAP output
|
|
5yyd
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - ternary complex 15 . SNAP output
|
|
5yye
|
DNA binding protein-DNA |
X-ray (2.325 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - ternary complex 16 . SNAP output
|
|
5yzy
|
transcription-DNA |
X-ray (2.61 Å) |
Wu BX, Zhang MM, Su SC, Liu HH, Gan JH, Ma JB |
(2018) "Structural
insight into the role of VAL1 B3 domain for targeting
to FLC locus in Arabidopsis thaliana." Biochem.
Biophys. Res. Commun. doi: 10.1016/j.bbrc.2018.05.002.
|
Atval1 b3 domain in complex with 13bp-DNA . SNAP output
|
|
5yzz
|
transcription-DNA |
X-ray (2.58 Å) |
Wu BX, Zhang MM, Su SC, Liu HH, Gan JH, Ma JB |
(2018) "Structural
insight into the role of VAL1 B3 domain for targeting
to FLC locus in Arabidopsis thaliana." Biochem.
Biophys. Res. Commun. doi: 10.1016/j.bbrc.2018.05.002.
|
Atval1 b3 domain in complex with 13bp-DNA . SNAP output
|
|
5z00
|
transcription-DNA |
X-ray (2.587 Å) |
Wu BX, Zhang MM, Su SC, Liu HH, Gan JH, Ma JB |
(2018) "Structural
insight into the role of VAL1 B3 domain for targeting
to FLC locus in Arabidopsis thaliana." Biochem.
Biophys. Res. Commun. doi: 10.1016/j.bbrc.2018.05.002.
|
Atval1 b3 domain in complex with 15bp-DNA . SNAP output
|
|
5z23
|
DNA binding protein-DNA |
X-ray (2.73 Å) |
Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H,
Fukagawa T, Kurumizaka H |
(2019) "The
CENP-A centromere targeting domain facilitates H4K20
monomethylation in the nucleosome by structural
polymorphism." Nat Commun,
10, 576. doi: 10.1038/s41467-019-08314-x.
|
Crystal structure of the nucleosome containing a
chimeric histone h3-cenp-a catd . SNAP output
|
|
5z2t
|
DNA binding protein-DNA |
X-ray (2.623 Å) |
Dong X, Zhang W, Wu H, Huang J, Zhang M, Wang P,
Zhang H, Chen Z, Chen SJ, Meng G |
(2018) "Structural
basis of DUX4/IGH-driven transactivation."
Leukemia, 32, 1466-1476. doi:
10.1038/s41375-018-0093-1.
|
Crystal structure of DNA-bound dux4-hd2 . SNAP output
|
|
5z30
|
DNA binding protein-DNA |
X-ray (2.45 Å) |
Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W,
Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa
Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H |
(2018) "Cancer-associated
mutations of histones H2B, H3.1 and H2A.Z.1 affect the
structure and stability of the nucleosome."
Nucleic Acids Res., 46,
10007-10018. doi: 10.1093/nar/gky661.
|
The crystal structure of the nucleosome containing a
cancer-associated histone h2a.z r80c mutant . SNAP output
|
|
5z3l
|
structural protein-hydrolase-DNA |
cryo-EM (4.31 Å) |
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X,
Chen Z |
(2019) "Mechanism
of DNA translocation underlying chromatin remodelling
by Snf2." Nature, 567,
409-413. doi: 10.1038/s41586-019-1029-2.
|
Structure of snf2-nucleosome complex in apo state .
SNAP output
|
|
5z3n
|
replication-DNA |
X-ray (1.91 Å) |
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu
C, He B, Gao YQ, Yi C |
(2019) "Unnatural
Cytosine Bases Recognized as Thymines by DNA
Polymerases by the Formation of the Watson-Crick
Geometry." Angew. Chem. Int. Ed. Engl.,
58, 130-133. doi: 10.1002/anie.201807845.
|
Structure of large fragment of DNA polymerase i from
thermus aquaticus host-guest complex with the unnatural
base 5fc pair with da . SNAP output
|
|
5z3o
|
structural protein-hydrolase-DNA |
cryo-EM (3.62 Å) |
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X,
Chen Z |
(2019) "Mechanism
of DNA translocation underlying chromatin remodelling
by Snf2." Nature, 567,
409-413. doi: 10.1038/s41586-019-1029-2.
|
Structure of snf2-nucleosome complex in adp state .
SNAP output
|
|
5z3u
|
structural protein-hydrolase-DNA |
cryo-EM (4.31 Å) |
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X,
Chen Z |
(2019) "Mechanism
of DNA translocation underlying chromatin remodelling
by Snf2." Nature, 567,
409-413. doi: 10.1038/s41586-019-1029-2.
|
Structure of snf2-nucleosome complex at shl2 in adp
befx state . SNAP
output
|
|
5z3v
|
structural protein-hydrolase-DNA |
cryo-EM (4.22 Å) |
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X,
Chen Z |
(2019) "Mechanism
of DNA translocation underlying chromatin remodelling
by Snf2." Nature, 567,
409-413. doi: 10.1038/s41586-019-1029-2.
|
Structure of snf2-nucleosome complex at shl-2 in adp
befx state . SNAP
output
|
|
5z6w
|
hydrolase-DNA |
X-ray (3.2 Å) |
Jin H, Roy U, Lee G, Scharer OD, Cho Y |
(2018) "Structural
mechanism of DNA interstrand cross-link unhooking by
the bacterial FAN1 nuclease." J. Biol.
Chem., 293, 6482-6496. doi:
10.1074/jbc.RA118.002171.
|
Crystal structure of pafan1 bound to 2nt 5'flap DNA
with gap with manganese . SNAP output
|
|
5z6z
|
transcription-DNA |
X-ray (2.301 Å) |
Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J,
Chen Y, Gu Y, Li J, Ma J, Gan J |
(2018) "Structural
basis for multiple gene regulation by human DUX4."
Biochem. Biophys. Res. Commun.,
505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056.
|
Crystal structure of human dux4 homeodomains bound to
DNA . SNAP output
|
|
5z7d
|
immune system |
X-ray (4.5 Å) |
Fan X, Jiang J, Zhao D, Chen F, Ma H, Smith P,
Unterholzner L, Xiao TS, Jin T |
(2021) "Structural
mechanism of DNA recognition by the p204 HIN
domain." Nucleic Acids Res. doi: 10.1093/nar/gkab076.
|
P204hinab-dsDNA complex structure . SNAP output
|
|
5z7i
|
DNA binding protein-DNA |
X-ray (1.601 Å) |
Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L,
Zhuang N, Laub MT, Zhang Y |
(2018) "Structural
insights into the unique mechanism of transcription
activation by Caulobacter crescentus GcrA."
Nucleic Acids Res., 46,
3245-3256. doi: 10.1093/nar/gky161.
|
Caulobacter crescentus gcra DNA-binding domain(dbd)in
complex with unmethylated dsDNA . SNAP output
|
|
5z98
|
antiviral protein-RNA |
X-ray (2.2 Å) |
Matsuoka T, Nagae T, Ode H, Awazu H, Kurosawa T,
Hamano A, Matsuoka K, Hachiya A, Imahashi M, Yokomaku Y,
Watanabe N, Iwatani Y |
(2018) "Structural
basis of chimpanzee APOBEC3H dimerization stabilized by
double-stranded RNA." Nucleic Acids Res.,
46, 10368-10379. doi: 10.1093/nar/gky676.
|
Crystal structure of the primate apobec3h dimer
mediated by RNA duplex . SNAP output
|
|
5zad
|
DNA binding protein-DNA |
X-ray (2.54 Å) |
Sun LY, Zhu LW, Tang YJ |
(2018) "Increasing
the distance between two monomers of topoisomerase II
beta under the action of antitumor agent 4
beta-sulfur-(benzimidazole)
4'-demethylepipodophyllotoxin." Sci Rep,
8, 14949. doi: 10.1038/s41598-018-33366-2.
|
Human topoisomerase ii beta in complex with DNA .
SNAP output
|
|
5zbx
|
DNA binding protein-DNA |
X-ray (2.58 Å) |
Arimura Y, Tachiwana H, Takagi H, Hori T, Kimura H,
Fukagawa T, Kurumizaka H |
(2019) "The
CENP-A centromere targeting domain facilitates H4K20
monomethylation in the nucleosome by structural
polymorphism." Nat Commun,
10, 576. doi: 10.1038/s41467-019-08314-x.
|
The crystal structure of the nucleosome containing
histone h3.1 catd(v76q, k77d) . SNAP output
|
|
5zcw
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Maestre-Reyna M, Yamamoto J, Huang WC, Tsai MD, Essen
LO, Bessho Y |
(2018) "Twist
and turn: a revised structural view on the unpaired
bubble of class II CPD photolyase in complex with
damaged DNA." IUCrJ, 5,
608-618. doi: 10.1107/S205225251800996X.
|
Structure of the methanosarcina mazei class ii
cpd-photolyase in complex with intact, phosphodiester
linked, cpd-lesion . SNAP output
|
|
5zd4
|
transcription |
X-ray (2.17 Å) |
Nosaki S, Miyakawa T, Xu Y, Nakamura A, Hirabayashi
K, Asami T, Nakano T, Tanokura M |
(2018) "Structural
basis for brassinosteroid response by BIL1/BZR1."
Nat Plants, 4, 771-776. doi:
10.1038/s41477-018-0255-1.
|
Crystal structure of mbp-fused bil1-bzr1 in complex
with double-stranded DNA . SNAP output
|
|
5zdz
|
DNA binding protein |
X-ray (2.8 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Hairpin forming complex, rag1-2-nicked 12rss-23rss
complex in ca2+ . SNAP
output
|
|
5ze0
|
DNA binding protein |
X-ray (2.75 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Hairpin forming complex, rag1-2-nicked(with dideoxy)
12rss-23rss complex in mg2+ . SNAP output
|
|
5ze1
|
DNA binding protein |
X-ray (3.0 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Hairpin forming complex, rag1-2-nicked 12rss-23rss
complex in 2mm mn2+ for 10 min at 4'c . SNAP output
|
|
5ze2
|
DNA binding protein |
X-ray (3.3 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Hairpin complex, rag1-2-hairpin 12rss-23rss complex in
5mm mn2+ for 2 min at 4'c . SNAP output
|
|
5zen
|
isomerase-DNA |
X-ray (2.75 Å) |
Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ,
Gilson MK, Chan NL |
(2018) "Structural
insights into the gating of DNA passage by the
topoisomerase II DNA-gate." Nat Commun,
9, 3085. doi: 10.1038/s41467-018-05406-y.
|
Crystal structure of human topoisomerase ii beta in
complex with DNA: a new quaternary conformation showing
opening of the protein-linked DNA-gate . SNAP output
|
|
5zfw
|
transcription-DNA |
X-ray (2.103 Å) |
Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J,
Chen Y, Gu Y, Li J, Ma J, Gan J |
(2018) "Structural
basis for multiple gene regulation by human DUX4."
Biochem. Biophys. Res. Commun.,
505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056.
|
Crystal structure of human dux4 homeodomains bound to
a11g DNA mutant . SNAP
output
|
|
5zfy
|
transcription-DNA |
X-ray (2.3 Å) |
Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J,
Chen Y, Gu Y, Li J, Ma J, Gan J |
(2018) "Structural
basis for multiple gene regulation by human DUX4."
Biochem. Biophys. Res. Commun.,
505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056.
|
Crystal structure of human dux4 homeodomains bound to
a12c DNA mutant . SNAP
output
|
|
5zfz
|
transcription-DNA |
X-ray (1.9 Å) |
Li Y, Wu B, Liu H, Gao Y, Yang C, Chen X, Zhang J,
Chen Y, Gu Y, Li J, Ma J, Gan J |
(2018) "Structural
basis for multiple gene regulation by human DUX4."
Biochem. Biophys. Res. Commun.,
505, 1161-1167. doi: 10.1016/j.bbrc.2018.10.056.
|
Crystal structure of human dux4 homeodomains bound to
a12t DNA mutant . SNAP
output
|
|
5zg9
|
DNA binding protein-DNA |
X-ray (2.04 Å) |
Zhao Y, Zhang Y, Huang J, Wang S, Yi L, Zhang X, Xu
M, Fang X, Liu J |
(2019) "The
effect of phosphate ion on the ssDNA binding mode of
MoSub1, a Sub1/PC4 homolog from rice blast fungus."
Proteins, 87, 257-264. doi:
10.1002/prot.25647.
|
Crystal structure of mosub1-ssDNA complex in phosphate
buffer . SNAP output
|
|
5zgn
|
toxin |
X-ray (2.24 Å) |
Qian HL, Yao QQ, Gan JH, Ou HY |
"The crystal structure of KacTA-DNA complex." |
The crystal structure of kacta-DNA complex . SNAP output
|
|
5zjq
|
transcription-DNA |
X-ray (2.443 Å) |
Zeiske T, Baburajendran N, Kaczynska A, Brasch J,
Palmer AG, Shapiro L, Honig B, Mann RS |
(2018) "Intrinsic
DNA Shape Accounts for Affinity Differences between
Hox-Cofactor Binding Sites." Cell Rep,
24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100.
|
Structure of abdb-exd complex bound to a 'red14' DNA
sequence . SNAP
output
|
|
5zjr
|
transcription-DNA |
X-ray (3.03 Å) |
Zeiske T, Baburajendran N, Kaczynska A, Brasch J,
Palmer AG, Shapiro L, Honig B, Mann RS |
(2018) "Intrinsic
DNA Shape Accounts for Affinity Differences between
Hox-Cofactor Binding Sites." Cell Rep,
24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100.
|
Structure of abdb-exd complex bound to a 'magenta14'
DNA sequence . SNAP
output
|
|
5zjs
|
transcription-DNA |
X-ray (2.896 Å) |
Zeiske T, Baburajendran N, Kaczynska A, Brasch J,
Palmer AG, Shapiro L, Honig B, Mann RS |
(2018) "Intrinsic
DNA Shape Accounts for Affinity Differences between
Hox-Cofactor Binding Sites." Cell Rep,
24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100.
|
Structure of abdb-exd complex bound to a 'blue14' DNA
sequence . SNAP
output
|
|
5zjt
|
transcription-DNA |
X-ray (2.4 Å) |
Zeiske T, Baburajendran N, Kaczynska A, Brasch J,
Palmer AG, Shapiro L, Honig B, Mann RS |
(2018) "Intrinsic
DNA Shape Accounts for Affinity Differences between
Hox-Cofactor Binding Sites." Cell Rep,
24, 2221-2230. doi: 10.1016/j.celrep.2018.07.100.
|
Structure of abdb-exd complex bound to a 'black14' DNA
sequence . SNAP
output
|
|
5zk1
|
transcription-DNA |
X-ray (3.05 Å) |
Song Y, Zhai L, Valencia Swain J, Chen Y, Wang P,
Chen L, Liu Y, Xiang S |
(2018) "Structural
Insights into the CRTC2-CREB Complex Assembly on
CRE." J. Mol. Biol., 430,
1926-1939. doi: 10.1016/j.jmb.2018.04.038.
|
Crystal structure of the crtc2(semet)-creb-cre complex
. SNAP output
|
|
5zki
|
hydrolase-DNA |
X-ray (2.321 Å) |
Wu CC, Lin JLJ, Yang-Yen HF, Yuan HS |
(2019) "A unique
exonuclease ExoG cleaves between RNA and DNA in
mitochondrial DNA replication." Nucleic Acids
Res., 47, 5405-5419. doi:
10.1093/nar/gkz241.
|
Human exog-h140a in complex with duplex DNA . SNAP output
|
|
5zkj
|
hydrolase-RNA-DNA |
X-ray (2.798 Å) |
Wu CC, Lin JLJ, Yang-Yen HF, Yuan HS |
(2019) "A unique
exonuclease ExoG cleaves between RNA and DNA in
mitochondrial DNA replication." Nucleic Acids
Res., 47, 5405-5419. doi:
10.1093/nar/gkz241.
|
Human exog-h140a in complex with RNA-DNA hybrid duplex
. SNAP output
|
|
5zkl
|
unknown function-DNA |
X-ray (1.951 Å) |
Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X,
Gong P, Zhang X, Liu M, Zhu J, Yang Y |
(2020) "Structural
insight into the length-dependent binding of ssDNA by
SP_0782 from Streptococcus pneumoniae, reveals a
divergence in the DNA-binding interface of PC4-like
proteins." Nucleic Acids Res.,
48, 432-444. doi: 10.1093/nar/gkz1045.
|
Crystal structure of streptococcus pneumoniae sp_0782
(residues 7-79) in complex with single-stranded DNA
dt12 . SNAP output
|
|
5zkm
|
unknown function-DNA |
X-ray (1.65 Å) |
Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X,
Gong P, Zhang X, Liu M, Zhu J, Yang Y |
(2020) "Structural
insight into the length-dependent binding of ssDNA by
SP_0782 from Streptococcus pneumoniae, reveals a
divergence in the DNA-binding interface of PC4-like
proteins." Nucleic Acids Res.,
48, 432-444. doi: 10.1093/nar/gkz1045.
|
Crystal structure of streptococcus pneumoniae sp_0782
(residues 7-79) in complex with single-stranded DNA
tcttcc . SNAP output
|
|
5zko
|
transcription-DNA |
X-ray (3.05 Å) |
Song Y, Zhai L, Valencia Swain J, Chen Y, Wang P,
Chen L, Liu Y, Xiang S |
(2018) "Structural
Insights into the CRTC2-CREB Complex Assembly on
CRE." J. Mol. Biol., 430,
1926-1939. doi: 10.1016/j.jmb.2018.04.038.
|
Crystal structure of the crtc2-creb-cre complex .
SNAP output
|
|
5zln
|
immune system |
X-ray (2.3 Å) |
Ishida H, Ohto U, Shibata T, Miyake K, Shimizu T |
(2018) "Structural
basis for species-specific activation of mouse
Toll-like receptor 9." FEBS Lett.,
592, 2636-2646. doi: 10.1002/1873-3468.13176.
|
Crystal structure of mouse tlr9 in complex with two
dnas (cpg DNA and tcgcca DNA) . SNAP output
|
|
5zlv
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex with 50mm mgcl2
. SNAP output
|
|
5zmc
|
transcription-DNA |
X-ray (2.99 Å) |
Xu X, Li Y, Bharath SR, Ozturk MB, Bowler MW, Loo
BZL, Tergaonkar V, Song H |
(2018) "Structural
basis for reactivating the mutant TERT promoter by
cooperative binding of p52 and ETS1." Nat
Commun, 9, 3183. doi: 10.1038/s41467-018-05644-0.
|
Structural basis for reactivation of -146c>t mutant
tert promoter by cooperative binding of p52 and ets1-2
. SNAP output
|
|
5zmd
|
oxidoreductase-DNA |
X-ray (3.3 Å) |
Zhang X, Wei LH, Wang Y, Xiao Y, Liu J, Zhang W, Yan
N, Amu G, Tang X, Zhang L, Jia G |
(2019) "Structural
insights into FTO's catalytic mechanism for the
demethylation of multiple RNA substrates."
Proc. Natl. Acad. Sci. U.S.A.,
116, 2919-2924. doi: 10.1073/pnas.1820574116.
|
Crystal structure of fto in complex with m6da modified
ssDNA . SNAP output
|
|
5zmn
|
DNA binding protein-DNA |
X-ray (3.29 Å) |
Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X,
Zhao Y, Deng Z, Wu G, He X |
(2018) "Structural
basis for the recognition of sulfur in
phosphorothioated DNA." Nat Commun,
9, 4689. doi: 10.1038/s41467-018-07093-1.
|
Sulfur binding domain and sra domain of scomcra
complexed with phosphorothioated DNA . SNAP output
|
|
5zmo
|
DNA binding protein-DNA |
X-ray (1.69 Å) |
Liu G, Fu W, Zhang Z, He Y, Yu H, Wang Y, Wang X,
Zhao Y, Deng Z, Wu G, He X |
(2018) "Structural
basis for the recognition of sulfur in
phosphorothioated DNA." Nat Commun,
9, 4689. doi: 10.1038/s41467-018-07093-1.
|
Sulfur binding domain of scomcra complexed with
phosphorothioated DNA . SNAP output
|
|
5zoe
|
hydrolase-DNA |
X-ray (1.95 Å) |
Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L,
Tian B, Zheng L, Shen B, Hua Y, Zhao Y |
(2018) "Structural
basis of 5' flap recognition and protein-protein
interactions of human flap endonuclease 1."
Nucleic Acids Res., 46,
11315-11325. doi: 10.1093/nar/gky911.
|
Crystal structure of d181a hfen1 in complex with DNA .
SNAP output
|
|
5zof
|
hydrolase-DNA |
X-ray (2.249 Å) |
Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L,
Tian B, Zheng L, Shen B, Hua Y, Zhao Y |
(2018) "Structural
basis of 5' flap recognition and protein-protein
interactions of human flap endonuclease 1."
Nucleic Acids Res., 46,
11315-11325. doi: 10.1093/nar/gky911.
|
Crystal structure of d181a-r192f hfen1 in complex with
DNA . SNAP output
|
|
5zog
|
hydrolase-DNA |
X-ray (2.299 Å) |
Xu H, Shi R, Han W, Cheng J, Xu X, Cheng K, Wang L,
Tian B, Zheng L, Shen B, Hua Y, Zhao Y |
(2018) "Structural
basis of 5' flap recognition and protein-protein
interactions of human flap endonuclease 1."
Nucleic Acids Res., 46,
11315-11325. doi: 10.1093/nar/gky911.
|
Crystal structure of r192f hfen1 in complex with DNA .
SNAP output
|
|
5zqf
|
isomerase-DNA |
X-ray (3.873 Å) |
Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ,
Gilson MK, Chan NL |
(2018) "Structural
insights into the gating of DNA passage by the
topoisomerase II DNA-gate." Nat Commun,
9, 3085. doi: 10.1038/s41467-018-05406-y.
|
Crystal structure of human topoisomerase ii beta in
complex with 5-iodouridine-containing-DNA in space
group p3221 . SNAP
output
|
|
5zr1
|
DNA binding protein-DNA |
cryo-EM (3.0 Å) |
Li N, Lam WH, Zhai Y, Cheng J, Cheng E, Zhao Y, Gao
N, Tye BK |
(2018) "Structure
of the origin recognition complex bound to DNA
replication origin." Nature,
559, 217-222. doi: 10.1038/s41586-018-0293-x.
|
Saccharomyces cerevisiae origin recognition complex
bound to a 72-bp origin DNA containing acs and b1
element . SNAP
output
|
|
5zrf
|
isomerase-DNA |
X-ray (2.3 Å) |
Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ,
Gilson MK, Chan NL |
(2018) "Structural
insights into the gating of DNA passage by the
topoisomerase II DNA-gate." Nat Commun,
9, 3085. doi: 10.1038/s41467-018-05406-y.
|
Crystal structure of human topoisomerase ii beta in
complex with 5-iodouridine-containing-DNA and etoposide
in space group p21 . SNAP output
|
|
5zu1
|
hydrolase-DNA |
X-ray (3.009 Å) |
Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S,
Sugiyama H, Kim KK |
(2018) "Sequence
preference and structural heterogeneity of BZ
junctions." Nucleic Acids Res.,
46, 10504-10513. doi: 10.1093/nar/gky784.
|
Crystal structure of bz junction in diverse sequence .
SNAP output
|
|
5zuo
|
hydrolase-DNA |
X-ray (2.902 Å) |
Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S,
Sugiyama H, Kim KK |
(2018) "Sequence
preference and structural heterogeneity of BZ
junctions." Nucleic Acids Res.,
46, 10504-10513. doi: 10.1093/nar/gky784.
|
Crystal structure of bz junction in diverse sequence .
SNAP output
|
|
5zup
|
hydrolase-DNA |
X-ray (2.9 Å) |
Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S,
Sugiyama H, Kim KK |
(2018) "Sequence
preference and structural heterogeneity of BZ
junctions." Nucleic Acids Res.,
46, 10504-10513. doi: 10.1093/nar/gky784.
|
Crystal structure of bz junction in diverse sequence .
SNAP output
|
|
5zux
|
DNA binding protein-DNA |
NMR |
Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia
B |
(2018) "How
bacterial xenogeneic silencer rok distinguishes foreign
from self DNA in its resident genome." Nucleic
Acids Res., 46, 10514-10529. doi:
10.1093/nar/gky836.
|
Solution structure of the DNA complex of the c-terminal
domain of rok . SNAP
output
|
|
5zva
|
structural protein-DNA |
X-ray (2.3 Å) |
Cheng C, Zhang T, Wang C, Lan W, Ding J, Cao C |
(2018) "Crystal Structure of Cytidine Deaminase Human
APOBEC3F Chimeric Catalytic Domain in Complex with
DNA." Chin.J.Chem., 36,
1241-1248. doi: 10.1002/cjoc.201800508.
|
Apobec3f chimeric catalytic domain in complex with
DNA(dc9) . SNAP
output
|
|
5zvb
|
structural protein-DNA |
X-ray (2.0 Å) |
Cheng C, Zhang T, Wang C, Lan W, Ding J, Cao C |
(2018) "Crystal Structure of Cytidine Deaminase Human
APOBEC3F Chimeric Catalytic Domain in Complex with
DNA." Chin.J.Chem., 36,
1241-1248. doi: 10.1002/cjoc.201800508.
|
Apobec3f chimeric catalytic domain in complex with
DNA(dt9) . SNAP
output
|
|
5zx2
|
transcription-DNA-RNA |
X-ray (2.8 Å) |
Li L, Fang C, Zhuang N, Wang T, Zhang Y |
(2019) "Structural
basis for transcription initiation by bacterial ECF
sigma factors." Nat Commun,
10, 1153. doi: 10.1038/s41467-019-09096-y.
|
Mycobacterium tuberculosis RNA polymerase transcription
initiation complex with ecf sigma factor sigma h and
7nt RNA . SNAP
output
|
|
5zyt
|
DNA binding protein |
X-ray (2.702 Å) |
Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma
J, Li J, Gan J |
(2018) "Structural
insights into DNA degradation by human mitochondrial
nuclease MGME1." Nucleic Acids Res.,
46, 11075-11088. doi: 10.1093/nar/gky855.
|
Crystal structure of human mgme1 with 3' overhang
double strand dna3 . SNAP output
|
|
5zyu
|
DNA binding protein-DNA |
X-ray (1.752 Å) |
Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma
J, Li J, Gan J |
(2018) "Structural
insights into DNA degradation by human mitochondrial
nuclease MGME1." Nucleic Acids Res.,
46, 11075-11088. doi: 10.1093/nar/gky855.
|
The crystal structure of humanmgme1 with single strand
dna2 . SNAP output
|
|
5zyv
|
DNA binding protein-DNA |
X-ray (2.72 Å) |
Yang C, Wu R, Liu H, Chen Y, Gao Y, Chen X, Li Y, Ma
J, Li J, Gan J |
(2018) "Structural
insights into DNA degradation by human mitochondrial
nuclease MGME1." Nucleic Acids Res.,
46, 11075-11088. doi: 10.1093/nar/gky855.
|
Crystal structure of human mgme1 with single strand
dna2 and ca2+ . SNAP
output
|
|
6a2h
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Zhang Z, Zhao M, Chen Y, Wang L, Liu Q, Dong Y, Gong
Y, Huang L |
(2019) "Architectural
roles of Cren7 in folding crenarchaeal chromatin
filament." Mol. Microbiol.,
111, 556-569. doi: 10.1111/mmi.14173.
|
Architectural roles of cren7 in folding crenarchaeal
chromatin filament . SNAP output
|
|
6a2i
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Zhang Z, Zhao M, Chen Y, Wang L, Liu Q, Dong Y, Gong
Y, Huang L |
(2019) "Architectural
roles of Cren7 in folding crenarchaeal chromatin
filament." Mol. Microbiol.,
111, 556-569. doi: 10.1111/mmi.14173.
|
Architectural roles of cren7 in folding crenarchaeal
chromatin filament . SNAP output
|
|
6a47
|
DNA binding protein |
X-ray (1.9 Å) |
Cheng HL, Lin CT, Huang KW, Wang S, Lin YT, Toh SI,
Hsiao YY |
(2018) "Structural
insights into the duplex DNA processing of TREX2."
Nucleic Acids Res., 46,
12166-12176. doi: 10.1093/nar/gky970.
|
Structure of trex2 in complex with a y structured dsDNA
. SNAP output
|
|
6a4b
|
DNA binding protein |
X-ray (2.7 Å) |
Cheng HL, Lin CT, Huang KW, Wang S, Lin YT, Toh SI,
Hsiao YY |
(2018) "Structural
insights into the duplex DNA processing of TREX2."
Nucleic Acids Res., 46,
12166-12176. doi: 10.1093/nar/gky970.
|
Structure of trex2 in complex with a duplex DNA with 2
nucleotide 3'-overhang . SNAP output
|
|
6a57
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Tian Z, Li X, Li M, Wu W, Zhang M, Tang C, Li Z, Liu
Y, Chen Z, Yang M, Ma L, Caba C, Tong Y, Lam HM, Dai S,
Chen Z |
(2020) "Crystal
structures of REF6 and its complex with DNA reveal
diverse recognition mechanisms." Cell
Discov, 6, 17. doi: 10.1038/s41421-020-0150-6.
|
Structure of histone demethylase ref6 complexed with
DNA . SNAP output
|
|
6a5l
|
transcription-RNA-DNA |
cryo-EM (5.6 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-1)
of the nucleosome, with foreign DNA . SNAP output
|
|
6a5n
|
gene regulation-DNA |
X-ray (2.4 Å) |
Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang
Z, Li S, Jacobsen SE, Du J |
(2018) "Mechanistic
insights into plant SUVH family H3K9 methyltransferases
and their binding to context-biased non-CG DNA
methylation." Proc. Natl. Acad. Sci.
U.S.A., 115, E8793-E8802. doi:
10.1073/pnas.1809841115.
|
Crystal structure of arabidopsis thaliana suvh6 in
complex with methylated DNA . SNAP output
|
|
6a5o
|
transcription-RNA-DNA |
cryo-EM (9.9 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-6)
of the nucleosome . SNAP
output
|
|
6a5p
|
transcription-RNA-DNA |
cryo-EM (7.0 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-5)
of the nucleosome . SNAP
output
|
|
6a5r
|
transcription-RNA-DNA |
cryo-EM (8.7 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-2)
of the nucleosome . SNAP
output
|
|
6a5t
|
transcription-RNA-DNA |
cryo-EM (6.7 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-1)
of the nucleosome . SNAP
output
|
|
6a5u
|
transcription-RNA-DNA |
cryo-EM (7.6 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine SI,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-1)
of the nucleosome, with foreign DNA, tilt conformation
. SNAP output
|
|
6a8r
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Dong X, Zhang H, Cheng N, Li K, Meng G |
(2019) "DUX4HD2-DNAERGstructure
reveals new insight into DUX4-Responsive-Element."
Leukemia, 33, 550-553. doi:
10.1038/s41375-018-0273-z.
|
Crystal structure of dux4 hd2 domain associated with
erg DNA binding site . SNAP output
|
|
6aeb
|
DNA binding protein-RNA |
X-ray (3.004 Å) |
Guo M, Ren K, Zhu Y, Tang Z, Wang Y, Zhang B, Huang
Z |
(2019) "Structural
insights into a high fidelity variant of SpCas9."
Cell Res., 29, 183-192. doi:
10.1038/s41422-018-0131-6.
|
Crystal structure of xcas9 in complex with sgrna and
target DNA (aag pam) . SNAP output
|
|
6aeg
|
DNA binding protein-DNA-RNA |
X-ray (2.701 Å) |
Guo M, Ren K, Zhu Y, Tang Z, Wang Y, Zhang B, Huang
Z |
(2019) "Structural
insights into a high fidelity variant of SpCas9."
Cell Res., 29, 183-192. doi:
10.1038/s41422-018-0131-6.
|
Crystal structure of xcas9 in complex with sgrna and
target DNA (gat pam) . SNAP output
|
|
6ai6
|
hydrolase-RNA-DNA |
X-ray (2.7 Å) |
Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S,
Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H,
Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani
H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O |
(2018) "Engineered
CRISPR-Cas9 nuclease with expanded targeting
space." Science, 361,
1259-1262. doi: 10.1126/science.aas9129.
|
Crystal structure of spcas9-ng . SNAP output
|
|
6ajo
|
DNA binding protein |
X-ray (2.269 Å) |
Ahn WC, Aroli S, Kim JH, Moon JH, Lee GS, Lee MH,
Sang PB, Oh BH, Varshney U, Woo EJ |
(2019) "Covalent
binding of uracil DNA glycosylase UdgX to abasic DNA
upon uracil excision." Nat.Chem.Biol.,
15, 607-614. doi: 10.1038/s41589-019-0289-3.
|
Complex form of uracil DNA glycosylase x and
uracil-DNA. . SNAP
output
|
|
6ak8
|
transferase-DNA |
X-ray (1.74 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with templating adenine and incoming ca-8oxodgtp .
SNAP output
|
|
6ak9
|
transferase-DNA |
X-ray (1.91 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with templating cytosine and incoming ca-8oxodgtp .
SNAP output
|
|
6akh
|
transferase-DNA |
X-ray (1.75 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with templating adenine and incoming mn-dumpnpp .
SNAP output
|
|
6ako
|
DNA binding protein-DNA |
X-ray (2.396 Å) |
Chen X, Wei H, Li J, Liang X, Dai S, Jiang L, Guo M,
Qu L, Chen Z, Chen L, Chen Y |
(2019) "Structural
basis for DNA recognition by FOXC2." Nucleic
Acids Res., 47, 3752-3764. doi:
10.1093/nar/gkz077.
|
Crystal structure of foxc2 dbd bound to dbe2 DNA .
SNAP output
|
|
6akp
|
DNA binding protein-DNA |
X-ray (2.323 Å) |
Chen X, Wei H, Li J, Liang X, Dai S, Jiang L, Guo M,
Qu L, Chen Z, Chen L, Chen Y |
(2019) "Structural
basis for DNA recognition by FOXC2." Nucleic
Acids Res., 47, 3752-3764. doi:
10.1093/nar/gkz077.
|
Crystal structural of foxc2 DNA binding domain bound to
pc promoter . SNAP
output
|
|
6alf
|
transcription-DNA-RNA |
cryo-EM (4.1 Å) |
Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A,
Chait BT, Gottesman ME, Darst SA |
(2017) "Structural
basis of transcription arrest by coliphage HK022 Nun in
anEscherichia coliRNA polymerase elongation
complex." Elife, 6. doi:
10.7554/eLife.25478.
|
Cryoem structure of crosslinked e.coli RNA polymerase
elongation complex . SNAP output
|
|
6alg
|
transcription-DNA-RNA |
cryo-EM (3.7 Å) |
Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A,
Chait BT, Gottesman ME, Darst SA |
(2017) "Structural
basis of transcription arrest by coliphage HK022 Nun in
anEscherichia coliRNA polymerase elongation
complex." Elife, 6. doi:
10.7554/eLife.25478.
|
Cryoem structure of hk022 nun - e.coli RNA polymerase
elongation complex . SNAP output
|
|
6alh
|
transcription-DNA-RNA |
cryo-EM (4.4 Å) |
Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A,
Chait BT, Gottesman ME, Darst SA |
(2017) "Structural
basis of transcription arrest by coliphage HK022 Nun in
anEscherichia coliRNA polymerase elongation
complex." Elife, 6. doi:
10.7554/eLife.25478.
|
Cryoem structure of e.coli RNA polymerase elongation
complex . SNAP
output
|
|
6ama
|
DNA binding protein-DNA |
X-ray (3.09 Å) |
Schumacher MA, den Hengst CD, Bush MJ, Le TBK, Tran
NT, Chandra G, Zeng W, Travis B, Brennan RG, Buttner
MJ |
(2018) "The
MerR-like protein BldC binds DNA direct repeats as
cooperative multimers to regulate Streptomyces
development." Nat Commun,
9, 1139. doi: 10.1038/s41467-018-03576-3.
|
Structure of s. coelicolor-s. venezuelae bldc-smea-ssfa
complex to 3.09 angstrom . SNAP output
|
|
6amk
|
DNA binding protein-DNA |
X-ray (3.288 Å) |
Schumacher MA, den Hengst CD, Bush MJ, Le TBK, Tran
NT, Chandra G, Zeng W, Travis B, Brennan RG, Buttner
MJ |
(2018) "The
MerR-like protein BldC binds DNA direct repeats as
cooperative multimers to regulate Streptomyces
development." Nat Commun,
9, 1139. doi: 10.1038/s41467-018-03576-3.
|
Structure of streptomyces venezuelae bldc-whii opt
complex . SNAP
output
|
|
6amo
|
transferase-DNA |
X-ray (2.497 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 7.0 . SNAP
output
|
|
6an2
|
transferase-DNA |
X-ray (2.7 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 7.5 . SNAP
output
|
|
6an8
|
transferase-DNA |
X-ray (2.596 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 8.0 . SNAP
output
|
|
6anq
|
transferase-DNA |
X-ray (2.586 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 8.5 . SNAP
output
|
|
6ar1
|
RNA binding protein-RNA-DNA |
X-ray (3.01 Å) |
Stamos JL, Lentzsch AM, Lambowitz AM |
(2017) "Structure
of a Thermostable Group II Intron Reverse Transcriptase
with Template-Primer and Its Functional and
Evolutionary Implications." Mol. Cell,
68, 926-939.e4. doi: 10.1016/j.molcel.2017.10.024.
|
Structure of a thermostable group ii intron reverse
transcriptase with template-primer and its functional
and evolutionary implications (rt-duplex (nat)) .
SNAP output
|
|
6ar3
|
RNA binding protein-RNA-DNA |
X-ray (3.41 Å) |
Stamos JL, Lentzsch AM, Lambowitz AM |
(2017) "Structure
of a Thermostable Group II Intron Reverse Transcriptase
with Template-Primer and Its Functional and
Evolutionary Implications." Mol. Cell,
68, 926-939.e4. doi: 10.1016/j.molcel.2017.10.024.
|
Structure of a thermostable group ii intron reverse
transcriptase with template-primer and its functional
and evolutionary implications (rt-duplex (se-met)) .
SNAP output
|
|
6as7
|
replication-DNA |
X-ray (2.95 Å) |
Baranovskiy AG, Duong VN, Babayeva ND, Zhang Y,
Pavlov YI, Anderson KS, Tahirov TH |
(2018) "Activity
and fidelity of human DNA polymerase alpha depend on
primer structure." J. Biol. Chem.,
293, 6824-6843. doi: 10.1074/jbc.RA117.001074.
|
Crystal structure of the catalytic core of human DNA
polymerase alpha in ternary complex with an DNA-primed
DNA template and dctp . SNAP output
|
|
6asb
|
DNA binding protein-DNA |
X-ray (2.85 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Cxxc and phd-type zinc finger regions of fbxl19 in
complex with DNA . SNAP
output
|
|
6asd
|
DNA binding protein-DNA |
X-ray (1.85 Å) |
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min
J |
(2018) "DNA
Sequence Recognition of Human CXXC Domains and Their
Structural Determinants." Structure,
26, 85-95.e3. doi: 10.1016/j.str.2017.11.022.
|
Zinc finger region of human tet1 in complex with cpg
DNA . SNAP output
|
|
6asw
|
transferase-DNA |
X-ray (2.605 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 9.0 . SNAP
output
|
|
6asx
|
transcription-DNA-RNA |
cryo-EM (3.8 Å) |
Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA,
Darst SA, Landick R |
(2018) "RNA
Polymerase Accommodates a Pause RNA Hairpin by Global
Conformational Rearrangements that Prolong
Pausing." Mol. Cell, 69,
802-815.e1. doi: 10.1016/j.molcel.2018.01.018.
|
Cryoem structure of e.coli his pause elongation complex
. SNAP output
|
|
6avm
|
transferase-DNA |
X-ray (2.502 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 9.5 with cross-linking to second base
template overhang . SNAP
output
|
|
6avt
|
transferase-DNA |
X-ray (2.603 Å) |
Martinez SE, Bauman JD, Das K, Arnold E |
(2019) "Structure
of HIV-1 reverse transcriptase/d4TTP complex: Novel DNA
cross-linking site and pH-dependent conformational
changes." Protein Sci.,
28, 587-597. doi: 10.1002/pro.3559.
|
Structure of hiv-1 reverse transcriptase (rt) ternary
complex with a double stranded DNA and an incoming
d4ttp at ph 9.5 with cross-linking to first base
template overhang . SNAP
output
|
|
6b0o
|
transcription-DNA |
X-ray (1.552 Å) |
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X,
Cheng X |
(2018) "Role for
first zinc finger of WT1 in DNA sequence specificity:
Denys-Drash syndrome-associated WT1 mutant in ZF1
enhances affinity for a subset of WT1 binding
sites." Nucleic Acids Res.,
46, 3864-3877. doi: 10.1093/nar/gkx1274.
|
Zinc finger domain of wt1(-kts form) with 12+1mer
oligonucleotide with 3' triplet tgt . SNAP output
|
|
6b0p
|
transcription-DNA |
X-ray (2.077 Å) |
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X,
Cheng X |
(2018) "Role for
first zinc finger of WT1 in DNA sequence specificity:
Denys-Drash syndrome-associated WT1 mutant in ZF1
enhances affinity for a subset of WT1 binding
sites." Nucleic Acids Res.,
46, 3864-3877. doi: 10.1093/nar/gkx1274.
|
Zinc finger domain of wt1(-kts form) with 12+1mer
oligonucleotide with 3' triplet ggt . SNAP output
|
|
6b0q
|
transcription-DNA |
X-ray (2.794 Å) |
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X,
Cheng X |
(2018) "Role for
first zinc finger of WT1 in DNA sequence specificity:
Denys-Drash syndrome-associated WT1 mutant in ZF1
enhances affinity for a subset of WT1 binding
sites." Nucleic Acids Res.,
46, 3864-3877. doi: 10.1093/nar/gkx1274.
|
Zinc finger domain of wt1(-kts form) with 13+1mer
oligonucleotide with 3' triplet tgt . SNAP output
|
|
6b0r
|
transcription-DNA |
X-ray (1.818 Å) |
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X,
Cheng X |
(2018) "Role for
first zinc finger of WT1 in DNA sequence specificity:
Denys-Drash syndrome-associated WT1 mutant in ZF1
enhances affinity for a subset of WT1 binding
sites." Nucleic Acids Res.,
46, 3864-3877. doi: 10.1093/nar/gkx1274.
|
Zinc finger domain of wt1(-kts form) with m342r
mutation and 14+1mer oligonucleotide with 3' triplet
tgg . SNAP output
|
|
6b19
|
viral protein-RNA |
cryo-EM (4.5 Å) |
Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH,
Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi
EV |
(2018) "Architecture
of an HIV-1 reverse transcriptase initiation
complex." Nature, 557,
118-122. doi: 10.1038/s41586-018-0055-9.
|
Architecture of hiv-1 reverse transcriptase initiation
complex core . SNAP
output
|
|
6b1q
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Hoshika S, Singh I, Switzer C, Molt Jr RW, Leal NA,
Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA |
(2018) ""Skinny"
and "Fat" DNA: Two New Double Helices." J. Am.
Chem. Soc., 140, 11655-11660.
doi: 10.1021/jacs.8b05042.
|
Hydrogen bonding complementary, not size
complementarity is key in the formation of the double
helix . SNAP output
|
|
6b1r
|
DNA binding protein-DNA |
X-ray (1.69 Å) |
Hoshika S, Singh I, Switzer C, Molt Jr RW, Leal NA,
Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA |
(2018) ""Skinny"
and "Fat" DNA: Two New Double Helices." J. Am.
Chem. Soc., 140, 11655-11660.
doi: 10.1021/jacs.8b05042.
|
Hydrogen bonding complementary, not size
complementarity is key in the formation of the double
helix . SNAP output
|
|
6b1s
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Hoshika S, Singh I, Switzer C, Molt Jr RW, Leal NA,
Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA |
(2018) ""Skinny"
and "Fat" DNA: Two New Double Helices." J. Am.
Chem. Soc., 140, 11655-11660.
doi: 10.1021/jacs.8b05042.
|
Hydrogen bonding complementary, not size
complementarity is key in the formation of the double
helix . SNAP output
|
|
6b40
|
recombination |
cryo-EM (4.3 Å) |
Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell
JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz
DG |
(2019) "Transposon
molecular domestication and the evolution of the RAG
recombinase." Nature,
569, 79-84. doi: 10.1038/s41586-019-1093-7.
|
Bbragl-3'tir synaptic complex with nicked DNA refined
with c2 symmetry . SNAP
output
|
|
6b44
|
immune system-RNA-DNA |
cryo-EM (2.9 Å) |
Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P,
Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ,
Subramaniam S |
(2017) "Cryo-EM
Structures Reveal Mechanism and Inhibition of DNA
Targeting by a CRISPR-Cas Surveillance Complex."
Cell, 171, 414-426.e12. doi:
10.1016/j.cell.2017.09.006.
|
cryo-EM structure of type i-f crispr crrna-guided csy
surveillance complex with bound target dsDNA . SNAP output
|
|
6b6h
|
transcription-transferase-DNA-RNA |
cryo-EM (3.9 Å) |
Liu B, Hong C, Huang RK, Yu Z, Steitz TA |
(2017) "Structural
basis of bacterial transcription activation."
Science, 358, 947-951. doi:
10.1126/science.aao1923.
|
The cryo-EM structure of a bacterial class i
transcription activation complex . SNAP output
|
|
6bce
|
hydrolase-DNA |
X-ray (1.75 Å) |
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop
MS, Gloor GB, Edgell DR |
(2018) "Active
site residue identity regulates cleavage preference of
LAGLIDADG homing endonucleases." Nucleic Acids
Res., 46, 11990-12007. doi:
10.1093/nar/gky976.
|
Wild-type i-ltri bound to cognate substrate
(pre-cleavage complex) . SNAP output
|
|
6bcf
|
hydrolase-DNA |
X-ray (2.92 Å) |
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop
MS, Gloor GB, Edgell DR |
(2018) "Active
site residue identity regulates cleavage preference of
LAGLIDADG homing endonucleases." Nucleic Acids
Res., 46, 11990-12007. doi:
10.1093/nar/gky976.
|
I-ltri g183a bound to cognate substrate (pre-cleavage
complex) . SNAP
output
|
|
6bcg
|
hydrolase-DNA |
X-ray (2.9 Å) |
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop
MS, Gloor GB, Edgell DR |
(2018) "Active
site residue identity regulates cleavage preference of
LAGLIDADG homing endonucleases." Nucleic Acids
Res., 46, 11990-12007. doi:
10.1093/nar/gky976.
|
I-ltri a28g bound to cognate substrate (pre-cleavage
complex) . SNAP
output
|
|
6bch
|
hydrolase-DNA |
X-ray (3.0 Å) |
McMurrough TA, Brown C, Zhang K, Junop M, Gloor GB,
Edgell DR |
"I-LtrI E29D bound to cognate substrate (nicked
complex)." |
I-ltri e29d bound to cognate substrate (nicked complex)
. SNAP output
|
|
6bci
|
hydrolase-DNA |
X-ray (2.28 Å) |
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop
MS, Gloor GB, Edgell DR |
(2018) "Active
site residue identity regulates cleavage preference of
LAGLIDADG homing endonucleases." Nucleic Acids
Res., 46, 11990-12007. doi:
10.1093/nar/gky976.
|
Wild-type i-ltri bound to non-cognate c4 substrate
(pre-cleavage complex) . SNAP output
|
|
6bcn
|
hydrolase-DNA |
X-ray (2.5 Å) |
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop
MS, Gloor GB, Edgell DR |
(2018) "Active
site residue identity regulates cleavage preference of
LAGLIDADG homing endonucleases." Nucleic Acids
Res., 46, 11990-12007. doi:
10.1093/nar/gky976.
|
I-ltri e184d bound to cognate substrate (pre-cleavage
complex) . SNAP
output
|
|
6bct
|
hydrolase-DNA |
X-ray (2.73 Å) |
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop
MS, Gloor GB, Edgell DR |
(2018) "Active
site residue identity regulates cleavage preference of
LAGLIDADG homing endonucleases." Nucleic Acids
Res., 46, 11990-12007. doi:
10.1093/nar/gky976.
|
I-ltri e184d bound to non-cognate c4 substrate
(pre-cleavage complex) . SNAP output
|
|
6bd0
|
hydrolase-DNA |
X-ray (1.45 Å) |
Laforet M, McMurrough TA, Brown C, Zhang K, Junop M,
Gloor GB, Edgell DR |
"I-OnuI K227Y, D236A bound to cognate substrate
(pre-cleavage complex)." |
I-onui k227y, d236a bound to cognate substrate
(pre-cleavage complex) . SNAP output
|
|
6bda
|
hydrolase-DNA |
X-ray (1.88 Å) |
Laforet M, McMurrough T, Brown C, Zhang K, Junop M,
Gloor GB, Edgell DR |
"Wild-type I-OnuI bound to A3G substrate
(post-cleavage complex)." |
Wild-type i-onui bound to a3g substrate (post-cleavage
complex) . SNAP
output
|
|
6bdb
|
hydrolase |
X-ray (1.5 Å) |
Laforet M, McMurrough TA, Brown C, Junop M, Zhang K,
Gloor GB |
"I-OnuI K227Y, D236A bound to A3G substrate
(pre-cleavage complex)." |
I-onui k227y, d236a bound to a3g substrate
(pre-cleavage complex) . SNAP output
|
|
6bek
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Nanji T, Gehrke EJ, Shen Y, Gloyd M, Zhang X, Firby
CD, Huynh A, Razi A, Ortega J, Elliot MA, Guarne A |
(2019) "Streptomyces
IHF uses multiple interfaces to bind DNA."
Biochim Biophys Acta Gen Subj,
1863, 129405. doi: 10.1016/j.bbagen.2019.07.014.
|
Structure of sihf bound to an 8bp palindromic DNA .
SNAP output
|
|
6bel
|
transferase-DNA |
X-ray (1.898 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with r-isomer of beta-gamma-chf-dctp . SNAP output
|
|
6bem
|
transferase-DNA |
X-ray (1.88 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with s-isomer of beta-gamma-chcl-dctp . SNAP output
|
|
6bhj
|
transferase-DNA |
X-ray (2.81 Å) |
Tuske S, Zheng J, Olson ED, Ruiz FX, Pascal BD,
Bauman JD, Das K, DeStefano JJ, Musier-Forsyth K, Griffin
PR, Arnold E |
(2020) "Integrative Structural Biology Studies of HIV-1
Reverse Transcriptase Binding to a High-Affinity DNA
Aptamer." Curr Res Struct Biol. doi: 10.1016/j.crstbi.2020.06.002.
|
Structure of hiv-1 reverse transcriptase bound to a
38-mer hairpin template-primer RNA-DNA aptamer .
SNAP output
|
|
6bhx
|
DNA binding protein-DNA |
X-ray (2.936 Å) |
Dubiel K, Myers AR, Kozlov AG, Yang O, Zhang J, Ha T,
Lohman TM, Keck JL |
(2019) "Structural
Mechanisms of Cooperative DNA Binding by Bacterial
Single-Stranded DNA-Binding Proteins." J. Mol.
Biol., 431, 178-195. doi:
10.1016/j.jmb.2018.11.019.
|
B. subtilis ssba with DNA . SNAP output
|
|
6bjs
|
transcription-DNA-RNA |
cryo-EM (5.5 Å) |
Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA,
Darst SA, Landick R |
(2018) "RNA
Polymerase Accommodates a Pause RNA Hairpin by Global
Conformational Rearrangements that Prolong
Pausing." Mol. Cell, 69,
802-815.e1. doi: 10.1016/j.molcel.2018.01.018.
|
Cryoem structure of e.coli his pause elongation complex
without pause hairpin . SNAP output
|
|
6bkf
|
ligase-DNA |
X-ray (3.25 Å) |
Kaminski AM, Tumbale PP, Schellenberg MJ, Williams
RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K |
(2018) "Structures
of DNA-bound human ligase IV catalytic core reveal
insights into substrate binding and catalysis."
Nat Commun, 9, 2642. doi:
10.1038/s41467-018-05024-8.
|
Lysyl-adenylate form of human ligiv catalytic domain
with bound DNA substrate in open conformation .
SNAP output
|
|
6bkg
|
ligase-DNA |
X-ray (2.402 Å) |
Kaminski AM, Tumbale PP, Schellenberg MJ, Williams
RS, Williams JG, Kunkel TA, Pedersen LC, Bebenek K |
(2018) "Structures
of DNA-bound human ligase IV catalytic core reveal
insights into substrate binding and catalysis."
Nat Commun, 9, 2642. doi:
10.1038/s41467-018-05024-8.
|
Human ligiv catalytic domain with bound DNA-adenylate
intermediate in closed conformation . SNAP output
|
|
6blo
|
transcription |
X-ray (3.401 Å) |
Wang W, Walmacq C, Chong J, Kashlev M, Wang D |
(2018) "Structural
basis of transcriptional stalling and bypass of abasic
DNA lesion by RNA polymerase II." Proc. Natl.
Acad. Sci. U.S.A., 115,
E2538-E2545. doi: 10.1073/pnas.1722050115.
|
Pol ii elongation complex with an abasic lesion at i+1
position . SNAP
output
|
|
6blp
|
transcription |
X-ray (3.203 Å) |
Wang W, Walmacq C, Chong J, Kashlev M, Wang D |
(2018) "Structural
basis of transcriptional stalling and bypass of abasic
DNA lesion by RNA polymerase II." Proc. Natl.
Acad. Sci. U.S.A., 115,
E2538-E2545. doi: 10.1073/pnas.1722050115.
|
Pol ii elongation complex with an abasic lesion at i+1
position, soaking ampcpp . SNAP output
|
|
6blw
|
DNA binding protein-DNA |
X-ray (1.835 Å) |
Wang D, Horton JR, Zheng Y, Blumenthal RM, Zhang X,
Cheng X |
(2018) "Role for
first zinc finger of WT1 in DNA sequence specificity:
Denys-Drash syndrome-associated WT1 mutant in ZF1
enhances affinity for a subset of WT1 binding
sites." Nucleic Acids Res.,
46, 3864-3877. doi: 10.1093/nar/gkx1274.
|
Zinc finger domain of wt1(+kts form) with m342r
mutation and 17+1mer oligonucleotide with triplet ggt .
SNAP output
|
|
6bm2
|
transcription |
X-ray (3.403 Å) |
Wang W, Walmacq C, Chong J, Kashlev M, Wang D |
(2018) "Structural
basis of transcriptional stalling and bypass of abasic
DNA lesion by RNA polymerase II." Proc. Natl.
Acad. Sci. U.S.A., 115,
E2538-E2545. doi: 10.1073/pnas.1722050115.
|
Pol ii elongation complex with an abasic lesion at i-1
position . SNAP
output
|
|
6bm4
|
transcription |
X-ray (2.951 Å) |
Wang W, Walmacq C, Chong J, Kashlev M, Wang D |
(2018) "Structural
basis of transcriptional stalling and bypass of abasic
DNA lesion by RNA polymerase II." Proc. Natl.
Acad. Sci. U.S.A., 115,
E2538-E2545. doi: 10.1073/pnas.1722050115.
|
Pol ii elongation complex with an abasic lesion at i-1
position,soaking umpnpp . SNAP output
|
|
6boq
|
DNA binding protein-DNA |
X-ray (1.96 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an a-a mismatch
adjacent the thf . SNAP
output
|
|
6bor
|
DNA binding protein-DNA |
X-ray (1.84 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an g-g mismatch
adjacent the thf . SNAP
output
|
|
6bos
|
DNA binding protein-DNA |
X-ray (2.304 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an a-c mismatch
adjacent the thf . SNAP
output
|
|
6bot
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an c-c mismatch
adjacent the thf . SNAP
output
|
|
6bou
|
DNA binding protein-DNA |
X-ray (2.538 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an t-c mismatch
adjacent the thf . SNAP
output
|
|
6bov
|
DNA binding protein-DNA |
X-ray (1.975 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an a-g mismatch
adjacent the thf . SNAP
output
|
|
6bow
|
DNA binding protein-DNA |
X-ray (1.59 Å) |
Fairlamb MS, Whitaker AM, Freudenthal BD |
(2018) "Apurinic/apyrimidinic
(AP) endonuclease 1 processing of AP sites with 5'
mismatches." Acta Crystallogr D Struct
Biol, 74, 760-768. doi: 10.1107/S2059798318003340.
|
Human ape1 substrate complex with an t-t mismatch
adjacent the thf . SNAP
output
|
|
6bqf
|
transferase-transcription |
X-ray (3.35 Å) |
Wang W, Walmacq C, Chong J, Kashlev M, Wang D |
(2018) "Structural
basis of transcriptional stalling and bypass of abasic
DNA lesion by RNA polymerase II." Proc. Natl.
Acad. Sci. U.S.A., 115,
E2538-E2545. doi: 10.1073/pnas.1722050115.
|
Pol ii elongation complex with 'dt-ap' at i+1, i-1
position . SNAP
output
|
|
6bqu
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Pufall MA |
"General and sequence-specific roles for DNA in
glucocorticoid receptor DNA-binding stoichiometry." |
Human gr (418-507) in complex with monomeric DNA
binding site . SNAP
output
|
|
6brr
|
transferase-DNA |
X-ray (2.97 Å) |
Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S,
Ji D, Rothbart SB, Wang Y, Wang GG, Song J |
(2018) "Structural
basis for DNMT3A-mediated de novo DNA methylation."
Nature, 554, 387-391. doi:
10.1038/nature25477.
|
Crystal structure of dnmt3a (r836a)-dnmt3l in complex
with DNA containing two cpg sites . SNAP output
|
|
6brx
|
replication |
X-ray (2.8 Å) |
Jha V, Ling H |
(2018) "Structural
Basis for Human DNA Polymerase Kappa to Bypass
Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an
Efficient and Accurate Extender." J. Mol.
Biol., 430, 1577-1589. doi:
10.1016/j.jmb.2018.04.023.
|
Crystal structure of human DNA polymerase kappa in
complex with DNA containing the major cisplatin lesion
. SNAP output
|
|
6bs1
|
replication |
X-ray (3.15 Å) |
Jha V, Ling H |
(2018) "Structural
Basis for Human DNA Polymerase Kappa to Bypass
Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an
Efficient and Accurate Extender." J. Mol.
Biol., 430, 1577-1589. doi:
10.1016/j.jmb.2018.04.023.
|
Crystal structure of human DNA polymerase kappa in
complex with DNA containing the major cisplatin lesion
. SNAP output
|
|
6bse
|
gene regulation |
X-ray (2.35 Å) |
Pufall MA, Zhang L |
"General and sequence-specific roles for DNA in
glucocorticoid receptor DNA-binding stoichiometry." |
Glucocorticoid receptor bound to high cooperativity
monomer sequence . SNAP
output
|
|
6bsf
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Pufall MA |
"General and sequence-specific roles for DNA in
glucocorticoid receptor DNA-binding stoichiometry." |
Human gr (418-507) in complex with monomeric DNA
binding site . SNAP
output
|
|
6bsg
|
viral protein-DNA-RNA-inhibitor |
X-ray (2.44 Å) |
Tian L, Kim MS, Li H, Wang J, Yang W |
(2018) "Structure
of HIV-1 reverse transcriptase cleaving RNA in an
RNA/DNA hybrid." Proc. Natl. Acad. Sci.
U.S.A., 115, 507-512. doi:
10.1073/pnas.1719746115.
|
Structure of hiv-1 rt complexed with RNA-DNA hybrid in
an RNA hydrolysis-off mode . SNAP output
|
|
6bsh
|
viral protein-DNA-RNA-inhibitor |
X-ray (2.649 Å) |
Tian L, Kim MS, Li H, Wang J, Yang W |
(2018) "Structure
of HIV-1 reverse transcriptase cleaving RNA in an
RNA/DNA hybrid." Proc. Natl. Acad. Sci.
U.S.A., 115, 507-512. doi:
10.1073/pnas.1719746115.
|
Structure of hiv-1 rt complexed with RNA-DNA hybrid in
the RNA hydrolysis mode . SNAP output
|
|
6bsi
|
viral protein-DNA-RNA-inhibitor |
X-ray (3.25 Å) |
Tian L, Kim MS, Li H, Wang J, Yang W |
(2018) "Structure
of HIV-1 reverse transcriptase cleaving RNA in an
RNA/DNA hybrid." Proc. Natl. Acad. Sci.
U.S.A., 115, 507-512. doi:
10.1073/pnas.1719746115.
|
Structure of hiv-1 rt complexed with an RNA-DNA hybrid
containing the polypurine-tract sequence . SNAP output
|
|
6bsj
|
viral protein-DNA-RNA-inhibitor |
X-ray (2.89 Å) |
Tian L, Kim MS, Li H, Wang J, Yang W |
(2018) "Structure
of HIV-1 reverse transcriptase cleaving RNA in an
RNA/DNA hybrid." Proc. Natl. Acad. Sci.
U.S.A., 115, 507-512. doi:
10.1073/pnas.1719746115.
|
Structure of hiv-1 rt complexed with an RNA-DNA hybrid
sequence non-preferred for RNA hydrolysis . SNAP output
|
|
6bte
|
transferase,lyase-DNA |
X-ray (2.2 Å) |
Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East
K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S,
Loria JP, Sweasy JB |
(2018) "I260Q
DNA polymerase beta highlights precatalytic
conformational rearrangements critical for
fidelity." Nucleic Acids Res.,
46, 10740-10756. doi: 10.1093/nar/gky825.
|
DNA polymerase beta i260q binary complex . SNAP output
|
|
6btf
|
transferase,lyase-DNA |
X-ray (1.75 Å) |
Liptak C, Mahmoud MM, Eckenroth BE, Moreno MV, East
K, Alnajjar KS, Huang J, Towle-Weicksel JB, Doublie S,
Loria JP, Sweasy JB |
(2018) "I260Q
DNA polymerase beta highlights precatalytic
conformational rearrangements critical for
fidelity." Nucleic Acids Res.,
46, 10740-10756. doi: 10.1093/nar/gky825.
|
DNA polymerase beta i260q ternary complex . SNAP output
|
|
6bux
|
hydrolase-DNA |
X-ray (1.856 Å) |
Maiti A, Myint W, Kanai T, Delviks-Frankenberry K,
Sierra Rodriguez C, Pathak VK, Schiffer CA, Matsuo H |
(2018) "Crystal
structure of the catalytic domain of HIV-1 restriction
factor APOBEC3G in complex with ssDNA." Nat
Commun, 9, 2460. doi: 10.1038/s41467-018-04872-8.
|
Crystal structure of apobec3g catalytic domain complex
with substrate ssDNA . SNAP output
|
|
6buz
|
structural protein-DNA |
cryo-EM (3.92 Å) |
Chittori S, Hong J, Saunders H, Feng H, Ghirlando R,
Kelly AE, Bai Y, Subramaniam S |
(2018) "Structural
mechanisms of centromeric nucleosome recognition by the
kinetochore protein CENP-N." Science,
359, 339-343. doi: 10.1126/science.aar2781.
|
cryo-EM structure of cenp-a nucleosome in complex with
kinetochore protein cenp-n . SNAP output
|
|
6bwy
|
hydrolase |
X-ray (2.9 Å) |
Ziegler SJ, Liu C, Landau M, Buzovetsky O, Desimmie
BA, Zhao Q, Sasaki T, Burdick RC, Pathak VK, Anderson KS,
Xiong Y |
(2018) "Insights
into DNA substrate selection by APOBEC3G from
structural, biochemical, and functional studies."
PLoS ONE, 13, e0195048. doi:
10.1371/journal.pone.0195048.
|
DNA substrate selection by apobec3g . SNAP output
|
|
6byy
|
transcription-DNA |
X-ray (2.3 Å) |
Lei X, Kou Y, Fu Y, Rajashekar N, Shi H, Wu F, Xu J,
Luo Y, Chen L |
(2018) "The
Cancer Mutation D83V Induces an alpha-Helix to
beta-Strand Conformation Switch in MEF2B." J.
Mol. Biol., 430, 1157-1172. doi:
10.1016/j.jmb.2018.02.012.
|
Mef2 chimera-DNA complex . SNAP output
|
|
6bz1
|
transcription-DNA |
X-ray (2.97 Å) |
Lei X, Kou Y, Fu Y, Rajashekar N, Shi H, Wu F, Xu J,
Luo Y, Chen L |
(2018) "The
Cancer Mutation D83V Induces an alpha-Helix to
beta-Strand Conformation Switch in MEF2B." J.
Mol. Biol., 430, 1157-1172. doi:
10.1016/j.jmb.2018.02.012.
|
Mef2 chimera d83v mutant-DNA complex . SNAP output
|
|
6bzo
|
transcription-DNA-antibiotic |
cryo-EM (3.38 Å) |
Boyaci H, Chen J, Lilic M, Palka M, Mooney RA,
Landick R, Darst SA, Campbell EA |
(2018) "Fidaxomicin
jamsMycobacterium tuberculosisRNA polymerase motions
needed for initiation via RbpA contacts."
Elife, 7. doi: 10.7554/eLife.34823.
|
Mtb rnap holo-rbpa-fidaxomicin-upstream fork DNA .
SNAP output
|
|
6c04
|
transcription-DNA |
cryo-EM (3.27 Å) |
Boyaci H, Chen J, Lilic M, Palka M, Mooney RA,
Landick R, Darst SA, Campbell EA |
(2018) "Fidaxomicin
jamsMycobacterium tuberculosisRNA polymerase motions
needed for initiation via RbpA contacts."
Elife, 7. doi: 10.7554/eLife.34823.
|
Mtb rnap holo-rbpa-double fork DNA -closed clamp .
SNAP output
|
|
6c0w
|
structural protein-DNA |
cryo-EM (4.0 Å) |
Pentakota S, Zhou K, Smith C, Maffini S, Petrovic A,
Morgan GP, Weir JR, Vetter IR, Musacchio A, Luger K |
(2017) "Decoding
the centromeric nucleosome through CENP-N."
Elife, 6. doi: 10.7554/eLife.33442.
|
cryo-EM structure of human kinetochore protein cenp-n
with the centromeric nucleosome containing cenp-a .
SNAP output
|
|
6c1a
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with methylated DNA . SNAP output
|
|
6c1t
|
DNA binding protein-DNA |
X-ray (1.84 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with a partially methylated DNA .
SNAP output
|
|
6c1u
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with a deoxy-oligonucleotide . SNAP output
|
|
6c1v
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with double-stranded DNA . SNAP output
|
|
6c1y
|
DNA binding protein-DNA |
X-ray (2.3 Å) |
Lei M, Tempel W, Chen S, Liu K, Min J |
(2019) "Plasticity
at the DNA recognition site of the MeCP2 mCG-binding
domain." Biochim Biophys Acta Gene Regul
Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409.
|
Mbd of human mecp2 in complex with methylated DNA .
SNAP output
|
|
6c2f
|
DNA binding protein-DNA |
X-ray (2.65 Å) |
Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C,
Edwards AM, Min J, Structural Genomics Consortium |
"MBD2 in complex with methylated DNA." |
Mbd2 in complex with methylated DNA . SNAP output
|
|
6c2s
|
DNA binding protein-DNA |
X-ray (2.85 Å) |
Cogan DP, Baraquet C, Harwood CS, Nair SK |
(2018) "Structural
basis of transcriptional regulation by CouR, a
repressor of coumarate catabolism, inRhodopseudomonas
palustris." J. Biol. Chem.,
293, 11727-11735. doi: 10.1074/jbc.RA118.003561.
|
Transcriptional repressor, cour, bound to a 23-mer DNA
duplex . SNAP output
|
|
6c31
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Samanovic MI, Hsu HC, Jones MB, Jones V, McNeil MR,
Becker SH, Jordan AT, Strnad M, Xu C, Jackson M, Li H,
Darwin KH |
(2018) "Cytokinin
Signaling in Mycobacterium tuberculosis."
MBio, 9. doi: 10.1128/mBio.00989-18.
|
Crystal structure of tetr family protein rv0078 in
complex with DNA . SNAP
output
|
|
6c66
|
DNA binding protein-DNA-RNA |
cryo-EM (3.66 Å) |
Xiao Y, Luo M, Dolan AE, Liao M, Ke A |
(2018) "Structure
basis for RNA-guided DNA degradation by Cascade and
Cas3." Science, 361. doi:
10.1126/science.aat0839.
|
Crispr RNA-guided surveillance complex, pre-nicking .
SNAP output
|
|
6c6s
|
transcription-DNA-RNA |
cryo-EM (3.7 Å) |
Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina
TV, Artsimovitch I, Landick R, Darst SA |
(2018) "Structural
Basis for Transcript Elongation Control by NusG Family
Universal Regulators." Cell,
173, 1650-1662.e14. doi: 10.1016/j.cell.2018.05.017.
|
Cryoem structure of e.coli RNA polymerase elongation
complex bound with rfah . SNAP output
|
|
6c6t
|
transcription-DNA-RNA |
cryo-EM (3.5 Å) |
Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina
TV, Artsimovitch I, Landick R, Darst SA |
(2018) "Structural
Basis for Transcript Elongation Control by NusG Family
Universal Regulators." Cell,
173, 1650-1662.e14. doi: 10.1016/j.cell.2018.05.017.
|
Cryoem structure of e.coli RNA polymerase elongation
complex bound with rfah . SNAP output
|
|
6c6u
|
transcription-DNA-RNA |
cryo-EM (3.7 Å) |
Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina
TV, Artsimovitch I, Landick R, Darst SA |
(2018) "Structural
Basis for Transcript Elongation Control by NusG Family
Universal Regulators." Cell,
173, 1650-1662.e14. doi: 10.1016/j.cell.2018.05.017.
|
Cryoem structure of e.coli RNA polymerase elongation
complex bound with nusg . SNAP output
|
|
6ca0
|
transcription-DNA |
cryo-EM (5.75 Å) |
Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D,
Jiang W, Murakami KS |
(2018) "Cryo-EM
structure ofEscherichia colisigma70RNA polymerase and
promoter DNA complex revealed a role of sigma
non-conserved region during the open complex
formation." J. Biol. Chem.,
293, 7367-7375. doi: 10.1074/jbc.RA118.002161.
|
cryo-EM structure of e. coli rnap sigma70 open complex
. SNAP output
|
|
6cc8
|
DNA binding protein-DNA |
X-ray (1.95 Å) |
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J |
(2019) "Structural
analyses reveal that MBD3 is a methylated CG
binder." Febs J., 286,
3240-3254. doi: 10.1111/febs.14850.
|
Crystal structure mbd3 mbd domain in complex with
methylated cpg DNA . SNAP output
|
|
6cce
|
transcription-DNA-antibiotic |
X-ray (3.05 Å) |
Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I,
Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T,
Saito K, Braffman N, Fay A, Glickman MS, Darst SA,
Campbell EA, Brady SF |
(2018) "Rifamycin
congeners kanglemycins are active against
rifampicin-resistant bacteria via a distinct
mechanism." Nat Commun,
9, 4147. doi: 10.1038/s41467-018-06587-2.
|
Crystal structure of a mycobacterium smegmatis RNA
polymerase transcription initiation complex with
inhibitor kanglemycin a . SNAP output
|
|
6ccg
|
transcription |
X-ray (1.9 Å) |
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J |
(2019) "Structural
analyses reveal that MBD3 is a methylated CG
binder." Febs J., 286,
3240-3254. doi: 10.1111/febs.14850.
|
Crystal structure mbd3 mbd domain in complex with
methylated cpg DNA . SNAP output
|
|
6ccv
|
transcription |
X-ray (3.05 Å) |
Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I,
Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T,
Saito K, Braffman N, Fay A, Glickman MS, Darst SA,
Campbell EA, Brady SF |
(2018) "Rifamycin
congeners kanglemycins are active against
rifampicin-resistant bacteria via a distinct
mechanism." Nat Commun,
9, 4147. doi: 10.1038/s41467-018-06587-2.
|
Crystal structure of a mycobacterium smegmatis RNA
polymerase transcription initiation complex with
inhibitor rifampicin . SNAP output
|
|
6ceu
|
transcription-DNA |
X-ray (2.005 Å) |
Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J |
(2019) "Structural
analyses reveal that MBD3 is a methylated CG
binder." Febs J., 286,
3240-3254. doi: 10.1111/febs.14850.
|
Mbd3 mbd in complex with methylated, non-palindromic
cpg DNA: alternative interpretation of crystallographic
data . SNAP output
|
|
6cfi
|
DNA binding protein-DNA |
X-ray (3.36 Å) |
Paul D, Mu H, Zhao H, Ouerfelli O, Jeffrey PD, Broyde
S, Min JH |
(2019) "Structure
and mechanism of pyrimidine-pyrimidone (6-4)
photoproduct recognition by the Rad4/XPC nucleotide
excision repair complex." Nucleic Acids
Res., 47, 6015-6028. doi:
10.1093/nar/gkz359.
|
Crystal structure of rad4-rad23 bound to a 6-4
photoproduct uv lesion . SNAP output
|
|
6cg0
|
recombination |
cryo-EM (3.17 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
cryo-EM structure of mouse rag1-2 hfc complex (3.17 a)
. SNAP output
|
|
6cg8
|
DNA binding protein-DNA |
X-ray (2.299 Å) |
Guo MS, Haakonsen DL, Zeng W, Schumacher MA, Laub
MT |
(2018) "A
Bacterial Chromosome Structuring Protein Binds
Overtwisted DNA to Stimulate Type II Topoisomerases and
Enable DNA Replication." Cell,
175, 583. doi: 10.1016/j.cell.2018.08.029.
|
Structure of c. crescentus gapr-DNA . SNAP output
|
|
6chv
|
antitoxin-DNA |
X-ray (2.9 Å) |
Schureck MA, Meisner J, Hoffer ED, Wang D, Onuoha N,
Ei Cho S, Lollar 3rd P, Dunham CM |
(2019) "Structural
basis of transcriptional regulation by the HigA
antitoxin." Mol.Microbiol.,
111, 1449-1462. doi: 10.1111/mmi.14229.
|
Proteus vulgaris higa antitoxin bound to DNA . SNAP output
|
|
6cij
|
recombination-DNA |
cryo-EM (3.9 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
cryo-EM structure of mouse rag1-2 hfc complex
containing partial hmgb1 linker(3.9 a) . SNAP output
|
|
6cik
|
recombination-DNA |
X-ray (3.15 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Pre-reaction complex, rag1(e962q)-2-intact-nicked
12-23rss complex in mn2+ . SNAP output
|
|
6cil
|
recombination-DNA |
X-ray (4.15 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Pre-reaction complex, rag1(e962q)-2-intact-intact
12-23rss complex in mn2+ . SNAP output
|
|
6cim
|
recombination-DNA |
X-ray (3.6 Å) |
Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH,
Gellert M, Yang W |
(2018) "Cracking
the DNA Code for V(D)J Recombination." Mol.
Cell, 70, 358-370.e4. doi:
10.1016/j.molcel.2018.03.008.
|
Pre-reaction complex, rag1(e962q)-2-nicked-intact
12-23rss complex in mn2+ . SNAP output
|
|
6cly
|
transferase, lyase-DNA |
X-ray (2.186 Å) |
Koag M-C, Lee S |
"Structure of human DNA polymerase beta complexed
with 8-ClG as the template base in a 1-nucleotide gapped
DNA." |
Structure of human DNA polymerase beta complexed with
8-clg as the template base in a 1-nucleotide gapped DNA
. SNAP output
|
|
6cnb
|
transcription-DNA |
cryo-EM (4.1 Å) |
Han Y, Yan C, Fishbain S, Ivanov I, He Y |
(2018) "Structural
visualization of RNA polymerase III transcription
machineries." Cell Discov,
4, 40. doi: 10.1038/s41421-018-0044-z.
|
Yeast RNA polymerase iii initial transcribing complex .
SNAP output
|
|
6cnc
|
transcription-DNA |
cryo-EM (4.1 Å) |
Han Y, Yan C, Fishbain S, Ivanov I, He Y |
(2018) "Structural
visualization of RNA polymerase III transcription
machineries." Cell Discov,
4, 40. doi: 10.1038/s41421-018-0044-z.
|
Yeast RNA polymerase iii open complex . SNAP output
|
|
6cnd
|
transcription-DNA |
cryo-EM (4.8 Å) |
Han Y, Yan C, Fishbain S, Ivanov I, He Y |
(2018) "Structural
visualization of RNA polymerase III transcription
machineries." Cell Discov,
4, 40. doi: 10.1038/s41421-018-0044-z.
|
Yeast RNA polymerase iii natural open complex (noc) .
SNAP output
|
|
6cnf
|
transcription-DNA |
cryo-EM (4.5 Å) |
Han Y, Yan C, Fishbain S, Ivanov I, He Y |
(2018) "Structural
visualization of RNA polymerase III transcription
machineries." Cell Discov,
4, 40. doi: 10.1038/s41421-018-0044-z.
|
Yeast RNA polymerase iii elongation complex . SNAP output
|
|
6cnp
|
transcription-DNA |
X-ray (2.1 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Crystal structure of mbd2 complex with methylated cpg
island . SNAP output
|
|
6cnq
|
transcription-DNA |
X-ray (2.151 Å) |
Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min
J |
(2018) "Structural
basis for the ability of MBD domains to bind methyl-CG
and TG sites in DNA." J. Biol. Chem.,
293, 7344-7354. doi: 10.1074/jbc.RA118.001785.
|
Mbd2 in complex with methylated DNA . SNAP output
|
|
6cpq
|
transferase-DNA |
X-ray (1.93 Å) |
Koag M-C, Lee S |
"Structure of human DNA polymerase beta complexed
with 8-ClG in the template base paired with incoming
non-hydrolyzable CTP." |
Structure of human DNA polymerase beta complexed with
8-clg in the template base paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
6cq2
|
isomerase-DNA |
X-ray (3.004 Å) |
Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh
YC |
(2018) "Investigating
mycobacterial topoisomerase I mechanism from the
analysis of metal and DNA substrate interactions at the
active site." Nucleic Acids Res.,
46, 7296-7308. doi: 10.1093/nar/gky492.
|
Crystal structure of mycobacterium tuberculosis
topoisomerase i in complex with oligonucleotide mts2-12
and magnesium . SNAP
output
|
|
6cqi
|
isomerase-DNA |
X-ray (2.42 Å) |
Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh
YC |
(2018) "Investigating
mycobacterial topoisomerase I mechanism from the
analysis of metal and DNA substrate interactions at the
active site." Nucleic Acids Res.,
46, 7296-7308. doi: 10.1093/nar/gky492.
|
2.42a crystal structure of mycobacterium tuberculosis
topoisomerase i in complex with an oligonucleotide
mts2-11 . SNAP
output
|
|
6cr3
|
transcription-DNA |
X-ray (1.95 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cbr2, beta,
gamma datp analogue . SNAP output
|
|
6cr4
|
transferase-DNA |
X-ray (1.8 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with datp .
SNAP output
|
|
6cr5
|
transferase-DNA |
X-ray (1.982 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with ch2-beta,
gamma datp analogue . SNAP output
|
|
6cr6
|
transferase-DNA |
X-ray (2.097 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with ch-ch3,
beta, gamma datp analogue . SNAP output
|
|
6cr7
|
transferase-DNA |
X-ray (2.29 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chf, beta,
gamma datp analogue . SNAP output
|
|
6cr8
|
transferase-DNA |
X-ray (2.05 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chcl (r & s
isomers), beta, gamma datp analogue . SNAP output
|
|
6cr9
|
transferase-DNA |
X-ray (1.96 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cfcl, beta,
gamma datp analogue . SNAP output
|
|
6crb
|
transferase-DNA |
X-ray (2.151 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cf2, beta,
gamma datp analogue . SNAP output
|
|
6crc
|
transferase-DNA |
X-ray (2.3 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with ccl2, beta,
gamma datp analogue . SNAP output
|
|
6crh
|
transferase, lyase-DNA |
X-ray (2.327 Å) |
Kou Y, Koag MC, Lee S |
(2019) "Promutagenicity
of 8-Chloroguanine, A Major Inflammation-Induced
Halogenated DNA Lesion." Molecules,
24. doi: 10.3390/molecules24193507.
|
Structure of human DNA polymerase beta complexed with
8-clg in the template base paired with incoming
non-hydrolyzable gtp . SNAP output
|
|
6crm
|
hydrolase-DNA |
X-ray (2.19 Å) |
Voter AF, Qiu Y, Tippana R, Myong S, Keck JL |
(2018) "A
guanine-flipping and sequestration mechanism for
G-quadruplex unwinding by RecQ helicases." Nat
Commun, 9, 4201. doi: 10.1038/s41467-018-06751-8.
|
Crystal structure of recq catalytic core from c.
sakazakii bound to an unfolded g-quadruplex . SNAP output
|
|
6cro
|
gene regulation-DNA |
X-ray (3.0 Å) |
Albright RA, Matthews BW |
(1998) "Crystal
structure of lambda-Cro bound to a consensus operator
at 3.0 A resolution." J.Mol.Biol.,
280, 137-151. doi: 10.1006/jmbi.1998.1848.
|
Crystal structure of lambda-cro bound to a consensus
operator at 3.0 angstrom resolution . SNAP output
|
|
6cst
|
replication, transferase-DNA |
X-ray (2.0 Å) |
Jha V, Ling H |
(2018) "2.0
angstrom resolution crystal structure of human pol
kappa reveals a new catalytic function of N-clasp in
DNA replication." Sci Rep,
8, 15125. doi: 10.1038/s41598-018-33371-5.
|
Structure of human DNA polymerase kappa with DNA .
SNAP output
|
|
6ct9
|
transferase-DNA |
X-ray (2.26 Å) |
Zhou W, Whiteley AT, de Oliveira Mann CC, Morehouse
BR, Nowak RP, Fischer ES, Gray NS, Mekalanos JJ,
Kranzusch PJ |
(2018) "Structure
of the Human cGAS-DNA Complex Reveals Enhanced Control
of Immune Surveillance." Cell,
174, 300-311.e11. doi: 10.1016/j.cell.2018.06.026.
|
Structure of the human cgas-DNA complex . SNAP output
|
|
6cta
|
transferase-DNA |
X-ray (2.779 Å) |
Zhou W, Whiteley AT, de Oliveira Mann CC, Morehouse
BR, Nowak RP, Fischer ES, Gray NS, Mekalanos JJ,
Kranzusch PJ |
(2018) "Structure
of the Human cGAS-DNA Complex Reveals Enhanced Control
of Immune Surveillance." Cell,
174, 300-311.e11. doi: 10.1016/j.cell.2018.06.026.
|
Structure of the human cgas-DNA complex with atp .
SNAP output
|
|
6cti
|
transcription-DNA |
X-ray (2.001 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with ccl2, beta,
gamma dttp analogue . SNAP output
|
|
6ctj
|
transcription-DNA |
X-ray (2.1 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chch3, beta,
gamma dttp analogue . SNAP output
|
|
6ctk
|
transcription-DNA |
X-ray (2.153 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chf-r-s
isomers, beta, gamma dttp analogue . SNAP output
|
|
6ctl
|
transcription-DNA |
X-ray (2.0 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chcl-r-s
isomers, beta, gamma dttp analogue . SNAP output
|
|
6ctm
|
transcription-DNA |
X-ray (2.101 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with
chcl(r-isomer), beta, gamma dttp analogue . SNAP output
|
|
6ctn
|
transcription-DNA |
X-ray (1.92 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with
cfcl,beta-gamma dttp analogue . SNAP output
|
|
6cto
|
transcription-DNA |
X-ray (2.04 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cf2, beta,
gamma dttp analogue . SNAP output
|
|
6ctp
|
transcription-DNA |
X-ray (2.2 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with ch2, beta,
gamma dttp analogue . SNAP output
|
|
6ctq
|
transcription-DNA |
X-ray (1.87 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with dctp .
SNAP output
|
|
6ctr
|
transcription-DNA |
X-ray (1.85 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chf (r & s
isomers), beta, gamma dctp analogue . SNAP output
|
|
6ctt
|
transcription-DNA |
X-ray (2.0 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chcl (r & s
isomers, beta, gamma dctp analogue . SNAP output
|
|
6ctu
|
transcription-DNA |
X-ray (1.9 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cfcl, beta,
gamma dctp analogue . SNAP output
|
|
6ctv
|
transcription-DNA |
X-ray (2.02 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cf2, beta,
gamma dctp analogue . SNAP output
|
|
6ctw
|
transcription-DNA |
X-ray (1.981 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with ccl2, beta,
gamma dctp analogue . SNAP output
|
|
6ctx
|
transcription-DNA |
X-ray (2.02 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with cbr2, beta,
gamma dctp analogue . SNAP output
|
|
6cu9
|
transferase, lyase-DNA |
X-ray (2.04 Å) |
Koag M-C, Lee S |
"Structure of human DNA polymerase beta complexed
with 8-ClG in the template base paired with incoming
non-hydrolyzable CTP and MANGANESE." |
Structure of human DNA polymerase beta complexed with
8-clg in the template base paired with incoming
non-hydrolyzable ctp and manganese . SNAP output
|
|
6cua
|
transferase, lyase-DNA |
X-ray (2.17 Å) |
Koag M-C, Lee S |
"Structure of human DNA polymerase beta complexed
with 8-ClG in the template base paired with incoming
non-hydrolyzable GTP and MANGANESE." |
Structure of human DNA polymerase beta complexed with
8-clg in the template base paired with incoming
non-hydrolyzable gtp and manganese . SNAP output
|
|
6cub
|
transferase, lyase-DNA |
X-ray (2.05 Å) |
Koag M-C, Lee S |
"Structure of human DNA polymerase beta complexed
with 8-ClG in the template base paired with incoming
non-hydrolyzable ATP and MANGANESE." |
Structure of human DNA polymerase beta complexed with
8-clg in the template base paired with incoming
non-hydrolyzable atp and manganese . SNAP output
|
|
6cuu
|
transcription-DNA-antibiotic |
X-ray (2.994 Å) |
Mosaei H, Molodtsov V, Kepplinger B, Harbottle J,
Moon CW, Jeeves RE, Ceccaroni L, Shin Y, Morton-Laing S,
Marrs ECL, Wills C, Clegg W, Yuzenkova Y, Perry JD, Bacon
J, Errington J, Allenby NEE, Hall MJ, Murakami KS, Zenkin
N |
(2018) "Mode of
Action of Kanglemycin A, an Ansamycin Natural Product
that Is Active against Rifampicin-Resistant
Mycobacterium tuberculosis." Mol. Cell,
72, 263-274.e5. doi: 10.1016/j.molcel.2018.08.028.
|
Thermus thermophiles RNA polymerase in complex with
promoter DNA and antibiotic kanglemycin a . SNAP output
|
|
6cvo
|
hydrolase-DNA-RNA |
X-ray (2.4 Å) |
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather
E, Watson M, Little JN, Krahn J, Waddell I, London RE,
Williams RS |
(2018) "Mechanism
of APTX nicked DNA sensing and pleiotropic inactivation
in neurodegenerative disease." EMBO J.,
37. doi: 10.15252/embj.201798875.
|
Human aprataxin (aptx) bound to nicked RNA-DNA, amp and
zn product complex . SNAP output
|
|
6cvp
|
hydrolase-DNA-RNA |
X-ray (1.999 Å) |
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather
E, Watson M, Little JN, Krahn J, Waddell I, London RE,
Williams RS |
(2018) "Mechanism
of APTX nicked DNA sensing and pleiotropic inactivation
in neurodegenerative disease." EMBO J.,
37. doi: 10.15252/embj.201798875.
|
Human aprataxin (aptx) r199h bound to RNA-DNA, amp and
zn product complex . SNAP output
|
|
6cvq
|
hydrolase-DNA-RNA |
X-ray (1.65 Å) |
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather
E, Watson M, Little JN, Krahn J, Waddell I, London RE,
Williams RS |
(2018) "Mechanism
of APTX nicked DNA sensing and pleiotropic inactivation
in neurodegenerative disease." EMBO J.,
37. doi: 10.15252/embj.201798875.
|
Human aprataxin (aptx) h201q bound to RNA-DNA, amp and
zn product complex . SNAP output
|
|
6cvr
|
hydrolase-DNA-RNA |
X-ray (1.88 Å) |
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather
E, Watson M, Little JN, Krahn J, Waddell I, London RE,
Williams RS |
(2018) "Mechanism
of APTX nicked DNA sensing and pleiotropic inactivation
in neurodegenerative disease." EMBO J.,
37. doi: 10.15252/embj.201798875.
|
Human aprataxin (aptx) s242n bound to RNA-DNA, amp and
zn product complex . SNAP output
|
|
6cvs
|
hydrolase-DNA |
X-ray (2.11 Å) |
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather
E, Watson M, Little JN, Krahn J, Waddell I, London RE,
Williams RS |
(2018) "Mechanism
of APTX nicked DNA sensing and pleiotropic inactivation
in neurodegenerative disease." EMBO J.,
37. doi: 10.15252/embj.201798875.
|
Human aprataxin (aptx) l248m bound to DNA, amp and zn
product . SNAP
output
|
|
6cvt
|
hydrolase-DNA-RNA |
X-ray (2.941 Å) |
Tumbale P, Schellenberg MJ, Mueller GA, Fairweather
E, Watson M, Little JN, Krahn J, Waddell I, London RE,
Williams RS |
(2018) "Mechanism
of APTX nicked DNA sensing and pleiotropic inactivation
in neurodegenerative disease." EMBO J.,
37. doi: 10.15252/embj.201798875.
|
Human aprataxin (aptx) v263g bound to RNA-DNA, amp and
zn product complex . SNAP output
|
|
6d0m
|
transferase-DNA |
X-ray (1.832 Å) |
Rechkoblit O, Choudhury JR, Buku A, Prakash L,
Prakash S, Aggarwal AK |
(2018) "Structural
basis for polymerase eta-promoted resistance to the
anticancer nucleoside analog cytarabine." Sci
Rep, 8, 12702. doi: 10.1038/s41598-018-30796-w.
|
Polymerase eta post-insertion binary complex with
cytarabine (arac) . SNAP
output
|
|
6d0z
|
transferase |
X-ray (1.75 Å) |
Rechkoblit O, Choudhury JR, Buku A, Prakash L,
Prakash S, Aggarwal AK |
(2018) "Structural
basis for polymerase eta-promoted resistance to the
anticancer nucleoside analog cytarabine." Sci
Rep, 8, 12702. doi: 10.1038/s41598-018-30796-w.
|
Polymerase eta cytarabine (arac) extension ternary
complex . SNAP
output
|
|
6d1t
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C,
Edwards AM, Min J, Structural Genomics Consortium |
"Complex of MBD1-MBD and methylated DNA." |
Complex of mbd1-mbd and methylated DNA . SNAP output
|
|
6d5f
|
virus |
cryo-EM (3.7 Å) |
Liu Y, Osinski T, Wang F, Krupovic M, Schouten S,
Kasson P, Prangishvili D, Egelman EH |
(2018) "Structural
conservation in a membrane-enveloped filamentous virus
infecting a hyperthermophilic acidophile." Nat
Commun, 9, 3360. doi: 10.1038/s41467-018-05684-6.
|
cryo-EM reconstruction of membrane-enveloped
filamentous virus sfv1 (sulfolobus filamentous virus 1)
. SNAP output
|
|
6d6q
|
hydrolase |
cryo-EM (3.45 Å) |
Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia
MA, Lima CD |
(2018) "Helicase-Dependent
RNA Decay Illuminated by a Cryo-EM Structure of a Human
Nuclear RNA Exosome-MTR4 Complex." Cell,
173, 1663. doi: 10.1016/j.cell.2018.05.041.
|
Human nuclear exosome-mtr4 RNA complex - overall
reconstruction . SNAP
output
|
|
6d6r
|
hydrolase |
cryo-EM (3.45 Å) |
Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia
MA, Lima CD |
(2018) "Helicase-Dependent
RNA Decay Illuminated by a Cryo-EM Structure of a Human
Nuclear RNA Exosome-MTR4 Complex." Cell,
173, 1663. doi: 10.1016/j.cell.2018.05.041.
|
Human nuclear exosome-mtr4 RNA complex - composite map
after focused reconstruction . SNAP output
|
|
6d6v
|
replication |
cryo-EM (4.8 Å) |
Jiang J, Wang Y, Susac L, Chan H, Basu R, Zhou ZH,
Feigon J |
(2018) "Structure
of Telomerase with Telomeric DNA." Cell,
173, 1179-1190.e13. doi: 10.1016/j.cell.2018.04.038.
|
Cryoem structure of tetrahymena telomerase with
telomeric DNA at 4.8 angstrom resolution . SNAP output
|
|
6d8a
|
RNA binding protein |
X-ray (2.251 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Rsago ternary complex with guide RNA and target DNA
containing a-a bulge within the seed segment of the
target strand . SNAP
output
|
|
6d8f
|
RNA binding protein |
X-ray (2.15 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Rsago ternary complex with guide RNA and target DNA
containing t-t bulge within the seed segment . SNAP output
|
|
6d8p
|
RNA binding protein |
X-ray (2.1 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Ternary rsago complex containing guide RNA paired with
target DNA . SNAP
output
|
|
6d92
|
RNA binding protein |
X-ray (1.81 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Ternary rsago complex with guide RNA and target DNA
containing a-a non-canonical pair at position 3 .
SNAP output
|
|
6d95
|
RNA binding protein |
X-ray (1.85 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Ternary rsago complex with guide RNA paired and target
DNA containing a8-a8' non-canonical pair . SNAP output
|
|
6d9k
|
RNA binding protein-RNA-DNA |
X-ray (2.0 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Ternary rsago complex with guide RNA and target DNA
containing a-g non-canonical pair . SNAP output
|
|
6d9l
|
RNA binding protein-RNA-DNA |
X-ray (2.6 Å) |
Liu Y, Esyunina D, Olovnikov I, Teplova M,
Kulbachinskiy A, Aravin AA, Patel DJ |
(2018) "Accommodation
of Helical Imperfections in Rhodobacter sphaeroides
Argonaute Ternary Complexes with Guide RNA and Target
DNA." Cell Rep, 24,
453-462. doi: 10.1016/j.celrep.2018.06.021.
|
Ternary rsago complex with guide RNA and target DNA
containing g-a non-canonical pair . SNAP output
|
|
6dbi
|
recombination-DNA |
cryo-EM (3.4 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss nicked DNA intermediates . SNAP output
|
|
6dbj
|
recombination-DNA |
cryo-EM (3.0 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss nicked DNA intermediates . SNAP output
|
|
6dbl
|
recombination-DNA |
cryo-EM (5.0 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss substrate dnas . SNAP output
|
|
6dbo
|
recombination-DNA |
cryo-EM (4.4 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss substrate dnas . SNAP output
|
|
6dbq
|
recombination-DNA |
cryo-EM (4.22 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss substrate dnas . SNAP output
|
|
6dbr
|
recombination-DNA |
cryo-EM (4.0 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with one melted rss
and one unmelted rss . SNAP output
|
|
6dbt
|
recombination-DNA |
cryo-EM (4.3 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss substrate dnas . SNAP output
|
|
6dbu
|
recombination-DNA |
cryo-EM (3.9 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss substrate dnas . SNAP output
|
|
6dbv
|
recombination-DNA |
cryo-EM (4.29 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss and
23-rss substrate dnas . SNAP output
|
|
6dbw
|
recombination-DNA |
cryo-EM (4.7 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss
substrate DNA . SNAP
output
|
|
6dbx
|
recombination-DNA |
cryo-EM (4.2 Å) |
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu
H |
(2018) "DNA
melting initiates the RAG catalytic pathway."
Nat. Struct. Mol. Biol., 25,
732-742. doi: 10.1038/s41594-018-0098-5.
|
cryo-EM structure of rag in complex with 12-rss
substrate DNA . SNAP
output
|
|
6dcf
|
transcription-DNA-antibiotic |
X-ray (3.45 Å) |
Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I,
Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T,
Saito K, Braffman N, Fay A, Glickman MS, Darst SA,
Campbell EA, Brady SF |
(2018) "Rifamycin
congeners kanglemycins are active against
rifampicin-resistant bacteria via a distinct
mechanism." Nat Commun,
9, 4147. doi: 10.1038/s41467-018-06587-2.
|
Crystal structure of a mycobacterium smegmatis
transcription initiation complex with
rifampicin-resistant RNA polymerase and bound to
kanglemycin a . SNAP
output
|
|
6df5
|
DNA binding protein-DNA |
X-ray (1.819 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
conformational switch in the zinc finger protein Kaiso
mediates differential readout of specific and
methylated DNA sequences." Biochemistry.
doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with the specific kaiso binding sequence (kbs)
. SNAP output
|
|
6df8
|
DNA binding protein-DNA |
X-ray (2.536 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
conformational switch in the zinc finger protein Kaiso
mediates differential readout of specific and
methylated DNA sequences." Biochemistry.
doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with the specific kaiso binding sequence (kbs),
ph 6.5 . SNAP output
|
|
6df9
|
DNA binding protein-DNA |
X-ray (2.319 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
conformational switch in the zinc finger protein Kaiso
mediates differential readout of specific and
methylated DNA sequences." Biochemistry.
doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) e535q zinc finger DNA binding domain in
complex with the specific kaiso binding sequence (kbs)
. SNAP output
|
|
6dfa
|
DNA binding protein-DNA |
X-ray (1.908 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
conformational switch in the zinc finger protein Kaiso
mediates differential readout of specific and
methylated DNA sequences." Biochemistry.
doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) e535a zinc finger DNA binding domain in
complex with the specific kaiso binding sequence (kbs)
. SNAP output
|
|
6dfb
|
DNA binding protein-DNA |
X-ray (1.66 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
conformational switch in the zinc finger protein Kaiso
mediates differential readout of specific and
methylated DNA sequences." Biochemistry.
doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) k539a zinc finger DNA binding domain in
complex with the specific kaiso binding sequence (kbs)
. SNAP output
|
|
6dfc
|
DNA binding protein-DNA |
X-ray (1.85 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
conformational switch in the zinc finger protein Kaiso
mediates differential readout of specific and
methylated DNA sequences." Biochemistry.
doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with the specific kaiso binding sequence (kbs)
with a t-to-u substitution . SNAP output
|
|
6dfy
|
DNA binding protein-DNA |
X-ray (2.623 Å) |
Aihara H, Shi K, Lee JK, Bosnakovski D, Kyba M |
(2018) "Comment
on structural basis of DUX4/IGH-driven
transactivation." Leukemia,
32, 2090-2092. doi: 10.1038/s41375-018-0217-7.
|
Remodeled crystal structure of DNA-bound dux4-hd2 .
SNAP output
|
|
6dg0
|
RNA binding protein-DNA |
X-ray (2.457 Å) |
Soufari H, Mackereth CD |
"Structure of MEC-8 RRM2 in complex with
AGCACA." |
Mec-8 c-terminal rrm domain bound to agcaca . SNAP output
|
|
6dgd
|
DNA binding protein-DNA |
X-ray (2.823 Å) |
Windgassen TA, Leroux M, Satyshur KA, Sandler SJ,
Keck JL |
(2018) "Structure-specific
DNA replication-fork recognition directs helicase and
replication restart activities of the PriA
helicase." Proc. Natl. Acad. Sci. U.S.A.,
115, E9075-E9084. doi: 10.1073/pnas.1809842115.
|
Pria helicase bound to dsDNA of a DNA replication fork
. SNAP output
|
|
6dia
|
DNA binding protein-DNA |
X-ray (1.969 Å) |
Smith MR, Shock DD, Beard WA, Greenberg MM,
Freudenthal BD, Wilson SH |
(2019) "A
guardian residue hinders insertion of a Fapy•dGTP
analog by modulating the open-closed DNA polymerase
transition." Nucleic Acids Res.,
47, 3197-3207. doi: 10.1093/nar/gkz002.
|
DNA polymerase beta substrate complex with templating
cytosine and incoming fapy-dgtp analog . SNAP output
|
|
6dic
|
DNA binding protein-DNA |
X-ray (1.992 Å) |
Smith MR, Shock DD, Beard WA, Greenberg MM,
Freudenthal BD, Wilson SH |
(2019) "A
guardian residue hinders insertion of a Fapy•dGTP
analog by modulating the open-closed DNA polymerase
transition." Nucleic Acids Res.,
47, 3197-3207. doi: 10.1093/nar/gkz002.
|
D276g DNA polymerase beta substrate complex with
templating cytosine and incoming fapy-dgtp analog .
SNAP output
|
|
6dks
|
transcription-DNA |
X-ray (2.78 Å) |
Yuan Z, VanderWielen BD, Giaimo BD, Pan L, Collins
CE, Turkiewicz A, Hein K, Oswald F, Borggrefe T, Kovall
RA |
(2019) "Structural
and Functional Studies of the RBPJ-SHARP Complex Reveal
a Conserved Corepressor Binding Site." Cell
Rep, 26, 845-854.e6. doi:
10.1016/j.celrep.2018.12.097.
|
Structure of the rbpj-sharp-DNA repressor complex .
SNAP output
|
|
6dmn
|
hydrolase-DNA-RNA |
X-ray (1.27 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: soaked in 2 mm
ca2+ and 200 mm k+ at 21 c . SNAP output
|
|
6dmv
|
hydrolase-DNA-RNA |
X-ray (1.52 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: soaked for 40 s
in 2 mm mg2+ and 200 mm k+ at 21 c . SNAP output
|
|
6dnw
|
DNA binding protein |
X-ray (2.849 Å) |
Li H, Sharp R, Rutherford K, Gupta K, Van Duyne
GD |
(2018) "Serine
Integrase attP Binding and Specificity." J.
Mol. Biol., 430, 4401-4418. doi:
10.1016/j.jmb.2018.09.007.
|
Sequence requirements of the listeria innocua prophage
attp site . SNAP
output
|
|
6do8
|
hydrolase-DNA-RNA |
X-ray (1.414 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 80 s at 21 c . SNAP output
|
|
6do9
|
hydrolase-DNA-RNA |
X-ray (1.36 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 120 s at 21 c . SNAP output
|
|
6doa
|
hydrolase-DNA-RNA |
X-ray (1.474 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 480 s at 21 c . SNAP output
|
|
6dob
|
hydrolase-DNA-RNA |
X-ray (1.343 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 200 s at 21 c . SNAP output
|
|
6doc
|
hydrolase-DNA-RNA |
X-ray (1.496 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 240 s at 21 c . SNAP output
|
|
6dod
|
hydrolase-DNA-RNA |
X-ray (1.535 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 360 s at 21 c . SNAP output
|
|
6doe
|
hydrolase-DNA-RNA |
X-ray (1.451 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 420 s at 21 c . SNAP output
|
|
6dof
|
hydrolase-DNA-RNA |
X-ray (1.433 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 540 s at 21 c . SNAP output
|
|
6dog
|
hydrolase-RNA-DNA |
X-ray (1.285 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 600 s at 21 c . SNAP output
|
|
6doh
|
hydrolase-RNA-DNA |
X-ray (1.363 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: soak in 0.5 mm
egta and 200 mm k+ at 21 c . SNAP output
|
|
6doi
|
hydrolase-RNA-DNA |
X-ray (1.948 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid (1.54 angstrom
wavelength): soak in 0.5 mm egta and 200 mm k+ at 21 c
. SNAP output
|
|
6doj
|
hydrolase-DNA-RNA |
X-ray (1.403 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 5 mm k+ for 120 s at 21 c . SNAP output
|
|
6dok
|
hydrolase-DNA-RNA |
X-ray (1.38 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 25 mm k+ for 120 s at 21 c (dataset 1) .
SNAP output
|
|
6dol
|
hydrolase-DNA-RNA |
X-ray (1.433 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 25 mm k+ for 120 s at 21 c (dataset 2) .
SNAP output
|
|
6dom
|
hydrolase-DNA-RNA |
X-ray (1.425 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 50 mm k+ for 120 s at 21 c . SNAP output
|
|
6don
|
hydrolase-DNA-RNA |
X-ray (1.422 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 100 mm k+ for 120 s at 21 c (dataset 1) .
SNAP output
|
|
6doo
|
hydrolase-DNA-RNA |
X-ray (1.44 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 100 mm k+ for 120 s at 21 c (dataset 2) .
SNAP output
|
|
6dop
|
hydrolase-DNA-RNA |
X-ray (1.25 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 120 s at 21 c (dataset 1) .
SNAP output
|
|
6doq
|
hydrolase-DNA-RNA |
X-ray (1.422 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm k+ for 120 s at 21 c (dataset 2) .
SNAP output
|
|
6dor
|
hydrolase-DNA-RNA |
X-ray (1.5 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 300 mm k+ for 120 s at 21 c (dataset 1) .
SNAP output
|
|
6dos
|
hydrolase-DNA-RNA |
X-ray (1.318 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 300 mm k+ for 120 s at 21 c (dataset 2) .
SNAP output
|
|
6dot
|
hydrolase-RNA-DNA |
X-ray (1.423 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm rb+ for 40 s at 21 c . SNAP output
|
|
6dou
|
hydrolase-RNA-DNA |
X-ray (1.487 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm rb+ for 120 s at 21 c . SNAP output
|
|
6dov
|
hydrolase-RNA-DNA |
X-ray (1.521 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm rb+ for 80 s at 21 c . SNAP output
|
|
6dow
|
hydrolase-RNA-DNA |
X-ray (1.495 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm rb+ for 160 s at 21 c . SNAP output
|
|
6dox
|
hydrolase-RNA-DNA |
X-ray (1.45 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm rb+ for 360 s at 21 c . SNAP output
|
|
6doy
|
hydrolase-DNA-RNA |
X-ray (1.45 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mg2+ and 200 mm li+ for 120 s at 21 c . SNAP output
|
|
6doz
|
hydrolase-DNA-RNA |
X-ray (1.573 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 1 mm
mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp0
|
hydrolase-DNA-RNA |
X-ray (1.451 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2.5
mm mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp1
|
hydrolase-DNA-RNA |
X-ray (1.42 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp2
|
hydrolase-DNA-RNA |
X-ray (1.662 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 7.5
mm mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp3
|
hydrolase-DNA-RNA |
X-ray (1.461 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 10 mm
mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp4
|
hydrolase-DNA-RNA |
X-ray (1.374 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 20 mm
mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp5
|
hydrolase-DNA-RNA |
X-ray (1.432 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 40 mm
mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp6
|
hydrolase-DNA-RNA |
X-ray (1.403 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 80 mm
mg2+ and 75 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp7
|
hydrolase-DNA-RNA |
X-ray (1.381 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 500
mm mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dp8
|
hydrolase-DNA-RNA |
X-ray (1.323 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm li+ for 240 s at 21 c . SNAP output
|
|
6dp9
|
hydrolase-DNA-RNA |
X-ray (1.4 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 2 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpa
|
hydrolase-DNA-RNA |
X-ray (1.489 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 4 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpb
|
hydrolase-DNA-RNA |
X-ray (1.324 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 8 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpc
|
hydrolase-DNA-RNA |
X-ray (1.34 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 12 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpd
|
hydrolase-DNA-RNA |
X-ray (1.46 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 16 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpe
|
hydrolase-DNA-RNA |
X-ray (1.56 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 20 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpf
|
hydrolase-DNA-RNA |
X-ray (1.56 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 40 mm
mn2+ and 200 mm k+ for 40 s at 21 c . SNAP output
|
|
6dpg
|
hydrolase-RNA-DNA |
X-ray (1.38 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 e188a in complex with an RNA-DNA hybrid: reaction in
4 mm mn2+ and 200 mm k+ for 240 s at 21 c . SNAP output
|
|
6dph
|
hydrolase-RNA-DNA |
X-ray (1.339 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 e188a in complex with an RNA-DNA hybrid: reaction in
2 mm mn2+ and 200 mm k+ for 120 s at 21 c . SNAP output
|
|
6dpi
|
hydrolase-RNA-DNA |
X-ray (1.347 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 k196a in complex with an RNA-DNA hybrid: reaction in
10 mm mg2+ and 200 mm rb+ for 40 s at 21 c . SNAP output
|
|
6dpj
|
hydrolase-RNA-DNA |
X-ray (1.55 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 k196a in complex with an RNA-DNA hybrid: reaction in
4 mm mn2+ and 200 mm k+ for 80 s at 21 c . SNAP output
|
|
6dpk
|
hydrolase-RNA-DNA |
X-ray (1.391 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 k196a in complex with an RNA-DNA hybrid: reaction in
4 mm mn2+ and 200 mm k+ for 240 s at 21 c . SNAP output
|
|
6dpl
|
hydrolase-RNA-DNA |
X-ray (1.45 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 k196a in complex with an RNA-DNA hybrid: reaction in
10 mm mg2+ and 200 mm rb+ for 720 s at 21 c . SNAP output
|
|
6dpm
|
hydrolase-RNA-DNA |
X-ray (1.677 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 k196a in complex with an RNA-DNA hybrid: reaction in
10 mm mg2+ and 200 mm rb+ for 1800 s at 21 c . SNAP output
|
|
6dpn
|
hydrolase-RNA-DNA |
X-ray (1.493 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 e188a in complex with an RNA-DNA hybrid: reaction in
2 mm mg2+ and 200 mm k+ for 200 s at 21 c . SNAP output
|
|
6dpo
|
hydrolase-RNA-DNA |
X-ray (1.45 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 e188a in complex with an RNA-DNA hybrid: reaction in
2 mm mg2+ and 200 mm k+ for 360 s at 21 c . SNAP output
|
|
6dpp
|
hydrolase-RNA-DNA |
X-ray (1.45 Å) |
Samara NL, Yang W |
(2018) "Cation
trafficking propels RNA hydrolysis." Nat.
Struct. Mol. Biol., 25, 715-721.
doi: 10.1038/s41594-018-0099-4.
|
Crystal structure of bacillus halodurans ribonuclease
h1 in complex with an RNA-DNA hybrid: reaction in 5 mm
mg2+ and 200 mm rb+ for 240 s at 21 c . SNAP output
|
|
6dsu
|
transferase-DNA |
X-ray (1.98 Å) |
Chim N, Jackson LN, Trinh AM, Chaput JC |
(2018) "Crystal
structures of DNA polymerase I capture novel
intermediates in the DNA synthesis pathway."
Elife, 7. doi: 10.7554/eLife.40444.
|
Bst DNA polymerase i pre-insertion complex structure .
SNAP output
|
|
6dsv
|
transferase-DNA |
X-ray (1.99 Å) |
Chim N, Jackson LN, Trinh AM, Chaput JC |
(2018) "Crystal
structures of DNA polymerase I capture novel
intermediates in the DNA synthesis pathway."
Elife, 7. doi: 10.7554/eLife.40444.
|
Bst DNA polymerase i post-chemistry (n+2) structure .
SNAP output
|
|
6dsw
|
transferase-DNA |
X-ray (1.589 Å) |
Chim N, Jackson LN, Trinh AM, Chaput JC |
(2018) "Crystal
structures of DNA polymerase I capture novel
intermediates in the DNA synthesis pathway."
Elife, 7. doi: 10.7554/eLife.40444.
|
Bst DNA polymerase i pre-chemistry (n) structure .
SNAP output
|
|
6dsx
|
transferase-DNA |
X-ray (1.99 Å) |
Chim N, Jackson LN, Trinh AM, Chaput JC |
(2018) "Crystal
structures of DNA polymerase I capture novel
intermediates in the DNA synthesis pathway."
Elife, 7. doi: 10.7554/eLife.40444.
|
Bst DNA polymerase i post-chemistry (n+1 with datp
soak) structure . SNAP
output
|
|
6dsy
|
transferase-DNA |
X-ray (1.98 Å) |
Chim N, Jackson LN, Trinh AM, Chaput JC |
(2018) "Crystal
structures of DNA polymerase I capture novel
intermediates in the DNA synthesis pathway."
Elife, 7. doi: 10.7554/eLife.40444.
|
Bst DNA polymerase i post-chemistry (n+1) structure .
SNAP output
|
|
6dt1
|
ligase-DNA |
X-ray (2.75 Å) |
Shi K, Bohl TE, Park J, Zasada A, Malik S, Banerjee
S, Tran V, Li N, Yin Z, Kurniawan F, Orellana K, Aihara
H |
(2018) "T4 DNA
ligase structure reveals a prototypical ATP-dependent
ligase with a unique mode of sliding clamp
interaction." Nucleic Acids Res.,
46, 10474-10488. doi: 10.1093/nar/gky776.
|
Crystal structure of the ligase from bacteriophage t4
complexed with DNA intermediate . SNAP output
|
|
6dt7
|
transcription-DNA |
X-ray (2.5 Å) |
Molodtsov V, Murakami KS |
(2018) "Minimalism
and functionality: Structural lessons from the
heterodimeric N4 bacteriophage RNA polymerase II."
J. Biol. Chem., 293,
13616-13625. doi: 10.1074/jbc.RA118.003447.
|
Bacteriophage n4 RNA polymerase ii and DNA complex .
SNAP output
|
|
6dt8
|
transcription-DNA-RNA |
X-ray (3.2 Å) |
Molodtsov V, Murakami KS |
(2018) "Minimalism
and functionality: Structural lessons from the
heterodimeric N4 bacteriophage RNA polymerase II."
J. Biol. Chem., 293,
13616-13625. doi: 10.1074/jbc.RA118.003447.
|
Bacteriophage n4 RNA polymerase ii elongation complex 1
. SNAP output
|
|
6dta
|
transcription-DNA-RNA |
X-ray (2.694 Å) |
Molodtsov V, Murakami KS |
(2018) "Minimalism
and functionality: Structural lessons from the
heterodimeric N4 bacteriophage RNA polymerase II."
J. Biol. Chem., 293,
13616-13625. doi: 10.1074/jbc.RA118.003447.
|
Bacteriophage n4 RNA polymerase ii elongation complex 2
. SNAP output
|
|
6dv9
|
transferase-DNA-RNA |
X-ray (3.8 Å) |
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K,
Ebright RH |
(2019) "Structural
basis of ECF-sigma-factor-dependent transcription
initiation." Nat Commun,
10, 710. doi: 10.1038/s41467-019-08443-3.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex(ecf sigma factor l)
containing 5nt RNA with 4nt spacer . SNAP output
|
|
6dvb
|
transferase-DNA-RNA |
X-ray (3.8 Å) |
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K,
Ebright RH |
(2019) "Structural
basis of ECF-sigma-factor-dependent transcription
initiation." Nat Commun,
10, 710. doi: 10.1038/s41467-019-08443-3.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex(ecf sigma factor l)
containing 5nt RNA with 5nt spacer . SNAP output
|
|
6dvc
|
transferase-DNA-RNA |
X-ray (3.3 Å) |
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K,
Ebright RH |
(2019) "Structural
basis of ECF-sigma-factor-dependent transcription
initiation." Nat Commun,
10, 710. doi: 10.1038/s41467-019-08443-3.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex(ecf sigma factor l)
containing 5nt RNA with 6nt spacer . SNAP output
|
|
6dvd
|
transferase-DNA |
X-ray (3.899 Å) |
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K,
Ebright RH |
(2019) "Structural
basis of ECF-sigma-factor-dependent transcription
initiation." Nat Commun,
10, 710. doi: 10.1038/s41467-019-08443-3.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex(ecf sigma factor l)
with 6 nt spacer and bromine labelled in position "-11
. SNAP output
|
|
6dve
|
transferase-DNA |
X-ray (3.812 Å) |
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K,
Ebright RH |
(2019) "Structural
basis of ECF-sigma-factor-dependent transcription
initiation." Nat Commun,
10, 710. doi: 10.1038/s41467-019-08443-3.
|
Crystal structure of mycobacterium tuberculosis
transcription initiation complex(ecf
selenomethionine-labelled sigma factor l) with 6 nt
spacer . SNAP output
|
|
6dww
|
DNA binding protein-DNA |
X-ray (2.851 Å) |
Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda
F |
(2018) "Structural
insights into the mechanism of double strand break
formation by Hermes, a hAT family eukaryotic DNA
transposase." Nucleic Acids Res.,
46, 10286-10301. doi: 10.1093/nar/gky838.
|
Hermes transposase deletion dimer complex with (a-t)
DNA and mn2+ . SNAP
output
|
|
6dwy
|
DNA binding protein-DNA |
X-ray (3.2 Å) |
Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda
F |
(2018) "Structural
insights into the mechanism of double strand break
formation by Hermes, a hAT family eukaryotic DNA
transposase." Nucleic Acids Res.,
46, 10286-10301. doi: 10.1093/nar/gky838.
|
Hermes transposase deletion dimer complex with (c-g)
DNA and ca2+ . SNAP
output
|
|
6dwz
|
DNA binding protein-DNA |
X-ray (3.2 Å) |
Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda
F |
(2018) "Structural
insights into the mechanism of double strand break
formation by Hermes, a hAT family eukaryotic DNA
transposase." Nucleic Acids Res.,
46, 10286-10301. doi: 10.1093/nar/gky838.
|
Hermes transposase deletion dimer complex with (c-g)
DNA . SNAP output
|
|
6dx0
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda
F |
(2018) "Structural
insights into the mechanism of double strand break
formation by Hermes, a hAT family eukaryotic DNA
transposase." Nucleic Acids Res.,
46, 10286-10301. doi: 10.1093/nar/gky838.
|
Hermes transposase deletion dimer complex with (a-t)
DNA . SNAP output
|
|
6dzt
|
nuclear protein |
cryo-EM (2.99 Å) |
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins
AL, Olins DE, Bai Y, Zhang P |
(2019) "Atomic
resolution cryo-EM structure of a native-like CENP-A
nucleosome aided by an antibody fragment." Nat
Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4.
|
cryo-EM structure of nucleosome in complex with a
single chain antibody fragment . SNAP output
|
|
6e0c
|
nuclear protein |
cryo-EM (2.63 Å) |
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins
AL, Olins DE, Bai Y, Zhang P |
(2019) "Atomic
resolution cryo-EM structure of a native-like CENP-A
nucleosome aided by an antibody fragment." Nat
Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4.
|
cryo-EM structure of the cenp-a nucleosome (w601) in
complex with a single chain antibody fragment .
SNAP output
|
|
6e0p
|
nuclear protein |
cryo-EM (2.6 Å) |
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins
AL, Olins DE, Bai Y, Zhang P |
(2019) "Atomic
resolution cryo-EM structure of a native-like CENP-A
nucleosome aided by an antibody fragment." Nat
Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4.
|
cryo-EM structure of the centromeric nucleosome (native
alpha satellite DNA) in complex with a single chain
antibody fragment . SNAP
output
|
|
6e33
|
transcription |
X-ray (1.705 Å) |
Garg A, Goldgur Y, Schwer B, Shuman S |
(2018) "Distinctive
structural basis for DNA recognition by the fission
yeast Zn2Cys6 transcription factor Pho7 and its role in
phosphate homeostasis." Nucleic Acids
Res., 46, 11262-11273. doi:
10.1093/nar/gky827.
|
Crystal structure of pho7-DNA complex . SNAP output
|
|
6e3r
|
DNA binding protein-DNA |
X-ray (2.26 Å) |
Koag MC, Jung H, Lee S |
(2019) "Mutagenic
Replication of the Major Oxidative Adenine Lesion
7,8-Dihydro-8-oxoadenine by Human DNA Polymerases."
J. Am. Chem. Soc., 141,
4584-4596. doi: 10.1021/jacs.8b08551.
|
Structure of human DNA polymerase beta complexed with
8oa as the template base in a 1-nucleotide gapped DNA .
SNAP output
|
|
6e3v
|
DNA binding protein-DNA |
X-ray (1.96 Å) |
Koag MC, Jung H, Lee S |
(2019) "Mutagenic
Replication of the Major Oxidative Adenine Lesion
7,8-Dihydro-8-oxoadenine by Human DNA Polymerases."
J. Am. Chem. Soc., 141,
4584-4596. doi: 10.1021/jacs.8b08551.
|
Structure of human DNA polymerase beta complexed with
8oa in the template base paired with incoming
non-hydrolyzable ttp . SNAP output
|
|
6e3w
|
DNA binding protein-DNA |
X-ray (2.02 Å) |
Koag MC, Jung H, Lee S |
(2019) "Mutagenic
Replication of the Major Oxidative Adenine Lesion
7,8-Dihydro-8-oxoadenine by Human DNA Polymerases."
J. Am. Chem. Soc., 141,
4584-4596. doi: 10.1021/jacs.8b08551.
|
Structure of human DNA polymerase beta complexed with
8oa in the template base paired with incoming
non-hydrolyzable gtp . SNAP output
|
|
6e3x
|
DNA binding protein-DNA |
X-ray (2.65 Å) |
Koag M-C, Lee S |
"Structure of human DNA polymerase beta complexed
with 8OA in the template base paired with incoming
non-hydrolyzable ATP." |
Structure of human DNA polymerase beta complexed with
8oa in the template base paired with incoming
non-hydrolyzable atp . SNAP output
|
|
6e53
|
transferase-transferase inhibitor |
X-ray (2.8 Å) |
Hernandez-Sanchez W, Huang W, Plucinsky B,
Garcia-Vazquez N, Robinson NJ, Schiemann WP, Berdis AJ,
Skordalakes E, Taylor DJ |
(2019) "A
non-natural nucleotide uses a specific pocket to
selectively inhibit telomerase activity." Plos
Biol., 17, e3000204. doi:
10.1371/journal.pbio.3000204.
|
Structure of tert in complex with a novel telomerase
inhibitor . SNAP
output
|
|
6e8c
|
DNA binding protein-DNA |
X-ray (2.12 Å) |
Lee JK, Bosnakovski D, Toso EA, Dinh T, Banerjee S,
Bohl TE, Shi K, Orellana K, Kyba M, Aihara H |
(2018) "Crystal
Structure of the Double Homeodomain of DUX4 in Complex
with DNA." Cell Rep, 25,
2955-2962.e3. doi: 10.1016/j.celrep.2018.11.060.
|
Crystal structure of the double homeodomain of dux4 in
complex with DNA . SNAP
output
|
|
6e93
|
DNA binding protein-DNA |
X-ray (1.747 Å) |
Hudson NO, Whitby FG, Buck-Koehntop BA |
(2018) "Structural
insights into methylated DNA recognition by the
C-terminal zinc fingers of the DNA reader protein
ZBTB38." J. Biol. Chem.,
293, 19835-19843. doi: 10.1074/jbc.RA118.005147.
|
Crystal structure of zbtb38 c-terminal zinc fingers 6-9
in complex with methylated DNA . SNAP output
|
|
6e94
|
DNA binding protein-DNA |
X-ray (1.594 Å) |
Hudson NO, Whitby FG, Buck-Koehntop BA |
(2018) "Structural
insights into methylated DNA recognition by the
C-terminal zinc fingers of the DNA reader protein
ZBTB38." J. Biol. Chem.,
293, 19835-19843. doi: 10.1074/jbc.RA118.005147.
|
Crystal structure of zbtb38 c-terminal zinc fingers 6-9
k1055r in complex with methylated DNA . SNAP output
|
|
6edb
|
transferase-DNA |
X-ray (3.209 Å) |
Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl
T, Patel DJ |
(2019) "Human
cGAS catalytic domain has an additional DNA-binding
interface that enhances enzymatic activity and
liquid-phase condensation."
Proc.Natl.Acad.Sci.USA, 116,
11946-11955. doi: 10.1073/pnas.1905013116.
|
Crystal structure of sry.hcgas-21bp dsDNA complex .
SNAP output
|
|
6edc
|
transferase-DNA |
X-ray (2.712 Å) |
Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl
T, Patel DJ |
(2019) "Human
cGAS catalytic domain has an additional DNA-binding
interface that enhances enzymatic activity and
liquid-phase condensation."
Proc.Natl.Acad.Sci.USA, 116,
11946-11955. doi: 10.1073/pnas.1905013116.
|
Hcgas-16bp dsDNA complex . SNAP output
|
|
6edt
|
transcription-DNA |
cryo-EM |
Boyaci H, Chen J, Jansen R, Darst SA, Campbell
EA |
(2019) "Structures
of an RNA polymerase promoter melting intermediate
elucidate DNA unwinding." Nature,
565, 382-385. doi: 10.1038/s41586-018-0840-5.
|
Mycobacterium tuberculosis rnap open promoter complex
with rbpa-card and ap3 promoter . SNAP output
|
|
6ee8
|
transcription-DNA |
cryo-EM (3.92 Å) |
Boyaci H, Chen J, Jansen R, Darst SA, Campbell
EA |
(2019) "Structures
of an RNA polymerase promoter melting intermediate
elucidate DNA unwinding." Nature,
565, 382-385. doi: 10.1038/s41586-018-0840-5.
|
Mycobacterium tuberculosis rnap promoter unwinding
intermediate complex with rbpa-card and ap3 promoter .
SNAP output
|
|
6eec
|
transcription-DNA |
cryo-EM (3.55 Å) |
Boyaci H, Chen J, Jansen R, Darst SA, Campbell
EA |
(2019) "Structures
of an RNA polymerase promoter melting intermediate
elucidate DNA unwinding." Nature,
565, 382-385. doi: 10.1038/s41586-018-0840-5.
|
Mycobacterium tuberculosis rnap promoter unwinding
intermediate complex with rbpa-card and ap3 promoter
captured by corallopyronin . SNAP output
|
|
6eht
|
DNA binding protein |
X-ray (3.2 Å) |
De March M, Barrera-Vilarmau S, Crespan E, Mentegari
E, Merino N, Gonzalez-Magana A, Romano-Moreno M, Maga G,
Crehuet R, Onesti S, Blanco FJ, De Biasio A |
(2018) "p15PAF
binding to PCNA modulates the DNA sliding surface."
Nucleic Acids Res., 46,
9816-9828. doi: 10.1093/nar/gky723.
|
Modulation of pcna sliding surface by p15paf suggests a
suppressive mechanism for cisplatin-induced DNA lesion
bypass by pol eta holoenzyme . SNAP output
|
|
6eko
|
hydrolase |
X-ray (2.284 Å) |
Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis
G, Grazulis S, Bochtler M, Siksnys V |
(2019) "Unique
mechanism of target recognition by PfoI restriction
endonuclease of the CCGG-family." Nucleic Acids
Res., 47, 997-1010. doi: 10.1093/nar/gky1137.
|
Crystal structure of type iip restriction endonuclease
pfoi with cognate DNA . SNAP output
|
|
6el8
|
DNA binding protein |
X-ray (1.61 Å) |
Newman JA, Aitkenhead HA, Pinkas DM, von Delft F,
Arrowsmith CH, Edwards A, Bountra C, Gileadi O |
"Crystal structure of the Forkhead domain of human
FOXN1 in complex with DNA." |
Crystal structure of the forkhead domain of human foxn1
in complex with DNA . SNAP output
|
|
6emy
|
recombination |
X-ray (2.5 Å) |
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev
G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork
P, Barabas O |
(2018) "Transposase-DNA
Complex Structures Reveal Mechanisms for Conjugative
Transposition of Antibiotic Resistance."
Cell, 173, 208-220.e20. doi:
10.1016/j.cell.2018.02.032.
|
Structure of the tn1549 transposon integrase (aa
82-397, y379f) in complex with transposon right end DNA
. SNAP output
|
|
6emz
|
recombination |
X-ray (2.79 Å) |
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev
G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork
P, Barabas O |
(2018) "Transposase-DNA
Complex Structures Reveal Mechanisms for Conjugative
Transposition of Antibiotic Resistance."
Cell, 173, 208-220.e20. doi:
10.1016/j.cell.2018.02.032.
|
Structure of the tn1549 transposon integrase (aa
82-397, r225k) in complex with circular intermediate
DNA (ci5-DNA) . SNAP
output
|
|
6en0
|
recombination |
X-ray (2.8 Å) |
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev
G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork
P, Barabas O |
(2018) "Transposase-DNA
Complex Structures Reveal Mechanisms for Conjugative
Transposition of Antibiotic Resistance."
Cell, 173, 208-220.e20. doi:
10.1016/j.cell.2018.02.032.
|
Structure of the tn1549 transposon integrase (aa
82-397) in complex with circular intermediate DNA
(ci5-DNA) . SNAP
output
|
|
6en1
|
recombination |
X-ray (2.67 Å) |
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev
G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork
P, Barabas O |
(2018) "Transposase-DNA
Complex Structures Reveal Mechanisms for Conjugative
Transposition of Antibiotic Resistance."
Cell, 173, 208-220.e20. doi:
10.1016/j.cell.2018.02.032.
|
Structure of the tn1549 transposon integrase (aa
82-397, r225k) in complex with a circular intermediate
DNA (ci6a-DNA) . SNAP
output
|
|
6en2
|
recombination |
X-ray (2.67 Å) |
Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev
G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork
P, Barabas O |
(2018) "Transposase-DNA
Complex Structures Reveal Mechanisms for Conjugative
Transposition of Antibiotic Resistance."
Cell, 173, 208-220.e20. doi:
10.1016/j.cell.2018.02.032.
|
Structure of the tn1549 transposon integrase (aa
82-397, r225k) in complex with a circular intermediate
DNA (ci6b-DNA) . SNAP
output
|
|
6en8
|
transcription |
X-ray (3.29 Å) |
Wang K, Sybers D, Maklad HR, Lemmens L, Lewyllie C,
Zhou X, Schult F, Brasen C, Siebers B, Valegard K, Lindas
AC, Peeters E |
(2019) "A
TetR-family transcription factor regulates fatty acid
metabolism in the archaeal model organism Sulfolobus
acidocaldarius." Nat Commun,
10, 1542. doi: 10.1038/s41467-019-09479-1.
|
Safadr in complex with dsDNA . SNAP output
|
|
6eo6
|
hydrolase-DNA |
X-ray (1.69 Å) |
Dolot R, Lam CH, Sierant M, Zhao Q, Liu FW, Nawrot B,
Egli M, Yang X |
(2018) "Crystal
structures of thrombin in complex with chemically
modified thrombin DNA aptamers reveal the origins of
enhanced affinity." Nucleic Acids Res.,
46, 4819-4830. doi: 10.1093/nar/gky268.
|
X-ray structure of the complex between human
alpha-thrombin and modified 15-mer DNA aptamer
containing
5-(3-(2-(1h-indol-3-yl)acetamide-n-yl)-1-propen-1-yl)-2'-deoxyuridine
residue . SNAP
output
|
|
6eo7
|
hydrolase-DNA |
X-ray (2.24 Å) |
Dolot R, Lam CH, Sierant M, Zhao Q, Liu FW, Nawrot B,
Egli M, Yang X |
(2018) "Crystal
structures of thrombin in complex with chemically
modified thrombin DNA aptamers reveal the origins of
enhanced affinity." Nucleic Acids Res.,
46, 4819-4830. doi: 10.1093/nar/gky268.
|
X-ray structure of the complex between human
alpha-thrombin and modified 15-mer DNA aptamer
containing
5-(3-(acetamide-n-yl)-1-propen-1-yl)-2'-deoxyuridine
residue . SNAP
output
|
|
6erf
|
DNA binding protein |
X-ray (3.01 Å) |
Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J,
Guerois R, Pitois A, Comte A, Delteil C, Barboule N,
Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E,
Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P,
Charbonnier JB |
(2018) "XLF and
APLF bind Ku80 at two remote sites to ensure DNA repair
by non-homologous end joining."
Nat.Struct.Mol.Biol., 25,
971-980. doi: 10.1038/s41594-018-0133-6.
|
Complex of aplf factor and ku heterodimer bound to DNA
. SNAP output
|
|
6erg
|
DNA binding protein |
X-ray (2.9 Å) |
Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J,
Guerois R, Pitois A, Comte A, Delteil C, Barboule N,
Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E,
Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P,
Charbonnier JB |
(2018) "XLF and
APLF bind Ku80 at two remote sites to ensure DNA repair
by non-homologous end joining." Nat. Struct.
Mol. Biol., 25, 971-980. doi:
10.1038/s41594-018-0133-6.
|
Complex of xlf and heterodimer ku bound to DNA .
SNAP output
|
|
6erh
|
DNA binding protein |
X-ray (2.8 Å) |
Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J,
Guerois R, Pitois A, Comte A, Delteil C, Barboule N,
Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E,
Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P,
Charbonnier JB |
(2018) "XLF and
APLF bind Ku80 at two remote sites to ensure DNA repair
by non-homologous end joining." Nat. Struct.
Mol. Biol., 25, 971-980. doi:
10.1038/s41594-018-0133-6.
|
Complex of xlf and heterodimer ku bound to DNA .
SNAP output
|
|
6erp
|
transcription |
X-ray (4.502 Å) |
Hillen HS, Morozov YI, Sarfallah A, Temiakov D,
Cramer P |
(2017) "Structural
Basis of Mitochondrial Transcription Initiation."
Cell, 171, 1072-1081.e10.
doi: 10.1016/j.cell.2017.10.036.
|
Structure of the human mitochondrial transcription
initiation complex at the lsp promoter . SNAP output
|
|
6erq
|
transcription |
X-ray (4.5 Å) |
Hillen HS, Morozov YI, Sarfallah A, Temiakov D,
Cramer P |
(2017) "Structural
Basis of Mitochondrial Transcription Initiation."
Cell, 171, 1072-1081.e10.
doi: 10.1016/j.cell.2017.10.036.
|
Structure of the human mitochondrial transcription
initiation complex at the hsp promoter . SNAP output
|
|
6es2
|
transcription |
X-ray (2.95 Å) |
Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A,
Xu Y, Nilsson L, Taipale J |
(2018) "Two
distinct DNA sequences recognized by transcription
factors represent enthalpy and entropy optima."
Elife, 7. doi: 10.7554/eLife.32963.
|
Structure of cdx2-DNA(caa) . SNAP output
|
|
6es3
|
transcription |
X-ray (2.57 Å) |
Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A,
Xu Y, Nilsson L, Taipale J |
(2018) "Two
distinct DNA sequences recognized by transcription
factors represent enthalpy and entropy optima."
Elife, 7. doi: 10.7554/eLife.32963.
|
Structure of cdx2-DNA(tcg) . SNAP output
|
|
6esf
|
gene regulation |
cryo-EM (3.7 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Histone
octamer rearranges to adapt to DNA unwrapping."
Nat. Struct. Mol. Biol., 25,
101-108. doi: 10.1038/s41594-017-0005-5.
|
Nucleosome : class 1 . SNAP output
|
|
6esg
|
gene regulation |
cryo-EM (5.4 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Histone
octamer rearranges to adapt to DNA unwrapping."
Nat. Struct. Mol. Biol., 25,
101-108. doi: 10.1038/s41594-017-0005-5.
|
Nucleosome breathing : class 2 . SNAP output
|
|
6esh
|
gene regulation |
cryo-EM (5.1 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Histone
octamer rearranges to adapt to DNA unwrapping."
Nat. Struct. Mol. Biol., 25,
101-108. doi: 10.1038/s41594-017-0005-5.
|
Nucleosome breathing : class 3 . SNAP output
|
|
6esi
|
gene regulation |
cryo-EM (6.3 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Histone
octamer rearranges to adapt to DNA unwrapping."
Nat. Struct. Mol. Biol., 25,
101-108. doi: 10.1038/s41594-017-0005-5.
|
Nucleosome breathing : class 4 . SNAP output
|
|
6eu0
|
transcription |
cryo-EM (4.0 Å) |
Abascal-Palacios G, Ramsay EP, Beuron F, Morris E,
Vannini A |
(2018) "Structural
basis of RNA polymerase III transcription
initiation." Nature, 553,
301-306. doi: 10.1038/nature25441.
|
RNA polymerase iii open pre-initiation complex (oc-pic)
. SNAP output
|
|
6eu1
|
transcription |
cryo-EM (3.4 Å) |
Abascal-Palacios G, Ramsay EP, Beuron F, Morris E,
Vannini A |
(2018) "Structural
basis of RNA polymerase III transcription
initiation." Nature, 553,
301-306. doi: 10.1038/nature25441.
|
RNA polymerase iii - open DNA complex (oc-pol3). .
SNAP output
|
|
6evv
|
hydrolase |
X-ray (2.5 Å) |
Troisi R, Napolitano V, Spiridonova V, Russo Krauss
I, Sica F |
(2018) "Several
structural motifs cooperate in determining the highly
effective anti-thrombin activity of NU172 aptamer."
Nucleic Acids Res., 46,
12177-12185. doi: 10.1093/nar/gky990.
|
X-ray structure of the complex between human alpha
thrombin and nu172, a duplex-quadruplex 26-mer DNA
aptamer, in the presence of potassium ions. . SNAP output
|
|
6exv
|
transcription |
cryo-EM (3.6 Å) |
Liu X, Farnung L, Wigge C, Cramer P |
(2018) "Cryo-EM
structure of a mammalian RNA polymerase II elongation
complex inhibited by alpha-amanitin." J. Biol.
Chem., 293, 7189-7194. doi:
10.1074/jbc.RA118.002545.
|
Structure of mammalian RNA polymerase ii elongation
complex inhibited by alpha-amanitin . SNAP output
|
|
6f0l
|
hydrolase |
cryo-EM (4.77 Å) |
Abid Ali F, Douglas ME, Locke J, Pye VE, Nans A,
Diffley JFX, Costa A |
(2017) "Cryo-EM
structure of a licensed DNA replication origin."
Nat Commun, 8, 2241. doi:
10.1038/s41467-017-02389-0.
|
S. cerevisiae mcm double hexamer bound to duplex DNA .
SNAP output
|
|
6f1k
|
DNA binding protein |
X-ray (2.2 Å) |
Obaji E, Haikarainen T, Lehtio L |
(2018) "Structural
basis for DNA break recognition by ARTD2/PARP2."
Nucleic Acids Res., 46,
12154-12165. doi: 10.1093/nar/gky927.
|
Structure of artd2-parp2 wgr domain bound to double
strand DNA without 5'phosphate . SNAP output
|
|
6f2s
|
virus |
cryo-EM (3.3 Å) |
Hesketh EL, Saunders K, Fisher C, Potze J, Stanley J,
Lomonossoff GP, Ranson NA |
(2018) "The 3.3
angstrom structure of a plant geminivirus using
cryo-EM." Nat Commun, 9,
2369. doi: 10.1038/s41467-018-04793-6.
|
Cryoem structure of ageratum yellow vein virus (ayvv) .
SNAP output
|
|
6f40
|
transcription |
cryo-EM (3.7 Å) |
Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller
CW |
(2018) "Molecular
mechanism of promoter opening by RNA polymerase
III." Nature, 553,
295-300. doi: 10.1038/nature25440.
|
RNA polymerase iii open complex . SNAP output
|
|
6f41
|
transcription |
cryo-EM (4.3 Å) |
Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller
CW |
(2018) "Molecular
mechanism of promoter opening by RNA polymerase
III." Nature, 553,
295-300. doi: 10.1038/nature25440.
|
RNA polymerase iii initially transcribing complex .
SNAP output
|
|
6f42
|
transcription |
cryo-EM (5.5 Å) |
Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller
CW |
(2018) "Molecular
mechanism of promoter opening by RNA polymerase
III." Nature, 553,
295-300. doi: 10.1038/nature25440.
|
RNA polymerase iii closed complex cc1. . SNAP output
|
|
6f44
|
transcription |
cryo-EM (4.2 Å) |
Vorlander MK, Khatter H, Wetzel R, Hagen WJH, Muller
CW |
(2018) "Molecular
mechanism of promoter opening by RNA polymerase
III." Nature, 553,
295-300. doi: 10.1038/nature25440.
|
RNA polymerase iii closed complex cc2. . SNAP output
|
|
6f57
|
transferase-DNA |
X-ray (3.098 Å) |
Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S,
Ji D, Rothbart SB, Wang Y, Wang GG, Song J |
(2018) "Structural
basis for DNMT3A-mediated de novo DNA methylation."
Nature, 554, 387-391. doi:
10.1038/nature25477.
|
Crystal structure of dnmt3a-dnmt3l in complex with
single cpg-containing DNA . SNAP output
|
|
6f58
|
transcription |
X-ray (2.253 Å) |
Newman JA, Gavard AE, Imprachim N, Aitkenhead H,
Sheppard HE, Te Poele R, Clarke PA, Hossain MA, Temme L,
Oh HJ, Wells CI, Davis-Gilbert ZW, Workman P, Gileadi O,
Drewry DH |
(2025) "Structural
insights into human brachyury DNA recognition and
discovery of progressible binders for cancer
therapy." Nat Commun, 16,
1596. doi: 10.1038/s41467-025-56213-1.
|
Crystal structure of human brachyury (t) in complex
with DNA . SNAP
output
|
|
6f59
|
transcription |
X-ray (2.151 Å) |
Newman JA, Gavard AE, Imprachim N, Aitkenhead H,
Sheppard HE, Te Poele R, Clarke PA, Hossain MA, Temme L,
Oh HJ, Wells CI, Davis-Gilbert ZW, Workman P, Gileadi O,
Drewry DH |
(2025) "Structural
insights into human brachyury DNA recognition and
discovery of progressible binders for cancer
therapy." Nat Commun, 16,
1596. doi: 10.1038/s41467-025-56213-1.
|
Crystal structure of human brachyury (t) g177d variant
in complex with DNA . SNAP output
|
|
6f5b
|
DNA binding protein |
X-ray (2.8 Å) |
Obaji E, Haikarainen T, Lehtio L |
(2018) "Structural
basis for DNA break recognition by ARTD2/PARP2."
Nucleic Acids Res., 46,
12154-12165. doi: 10.1093/nar/gky927.
|
Structure of artd2-parp2 wgr domain bound to double
stranded DNA with 5'phosphate . SNAP output
|
|
6f5f
|
DNA binding protein |
X-ray (2.98 Å) |
Obaji E, Haikarainen T, Lehtio L |
(2018) "Structural
basis for DNA break recognition by ARTD2/PARP2."
Nucleic Acids Res., 46,
12154-12165. doi: 10.1093/nar/gky927.
|
Structure of artd2-parp2 wgr domain bound to double
strand DNA with 5 nucleotide overhang and 5'phosphate .
SNAP output
|
|
6fas
|
DNA binding protein |
X-ray (1.9 Å) |
Sasnauskas G, Kauneckaite K, Siksnys V |
(2018) "Structural
basis of DNA target recognition by the B3 domain of
Arabidopsis epigenome reader VAL1." Nucleic
Acids Res., 46, 4316-4324. doi:
10.1093/nar/gky256.
|
Crystal structure of val1 b3 domain in complex with
cognate DNA . SNAP
output
|
|
6fb0
|
DNA binding protein |
X-ray (2.15 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of a tailored i-crei homing
endonuclease protein (3115 variant) in complex with its
target DNA (haemoglobin beta subunit gene) in the
presence of calcium . SNAP output
|
|
6fb1
|
DNA binding protein |
X-ray (3.024 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of a tailored i-crei homing
endonuclease protein (3115 variant) in complex with its
target DNA (haemoglobin beta subunit gene) in the
presence of magnesium . SNAP output
|
|
6fb2
|
DNA binding protein |
X-ray (2.95 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of a tailored i-crei homing
endonuclease protein (3115 variant) in complex with its
target DNA (haemoglobin beta subunit gene) in the
presence of manganese . SNAP output
|
|
6fb5
|
DNA binding protein |
X-ray (2.2 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of a tailored i-crei homing
endonuclease protein (3115 variant) in complex with an
altered version of its target DNA (haemoglobin beta
subunit gene) at 5nnn region in the presence of
magnesium . SNAP
output
|
|
6fb6
|
DNA binding protein |
X-ray (2.6 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of a tailored i-crei homing
endonuclease protein (3115 variant) in complex with an
altered version of its target DNA (haemoglobin beta
subunit gene) at 5nnn region in the presence of
manganese . SNAP
output
|
|
6fb7
|
DNA binding protein |
X-ray (2.689 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of the i-crei homing endonuclease
d75n variant in complex with its target DNA in the
presence of manganese . SNAP output
|
|
6fb8
|
DNA binding protein |
X-ray (2.45 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of the i-crei homing endonuclease
d75n variant in complex with an altered version of its
target DNA at 5nnn region in the presence of magnesium
. SNAP output
|
|
6fb9
|
DNA binding protein |
X-ray (2.95 Å) |
Prieto J, Redondo P, Lopez-Mendez B, D'Abramo M,
Merino N, Blanco FJ, Duchateau P, Montoya G, Molina
R |
(2018) "Understanding
the indirect DNA read-out specificity of I-CreI
Meganuclease." Sci Rep,
8, 10286. doi: 10.1038/s41598-018-28599-0.
|
Crystal structure of the i-crei homing endonuclease
d75n variant in complex with an altered version of its
target DNA at 5nnn region in the presence of manganese
. SNAP output
|
|
6fbc
|
DNA binding protein |
X-ray (1.54 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase processing a modified primer -
bearing the modification at the 3'-terminus of the
primer. . SNAP
output
|
|
6fbd
|
DNA binding protein |
X-ray (2.099 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase processing a modified primer -
bearing the modification upstream at the second primer
nucleotide. . SNAP
output
|
|
6fbe
|
DNA binding protein |
X-ray (1.589 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase processing a modified primer -
bearing the modification upstream at the third primer
nucleotide. . SNAP
output
|
|
6fbf
|
DNA binding protein |
X-ray (2.001 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase processing a modified primer -
bearing the modification upstream at the fourth primer
nucleotide. . SNAP
output
|
|
6fbg
|
DNA binding protein |
X-ray (1.702 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase processing a modified primer -
bearing the modification upstream at the fifth primer
nucleotide. . SNAP
output
|
|
6fbh
|
DNA binding protein |
X-ray (1.8 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase processing a modified primer -
bearing the modification upstream at the sixth primer
nucleotide. . SNAP
output
|
|
6fbi
|
DNA binding protein |
X-ray (1.9 Å) |
Kropp HM, Durr SL, Peter C, Diederichs K, Marx A |
(2018) "Snapshots
of a modified nucleotide moving through the confines of
a DNA polymerase." Proc. Natl. Acad. Sci.
U.S.A., 115, 9992-9997. doi:
10.1073/pnas.1811518115.
|
Klentaq DNA polymerase in a closed, ternary complex
with dgpnhpp bound in the active site . SNAP output
|
|
6fbq
|
transcription |
X-ray (1.6 Å) |
Osz J, McEwen AG, Wolf J, Poussin-Courmontagne P,
Peluso-Iltis C, Chebaro Y, Kieffer B, Rochel N |
(2019) "Modulation
of RXR-DNA complex assembly by DNA context."
Mol. Cell. Endocrinol., 481,
44-52. doi: 10.1016/j.mce.2018.11.008.
|
Crystal structure of the human retinoid x receptor
DNA-binding domain bound to the human mep dr1 response
element, ph 7.0 . SNAP
output
|
|
6fbr
|
transcription |
X-ray (2.1 Å) |
Osz J, McEwen AG, Wolf J, Poussin-Courmontagne P,
Peluso-Iltis C, Chebaro Y, Kieffer B, Rochel N |
(2019) "Modulation
of RXR-DNA complex assembly by DNA context."
Mol. Cell. Endocrinol., 481,
44-52. doi: 10.1016/j.mce.2018.11.008.
|
Crystal structure of the human retinoid x receptor
DNA-binding domain bound to the human mep dr1 response
element, ph 4.2 . SNAP
output
|
|
6fbu
|
hydrolase |
X-ray (2.0 Å) |
Pomyalov S, Lansky S, Golan G, Zharkov DO, Grollman
AP, Shoham G |
"Crystal structure of the DNA repair enzyme
endonuclease-VIII (Nei) from E. coli (E2Q) in complex
with AP-site containing DNA substrate." |
Crystal structure of the DNA repair enzyme
endonuclease-viii (nei) from e. coli (e2q) in complex
with ap-site containing DNA substrate . SNAP output
|
|
6fi8
|
DNA binding protein |
X-ray (2.598 Å) |
Morero NR, Zuliani C, Kumar B, Bebel A, Okamoto S,
Guynet C, Hickman AB, Chandler M, Dyda F, Barabas O |
(2018) "Targeting
IS608 transposon integration to highly specific
sequences by structure-based transposon
engineering." Nucleic Acids Res.,
46, 4152-4163. doi: 10.1093/nar/gky235.
|
Crystal structure of the is608 transposase in complex
with left end 29-mer DNA hairpin and a 6-mer DNA
representing the intact target site: pre-cleavage
target capture complex . SNAP output
|
|
6fix
|
antitoxin |
X-ray (3.8 Å) |
Talavera A, Tamman H, Ainelo A, Konijnenberg A, Hadzi
S, Sobott F, Garcia-Pino A, Horak R, Loris R |
(2019) "A dual
role in regulation and toxicity for the disordered
N-terminus of the toxin GraT." Nat Commun,
10, 972. doi: 10.1038/s41467-019-08865-z.
|
Antitoxin graa in complex with its operator . SNAP output
|
|
6fj5
|
transcription |
X-ray (2.051 Å) |
Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg
H, Shakked Z |
(2018) "New
Insights into the Role of DNA Shape on Its Recognition
by p53 Proteins." Structure,
26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006.
|
New insights into the role of DNA shape on its
recognition by p53 proteins (complex p53dbd-agg-hg) .
SNAP output
|
|
6fk4
|
DNA binding protein |
X-ray (2.297 Å) |
Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang
CM, Freemont PS, Baldwin GS |
(2018) "Structural
basis for recognition and repair of the 3'-phosphate by
NExo, a base excision DNA repair nuclease from
Neisseria meningitidis." Nucleic Acids
Res., 46, 11980-11989. doi:
10.1093/nar/gky934.
|
Structure of 3' phosphatase nexo (wt) from neisseria
bound to DNA substrate . SNAP output
|
|
6fk5
|
DNA binding protein |
X-ray (2.02 Å) |
Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang
CM, Freemont PS, Baldwin GS |
(2018) "Structural
basis for recognition and repair of the 3'-phosphate by
NExo, a base excision DNA repair nuclease from
Neisseria meningitidis." Nucleic Acids
Res., 46, 11980-11989. doi:
10.1093/nar/gky934.
|
Structure of 3' phosphatase nexo (d146n) from neisseria
bound to DNA substrate in presence of magnesium ion .
SNAP output
|
|
6fke
|
DNA binding protein |
X-ray (2.151 Å) |
Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang
CM, Freemont PS, Baldwin GS |
(2018) "Structural
basis for recognition and repair of the 3'-phosphate by
NExo, a base excision DNA repair nuclease from
Neisseria meningitidis." Nucleic Acids
Res., 46, 11980-11989. doi:
10.1093/nar/gky934.
|
Structure of 3' phosphatase nexo (d146n) from neisseria
bound to product DNA hairpin . SNAP output
|
|
6fl1
|
hydrolase |
X-ray (1.6 Å) |
Coste F, Castaing B, Ober M, Carell T |
"Crystal structure of the complex between the
Lactococcus lactis FPG mutant T221P and a Fapy-dG
containing DNA." |
Crystal structure of the complex between the
lactococcus lactis fpg mutant t221p and a fapy-dg
containing DNA . SNAP
output
|
|
6flp
|
transcription |
cryo-EM (4.1 Å) |
Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G,
Takacs M, Schultz P, Weixlbaumer A |
(2018) "Structural
Basis for NusA Stabilized Transcriptional Pausing."
Mol. Cell, 69, 816-827.e4.
doi: 10.1016/j.molcel.2018.02.008.
|
Cryoem structure of e.coli RNA polymerase paused
elongation complex without RNA hairpin bound to nusa .
SNAP output
|
|
6flq
|
transcription |
cryo-EM (3.6 Å) |
Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G,
Takacs M, Schultz P, Weixlbaumer A |
(2018) "Structural
Basis for NusA Stabilized Transcriptional Pausing."
Mol. Cell, 69, 816-827.e4.
doi: 10.1016/j.molcel.2018.02.008.
|
Cryoem structure of e.coli RNA polymerase paused
elongation complex bound to nusa . SNAP output
|
|
6fm4
|
isomerase |
X-ray (2.7 Å) |
Magaro G, Prati F, Garofalo B, Corso G, Furlotti G,
Apicella C, Mangano G, D'Atanasio N, Robinson D, Di
Giorgio FP, Ombrato R |
(2019) "Virtual
Screening Approach and Investigation of
Structure-Activity Relationships To Discover Novel
Bacterial Topoisomerase Inhibitors Targeting
Gram-Positive and Gram-Negative Pathogens."
J.Med.Chem., 62, 7445-7472.
doi: 10.1021/acs.jmedchem.9b00394.
|
The crystal structure of s. aureus gyrase complex with
id-130 and DNA . SNAP
output
|
|
6fml
|
DNA binding protein |
cryo-EM (4.34 Å) |
Eustermann S, Schall K, Kostrewa D, Lakomek K,
Strauss M, Moldt M, Hopfner KP |
(2018) "Structural
basis for ATP-dependent chromatin remodelling by the
INO80 complex." Nature,
556, 386-390. doi: 10.1038/s41586-018-0029-y.
|
Cryoem structure ino80core nucleosome complex .
SNAP output
|
|
6fn0
|
flavoprotein |
X-ray (2.9 Å) |
Franz S, Ignatz E, Wenzel S, Zielosko H, Putu EPGN,
Maestre-Reyna M, Tsai MD, Yamamoto J, Mittag M, Essen
LO |
(2018) "Structure
of the bifunctional cryptochrome aCRY from
Chlamydomonas reinhardtii." Nucleic Acids
Res., 46, 8010-8022. doi:
10.1093/nar/gky621.
|
The animal-like cryptochrome from chlamydomonas
reinhardtii in complex with 6-4 DNA . SNAP output
|
|
6fq5
|
gene regulation |
cryo-EM (3.8 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Structural
rearrangements of the histone octamer translocate
DNA." Nat Commun, 9,
1330. doi: 10.1038/s41467-018-03677-z.
|
Class 1 : canonical nucleosome . SNAP output
|
|
6fq6
|
gene regulation |
cryo-EM (4.0 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Structural
rearrangements of the histone octamer translocate
DNA." Nat Commun, 9,
1330. doi: 10.1038/s41467-018-03677-z.
|
Class 2 : distorted nucleosome . SNAP output
|
|
6fq8
|
gene regulation |
cryo-EM (4.8 Å) |
Bilokapic S, Strauss M, Halic M |
(2018) "Structural
rearrangements of the histone octamer translocate
DNA." Nat Commun, 9,
1330. doi: 10.1038/s41467-018-03677-z.
|
Class 3 : translocated nucleosome . SNAP output
|
|
6fqm
|
isomerase |
X-ray (3.06 Å) |
Germe T, Voros J, Jeannot F, Taillier T, Stavenger
RA, Bacque E, Maxwell A, Bax BD |
(2018) "A new
class of antibacterials, the imidazopyrazinones, reveal
structural transitions involved in DNA gyrase poisoning
and mechanisms of resistance." Nucleic Acids
Res., 46, 4114-4128. doi:
10.1093/nar/gky181.
|
3.06a complex of s.aureus gyrase with imidazopyrazinone
t1 and DNA . SNAP
output
|
|
6fqp
|
transcription |
X-ray (2.42 Å) |
Guca E, Sunol D, Ruiz L, Konkol A, Cordero J, Torner
C, Aragon E, Martin-Malpartida P, Riera A, Macias MJ |
(2018) "TGIF1
homeodomain interacts with Smad MH1 domain and
represses TGF-beta signaling." Nucleic Acids
Res., 46, 9220-9235. doi:
10.1093/nar/gky680.
|
Crystal structure of tale homeobox domain transcription
factor tgif1 with its consensus DNA . SNAP output
|
|
6fqq
|
transcription |
X-ray (3.25 Å) |
Guca E, Sunol D, Ruiz L, Konkol A, Cordero J, Torner
C, Aragon E, Martin-Malpartida P, Riera A, Macias MJ |
(2018) "TGIF1
homeodomain interacts with Smad MH1 domain and
represses TGF-beta signaling." Nucleic Acids
Res., 46, 9220-9235. doi:
10.1093/nar/gky680.
|
Crystal structure of tale homeobox domain transcription
factor tgif1 double alanine mutant bound to its
consensus DNA . SNAP
output
|
|
6fqs
|
isomerase |
X-ray (3.11 Å) |
Germe T, Voros J, Jeannot F, Taillier T, Stavenger
RA, Bacque E, Maxwell A, Bax BD |
(2018) "A new
class of antibacterials, the imidazopyrazinones, reveal
structural transitions involved in DNA gyrase poisoning
and mechanisms of resistance." Nucleic Acids
Res., 46, 4114-4128. doi:
10.1093/nar/gky181.
|
3.11a complex of s.aureus gyrase with imidazopyrazinone
t3 and DNA . SNAP
output
|
|
6fqv
|
isomerase |
X-ray (2.6 Å) |
Germe T, Voros J, Jeannot F, Taillier T, Stavenger
RA, Bacque E, Maxwell A, Bax BD |
(2018) "A new
class of antibacterials, the imidazopyrazinones, reveal
structural transitions involved in DNA gyrase poisoning
and mechanisms of resistance." Nucleic Acids
Res., 46, 4114-4128. doi:
10.1093/nar/gky181.
|
2.60a binary complex of s.aureus gyrase with uncleaved
DNA . SNAP output
|
|
6frk
|
translation |
cryo-EM (3.7 Å) |
Kobayashi K, Jomaa A, Lee JH, Chandrasekar S,
Boehringer D, Shan SO, Ban N |
(2018) "Structure
of a prehandover mammalian ribosomal SRP·SRP receptor
targeting complex." Science,
360, 323-327. doi: 10.1126/science.aar7924.
|
Structure of a prehandover mammalian ribosomal srp and
srp receptor targeting complex . SNAP output
|
|
6ftg
|
protein transport |
cryo-EM (9.1 Å) |
Braunger K, Pfeffer S, Shrimal S, Gilmore R,
Berninghausen O, Mandon EC, Becker T, Forster F, Beckmann
R |
(2018) "Structural
basis for coupling protein transport and
N-glycosylation at the mammalian endoplasmic
reticulum." Science, 360,
215-219. doi: 10.1126/science.aar7899.
|
Subtomogram average of ost-containing
ribosome-translocon complexes from canine rough
microsomal membranes . SNAP output
|
|
6fti
|
protein transport |
cryo-EM (4.2 Å) |
Braunger K, Pfeffer S, Shrimal S, Gilmore R,
Berninghausen O, Mandon EC, Becker T, Forster F, Beckmann
R |
(2018) "Structural
basis for coupling protein transport and
N-glycosylation at the mammalian endoplasmic
reticulum." Science, 360,
215-219. doi: 10.1126/science.aar7899.
|
cryo-EM structure of the mammalian
oligosaccharyltransferase bound to sec61 and the
programmed 80s ribosome . SNAP output
|
|
6ftj
|
protein transport |
cryo-EM (4.7 Å) |
Braunger K, Pfeffer S, Shrimal S, Gilmore R,
Berninghausen O, Mandon EC, Becker T, Forster F, Beckmann
R |
(2018) "Structural
basis for coupling protein transport and
N-glycosylation at the mammalian endoplasmic
reticulum." Science, 360,
215-219. doi: 10.1126/science.aar7899.
|
cryo-EM structure of the mammalian
oligosaccharyltransferase bound to sec61 and the
non-programmed 80s ribosome . SNAP output
|
|
6ftx
|
motor protein |
cryo-EM (4.5 Å) |
Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG,
Ferreira H, Owen-Hughes T |
(2018) "Structure
of the chromatin remodelling enzyme Chd1 bound to a
ubiquitinylated nucleosome." Elife,
7. doi: 10.7554/eLife.35720.
|
Structure of the chromatin remodelling enzyme chd1
bound to a ubiquitinylated nucleosome . SNAP output
|
|
6fwk
|
DNA binding protein |
X-ray (2.503 Å) |
Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV,
Kamerlin SCL, Johansson E |
(2019) "Structural
consequence of the most frequently recurring
cancer-associated substitution in DNA polymerase
epsilon." Nat Commun, 10,
373. doi: 10.1038/s41467-018-08114-9.
|
The crystal structure of pol2core-m644g in complex with
DNA and an incoming nucleotide . SNAP output
|
|
6fwr
|
DNA binding protein |
X-ray (2.5 Å) |
Cheng K, Wigley DB |
(2018) "DNA
translocation mechanism of an XPD family helicase."
Elife, 7. doi: 10.7554/eLife.42400.
|
Structure of ding in complex with ssDNA . SNAP output
|
|
6fws
|
DNA binding protein |
X-ray (2.5 Å) |
Cheng K, Wigley DB |
(2018) "DNA
translocation mechanism of an XPD family helicase."
Elife, 7. doi: 10.7554/eLife.42400.
|
Structure of ding in complex with ssDNA and adpbef .
SNAP output
|
|
6fzs
|
transcription |
X-ray (2.31 Å) |
Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C,
Freier R, Baginski B, Martin-Malpartida P, Marquez JA,
Cordeiro TN, Pluta R, Macias MJ |
(2021) "Unveiling the dimer/monomer propensities of
Smad MH1-DNA complexes." Computational and
Structural Biotechnology Journal,
19. doi: 10.1016/j.csbj.2020.12.044.
|
Crystal structure of smad5-mh1 bound to the ggcgc site.
. SNAP output
|
|
6fzt
|
transcription |
X-ray (2.46 Å) |
Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C,
Freier R, Baginski B, Martin-Malpartida P, Marquez JA,
Cordeiro TN, Pluta R, Macias MJ |
(2021) "Unveiling the dimer/monomer propensities of
Smad MH1-DNA complexes." Computational and
Structural Biotechnology Journal,
19. doi: 10.1016/j.csbj.2020.12.044.
|
Crystal structure of smad8_9-mh1 bound to the ggcgc
site. . SNAP output
|
|
6g0a
|
DNA binding protein |
X-ray (2.62 Å) |
Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV,
Kamerlin SCL, Johansson E |
(2019) "Structural
consequence of the most frequently recurring
cancer-associated substitution in DNA polymerase
epsilon." Nat Commun, 10,
373. doi: 10.1038/s41467-018-08114-9.
|
The crystal structure of the pol2 catalytic domain of
DNA polymerase epsilon carrying a p301r substitution. .
SNAP output
|
|
6g0l
|
motor protein |
cryo-EM (10.0 Å) |
Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG,
Ferreira H, Owen-Hughes T |
(2018) "Structure
of the chromatin remodelling enzyme Chd1 bound to a
ubiquitinylated nucleosome." Elife,
7. doi: 10.7554/eLife.35720.
|
Structure of two molecules of the chromatin remodelling
enzyme chd1 bound to a nucleosome . SNAP output
|
|
6g1l
|
transcription |
X-ray (2.4 Å) |
Moller K, Sigurbjornsdottir S, Arnthorsson AO,
Pogenberg V, Dilshat R, Fock V, Brynjolfsdottir SH,
Bindesboll C, Bessadottir M, Ogmundsdottir HM, Simonsen
A, Larue L, Wilmanns M, Thorsson V, Steingrimsson E,
Ogmundsdottir MH |
(2019) "MITF has
a central role in regulating starvation-induced
autophagy in melanoma." Sci Rep,
9, 1055. doi: 10.1038/s41598-018-37522-6.
|
Mitf-clearbox structure . SNAP output
|
|
6g1t
|
DNA binding protein |
X-ray (1.93 Å) |
Kohler V, Goessweiner-Mohr N, Aufschnaiter A, Fercher
C, Probst I, Pavkov-Keller T, Hunger K, Wolinski H,
Buttner S, Grohmann E, Keller W |
(2018) "TraN: A
novel repressor of an Enterococcus conjugative type IV
secretion system." Nucleic Acids Res.,
46, 9201-9219. doi: 10.1093/nar/gky671.
|
Tran, a repressor of an enterococcus conjugative type
iv secretion system . SNAP output
|
|
6g2q
|
replication |
X-ray (2.148 Å) |
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna
CE, Goodman MF, Wilson SH |
(2018) "Mapping
Functional Substrate-Enzyme Interactions in the pol
beta Active Site through Chemical Biology: Structural
Responses to Acidity Modification of Incoming
dNTPs." Biochemistry, 57,
3934-3944. doi: 10.1021/acs.biochem.8b00418.
|
Ternary complex crystal structure of DNA polymerase
beta with a dideoxy terminated primer with chcl
(s-isomer), beta, gamma dttp analogue . SNAP output
|
|
6g3b
|
hydrolase |
X-ray (1.8 Å) |
Kisiala M, Kowalska M, Pastor M, Korza H, Czapinska
H, Bochtler M |
(2020) "Restriction endonucleases that cleave RNA/DNA
heteroduplexes bind dsDNA in A-like conformation."
Nucleic Acids Res. |
Avaii restriction endonuclease in complex with an
RNA-DNA hybrid . SNAP
output
|
|
6gat
|
transcription-DNA |
NMR |
Starich MR, Wikstrom M, Schumacher S, Arst Jr HN,
Gronenborn AM, Clore GM |
(1998) "The
solution structure of the Leu22-->Val mutant AREA
DNA binding domain complexed with a TGATAG core element
defines a role for hydrophobic packing in the
determination of specificity."
J.Mol.Biol., 277, 621-634.
doi: 10.1006/jmbi.1997.1626.
|
Solution NMR structure of the l22v mutant DNA binding
domain of area complexed to a 13 bp DNA containing a
tgata site, regularized mean structure . SNAP output
|
|
6gcd
|
DNA binding protein |
X-ray (1.8 Å) |
Zagorskaite E, Manakova E, Sasnauskas G |
(2018) "Recognition
of modified cytosine variants by the DNA-binding domain
of methyl-directed endonuclease McrBC." FEBS
Lett., 592, 3335-3345. doi:
10.1002/1873-3468.13244.
|
DNA binding domain of restriction endonuclease mcrbc in
complex with 5-hydroxymethylcytosine DNA . SNAP output
|
|
6gce
|
DNA binding protein |
X-ray (1.6 Å) |
Zagorskaite E, Manakova E, Sasnauskas G |
(2018) "Recognition
of modified cytosine variants by the DNA-binding domain
of methyl-directed endonuclease McrBC." FEBS
Lett., 592, 3335-3345. doi:
10.1002/1873-3468.13244.
|
DNA binding domain of restriction endonuclease mcrbc in
complex with 5-formylcytosine DNA . SNAP output
|
|
6gcf
|
DNA binding protein |
X-ray (1.55 Å) |
Zagorskaite E, Manakova E, Sasnauskas G |
(2018) "Recognition
of modified cytosine variants by the DNA-binding domain
of methyl-directed endonuclease McrBC." FEBS
Lett., 592, 3335-3345. doi:
10.1002/1873-3468.13244.
|
DNA binding domain of restriction endonuclease mcrbc in
complex with n4-methylcytosine DNA . SNAP output
|
|
6gdr
|
ligase |
X-ray (2.33 Å) |
Williamson A, Grgic M, Leiros HS |
(2018) "DNA
binding with a minimal scaffold: structure-function
analysis of Lig E DNA ligases." Nucleic Acids
Res., 46, 8616-8629. doi:
10.1093/nar/gky622.
|
DNA binding with a minimal scaffold: structure-function
analysis of lig e DNA ligases . SNAP output
|
|
6ged
|
cell adhesion |
X-ray (1.794 Å) |
Schmitt A, Jiang K, Camacho MI, Jonna VR, Hofer A,
Westerlund F, Christie PJ, Berntsson RP |
(2018) "PrgB
promotes aggregation, biofilm formation, and
conjugation through DNA binding and compaction."
Mol. Microbiol., 109,
291-305. doi: 10.1111/mmi.13980.
|
Adhesin domain of prgb from enterococcus faecalis bound
to DNA . SNAP output
|
|
6gej
|
nuclear protein |
cryo-EM (3.6 Å) |
Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M,
Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS,
Wigley DB |
(2018) "Structure
and dynamics of the yeast SWR1-nucleosome complex."
Science, 362. doi: 10.1126/science.aat7716.
|
Chromatin remodeller-nucleosome complex at 3.6 Å
resolution. . SNAP
output
|
|
6gen
|
nuclear protein |
cryo-EM (3.6 Å) |
Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M,
Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS,
Wigley DB |
(2018) "Structure
and dynamics of the yeast SWR1-nucleosome complex."
Science, 362. doi: 10.1126/science.aat7716.
|
Chromatin remodeller-nucleosome complex at 4.5 Å
resolution. . SNAP
output
|
|
6gfw
|
transcription |
cryo-EM (3.7 Å) |
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M,
Zhang X |
(2018) "Structures
of Bacterial RNA Polymerase Complexes Reveal the
Mechanism of DNA Loading and Transcription
Initiation." Mol. Cell,
70, 1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021.
|
cryo-EM structure of bacterial RNA polymerase-sigma54
holoenzyme initial transcribing complex . SNAP output
|
|
6gh5
|
transcription |
cryo-EM (3.4 Å) |
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M,
Zhang X |
(2018) "Structures
of Bacterial RNA Polymerase Complexes Reveal the
Mechanism of DNA Loading and Transcription
Initiation." Mol. Cell,
70, 1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021.
|
cryo-EM structure of bacterial RNA polymerase-sigma54
holoenzyme transcription open complex . SNAP output
|
|
6gh6
|
transcription |
cryo-EM (4.1 Å) |
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M,
Zhang X |
(2018) "Structures
of Bacterial RNA Polymerase Complexes Reveal the
Mechanism of DNA Loading and Transcription
Initiation." Mol. Cell,
70, 1111-1120.e3. doi: 10.1016/j.molcel.2018.05.021.
|
cryo-EM structure of bacterial RNA polymerase-sigma54
holoenzyme intermediate partially loaded complex .
SNAP output
|
|
6gis
|
DNA binding protein |
X-ray (2.82 Å) |
De March M, Merino N, Barrera-Vilarmau S, Crehuet R,
Onesti S, Blanco FJ, De Biasio A |
(2017) "Structural
basis of human PCNA sliding on DNA." Nat
Commun, 8, 13935. doi: 10.1038/ncomms13935.
|
Structural basis of human clamp sliding on DNA .
SNAP output
|
|
6gmh
|
transcription |
cryo-EM (3.1 Å) |
Vos SM, Farnung L, Boehning M, Wigge C, Linden A,
Urlaub H, Cramer P |
(2018) "Structure
of activated transcription complex Pol
II-DSIF-PAF-SPT6." Nature,
560, 607-612. doi: 10.1038/s41586-018-0440-4.
|
Structure of activated transcription complex pol
ii-dsif-paf-spt6 . SNAP
output
|
|
6gml
|
transcription |
cryo-EM (3.2 Å) |
Vos SM, Farnung L, Urlaub H, Cramer P |
(2018) "Structure
of paused transcription complex Pol II-DSIF-NELF."
Nature, 560, 601-606. doi:
10.1038/s41586-018-0442-2.
|
Structure of paused transcription complex pol
ii-dsif-nelf . SNAP
output
|
|
6gn7
|
hydrolase |
X-ray (2.8 Å) |
Troisi R, Napolitano V, Spiridonova V, Russo Krauss
I, Sica F |
(2018) "Several
structural motifs cooperate in determining the highly
effective anti-thrombin activity of NU172 aptamer."
Nucleic Acids Res., 46,
12177-12185. doi: 10.1093/nar/gky990.
|
X-ray structure of the complex between human alpha
thrombin and nu172, a duplex-quadruplex 26-mer DNA
aptamer, in the presence of sodium ions. . SNAP output
|
|
6go5
|
DNA binding protein |
X-ray (2.35 Å) |
Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber
MR, Delarue M |
(2019) "Structural
evidence for an intransbase selection mechanism
involving Loop1 in polymerase mu at an NHEJ
double-strand break junction."
J.Biol.Chem., 294,
10579-10595. doi: 10.1074/jbc.RA119.008739.
|
Tdt chimera (loop1 of pol mu) - ternary complex with
1-nt gapped DNA substrate . SNAP output
|
|
6go6
|
DNA binding protein |
X-ray (2.09 Å) |
Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber
MR, Delarue M |
(2019) "Structural
evidence for an intransbase selection mechanism
involving Loop1 in polymerase mu at an NHEJ
double-strand break junction."
J.Biol.Chem., 294,
10579-10595. doi: 10.1074/jbc.RA119.008739.
|
Tdt chimera (loop1 of pol mu) - ternary complex with
downstream dsDNA . SNAP
output
|
|
6go7
|
DNA binding protein |
X-ray (2.55 Å) |
Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber
MR, Delarue M |
(2019) "Structural
evidence for an intransbase selection mechanism
involving Loop1 in polymerase mu at an NHEJ
double-strand break junction."
J.Biol.Chem., 294,
10579-10595. doi: 10.1074/jbc.RA119.008739.
|
Tdt chimera (loop1 of pol mu) - full DNA synapsis
complex . SNAP
output
|
|
6gov
|
transcription |
cryo-EM (3.7 Å) |
Krupp F, Said N, Huang YH, Loll B, Burger J, Mielke
T, Spahn CMT, Wahl MC |
(2019) "Structural
Basis for the Action of an All-Purpose Transcription
Anti-termination Factor." Mol.Cell,
74, 143-157.e5. doi: 10.1016/j.molcel.2019.01.016.
|
Structure of the RNA polymerase lambda-based
antitermination complex . SNAP output
|
|
6grb
|
DNA |
X-ray (2.4 Å) |
Liu Y, Freeman AD, Declais AC, Lilley DMJ |
(2018) "A
monovalent ion in the DNA binding interface of the
eukaryotic junction-resolving enzyme GEN1."
Nucleic Acids Res., 46,
11089-11098. doi: 10.1093/nar/gky863.
|
Eukaryotic junction-resolving enzyme gen-1 binding with
potassium . SNAP
output
|
|
6grc
|
DNA |
X-ray (2.452 Å) |
Liu Y, Freeman AD, Declais AC, Lilley DMJ |
(2018) "A
monovalent ion in the DNA binding interface of the
eukaryotic junction-resolving enzyme GEN1."
Nucleic Acids Res., 46,
11089-11098. doi: 10.1093/nar/gky863.
|
Eukaryotic junction-resolving enzyme gen-1 binding with
sodium . SNAP output
|
|
6grd
|
DNA |
X-ray (2.66 Å) |
Liu Y, Freeman AD, Declais AC, Lilley DMJ |
(2018) "A
monovalent ion in the DNA binding interface of the
eukaryotic junction-resolving enzyme GEN1."
Nucleic Acids Res., 46,
11089-11098. doi: 10.1093/nar/gky863.
|
Eukaryotic junction-resolving enzyme gen-1 binding with
cesium . SNAP output
|
|
6gtc
|
hydrolase |
cryo-EM (3.91 Å) |
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen
SB, Saligram B, Moses ME, Hatzakis NS, Montoya G |
(2018) "Conformational
Activation Promotes CRISPR-Cas12a Catalysis and
Resetting of the Endonuclease Activity."
Cell, 175, 1856-1871.e21.
doi: 10.1016/j.cell.2018.10.045.
|
Transition state structure of cpf1(cas12a) i1
conformation . SNAP
output
|
|
6gtd
|
hydrolase |
cryo-EM (4.24 Å) |
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen
SB, Saligram B, Moses ME, Hatzakis NS, Montoya G |
(2018) "Conformational
Activation Promotes CRISPR-Cas12a Catalysis and
Resetting of the Endonuclease Activity."
Cell, 175, 1856-1871.e21.
doi: 10.1016/j.cell.2018.10.045.
|
Transient state structure of crispr-cpf1 (cas12a) i2
conformation . SNAP
output
|
|
6gte
|
hydrolase |
cryo-EM (4.07 Å) |
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen
SB, Saligram B, Moses ME, Hatzakis NS, Montoya G |
(2018) "Conformational
Activation Promotes CRISPR-Cas12a Catalysis and
Resetting of the Endonuclease Activity."
Cell, 175, 1856-1871.e21.
doi: 10.1016/j.cell.2018.10.045.
|
Transient state structure of crispr-cpf1 (cas12a) i3
conformation . SNAP
output
|
|
6gtf
|
hydrolase |
cryo-EM (3.63 Å) |
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen
SB, Saligram B, Moses ME, Hatzakis NS, Montoya G |
(2018) "Conformational
Activation Promotes CRISPR-Cas12a Catalysis and
Resetting of the Endonuclease Activity."
Cell, 175, 1856-1871.e21.
doi: 10.1016/j.cell.2018.10.045.
|
Transient state structure of crispr-cpf1 (cas12a) i5
conformation . SNAP
output
|
|
6gtg
|
hydrolase |
cryo-EM (3.27 Å) |
Stella S, Mesa P, Thomsen J, Paul B, Alcon P, Jensen
SB, Saligram B, Moses ME, Hatzakis NS, Montoya G |
(2018) "Conformational
Activation Promotes CRISPR-Cas12a Catalysis and
Resetting of the Endonuclease Activity."
Cell, 175, 1856-1871.e21.
doi: 10.1016/j.cell.2018.10.045.
|
Transition state structure of cpf1(cas12a) i4
conformation . SNAP
output
|
|
6gts
|
transcription |
X-ray (3.357 Å) |
Jurenas D, Van Melderen L, Garcia-Pino A |
(2019) "Mechanism
of regulation and neutralization of the AtaR-AtaT
toxin-antitoxin system." Nat. Chem. Biol.,
15, 285-294. doi: 10.1038/s41589-018-0216-z.
|
Structure of the atat-atar complex bound DNA . SNAP output
|
|
6gvq
|
DNA binding protein |
NMR |
Boudet J, Devillier JC, Wiegand T, Salmon L, Meier
BH, Lipps G, Allain FH |
(2019) "A Small
Helical Bundle Prepares Primer Synthesis by Binding Two
Nucleotides that Enhance Sequence-Specific Recognition
of the DNA Template." Cell,
176, 154-166.e13. doi: 10.1016/j.cell.2018.11.031.
|
DNA-bound prn1 helix bundle domain with atp and
magnesium in the interaction buffer . SNAP output
|
|
6gvt
|
DNA binding protein |
multiple methods: solution nmr, solid-state nmr |
Boudet J, Devillier JC, Wiegand T, Salmon L, Meier
BH, Lipps G, Allain FH |
(2019) "A Small
Helical Bundle Prepares Primer Synthesis by Binding Two
Nucleotides that Enhance Sequence-Specific Recognition
of the DNA Template." Cell,
176, 154-166.e13. doi: 10.1016/j.cell.2018.11.031.
|
Hybrid structure of the prn1 helix bundle domain in
complex with DNA and 2 atp molecules . SNAP output
|
|
6gvu
|
DNA binding protein |
NMR |
Boudet J, Devillier JC, Wiegand T, Salmon L, Meier
BH, Lipps G, Allain FH |
(2019) "A Small
Helical Bundle Prepares Primer Synthesis by Binding Two
Nucleotides that Enhance Sequence-Specific Recognition
of the DNA Template." Cell,
176, 154-166.e13. doi: 10.1016/j.cell.2018.11.031.
|
NMR structure of the DNA-bound helix bundle domain from
the functional prn1 primase . SNAP output
|
|
6gy3
|
transcription |
X-ray (2.68 Å) |
Schwab C, Sevvana M, Seidel G, Sandmann A, Grau FC,
Muller YA |
"The role of DNA flexibility in transcription
regulator AmtR-DNA interaction." |
Crystal structure of c. glutamicum amtr bound to glna
operator DNA . SNAP
output
|
|
6gyk
|
transcription |
cryo-EM (5.1 Å) |
Dienemann C, Schwalb B, Schilbach S, Cramer P |
(2019) "Promoter
Distortion and Opening in the RNA Polymerase II
Cleft." Mol. Cell, 73,
97-106.e4. doi: 10.1016/j.molcel.2018.10.014.
|
Structure of a yeast closed complex (core cc1) .
SNAP output
|
|
6gyl
|
transcription |
cryo-EM (4.8 Å) |
Dienemann C, Schwalb B, Schilbach S, Cramer P |
(2019) "Promoter
Distortion and Opening in the RNA Polymerase II
Cleft." Mol. Cell, 73,
97-106.e4. doi: 10.1016/j.molcel.2018.10.014.
|
Structure of a yeast closed complex with distorted DNA
(core ccdist) . SNAP
output
|
|
6gym
|
transcription |
cryo-EM (6.7 Å) |
Dienemann C, Schwalb B, Schilbach S, Cramer P |
(2019) "Promoter
Distortion and Opening in the RNA Polymerase II
Cleft." Mol. Cell, 73,
97-106.e4. doi: 10.1016/j.molcel.2018.10.014.
|
Structure of a yeast closed complex with distorted DNA
(ccdist) . SNAP
output
|
|
6gys
|
DNA binding protein |
cryo-EM (4.4 Å) |
Yan K, Zhang Z, Yang J, McLaughlin SH, Barford D |
(2018) "Architecture
of the CBF3-centromere complex of the budding yeast
kinetochore." Nat. Struct. Mol. Biol.,
25, 1103-1110. doi: 10.1038/s41594-018-0154-1.
|
cryo-EM structure of the cbf3-cen3 complex of the
budding yeast kinetochore . SNAP output
|
|
6h0s
|
hydrolase |
X-ray (1.75 Å) |
Coste F, Castaing B, Carell T |
"Crystal structure of the complex between the
Lactococcus lactis FPG mutant G226P and a Fapy-dG
containing DNA." |
Crystal structure of the complex between the
lactococcus lactis fpg mutant g226p and a fapy-dg
containing DNA . SNAP
output
|
|
6h1v
|
DNA binding protein |
X-ray (2.7 Å) |
Ter Beek J, Parkash V, Bylund GO, Osterman P,
Sauer-Eriksson AE, Johansson E |
(2019) "Structural
evidence for an essential Fe-S cluster in the catalytic
core domain of DNA polymerase ε." Nucleic Acids
Res., 47, 5712-5722. doi:
10.1093/nar/gkz248.
|
The crystal structure of pol2core in complex with DNA
and an incoming nucleotide, carrying an fe-s cluster .
SNAP output
|
|
6h3r
|
transcription |
X-ray (2.75 Å) |
Aragon E, Wang Q, Zou Y, Morgani SM, Ruiz L,
Kaczmarska Z, Su J, Torner C, Tian L, Hu J, Shu W,
Agrawal S, Gomes T, Marquez JA, Hadjantonakis A-K, Macias
MJ, Massague J |
(2020) "Structural basis for distinct roles of SMAD2
and SMAD3 in FOXH1 pioneer-directed TGF-beta
signaling." Genes Dev. doi: 10.1101/gad.330837.119.
|
Crystal structure of smad2 without exon -mh1 bound to
the cagac site. . SNAP
output
|
|
6h67
|
transcription |
cryo-EM (3.6 Å) |
Sanz-Murillo M, Xu J, Belogurov GA, Calvo O,
Gil-Carton D, Moreno-Morcillo M, Wang D,
Fernandez-Tornero C |
(2018) "Structural
basis of RNA polymerase I stalling at UV light-induced
DNA damage." Proc. Natl. Acad. Sci.
U.S.A., 115, 8972-8977. doi:
10.1073/pnas.1802626115.
|
Yeast RNA polymerase i elongation complex stalled by
cyclobutane pyrimidine dimer (cpd) . SNAP output
|
|
6h68
|
transcription |
cryo-EM (4.6 Å) |
Sanz-Murillo M, Xu J, Belogurov GA, Calvo O,
Gil-Carton D, Moreno-Morcillo M, Wang D,
Fernandez-Tornero C |
(2018) "Structural
basis of RNA polymerase I stalling at UV light-induced
DNA damage." Proc. Natl. Acad. Sci.
U.S.A., 115, 8972-8977. doi:
10.1073/pnas.1802626115.
|
Yeast RNA polymerase i elongation complex stalled by
cyclobutane pyrimidine dimer (cpd) with fully-ordered
a49 . SNAP output
|
|
6h8q
|
cell cycle |
X-ray (3.631 Å) |
Li Y, Muir K, Bowler MW, Metz J, Haering CH, Panne
D |
(2018) "Structural
basis for Scc3-dependent cohesin recruitment to
chromatin." Elife, 7.
doi: 10.7554/eLife.38356.
|
Structural basis for scc3-dependent cohesin recruitment
to chromatin . SNAP
output
|
|
6hb4
|
DNA binding protein |
X-ray (3.05 Å) |
Cuppari A, Fernandez-Millan P, Battistini F,
Tarres-Sole A, Lyonnais S, Iruela G, Ruiz-Lopez E, Enciso
Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Toth K,
Rivas G, Orozco M, Sola M |
(2019) "DNA
specificities modulate the binding of human
transcription factor A to mitochondrial DNA control
region." Nucleic Acids Res.,
47, 6519-6537. doi: 10.1093/nar/gkz406.
|
Tfam in complex with site-y . SNAP output
|
|
6hc3
|
DNA binding protein |
X-ray (3.1 Å) |
Cuppari A, Fernandez-Millan P, Battistini F,
Tarres-Sole A, Lyonnais S, Iruela G, Ruiz-Lopez E, Enciso
Y, Rubio-Cosials A, Prohens R, Pons M, Alfonso C, Toth K,
Rivas G, Orozco M, Sola M |
(2019) "DNA
specificities modulate the binding of human
transcription factor A to mitochondrial DNA control
region." Nucleic Acids Res.,
47, 6519-6537. doi: 10.1093/nar/gkz406.
|
Tfam bound to site-x . SNAP output
|
|
6hcf
|
ribosome |
cryo-EM (3.9 Å) |
Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S,
Ramakrishnan V, Hegde RS |
(2018) "ZNF598
Is a Quality Control Sensor of Collided Ribosomes."
Mol. Cell, 72, 469-481.e7.
doi: 10.1016/j.molcel.2018.08.037.
|
Structure of the rabbit 80s ribosome stalled on globin
mrna at the stop codon . SNAP output
|
|
6hcj
|
ribosome |
cryo-EM (3.8 Å) |
Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S,
Ramakrishnan V, Hegde RS |
(2018) "ZNF598
Is a Quality Control Sensor of Collided Ribosomes."
Mol. Cell, 72, 469-481.e7.
doi: 10.1016/j.molcel.2018.08.037.
|
Structure of the rabbit 80s ribosome on globin mrna in
the rotated state with a-p and p-e trnas . SNAP output
|
|
6hcm
|
ribosome |
cryo-EM (6.8 Å) |
Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S,
Ramakrishnan V, Hegde RS |
(2018) "ZNF598
Is a Quality Control Sensor of Collided Ribosomes."
Mol. Cell, 72, 469-481.e7.
doi: 10.1016/j.molcel.2018.08.037.
|
Structure of the rabbit collided di-ribosome (stalled
monosome) . SNAP
output
|
|
6hcq
|
ribosome |
cryo-EM (6.5 Å) |
Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S,
Ramakrishnan V, Hegde RS |
(2018) "ZNF598
Is a Quality Control Sensor of Collided Ribosomes."
Mol. Cell, 72, 469-481.e7.
doi: 10.1016/j.molcel.2018.08.037.
|
Structure of the rabbit collided di-ribosome (collided
monosome) . SNAP
output
|
|
6hko
|
transcription |
cryo-EM (3.42 Å) |
Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Muller
CW |
(2019) "The
cryo-EM structure of a 12-subunit variant of RNA
polymerase I reveals dissociation of the A49-A34.5
heterodimer and rearrangement of subunit A12.2."
Elife, 8. doi: 10.7554/eLife.43204.
|
Yeast RNA polymerase i elongation complex bound to
nucleotide analog gmpcpp . SNAP output
|
|
6hkt
|
DNA binding protein |
X-ray (9.7 Å) |
Garcia-Saez I, Menoni H, Boopathi R, Shukla MS,
Soueidan L, Noirclerc-Savoye M, Le Roy A, Skoufias DA,
Bednar J, Hamiche A, Angelov D, Petosa C, Dimitrov S |
(2018) "Structure
of an H1-Bound 6-Nucleosome Array Reveals an Untwisted
Two-Start Chromatin Fiber Conformation." Mol.
Cell, 72, 902-915.e7. doi:
10.1016/j.molcel.2018.09.027.
|
Structure of an h1-bound 6-nucleosome array . SNAP output
|
|
6hlq
|
transcription |
cryo-EM (3.18 Å) |
Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Muller
CW |
(2019) "The
cryo-EM structure of a 12-subunit variant of RNA
polymerase I reveals dissociation of the A49-A34.5
heterodimer and rearrangement of subunit A12.2."
Elife, 8. doi: 10.7554/eLife.43204.
|
Yeast RNA polymerase i* elongation complex bound to
nucleotide analog gmpcpp . SNAP output
|
|
6hlr
|
transcription |
cryo-EM (3.18 Å) |
Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Muller
CW |
(2019) "The
cryo-EM structure of a 12-subunit variant of RNA
polymerase I reveals dissociation of the A49-A34.5
heterodimer and rearrangement of subunit A12.2."
Elife, 8. doi: 10.7554/eLife.43204.
|
Yeast RNA polymerase i elongation complex bound to
nucleotide analog gmpcpp (core focused) . SNAP output
|
|
6hp7
|
DNA binding protein |
X-ray (2.2 Å) |
Gallego Del Sol F, Penades JR, Marina A |
(2019) "Deciphering
the Molecular Mechanism Underpinning Phage Arbitrium
Communication Systems." Mol.Cell,
74, 59-72.e3. doi: 10.1016/j.molcel.2019.01.025.
|
Arbitrium peptide receptor from spbeta phage in complex
with 43 mer DNA . SNAP
output
|
|
6ht5
|
transcription |
X-ray (3.451 Å) |
Vahokoski J, Pogenberg V, Wilmanns M |
"Oct4/Sox2:UTF1 structure." |
Oct4-sox2:utf1 structure . SNAP output
|
|
6hts
|
DNA binding protein |
cryo-EM (4.8 Å) |
Ayala R, Willhoft O, Aramayo RJ, Wilkinson M,
McCormack EA, Ocloo L, Wigley DB, Zhang X |
(2018) "Structure
and regulation of the human INO80-nucleosome
complex." Nature, 556,
391-395. doi: 10.1038/s41586-018-0021-6.
|
cryo-EM structure of the human ino80 complex bound to
nucleosome . SNAP
output
|
|
6hv9
|
DNA binding protein |
cryo-EM (4.98 Å) |
Goswami P, Abid Ali F, Douglas ME, Locke J, Purkiss
A, Janska A, Eickhoff P, Early A, Nans A, Cheung AMC,
Diffley JFX, Costa A |
(2018) "Structure
of DNA-CMG-Pol epsilon elucidates the roles of the
non-catalytic polymerase modules in the eukaryotic
replisome." Nat Commun,
9, 5061. doi: 10.1038/s41467-018-07417-1.
|
S. cerevisiae cmg-pol epsilon-DNA . SNAP output
|
|
6hyu
|
RNA binding protein |
X-ray (3.22 Å) |
Felisberto-Rodrigues C, Thomas JC, McAndrew C, Le
Bihan YV, Burke R, Workman P, van Montfort RLM |
(2019) "Structural
and functional characterisation of human RNA helicase
DHX8 provides insights into the mechanism of
RNA-stimulated ADP release." Biochem.J.,
476, 2521-2543. doi: 10.1042/BCJ20190383.
|
Crystal structure of dhx8 helicase bound to single
stranded poly-adenine RNA . SNAP output
|
|
6i1k
|
hydrolase |
X-ray (2.65 Å) |
Swarts DC, Jinek M |
(2019) "Mechanistic
Insights into the cis- and trans-Acting DNase
Activities of Cas12a." Mol. Cell,
73, 589-600.e4. doi: 10.1016/j.molcel.2018.11.021.
|
Crystal structure of catalytically inactive fncas12a in
complex with a crrna guide and a dsDNA target .
SNAP output
|
|
6i1l
|
hydrolase |
X-ray (2.98 Å) |
Swarts DC, Jinek M |
(2019) "Mechanistic
Insights into the cis- and trans-Acting DNase
Activities of Cas12a." Mol. Cell,
73, 589-600.e4. doi: 10.1016/j.molcel.2018.11.021.
|
Crystal structure of fncas12a in complex with a crrna
guide and ssDNA target . SNAP output
|
|
6i52
|
DNA binding protein |
cryo-EM (4.7 Å) |
Yates LA, Aramayo RJ, Pokhrel N, Caldwell CC, Kaplan
JA, Perera RL, Spies M, Antony E, Zhang X |
(2018) "A
structural and dynamic model for the assembly of
Replication Protein A on single-stranded DNA."
Nat Commun, 9, 5447. doi:
10.1038/s41467-018-07883-7.
|
Yeast rpa bound to ssDNA . SNAP output
|
|
6i84
|
transcription |
cryo-EM (4.4 Å) |
Farnung L, Vos SM, Cramer P |
(2018) "Structure
of transcribing RNA polymerase II-nucleosome
complex." Nat Commun, 9,
5432. doi: 10.1038/s41467-018-07870-y.
|
Structure of transcribing RNA polymerase ii-nucleosome
complex . SNAP
output
|
|
6i8a
|
DNA binding protein |
X-ray (2.652 Å) |
Parkash V, Kulkarni Y, Ter Beek J, Shcherbakova PV,
Kamerlin SCL, Johansson E |
(2019) "Structural
consequence of the most frequently recurring
cancer-associated substitution in DNA polymerase
epsilon." Nat Commun, 10,
373. doi: 10.1038/s41467-018-08114-9.
|
The crystal structure of the pol2 catalytic domain of
DNA polymerase epsilon carrying a p301r substitution. .
SNAP output
|
|
6ide
|
transcription-DNA |
X-ray (2.51 Å) |
Wu H, Li M, Guo H, Zhou H, Li B, Xu Q, Xu C, Yu F, He
J |
(2019) "Crystal
structure of theVibrio choleraeVqmA-ligand-DNA complex
provides insight into ligand-binding mechanisms
relevant for drug design." J. Biol. Chem.,
294, 2580-2592. doi: 10.1074/jbc.RA118.006082.
|
Crystal structure of the vibrio cholera vqma-ligand-DNA
complex provides molecular mechanisms for drug design .
SNAP output
|
|
6idg
|
immune system |
X-ray (2.0 Å) |
Yokoyama H, Mizutani R, Noguchi S, Hayashida N |
(2019) "Structures
of the antibody 64M-5 Fab and its complex with dT(6-4)T
indicate induced-fit and high-affinity mechanisms."
Acta Crystallogr.,Sect.F, 75,
80-88. doi: 10.1107/S2053230X18017661.
|
Antibody 64m-5 fab in complex with dt(6-4)t . SNAP output
|
|
6ido
|
transcription |
X-ray (3.748 Å) |
Lou YC, Chou CC, Yeh HH, Chien CY, Sadotra S, Hsu CH,
Chen C |
(2020) "Structural
basis for -35 element recognition by sigma4chimera
proteins and their interactions with PmrA response
regulator." Proteins, 88,
69-81. doi: 10.1002/prot.25768.
|
Crystal structure of klebsiella pneumoniae sigma4 of
sigmas fusing with the RNA polymerase
beta-flap-tip-helix in complex with -35 element DNA .
SNAP output
|
|
6ifm
|
toxin-antitoxin-DNA |
X-ray (2.804 Å) |
Park D, Yoon HJ, Lee KY, Park SJ, Cheon SH, Lee HH,
Lee SJ, Lee BJ |
(2020) "Crystal
structure of proteolyzed VapBC and DNA-bound VapBC from
Salmonella enterica Typhimurium LT2 and VapC as a
putative Ca2+-dependent ribonuclease." Faseb
J., 34, 3051-3068. doi: 10.1096/fj.201901989R.
|
Crystal structure of DNA bound vapbc from salmonella
typhimurium . SNAP
output
|
|
6ig1
|
DNA binding protein |
X-ray (1.97 Å) |
Kottur J, Nair DT |
(2018) "Pyrophosphate
hydrolysis is an intrinsic and critical step of the DNA
synthesis reaction." Nucleic Acids Res.,
46, 5875-5885. doi: 10.1093/nar/gky402.
|
DNA polymerase iv - DNA ternary complex 10 . SNAP output
|
|
6iid
|
hydrolase-DNA |
X-ray (2.986 Å) |
Wu CC, Lin JLJ, Yang-Yen HF, Yuan HS |
(2019) "A unique
exonuclease ExoG cleaves between RNA and DNA in
mitochondrial DNA replication." Nucleic Acids
Res., 47, 5405-5419. doi:
10.1093/nar/gkz241.
|
Human exog-h140a in complex with RNA-DNA chimeric
duplex . SNAP output
|
|
6iiq
|
DNA binding protein-DNA |
X-ray (1.85 Å) |
Wang Z, Tian W |
(2019) "Complex structure of the HRP3 PWWP domain
with a 16-bp TA-rich DNA." Nucleic Acids
Res. |
Complex structure of the hrp3 pwwp domain with a 16-bp
ta-rich DNA . SNAP
output
|
|
6iir
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Wang Z, Tian W |
(2019) "Complex structure of the HRP3 PWWP domain
with a 10-bp GC-rich DNA." Nucleic Acids
Res. |
Complex structure of the hrp3 pwwp domain with a 10-bp
gc-rich DNA . SNAP
output
|
|
6iis
|
DNA binding protein-DNA |
X-ray (2.358 Å) |
Wang Z, Tian W |
(2019) "Complex structure of the HRP3 PWWP domain
with both a 16-bp TA-rich DNA and an H3K36me3-containing
histone peptide." Nucleic Acids Res. |
Complex structure of the hrp3 pwwp domain with both a
16-bp ta-rich DNA and an h3k36me3-containing histone
peptide . SNAP
output
|
|
6iit
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Wang Z, Tian W |
(2019) "Complex structure of the HRP3 PWWP domain
with both a 16-bp TA-rich DNA and a H3K36me2-containing
histone peptide." Nucleic Acids Res. |
Complex structure of the hrp3 pwwp domain with both a
16-bp ta-rich DNA and an h3k36me2-containing histone
peptide . SNAP
output
|
|
6ik9
|
transferase-DNA |
X-ray (2.435 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2019) "Active-site
deformation in the structure of HIV-1 RT with
HBV-associated septuple amino acid substitutions
rationalizes the differential susceptibility of HIV-1
and HBV against 4'-modified nucleoside RT
inhibitors." Biochem. Biophys. Res.
Commun., 509, 943-948. doi:
10.1016/j.bbrc.2019.01.026.
|
Hiv-1 reverse transcriptase with
q151m-g112s-d113a-y115f-f116y-f160l-i159l:DNA:dgtp
ternary complex . SNAP
output
|
|
6ika
|
transferase-DNA |
X-ray (2.598 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2019) "Active-site
deformation in the structure of HIV-1 RT with
HBV-associated septuple amino acid substitutions
rationalizes the differential susceptibility of HIV-1
and HBV against 4'-modified nucleoside RT
inhibitors." Biochem. Biophys. Res.
Commun., 509, 943-948. doi:
10.1016/j.bbrc.2019.01.026.
|
Hiv-1 reverse transcriptase with
q151m-g112s-d113a-y115f-f116y-f160l-i159l:DNA:entecavir-triphosphate
ternary complex . SNAP
output
|
|
6imj
|
ligase-DNA |
X-ray (2.554 Å) |
Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R,
Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J |
(2019) "Structure
of the error-prone DNA ligase of African swine fever
virus identifies critical active site residues."
Nat Commun, 10, 387. doi:
10.1038/s41467-019-08296-w.
|
The crystal structure of se-asfvlig:DNA complex .
SNAP output
|
|
6imk
|
ligase-DNA |
X-ray (2.502 Å) |
Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R,
Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J |
(2019) "Structure
of the error-prone DNA ligase of African swine fever
virus identifies critical active site residues."
Nat Commun, 10, 387. doi:
10.1038/s41467-019-08296-w.
|
The crystal structure of asfvlig:cg complex . SNAP output
|
|
6iml
|
ligase-DNA |
X-ray (2.35 Å) |
Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R,
Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J |
(2019) "Structure
of the error-prone DNA ligase of African swine fever
virus identifies critical active site residues."
Nat Commun, 10, 387. doi:
10.1038/s41467-019-08296-w.
|
The crystal structure of asfvlig:ct1 complex . SNAP output
|
|
6imn
|
ligase-DNA |
X-ray (2.7 Å) |
Chen Y, Liu H, Yang C, Gao Y, Yu X, Chen X, Cui R,
Zheng L, Li S, Li X, Ma J, Huang Z, Li J, Gan J |
(2019) "Structure
of the error-prone DNA ligase of African swine fever
virus identifies critical active site residues."
Nat Commun, 10, 387. doi:
10.1038/s41467-019-08296-w.
|
The crystal structure of asfvlig:ct2 complex . SNAP output
|
|
6inq
|
transcription-RNA-DNA |
cryo-EM (6.9 Å) |
Kujirai T, Ehara H, Fujino Y, Shirouzu M, Sekine S,
Kurumizaka H |
(2018) "Structural
basis of the nucleosome transition during RNA
polymerase II passage." Science,
362, 595-598. doi: 10.1126/science.aau9904.
|
RNA polymerase ii elongation complex stalled at shl(-1)
of the nucleosome, with foreign DNA (+1 position) .
SNAP output
|
|
6iod
|
DNA binding protein-DNA |
X-ray (1.66 Å) |
Tu J, Chen R, Yang Y, Cao W, Xie W |
(2019) "Suicide
inactivation of the uracil DNA glycosylase UdgX by
covalent complex formation."
Nat.Chem.Biol., 15, 615-622.
doi: 10.1038/s41589-019-0290-x.
|
The structure of udgx in complex with single-stranded
DNA . SNAP output
|
|
6ip5
|
ribosome |
cryo-EM (3.9 Å) |
Yokoyama T, Machida K, Iwasaki W, Shigeta T,
Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Harada
Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito
T |
(2019) "HCV IRES
Captures an Actively Translating 80S Ribosome."
Mol.Cell, 74, 1205-1214.e8.
doi: 10.1016/j.molcel.2019.04.022.
|
cryo-EM structure of the cmv-stalled human 80s ribosome
(structure ii) . SNAP
output
|
|
6ip6
|
ribosome |
cryo-EM (4.5 Å) |
Yokoyama T, Machida K, Iwasaki W, Shigeta T,
Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Harada
Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito
T |
(2019) "HCV IRES
Captures an Actively Translating 80S Ribosome."
Mol.Cell, 74, 1205-1214.e8.
doi: 10.1016/j.molcel.2019.04.022.
|
cryo-EM structure of the cmv-stalled human 80s ribosome
with hcv ires (structure iii) . SNAP output
|
|
6ip8
|
ribosome |
cryo-EM (3.9 Å) |
Yokoyama T, Machida K, Iwasaki W, Shigeta T,
Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Harada
Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito
T |
(2019) "HCV IRES
Captures an Actively Translating 80S Ribosome."
Mol.Cell, 74, 1205-1214.e8.
doi: 10.1016/j.molcel.2019.04.022.
|
cryo-EM structure of the hcv ires dependently initiated
cmv-stalled 80s ribosome (structure iv) . SNAP output
|
|
6ipd
|
transferase-DNA |
X-ray (1.7 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Post-catalytic complex of human DNA polymerase mu with
templating adenine and mn-8oxodgmp . SNAP output
|
|
6ipe
|
transferase-DNA |
X-ray (1.7 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Post-catalytic complex of human DNA polymerase mu with
templating adenine and mg-8oxodgmp . SNAP output
|
|
6ipf
|
transferase-DNA |
X-ray (1.77 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Post-catalytic complex of human DNA polymerase mu with
templating cytosine and mn-8oxodgmp . SNAP output
|
|
6ipg
|
transferase-DNA |
X-ray (1.62 Å) |
Chang YK, Huang YP, Liu XX, Ko TP, Bessho Y, Kawano
Y, Maestre-Reyna M, Wu WJ, Tsai MD |
(2019) "Human
DNA Polymerase mu Can Use a Noncanonical Mechanism for
Multiple Mn2+-Mediated Functions."
J.Am.Chem.Soc., 141,
8489-8502. doi: 10.1021/jacs.9b01741.
|
Post-catalytic complex of human DNA polymerase mu with
templating cytosine and mg-8oxodgmp . SNAP output
|
|
6ipu
|
DNA binding protein-DNA |
X-ray (1.99 Å) |
Sharma D, De Falco L, Padavattan S, Rao C,
Geifman-Shochat S, Liu CF, Davey CA |
(2019) "PARP1
exhibits enhanced association and catalytic efficiency
with gamma H2A.X-nucleosome." Nat Commun,
10, 5751. doi: 10.1038/s41467-019-13641-0.
|
Human nucleosome core particle containing 145 bp of DNA
. SNAP output
|
|
6iq4
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Batchelor LK, De Falco L, von Erlach T, Sharma D,
Adhireksan Z, Roethlisberger U, Davey CA, Dyson PJ |
(2019) "Crosslinking
Allosteric Sites on the Nucleosome."
Angew.Chem.Int.Ed.Engl., 58,
15660-15664. doi: 10.1002/anie.201906423.
|
Nucleosome core particle cross-linked with a
hetero-binuclear molecule possessing rapta and gold(i)
4-(diphenylphosphino)benzoic acid groups. . SNAP output
|
|
6ir8
|
transcription-DNA |
X-ray (2.3 Å) |
Cheng X, Zhao Y, Jiang Q, Yang J, Zhao W, Taylor IA,
Peng YL, Wang D, Liu J |
(2019) "Structural
basis of dimerization and dual W-box DNA recognition by
rice WRKY domain." Nucleic Acids Res.,
47, 4308-4318. doi: 10.1093/nar/gkz113.
|
Rice wrky-DNA complex . SNAP output
|
|
6ir9
|
transcription-RNA-DNA |
cryo-EM (3.8 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with elf1
and spt4-5, stalled at shl(-1) of the nucleosome .
SNAP output
|
|
6iro
|
DNA binding protein-DNA |
cryo-EM (3.4 Å) |
Yan L, Wu H, Li X, Gao N, Chen Z |
(2019) "Structures
of the ISWI-nucleosome complex reveal a conserved
mechanism of chromatin remodeling." Nat.
Struct. Mol. Biol., 26, 258-266.
doi: 10.1038/s41594-019-0199-9.
|
The crosslinked complex of iswi-nucleosome in the
adp-bound state . SNAP
output
|
|
6irq
|
DNA binding protein-DNA |
X-ray (1.91 Å) |
Huang YH, Chen IC, Huang CY |
(2019) "Characterization of an SSB-dT25 complex:
structural insights into the S-shaped ssDNA binding
conformation." Rsc Adv, 9,
40388-40396. doi: 10.1039/C9RA09406G.
|
Complexed crystal structure of passb with ssDNA dt25 at
1.91 angstrom resolution . SNAP output
|
|
6is7
|
transferase-DNA |
X-ray (2.8 Å) |
LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu
WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J,
Tsai MD |
(2019) "Thermococcus
sp. 9°N DNA polymerase exhibits 3'-esterase activity
that can be harnessed for DNA sequencing."
Commun Biol, 2, 224. doi:
10.1038/s42003-019-0458-7.
|
Structure of 9n-i DNA polymerase incorporation with da
in the active site . SNAP output
|
|
6is8
|
DNA binding protein-DNA |
X-ray (1.68 Å) |
Lin H, Zhang D, Zuo K, Yuan C, Li J, Huang M, Lin
Z |
(2019) "Structural
basis of sequence-specific Holliday junction cleavage
by MOC1." Nat.Chem.Biol.,
15, 1241-1248. doi: 10.1038/s41589-019-0377-4.
|
Crystal structure of zmmoc1 d115n mutant in complex
with holliday junction . SNAP output
|
|
6isf
|
transferase-DNA |
X-ray (2.8 Å) |
LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu
WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J,
Tsai MD |
(2019) "Thermococcus
sp. 9°N DNA polymerase exhibits 3'-esterase activity
that can be harnessed for DNA sequencing."
Commun Biol, 2, 224. doi:
10.1038/s42003-019-0458-7.
|
Structure of 9n-i DNA polymerase incorporation with dt
in the active site . SNAP output
|
|
6isg
|
transferase-DNA |
X-ray (3.401 Å) |
LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu
WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J,
Tsai MD |
(2019) "Thermococcus
sp. 9°N DNA polymerase exhibits 3'-esterase activity
that can be harnessed for DNA sequencing."
Commun Biol, 2, 224. doi:
10.1038/s42003-019-0458-7.
|
Structure of 9n-i DNA polymerase incorporation with dg
in the active site . SNAP output
|
|
6ish
|
transferase-DNA |
X-ray (3.3 Å) |
LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu
WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J,
Tsai MD |
(2019) "Thermococcus
sp. 9°N DNA polymerase exhibits 3'-esterase activity
that can be harnessed for DNA sequencing."
Commun Biol, 2, 224. doi:
10.1038/s42003-019-0458-7.
|
Structure of 9n-i DNA polymerase incorporation with
3'-al in the active site . SNAP output
|
|
6isi
|
transferase-DNA |
X-ray (3.2 Å) |
LinWu SW, Tu YH, Tsai TY, Maestre-Reyna M, Liu MS, Wu
WJ, Huang JY, Chi HW, Chang WH, Chiou CF, Wang AH, Lee J,
Tsai MD |
(2019) "Thermococcus
sp. 9°N DNA polymerase exhibits 3'-esterase activity
that can be harnessed for DNA sequencing."
Commun Biol, 2, 224. doi:
10.1038/s42003-019-0458-7.
|
Structure of 9n-i DNA polymerase incorporation with
3'-cl in the active site . SNAP output
|
|
6iuc
|
DNA binding protein-DNA |
X-ray (3.4 Å) |
Chu CH, Yen CY, Chen BW, Lin MG, Wang LH, Tang KZ,
Hsiao CD, Sun YJ |
(2019) "Crystal
structures of HpSoj-DNA complexes and the
nucleoid-adaptor complex formation in chromosome
segregation." Nucleic Acids Res.,
47, 2113-2129. doi: 10.1093/nar/gky1251.
|
Structure of helicobacter pylori soj-atp complex bound
to DNA . SNAP output
|
|
6iud
|
DNA binding protein-DNA |
X-ray (2.506 Å) |
Chu CH, Yen CY, Chen BW, Lin MG, Wang LH, Tang KZ,
Hsiao CD, Sun YJ |
(2019) "Crystal
structures of HpSoj-DNA complexes and the
nucleoid-adaptor complex formation in chromosome
segregation." Nucleic Acids Res.,
47, 2113-2129. doi: 10.1093/nar/gky1251.
|
Structure of helicobacter pylori soj-adp complex bound
to DNA . SNAP output
|
|
6iy2
|
structural protein-hydrolase-DNA |
cryo-EM (3.47 Å) |
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X,
Chen Z |
(2019) "Mechanism
of DNA translocation underlying chromatin remodelling
by Snf2." Nature, 567,
409-413. doi: 10.1038/s41586-019-1029-2.
|
Structure of snf2-mmtv-a nucleosome complex at shl2 in
adp state . SNAP
output
|
|
6iy3
|
structural protein-hydrolase-DNA |
cryo-EM (3.67 Å) |
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X,
Chen Z |
(2019) "Mechanism
of DNA translocation underlying chromatin remodelling
by Snf2." Nature, 567,
409-413. doi: 10.1038/s41586-019-1029-2.
|
Structure of snf2-mmtv-a nucleosome complex at shl-2 in
adp state . SNAP
output
|
|
6j0h
|
DNA-antibiotic |
X-ray (1.52 Å) |
Satange R, Chuang CY, Neidle S, Hou MH |
(2019) "Polymorphic
G:G mismatches act as hotspots for inducing
right-handed Z DNA by DNA intercalation."
Nucleic Acids Res., 47,
8899-8912. doi: 10.1093/nar/gkz653.
|
Crystal structure of actinomycin d- d(ttggcgaa) complex
. SNAP output
|
|
6j4e
|
DNA binding protein-DNA |
X-ray (3.126 Å) |
Xu YP, Xu H, Wang B, Su XD |
"Crystal structure of the AtWRKY1 domain." |
Crystal structure of the atwrky1 domain . SNAP output
|
|
6j4f
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Xu YP, Xu H, Wang B, Su XD |
"Crystal structure of the AtWRKY2 domain." |
Crystal structure of the atwrky2 domain . SNAP output
|
|
6j4g
|
DNA binding protein |
X-ray (3.0 Å) |
Xu YP, Xu H, Wang B, Su XD |
"Crystal structure of the N-terminal DNA binding
domain of AtWRKY33." |
Crystal structure of the atwrky33 domain . SNAP output
|
|
6j4r
|
transcription-DNA |
X-ray (2.8 Å) |
Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang
Q, Wang Q, Yang W, Wu Y |
(2019) "Structural
basis for the Target DNA recognition and binding by the
MYB domain of phosphate starvation response 1."
Febs J., 286, 2809-2821. doi:
10.1111/febs.14846.
|
Structural basis for the target DNA recognition and
binding by the myb domain of phosphate starvation
response regulator 1 . SNAP output
|
|
6j4w
|
transcription-RNA-DNA |
cryo-EM (7.9 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with elf1
and spt4-5, stalled at shl(-5) of the nucleosome .
SNAP output
|
|
6j4x
|
transcription-RNA-DNA |
cryo-EM (4.3 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with elf1
and spt4-5, stalled at shl(-1) of the nucleosome (+1a)
. SNAP output
|
|
6j4y
|
transcription-RNA-DNA |
cryo-EM (4.3 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with elf1
and spt4-5, stalled at shl(-1) of the nucleosome (+1b)
. SNAP output
|
|
6j4z
|
transcription-RNA-DNA |
cryo-EM (4.1 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with spt4-5
and foreign DNA, stalled at shl(-1) of the nucleosome .
SNAP output
|
|
6j50
|
transcription-RNA-DNA |
cryo-EM (4.7 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with spt4-5
and foreign DNA, stalled at shl(-1) of the nucleosome
(tilted conformation) . SNAP output
|
|
6j51
|
transcription-RNA-DNA |
cryo-EM (4.2 Å) |
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka
H, Sekine SI |
(2019) "Structural
insight into nucleosome transcription by RNA polymerase
II with elongation factors." Science,
363, 744-747. doi: 10.1126/science.aav8912.
|
RNA polymerase ii elongation complex bound with spt4-5
and foreign DNA, stalled at shl(-1) of the nucleosome,
weak elf1 (+1 position) . SNAP output
|
|
6j5b
|
transcription-DNA |
X-ray (2.7 Å) |
Jiang M, Sun L, Isupov MN, Littlechild JA, Wu X, Wang
Q, Wang Q, Yang W, Wu Y |
(2019) "Structural
basis for the Target DNA recognition and binding by the
MYB domain of phosphate starvation response 1."
Febs J., 286, 2809-2821. doi:
10.1111/febs.14846.
|
Structural basis for the target DNA recognition and
binding by the myb domain of phosphate starvation
response regulator 1 . SNAP output
|
|
6j7y
|
hydrolase |
X-ray (2.203 Å) |
Chu LY, Agrawal S, Chen YP, Yang WZ, Yuan HS |
(2019) "Structural
insights into nanoRNA degradation by human Rexo2."
Rna, 25, 737-746. doi:
10.1261/rna.070557.119.
|
Human mitochondrial oligoribonuclease in complex with
DNA . SNAP output
|
|
6j80
|
hydrolase-DNA |
X-ray (1.812 Å) |
Chu LY, Agrawal S, Chen YP, Yang WZ, Yuan HS |
(2019) "Structural
insights into nanoRNA degradation by human Rexo2."
Rna, 25, 737-746. doi:
10.1261/rna.070557.119.
|
Human mitochondrial oligoribonuclease in complex with
poly-dt DNA . SNAP
output
|
|
6j99
|
transcription |
cryo-EM (4.1 Å) |
Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan
G, Lei M, Huang J |
(2019) "Structural
basis of the crosstalk between histone H2B
monoubiquitination and H3 lysine 79 methylation on
nucleosome." Cell Res.,
29, 330-333. doi: 10.1038/s41422-019-0146-7.
|
cryo-EM structure of human dot1l in complex with an
h2b-monoubiquitinated nucleosome . SNAP output
|
|
6j9a
|
transcription-DNA |
X-ray (2.915 Å) |
Tao Z, Hu H, Luo X, Jia B, Du J, He Y |
(2019) "Embryonic
resetting of the parental vernalized state by two B3
domain transcription factors in Arabidopsis."
Nat.Plants, 5, 424-435. doi:
10.1038/s41477-019-0402-3.
|
Crystal structure of arabidopsis thaliana val1 in
complex with flc DNA fragment . SNAP output
|
|
6j9b
|
transcription-DNA |
X-ray (1.9 Å) |
Tao Z, Hu H, Luo X, Jia B, Du J, He Y |
(2019) "Embryonic
resetting of the parental vernalized state by two B3
domain transcription factors in Arabidopsis."
Nat.Plants, 5, 424-435. doi:
10.1038/s41477-019-0402-3.
|
Arabidopsis fus3-DNA complex . SNAP output
|
|
6j9c
|
transcription-DNA |
X-ray (3.102 Å) |
Tao Z, Hu H, Luo X, Jia B, Du J, He Y |
(2019) "Embryonic
resetting of the parental vernalized state by two B3
domain transcription factors in Arabidopsis."
Nat.Plants, 5, 424-435. doi:
10.1038/s41477-019-0402-3.
|
Crystal structure of arabidopsis thaliana transcription
factor lec2-DNA complex . SNAP output
|
|
6j9e
|
transcription |
cryo-EM (3.41 Å) |
You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W,
Feng Y, Zhang Y |
(2019) "Structural
basis for transcription antitermination at bacterial
intrinsic terminator." Nat Commun,
10, 3048. doi: 10.1038/s41467-019-10955-x.
|
cryo-EM structure of xanthomonos oryzae transcription
elongation complex with nusa and the bacteriophage
protein p7 . SNAP
output
|
|
6j9f
|
transcription |
cryo-EM (3.95 Å) |
You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W,
Feng Y, Zhang Y |
(2019) "Structural
basis for transcription antitermination at bacterial
intrinsic terminator." Nat Commun,
10, 3048. doi: 10.1038/s41467-019-10955-x.
|
cryo-EM structure of xanthomonos oryzae transcription
elongation complex with the bacteriophage protein p7 .
SNAP output
|
|
6jbq
|
transcription-DNA-RNA |
cryo-EM (4.02 Å) |
Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang
Y |
(2019) "Structures
and mechanism of transcription initiation by bacterial
ECF factors." Nucleic Acids Res.,
47, 7094-7104. doi: 10.1093/nar/gkz470.
|
Cryoem structure of escherichia coli sigmae
transcription initiation complex containing 5nt of RNA
. SNAP output
|
|
6jbx
|
transcription-DNA |
X-ray (2.2 Å) |
Zuo G, Chen ZP, Jiang YL, Zhu Z, Ding C, Zhang Z,
Chen Y, Zhou CZ, Li Q |
(2019) "Structural
insights into repression of the Pneumococcal fatty acid
synthesis pathway by repressor FabT and co-repressor
acyl-ACP." Febs Lett.,
593, 2730-2741. doi: 10.1002/1873-3468.13534.
|
Crystal structure of streptococcus pneumoniae fabt in
complex with DNA . SNAP
output
|
|
6jcx
|
transcription |
X-ray (2.903 Å) |
Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang
Y |
(2019) "Structures
and mechanism of transcription initiation by bacterial
ECF factors." Nucleic Acids Res.,
47, 7094-7104. doi: 10.1093/nar/gkz470.
|
Mycobacterium tuberculosis transcription initiation
complex with ecf sigma factor sigma h and 6nt RNA .
SNAP output
|
|
6jcy
|
transcription |
X-ray (3.106 Å) |
Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang
Y |
(2019) "Structures
and mechanism of transcription initiation by bacterial
ECF factors." Nucleic Acids Res.,
47, 7094-7104. doi: 10.1093/nar/gkz470.
|
Mycobacterium tuberculosis RNA polymerase transcription
initiation open complex with a chimeric ecf sigma
factor sigh-e . SNAP
output
|
|
6jdg
|
DNA binding protein-DNA |
X-ray (2.388 Å) |
Huang YH, Lin ES, Huang CY |
(2019) "Complexed
crystal structure of SSB reveals a novel
single-stranded DNA binding mode (SSB)3:1: Phe60 is not
crucial for defining binding paths."
Biochem.Biophys.Res.Commun.,
520, 353-358. doi: 10.1016/j.bbrc.2019.10.036.
|
Complexed crystal structure of passb with ssDNA dt20 at
2.39 angstrom resolution . SNAP output
|
|
6jdv
|
hydrolase-RNA-DNA |
X-ray (3.1 Å) |
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K,
Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L,
Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y |
(2019) "Structures
of Neisseria meningitidis Cas9 Complexes in
Catalytically Poised and Anti-CRISPR-Inhibited
States." Mol.Cell, 76,
938. doi: 10.1016/j.molcel.2019.09.025.
|
Crystal structure of nme1cas9 in complex with sgrna and
target DNA (atatgatt pam) in catalytic state . SNAP output
|
|
6je3
|
hydrolase-RNA-DNA |
X-ray (2.931 Å) |
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K,
Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L,
Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y |
(2019) "Structures
of Neisseria meningitidis Cas9 Complexes in
Catalytically Poised and Anti-CRISPR-Inhibited
States." Mol.Cell, 76,
938. doi: 10.1016/j.molcel.2019.09.025.
|
Crystal structure of nme2cas9 in complex with sgrna and
target DNA (aggccc pam) with 5 nt overhang . SNAP output
|
|
6je4
|
hydrolase-hydrolase inhibitor-DNA-RNA |
X-ray (3.069 Å) |
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K,
Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L,
Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y |
(2019) "Structures
of Neisseria meningitidis Cas9 Complexes in
Catalytically Poised and Anti-CRISPR-Inhibited
States." Mol.Cell, 76,
938. doi: 10.1016/j.molcel.2019.09.025.
|
Crystal structure of nme1cas9-sgrna-dsDNA dimer
mediated by double protein inhibitor acriic3 monomers .
SNAP output
|
|
6jfu
|
hydrolase-RNA-DNA |
X-ray (3.2 Å) |
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K,
Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L,
Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y |
(2019) "Structures
of Neisseria meningitidis Cas9 Complexes in
Catalytically Poised and Anti-CRISPR-Inhibited
States." Mol.Cell, 76,
938. doi: 10.1016/j.molcel.2019.09.025.
|
Crystal structure of nme2cas9 in complex with sgrna and
target DNA (aggccc pam) . SNAP output
|
|
6jg8
|
peptide binding protein-DNA |
X-ray (2.097 Å) |
Guan ZY, Pei K, Wang J, Cui YQ, Zhu X, Su X, Zhou YB,
Zhang DL, Tang C, Yin P, Liu Z, Zou TT |
(2019) "Structural
insights into DNA recognition by AimR of the arbitrium
communication system in the SPbeta phage." Cell
Discov, 5, 29. doi: 10.1038/s41421-019-0101-2.
|
Crystal structure of aimr in complex with DNA .
SNAP output
|
|
6jgw
|
transcription-DNA |
X-ray (2.8 Å) |
Liu X, Hu Q, Yang J, Huang S, Wei T, Chen W, He Y,
Wang D, Liu Z, Wang K, Gan J, Chen H |
(2019) "Selective
cadmium regulation mediated by a cooperative binding
mechanism in CadR."
Proc.Natl.Acad.Sci.USA, 116,
20398-20403. doi: 10.1073/pnas.1908610116.
|
Crystal structure of the transcriptional regulator cadr
from p. putida in complex with DNA . SNAP output
|
|
6jgx
|
transcription-DNA |
X-ray (2.71 Å) |
Liu X, Hu Q, Yang J, Huang S, Wei T, Chen W, He Y,
Wang D, Liu Z, Wang K, Gan J, Chen H |
(2019) "Selective
cadmium regulation mediated by a cooperative binding
mechanism in CadR."
Proc.Natl.Acad.Sci.USA, 116,
20398-20403. doi: 10.1073/pnas.1908610116.
|
Crystal structure of the transcriptional regulator cadr
from p. putida in complex with cadmium(ii) and DNA .
SNAP output
|
|
6jhe
|
transcription-DNA |
X-ray (3.101 Å) |
Kwon E, Devkota SR, Pathak D, Dahal P, Kim DY |
(2019) "Structural
analysis of the recognition of the -35 promoter element
by SigW from Bacillus subtilis." Plos One,
14, e0221666. doi: 10.1371/journal.pone.0221666.
|
Crystal structure of bacillus subtilis sigw domain 4 in
complexed with -35 element DNA . SNAP output
|
|
6jip
|
DNA binding protein-DNA |
X-ray (1.659 Å) |
Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X,
Gong P, Zhang X, Liu M, Zhu J, Yang Y |
(2020) "Structural
insight into the length-dependent binding of ssDNA by
SP_0782 from Streptococcus pneumoniae, reveals a
divergence in the DNA-binding interface of PC4-like
proteins." Nucleic Acids Res.,
48, 432-444. doi: 10.1093/nar/gkz1045.
|
Crystal structure of streptococcus pneumoniae sp_0782
(residues 7-79) in complex with single-stranded DNA dt6
. SNAP output
|
|
6jiq
|
DNA binding protein-DNA |
X-ray (1.67 Å) |
Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X,
Gong P, Zhang X, Liu M, Zhu J, Yang Y |
(2020) "Structural
insight into the length-dependent binding of ssDNA by
SP_0782 from Streptococcus pneumoniae, reveals a
divergence in the DNA-binding interface of PC4-like
proteins." Nucleic Acids Res.,
48, 432-444. doi: 10.1093/nar/gkz1045.
|
Crystal structure of streptococcus pneumoniae sp_0782
(residues 7-79) in complex with single-stranded DNA dt6
. SNAP output
|
|
6jm9
|
gene regulation |
cryo-EM (7.3 Å) |
Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY,
Kim SJ, Hohng S, Song JJ |
(2019) "Structural
basis of recognition and destabilization of the histone
H2B ubiquitinated nucleosome by the DOT1L histone H3
Lys79 methyltransferase." Genes Dev.,
33, 620-625. doi: 10.1101/gad.323790.118.
|
cryo-EM structure of dot1l bound to unmodified
nucleosome . SNAP
output
|
|
6jma
|
gene regulation |
cryo-EM (6.8 Å) |
Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY,
Kim SJ, Hohng S, Song JJ |
(2019) "Structural
basis of recognition and destabilization of the histone
H2B ubiquitinated nucleosome by the DOT1L histone H3
Lys79 methyltransferase." Genes Dev.,
33, 620-625. doi: 10.1101/gad.323790.118.
|
cryo-EM structure of dot1l bound to h2b ubiquitinated
nucleosome . SNAP
output
|
|
6jni
|
transcription-DNA |
X-ray (2.9 Å) |
Liu X, Hu Q, Yang J, Huang S, Wei T, Chen W, He Y,
Wang D, Liu Z, Wang K, Gan J, Chen H |
(2019) "Selective
cadmium regulation mediated by a cooperative binding
mechanism in CadR."
Proc.Natl.Acad.Sci.USA, 116,
20398-20403. doi: 10.1073/pnas.1908610116.
|
Crystal structure of the transcriptional regulator cadr
from p. putida in complex with zinc(ii) and DNA .
SNAP output
|
|
6jnl
|
DNA binding protein-DNA |
X-ray (2.15 Å) |
Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu
F, Ma J, Cao X |
(2019) "DNA
methylation repels targeting of Arabidopsis REF6."
Nat Commun, 10, 2063. doi:
10.1038/s41467-019-10026-1.
|
Ref6 znf2-4-nac004 complex . SNAP output
|
|
6jnm
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu
F, Ma J, Cao X |
(2019) "DNA
methylation repels targeting of Arabidopsis REF6."
Nat Commun, 10, 2063. doi:
10.1038/s41467-019-10026-1.
|
Ref6 znf2-4-nac004-mc3 complex . SNAP output
|
|
6jnn
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu
F, Ma J, Cao X |
(2019) "DNA
methylation repels targeting of Arabidopsis REF6."
Nat Commun, 10, 2063. doi:
10.1038/s41467-019-10026-1.
|
Ref6 znf2-4-nac004-mc1 complex . SNAP output
|
|
6jnx
|
transcription,DNA,RNA |
cryo-EM (4.08 Å) |
Shi J, Gao X, Tian T, Yu Z, Gao B, Wen A, You L,
Chang S, Zhang X, Zhang Y, Feng Y |
(2019) "Structural
basis of Q-dependent transcription
antitermination." Nat Commun,
10, 2925. doi: 10.1038/s41467-019-10958-8.
|
cryo-EM structure of a q-engaged arrested complex .
SNAP output
|
|
6joo
|
hydrolase-DNA-RNA |
X-ray (2.9 Å) |
Hirano S, Abudayyeh OO, Gootenberg JS, Horii T,
Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O |
(2019) "Structural
basis for the promiscuous PAM recognition by
Corynebacterium diphtheriae Cas9." Nat
Commun, 10, 1968. doi: 10.1038/s41467-019-09741-6.
|
Crystal structure of corynebacterium diphtheriae cas9
in complex with sgrna and target DNA . SNAP output
|
|
6jou
|
DNA binding protein-DNA |
X-ray (2.17 Å) |
Horikoshi N, Kujirai T, Sato K, Kimura H, Kurumizaka
H |
(2019) "Structure-based
design of an H2A.Z.1 mutant stabilizing a nucleosome in
vitro and in vivo."
Biochem.Biophys.Res.Commun.,
515, 719-724. doi: 10.1016/j.bbrc.2019.06.012.
|
Crystal structure of the human nucleosome containing
h2a.z.1 s42r . SNAP
output
|
|
6jpi
|
antitoxin-DNA |
X-ray (3.143 Å) |
Liu Y, Gao Z, Zhang H, Dong Y |
"Crystal structure of PA4674 in complex with its
operator DNA (28bp) from Pseudomonas aeruginosa." |
Crystal structure of pa4674 in complex with its
operator DNA (28bp) from pseudomonas aeruginosa .
SNAP output
|
|
6jr0
|
gene regulation-DNA |
X-ray (2.5 Å) |
Saotome M, Horikoshi N, Urano K, Kujirai T,
Yuzurihara H, Kurumizaka H, Kagawa W |
(2019) "Structure
determination of the nucleosome core particle by
selenium SAD phasing." Acta Crystallogr D
Struct Biol, 75, 930-936. doi:
10.1107/S2059798319012713.
|
Crystal structure of the human nucleosome phased with
12 selenium atoms . SNAP
output
|
|
6jr1
|
gene regulation-DNA |
X-ray (2.4 Å) |
Saotome M, Horikoshi N, Urano K, Kujirai T,
Yuzurihara H, Kurumizaka H, Kagawa W |
(2019) "Structure
determination of the nucleosome core particle by
selenium SAD phasing." Acta Crystallogr D
Struct Biol, 75, 930-936. doi:
10.1107/S2059798319012713.
|
Crystal structure of the human nucleosome phased with
16 selenium atoms . SNAP
output
|
|
6jrf
|
DNA binding protein-DNA |
X-ray (2.047 Å) |
Lin H, Zhang D, Zuo K, Yuan C, Li J, Huang M, Lin
Z |
(2019) "Structural
basis of sequence-specific Holliday junction cleavage
by MOC1." Nat.Chem.Biol.,
15, 1241-1248. doi: 10.1038/s41589-019-0377-4.
|
Crystal structure of zmmoc1-holliday junction complex
in the presence of calcium . SNAP output
|
|
6jrg
|
DNA binding protein-DNA |
X-ray (2.005 Å) |
Lin H, Zhang D, Zuo K, Yuan C, Li J, Huang M, Lin
Z |
(2019) "Structural
basis of sequence-specific Holliday junction cleavage
by MOC1." Nat.Chem.Biol.,
15, 1241-1248. doi: 10.1038/s41589-019-0377-4.
|
Crystal structure of zmmoc1 h253a mutant in complex
with holliday junction . SNAP output
|
|
6jrp
|
transcription |
X-ray (3.0 Å) |
Lee H, Song JJ |
(2019) "The
crystal structure of Capicua HMG-box domain complexed
with the ETV5-DNA and its implications for
Capicua-mediated cancers." Febs J.,
286, 4951-4963. doi: 10.1111/febs.15008.
|
Crystal structure of cic-hmg-etv5-DNA complex .
SNAP output
|
|
6jtq
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Liu L, Yi C |
"RVD HA specifically contacts 5mC through van der
Waals interactions." |
Rvd ha specifically contacts 5mc through van der waals
interactions . SNAP
output
|
|
6jul
|
replication-DNA |
X-ray (2.3 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Msdpo4-DNA complex 1 . SNAP output
|
|
6jum
|
replication-DNA |
X-ray (1.78 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Msdpo4-DNA complex 2 . SNAP output
|
|
6jun
|
replication-DNA |
X-ray (2.51 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Msdpo4-DNA complex 3 . SNAP output
|
|
6juo
|
replication-DNA |
X-ray (2.16 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Msdpo4-DNA complex 4 . SNAP output
|
|
6jup
|
replication-DNA |
X-ray (2.44 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Mutant poliv-DNA incoming nucleotide complex . SNAP output
|
|
6juq
|
replication-DNA |
X-ray (2.74 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Mutant poliv-DNA incoming nucleotide complex 2 .
SNAP output
|
|
6jur
|
replication-DNA |
X-ray (2.06 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Msdpo4-DNA complex 5 . SNAP output
|
|
6jus
|
replication-DNA |
X-ray (2.5 Å) |
Johnson MK, Kottur J, Nair DT |
(2019) "A polar
filter in DNA polymerases prevents ribonucleotide
incorporation." Nucleic Acids Res.,
47, 10693-10705. doi: 10.1093/nar/gkz792.
|
Msdpo4-DNA complex 6 . SNAP output
|
|
6jvy
|
RNA binding protein-DNA |
X-ray (2.003 Å) |
Qian K, Li M, Wang J, Zhang M, Wang M |
(2020) "Structural
basis for mRNA recognition by human RBM38."
Biochem.J., 477, 161-172.
doi: 10.1042/BCJ20190652.
|
Crystal structure of rbm38 in complex with
single-stranded DNA . SNAP output
|
|
6jvz
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Rvd ha specifically contacts 5mc through van der waals
interactions . SNAP
output
|
|
6jw0
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Universal rvd r* accommodates cytosine via
water-mediated interactions . SNAP output
|
|
6jw1
|
DNA binding protein-DNA |
X-ray (2.49 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Universal rvd r* accommodates 5mc via water-mediated
interactions . SNAP
output
|
|
6jw2
|
DNA binding protein-DNA |
X-ray (3.03 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Universal rvd r* accommodates 5hmc via water-mediated
interactions . SNAP
output
|
|
6jw3
|
DNA binding protein-DNA |
X-ray (3.1 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Degenerate rvd rg forms a distinct loop conformation .
SNAP output
|
|
6jw4
|
DNA binding protein-DNA |
X-ray (3.09 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Degenerate rvd rg forms a distinct loop conformation .
SNAP output
|
|
6jw5
|
DNA binding protein-DNA |
X-ray (2.99 Å) |
Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J |
(2020) "Structural
Insights into the Specific Recognition of
5-methylcytosine and 5-hydroxymethylcytosine by TAL
Effectors." J.Mol.Biol.,
432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023.
|
Rvd q* recognizes 5hmc through water-mediated h bonds .
SNAP output
|
|
6jxd
|
DNA binding protein-DNA |
X-ray (2.25 Å) |
Sharma D, De Falco L, Padavattan S, Rao C,
Geifman-Shochat S, Liu CF, Davey CA |
(2019) "PARP1
exhibits enhanced association and catalytic efficiency
with gamma H2A.X-nucleosome." Nat Commun,
10, 5751. doi: 10.1038/s41467-019-13641-0.
|
Human nucleosome core particle with cohesive end DNA
termini . SNAP
output
|
|
6jyl
|
DNA binding protein-DNA |
cryo-EM (3.37 Å) |
Yan L, Wu H, Li X, Gao N, Chen Z |
(2019) "Structures
of the ISWI-nucleosome complex reveal a conserved
mechanism of chromatin remodeling."
Nat.Struct.Mol.Biol., 26,
258-266. doi: 10.1038/s41594-019-0199-9.
|
The crosslinked complex of iswi-nucleosome in the
adp.bef-bound state . SNAP output
|
|
6jyw
|
transcription-DNA |
X-ray (2.95 Å) |
Liu XC, Chen H |
"Crystal structure of the transcription regulator
CadR N81M mutant from P. putida in complex with
Cadmium(II) and DNA." |
Crystal structure of the transcription regulator cadr
n81m mutant from p. putida in complex with cadmium(ii)
and DNA . SNAP
output
|
|
6k1i
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Sharma D, De Falco L, Padavattan S, Rao C,
Geifman-Shochat S, Liu CF, Davey CA |
(2019) "PARP1
exhibits enhanced association and catalytic efficiency
with gamma H2A.X-nucleosome." Nat Commun,
10, 5751. doi: 10.1038/s41467-019-13641-0.
|
Human nucleosome core particle with gammah2a.x variant
. SNAP output
|
|
6k1j
|
DNA binding protein-DNA |
X-ray (2.85 Å) |
Sharma D, De Falco L, Padavattan S, Rao C,
Geifman-Shochat S, Liu CF, Davey CA |
(2019) "PARP1
exhibits enhanced association and catalytic efficiency
with gamma H2A.X-nucleosome." Nat Commun,
10, 5751. doi: 10.1038/s41467-019-13641-0.
|
Human nucleosome core particle with h2a.x variant .
SNAP output
|
|
6k1k
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Sharma D, De Falco L, Padavattan S, Rao C,
Geifman-Shochat S, Liu CF, Davey CA |
(2019) "PARP1
exhibits enhanced association and catalytic efficiency
with gamma H2A.X-nucleosome." Nat Commun,
10, 5751. doi: 10.1038/s41467-019-13641-0.
|
Human nucleosome core particle with h2a.x s139e variant
. SNAP output
|
|
6k1p
|
DNA binding protein-DNA |
cryo-EM (3.87 Å) |
Yan L, Wu H, Li X, Gao N, Chen Z |
(2019) "Structures
of the ISWI-nucleosome complex reveal a conserved
mechanism of chromatin remodeling."
Nat.Struct.Mol.Biol., 26,
258-266. doi: 10.1038/s41594-019-0199-9.
|
The complex of iswi-nucleosome in the adp.bef-bound
state . SNAP output
|
|
6k2j
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Huang Q, Duan B, Dong X, Fan S, Xia B |
(2020) "GapR
binds DNA through dynamic opening of its tetrameric
interface." Nucleic Acids Res.,
48, 9372-9386. doi: 10.1093/nar/gkaa644.
|
Crystal structure of the DNA complex of c. crescentus
gapr . SNAP output
|
|
6k3j
|
hydrolase-DNA |
NMR |
Yan X, Lan W, Wang C, Cao C |
(2019) "Structural
Investigations on the Interactions between Cytidine
Deaminase Human APOBEC3G and DNA." Chem Asian
J, 14, 2235-2241. doi: 10.1002/asia.201900480.
|
Solution structure of apobec3g-cd2 with ssDNA, product
a . SNAP output
|
|
6k3k
|
hydrolase-DNA |
NMR |
Yan X, Lan W, Wang C, Cao C |
(2019) "Structural
Investigations on the Interactions between Cytidine
Deaminase Human APOBEC3G and DNA." Chem Asian
J, 14, 2235-2241. doi: 10.1002/asia.201900480.
|
Solution structure of apobec3g-cd2 with ssDNA, product
b . SNAP output
|
|
6k3z
|
hydrolase-DNA-RNA |
X-ray (3.2 Å) |
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q |
(2019) "Molecular
basis for the PAM expansion and fidelity enhancement of
an evolved Cas9 nuclease." Plos Biol.,
17, e3000496. doi: 10.1371/journal.pbio.3000496.
|
Crystal structure of dcas9 in complex with sgrna and
DNA (tga pam) . SNAP
output
|
|
6k4p
|
hydrolase-DNA-RNA |
X-ray (2.9 Å) |
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q |
(2019) "Molecular
basis for the PAM expansion and fidelity enhancement of
an evolved Cas9 nuclease." Plos Biol.,
17, e3000496. doi: 10.1371/journal.pbio.3000496.
|
Crystal structure of xcas9 in complex with sgrna and
DNA (tgg pam) . SNAP
output
|
|
6k4q
|
hydrolase-DNA-RNA |
X-ray (2.7 Å) |
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q |
(2019) "Molecular
basis for the PAM expansion and fidelity enhancement of
an evolved Cas9 nuclease." Plos Biol.,
17, e3000496. doi: 10.1371/journal.pbio.3000496.
|
Crystal structure of xcas9 in complex with sgrna and
DNA (cgg pam) . SNAP
output
|
|
6k4s
|
hydrolase-DNA-RNA |
X-ray (3.01 Å) |
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q |
(2019) "Molecular
basis for the PAM expansion and fidelity enhancement of
an evolved Cas9 nuclease." Plos Biol.,
17, e3000496. doi: 10.1371/journal.pbio.3000496.
|
Crystal structure of xcas9 in complex with sgrna and
DNA (tgc pam) . SNAP
output
|
|
6k4u
|
hydrolase-DNA |
X-ray (3.2 Å) |
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q |
(2019) "Molecular
basis for the PAM expansion and fidelity enhancement of
an evolved Cas9 nuclease." Plos Biol.,
17, e3000496. doi: 10.1371/journal.pbio.3000496.
|
Crystal structure of xcas9 in complex with sgrna and
DNA (tga pam) . SNAP
output
|
|
6k4y
|
transcription |
cryo-EM (3.79 Å) |
Shi J, Wen A, Zhao M, You L, Zhang Y, Feng Y |
(2019) "Structural
basis of sigma appropriation." Nucleic Acids
Res., 47, 9423-9432. doi:
10.1093/nar/gkz682.
|
Cryoem structure of sigma appropriation complex .
SNAP output
|
|
6k57
|
hydrolase-RNA-DNA |
X-ray (2.98 Å) |
Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q |
(2019) "Molecular
basis for the PAM expansion and fidelity enhancement of
an evolved Cas9 nuclease." Plos Biol.,
17, e3000496. doi: 10.1371/journal.pbio.3000496.
|
Crystal structure of dcas9 in complex with sgrna and
DNA (cga pam) . SNAP
output
|
|
6k8o
|
isomerase, DNA binding protein-DNA |
X-ray (2.5 Å) |
Wang HQ, Zhang JH, Zheng X, Zheng ZF, Dong YH, Huang
L, Gong Y |
"Crystal structures of the Sulfolobus solfataricus
topoisomerase III reveal that its C-terminal novel zinc
finger part is a unique decatenation domain." |
Crystal structure of the sulfolobus solfataricus
topoisomerase iii in complex with DNA . SNAP output
|
|
6kbs
|
DNA binding protein |
X-ray (1.601 Å) |
Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang
H |
(2019) "Molecular
basis of abasic site sensing in single-stranded DNA by
the SRAP domain of E. coli yedK." Nucleic Acids
Res., 47, 10388-10399. doi:
10.1093/nar/gkz744.
|
Crystal structure of yedk in complex with ssDNA .
SNAP output
|
|
6kbx
|
DNA binding protein |
X-ray (1.221 Å) |
Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang
H |
(2019) "Molecular
basis of abasic site sensing in single-stranded DNA by
the SRAP domain of E. coli yedK." Nucleic Acids
Res., 47, 10388-10399. doi:
10.1093/nar/gkz744.
|
Crystal structure of yedk in complex with ssDNA
containing abasic site . SNAP output
|
|
6kbz
|
DNA binding protein |
X-ray (1.653 Å) |
Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang
H |
(2019) "Molecular
basis of abasic site sensing in single-stranded DNA by
the SRAP domain of E. coli yedK." Nucleic Acids
Res., 47, 10388-10399. doi:
10.1093/nar/gkz744.
|
Crystal structure of yedk with ssDNA containing a
tetrahydrofuran abasic site . SNAP output
|
|
6kc7
|
hydrolase-RNA-DNA |
X-ray (3.3 Å) |
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K,
Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L,
Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y |
(2019) "Structures
of Neisseria meningitidis Cas9 Complexes in
Catalytically Poised and Anti-CRISPR-Inhibited
States." Mol.Cell, 76,
938. doi: 10.1016/j.molcel.2019.09.025.
|
Crystal structure of nme1cas9 in complex with sgrna and
target DNA (atatgatt pam) in seed-base paring state .
SNAP output
|
|
6kc8
|
hydrolase-RNA-DNA |
X-ray (2.9 Å) |
Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K,
Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L,
Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y |
(2019) "Structures
of Neisseria meningitidis Cas9 Complexes in
Catalytically Poised and Anti-CRISPR-Inhibited
States." Mol.Cell, 76,
938. doi: 10.1016/j.molcel.2019.09.025.
|
Crystal structure of wt nme1cas9 in complex with sgrna
and target DNA (atatgatt pam) in post-cleavage state .
SNAP output
|
|
6kco
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Liu YC, Huang Y |
"Shuguo PWWP in complex with ssDNA." |
Shuguo pwwp in complex with ssDNA . SNAP output
|
|
6kcp
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Liu YC, Huang Y |
"Shuguo PWWP in complex with ssDNA." |
Shuguo pwwp in complex with ssDNA . SNAP output
|
|
6kcq
|
DNA binding protein |
X-ray (1.701 Å) |
Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang
H |
(2019) "Molecular
basis of abasic site sensing in single-stranded DNA by
the SRAP domain of E. coli yedK." Nucleic Acids
Res., 47, 10388-10399. doi:
10.1093/nar/gkz744.
|
Crystal structure of yedk with ssDNA containing an
abasic site . SNAP
output
|
|
6kcs
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Hishiki A, Sato M, Hashimoto H |
(2020) "Structure
of HIRAN domain of human HLTF bound to duplex DNA
provides structural basis for DNA unwinding to initiate
replication fork regression." J.Biochem.,
167, 597-602. doi: 10.1093/jb/mvaa008.
|
Crystal structure of hiran domain of hltf in complex
with duplex DNA . SNAP
output
|
|
6kda
|
transferase-DNA |
X-ray (2.909 Å) |
Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS |
(2020) "Structural
insights into CpG-specific DNA methylation by human DNA
methyltransferase 3B." Nucleic Acids Res.,
48, 3949-3961. doi: 10.1093/nar/gkaa111.
|
Crystal structure of human dnmt3b-dnmt3l in complex
with DNA containing cpgpg site . SNAP output
|
|
6kdb
|
transferase-DNA |
X-ray (2.862 Å) |
Lin CC, Chen YP, Yang WZ, Shen JCK, Yuan HS |
(2020) "Structural
insights into CpG-specific DNA methylation by human DNA
methyltransferase 3B." Nucleic Acids Res.,
48, 3949-3961. doi: 10.1093/nar/gkaa111.
|
Crystal structure of human dnmt3b-dnmt3l in complex
with DNA containing cpgpt site . SNAP output
|
|
6kdi
|
immune system |
X-ray (2.7 Å) |
Yokoyama H, Mizutani R, Noguchi S, Hayashida N |
(2019) "Structural
and biochemical basis of the formation of isoaspartate
in the complementarity-determining region of antibody
64M-5 Fab." Sci Rep, 9,
18494. doi: 10.1038/s41598-019-54918-0.
|
Antibody 64m-5 fab including isoasp in complex with
dt(6-4)t . SNAP
output
|
|
6kdj
|
transferase-DNA |
X-ray (2.51 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2020) "Structural
features in common of HBV and HIV-1 resistance against
chirally-distinct nucleoside analogues entecavir and
lamivudine." Sci Rep, 10,
3021. doi: 10.1038/s41598-020-59775-w.
|
Hiv-1 reverse transcriptase with
q151m-y115f-f116y:DNA:lamivudine 5'-triphosphate
ternary complex . SNAP
output
|
|
6kdk
|
transferase-DNA |
X-ray (2.56 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2020) "Structural
features in common of HBV and HIV-1 resistance against
chirally-distinct nucleoside analogues entecavir and
lamivudine." Sci Rep, 10,
3021. doi: 10.1038/s41598-020-59775-w.
|
Hiv-1 reverse transcriptase with
q151m-y115f-f116y:DNA:dctp ternary complex . SNAP output
|
|
6kdm
|
transferase-DNA |
X-ray (2.32 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2020) "Structural
features in common of HBV and HIV-1 resistance against
chirally-distinct nucleoside analogues entecavir and
lamivudine." Sci Rep, 10,
3021. doi: 10.1038/s41598-020-59775-w.
|
Hiv-1 reverse transcriptase with
q151m-y115f-f116y:DNA:entecavir 5'-triphosphate ternary
complex . SNAP
output
|
|
6kdn
|
transferase-DNA |
X-ray (2.303 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2020) "Structural
features in common of HBV and HIV-1 resistance against
chirally-distinct nucleoside analogues entecavir and
lamivudine." Sci Rep, 10,
3021. doi: 10.1038/s41598-020-59775-w.
|
Hiv-1 reverse transcriptase with
q151m-y115f-f116y:DNA:dgtp ternary complex . SNAP output
|
|
6kdo
|
transferase-DNA |
X-ray (2.573 Å) |
Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S,
Maeda K, Mitsuya H |
(2020) "Structural
features in common of HBV and HIV-1 resistance against
chirally-distinct nucleoside analogues entecavir and
lamivudine." Sci Rep, 10,
3021. doi: 10.1038/s41598-020-59775-w.
|
Hiv-1 reverse transcriptase with
q151m-y115f-f116y-m184v-f160m:DNA:lamivudine
5'-triphosphate ternary complex . SNAP output
|
|
6kdv
|
DNA binding protein-DNA |
X-ray (3.11 Å) |
Yang J, Li J, Wang J, Sheng G, Wang M, Zhao H, Yang
Y, Wang Y |
(2020) "Crystal
structure of Cas1 in complex with branched DNA."
Sci China Life Sci, 63,
516-528. doi: 10.1007/s11427-019-9827-x.
|
Crystal structure of ttcas1-DNA complex . SNAP output
|
|
6ke9
|
DNA binding protein-DNA |
X-ray (2.22 Å) |
Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V,
Korolev N, Rhodes D, Nordenskiold L |
(2020) "The
human telomeric nucleosome displays distinct structural
and dynamic properties." Nucleic Acids
Res., 48, 5383-5396. doi:
10.1093/nar/gkaa289.
|
The human telomeric nucleosome displays distinct
structural and dynamic properties . SNAP output
|
|
6kf9
|
transcription |
cryo-EM (3.79 Å) |
Jun SH, Hyun J, Cha JS, Kim H, Bartlett MS, Cho HS,
Murakami KS |
(2020) "Direct
binding of TFE alpha opens DNA binding cleft of RNA
polymerase." Nat Commun,
11, 6123. doi: 10.1038/s41467-020-19998-x.
|
cryo-EM structure of thermococcus kodakarensis RNA
polymerase . SNAP
output
|
|
6khy
|
DNA binding protein |
X-ray (3.008 Å) |
Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C,
Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J |
(2020) "A unique
DNA-binding mode of African swine fever virus AP
endonuclease." Cell Discov,
6, 13. doi: 10.1038/s41421-020-0146-2.
|
The crystal structure of asfvap:ag . SNAP output
|
|
6ki3
|
DNA binding protein-DNA |
X-ray (2.354 Å) |
Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C,
Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J |
(2020) "A unique
DNA-binding mode of African swine fever virus AP
endonuclease." Cell Discov,
6, 13. doi: 10.1038/s41421-020-0146-2.
|
The crystal structure of asfvap:df commplex . SNAP output
|
|
6ki6
|
transcription-DNA |
X-ray (2.5 Å) |
Yang Y, Xu Z, He C, Zhang B, Shi Y, Li F |
(2019) "Structural
insights into the recognition of gamma-globin gene
promoter by BCL11A." Cell Res.,
29, 960-963. doi: 10.1038/s41422-019-0221-0.
|
Crystal structure of bcl11a in complex with
gamma-globin -115 hpfh region . SNAP output
|
|
6kij
|
DNA binding protein |
X-ray (1.58 Å) |
Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang
H |
(2019) "Molecular
basis of abasic site sensing in single-stranded DNA by
the SRAP domain of E. coli yedK." Nucleic Acids
Res., 47, 10388-10399. doi:
10.1093/nar/gkz744.
|
Crystal structure of yedk with ssDNA containing an
abasic site . SNAP
output
|
|
6kiu
|
transcription-DNA |
cryo-EM (3.2 Å) |
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei
M, Huang J |
(2019) "Structural
basis of nucleosome recognition and modification by MLL
methyltransferases." Nature,
573, 445-449. doi: 10.1038/s41586-019-1528-1.
|
cryo-EM structure of human mll1-ubncp complex (3.2
angstrom) . SNAP
output
|
|
6kiv
|
transcription-DNA |
cryo-EM (4.0 Å) |
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei
M, Huang J |
(2019) "Structural
basis of nucleosome recognition and modification by MLL
methyltransferases." Nature,
573, 445-449. doi: 10.1038/s41586-019-1528-1.
|
cryo-EM structure of human mll1-ubncp complex (4.0
angstrom) . SNAP
output
|
|
6kiw
|
transcription-DNA |
cryo-EM (4.0 Å) |
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei
M, Huang J |
(2019) "Structural
basis of nucleosome recognition and modification by MLL
methyltransferases." Nature,
573, 445-449. doi: 10.1038/s41586-019-1528-1.
|
cryo-EM structure of human mll3-ubncp complex (4.0
angstrom) . SNAP
output
|
|
6kix
|
transcription-DNA |
cryo-EM (4.1 Å) |
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei
M, Huang J |
(2019) "Structural
basis of nucleosome recognition and modification by MLL
methyltransferases." Nature,
573, 445-449. doi: 10.1038/s41586-019-1528-1.
|
cryo-EM structure of human mll1-ncp complex, binding
mode1 . SNAP output
|
|
6kiz
|
transcription-DNA |
cryo-EM (4.5 Å) |
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei
M, Huang J |
(2019) "Structural
basis of nucleosome recognition and modification by MLL
methyltransferases." Nature,
573, 445-449. doi: 10.1038/s41586-019-1528-1.
|
cryo-EM structure of human mll1-ncp complex, binding
mode2 . SNAP output
|
|
6kj6
|
transcription |
cryo-EM (3.8 Å) |
Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao
G, Feng Y, Yang B, Zhang Y |
(2019) "Crl
activates transcription by stabilizing active
conformation of the master stress transcription
initiation factor." Elife,
8. doi: 10.7554/eLife.50928.
|
cryo-EM structure of escherichia coli crl transcription
activation complex . SNAP output
|
|
6kks
|
DNA binding protein-DNA |
X-ray (2.15 Å) |
Wang B, Luo Q, Li Y, Yin L, Zhou N, Li X, Gan J, Dong
A |
(2020) "Structural
insights into target DNA recognition by R2R3-MYB
transcription factors." Nucleic Acids
Res., 48, 460-471. doi: 10.1093/nar/gkz1081.
|
Structural insights into target DNA recognition by
r2r3-type myb transcription factor . SNAP output
|
|
6knb
|
replication-DNA |
cryo-EM (6.9 Å) |
Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T,
Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y |
(2020) "Two
conformations of DNA polymerase D-PCNA-DNA, an archaeal
replisome complex, revealed by cryo-electron
microscopy." Bmc Biol.,
18, 152. doi: 10.1186/s12915-020-00889-y.
|
Pold-pcna-DNA (form a) . SNAP output
|
|
6knc
|
replication-DNA |
cryo-EM (9.3 Å) |
Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T,
Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y |
(2020) "Two
conformations of DNA polymerase D-PCNA-DNA, an archaeal
replisome complex, revealed by cryo-electron
microscopy." Bmc Biol.,
18, 152. doi: 10.1186/s12915-020-00889-y.
|
Pold-pcna-DNA (form b) . SNAP output
|
|
6kon
|
transcription |
X-ray (3.0 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Mycobacterium tuberculosis initial transcription
complex comprising sigma h and 5'-oh RNA of 5 nt .
SNAP output
|
|
6koo
|
transcription |
X-ray (2.8 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Mycobacterium tuberculosis initial transcription
complex comprising sigma h and 5'-oh RNA of 7 nt .
SNAP output
|
|
6kop
|
transcription |
X-ray (3.303 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Mycobacterium tuberculosis initial transcription
complex comprising sigma h and 5'-oh RNA of 9 nt .
SNAP output
|
|
6koq
|
transcription |
X-ray (3.353 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Mycobacterium tuberculosis initial transcription
complex comprising sigma h and 5'-oh RNA of 10 nt .
SNAP output
|
|
6kqd
|
transcription |
X-ray (3.3 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-oh RNA of 3 nt . SNAP output
|
|
6kqe
|
translation |
X-ray (3.3 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-oh RNA of 4 nt . SNAP output
|
|
6kqf
|
transcription |
X-ray (2.45 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-oh RNA of 5 nt . SNAP output
|
|
6kqg
|
transcription |
X-ray (2.783 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-oh RNA of 6 nt . SNAP output
|
|
6kqh
|
transcription |
X-ray (3.18 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-oh RNA of 7 nt . SNAP output
|
|
6kql
|
transcription |
X-ray (2.89 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-triphosphate RNA of 4 nt .
SNAP output
|
|
6kqm
|
transcription |
X-ray (3.197 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-triphosphate RNA of 5 nt .
SNAP output
|
|
6kqn
|
transcription |
X-ray (3.489 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-triphosphate RNA of 6 nt .
SNAP output
|
|
6ksf
|
gene regulation |
X-ray (2.4 Å) |
Zhang M, Yang S, Nelakanti R, Zhao W, Liu G, Li Z,
Liu X, Wu T, Xiao A, Li H |
(2020) "Mammalian
ALKBH1 serves as an N6-mA demethylase of unpairing
DNA." Cell Res., 30,
197-210. doi: 10.1038/s41422-019-0237-5.
|
Crystal structure of alkbh1 bound to 21-mer DNA bulge .
SNAP output
|
|
6kvd
|
DNA binding protein-DNA |
X-ray (2.21 Å) |
Tanaka H, Sato S, Koyama M, Kujirai T, Kurumizaka
H |
(2020) "Biochemical
and structural analyses of the nucleosome containing
human histone H2A.J." J.Biochem.,
167, 419-427. doi: 10.1093/jb/mvz109.
|
Crystal structure of human nucleosome containing h2a.j
. SNAP output
|
|
6kvo
|
plant protein-DNA |
X-ray (2.5 Å) |
Yan J, Hong S, Guan Z, He W, Zhang D, Yin P |
(2020) "Structural
insights into sequence-dependent Holliday junction
resolution by the chloroplast resolvase MOC1."
Nat Commun, 11, 1417. doi:
10.1038/s41467-020-15242-8.
|
Crystal structure of chloroplast resolvase in complex
with holliday junction . SNAP output
|
|
6kw3
|
DNA binding protein-DNA |
cryo-EM (7.13 Å) |
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W,
Deng H, Cairns BR, Gao N, Chen Z |
(2019) "Structure
of the RSC complex bound to the nucleosome."
Science, 366, 838-843. doi:
10.1126/science.aay0033.
|
The classa rsc-nucleosome complex . SNAP output
|
|
6kw4
|
DNA binding protein-DNA |
cryo-EM (7.55 Å) |
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W,
Deng H, Cairns BR, Gao N, Chen Z |
(2019) "Structure
of the RSC complex bound to the nucleosome."
Science, 366, 838-843. doi:
10.1126/science.aay0033.
|
The classb rsc-nucleosome complex . SNAP output
|
|
6kw5
|
DNA binding protein-DNA |
cryo-EM (10.13 Å) |
Ye YP, Wu H, Chen KJ, Verma N, Cairns B, Gao N, Chen
ZC |
"Structure of the RSC complex bound to the
nucleosome." |
The classc rsc-nucleosome complex . SNAP output
|
|
6kxv
|
DNA binding protein-DNA |
X-ray (3.63 Å) |
Dacher M, Tachiwana H, Horikoshi N, Kujirai T,
Taguchi H, Kimura H, Kurumizaka H |
(2019) "Incorporation
and influence of Leishmania histone H3 in
chromatin." Nucleic Acids Res.,
47, 11637-11648. doi: 10.1093/nar/gkz1040.
|
Crystal structure of a nucleosome containing leishmania
histone h3 . SNAP
output
|
|
6l2n
|
hydrolase-DNA |
X-ray (2.45 Å) |
Miyazono KI, Wang D, Ito T, Tanokura M |
(2020) "Distortion
of double-stranded DNA structure by the binding of the
restriction DNA glycosylase R.PabI." Nucleic
Acids Res., 48, 5106-5118. doi:
10.1093/nar/gkaa184.
|
Crystal structure of the
r.pabi(y68f-k154a)-dsDNA(gtac-3bp-gtac) complex .
SNAP output
|
|
6l2o
|
hydrolase-DNA |
X-ray (2.2 Å) |
Miyazono KI, Wang D, Ito T, Tanokura M |
(2020) "Distortion
of double-stranded DNA structure by the binding of the
restriction DNA glycosylase R.PabI." Nucleic
Acids Res., 48, 5106-5118. doi:
10.1093/nar/gkaa184.
|
Crystal structure of the
r.pabi(y68f-k154a)-dsDNA(gtac-5bp-gtac) complex .
SNAP output
|
|
6l3g
|
hydrolase-DNA |
X-ray (3.3 Å) |
Su N, Byrd AK, Bharath SR, Yang O, Jia Y, Tang X, Ha
T, Raney KD, Song H |
(2019) "Structural
basis for DNA unwinding at forked dsDNA by two
coordinating Pif1 helicases." Nat Commun,
10, 5375. doi: 10.1038/s41467-019-13414-9.
|
Structural basis for DNA unwinding at forked dsDNA by
two coordinating pif1 helicases . SNAP output
|
|
6l49
|
nuclear protein |
cryo-EM (18.9 Å) |
Takizawa Y, Ho CH, Tachiwana H, Matsunami H,
Kobayashi W, Suzuki M, Arimura Y, Hori T, Fukagawa T, Ohi
MD, Wolf M, Kurumizaka H |
(2020) "Cryo-EM
Structures of Centromeric Tri-nucleosomes Containing a
Central CENP-A Nucleosome." Structure,
28, 44. doi: 10.1016/j.str.2019.10.016.
|
H3-ca-h3 tri-nucleosome with the 22 base-pair linker
DNA . SNAP output
|
|
6l4a
|
nuclear protein |
cryo-EM (12.3 Å) |
Takizawa Y, Ho CH, Tachiwana H, Matsunami H,
Kobayashi W, Suzuki M, Arimura Y, Hori T, Fukagawa T, Ohi
MD, Wolf M, Kurumizaka H |
(2020) "Cryo-EM
Structures of Centromeric Tri-nucleosomes Containing a
Central CENP-A Nucleosome." Structure,
28, 44. doi: 10.1016/j.str.2019.10.016.
|
H3-h3-h3 tri-nucleosome with the 22 base-pair linker
DNA . SNAP output
|
|
6l6l
|
DNA binding protein |
X-ray (2.781 Å) |
Jiang L, Dai S, Li J, Liang X, Qu L, Chen X, Guo M,
Chen Z, Chen L, Wei H, Chen Y |
(2019) "Structural
basis of binding of homodimers of the nuclear receptor
NR4A2 to selective Nur-responsive DNA elements."
J.Biol.Chem., 294,
19795-19803. doi: 10.1074/jbc.RA119.010730.
|
Structural basis of nr4a2 homodimers binding to
selective nur-responsive elements . SNAP output
|
|
6l6q
|
DNA binding protein |
X-ray (2.601 Å) |
Jiang L, Dai S, Li J, Liang X, Qu L, Chen X, Guo M,
Chen Z, Chen L, Wei H, Chen Y |
(2019) "Structural
basis of binding of homodimers of the nuclear receptor
NR4A2 to selective Nur-responsive DNA elements."
J.Biol.Chem., 294,
19795-19803. doi: 10.1074/jbc.RA119.010730.
|
Structural basis of nr4a2 homodimers binding to
selective nur-responsive elements . SNAP output
|
|
6l6s
|
DNA binding protein |
X-ray (2.06 Å) |
Jia Q, Zeng H, Tu J, Sun L, Cao W, Xie W |
(2021) "Structural
insights into an MsmUdgX mutant capable of both
crosslinking and uracil excision capability."
DNA Repair (Amst), 97,
103008. doi: 10.1016/j.dnarep.2020.103008.
|
The structure of the udgx mutant h109e crosslinked to
single-stranded DNA . SNAP output
|
|
6l6y
|
DNA binding protein-DNA,transcription |
X-ray (3.0 Å) |
Balasubramanian M, Kolatkar PR |
"Crystal Structure of Pluripotency Reprogramming
Factor Sox17 mutant (Sox17EK) HMG Domain bound to
DNA." |
Crystal structure of pluripotency reprogramming factor
sox17 mutant (sox17ek) hmg domain bound to DNA .
SNAP output
|
|
6l74
|
transcription |
X-ray (3.12 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Thermus thermophilus initial transcription complex
comprising sigma a and 5'-triphosphate RNA of 2 nt .
SNAP output
|
|
6l84
|
DNA binding protein-DNA |
X-ray (2.602 Å) |
An J, Choi J, Hwang D, Park J, Pemble 4th CW, Duong
THM, Kim KR, Ahn H, Chung HS, Ahn DR |
(2020) "The
crystal structure of a natural DNA polymerase complexed
with mirror DNA." Chem.Commun.(Camb.),
56, 2186-2189. doi: 10.1039/c9cc09351f.
|
Complex of DNA polymerase iv and d-DNA duplex .
SNAP output
|
|
6l8e
|
antitoxin-toxin-DNA |
X-ray (2.35 Å) |
Xue L, Yue J, Ke J, Khan MH, Wen W, Sun B, Zhu Z, Niu
L |
(2020) "Distinct
oligomeric structures of the YoeB-YefM complex provide
insights into the conditional cooperativity of type II
toxin-antitoxin system." Nucleic Acids
Res., 48, 10527-10541. doi:
10.1093/nar/gkaa706.
|
Crystal structure of heterohexameric yoeb-yefm complex
bound to 26bp-DNA . SNAP
output
|
|
6l97
|
DNA binding protein-DNA |
X-ray (2.362 Å) |
An J, Choi J, Hwang D, Park J, Pemble 4th CW, Duong
THM, Kim KR, Ahn H, Chung HS, Ahn DR |
(2020) "The
crystal structure of a natural DNA polymerase complexed
with mirror DNA." Chem.Commun.(Camb.),
56, 2186-2189. doi: 10.1039/c9cc09351f.
|
Complex of DNA polymerase iv and l-DNA duplex .
SNAP output
|
|
6l9h
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V,
Korolev N, Rhodes D, Nordenskiold L |
(2020) "The
human telomeric nucleosome displays distinct structural
and dynamic properties." Nucleic Acids
Res., 48, 5383-5396. doi:
10.1093/nar/gkaa289.
|
The human telomeric nucleosome displays distinct
structural and dynamic properties . SNAP output
|
|
6l9z
|
DNA binding protein |
X-ray (2.5 Å) |
Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S,
Shum WK, Davey GE, Davey CA |
(2021) "Engineering
nucleosomes for generating diverse chromatin
assemblies." Nucleic Acids Res.,
49, e52. doi: 10.1093/nar/gkab070.
|
338 bp di-nucleosome assembled with linker histone h1.x
. SNAP output
|
|
6la2
|
DNA binding protein |
X-ray (3.89 Å) |
Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S,
Shum WK, Davey GE, Davey CA |
(2021) "Engineering
nucleosomes for generating diverse chromatin
assemblies." Nucleic Acids Res.,
49, e52. doi: 10.1093/nar/gkab070.
|
343 bp di-nucleosome harboring cohesive DNA termini
assembled with linker histone h1.0 . SNAP output
|
|
6la8
|
DNA binding protein |
X-ray (3.4 Å) |
Adhireksan Z, Sharma D, Lee PL, Davey CA |
(2020) "Near-atomic
resolution structures of interdigitated nucleosome
fibres." Nat Commun, 11,
4747. doi: 10.1038/s41467-020-18533-2.
|
349 bp di-nucleosome harboring cohesive DNA termini
assembled with linker histone h1.0 . SNAP output
|
|
6la9
|
DNA binding protein |
X-ray (3.7 Å) |
Adhireksan Z, Sharma D, Lee PL, Davey CA |
(2020) "Near-atomic
resolution structures of interdigitated nucleosome
fibres." Nat Commun, 11,
4747. doi: 10.1038/s41467-020-18533-2.
|
349 bp di-nucleosome harboring cohesive DNA termini
assembled with linker histone h1.0 (high
cryoprotectant) . SNAP
output
|
|
6lab
|
DNA binding protein |
X-ray (3.2 Å) |
Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S,
Shum WK, Davey GE, Davey CA |
(2021) "Engineering
nucleosomes for generating diverse chromatin
assemblies." Nucleic Acids Res.,
49, e52. doi: 10.1093/nar/gkab070.
|
169 bp nucleosome, harboring cohesive DNA termini,
assembled with linker histone h1.0 . SNAP output
|
|
6lae
|
DNA binding protein-DNA |
X-ray (2.81 Å) |
Lian FM, Yang X, Jiang YL, Yang F, Li C, Yang W, Qian
C |
(2020) "New
structural insights into the recognition of undamaged
splayed-arm DNA with a single pair of non-complementary
nucleotides by human nucleotide excision repair protein
XPA." Int.J.Biol.Macromol.,
148, 466-474. doi: 10.1016/j.ijbiomac.2020.01.169.
|
Crystal structure of the DNA-binding domain of human
xpa in complex with DNA . SNAP output
|
|
6lb3
|
antitoxin-DNA |
X-ray (2.497 Å) |
Liu Y, Zhang H, Gao Z, Dong Y |
"Crystal structure of PA4674 in complex with its
operator DNA (18bp) from Pseudomonas aeruginosa." |
Crystal structure of pa4674 in complex with its
operator DNA (18bp) from pseudomonas aeruginosa .
SNAP output
|
|
6lbi
|
DNA binding protein |
X-ray (3.067 Å) |
Li J, Dai S, Chen X, Liang X, Qu L, Jiang L, Guo M,
Zhou Z, Wei H, Zhang H, Chen Z, Chen L, Chen Y |
(2021) "Mechanism
of forkhead transcription factors binding to a novel
palindromic DNA site." Nucleic Acids Res.,
49, 3573-3583. doi: 10.1093/nar/gkab086.
|
Crystal structure of foxo1-dbd homodimer bound to a
palindromic DNA sequence . SNAP output
|
|
6lbm
|
transcription |
X-ray (2.841 Å) |
Li J, Dai S, Chen X, Liang X, Qu L, Jiang L, Guo M,
Zhou Z, Wei H, Zhang H, Chen Z, Chen L, Chen Y |
(2021) "Mechanism
of forkhead transcription factors binding to a novel
palindromic DNA site." Nucleic Acids Res.,
49, 3573-3583. doi: 10.1093/nar/gkab086.
|
Crystal structure of foxc2-dbd bound to a palindromic
DNA sequence . SNAP
output
|
|
6lbr
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Ge Y, Wu Z, Chen H, Zhong Q, Shi S, Li G, Wu J, Lei
M |
(2020) "Structural
insights into telomere protection and homeostasis
regulation by yeast CST complex."
Nat.Struct.Mol.Biol., 27,
752-762. doi: 10.1038/s41594-020-0459-8.
|
Crystal structure of yeast cdc13 and ssDNA . SNAP output
|
|
6lc1
|
DNA binding protein-DNA |
X-ray (3.12 Å) |
Jiang L, Wei H, Yan N, Dai S, Li J, Qu L, Chen X, Guo
M, Chen Z, Chen Y |
(2020) "Structural
basis of NR4A1 bound to the human pituitary
proopiomelanocortin gene promoter."
Biochem.Biophys.Res.Commun.,
523, 1-5. doi: 10.1016/j.bbrc.2019.11.192.
|
Structural basis of nr4a1 bound to the human pituitary
proopiomelanocortin gene promoter . SNAP output
|
|
6lct
|
hydrolase-DNA |
X-ray (2.55 Å) |
Yan J, Hong S, Guan Z, He W, Zhang D, Yin P |
(2020) "Structural
insights into sequence-dependent Holliday junction
resolution by the chloroplast resolvase MOC1."
Nat Commun, 11, 1417. doi:
10.1038/s41467-020-15242-8.
|
Crystal structure of catalytic inactive chloroplast
resolvase ntmoc1 in complex with holliday junction .
SNAP output
|
|
6ldi
|
transcription (DNA to RNA) |
cryo-EM (3.69 Å) |
Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu
J, Feng Y, O'Halloran TV, Zhang Y |
(2021) "CueR
activates transcription through a DNA distortion
mechanism." Nat.Chem.Biol.,
17, 57-64. doi: 10.1038/s41589-020-00653-x.
|
The cryo-EM structure of e. coli cuer transcription
activation complex . SNAP output
|
|
6ldm
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Traczyk A, Liew CW, Gill DJ, Rhodes D |
(2020) "Structural
basis of G-quadruplex DNA recognition by the yeast
telomeric protein Rap1." Nucleic Acids
Res., 48, 4562-4571. doi:
10.1093/nar/gkaa171.
|
Structural basis of g-quadruplex DNA recognition by the
yeast telomeric protein rap1 . SNAP output
|
|
6le9
|
DNA binding protein-DNA |
X-ray (2.6 Å) |
Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V,
Korolev N, Rhodes D, Nordenskiold L |
(2020) "The
human telomeric nucleosome displays distinct structural
and dynamic properties." Nucleic Acids
Res., 48, 5383-5396. doi:
10.1093/nar/gkaa289.
|
The human telomeric nucleosome displays distinct
structural and dynamic properties . SNAP output
|
|
6ler
|
DNA binding protein |
X-ray (3.0 Å) |
Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S,
Shum WK, Davey GE, Davey CA |
(2021) "Engineering
nucleosomes for generating diverse chromatin
assemblies." Nucleic Acids Res.,
49, e52. doi: 10.1093/nar/gkab070.
|
169 bp nucleosome harboring non-identical cohesive DNA
termini. . SNAP
output
|
|
6lew
|
DNA binding protein-DNA |
X-ray (2.48 Å) |
Liu L, Yi C |
"RVD HA specifically contacts 5mC through van der
Waals interactions." |
Rvd ha specifically contacts 5mc through van der waals
interactions . SNAP
output
|
|
6lff
|
transcription-DNA |
X-ray (1.79 Å) |
Yamasaki K, Akutsu Y, Yamasaki T, Miyagishi M, Kubota
T |
(2020) "Enhanced
affinity of racemic phosphorothioate DNA with
transcription factor SATB1 arising from
diastereomer-specific hydrogen bonds and hydrophobic
contacts." Nucleic Acids Res.,
48, 4551-4561. doi: 10.1093/nar/gkaa170.
|
Transcription factor satb1 cutr1 domain in complex with
a phosphorothioate DNA . SNAP output
|
|
6lmj
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Liu R, Sun Y, Chai Y, Li S, Li S, Wang L, Su J, Yu S,
Yan J, Gao F, Zhang G, Qiu HJ, Gao GF, Qi J, Wang H |
(2020) "The
structural basis of African swine fever virus pA104R
binding to DNA and its inhibition by stilbene
derivatives." Proc.Natl.Acad.Sci.USA,
117, 11000-11009. doi: 10.1073/pnas.1922523117.
|
Asfv pa104r in complex with double-strand DNA .
SNAP output
|
|
6lmr
|
DNA binding protein |
NMR |
Zhang J, Fan JS, Li S, Yang Y, Sun P, Zhu Q, Wang J,
Jiang B, Yang D, Liu M |
(2020) "Structural
basis of DNA binding to human YB-1 cold shock domain
regulated by phosphorylation." Nucleic Acids
Res., 48, 9361-9371. doi:
10.1093/nar/gkaa619.
|
Solution structure of cold shock domain and ssDNA
complex . SNAP
output
|
|
6lnb
|
immune system |
cryo-EM (3.18 Å) |
Wang B, Xu W, Yang H |
(2020) "Structural
basis of a Tn7-like transposase recruitment and DNA
loading to CRISPR-Cas surveillance complex."
Cell Res., 30, 185-187. doi:
10.1038/s41422-020-0274-0.
|
Cryoem structure of cascade-tniq-dsDNA complex .
SNAP output
|
|
6lqf
|
gene regulation |
X-ray (1.5 Å) |
Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y,
Chen L, Du X, Li S, Shao CR, Su YN, Cai XW, Lin RN, Li L,
Chen S, Du J, He XJ |
(2020) "Dual
Recognition of H3K4me3 and DNA by the ISWI Component
ARID5 Regulates the Floral Transition in
Arabidopsis." Plant Cell,
32, 2178-2195. doi: 10.1105/tpc.19.00944.
|
Crystal structure of arabidopsis arid5 arid-phd
cassette in complex with h3k4me3 peptide and DNA .
SNAP output
|
|
6lrd
|
DNA binding protein-DNA |
X-ray (1.9 Å) |
Cheng K, Xu Y, Chen X, Lu H, He Y, Wang L, Hua Y |
(2020) "Participation
of RecJ in the base excision repair pathway of
Deinococcus radiodurans." Nucleic Acids
Res., 48, 9859-9871. doi:
10.1093/nar/gkaa714.
|
Structure of recj complexed with a
5'-p-dspacer-modified ssDNA . SNAP output
|
|
6ltj
|
gene regulation |
cryo-EM (3.7 Å) |
He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, Li J, Liu B,
Xu Y |
(2020) "Structure
of nucleosome-bound human BAF complex."
Science, 367, 875-881. doi:
10.1126/science.aaz9761.
|
Structure of nucleosome-bound human baf complex .
SNAP output
|
|
6ltr
|
hydrolase-RNA-DNA |
X-ray (2.51 Å) |
Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng
G, Gong W, Wang Y |
(2020) "Structural
basis for two metal-ion catalysis of DNA cleavage by
Cas12i2." Nat Commun, 11,
5241. doi: 10.1038/s41467-020-19072-6.
|
Crystal structure of cas12i2 ternary complex with
single mg2+ bound in catalytic pocket . SNAP output
|
|
6lts
|
transcription |
X-ray (3.45 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Crystal structure of thermus thermophilus transcription
initiation complex comprising a truncated sigma finger
. SNAP output
|
|
6ltu
|
hydrolase-RNA-DNA |
X-ray (2.57 Å) |
Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng
G, Gong W, Wang Y |
(2020) "Structural
basis for two metal-ion catalysis of DNA cleavage by
Cas12i2." Nat Commun, 11,
5241. doi: 10.1038/s41467-020-19072-6.
|
Crystal structure of cas12i2 ternary complex with
double mg2+ bound in catalytic pocket . SNAP output
|
|
6lty
|
antitoxin, DNA binding protein-DNA |
X-ray (3.28 Å) |
Park JY, Kim HJ, Pathak C, Yoon HJ, Kim DH, Park SJ,
Lee BJ |
(2020) "Induced
DNA bending by unique dimerization of HigA
antitoxin." Iucrj, 7,
748-760. doi: 10.1107/S2052252520006466.
|
DNA bound antitoxin higa3 . SNAP output
|
|
6lu0
|
hydrolase-RNA-DNA |
X-ray (3.22 Å) |
Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng
G, Gong W, Wang Y |
(2020) "Structural
basis for two metal-ion catalysis of DNA cleavage by
Cas12i2." Nat Commun, 11,
5241. doi: 10.1038/s41467-020-19072-6.
|
Crystal structure of cas12i2 ternary complex with 12 nt
spacer . SNAP output
|
|
6lui
|
DNA binding protein |
X-ray (1.781 Å) |
Stielow B, Zhou Y, Cao Y, Simon C, Pogoda HM, Jiang
J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T,
Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R |
(2021) "The SAM
domain-containing protein 1 (SAMD1) acts as a
repressive chromatin regulator at unmethylated CpG
islands." Sci Adv, 7.
doi: 10.1126/sciadv.abf2229.
|
Crystal structure of the samd1 wh domain and DNA
complex . SNAP
output
|
|
6lwa
|
DNA binding protein-DNA |
X-ray (2.76 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, k242) bound
to duplex DNA containing 5-hydroxyuracil (5-ohu) .
SNAP output
|
|
6lwb
|
DNA binding protein-DNA |
X-ray (2.55 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, r242) bound
to duplex DNA containing 5-hydroxyuracil (5-ohu) .
SNAP output
|
|
6lwc
|
DNA binding protein-DNA |
X-ray (2.91 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, k242) bound
to duplex DNA containing spiroiminodihydantoin (sp) .
SNAP output
|
|
6lwd
|
DNA binding protein-DNA |
X-ray (2.41 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, r242) bound
to duplex DNA containing spiroiminodihydantoin (sp) .
SNAP output
|
|
6lwf
|
DNA binding protein-DNA |
X-ray (2.79 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, k242) bound
to duplex DNA containing guanidinohydantoin (gh) .
SNAP output
|
|
6lwg
|
DNA binding protein-DNA |
X-ray (2.53 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, r242) bound
to duplex DNA containing guanidinohydantoin (gh) .
SNAP output
|
|
6lwh
|
DNA binding protein-DNA |
X-ray (2.78 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, k242) bound
to duplex DNA containing dihydrothymine (dht) .
SNAP output
|
|
6lwi
|
DNA binding protein-DNA |
X-ray (2.72 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, r242) bound
to duplex DNA containing dihydrothymine (dht) .
SNAP output
|
|
6lwj
|
DNA binding protein-DNA |
X-ray (2.83 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, k242) bound
to duplex DNA containing dihydrouracil (dhu) . SNAP output
|
|
6lwk
|
DNA binding protein-DNA |
X-ray (2.88 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(p2g, e3q, r242) bound
to duplex DNA containing dihydrouracil (dhu) . SNAP output
|
|
6lwl
|
DNA binding protein-DNA |
X-ray (2.55 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(r242) bound to duplex
DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine .
SNAP output
|
|
6lwm
|
DNA binding protein-DNA |
X-ray (2.67 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(k242) bound to duplex
DNA containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine .
SNAP output
|
|
6lwn
|
DNA binding protein-DNA |
X-ray (2.74 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(r242, g249p) bound to
duplex DNA containing
2'-fluoro-2'-deoxy-5,6-dihydrouridine . SNAP output
|
|
6lwo
|
DNA binding protein-DNA |
X-ray (2.51 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(r242, y244h) bound to
duplex DNA containing
2'-fluoro-2'-deoxy-5,6-dihydrouridine . SNAP output
|
|
6lwp
|
DNA binding protein-DNA |
X-ray (2.64 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(r242, y244r) bound to
duplex DNA containing
2'-fluoro-2'-deoxy-5,6-dihydrouridine . SNAP output
|
|
6lwq
|
DNA binding protein |
X-ray (2.89 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(r242) bound to duplex
DNA containing a c:t mismatch . SNAP output
|
|
6lwr
|
DNA binding protein-DNA |
X-ray (2.9 Å) |
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L,
Zeng H, Gao YQ, Yi C |
(2021) "DNA
repair glycosylase hNEIL1 triages damaged bases via
competing interaction modes." Nat Commun,
12, 4108. doi: 10.1038/s41467-021-24431-y.
|
Crystal structure of human neil1(k242) bound to duplex
DNA containing a cleaved c:t mismatch . SNAP output
|
|
6lxn
|
DNA binding protein |
X-ray (2.93 Å) |
Sadotra S, Lou YC, Tang HC, Chiu YC, Hsu CH, Chen
C |
(2020) "Structural
basis for promoter DNA recognition by the response
regulator OmpR." J.Struct.Biol.,
213, 107638. doi: 10.1016/j.jsb.2020.107638.
|
Crystal structure of c-terminal DNA-binding domain of
escherichia coli ompr in complex with f1-DNA . SNAP output
|
|
6m0v
|
hydrolase-DNA-RNA |
X-ray (3.0 Å) |
Zhang Y, Zhang H, Xu X, Wang Y, Chen W, Wang Y, Wu Z,
Tang N, Wang Y, Zhao S, Gan J, Ji Q |
(2020) "Catalytic-state structure and engineering of
Streptococcus thermophilus Cas9." Nat Catal.
doi: 10.1038/s41929-020-00506-9.
|
Crsytal structure of streptococcus thermophilus cas9 in
complex with the ggaa pam . SNAP output
|
|
6m0w
|
hydrolase-DNA-RNA |
X-ray (2.76 Å) |
Zhang Y, Zhang H, Xu X, Wang Y, Chen W, Wang Y, Wu Z,
Tang N, Wang Y, Zhao S, Gan J, Ji Q |
(2020) "Catalytic-state structure and engineering of
Streptococcus thermophilus Cas9." Nat Catal.
doi: 10.1038/s41929-020-00506-9.
|
Crystal structure of streptococcus thermophilus cas9 in
complex with the agaa pam . SNAP output
|
|
6m0x
|
DNA binding protein |
X-ray (2.561 Å) |
Zhang Y, Zhang H, Xu X, Wang Y, Chen W, Wang Y, Wu Z,
Tang N, Wang Y, Zhao S, Gan J, Ji Q |
(2020) "Catalytic-state structure and engineering of
Streptococcus thermophilus Cas9." Nat Catal.
doi: 10.1038/s41929-020-00506-9.
|
Crystal structure of streptococcus thermophilus cas9 in
complex with agga pam . SNAP output
|
|
6m2v
|
DNA binding protein-DNA |
X-ray (3.0 Å) |
Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara
E |
(2021) "Mechanistic
insights into recognition of symmetric methylated
cytosines in CpG and non-CpG DNA by UHRF1 SRA."
Int.J.Biol.Macromol., 170,
514-522. doi: 10.1016/j.ijbiomac.2020.12.149.
|
Crystal structure of uhrf1 sra complexed with
fully-mchg DNA. . SNAP
output
|
|
6m3d
|
DNA binding protein-DNA |
X-ray (1.6 Å) |
Sunami T, Hirano Y, Tamada T, Kono H |
(2020) "Structural
basis for designing an array of engrailed
homeodomains." Acta Crystallogr D Struct
Biol, 76, 824-833. doi: 10.1107/S2059798320009237.
|
X-ray crystal structure of tandemly connected engrailed
homeodomains (ehd) with r53a mutations and DNA complex
. SNAP output
|
|
6m3l
|
hydrolase-DNA |
X-ray (2.75 Å) |
Miyazono KI, Wang D, Ito T, Tanokura M |
(2020) "Distortion
of double-stranded DNA structure by the binding of the
restriction DNA glycosylase R.PabI." Nucleic
Acids Res., 48, 5106-5118. doi:
10.1093/nar/gkaa184.
|
Crystal structure of the
r.pabi(y68f-k154a)-dsDNA(nonspecific) complex .
SNAP output
|
|
6m3v
|
DNA binding protein |
X-ray (4.6 Å) |
Adhireksan Z, Sharma D, Lee PL, Davey CA |
(2020) "Near-atomic
resolution structures of interdigitated nucleosome
fibres." Nat Commun, 11,
4747. doi: 10.1038/s41467-020-18533-2.
|
355 bp di-nucleosome harboring cohesive DNA termini .
SNAP output
|
|
6m44
|
DNA binding protein |
X-ray (3.81 Å) |
Adhireksan Z, Sharma D, Lee PL, Davey CA |
(2020) "Near-atomic
resolution structures of interdigitated nucleosome
fibres." Nat Commun, 11,
4747. doi: 10.1038/s41467-020-18533-2.
|
355 bp di-nucleosome harboring cohesive DNA termini
(high cryoprotectant) . SNAP output
|
|
6m4d
|
nuclear protein |
cryo-EM (4.4 Å) |
Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu
P, Zhou Z |
(2021) "Structural
basis of nucleosome dynamics modulation by histone
variants H2A.B and H2A.Z.2.2." Embo J.,
40, e105907. doi: 10.15252/embj.2020105907.
|
Structural mechanism of nucleosome dynamics governed by
human histone variants h2a.b and h2a.z.2.2 . SNAP output
|
|
6m4g
|
nuclear protein |
cryo-EM (2.8 Å) |
Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu
P, Zhou Z |
(2021) "Structural
basis of nucleosome dynamics modulation by histone
variants H2A.B and H2A.Z.2.2." Embo J.,
40, e105907. doi: 10.15252/embj.2020105907.
|
Structural mechanism of nucleosome dynamics governed by
human histone variants h2a.b and h2a.z.2.2 . SNAP output
|
|
6m4h
|
nuclear protein |
cryo-EM (3.9 Å) |
Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu
P, Zhou Z |
(2021) "Structural
basis of nucleosome dynamics modulation by histone
variants H2A.B and H2A.Z.2.2." Embo J.,
40, e105907. doi: 10.15252/embj.2020105907.
|
Structural mechanism of nucleosome dynamics governed by
human histone variants h2a.b and h2a.z.2.2 . SNAP output
|
|
6m6a
|
transcription |
cryo-EM (5.0 Å) |
Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S,
Hua X, Zhang Y, Feng Y |
(2020) "Structural
basis of Mfd-dependent transcription termination."
Nucleic Acids Res., 48,
11762-11772. doi: 10.1093/nar/gkaa904.
|
cryo-EM structure of thermus thermophilus mfd in
complex with RNA polymerase . SNAP output
|
|
6m6b
|
transcription |
cryo-EM (4.1 Å) |
Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S,
Hua X, Zhang Y, Feng Y |
(2020) "Structural
basis of Mfd-dependent transcription termination."
Nucleic Acids Res., 48,
11762-11772. doi: 10.1093/nar/gkaa904.
|
cryo-EM structure of thermus thermophilus mfd in
complex with RNA polymerase and atp-gamma-s . SNAP output
|
|
6m6c
|
transcription |
cryo-EM (3.1 Å) |
Shi J, Wen A, Zhao M, Jin S, You L, Shi Y, Dong S,
Hua X, Zhang Y, Feng Y |
(2020) "Structural
basis of Mfd-dependent transcription termination."
Nucleic Acids Res., 48,
11762-11772. doi: 10.1093/nar/gkaa904.
|
Cryoem structure of thermus thermophilus RNA polymerase
elongation complex . SNAP output
|
|
6m75
|
DNA binding protein-DNA |
X-ray (2.57 Å) |
Aggarwal P, Bhavesh NS |
(2021) "Hinge
like domain motion facilitates human RBMS1 protein
binding to proto-oncogene c-myc promoter."
Nucleic Acids Res., 49,
5943-5955. doi: 10.1093/nar/gkab363.
|
C-myc DNA binding protein complex . SNAP output
|
|
6m7j
|
transcription |
cryo-EM (4.4 Å) |
Boyaci H, Chen J, Jansen R, Darst SA, Campbell
EA |
(2019) "Structures
of an RNA polymerase promoter melting intermediate
elucidate DNA unwinding." Nature,
565, 382-385. doi: 10.1038/s41586-018-0840-5.
|
Mycobacterium tuberculosis rnap with rbpa-us fork and
corallopyronin . SNAP
output
|
|
6m7o
|
transferase-DNA |
X-ray (3.0 Å) |
Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang
W |
(2018) "Bypassing
a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA
polymerase eta at atomic resolution." Proc.
Natl. Acad. Sci. U.S.A., 115,
10660-10665. doi: 10.1073/pnas.1812856115.
|
Human DNA polymerase eta ternary complex with mn2+ and
dtmpnpp oppositing cda . SNAP output
|
|
6m7p
|
transferase-DNA |
X-ray (1.75 Å) |
Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang
W |
(2018) "Bypassing
a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA
polymerase eta at atomic resolution." Proc.
Natl. Acad. Sci. U.S.A., 115,
10660-10665. doi: 10.1073/pnas.1812856115.
|
Human DNA polymerase eta extension complex with cda at
the -2 position . SNAP
output
|
|
6m7t
|
transferase-DNA |
X-ray (2.8 Å) |
Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang
W |
(2018) "Bypassing
a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA
polymerase eta at atomic resolution." Proc.
Natl. Acad. Sci. U.S.A., 115,
10660-10665. doi: 10.1073/pnas.1812856115.
|
Human DNA polymerase eta in a non-productive ternary
complex with ca2+ and dttp oppositing cda . SNAP output
|
|
6m7u
|
transferase-DNA |
X-ray (3.4 Å) |
Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang
W |
(2018) "Bypassing
a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA
polymerase eta at atomic resolution." Proc.
Natl. Acad. Sci. U.S.A., 115,
10660-10665. doi: 10.1073/pnas.1812856115.
|
Human DNA polymerase eta in a non-productive ternary
complex with mg2+ and dtmpnpp oppositing cda . SNAP output
|
|
6m7v
|
transferase-DNA |
X-ray (3.062 Å) |
Weng PJ, Gao Y, Gregory MT, Wang P, Wang Y, Yang
W |
(2018) "Bypassing
a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA
polymerase eta at atomic resolution." Proc.
Natl. Acad. Sci. U.S.A., 115,
10660-10665. doi: 10.1073/pnas.1812856115.
|
Human DNA polymerase eta extension complex with cda at
the -1 position . SNAP
output
|
|
6mdz
|
hydrolase-RNA |
X-ray (3.4 Å) |
Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S,
Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ |
(2019) "Structural
Basis for Target-Directed MicroRNA Degradation."
Mol.Cell, 75, 1243-1255.e7.
doi: 10.1016/j.molcel.2019.06.019.
|
Human argonaute2-mir-122 bound to a target RNA with two
central mismatches (bu2) . SNAP output
|
|
6me0
|
RNA-DNA-nucleic acid binding protein |
cryo-EM (3.6 Å) |
Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker
TS, Toor N |
(2019) "Cryo-EM
Structures of a Group II Intron Reverse Splicing into
DNA." Cell, 178,
612-623.e12. doi: 10.1016/j.cell.2019.06.035.
|
Structure of a group ii intron retroelement prior to
DNA integration . SNAP
output
|
|
6mec
|
RNA-DNA-RNA binding protein |
cryo-EM (3.6 Å) |
Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker
TS, Toor N |
(2019) "Cryo-EM
Structures of a Group II Intron Reverse Splicing into
DNA." Cell, 178,
612-623.e12. doi: 10.1016/j.cell.2019.06.035.
|
Structure of a group ii intron retroelement after DNA
integration . SNAP
output
|
|
6mfr
|
hydrolase-RNA |
X-ray (3.6 Å) |
Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S,
Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ |
(2019) "Structural
Basis for Target-Directed MicroRNA Degradation."
Mol.Cell, 75, 1243-1255.e7.
doi: 10.1016/j.molcel.2019.06.019.
|
Human argonaute2-mir-122 bound to a target RNA with
three central mismatches (bu3) . SNAP output
|
|
6mg1
|
transcription-DNA |
X-ray (1.75 Å) |
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang
Y, Zhang X, Blumenthal RM, Cheng X |
(2019) "Structural
basis for effects of CpA modifications on C/EBP beta
binding of DNA." Nucleic Acids Res.,
47, 1774-1785. doi: 10.1093/nar/gky1264.
|
C-terminal bzip domain of human c-ebpbeta with 16bp
methylated oligonucleotide containing consensus
recognition sequence-c2 crystal form . SNAP output
|
|
6mg2
|
transcription-DNA |
X-ray (1.928 Å) |
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang
Y, Zhang X, Blumenthal RM, Cheng X |
(2019) "Structural
basis for effects of CpA modifications on C/EBP beta
binding of DNA." Nucleic Acids Res.,
47, 1774-1785. doi: 10.1093/nar/gky1264.
|
C-terminal bzip domain of human c-ebpbeta with 16bp
methylated oligonucleotide containing consensus
recognition sequence-c2221 crystal form . SNAP output
|
|
6mg3
|
transcription-DNA |
X-ray (2.05 Å) |
Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang
Y, Zhang X, Blumenthal RM, Cheng X |
(2019) "Structural
basis for effects of CpA modifications on C/EBP beta
binding of DNA." Nucleic Acids Res.,
47, 1774-1785. doi: 10.1093/nar/gky1264.
|
V285a mutant of the c-terminal bzip domain of human
c-ebpbeta with 16bp methylated oligonucleotide
containing consensus recognition sequence . SNAP output
|
|
6mht
|
transferase-DNA |
X-ray (2.05 Å) |
Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ,
Cheng X |
(1997) "DNA
containing 4'-thio-2'-deoxycytidine inhibits
methylation by HhaI methyltransferase." Nucleic
Acids Res., 25, 2773-2783. doi:
10.1093/nar/25.14.2773.
|
Ternary structure of hhai methyltransferase with adohcy
and DNA containing 4'-thio-2'deoxycytidine at the
target . SNAP output
|
|
6mig
|
hydrolase-DNA |
X-ray (1.7 Å) |
Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim
HJ, Bates AM, Watkins Jr NE, SantaLucia HA, Meyer AJ,
DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr J,
Georgiadis MM, Benner SA |
(2019) "Hachimoji
DNA and RNA: A genetic system with eight building
blocks." Science, 363,
884-887. doi: 10.1126/science.aat0971.
|
Crystal structure of host-guest complex with pb
hachimoji DNA . SNAP
output
|
|
6mih
|
hydrolase-DNA |
X-ray (1.6 Å) |
Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim
HJ, Bates AM, Watkins Jr NE, SantaLucia HA, Meyer AJ,
DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr J,
Georgiadis MM, Benner SA |
(2019) "Hachimoji
DNA and RNA: A genetic system with eight building
blocks." Science, 363,
884-887. doi: 10.1126/science.aat0971.
|
Crystal structure of host-guest complex with pc
hachimoji DNA . SNAP
output
|
|
6mii
|
hydrolase-DNA |
X-ray (3.15 Å) |
Meagher M, Epling LB, Enemark EJ |
(2019) "DNA
translocation mechanism of the MCM complex and
implications for replication initiation." Nat
Commun, 10, 3117. doi: 10.1038/s41467-019-11074-3.
|
Crystal structure of minichromosome maintenance protein
mcm-DNA complex . SNAP
output
|
|
6mik
|
hydrolase-DNA |
X-ray (1.7 Å) |
Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim
HJ, Bates AM, Watkins Jr NE, SantaLucia HA, Meyer AJ,
DasGupta S, Piccirilli JA, Ellington AD, SantaLucia Jr J,
Georgiadis MM, Benner SA |
(2019) "Hachimoji
DNA and RNA: A genetic system with eight building
blocks." Science, 363,
884-887. doi: 10.1126/science.aat0971.
|
Crystal structure of host-guest complex with pp
hachimoji DNA . SNAP
output
|
|
6ml2
|
transcription-DNA |
X-ray (1.874 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 1) . SNAP output
|
|
6ml3
|
transcription-DNA |
X-ray (1.683 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 2) . SNAP output
|
|
6ml4
|
transcription-DNA |
X-ray (1.482 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Btb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide
(sequence 3) . SNAP
output
|
|
6ml5
|
transcription-DNA |
X-ray (1.65 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 4) . SNAP output
|
|
6ml6
|
transcription-DNA |
X-ray (1.54 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 4 with a cpa 5mc
modification) . SNAP
output
|
|
6ml7
|
transcription-DNA |
X-ray (1.75 Å) |
Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK,
Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H,
Zhang X, Chen T, Cheng X |
(2019) "Structural
basis of specific DNA binding by the transcription
factor ZBTB24." Nucleic Acids Res.,
47, 8388-8398. doi: 10.1093/nar/gkz557.
|
Zbtb24 zinc fingers 4-8 with 19+1mer DNA
oligonucleotide (sequence 4 with a cpg 5mc
modification) . SNAP
output
|
|
6mp3
|
transferase-DNA |
X-ray (1.907 Å) |
Hawkins MA, Hunmin J, Lee S |
"Structural Analysis of Translesion Synthesis Across
Hypoxanthine Lesion Using Human DNA Polymerase Eta." |
Binary structure of DNA polymerase eta in complex with
templating hypoxanthine . SNAP output
|
|
6mq8
|
transferase-DNA |
X-ray (1.969 Å) |
Jung H, Hawkins M, Lee S |
(2020) "Structural
insights into the bypass of the major deaminated
purines by translesion synthesis DNA polymerase."
Biochem.J. doi: 10.1042/BCJ20200800.
|
Binary structure of DNA polymerase eta in complex with
templating hypoxanthine . SNAP output
|
|
6mr7
|
DNA binding protein-DNA |
X-ray (2.144 Å) |
Smith MR, Shock DD, Beard WA, Greenberg MM,
Freudenthal BD, Wilson SH |
(2019) "A
guardian residue hinders insertion of a Fapy•dGTP
analog by modulating the open-closed DNA polymerase
transition." Nucleic Acids Res.,
47, 3197-3207. doi: 10.1093/nar/gkz002.
|
DNA polymerase beta substrate complex with templating
adenine and incoming fapy-dgtp analog . SNAP output
|
|
6mr8
|
DNA binding protein-DNA |
X-ray (1.897 Å) |
Smith MR, Shock DD, Beard WA, Greenberg MM,
Freudenthal BD, Wilson SH |
(2019) "A
guardian residue hinders insertion of a Fapy•dGTP
analog by modulating the open-closed DNA polymerase
transition." Nucleic Acids Res.,
47, 3197-3207. doi: 10.1093/nar/gkz002.
|
D276g DNA polymerase beta substrate complex with
templating adenine and incoming fapy-dgtp analog .
SNAP output
|
|
6mrj
|
DNA binding protein-DNA |
X-ray (2.8 Å) |
Pozharski E, de Serrano V |
"Crystal structure of H.pylori NikR in complex with
DNA." |
Crystal structure of h.pylori nikr in complex with DNA
. SNAP output
|
|
6mu4
|
transferase-DNA |
X-ray (1.62 Å) |
Jackson LN, Chim N, Shi C, Chaput JC |
(2019) "Crystal
structures of a natural DNA polymerase that functions
as an XNA reverse transcriptase." Nucleic Acids
Res., 47, 6973-6983. doi:
10.1093/nar/gkz513.
|
Bst DNA polymerase i fana-DNA binary complex . SNAP output
|
|
6mu5
|
transferase-DNA |
X-ray (1.912 Å) |
Jackson LN, Chim N, Shi C, Chaput JC |
(2019) "Crystal
structures of a natural DNA polymerase that functions
as an XNA reverse transcriptase." Nucleic Acids
Res., 47, 6973-6983. doi:
10.1093/nar/gkz513.
|
Bst DNA polymerase i tna-DNA binary complex . SNAP output
|
|
6muo
|
nuclear protein |
cryo-EM (3.6 Å) |
Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M,
Braitbard M, Xu C, Kalisman N, Murakami K, Black BE |
(2019) "Structure
of the Human Core Centromeric Nucleosome Complex."
Curr.Biol., 29, 2625-2639.e5.
doi: 10.1016/j.cub.2019.06.062.
|
Cenp-a nucleosome bound by two copies of cenp-c(cd) and
one copy cenp-n(nt) . SNAP output
|
|
6mup
|
nuclear protein |
cryo-EM (3.5 Å) |
Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M,
Braitbard M, Xu C, Kalisman N, Murakami K, Black BE |
(2019) "Structure
of the Human Core Centromeric Nucleosome Complex."
Curr.Biol., 29, 2625-2639.e5.
doi: 10.1016/j.cub.2019.06.062.
|
Cenp-a nucleosome bound by two copies of cenp-c(cd) and
two copies cenp-n(nt) . SNAP output
|
|
6mxo
|
nuclear protein-DNA |
X-ray (2.04 Å) |
Ouzon-Shubeita H, Baker M, Koag MC, Lee S |
(2019) "Structural
basis for the bypass of the major oxaliplatin-DNA
adducts by human DNA polymerase eta." Biochem.
J., 476, 747-758. doi: 10.1042/BCJ20180848.
|
Structure of hpoleta incorporating dctp opposite the
3-prime pt(dach)-gg . SNAP output
|
|
6mzm
|
transcription-DNA |
cryo-EM (7.5 Å) |
Patel AB, Louder RK, Greber BJ, Grunberg S, Luo J,
Fang J, Liu Y, Ranish J, Hahn S, Nogales E |
(2018) "Structure
of human TFIID and mechanism of TBP loading onto
promoter DNA." Science,
362. doi: 10.1126/science.aau8872.
|
Human tfiid bound to promoter DNA and tfiia . SNAP output
|
|
6n1p
|
isomerase-DNA |
cryo-EM (6.35 Å) |
Soczek KM, Grant T, Rosenthal PB, Mondragon A |
(2018) "CryoEM
structures of open dimers of Gyrase A in complex with
DNA illuminate mechanism of strand passage."
Elife, 7. doi: 10.7554/eLife.41215.
|
Dihedral oligomeric complex of gyra n-terminal fragment
with DNA, solved by cryoem in c2 symmetry . SNAP output
|
|
6n2r
|
gene regulation-DNA |
X-ray (2.1 Å) |
Howard MJ, Foley KG, Shock DD, Batra VK, Wilson
SH |
(2019) "Molecular
basis for the faithful replication of 5-methylcytosine
and its oxidized forms by DNA polymerase beta."
J.Biol.Chem., 294, 7194-7201.
doi: 10.1074/jbc.RA118.006809.
|
Binary complex crystal structure of DNA polymerase beta
with 5-carboxy-dc (5-cac) at the templating position .
SNAP output
|
|
6n2s
|
gene regulation-DNA |
X-ray (2.457 Å) |
Howard MJ, Foley KG, Shock DD, Batra VK, Wilson
SH |
(2019) "Molecular
basis for the faithful replication of 5-methylcytosine
and its oxidized forms by DNA polymerase beta."
J.Biol.Chem., 294, 7194-7201.
doi: 10.1074/jbc.RA118.006809.
|
Ternary complex crystal structure of DNA polymerase
beta with 5-carboxy-dc (5-cac) at the templating
position . SNAP
output
|
|
6n2t
|
gene regulation-DNA |
X-ray (2.6 Å) |
Howard MJ, Foley KG, Shock DD, Batra VK, Wilson
SH |
(2019) "Molecular
basis for the faithful replication of 5-methylcytosine
and its oxidized forms by DNA polymerase beta."
J.Biol.Chem., 294, 7194-7201.
doi: 10.1074/jbc.RA118.006809.
|
Ternary complex crystal structure of DNA polymerase
beta with 5-hydroxymethyl-dc (5-hmc) at the templating
position . SNAP
output
|
|
6n4c
|
transcription-DNA |
cryo-EM (17.0 Å) |
Sosa R, Florez-Ariza A, Diaz-Celis C, Onoa B, Cassago
A, de Oliveira PSL, Portugal RV, Guerra DG, Bustamante
C |
(2020) "Interactions of Upstream and Downstream
Promoter Regions with RNA Polymerase are Energetically
Coupled and a Target of Regulation in Transcription
Initiation." Biorxiv. doi: 10.1101/2020.05.13.070375.
|
Em structure of the DNA wrapping in bacterial open
transcription initiation complex . SNAP output
|
|
6n60
|
transferase-DNA |
X-ray (3.68 Å) |
Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link
AJ, Darst SA |
(2019) "Structural
mechanism of transcription inhibition by lasso peptides
microcin J25 and capistruin." Proc. Natl. Acad.
Sci. U.S.A., 116, 1273-1278. doi:
10.1073/pnas.1817352116.
|
Escherichia coli RNA polymerase sigma70-holoenzyme
bound to upstream fork promoter DNA and microcin j25
(mccj25) . SNAP
output
|
|
6n61
|
transferase-DNA |
X-ray (3.253 Å) |
Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link
AJ, Darst SA |
(2019) "Structural
mechanism of transcription inhibition by lasso peptides
microcin J25 and capistruin." Proc. Natl. Acad.
Sci. U.S.A., 116, 1273-1278. doi:
10.1073/pnas.1817352116.
|
Escherichia coli RNA polymerase sigma70-holoenzyme
bound to upstream fork promoter DNA and capistruin .
SNAP output
|
|
6n62
|
transferase-DNA |
X-ray (3.803 Å) |
Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link
AJ, Darst SA |
(2019) "Structural
mechanism of transcription inhibition by lasso peptides
microcin J25 and capistruin." Proc. Natl. Acad.
Sci. U.S.A., 116, 1273-1278. doi:
10.1073/pnas.1817352116.
|
Escherichia coli RNA polymerase sigma70-holoenzyme
bound to upstream fork promoter DNA . SNAP output
|
|
6n7i
|
hydrolase,transferase-DNA |
cryo-EM (3.2 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 e343q mutant gp4
helicase-primase in complex with ssDNA, dttp, ac
dinucleotide and ctp (gp4(5)-DNA) . SNAP output
|
|
6n7n
|
hydrolase,transferase-DNA |
cryo-EM (3.5 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 e343q mutant gp4
helicase-primase in complex with ssDNA, dttp, ac
dinucleotide and ctp (form i) . SNAP output
|
|
6n7s
|
hydrolase,transferase-DNA |
cryo-EM (4.6 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 e343q mutant gp4
helicase-primase in complex with ssDNA, dttp, ac
dinucleotide and ctp (form ii) . SNAP output
|
|
6n7t
|
hydrolase,transferase-DNA |
cryo-EM (3.9 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 e343q mutant gp4
helicase-primase in complex with ssDNA, dttp, ac
dinucleotide and ctp (form iii) . SNAP output
|
|
6n7v
|
hydrolase,transferase-DNA |
cryo-EM (3.8 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 gp4 (helicase-primase,
e343q mutant) in complex with ssDNA, dttp, ac
dinucleotide, and ctp (from multiple lead complexes) .
SNAP output
|
|
6n7w
|
transferase-DNA |
cryo-EM (4.5 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 leading-strand DNA
polymerase (d5a-e7a)-trx in complex with a DNA fork and
incoming dttp (from multiple lead complexes) . SNAP output
|
|
6n9u
|
hydrolase,transferase-DNA |
cryo-EM (3.7 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 lagging-strand DNA
polymerase (d5a-e7a) interacting with primase domains
of two gp4 subunits bound to an RNA-DNA hybrid and dttp
(from lags1) . SNAP
output
|
|
6n9v
|
hydrolase,transferase-DNA |
cryo-EM (4.0 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 lagging-strand DNA
polymerase (d5a-e7a) and gp4 (helicase-primase) bound
to DNA including RNA-DNA hybrid, and an incoming dttp
(lags1) . SNAP
output
|
|
6n9w
|
hydrolase,transferase-DNA |
cryo-EM (4.0 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 lagging-strand DNA
polymerase (d5a-e7a) and gp4 (helicase-primase) bound
to DNA including RNA-DNA hybrid, and an incoming dttp
(lags2) . SNAP
output
|
|
6n9x
|
hydrolase,transferase-DNA |
cryo-EM (4.1 Å) |
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou
ZH, Yang W |
(2019) "Structures
and operating principles of the replisome."
Science, 363. doi: 10.1126/science.aav7003.
|
Structure of bacteriophage t7 lagging-strand DNA
polymerase (d5a-e7a) and gp4 (helicase-primase) bound
to DNA including RNA-DNA hybrid, and an incoming dttp
(lags3) . SNAP
output
|
|
6nce
|
DNA binding protein-DNA |
X-ray (2.598 Å) |
Rogers JM, Waters CT, Seegar TCM, Jarrett SM,
Hallworth AN, Blacklow SC, Bulyk ML |
(2019) "Bispecific
Forkhead Transcription Factor FoxN3 Recognizes Two
Distinct Motifs with Different DNA Shapes."
Mol. Cell, 74, 245. doi:
10.1016/j.molcel.2019.01.019.
|
Crystal structure of the human foxn3 DNA binding domain
in complex with a forkhead DNA sequence . SNAP output
|
|
6ncm
|
DNA binding protein-DNA |
X-ray (2.704 Å) |
Rogers JM, Waters CT, Seegar TCM, Jarrett SM,
Hallworth AN, Blacklow SC, Bulyk ML |
(2019) "Bispecific
Forkhead Transcription Factor FoxN3 Recognizes Two
Distinct Motifs with Different DNA Shapes."
Mol. Cell, 74, 245. doi:
10.1016/j.molcel.2019.01.019.
|
Crystal structure of the human foxn3 DNA binding domain
in complex with a forkhead-like (fhl) DNA sequence .
SNAP output
|
|
6ne0
|
immune system-RNA |
cryo-EM (3.4 Å) |
Rollins MF, Chowdhury S, Carter J, Golden SM,
Miettinen HM, Santiago-Frangos A, Faith D, Lawrence CM,
Lander GC, Wiedenheft B |
(2019) "Structure
Reveals a Mechanism of CRISPR-RNA-Guided Nuclease
Recruitment and Anti-CRISPR Viral Mimicry."
Mol. Cell, 74, 132-142.e5.
doi: 10.1016/j.molcel.2019.02.001.
|
Structure of double-stranded target DNA engaged csy
complex from pseudomonas aeruginosa (pa-14) . SNAP output
|
|
6ne3
|
DNA binding protein-DNA |
cryo-EM (3.9 Å) |
Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S,
Narlikar GJ, Cheng Y |
(2019) "Cryo-EM
structures of remodeler-nucleosome intermediates
suggest allosteric control through the nucleosome."
Elife, 8. doi: 10.7554/eLife.46057.
|
cryo-EM structure of singly-bound snf2h-nucleosome
complex with snf2h bound at shl-2 . SNAP output
|
|
6nit
|
RNA binding protein-RNA |
X-ray (3.8 Å) |
Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S,
Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ |
(2019) "Structural
Basis for Target-Directed MicroRNA Degradation."
Mol.Cell, 75, 1243-1255.e7.
doi: 10.1016/j.molcel.2019.06.019.
|
Human argonaute2-mir-122 bound to a target RNA with
four central mismatches (bu4) . SNAP output
|
|
6nj9
|
structural protein-transferase-DNA |
cryo-EM (2.96 Å) |
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C |
(2019) "Mechanism
of Cross-talk between H2B Ubiquitination and H3
Methylation by Dot1L." Cell,
176, 1490-1501.e12. doi: 10.1016/j.cell.2019.02.002.
|
Active state dot1l bound to the h2b-ubiquitinated
nucleosome, 2-to-1 complex . SNAP output
|
|
6njq
|
DNA binding protein-DNA |
X-ray (2.75 Å) |
Stelling AL, Liu AY, Zeng W, Salinas R, Schumacher
MA, Al-Hashimi HM |
(2019) "Infrared
Spectroscopic Observation of a G-C+Hoogsteen Base Pair
in the DNA:TATA-Box Binding Protein Complex Under
Solution Conditions."
Angew.Chem.Int.Ed.Engl., 58,
12010-12013. doi: 10.1002/anie.201902693.
|
Structure of tbp-hoogsteen containing DNA complex .
SNAP output
|
|
6nju
|
recombination |
X-ray (2.35 Å) |
Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho
PS |
(2020) "Structural
adaptation of vertebrate endonuclease G for
5-hydroxymethylcytosine recognition and function."
Nucleic Acids Res., 48,
3962-3974. doi: 10.1093/nar/gkaa117.
|
Mouse endonuclease g mutant h97a bound to a-DNA .
SNAP output
|
|
6nkr
|
transcription-DNA |
X-ray (2.45 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with dgtp . SNAP output
|
|
6nks
|
transcription-DNA |
X-ray (2.349 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with beta-gamma chf analog of dgtp
. SNAP output
|
|
6nkt
|
transcription-DNA |
X-ray (2.6 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with beta-gamma difluoro analogue
of dgtp . SNAP
output
|
|
6nku
|
transcription-DNA |
X-ray (1.9 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of DNA polymerase
beta with "hot-spot sequence" with dgtp . SNAP output
|
|
6nkv
|
transcription-DNA |
X-ray (1.85 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of DNA polymerase
beta with "hot-spot sequence" with beta-gamma chf
analogue of dgtp . SNAP
output
|
|
6nkw
|
transcription-DNA |
X-ray (1.98 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of DNA polymerase
beta with "hot-spot sequence" with beta-gamma-methylene
dgtp . SNAP output
|
|
6nkx
|
transcription-DNA |
X-ray (1.98 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with "hot-spot sequence" with dgtp
. SNAP output
|
|
6nky
|
transcription-DNA |
X-ray (2.094 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with "hot-spot sequence" with
beta-gamma chf analogue of dgtp . SNAP output
|
|
6nkz
|
transcription-DNA |
X-ray (2.01 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with "hot-spot sequence" with
beta-gamma methylene dgtp . SNAP output
|
|
6nl0
|
transcription-DNA |
X-ray (1.97 Å) |
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman
MF, Wilson SH |
(2020) "Revealing
an Internal Stabilization Deficiency in the DNA
Polymerase beta K289M Cancer Variant through the
Combined Use of Chemical Biology and X-ray
Crystallography." Biochemistry,
59, 955-963. doi: 10.1021/acs.biochem.9b01072.
|
Ternary complex crystal structure of k289m variant of
DNA polymerase beta with "hot-spot sequence" with
beta-gamma cf2 analogue of dgtp . SNAP output
|
|
6nn6
|
gene regulation |
cryo-EM (3.9 Å) |
Anderson CJ, Baird MR, Hsu A, Barbour EH, Koyama Y,
Borgnia MJ, McGinty RK |
(2019) "Structural
Basis for Recognition of Ubiquitylated Nucleosome by
Dot1L Methyltransferase." Cell Rep,
26, 1681-1690.e5. doi: 10.1016/j.celrep.2019.01.058.
|
Structure of dot1l-h2bk120ub nucleosome complex .
SNAP output
|
|
6nog
|
structural protein-transferase-DNA |
cryo-EM (3.9 Å) |
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C |
(2019) "Mechanism
of Cross-talk between H2B Ubiquitination and H3
Methylation by Dot1L." Cell,
176, 1490-1501.e12. doi: 10.1016/j.cell.2019.02.002.
|
Poised-state dot1l bound to the h2b-ubiquitinated
nucleosome . SNAP
output
|
|
6nqa
|
structural protein-transferase-DNA |
cryo-EM (3.54 Å) |
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C |
(2019) "Mechanism
of Cross-talk between H2B Ubiquitination and H3
Methylation by Dot1L." Cell,
176, 1490-1501.e12. doi: 10.1016/j.cell.2019.02.002.
|
Active state dot1l bound to the h2b-ubiquitinated
nucleosome, 1-to-1 complex . SNAP output
|
|
6nsm
|
transcription-DNA |
X-ray (2.8 Å) |
He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ,
Bahl CD, Hickman AB, Dyda F, Madden DR |
(2024) "Molecular
basis for the transcriptional regulation of an
epoxide-based virulence circuit in Pseudomonas
aeruginosa." Nucleic Acids Res. doi:
10.1093/nar/gkae889.
|
Tetr family transcriptional regulator cifr
c99t-c107s-c181r cysteines mutant complexed with 26bp
double-strand operator DNA . SNAP output
|
|
6nsn
|
transcription-DNA |
X-ray (2.6 Å) |
He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ,
Bahl CD, Hickman AB, Dyda F, Madden DR |
(2024) "Molecular
basis for the transcriptional regulation of an
epoxide-based virulence circuit in Pseudomonas
aeruginosa." Nucleic Acids Res. doi:
10.1093/nar/gkae889.
|
Tetr family transcriptional regulator cifr c99t-c181r
cysteines mutant complexed with 26bp double-strand
operator DNA . SNAP
output
|
|
6nsr
|
transcription-DNA |
X-ray (3.0 Å) |
He S, Taher NM, Simard AR, Hvorecny KL, Ragusa MJ,
Bahl CD, Hickman AB, Dyda F, Madden DR |
(2024) "Molecular
basis for the transcriptional regulation of an
epoxide-based virulence circuit in Pseudomonas
aeruginosa." Nucleic Acids Res. doi:
10.1093/nar/gkae889.
|
Tetr family transcriptional regulator cifr c99t-c181r
cysteine mutant complexed with 26bp double-strand
operator DNA and apo-cifr c99t-c181r . SNAP output
|
|
6nua
|
DNA binding protein-DNA |
X-ray (1.64 Å) |
Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman
BF |
(2019) "Protection
of abasic sites during DNA replication by a stable
thiazolidine protein-DNA cross-link."
Nat.Struct.Mol.Biol., 26,
613-618. doi: 10.1038/s41594-019-0255-5.
|
DNA-protein crosslink between e. coli yedk and ssDNA
containing an abasic site . SNAP output
|
|
6nuh
|
DNA binding protein-DNA |
X-ray (1.594 Å) |
Thompson PS, Amidon KM, Mohni KN, Cortez D, Eichman
BF |
(2019) "Protection
of abasic sites during DNA replication by a stable
thiazolidine protein-DNA cross-link."
Nat.Struct.Mol.Biol., 26,
613-618. doi: 10.1038/s41594-019-0255-5.
|
Non-covalent DNA-protein complex between e. coli yedk
and ssDNA containing an abasic site analog . SNAP output
|
|
6ny1
|
RNA binding protein-RNA-DNA |
cryo-EM (4.2 Å) |
Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney
KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb
B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais
J, Nogales E, Doudna JA |
(2019) "CasX
enzymes comprise a distinct family of RNA-guided genome
editors." Nature, 566,
218-223. doi: 10.1038/s41586-019-0908-x.
|
Casx-grna-DNA(30bp) state ii . SNAP output
|
|
6ny2
|
RNA binding protein-RNA-DNA |
cryo-EM (3.2 Å) |
Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney
KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb
B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais
J, Nogales E, Doudna JA |
(2019) "CasX
enzymes comprise a distinct family of RNA-guided genome
editors." Nature, 566,
218-223. doi: 10.1038/s41586-019-0908-x.
|
Casx-grna-DNA(45bp) state i . SNAP output
|
|
6ny3
|
RNA binding protein-RNA-DNA |
cryo-EM (3.7 Å) |
Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney
KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb
B, Wagner A, Brotzmann J, Staahl BT, Taylor KL, Desmarais
J, Nogales E, Doudna JA |
(2019) "CasX
enzymes comprise a distinct family of RNA-guided genome
editors." Nature, 566,
218-223. doi: 10.1038/s41586-019-0908-x.
|
Casx ternary complex with 30bp target DNA . SNAP output
|
|
6nzo
|
gene regulation |
cryo-EM (3.8 Å) |
Bilokapic S, Halic M |
(2019) "Nucleosome
and ubiquitin position Set2 to methylate H3K36."
Nat Commun, 10, 3795. doi:
10.1038/s41467-019-11726-4.
|
Set2 bound to nucleosome . SNAP output
|
|
6o0x
|
hydrolase-RNA-DNA |
cryo-EM (3.28 Å) |
Zhu X, Clarke R, Puppala AK, Chittori S, Merk A,
Merrill BJ, Simonovic M, Subramaniam S |
(2019) "Cryo-EM
structures reveal coordinated domain motions that
govern DNA cleavage by Cas9."
Nat.Struct.Mol.Biol., 26,
679-685. doi: 10.1038/s41594-019-0258-2.
|
Conformational states of cas9-sgrna-DNA ternary complex
in the presence of magnesium . SNAP output
|
|
6o0y
|
hydrolase-RNA-DNA |
cryo-EM (3.37 Å) |
Zhu X, Clarke R, Puppala AK, Chittori S, Merk A,
Merrill BJ, Simonovic M, Subramaniam S |
(2019) "Cryo-EM
structures reveal coordinated domain motions that
govern DNA cleavage by Cas9."
Nat.Struct.Mol.Biol., 26,
679-685. doi: 10.1038/s41594-019-0258-2.
|
Conformational states of cas9-sgrna-DNA ternary complex
in the presence of magnesium . SNAP output
|
|
6o0z
|
hydrolase-RNA-DNA |
cryo-EM (3.3 Å) |
Zhu X, Clarke R, Puppala AK, Chittori S, Merk A,
Merrill BJ, Simonovic M, Subramaniam S |
(2019) "Cryo-EM
structures reveal coordinated domain motions that
govern DNA cleavage by Cas9."
Nat.Struct.Mol.Biol., 26,
679-685. doi: 10.1038/s41594-019-0258-2.
|
Conformational states of cas9-sgrna-DNA ternary complex
in the presence of magnesium . SNAP output
|
|
6o19
|
transcription-DNA |
X-ray (1.596 Å) |
Garg A, Goldgur Y, Sanchez AM, Schwer B, Shuman
S |
(2019) "Structure
of Fission Yeast Transcription Factor Pho7 Bound
topho1Promoter DNA and Effect of Pho7 Mutations on DNA
Binding and Phosphate Homeostasis."
Mol.Cell.Biol., 39. doi:
10.1128/MCB.00132-19.
|
Crystal structure of pho7 complex with pho1 promoter
site 2 . SNAP output
|
|
6o1d
|
nuclear protein |
cryo-EM (3.395 Å) |
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins
AL, Olins DE, Bai Y, Zhang P |
(2019) "Atomic
resolution cryo-EM structure of a native-like CENP-A
nucleosome aided by an antibody fragment." Nat
Commun, 10, 2301. doi: 10.1038/s41467-019-10247-4.
|
cryo-EM structure of the centromeric nucleosome with
native alpha satellite DNA . SNAP output
|
|
6o3t
|
gene regulation-DNA |
X-ray (3.06 Å) |
Li S, Pradhan L, Ashur S, Joshi A, Nam HJ |
(2019) "Crystal
Structure of FOXC2 in Complex with DNA Target."
Acs Omega, 4, 10906-10914.
doi: 10.1021/acsomega.9b00756.
|
Structural basis of foxc2 and DNA interactions .
SNAP output
|
|
6o6c
|
transferase-DNA-RNA |
cryo-EM (3.1 Å) |
Lahiri I, Xu J, Han BG, Oh J, Wang D, DiMaio F,
Leschziner AE |
(2019) "3.1
angstrom structure of yeast RNA polymerase II
elongation complex stalled at a cyclobutane pyrimidine
dimer lesion solved using streptavidin affinity
grids." J.Struct.Biol.,
207, 270-278. doi: 10.1016/j.jsb.2019.06.004.
|
RNA polymerase ii elongation complex arrested at a cpd
lesion . SNAP output
|
|
6o6k
|
DNA binding protein-DNA |
X-ray (3.601 Å) |
Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA,
Adhya S, Hammel M |
(2020) "Nucleoid
remodeling during environmental adaptation is regulated
by HU-dependent DNA bundling." Nat Commun,
11, 2905. doi: 10.1038/s41467-020-16724-5.
|
Huaa 19bp sym DNA ph 5.5 . SNAP output
|
|
6o6p
|
transcription-DNA |
X-ray (3.851 Å) |
Lara J, Diacovich L, Trajtenberg F, Larrieux N,
Malchiodi EL, Fernandez MM, Gago G, Gramajo H, Buschiazzo
A |
(2020) "Mycobacterium
tuberculosis FasR senses long fatty acyl-CoA through a
tunnel and a hydrophobic transmission spine."
Nat Commun, 11, 3703. doi:
10.1038/s41467-020-17504-x.
|
Structure of the regulator fasr from mycobacterium
tuberculosis in complex with DNA . SNAP output
|
|
6o71
|
immune system-DNA |
X-ray (2.55 Å) |
Jia N, Jones R, Yang G, Ouerfelli O, Patel DJ |
(2019) "CRISPR-Cas
III-A Csm6 CARF Domain Is a Ring Nuclease Triggering
Stepwise cA4Cleavage with ApA>p Formation
Terminating RNase Activity." Mol.Cell,
75, 944-956.e6. doi: 10.1016/j.molcel.2019.06.014.
|
Crystal structure of csm6 in complex with cda4 by
soaking cda4 into csm6 . SNAP output
|
|
6o8e
|
DNA binding protein-DNA |
X-ray (2.61 Å) |
Lee SJ, Sung RJ, Verdine GL |
(2019) "Mechanism
of DNA Lesion Homing and Recognition by the Uvr
Nucleotide Excision Repair System." Res,
2019, 5641746. doi: 10.34133/2019/5641746.
|
Crystal structure of uvrb bound to duplex DNA with adp
. SNAP output
|
|
6o8f
|
DNA binding protein-DNA |
X-ray (2.81 Å) |
Lee SJ, Sung RJ, Verdine GL |
(2019) "Mechanism
of DNA Lesion Homing and Recognition by the Uvr
Nucleotide Excision Repair System." Res,
2019, 5641746. doi: 10.34133/2019/5641746.
|
Crystal structure of uvrb bound to duplex DNA .
SNAP output
|
|
6o8g
|
DNA binding protein-DNA |
X-ray (2.64 Å) |
Lee SJ, Sung RJ, Verdine GL |
(2019) "Mechanism
of DNA Lesion Homing and Recognition by the Uvr
Nucleotide Excision Repair System." Res,
2019, 5641746. doi: 10.34133/2019/5641746.
|
Crystal structure of uvrb bound to fully duplex DNA .
SNAP output
|
|
6o8h
|
DNA binding protein-DNA |
X-ray (2.39 Å) |
Lee SJ, Sung RJ, Verdine GL |
(2019) "Mechanism
of DNA Lesion Homing and Recognition by the Uvr
Nucleotide Excision Repair System." Res,
2019, 5641746. doi: 10.34133/2019/5641746.
|
Crystal structure of uvrb mutant bound to duplex DNA .
SNAP output
|
|
6o8q
|
DNA binding protein-DNA |
X-ray (3.216 Å) |
Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA,
Adhya S, Hammel M |
(2020) "Nucleoid
remodeling during environmental adaptation is regulated
by HU-dependent DNA bundling." Nat Commun,
11, 2905. doi: 10.1038/s41467-020-16724-5.
|
Huaa 19bp sym DNA ph 4.5 . SNAP output
|
|
6o96
|
structural protein-DNA-transferase |
cryo-EM (3.5 Å) |
Valencia-Sanchez MI, De Ioannes P, Wang M, Vasilyev
N, Chen R, Nudler E, Armache J-P, Armache KJ |
(2019) "Structural
Basis of Dot1L Stimulation by Histone H2B Lysine 120
Ubiquitination." Mol.Cell,
74, 1010. doi: 10.1016/j.molcel.2019.03.029.
|
Dot1l bound to the h2bk120 ubiquitinated nucleosome .
SNAP output
|
|
6o9e
|
transferase-DNA |
X-ray (2.4 Å) |
Ruiz FX, Hoang A, Das K, Arnold E |
(2019) "Structural
Basis of HIV-1 Inhibition by Nucleotide-Competing
Reverse Transcriptase Inhibitor INDOPY-1."
J.Med.Chem., 62, 9996-10002.
doi: 10.1021/acs.jmedchem.9b01289.
|
Structure of hiv-1 reverse transcriptase in complex
with DNA and indopy-1 . SNAP output
|
|
6o9l
|
transcription-DNA |
cryo-EM (7.2 Å) |
Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov
I |
(2019) "Transcription
preinitiation complex structure and dynamics provide
insight into genetic diseases."
Nat.Struct.Mol.Biol., 26,
397-406. doi: 10.1038/s41594-019-0220-3.
|
Human holo-pic in the closed state . SNAP output
|
|
6oaj
|
DNA binding protein-DNA |
X-ray (4.092 Å) |
Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA,
Adhya S, Hammel M |
(2020) "Nucleoid
remodeling during environmental adaptation is regulated
by HU-dependent DNA bundling." Nat Commun,
11, 2905. doi: 10.1038/s41467-020-16724-5.
|
Huae34k 19bp sym DNA . SNAP output
|
|
6obj
|
hydrolase-DNA |
cryo-EM (3.5 Å) |
Polley S, Lyumkis D, Horton NC |
(2019) "Mechanism
of Filamentation-Induced Allosteric Activation of the
SgrAI Endonuclease." Structure,
27, 1497-1507.e3. doi: 10.1016/j.str.2019.08.001.
|
Structure of a DNA-bound dimer extracted from
filamentous sgrai endonuclease in its activated form .
SNAP output
|
|
6od3
|
transcription-DNA |
X-ray (1.494 Å) |
Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal
RM, Cheng X |
(2019) "Structural
basis for preferential binding of human TCF4 to DNA
containing 5-carboxylcytosine." Nucleic Acids
Res., 47, 8375-8387. doi:
10.1093/nar/gkz381.
|
Human tcf4 c-terminal bhlh domain in complex with 13-bp
oligonucleotide containing e-box sequence . SNAP output
|
|
6od4
|
transcription-DNA |
X-ray (1.699 Å) |
Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal
RM, Cheng X |
(2019) "Structural
basis for preferential binding of human TCF4 to DNA
containing 5-carboxylcytosine." Nucleic Acids
Res., 47, 8375-8387. doi:
10.1093/nar/gkz381.
|
Human tcf4 c-terminal bhlh domain in complex with 11-bp
oligonucleotide containing e-box sequence . SNAP output
|
|
6od5
|
transcription-DNA |
X-ray (2.05 Å) |
Yang J, Horton JR, Li J, Huang Y, Zhang X, Blumenthal
RM, Cheng X |
(2019) "Structural
basis for preferential binding of human TCF4 to DNA
containing 5-carboxylcytosine." Nucleic Acids
Res., 47, 8375-8387. doi:
10.1093/nar/gkz381.
|
Human tcf4 c-terminal bhlh domain in complex with 12-bp
oligonucleotide containing e-box sequence with
5-carboxylcytosines . SNAP output
|
|
6oe7
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A,
Aravind L, Arrowsmith CH |
(2019) "Structural
basis of HMCES interactions with abasic DNA and
multivalent substrate recognition."
Nat.Struct.Mol.Biol., 26,
607-612. doi: 10.1038/s41594-019-0246-6.
|
Crystal structure of hmces cross-linked to DNA abasic
site . SNAP output
|
|
6oea
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A,
Aravind L, Arrowsmith CH |
(2019) "Structural
basis of HMCES interactions with abasic DNA and
multivalent substrate recognition."
Nat.Struct.Mol.Biol., 26,
607-612. doi: 10.1038/s41594-019-0246-6.
|
Crystal structure of hmces srap domain in complex with
longer 3' overhang DNA . SNAP output
|
|
6oeb
|
DNA binding protein-DNA |
X-ray (2.1 Å) |
Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A,
Aravind L, Arrowsmith CH |
(2019) "Structural
basis of HMCES interactions with abasic DNA and
multivalent substrate recognition."
Nat.Struct.Mol.Biol., 26,
607-612. doi: 10.1038/s41594-019-0246-6.
|
Crystal structure of hmces srap domain in complex with
3' overhang DNA . SNAP
output
|
|
6oem
|
recombination-DNA |
cryo-EM (3.6 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse rag1-2 prc complex (dna0) .
SNAP output
|
|
6oen
|
recombination-DNA |
cryo-EM (4.3 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse rag1-2 prc complex (dna1) .
SNAP output
|
|
6oeo
|
recombination-DNA |
cryo-EM (3.69 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse rag1-2 nfc complex (dna1) .
SNAP output
|
|
6oep
|
recombination-DNA |
cryo-EM (3.7 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse rag1-2 12rss-nfc-23rss-prc
complex (dna1) . SNAP
output
|
|
6oeq
|
recombination-DNA |
cryo-EM (4.3 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse rag1-2 12rss-prc-23rss-nfc
complex (dna1) . SNAP
output
|
|
6oer
|
recombination-DNA |
cryo-EM (3.29 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse rag1-2 nfc complex (dna2) .
SNAP output
|
|
6oes
|
recombination-DNA |
cryo-EM (3.06 Å) |
Chen X, Cui Y, Wang H, Zhou ZH, Gellert M, Yang
W |
(2020) "How
mouse RAG recombinase avoids DNA transposition."
Nat.Struct.Mol.Biol., 27,
127-133. doi: 10.1038/s41594-019-0366-z.
|
cryo-EM structure of mouse rag1-2 stc complex (without
nbd domain) . SNAP
output
|
|
6oet
|
recombination-DNA |
cryo-EM (3.4 Å) |
Chen X, Cui Y, Wang H, Zhou ZH, Gellert M, Yang
W |
(2020) "How
mouse RAG recombinase avoids DNA transposition."
Nat.Struct.Mol.Biol., 27,
127-133. doi: 10.1038/s41594-019-0366-z.
|
cryo-EM structure of mouse rag1-2 stc complex .
SNAP output
|
|
6ogj
|
DNA binding protein-DNA |
X-ray (1.8 Å) |
Lei M, Tempel W, Chen S, Liu K, Min J |
(2019) "Plasticity
at the DNA recognition site of the MeCP2 mCG-binding
domain." Biochim Biophys Acta Gene Regul
Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409.
|
Mecp2 mbd in complex with DNA . SNAP output
|
|
6ogk
|
DNA binding protein-DNA |
X-ray (1.65 Å) |
Lei M, Tempel W, Chen S, Liu K, Min J |
(2019) "Plasticity
at the DNA recognition site of the MeCP2 mCG-binding
domain." Biochim Biophys Acta Gene Regul
Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409.
|
Mecp2 mbd in complex with DNA . SNAP output
|
|
6ola
|
virus like particle |
cryo-EM (3.3 Å) |
Khayat R, Wen K, Alimova A, Gavrilov B, Katz A,
Galarza JM, Gottlieb P |
(2019) "Structural
characterization of the PCV2d virus-like particle at
3.3 angstrom resolution reveals differences to PCV2a
and PCV2b capsids, a tetranucleotide, and an N-terminus
near the icosahedral 3-fold axes."
Virology, 537, 186-197. doi:
10.1016/j.virol.2019.09.001.
|
Structure of the pcv2d virus-like particle . SNAP output
|
|
6ole
|
ribosome |
cryo-EM (3.1 Å) |
Li W, Ward FR, McClure KF, Chang ST, Montabana E,
Liras S, Dullea RG, Cate JHD |
(2019) "Structural
basis for selective stalling of human ribosome nascent
chain complexes by a drug-like molecule."
Nat.Struct.Mol.Biol., 26,
501-509. doi: 10.1038/s41594-019-0236-8.
|
Human ribosome nascent chain complex (cdh1-rnc) stalled
by a drug-like molecule with ap and pe trnas . SNAP output
|
|
6olf
|
ribosome |
cryo-EM (3.9 Å) |
Li W, Ward FR, McClure KF, Chang ST, Montabana E,
Liras S, Dullea RG, Cate JHD |
(2019) "Structural
basis for selective stalling of human ribosome nascent
chain complexes by a drug-like molecule."
Nat.Struct.Mol.Biol., 26,
501-509. doi: 10.1038/s41594-019-0236-8.
|
Human ribosome nascent chain complex (cdh1-rnc) stalled
by a drug-like molecule with aa and pe trnas . SNAP output
|
|
6oli
|
ribosome |
cryo-EM (3.5 Å) |
Li W, Ward FR, McClure KF, Chang ST, Montabana E,
Liras S, Dullea RG, Cate JHD |
(2019) "Structural
basis for selective stalling of human ribosome nascent
chain complexes by a drug-like molecule."
Nat.Struct.Mol.Biol., 26,
501-509. doi: 10.1038/s41594-019-0236-8.
|
Structure of human ribosome nascent chain complex
selectively stalled by a drug-like small molecule
(uso1-rnc) . SNAP
output
|
|
6om0
|
ribosome |
cryo-EM (3.1 Å) |
Li W, Ward FR, McClure KF, Chang ST, Montabana E,
Liras S, Dullea RG, Cate JHD |
(2019) "Structural
basis for selective stalling of human ribosome nascent
chain complexes by a drug-like molecule."
Nat.Struct.Mol.Biol., 26,
501-509. doi: 10.1038/s41594-019-0236-8.
|
Human ribosome nascent chain complex (pcsk9-rnc)
stalled by a drug-like molecule with ap and pe trnas .
SNAP output
|
|
6om3
|
structural protein-DNA |
X-ray (3.3 Å) |
De Ioannes P, Leon VA, Kuang Z, Wang M, Boeke JD,
Hochwagen A, Armache KJ |
(2019) "Structure
and function of the Orc1 BAH-nucleosome complex."
Nat Commun, 10, 2894. doi:
10.1038/s41467-019-10609-y.
|
Crystal structure of the orc1 bah domain in complex
with a nucleosome core particle . SNAP output
|
|
6om7
|
ribosome |
cryo-EM (3.7 Å) |
Li W, Ward FR, McClure KF, Chang ST, Montabana E,
Liras S, Dullea RG, Cate JHD |
(2019) "Structural
basis for selective stalling of human ribosome nascent
chain complexes by a drug-like molecule."
Nat.Struct.Mol.Biol., 26,
501-509. doi: 10.1038/s41594-019-0236-8.
|
Human ribosome nascent chain complex (pcsk9-rnc)
stalled by a drug-like small molecule with aa and pe
trnas . SNAP output
|
|
6omf
|
transcription, transferase-DNA |
cryo-EM (3.26 Å) |
Cartagena AJ, Banta AB, Sathyan N, Ross W, Gourse RL,
Campbell EA, Darst SA |
(2019) "Structural
basis for transcription activation by Crl through
tethering of sigmaSand RNA polymerase."
Proc.Natl.Acad.Sci.USA, 116,
18923-18927. doi: 10.1073/pnas.1910827116.
|
Cryoem structure of sigmas-transcription initiation
complex with activator crl . SNAP output
|
|
6omv
|
unknown function-DNA-RNA |
cryo-EM (3.9 Å) |
Zhang H, Li Z, Daczkowski CM, Gabel C, Mesecar AD,
Chang L |
(2019) "Structural
Basis for the Inhibition of CRISPR-Cas12a by
Anti-CRISPR Proteins." Cell Host Microbe,
25, 815. doi: 10.1016/j.chom.2019.05.004.
|
Cryoem structure of the lbcas12a-crrna-acrva4-DNA
complex . SNAP
output
|
|
6on0
|
transcription-DNA |
X-ray (1.6 Å) |
Hall BM, Roberts SA, Cordes MHJ |
(2019) "Extreme
divergence between one-to-one orthologs: the structure
of N15 Cro bound to operator DNA and its relationship
to the lambda Cro complex." Nucleic Acids
Res., 47, 7118-7129. doi:
10.1093/nar/gkz507.
|
Structure of n15 cro complexed with consensus operator
DNA . SNAP output
|
|
6oov
|
DNA binding protein-DNA |
X-ray (2.2 Å) |
Halabelian L, Zeng H, Li Y, Bountra C, Edwards AM,
Arrowsmith CH, Structural Genomics Consortium (SGC) |
"Crystal structure of HMCES SRAP domain in complex
with palindromic 3' overhang DNA." |
Crystal structure of hmces srap domain in complex with
palindromic 3' overhang DNA . SNAP output
|
|
6opm
|
hydrolase-DNA |
X-ray (3.1 Å) |
Hickman AB, Kailasan S, Genzor P, Haase AD, Dyda
F |
(2020) "Casposase
structure and the mechanistic link between DNA
transposition and spacer acquisition by
CRISPR-Cas." Elife, 9.
doi: 10.7554/eLife.50004.
|
Casposase bound to integration product . SNAP output
|
|
6or7
|
transferase-DNA |
X-ray (2.53 Å) |
Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson
KS |
(2019) "Structural
insights into the recognition of nucleoside reverse
transcriptase inhibitors by HIV-1 reverse
transcriptase: First crystal structures with reverse
transcriptase and the active triphosphate forms of
lamivudine and emtricitabine." Protein
Sci., 28, 1664-1675. doi:
10.1002/pro.3681.
|
Structure of hiv-1 reverse transcriptase (rt) in
complex with DNA and (-)ftc-tp . SNAP output
|
|
6otz
|
transferase-DNA |
X-ray (2.857 Å) |
Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson
KS |
(2019) "Structural
insights into the recognition of nucleoside reverse
transcriptase inhibitors by HIV-1 reverse
transcriptase: First crystal structures with reverse
transcriptase and the active triphosphate forms of
lamivudine and emtricitabine." Protein
Sci., 28, 1664-1675. doi:
10.1002/pro.3681.
|
Structure of hiv-1 reverse transcriptase (rt) in
complex with dsDNA and (+)ftc-tp . SNAP output
|
|
6oul
|
transcription |
cryo-EM (3.4 Å) |
Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell
EA, Gourse RL, Ross W, Darst SA |
(2019) "E.
coliTraR allosterically regulates transcription
initiation by altering RNA polymerase
conformation." Elife, 8.
doi: 10.7554/eLife.49375.
|
cryo-EM structure of escherichia coli rnap polymerase
bound to rpstp2 promoter DNA . SNAP output
|
|
6oun
|
transferase-DNA |
X-ray (2.656 Å) |
Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson
KS |
(2019) "Structural
insights into the recognition of nucleoside reverse
transcriptase inhibitors by HIV-1 reverse
transcriptase: First crystal structures with reverse
transcriptase and the active triphosphate forms of
lamivudine and emtricitabine." Protein
Sci., 28, 1664-1675. doi:
10.1002/pro.3681.
|
Structure of hiv-1 reverse transcriptase (rt) in
complex with dsDNA and (-)3tc-tp . SNAP output
|
|
6ovr
|
transcription-DNA-RNA |
X-ray (2.843 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter variant -1g .
SNAP output
|
|
6ovy
|
transcription-DNA-RNA |
X-ray (2.999 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter variant -1c .
SNAP output
|
|
6ow3
|
transcription-DNA-RNA |
X-ray (2.766 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter variant -1t .
SNAP output
|
|
6oy5
|
transcription-DNA-RNA |
X-ray (3.1 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter at 3 min .
SNAP output
|
|
6oy6
|
transcription-DNA-RNA |
X-ray (3.096 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter at 5 min .
SNAP output
|
|
6oy7
|
transcription-DNA-RNA |
X-ray (3.04 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrg promoter at 7 min .
SNAP output
|
|
6ozf
|
hydrolase |
X-ray (1.8 Å) |
Wu J, Samara NL, Kuraoka I, Yang W |
(2019) "Evolution
of Inosine-Specific Endonuclease V from Bacterial DNase
to Eukaryotic RNase." Mol.Cell,
76, 44. doi: 10.1016/j.molcel.2019.06.046.
|
Crystal structure of thermotoga maritima (tm)
endonuclease v (d110n) in complex with a 12mer DNA
containing an inosine followed by a ribo-adenosine .
SNAP output
|
|
6ozg
|
hydrolase |
X-ray (1.93 Å) |
Wu J, Samara NL, Kuraoka I, Yang W |
(2019) "Evolution
of Inosine-Specific Endonuclease V from Bacterial DNase
to Eukaryotic RNase." Mol.Cell,
76, 44. doi: 10.1016/j.molcel.2019.06.046.
|
Crystal structure of thermotoga maritima (tm)
endonuclease v (e89q) in complex with a 12mer DNA
containing an inosine followed by a ribo-adenosine .
SNAP output
|
|
6ozh
|
hydrolase |
X-ray (3.026 Å) |
Wu J, Samara NL, Kuraoka I, Yang W |
(2019) "Evolution
of Inosine-Specific Endonuclease V from Bacterial DNase
to Eukaryotic RNase." Mol.Cell,
76, 44. doi: 10.1016/j.molcel.2019.06.046.
|
Crystal structure of ciona intestinalis (ci)
endonuclease v in complex with a 24mer DNA containing
an inosine followed by a ribo-adenosine . SNAP output
|
|
6ozi
|
hydrolase |
X-ray (2.302 Å) |
Wu J, Samara NL, Kuraoka I, Yang W |
(2019) "Evolution
of Inosine-Specific Endonuclease V from Bacterial DNase
to Eukaryotic RNase." Mol.Cell,
76, 44. doi: 10.1016/j.molcel.2019.06.046.
|
Crystal structure of ciona intestinalis (ci)
endonuclease v (d234n) in complex with a 23mer DNA
containing an inosine followed by a ribo-adenosine .
SNAP output
|
|
6p09
|
ligase-DNA |
X-ray (2.052 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 bound to an adenylated, dideoxy
terminated DNA nick with 200 mm mg2+ . SNAP output
|
|
6p0a
|
ligase |
X-ray (2.05 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 bound to an adenylated, dideoxy
terminated DNA nick with 2 mm mg2+ . SNAP output
|
|
6p0b
|
ligase |
X-ray (2.203 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 (e346a-e592a) bound to an
adenylated, dideoxy terminated DNA nick with 200 mm
mg2+ . SNAP output
|
|
6p0c
|
ligase-DNA |
X-ray (1.55 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 bound to an adenylated, hydroxyl
terminated DNA nick in edta . SNAP output
|
|
6p0d
|
ligase |
X-ray (1.75 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 (e346a-e592a) bound to an
adenylated, hydroxyl terminated DNA nick . SNAP output
|
|
6p0e
|
ligase |
X-ray (1.85 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 (e346a,e592a) bound to adenylated
DNA containing an 8-oxo guanine:adenine base-pair .
SNAP output
|
|
6p0g
|
DNA binding protein-DNA |
X-ray (2.27 Å) |
Hosford CJ, Bui AQ, Chappie JS |
(2020) "The
structure of theThermococcus gammatoleransMcrB
N-terminal domain reveals a new mode of substrate
recognition and specificity among McrB homologs."
J.Biol.Chem., 295, 743-756.
doi: 10.1074/jbc.RA119.010188.
|
N-terminal domain of thermococcus gammatolerans mcrb
bound to m5c DNA . SNAP
output
|
|
6p0s
|
DNA binding protein-DNA |
X-ray (2.7 Å) |
Hancock SP, Cascio D, Johnson RC |
(2019) "Cooperative
DNA binding by proteins through DNA shape
complementarity." Nucleic Acids Res.,
47, 8874-8887. doi: 10.1093/nar/gkz642.
|
Crystal structure of ternary DNA complex "fx2"
containing e. coli fis and phage lambda xis . SNAP output
|
|
6p0t
|
DNA binding protein-DNA |
X-ray (3.603 Å) |
Hancock SP, Cascio D, Johnson RC |
(2019) "Cooperative
DNA binding by proteins through DNA shape
complementarity." Nucleic Acids Res.,
47, 8874-8887. doi: 10.1093/nar/gkz642.
|
Crystal structure of ternary DNA complex "fx(1-2)-1xis"
containing e. coli fis and phage lambda xis . SNAP output
|
|
6p0u
|
DNA binding protein-DNA |
X-ray (3.3 Å) |
Hancock SP, Cascio D, Johnson RC |
(2019) "Cooperative
DNA binding by proteins through DNA shape
complementarity." Nucleic Acids Res.,
47, 8874-8887. doi: 10.1093/nar/gkz642.
|
Crystal structure of ternary DNA complex "
fx(1-2)-2xis" containing e. coli fis and phage lambda
xis . SNAP output
|
|
6p18
|
gene regulation |
cryo-EM (3.5 Å) |
Yin Z, Kaelber JT, Ebright RH |
(2019) "Structural
basis of Q-dependent antitermination."
Proc.Natl.Acad.Sci.USA, 116,
18384-18390. doi: 10.1073/pnas.1909801116.
|
Q21 transcription antitermination complex: loading
complex . SNAP
output
|
|
6p19
|
gene regulation |
cryo-EM (3.8 Å) |
Yin Z, Kaelber JT, Ebright RH |
(2019) "Structural
basis of Q-dependent antitermination."
Proc.Natl.Acad.Sci.USA, 116,
18384-18390. doi: 10.1073/pnas.1909801116.
|
Q21 transcription antitermination complex: loaded
complex . SNAP
output
|
|
6p1a
|
gene regulation |
X-ray (2.837 Å) |
Yin Z, Kaelber JT, Ebright RH |
(2019) "Structural
basis of Q-dependent antitermination."
Proc.Natl.Acad.Sci.USA, 116,
18384-18390. doi: 10.1073/pnas.1909801116.
|
Transcription antitermination factor q21 in complex
with q21-binding-element DNA . SNAP output
|
|
6p1h
|
DNA binding protein-DNA |
cryo-EM (3.2 Å) |
Jain R, Rice WJ, Malik R, Johnson RE, Prakash L,
Prakash S, Ubarretxena-Belandia I, Aggarwal AK |
(2019) "Cryo-EM
structure and dynamics of eukaryotic DNA polymerase
delta holoenzyme." Nat.Struct.Mol.Biol.,
26, 955-962. doi: 10.1038/s41594-019-0305-z.
|
cryo-EM structure of DNA polymerase delta holoenzyme .
SNAP output
|
|
6p1i
|
transferase-DNA |
X-ray (2.74 Å) |
Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson
KS |
(2019) "Structural
insights into the recognition of nucleoside reverse
transcriptase inhibitors by HIV-1 reverse
transcriptase: First crystal structures with reverse
transcriptase and the active triphosphate forms of
lamivudine and emtricitabine." Protein
Sci., 28, 1664-1675. doi:
10.1002/pro.3681.
|
Structure of hiv-1 reverse transcriptase (rt) in
complex with dsDNA and dctp . SNAP output
|
|
6p1m
|
transferase |
X-ray (1.65 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Binary complex of human DNA polymerase mu with 1-nt
gapped substrate containing template 8og . SNAP output
|
|
6p1n
|
transferase |
X-ray (1.6 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and bound incoming dampnpp . SNAP output
|
|
6p1o
|
transferase |
X-ray (1.65 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Post-catalytic nicked complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and newly incorporated damp . SNAP output
|
|
6p1p
|
transferase |
X-ray (1.75 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and bound incoming dcmpnpp . SNAP output
|
|
6p1q
|
transferase |
X-ray (1.9 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Post-catalytic nicked complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and newly incorporated dcmp . SNAP output
|
|
6p1r
|
transferase |
X-ray (1.701 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and bound incoming ampnpp . SNAP output
|
|
6p1s
|
transferase-DNA |
X-ray (1.75 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Post-catalytic nicked complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and newly incorporated amp . SNAP output
|
|
6p1t
|
transferase |
X-ray (1.7 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and bound cmpcpp . SNAP
output
|
|
6p1u
|
transferase |
X-ray (1.75 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Post-catalytic nicked complex of human DNA polymerase
mu with 1-nt gapped substrate containing template 8og
and newly incorporated cmp . SNAP output
|
|
6p1v
|
transferase |
X-ray (1.95 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with 1-nt gapped substrate containing undamaged
template dg and bound incoming dcmpnpp . SNAP output
|
|
6p1w
|
transferase |
X-ray (1.751 Å) |
Kaminski AM, Chiruvella KK, Ramsden DA, Kunkel TA,
Bebenek K, Pedersen LC |
(2019) "Unexpected
behavior of DNA polymerase Mu opposite template
8-oxo-7,8-dihydro-2'-guanosine." Nucleic Acids
Res., 47, 9410-9422. doi:
10.1093/nar/gkz680.
|
Pre-catalytic ternary complex of human DNA polymerase
mu with 1-nt gapped substrate containing undamaged
template dg and bound incoming cmpcpp . SNAP output
|
|
6p1x
|
transferase-DNA |
X-ray (2.553 Å) |
Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson
KS |
(2019) "Structural
insights into the recognition of nucleoside reverse
transcriptase inhibitors by HIV-1 reverse
transcriptase: First crystal structures with reverse
transcriptase and the active triphosphate forms of
lamivudine and emtricitabine." Protein
Sci., 28, 1664-1675. doi:
10.1002/pro.3681.
|
Structure of hiv-1 reverse transcriptase (rt) in
complex with dsDNA and l-ddctp . SNAP output
|
|
6p2g
|
transferase-DNA |
X-ray (2.99 Å) |
Bertoletti N, Chan AH, Schinazi RF, Yin YW, Anderson
KS |
(2019) "Structural
insights into the recognition of nucleoside reverse
transcriptase inhibitors by HIV-1 reverse
transcriptase: First crystal structures with reverse
transcriptase and the active triphosphate forms of
lamivudine and emtricitabine." Protein
Sci., 28, 1664-1675. doi:
10.1002/pro.3681.
|
Structure of hiv-1 reverse transcriptase (rt) in
complex with dsDNA and d-ddctp . SNAP output
|
|
6p4f
|
hydrolase-DNA |
X-ray (3.55 Å) |
He F, DuPrez K, Hilario E, Chen Z, Fan L |
(2020) "Structural
basis of the XPB helicase-Bax1 nuclease complex
interacting with the repair bubble DNA."
Nucleic Acids Res., 48,
11695-11705. doi: 10.1093/nar/gkaa801.
|
Crystal structure of the xpb-bax1-forked DNA ternary
complex . SNAP
output
|
|
6p5a
|
transferase-DNA |
cryo-EM (3.6 Å) |
Ghanim GE, Kellogg EH, Nogales E, Rio DC |
(2019) "Structure
of a P element transposase-DNA complex reveals unusual
DNA structures and GTP-DNA contacts."
Nat.Struct.Mol.Biol., 26,
1013-1022. doi: 10.1038/s41594-019-0319-6.
|
Drosophila p element transposase strand transfer
complex . SNAP
output
|
|
6p5c
|
replication-DNA |
X-ray (2.2 Å) |
Hamm ML, Garcia AA, Gilbert R, Johri M, Ricart M,
Sholes SL, Murray-Nerger LA, Wu EY |
(2020) "The
importance of Ile716 toward the mutagenicity of
8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA
polymerase." DNA Repair (Amst.),
89, 102826. doi: 10.1016/j.dnarep.2020.102826.
|
Bacillus fragment DNA polymerase mutant i716m .
SNAP output
|
|
6p70
|
transcription-DNA |
X-ray (3.052 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of bacterial RNA polymerase and
pyrbi promoter complex . SNAP output
|
|
6p71
|
transcription-DNA-RNA |
X-ray (2.92 Å) |
Shin Y, Hedglin M, Murakami KS |
(2020) "Structural
basis of reiterative transcription from the pyrG and
pyrBI promoters by bacterial RNA polymerase."
Nucleic Acids Res., 48,
2144-2155. doi: 10.1093/nar/gkz1221.
|
X-ray crystal structure of a bacterial reiterative
transcription complex of pyrbi promoter . SNAP output
|
|
6p7b
|
hydrolase-DNA |
X-ray (3.317 Å) |
Li N, Shi K, Rao T, Banerjee S, Aihara H |
(2020) "Structural
insights into the promiscuous DNA binding and broad
substrate selectivity of fowlpox virus resolvase."
Sci Rep, 10, 393. doi:
10.1038/s41598-019-56825-w.
|
Crystal structure of fowlpox virus resolvase and
substrate holliday junction DNA complex . SNAP output
|
|
6p7e
|
transferase-DNA binding protein-DNA |
X-ray (3.001 Å) |
Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz
BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR |
(2019) "Combined
Solution and Crystal Methods Reveal the Electrostatic
Tethers That Provide a Flexible Platform for
Replication Activities in the Bacteriophage T7
Replisome." Biochemistry,
58, 4466-4479. doi: 10.1021/acs.biochem.9b00525.
|
Structure of t7 DNA polymerase bound to a
primer-template DNA and a peptide that mimics the
c-terminal tail of the primase-helicase . SNAP output
|
|
6p93
|
lyase-DNA |
X-ray (2.1 Å) |
McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL,
McKinnon PJ, Freudenthal BD, Wilson DM |
(2020) "Functions
of the major abasic endonuclease (APE1) in cell
viability and genotoxin resistance."
Mutagenesis, 35, 27-38. doi:
10.1093/mutage/gez046.
|
Human ape1 k98a ap-endonuclease product complex .
SNAP output
|
|
6p94
|
lyase-DNA |
X-ray (2.09 Å) |
McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL,
McKinnon PJ, Freudenthal BD, Wilson DM |
(2020) "Functions
of the major abasic endonuclease (APE1) in cell
viability and genotoxin resistance."
Mutagenesis, 35, 27-38. doi:
10.1093/mutage/gez046.
|
Human ape1 c65a ap-endonuclease product complex .
SNAP output
|
|
6pa7
|
transferase-DNA |
cryo-EM (2.94 Å) |
Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE,
Melcher K, Jones PA |
(2020) "Structure
of nucleosome-bound DNA methyltransferases DNMT3A and
DNMT3B." Nature, 586,
151-155. doi: 10.1038/s41586-020-2747-1.
|
The cryo-EM structure of the human dnmt3a2-dnmt3b3
complex bound to nucleosome. . SNAP output
|
|
6pax
|
gene regulation-DNA |
X-ray (2.5 Å) |
Xu HE, Rould MA, Xu W, Epstein JA, Maas RL, Pabo
CO |
(1999) "Crystal
structure of the human Pax6 paired domain-DNA complex
reveals specific roles for the linker region and
carboxy-terminal subdomain in DNA binding."
Genes Dev., 13, 1263-1275.
|
Crystal structure of the human pax-6 paired domain-DNA
complex reveals a general model for pax protein-DNA
interactions . SNAP
output
|
|
6pb4
|
transcription-DNA-RNA |
cryo-EM (4.35 Å) |
Shi W, Jiang Y, Deng Y, Dong Z, Liu B |
(2020) "Visualization of two architectures in class-II
CAP-dependent transcription activation." Plos
Biol., 18, e3000706. doi:
10.1371/journal.pbio.3000706.
|
The e. coli class-ii cap-dependent transcription
activation complex with de novo RNA transcript at the
state 2 . SNAP
output
|
|
6pb5
|
transcription-DNA |
cryo-EM (4.52 Å) |
Shi W, Jiang Y, Deng Y, Dong Z, Liu B |
(2020) "Visualization of two architectures in class-II
CAP-dependent transcription activation." Plos
Biol., 18, e3000706. doi:
10.1371/journal.pbio.3000706.
|
The e. coli class-ii cap-dependent transcription
activation complex at the state 1 architecture .
SNAP output
|
|
6pb6
|
transcription-DNA |
cryo-EM (4.29 Å) |
Shi W, Jiang Y, Deng Y, Dong Z, Liu B |
(2020) "Visualization of two architectures in class-II
CAP-dependent transcription activation." Plos
Biol., 18, e3000706. doi:
10.1371/journal.pbio.3000706.
|
The e. coli class-ii cap-dependent transcription
activation complex at the state 2 . SNAP output
|
|
6pbd
|
transferase-DNA |
X-ray (2.343 Å) |
Horton JR, Woodcock CB, Opot SB, Reich NO, Zhang X,
Cheng X |
(2019) "The cell
cycle-regulated DNA adenine methyltransferase CcrM
opens a bubble at its DNA recognition site."
Nat Commun, 10, 4600. doi:
10.1038/s41467-019-12498-7.
|
DNA n6-adenine methyltransferase ccrm in complex with
double-stranded DNA oligonucleotide containing its
recognition sequence gaatc . SNAP output
|
|
6pcm
|
isomerase-DNA |
X-ray (3.107 Å) |
Cao N, Tan K, Zuo X, Annamalai T, Tse-Dinh YC |
(2020) "Mechanistic
insights from structure of Mycobacterium smegmatis
topoisomerase I with ssDNA bound to both N- and
C-terminal domains." Nucleic Acids Res.,
48, 4448-4462. doi: 10.1093/nar/gkaa201.
|
Crystal structure of mycobacterium smegmatis
topoisomerase i with ssDNA bound to both n- and
c-terminal domains . SNAP output
|
|
6pe2
|
transferase-DNA |
cryo-EM (4.0 Å) |
Ghanim GE, Kellogg EH, Nogales E, Rio DC |
(2019) "Structure
of a P element transposase-DNA complex reveals unusual
DNA structures and GTP-DNA contacts."
Nat.Struct.Mol.Biol., 26,
1013-1022. doi: 10.1038/s41594-019-0319-6.
|
Drosophila p element transposase strand transfer
complex . SNAP
output
|
|
6ph5
|
transcription-DNA |
X-ray (2.602 Å) |
Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard
WA, Wilson SH |
(2020) "DNA
polymerase beta nucleotide-stabilized template
misalignment fidelity depends on local sequence
context." J.Biol.Chem.,
295, 529-538. doi: 10.1074/jbc.RA119.010594.
|
Binary product complex crystal structure of DNA
polymerase beta with an extra-helical template base .
SNAP output
|
|
6ph6
|
transcription-DNA |
X-ray (2.6 Å) |
Howard MJ, Cavanaugh NA, Batra VK, Shock DD, Beard
WA, Wilson SH |
(2020) "DNA
polymerase beta nucleotide-stabilized template
misalignment fidelity depends on local sequence
context." J.Biol.Chem.,
295, 529-538. doi: 10.1074/jbc.RA119.010594.
|
Ternary complex crystal structure of DNA polymerase
beta with 2nt-gap with dctp bound downstream . SNAP output
|
|
6pij
|
RNA binding protein-RNA-DNA |
cryo-EM (2.9 Å) |
Halpin-Healy TS, Klompe SE, Sternberg SH, Fernandez
IS |
(2020) "Structural
basis of DNA targeting by a transposon-encoded
CRISPR-Cas system." Nature,
577, 271-274. doi: 10.1038/s41586-019-1849-0.
|
Target DNA-bound v. cholerae tniq-cascade complex,
closed conformation . SNAP output
|
|
6pkz
|
DNA binding protein-DNA |
X-ray (2.74 Å) |
Koag MC, Lee S |
"Structure of human DNA polymerase beta N279A
complexed with 8OA in the template base paired with
incoming non-hydrolyzable GTP." |
Structure of human DNA polymerase beta n279a complexed
with 8oa in the template base paired with incoming
non-hydrolyzable gtp . SNAP output
|
|
6pl7
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Koag MC, Lee S |
"Structure of human DNA polymerase eta complexed with
A in the template base paired with incoming
non-hydrolyzable TTP." |
Structure of human DNA polymerase eta complexed with a
in the template base paired with incoming
non-hydrolyzable ttp . SNAP output
|
|
6pl8
|
DNA binding protein-DNA |
X-ray (2.17 Å) |
Koag MC, Lee S |
"Structure of human DNA polymerase eta complexed with
8OA in the template base paired with incoming
non-hydrolyzable TTP." |
Structure of human DNA polymerase eta complexed with
8oa in the template base paired with incoming
non-hydrolyzable ttp . SNAP output
|
|
6plc
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Koag MC, Jung H, Lee S |
(2020) "Mutagenesis
mechanism of the major oxidative adenine lesion
7,8-dihydro-8-oxoadenine." Nucleic Acids
Res., 48, 5119-5134. doi:
10.1093/nar/gkaa193.
|
Structure of human DNA polymerase eta complexed with
8oa in the template base paired with incoming
non-hydrolyzable gtp . SNAP output
|
|
6pmi
|
transcription |
cryo-EM (3.86 Å) |
Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A,
Hu Y, Liu B |
(2020) "Structural
basis of bacterial sigma28-mediated transcription
reveals roles of the RNA polymerase zinc-binding
domain." Embo J., 39,
e104389. doi: 10.15252/embj.2020104389.
|
Sigm28-transcription initiation complex with specific
promoter at the state 1 . SNAP output
|
|
6pmj
|
transcription |
cryo-EM (3.91 Å) |
Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A,
Hu Y, Liu B |
(2020) "Structural
basis of bacterial sigma28-mediated transcription
reveals roles of the RNA polymerase zinc-binding
domain." Embo J., 39,
e104389. doi: 10.15252/embj.2020104389.
|
Sigm28-transcription initiation complex with specific
promoter at the state 2 . SNAP output
|
|
6ppr
|
DNA binding protein-DNA |
cryo-EM (3.5 Å) |
Jia N, Unciuleac MC, Xue C, Greene EC, Patel DJ,
Shuman S |
(2019) "Structures
and single-molecule analysis of bacterial motor
nuclease AdnAB illuminate the mechanism of DNA
double-strand break resection."
Proc.Natl.Acad.Sci.USA, 116,
24507-24516. doi: 10.1073/pnas.1913546116.
|
cryo-EM structure of aDNA(d934a)-adnb(d1014a) in
complex with amppnp and DNA . SNAP output
|
|
6ppu
|
DNA binding protein-DNA |
cryo-EM (3.5 Å) |
Jia N, Unciuleac MC, Xue C, Greene EC, Patel DJ,
Shuman S |
(2019) "Structures
and single-molecule analysis of bacterial motor
nuclease AdnAB illuminate the mechanism of DNA
double-strand break resection."
Proc.Natl.Acad.Sci.USA, 116,
24507-24516. doi: 10.1073/pnas.1913546116.
|
cryo-EM structure of adnab-amppnp-DNA complex .
SNAP output
|
|
6pqr
|
recombination-DNA |
cryo-EM (3.4 Å) |
Liu C, Yang Y, Schatz DG |
(2019) "Structures
of a RAG-like transposase during cut-and-paste
transposition." Nature,
575, 540-544. doi: 10.1038/s41586-019-1753-7.
|
cryo-EM structure of hztransib-intact tir substrate DNA
pre-reaction complex (prc) . SNAP output
|
|
6pqu
|
recombination-DNA |
cryo-EM (3.3 Å) |
Liu C, Yang Y, Schatz DG |
(2019) "Structures
of a RAG-like transposase during cut-and-paste
transposition." Nature,
575, 540-544. doi: 10.1038/s41586-019-1753-7.
|
cryo-EM structure of hztransib-nicked tir substrate DNA
pre-reaction complex (prc) . SNAP output
|
|
6pqx
|
recombination-DNA |
cryo-EM (4.6 Å) |
Liu C, Yang Y, Schatz DG |
(2019) "Structures
of a RAG-like transposase during cut-and-paste
transposition." Nature,
575, 540-544. doi: 10.1038/s41586-019-1753-7.
|
cryo-EM structure of hztransib-nicked tir substrate DNA
hairpin forming complex (hfc) . SNAP output
|
|
6pqy
|
recombination |
cryo-EM (4.2 Å) |
Liu C, Yang Y, Schatz DG |
(2019) "Structures
of a RAG-like transposase during cut-and-paste
transposition." Nature,
575, 540-544. doi: 10.1038/s41586-019-1753-7.
|
cryo-EM structure of hztransib-tir DNA transposon end
complex (tec) . SNAP
output
|
|
6pr5
|
recombination-DNA |
cryo-EM (3.3 Å) |
Liu C, Yang Y, Schatz DG |
(2019) "Structures
of a RAG-like transposase during cut-and-paste
transposition." Nature,
575, 540-544. doi: 10.1038/s41586-019-1753-7.
|
cryo-EM structure of hztransib strand transfer complex
(stc) . SNAP output
|
|
6psq
|
transcription-DNA |
cryo-EM (3.4 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase closed complex (trpc)
with trar and rpst p2 promoter . SNAP output
|
|
6psr
|
transcription-DNA |
cryo-EM (3.4 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase promoter unwinding
intermediate (trpi1) with trar and rpst p2 promoter .
SNAP output
|
|
6pss
|
transcription-DNA |
cryo-EM (3.5 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase promoter unwinding
intermediate (trpi1.5a) with trar and mutant rpst p2
promoter . SNAP
output
|
|
6pst
|
transcription-DNA |
cryo-EM (3.0 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase promoter unwinding
intermediate (trpi1.5b) with trar and mutant rpst p2
promoter . SNAP
output
|
|
6psu
|
transcription-DNA |
cryo-EM (3.9 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase promoter unwinding
intermediate (trpi2) with trar and rpst p2 promoter .
SNAP output
|
|
6psv
|
transcription-DNA |
cryo-EM (3.5 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase promoter unwinding
intermediate (tprerpo) with trar and rpst p2 promoter .
SNAP output
|
|
6psw
|
transcription-DNA |
cryo-EM (3.7 Å) |
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares
PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross
W, Gourse RL, Campbell EA, Darst SA |
(2020) "Stepwise
Promoter Melting by Bacterial RNA Polymerase."
Mol.Cell, 78, 275. doi:
10.1016/j.molcel.2020.02.017.
|
Escherichia coli RNA polymerase promoter unwinding
intermediate (trpo) with trar and rpst p2 promoter .
SNAP output
|
|
6put
|
viral protein-DNA |
cryo-EM (2.9 Å) |
Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins
D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr
TR, Craigie R, Lyumkis D |
(2020) "Structural
basis for strand-transfer inhibitor binding to HIV
intasomes." Science, 367,
810-814. doi: 10.1126/science.aay8015.
|
Structure of hiv cleaved synaptic complex (csc)
intasome bound with calcium . SNAP output
|
|
6puw
|
viral protein-DNA |
cryo-EM (2.9 Å) |
Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins
D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr
TR, Craigie R, Lyumkis D |
(2020) "Structural
basis for strand-transfer inhibitor binding to HIV
intasomes." Science, 367,
810-814. doi: 10.1126/science.aay8015.
|
Structure of hiv cleaved synaptic complex (csc)
intasome bound with magnesium and bictegravir (bic) .
SNAP output
|
|
6puy
|
viral protein-DNA |
cryo-EM (2.8 Å) |
Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins
D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr
TR, Craigie R, Lyumkis D |
(2020) "Structural
basis for strand-transfer inhibitor binding to HIV
intasomes." Science, 367,
810-814. doi: 10.1126/science.aay8015.
|
Structure of hiv cleaved synaptic complex (csc)
intasome bound with magnesium and insti xz426 (compound
4d) . SNAP output
|
|
6puz
|
viral protein-DNA |
cryo-EM (2.8 Å) |
Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins
D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr
TR, Craigie R, Lyumkis D |
(2020) "Structural
basis for strand-transfer inhibitor binding to HIV
intasomes." Science, 367,
810-814. doi: 10.1126/science.aay8015.
|
Structure of hiv cleaved synaptic complex (csc)
intasome bound with magnesium and insti xz446 (compound
4f) . SNAP output
|
|
6pw2
|
viral protein-DNA |
X-ray (3.01 Å) |
Malecka KA, Dheekollu J, Deakyne JS, Wiedmer A,
Ramirez UD, Lieberman PM, Messick TE |
(2019) "Structural
Basis for Cooperative Binding of EBNA1 to the
Epstein-Barr Virus Dyad Symmetry Minimal Origin of
Replication." J.Virol.,
93. doi: 10.1128/JVI.00487-19.
|
Structural basis for cooperative binding of ebna1 to
the epstein-barr virus dyad symmetry minimal origin of
replication . SNAP
output
|
|
6pwe
|
structural protein-DNA |
cryo-EM (3.95 Å) |
Chittori S, Hong J, Bai Y, Subramaniam S |
(2019) "Structure
of the primed state of the ATPase domain of chromatin
remodeling factor ISWI bound to the nucleosome."
Nucleic Acids Res., 47,
9400-9409. doi: 10.1093/nar/gkz670.
|
cryo-EM structure of nucleosome core particle .
SNAP output
|
|
6pwf
|
structural protein-DNA |
cryo-EM (4.07 Å) |
Chittori S, Hong J, Bai Y, Subramaniam S |
(2019) "Structure
of the primed state of the ATPase domain of chromatin
remodeling factor ISWI bound to the nucleosome."
Nucleic Acids Res., 47,
9400-9409. doi: 10.1093/nar/gkz670.
|
cryo-EM structure of the atpase domain of chromatin
remodeling factor iswi bound to the nucleosome .
SNAP output
|
|
6pwv
|
histone binding-DNA binding-DNA |
cryo-EM (6.2 Å) |
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang
B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho
US |
(2019) "Cryo-EM
structure of the human MLL1 core complex bound to the
nucleosome." Nat Commun,
10, 5540. doi: 10.1038/s41467-019-13550-2.
|
cryo-EM structure of mll1 core complex bound to the
nucleosome . SNAP
output
|
|
6pww
|
histone binding-DNA binding-DNA |
cryo-EM (4.4 Å) |
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang
B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho
US |
(2019) "Cryo-EM
structure of the human MLL1 core complex bound to the
nucleosome." Nat Commun,
10, 5540. doi: 10.1038/s41467-019-13550-2.
|
cryo-EM structure of mll1 in complex with rbbp5 and
wdr5 bound to the nucleosome . SNAP output
|
|
6pwx
|
histone binding-DNA binding-DNA |
cryo-EM (4.2 Å) |
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang
B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho
US |
(2019) "Cryo-EM
structure of the human MLL1 core complex bound to the
nucleosome." Nat Commun,
10, 5540. doi: 10.1038/s41467-019-13550-2.
|
cryo-EM structure of rbbp5 bound to the nucleosome .
SNAP output
|
|
6px1
|
gene regulation |
cryo-EM (3.3 Å) |
Bilokapic S, Halic M |
(2019) "Nucleosome
and ubiquitin position Set2 to methylate H3K36."
Nat Commun, 10, 3795. doi:
10.1038/s41467-019-11726-4.
|
Set2 bound to nucleosome . SNAP output
|
|
6px3
|
gene regulation |
cryo-EM (4.1 Å) |
Bilokapic S, Halic M |
(2019) "Nucleosome
and ubiquitin position Set2 to methylate H3K36."
Nat Commun, 10, 3795. doi:
10.1038/s41467-019-11726-4.
|
Set2 bound to nucleosome . SNAP output
|
|
6py8
|
DNA binding protein-DNA |
X-ray (3.75 Å) |
Jarrett SM, Seegar TCM, Andrews M, Adelmant G, Marto
JA, Aster JC, Blacklow SC |
(2019) "Extension
of the Notch intracellular domain ankyrin repeat stack
by NRARP promotes feedback inhibition of Notch
signaling." Sci.Signal.,
12. doi: 10.1126/scisignal.aay2369.
|
Crystal structure of the rbpj-notch1-nrarp ternary
complex bound to DNA . SNAP output
|
|
6pz3
|
transferase |
X-ray (2.395 Å) |
Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash
S, Aggarwal AK |
(2019) "Structural
insights into mutagenicity of anticancer nucleoside
analog cytarabine during replication by DNA polymerase
eta." Sci Rep, 9, 16400.
doi: 10.1038/s41598-019-52703-7.
|
Polymerase eta-catalyzed insertion of correct g
opposite template cytarabine (arac) residue . SNAP output
|
|
6q02
|
transferase-DNA |
X-ray (2.09 Å) |
Rechkoblit O, Johnson RE, Buku A, Prakash L, Prakash
S, Aggarwal AK |
(2019) "Structural
insights into mutagenicity of anticancer nucleoside
analog cytarabine during replication by DNA polymerase
eta." Sci Rep, 9, 16400.
doi: 10.1038/s41598-019-52703-7.
|
Polymerase eta-catalyzed insertion of the mismatched a
opposite template cytarabine (arac) residue . SNAP output
|
|
6q0c
|
hydrolase-DNA |
X-ray (2.0 Å) |
Russelburg LP, O'Shea Murray VL, Demir M, Knutsen KR,
Sehgal SL, Cao S, David SS, Horvath MP |
(2020) "Structural
Basis for Finding OG Lesions and Avoiding Undamaged G
by the DNA Glycosylase MutY." Acs
Chem.Biol., 15, 93-102. doi:
10.1021/acschembio.9b00639.
|
Muty adenine glycosylase bound to DNA containing a
transition state analog (1n) paired with undamaged dg .
SNAP output
|
|
6q1v
|
ligase-DNA |
X-ray (1.85 Å) |
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA,
O'Brien PJ, Williams RS |
(2019) "Two-tiered
enforcement of high-fidelity DNA ligation." Nat
Commun, 10, 5431. doi: 10.1038/s41467-019-13478-7.
|
Human DNA ligase 1 (e592r) bound to an adenylated,
hydroxyl terminated DNA nick . SNAP output
|
|
6q2b
|
transcription |
X-ray (2.72 Å) |
Kim Y, Tesar C, Clancy S, Joachimiak A, Midwest
Center for Structural Genomics (MCSG) |
"Crystal Structure of Putative MarR Family
Transcriptional Regulator from Listeria monocytogenes
complexed with 26mer DNA." |
Crystal structure of putative marr family
transcriptional regulator from listeria monocytogenes
complexed with 26mer DNA . SNAP output
|
|
6q4t
|
DNA binding protein |
X-ray (1.997 Å) |
Kropp HM, Diederichs K, Marx A |
(2019) "The
Structure of an Archaeal B-Family DNA Polymerase in
Complex with a Chemically Modified Nucleotide."
Angew.Chem.Int.Ed.Engl., 58,
5457-5461. doi: 10.1002/anie.201900315.
|
Kod DNA pol in a closed ternary complex with
7-deaza-7-(2-(2-hydroxyethoxy)-n-(prop-2-yn-1-yl)acetamide)-2-datp
. SNAP output
|
|
6q4u
|
DNA binding protein |
X-ray (2.005 Å) |
Kropp HM, Diederichs K, Marx A |
(2019) "The
Structure of an Archaeal B-Family DNA Polymerase in
Complex with a Chemically Modified Nucleotide."
Angew.Chem.Int.Ed.Engl., 58,
5457-5461. doi: 10.1002/anie.201900315.
|
Klentaq DNA pol in a closed ternary complex with
7-deaza-7-(2-(2-hydroxyethoxy)-n-(prop-2-yn-1-yl)acetamide)-2-datp
. SNAP output
|
|
6q4v
|
DNA binding protein |
X-ray (2.006 Å) |
Kropp HM, Diederichs K, Marx A |
(2019) "The
Structure of an Archaeal B-Family DNA Polymerase in
Complex with a Chemically Modified Nucleotide."
Angew.Chem.Int.Ed.Engl., 58,
5457-5461. doi: 10.1002/anie.201900315.
|
Klentaq DNA polymerase in complex with datp . SNAP output
|
|
6q6r
|
DNA binding protein |
X-ray (1.5 Å) |
Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan
AT |
(2020) "Recognition
of different base tetrads by RHAU (DHX36): X-ray
crystal structure of the G4 recognition motif bound to
the 3'-end tetrad of a DNA G-quadruplex."
J.Struct.Biol., 209, 107399.
doi: 10.1016/j.jsb.2019.10.001.
|
Recognition of different base tetrads by rhau: x-ray
crystal structure of g4 recognition motif bound to the
3-end tetrad of a DNA g-quadruplex . SNAP output
|
|
6qec
|
circadian clock protein |
X-ray (1.9 Å) |
Silva CS, Nayak A, Lai X, Hutin S, Hugouvieux V, Jung
JH, Lopez-Vidriero I, Franco-Zorrilla JM, Panigrahi KCS,
Nanao MH, Wigge PA, Zubieta C |
(2020) "Molecular
mechanisms of Evening Complex activity
inArabidopsis." Proc.Natl.Acad.Sci.USA,
117, 6901-6909. doi: 10.1073/pnas.1920972117.
|
DNA binding domain of lux arrythmo in complex with DNA
. SNAP output
|
|
6qem
|
replication |
cryo-EM (3.4 Å) |
Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q,
Berger JM |
(2019) "Physical
Basis for the Loading of a Bacterial Replicative
Helicase onto DNA." Mol.Cell,
74, 173-184.e4. doi: 10.1016/j.molcel.2019.01.023.
|
E. coli dnabc complex bound to ssDNA . SNAP output
|
|
6qfd
|
DNA binding protein |
X-ray (2.133 Å) |
Kutnowski N, Shmulevich F, Davidov G, Shahar A,
Bar-Zvi D, Eichler J, Zarivach R, Shaanan B |
(2019) "Specificity
of protein-DNA interactions in hypersaline environment:
structural studies on complexes of Halobacterium
salinarum oxidative stress-dependent protein
hsRosR." Nucleic Acids Res.,
47, 8860-8873. doi: 10.1093/nar/gkz604.
|
The complex structure of hsrosr-s4 (vng0258-rosr-s4) .
SNAP output
|
|
6qh0
|
DNA binding protein |
X-ray (2.436 Å) |
Kutnowski N, Shmulevich F, Davidov G, Shahar A,
Bar-Zvi D, Eichler J, Zarivach R, Shaanan B |
(2019) "Specificity
of protein-DNA interactions in hypersaline environment:
structural studies on complexes of Halobacterium
salinarum oxidative stress-dependent protein
hsRosR." Nucleic Acids Res.,
47, 8860-8873. doi: 10.1093/nar/gkz604.
|
The complex structure of hsrosr-s5 (vng0258h-rosr-s5) .
SNAP output
|
|
6qhd
|
transcription |
X-ray (2.85 Å) |
Belo Y, Mielko Z, Nudelman H, Afek A, Ben-David O,
Shahar A, Zarivach R, Gordan R, Arbely E |
(2019) "Unexpected
implications of STAT3 acetylation revealed by genetic
encoding of acetyl-lysine." Biochim Biophys
Acta Gen Subj, 1863, 1343-1350.
doi: 10.1016/j.bbagen.2019.05.019.
|
Lysine acetylated and tyrosine phosphorylated stat3 in
a complex with DNA . SNAP output
|
|
6qib
|
DNA binding protein |
X-ray (2.8 Å) |
Ter Beek J, Parkash V, Bylund GO, Osterman P,
Sauer-Eriksson AE, Johansson E |
(2019) "Structural
evidence for an essential Fe-S cluster in the catalytic
core domain of DNA polymerase ε." Nucleic Acids
Res., 47, 5712-5722. doi:
10.1093/nar/gkz248.
|
The crystal structure of pol2core in complex with DNA
and an incoming nucleotide, carrying an fe-s cluster .
SNAP output
|
|
6qil
|
DNA binding protein |
X-ray (2.0 Å) |
Kutnowski N, Shmulevich F, Davidov G, Shahar A,
Bar-Zvi D, Eichler J, Zarivach R, Shaanan B |
(2019) "Specificity
of protein-DNA interactions in hypersaline environment:
structural studies on complexes of Halobacterium
salinarum oxidative stress-dependent protein
hsRosR." Nucleic Acids Res.,
47, 8860-8873. doi: 10.1093/nar/gkz604.
|
The complex structure of hsrosr-s1 (vng0258h-rosr-s1) .
SNAP output
|
|
6qld
|
DNA binding protein |
cryo-EM (4.15 Å) |
Yan K, Yang J, Zhang Z, McLaughlin SH, Chang L, Fasci
D, Ehrenhofer-Murray AE, Heck AJR, Barford D |
(2019) "Structure
of the inner kinetochore CCAN complex assembled onto a
centromeric nucleosome." Nature,
574, 278-282. doi: 10.1038/s41586-019-1609-1.
|
Structure of inner kinetochore ccan-cenp-a complex .
SNAP output
|
|
6qtk
|
isomerase |
X-ray (2.31 Å) |
Gibson EG, Bax B, Chan PF, Osheroff N |
(2019) "Mechanistic
and Structural Basis for the Actions of the
Antibacterial Gepotidacin against Staphylococcus aureus
Gyrase." Acs Infect Dis.,
5, 570-581. doi: 10.1021/acsinfecdis.8b00315.
|
2.31a structure of gepotidacin with s.aureus DNA gyrase
and doubly nicked DNA . SNAP output
|
|
6qtp
|
isomerase |
X-ray (2.37 Å) |
Gibson EG, Bax B, Chan PF, Osheroff N |
(2019) "Mechanistic
and Structural Basis for the Actions of the
Antibacterial Gepotidacin against Staphylococcus aureus
Gyrase." Acs Infect Dis.,
5, 570-581. doi: 10.1021/acsinfecdis.8b00315.
|
2.37a structure of gepotidacin with s.aureus DNA gyrase
and uncleaved DNA . SNAP
output
|
|
6qua
|
DNA binding protein |
X-ray (2.681 Å) |
Kutnowski N, Shmulevich F, Davidov G, Shahar A,
Bar-Zvi D, Eichler J, Zarivach R, Shaanan B |
(2019) "Specificity
of protein-DNA interactions in hypersaline environment:
structural studies on complexes of Halobacterium
salinarum oxidative stress-dependent protein
hsRosR." Nucleic Acids Res.,
47, 8860-8873. doi: 10.1093/nar/gkz604.
|
The complex structure of hsrosr-sg (vng0258-rosr-sg) .
SNAP output
|
|
6qwf
|
DNA binding protein |
X-ray (2.7 Å) |
Hansen S, Hall M, Grundstrom C, Brannstrom K,
Sauer-Eriksson AE, Johansson J |
(2020) "A Novel
Growth-Based Selection Strategy Identifies New
Constitutively Active Variants of the Major Virulence
Regulator PrfA in Listeria monocytogenes."
J.Bacteriol., 202. doi:
10.1128/JB.00115-20.
|
The transcriptional regulator prfa-a94v mutant from
listeria monocytogenes in complex with a 30-bp operator
prfa-box motif . SNAP
output
|
|
6qwh
|
DNA binding protein |
X-ray (2.9 Å) |
Hansen S, Hall M, Grundstrom C, Brannstrom K,
Sauer-Eriksson AE, Johansson J |
(2020) "A Novel
Growth-Based Selection Strategy Identifies New
Constitutively Active Variants of the Major Virulence
Regulator PrfA in Listeria monocytogenes."
J.Bacteriol., 202. doi:
10.1128/JB.00115-20.
|
The transcriptional regulator prfa-l140h mutant from
listeria monocytogenes in complex with a 30-bp operator
prfa-box motif . SNAP
output
|
|
6qwk
|
DNA binding protein |
X-ray (2.9 Å) |
Hansen S, Hall M, Grundstrom C, Brannstrom K,
Sauer-Eriksson AE, Johansson J |
(2020) "A Novel
Growth-Based Selection Strategy Identifies New
Constitutively Active Variants of the Major Virulence
Regulator PrfA in Listeria monocytogenes."
J.Bacteriol., 202. doi:
10.1128/JB.00115-20.
|
The transcriptional regulator prfa-l140f mutant from
listeria monocytogenes in complex with a 30-bp operator
prfa-box motif . SNAP
output
|
|
6qwm
|
DNA binding protein |
X-ray (2.9 Å) |
Hansen S, Hall M, Grundstrom C, Brannstrom K,
Sauer-Eriksson AE, Johansson J |
(2020) "A Novel
Growth-Based Selection Strategy Identifies New
Constitutively Active Variants of the Major Virulence
Regulator PrfA in Listeria monocytogenes."
J.Bacteriol., 202. doi:
10.1128/JB.00115-20.
|
The transcriptional regulator prfa-a218g mutant from
listeria monocytogenes in complex with a 30-bp operator
prfa-box motif . SNAP
output
|
|
6qx1
|
isomerase |
X-ray (2.65 Å) |
Thalji RK, Raha K, Andreotti D, Checchia A, Cui H,
Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T,
Donovan BT, Howells A, Jain S, Nixon C, Quinque G,
McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA |
(2019) "Structure-guided
design of antibacterials that allosterically inhibit
DNA gyrase." Bioorg.Med.Chem.Lett.,
29, 1407-1412. doi: 10.1016/j.bmcl.2019.03.029.
|
2.7a structure of benzoisoxazole 3 with s.aureus DNA
gyrase and DNA. . SNAP
output
|
|
6qx2
|
isomerase |
X-ray (3.4 Å) |
Thalji RK, Raha K, Andreotti D, Checchia A, Cui H,
Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T,
Donovan BT, Howells A, Jain S, Nixon C, Quinque G,
McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA |
(2019) "Structure-guided
design of antibacterials that allosterically inhibit
DNA gyrase." Bioorg.Med.Chem.Lett.,
29, 1407-1412. doi: 10.1016/j.bmcl.2019.03.029.
|
3.4a structure of benzoisoxazole 3 with s.aureus DNA
gyrase and DNA . SNAP
output
|
|
6qxf
|
DNA binding protein |
cryo-EM (3.6 Å) |
Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G,
Siksnys V, Wigley DB |
(2019) "Structure
of the DNA-Bound Spacer Capture Complex of a Type II
CRISPR-Cas System." Mol.Cell,
75, 90-101.e5. doi: 10.1016/j.molcel.2019.04.020.
|
Cas1-cas2-csn2-DNA complex from the type ii-a
crispr-cas system . SNAP
output
|
|
6qxt
|
DNA binding protein |
cryo-EM (8.9 Å) |
Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G,
Siksnys V, Wigley DB |
(2019) "Structure
of the DNA-Bound Spacer Capture Complex of a Type II
CRISPR-Cas System." Mol.Cell,
75, 90-101.e5. doi: 10.1016/j.molcel.2019.04.020.
|
Cas1-cas2-csn2-DNA dimer complex from the type ii-a
crispr-cas system . SNAP
output
|
|
6qy3
|
DNA binding protein |
cryo-EM (9.1 Å) |
Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G,
Siksnys V, Wigley DB |
(2019) "Structure
of the DNA-Bound Spacer Capture Complex of a Type II
CRISPR-Cas System." Mol.Cell,
75, 90-101.e5. doi: 10.1016/j.molcel.2019.04.020.
|
Segment of the cas1-cas2-csn2-DNA filament complex from
the type ii-a crispr-cas system . SNAP output
|
|
6qzk
|
hydrolase |
X-ray (3.548 Å) |
Hegge JW, Swarts DC, Chandradoss SD, Cui TJ, Kneppers
J, Jinek M, Joo C, van der Oost J |
(2019) "DNA-guided
DNA cleavage at moderate temperatures by Clostridium
butyricum Argonaute." Nucleic Acids Res.,
47, 5809-5821. doi: 10.1093/nar/gkz306.
|
Structure of clostridium butyricum argonaute bound to a
guide DNA (5' deoxycytidine) and a 19-mer target DNA .
SNAP output
|
|
6qzp
|
ribosome |
cryo-EM (2.9 Å) |
Natchiar SK, Myasnikov AG, Kratzat H, Hazemann I,
Klaholz BP |
(2017) "Visualization
of chemical modifications in the human 80S ribosome
structure." Nature, 551,
472-477. doi: 10.1038/nature24482.
|
High-resolution cryo-EM structure of the human 80s
ribosome . SNAP
output
|
|
6r0c
|
DNA binding protein |
cryo-EM (4.2 Å) |
Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE,
Nans A, Rueda DS, Cherepanov P, Costa A |
(2019) "Retroviral
integration into nucleosomes through DNA looping and
sliding along the histone octamer." Nat
Commun, 10, 4189. doi: 10.1038/s41467-019-12007-w.
|
Human-d02 nucleosome core particle with
biotin-streptavidin label . SNAP output
|
|
6r1t
|
gene regulation |
cryo-EM (4.02 Å) |
Marabelli C, Marrocco B, Pilotto S, Chittori S,
Picaud S, Marchese S, Ciossani G, Forneris F,
Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S,
Mattevi A |
(2019) "A
Tail-Based Mechanism Drives Nucleosome Demethylation by
the LSD2/NPAC Multimeric Complex." Cell
Rep, 27, 387-399.e7. doi:
10.1016/j.celrep.2019.03.061.
|
Structure of lsd2-npac-linker-nucleosome core particle
complex: class 1, free nuclesome . SNAP output
|
|
6r1u
|
gene regulation |
cryo-EM (4.36 Å) |
Marabelli C, Marrocco B, Pilotto S, Chittori S,
Picaud S, Marchese S, Ciossani G, Forneris F,
Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S,
Mattevi A |
(2019) "A
Tail-Based Mechanism Drives Nucleosome Demethylation by
the LSD2/NPAC Multimeric Complex." Cell
Rep, 27, 387-399.e7. doi:
10.1016/j.celrep.2019.03.061.
|
Structure of lsd2-npac-linker-nucleosome core particle
complex: class 2 . SNAP
output
|
|
6r25
|
gene regulation |
cryo-EM (4.61 Å) |
Marabelli C, Marrocco B, Pilotto S, Chittori S,
Picaud S, Marchese S, Ciossani G, Forneris F,
Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S,
Mattevi A |
(2019) "A
Tail-Based Mechanism Drives Nucleosome Demethylation by
the LSD2/NPAC Multimeric Complex." Cell
Rep, 27, 387-399.e7. doi:
10.1016/j.celrep.2019.03.061.
|
Structure of lsd2-npac-linker-nucleosome core particle
complex: class 3 . SNAP
output
|
|
6r2v
|
transcription |
X-ray (2.503 Å) |
Chaves-Sanjuan A, Gnesutta N, Gobbini A, Martignago
D, Bernardini A, Fornara F, Mantovani R, Nardini M |
(2021) "Structural
determinants for NF-Y subunit organization and NF-Y/DNA
association in plants." Plant J.,
105, 49-61. doi: 10.1111/tpj.15038.
|
Arabidopsis nf-y-ccaat-box complex . SNAP output
|
|
6r64
|
hydrolase |
X-ray (2.64 Å) |
Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G,
Bochtler M |
(2019) "Crystal
structure of the EcoKMcrA N-terminal domain (NEco):
recognition of modified cytosine bases without
flipping." Nucleic Acids Res.,
47, 11943-11955. doi: 10.1093/nar/gkz1017.
|
N-terminal domain of modification dependent ecokmcra
restriction endonuclease (neco) in complex with c5mcgg
target sequence . SNAP
output
|
|
6r6p
|
ribosome |
cryo-EM (3.1 Å) |
Shanmuganathan V, Schiller N, Magoulopoulou A, Cheng
J, Braunger K, Cymer F, Berninghausen O, Beatrix B, Kohno
K, Heijne GV, Beckmann R |
(2019) "Structural
and mutational analysis of the ribosome-arresting human
XBP1u." Elife, 8. doi:
10.7554/eLife.46267.
|
Structure of xbp1u-paused ribosome nascent chain
complex (rotated state) . SNAP output
|
|
6r8y
|
DNA binding protein |
cryo-EM (4.3 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp-6-4pp(-1)-uv-ddb . SNAP output
|
|
6r8z
|
DNA binding protein |
cryo-EM (3.9 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp_thf2(-1)-uv-ddb . SNAP output
|
|
6r90
|
DNA binding protein |
cryo-EM (4.5 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp-thf2(+1)-uv-ddb class a .
SNAP output
|
|
6r91
|
DNA binding protein |
cryo-EM (4.1 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp_thf2(-3)-uv-ddb . SNAP output
|
|
6r92
|
DNA binding protein |
cryo-EM (4.8 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp-thf2(+1)-uv-ddb class b .
SNAP output
|
|
6r93
|
DNA |
cryo-EM (4.0 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp-6-4pp . SNAP output
|
|
6r94
|
DNA binding protein |
cryo-EM (3.5 Å) |
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza
A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S,
Sugasawa K, Kurumizaka H, Thoma NH |
(2019) "DNA
damage detection in nucleosomes involves DNA register
shifting." Nature, 571,
79-84. doi: 10.1038/s41586-019-1259-3.
|
cryo-EM structure of ncp_thf2(-3) . SNAP output
|
|
6rar
|
DNA binding protein |
X-ray (1.785 Å) |
Williamson A, Leiros HS |
(2019) "Structural
intermediates of a DNA-ligase complex illuminate the
role of the catalytic metal ion and mechanism of
phosphodiester bond formation." Nucleic Acids
Res., 47, 7147-7162. doi:
10.1093/nar/gkz596.
|
Pmar-lig_pres3-mn . SNAP
output
|
|
6ras
|
DNA binding protein |
X-ray (2.75 Å) |
Williamson A, Leiros HS |
(2019) "Structural
intermediates of a DNA-ligase complex illuminate the
role of the catalytic metal ion and mechanism of
phosphodiester bond formation." Nucleic Acids
Res., 47, 7147-7162. doi:
10.1093/nar/gkz596.
|
Pmar-lig_pre. . SNAP
output
|
|
6rau
|
DNA binding protein |
X-ray (1.99 Å) |
Williamson A, Leiros HS |
(2019) "Structural
intermediates of a DNA-ligase complex illuminate the
role of the catalytic metal ion and mechanism of
phosphodiester bond formation." Nucleic Acids
Res., 47, 7147-7162. doi:
10.1093/nar/gkz596.
|
Posts3_pmar_lig4_wt . SNAP output
|
|
6raw
|
replication |
cryo-EM (3.7 Å) |
Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali
F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR,
Yardimci H, Costa A |
(2019) "Molecular
Basis for ATP-Hydrolysis-Driven DNA Translocation by
the CMG Helicase of the Eukaryotic Replisome."
Cell Rep, 28, 2673-2688.e8.
doi: 10.1016/j.celrep.2019.07.104.
|
D. melanogaster cmg-DNA, state 1a . SNAP output
|
|
6rax
|
hydolase |
cryo-EM (3.99 Å) |
Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali
F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR,
Yardimci H, Costa A |
(2019) "Molecular
Basis for ATP-Hydrolysis-Driven DNA Translocation by
the CMG Helicase of the Eukaryotic Replisome."
Cell Rep, 28, 2673-2688.e8.
doi: 10.1016/j.celrep.2019.07.104.
|
D. melanogaster cmg-DNA, state 1b . SNAP output
|
|
6ray
|
replication |
cryo-EM (4.28 Å) |
Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali
F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR,
Yardimci H, Costa A |
(2019) "Molecular
Basis for ATP-Hydrolysis-Driven DNA Translocation by
the CMG Helicase of the Eukaryotic Replisome."
Cell Rep, 28, 2673-2688.e8.
doi: 10.1016/j.celrep.2019.07.104.
|
D. melanogaster cmg-DNA, state 2a . SNAP output
|
|
6raz
|
hydrolase |
cryo-EM (4.46 Å) |
Eickhoff P, Kose HB, Martino F, Petojevic T, Abid Ali
F, Locke J, Tamberg N, Nans A, Berger JM, Botchan MR,
Yardimci H, Costa A |
(2019) "Molecular
Basis for ATP-Hydrolysis-Driven DNA Translocation by
the CMG Helicase of the Eukaryotic Replisome."
Cell Rep, 28, 2673-2688.e8.
doi: 10.1016/j.celrep.2019.07.104.
|
D. melanogaster cmg-DNA, state 2b . SNAP output
|
|
6rce
|
DNA binding protein |
X-ray (1.946 Å) |
Williamson A, Leiros HS |
(2019) "Structural
intermediates of a DNA-ligase complex illuminate the
role of the catalytic metal ion and mechanism of
phosphodiester bond formation." Nucleic Acids
Res., 47, 7147-7162. doi:
10.1093/nar/gkz596.
|
Pmar-lig_pres3 . SNAP
output
|
|
6rcn
|
hydrolase |
X-ray (2.25 Å) |
Nicholls TJ, Spahr H, Jiang S, Siira SJ, Koolmeister
C, Sharma S, Kauppila JHK, Jiang M, Kaever V, Rackham O,
Chabes A, Falkenberg M, Filipovska A, Larsson NG,
Gustafsson CM |
(2019) "Dinucleotide
Degradation by REXO2 Maintains Promoter Specificity in
Mammalian Mitochondria." Mol.Cell,
76, 784-796.e6. doi: 10.1016/j.molcel.2019.09.010.
|
Crystal structure of rexo2-d199a-dada . SNAP output
|
|
6rh3
|
transcription |
cryo-EM (3.6 Å) |
Abdelkareem M, Saint-Andre C, Takacs M, Papai G,
Crucifix C, Guo X, Ortiz J, Weixlbaumer A |
(2019) "Structural
Basis of Transcription: RNA Polymerase Backtracking and
Its Reactivation." Mol.Cell,
75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029.
|
cryo-EM structure of e. coli RNA polymerase elongation
complex bound to ctp substrate . SNAP output
|
|
6ri7
|
transcription |
cryo-EM (3.9 Å) |
Abdelkareem M, Saint-Andre C, Takacs M, Papai G,
Crucifix C, Guo X, Ortiz J, Weixlbaumer A |
(2019) "Structural
Basis of Transcription: RNA Polymerase Backtracking and
Its Reactivation." Mol.Cell,
75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029.
|
cryo-EM structure of e. coli RNA polymerase elongation
complex bound to greb transcription factor . SNAP output
|
|
6ri9
|
transcription |
cryo-EM (3.7 Å) |
Abdelkareem M, Saint-Andre C, Takacs M, Papai G,
Crucifix C, Guo X, Ortiz J, Weixlbaumer A |
(2019) "Structural
Basis of Transcription: RNA Polymerase Backtracking and
Its Reactivation." Mol.Cell,
75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029.
|
cryo-EM structure of e. coli RNA polymerase backtracked
elongation complex in non-swiveled state . SNAP output
|
|
6rid
|
viral protein |
cryo-EM (2.9 Å) |
Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K,
Szalay AA, Fischer U, Cramer P |
(2019) "Structural
Basis of Poxvirus Transcription: Transcribing and
Capping Vaccinia Complexes." Cell,
179, 1525. doi: 10.1016/j.cell.2019.11.023.
|
Structure of vaccinia virus DNA-dependent RNA
polymerase elongation complex . SNAP output
|
|
6rie
|
viral protein |
cryo-EM (3.1 Å) |
Hillen HS, Bartuli J, Grimm C, Dienemann C, Bedenk K,
Szalay AA, Fischer U, Cramer P |
(2019) "Structural
Basis of Poxvirus Transcription: Transcribing and
Capping Vaccinia Complexes." Cell,
179, 1525. doi: 10.1016/j.cell.2019.11.023.
|
Structure of vaccinia virus DNA-dependent RNA
polymerase co-transcriptional capping complex .
SNAP output
|
|
6rin
|
transcription |
cryo-EM (3.7 Å) |
Abdelkareem M, Saint-Andre C, Takacs M, Papai G,
Crucifix C, Guo X, Ortiz J, Weixlbaumer A |
(2019) "Structural
Basis of Transcription: RNA Polymerase Backtracking and
Its Reactivation." Mol.Cell,
75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029.
|
cryo-EM structure of e. coli RNA polymerase backtracked
elongation complex bound to greb transcription factor .
SNAP output
|
|
6rip
|
transcription |
cryo-EM (3.4 Å) |
Abdelkareem M, Saint-Andre C, Takacs M, Papai G,
Crucifix C, Guo X, Ortiz J, Weixlbaumer A |
(2019) "Structural
Basis of Transcription: RNA Polymerase Backtracking and
Its Reactivation." Mol.Cell,
75, 298-309.e4. doi: 10.1016/j.molcel.2019.04.029.
|
cryo-EM structure of e. coli RNA polymerase backtracked
elongation complex in swiveled state . SNAP output
|
|
6rj9
|
hydrolase |
cryo-EM (3.2 Å) |
Fuchsbauer O, Swuec P, Zimberger C, Amigues B,
Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A,
Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M,
Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A |
(2019) "Cas9
Allosteric Inhibition by the Anti-CRISPR Protein
AcrIIA6." Mol.Cell, 76,
922. doi: 10.1016/j.molcel.2019.09.012.
|
cryo-EM structure of st1cas9-sgrna-tdna20-acriia6
monomeric assembly. . SNAP output
|
|
6rja
|
hydrolase |
cryo-EM (3.0 Å) |
Fuchsbauer O, Swuec P, Zimberger C, Amigues B,
Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A,
Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M,
Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A |
(2019) "Cas9
Allosteric Inhibition by the Anti-CRISPR Protein
AcrIIA6." Mol.Cell, 76,
922. doi: 10.1016/j.molcel.2019.09.012.
|
cryo-EM structure of st1cas9-sgrna-tdna20-acriia6
dimeric assembly. . SNAP
output
|
|
6rjd
|
hydrolase |
cryo-EM (3.3 Å) |
Fuchsbauer O, Swuec P, Zimberger C, Amigues B,
Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A,
Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M,
Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A |
(2019) "Cas9
Allosteric Inhibition by the Anti-CRISPR Protein
AcrIIA6." Mol.Cell, 76,
922. doi: 10.1016/j.molcel.2019.09.012.
|
cryo-EM structure of st1cas9-sgrna-tdna59-ntpam
complex. . SNAP
output
|
|
6rjg
|
hydrolase |
cryo-EM (3.2 Å) |
Fuchsbauer O, Swuec P, Zimberger C, Amigues B,
Levesque S, Agudelo D, Duringer A, Chaves-Sanjuan A,
Spinelli S, Rousseau GM, Velimirovic M, Bolognesi M,
Roussel A, Cambillau C, Moineau S, Doyon Y, Goulet A |
(2019) "Cas9
Allosteric Inhibition by the Anti-CRISPR Protein
AcrIIA6." Mol.Cell, 76,
922. doi: 10.1016/j.molcel.2019.09.012.
|
cryo-EM structure of st1cas9-sgrna-acriia6-tdna59-ntpam
complex. . SNAP
output
|
|
6rks
|
isomerase |
cryo-EM (4.0 Å) |
Vanden Broeck A, Lotz C, Ortiz J, Lamour V |
(2019) "Cryo-EM
structure of the complete E. coli DNA gyrase
nucleoprotein complex." Nat Commun,
10, 4935. doi: 10.1038/s41467-019-12914-y.
|
E. coli DNA gyrase - DNA binding and cleavage domain in
state 1 without toprim insertion . SNAP output
|
|
6rku
|
isomerase |
cryo-EM (4.0 Å) |
Vanden Broeck A, Lotz C, Ortiz J, Lamour V |
(2019) "Cryo-EM
structure of the complete E. coli DNA gyrase
nucleoprotein complex." Nat Commun,
10, 4935. doi: 10.1038/s41467-019-12914-y.
|
E. coli DNA gyrase - DNA binding and cleavage domain in
state 1 . SNAP
output
|
|
6rkv
|
isomerase |
cryo-EM (4.6 Å) |
Vanden Broeck A, Lotz C, Ortiz J, Lamour V |
(2019) "Cryo-EM
structure of the complete E. coli DNA gyrase
nucleoprotein complex." Nat Commun,
10, 4935. doi: 10.1038/s41467-019-12914-y.
|
E. coli DNA gyrase - DNA binding and cleavage domain in
state 2 . SNAP
output
|
|
6rkw
|
isomerase |
cryo-EM (6.6 Å) |
Vanden Broeck A, Lotz C, Ortiz J, Lamour V |
(2019) "Cryo-EM
structure of the complete E. coli DNA gyrase
nucleoprotein complex." Nat Commun,
10, 4935. doi: 10.1038/s41467-019-12914-y.
|
Cryoem structure of the complete e. coli DNA gyrase
complex bound to a 130 bp DNA duplex . SNAP output
|
|
6rnm
|
hydrolase |
X-ray (1.76 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
Crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6rno
|
hydrolase |
X-ray (2.25 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
Crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6rnr
|
hydrolase |
X-ray (2.003 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
The crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6rny
|
DNA binding protein |
cryo-EM (3.9 Å) |
Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE,
Nans A, Rueda DS, Cherepanov P, Costa A |
(2019) "Retroviral
integration into nucleosomes through DNA looping and
sliding along the histone octamer." Nat
Commun, 10, 4189. doi: 10.1038/s41467-019-12007-w.
|
Pfv intasome - nucleosome strand transfer complex .
SNAP output
|
|
6ro2
|
hydrolase |
X-ray (1.821 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
The crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6ro4
|
translocase |
cryo-EM (3.5 Å) |
Kokic G, Chernev A, Tegunov D, Dienemann C, Urlaub H,
Cramer P |
(2019) "Structural
basis of TFIIH activation for nucleotide excision
repair." Nat Commun, 10,
2885. doi: 10.1038/s41467-019-10745-5.
|
Structure of the core tfiih-xpa-DNA complex . SNAP output
|
|
6rok
|
hydrolase |
X-ray (1.95 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
The crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6rp0
|
hydrolase |
X-ray (2.25 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
The crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6rp7
|
hydrolase |
X-ray (2.0 Å) |
Rieux C, Goffinont S, Coste F, Tber Z, Cros J, Roy V,
Guerin M, Gaudon V, Bourg S, Biela A, Aucagne V,
Agrofoglio L, Garnier N, Castaing B |
(2020) "Thiopurine
Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition:
Structural, Dynamic and Functional Insights."
Int J Mol Sci, 21. doi:
10.3390/ijms21062058.
|
The crystal structure of a complex between the llfpg
protein, a thf-DNA and an inhibitor . SNAP output
|
|
6rqc
|
replication |
cryo-EM (4.4 Å) |
Miller TCR, Locke J, Greiwe JF, Diffley JFX, Costa
A |
(2019) "Mechanism
of head-to-head MCM double-hexamer formation revealed
by cryo-EM." Nature, 575,
704-710. doi: 10.1038/s41586-019-1768-0.
|
cryo-EM structure of an mcm loading intermediate .
SNAP output
|
|
6rqh
|
transcription |
cryo-EM (3.7 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i closed conformation 1 (cc1) . SNAP output
|
|
6rql
|
transcription |
cryo-EM (2.9 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i closed conformation 2 (cc2) . SNAP output
|
|
6rqt
|
transcription |
cryo-EM (4.0 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i-twh-rrn3-DNA . SNAP output
|
|
6rrd
|
transcription |
cryo-EM (3.1 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i pre-initiation complex DNA opening
intermediate 1 . SNAP
output
|
|
6rt4
|
RNA binding protein |
X-ray (1.49 Å) |
Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch
A |
(2019) "Flexible
Binding of m6A Reader Protein YTHDC1 to Its Preferred
RNA Motif." J Chem Theory Comput,
15, 7004-7014. doi: 10.1021/acs.jctc.9b00987.
|
The yth domain of ythdc1 protein in complex with m6acu
oligonucleotide . SNAP
output
|
|
6rt5
|
RNA binding protein |
X-ray (2.303 Å) |
Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch
A |
(2019) "Flexible
Binding of m6A Reader Protein YTHDC1 to Its Preferred
RNA Motif." J Chem Theory Comput,
15, 7004-7014. doi: 10.1021/acs.jctc.9b00987.
|
The yth domain of ythdc1 protein in complex with gm6ac
oligonucleotide . SNAP
output
|
|
6rt6
|
RNA binding protein |
X-ray (1.461 Å) |
Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch
A |
(2019) "Flexible
Binding of m6A Reader Protein YTHDC1 to Its Preferred
RNA Motif." J Chem Theory Comput,
15, 7004-7014. doi: 10.1021/acs.jctc.9b00987.
|
The yth domain of ythdc1 protein in complex with ggm6ac
oligonucleotide . SNAP
output
|
|
6rt7
|
RNA binding protein |
X-ray (1.73 Å) |
Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch
A |
(2019) "Flexible
Binding of m6A Reader Protein YTHDC1 to Its Preferred
RNA Motif." J Chem Theory Comput,
15, 7004-7014. doi: 10.1021/acs.jctc.9b00987.
|
The yth domain of ythdc1 protein in complex with gm6acu
oligonucleotide . SNAP
output
|
|
6rui
|
transcription |
cryo-EM (2.7 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i pre-initiation complex DNA opening
intermediate 2 . SNAP
output
|
|
6ruo
|
transcription |
cryo-EM (3.5 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i open complex conformation 1 . SNAP output
|
|
6rwe
|
transcription |
cryo-EM (3.0 Å) |
Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R,
Weis F, Muller CW |
(2019) "Molecular
insight into RNA polymerase I promoter recognition and
promoter melting." Nat Commun,
10, 5543. doi: 10.1038/s41467-019-13510-w.
|
RNA polymerase i open complex conformation 2 . SNAP output
|
|
6rwl
|
recombination |
cryo-EM (3.36 Å) |
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas
A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov
P |
(2020) "Structural
basis of second-generation HIV integrase inhibitor
action and viral resistance." Science,
367, 806-810. doi: 10.1126/science.aay4919.
|
Sivrcm intasome . SNAP
output
|
|
6rwm
|
recombination |
cryo-EM (2.81 Å) |
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas
A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov
P |
(2020) "Structural
basis of second-generation HIV integrase inhibitor
action and viral resistance." Science,
367, 806-810. doi: 10.1126/science.aay4919.
|
Sivrcm intasome in complex with bictegravir . SNAP output
|
|
6rwn
|
recombination |
cryo-EM (3.1 Å) |
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas
A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov
P |
(2020) "Structural
basis of second-generation HIV integrase inhibitor
action and viral resistance." Science,
367, 806-810. doi: 10.1126/science.aay4919.
|
Sivrcm intasome in complex with dolutegravir . SNAP output
|
|
6rwo
|
recombination |
cryo-EM (3.05 Å) |
Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas
A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov
P |
(2020) "Structural
basis of second-generation HIV integrase inhibitor
action and viral resistance." Science,
367, 806-810. doi: 10.1126/science.aay4919.
|
Sivrcm intasome (q148h-g140s) in complex with
bictegravir . SNAP
output
|
|
6ryd
|
DNA binding protein |
X-ray (1.575 Å) |
Sloan J, Hakenjos JP, Gebert M, Ermakova O, Gumiero
A, Stier G, Wild K, Sinning I, Lohmann JU |
(2020) "Structural
basis for the complex DNA binding behavior of the plant
stem cell regulator WUSCHEL." Nat Commun,
11, 2223. doi: 10.1038/s41467-020-16024-y.
|
Wus-hd bound to tgaa DNA . SNAP output
|
|
6ryi
|
DNA binding protein |
X-ray (2.691 Å) |
Sloan J, Hakenjos JP, Gebert M, Ermakova O, Gumiero
A, Stier G, Wild K, Sinning I, Lohmann JU |
(2020) "Structural
basis for the complex DNA binding behavior of the plant
stem cell regulator WUSCHEL." Nat Commun,
11, 2223. doi: 10.1038/s41467-020-16024-y.
|
Wus-hd bound to g-box DNA . SNAP output
|
|
6ryl
|
DNA binding protein |
X-ray (2.63 Å) |
Sloan J, Hakenjos JP, Gebert M, Ermakova O, Gumiero
A, Stier G, Wild K, Sinning I, Lohmann JU |
(2020) "Structural
basis for the complex DNA binding behavior of the plant
stem cell regulator WUSCHEL." Nat Commun,
11, 2223. doi: 10.1038/s41467-020-16024-y.
|
Wus-hd bound to taat DNA . SNAP output
|
|
6ryr
|
transcription |
cryo-EM (3.1 Å) |
Farnung L, Ochmann M, Cramer P |
(2020) "Nucleosome-CHD4
chromatin remodeller structure maps human disease
mutations." Elife, 9.
doi: 10.7554/eLife.56178.
|
Nucleosome-chd4 complex structure (single chd4 copy) .
SNAP output
|
|
6ryu
|
transcription |
cryo-EM (4.0 Å) |
Farnung L, Ochmann M, Cramer P |
(2020) "Nucleosome-CHD4
chromatin remodeller structure maps human disease
mutations." Elife, 9.
doi: 10.7554/eLife.56178.
|
Nucleosome-chd4 complex structure (two chd4 copies) .
SNAP output
|
|
6s01
|
transcription |
cryo-EM (3.2 Å) |
Wang H, Farnung L, Dienemann C, Cramer P |
(2020) "Structure
of H3K36-methylated nucleosome-PWWP complex reveals
multivalent cross-gyre binding."
Nat.Struct.Mol.Biol., 27,
8-13. doi: 10.1038/s41594-019-0345-4.
|
Structure of ledgf pwwp domain bound h3k36 methylated
nucleosome . SNAP
output
|
|
6s16
|
hydrolase |
X-ray (3.409 Å) |
Gorecka KM, Krepl M, Szlachcic A, Poznanski J, Sponer
J, Nowotny M |
(2019) "RuvC
uses dynamic probing of the Holliday junction to
achieve sequence specificity and efficient
resolution." Nat Commun,
10, 4102. doi: 10.1038/s41467-019-11900-8.
|
T. thermophilus ruvc in complex with holliday junction
substrate . SNAP
output
|
|
6s1m
|
replication |
cryo-EM (4.27 Å) |
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N,
Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ,
Hamdan SM, De Biasio A |
(2020) "Structure
of the processive human Pol delta holoenzyme."
Nat Commun, 11, 1109. doi:
10.1038/s41467-020-14898-6.
|
Human polymerase delta holoenzyme conformer 1 .
SNAP output
|
|
6s1n
|
replication |
cryo-EM (4.86 Å) |
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N,
Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ,
Hamdan SM, De Biasio A |
(2020) "Structure
of the processive human Pol delta holoenzyme."
Nat Commun, 11, 1109. doi:
10.1038/s41467-020-14898-6.
|
Human polymerase delta holoenzyme conformer 2 .
SNAP output
|
|
6s1o
|
replication |
cryo-EM (8.1 Å) |
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N,
Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ,
Hamdan SM, De Biasio A |
(2020) "Structure
of the processive human Pol delta holoenzyme."
Nat Commun, 11, 1109. doi:
10.1038/s41467-020-14898-6.
|
Human polymerase delta holoenzyme conformer 3 .
SNAP output
|
|
6s3h
|
hydrolase |
X-ray (2.06 Å) |
Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou
SX, Rety S, Xi XG |
(2021) "Structural
and functional studies of SF1B Pif1 from Thermus
oshimai reveal dimerization-induced helicase
inhibition." Nucleic Acids Res.,
49, 4129-4143. doi: 10.1093/nar/gkab188.
|
Crystal structure of helicase pif1 from thermus oshimai
in complex with adp-alf4 and (dt)7ds11bp . SNAP output
|
|
6s3i
|
hydrolase |
X-ray (2.455 Å) |
Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou
SX, Rety S, Xi XG |
(2021) "Structural
and functional studies of SF1B Pif1 from Thermus
oshimai reveal dimerization-induced helicase
inhibition." Nucleic Acids Res.,
49, 4129-4143. doi: 10.1093/nar/gkab188.
|
Crystal structure of helicase pif1 from thermus oshimai
in complex with ssDNA (dt)18 and adp-mgf4 . SNAP output
|
|
6s3m
|
hydrolase |
X-ray (2.113 Å) |
Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou
SX, Rety S, Xi XG |
(2021) "Structural
and functional studies of SF1B Pif1 from Thermus
oshimai reveal dimerization-induced helicase
inhibition." Nucleic Acids Res.,
49, 4129-4143. doi: 10.1093/nar/gkab188.
|
Crystal structure of helicase pif1 from thermus oshimai
in complex with ssDNA (dt)18 and adp-alf4 . SNAP output
|
|
6s3n
|
hydrolase |
X-ray (2.533 Å) |
Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou
SX, Rety S, Xi XG |
(2021) "Structural
and functional studies of SF1B Pif1 from Thermus
oshimai reveal dimerization-induced helicase
inhibition." Nucleic Acids Res.,
49, 4129-4143. doi: 10.1093/nar/gkab188.
|
Crystal structure of helicase pif1 from thermus oshimai
in complex with ssDNA (dt)18 and adp-vo4 . SNAP output
|
|
6s3o
|
hydrolase |
X-ray (1.974 Å) |
Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou
SX, Rety S, Xi XG |
(2021) "Structural
and functional studies of SF1B Pif1 from Thermus
oshimai reveal dimerization-induced helicase
inhibition." Nucleic Acids Res.,
49, 4129-4143. doi: 10.1093/nar/gkab188.
|
Crystal structure of helicase pif1 from thermus oshimai
in complex with ssDNA (dt)18 and adp . SNAP output
|
|
6s3p
|
hydrolase |
X-ray (1.926 Å) |
Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou
SX, Rety S, Xi XG |
(2021) "Structural
and functional studies of SF1B Pif1 from Thermus
oshimai reveal dimerization-induced helicase
inhibition." Nucleic Acids Res.,
49, 4129-4143. doi: 10.1093/nar/gkab188.
|
Crystal structure of helicase pif1 from thermus oshimai
in complex with (dt)18 . SNAP output
|
|
6s48
|
hydrolase |
X-ray (1.9 Å) |
Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska
H, Bochtler M |
(2020) "Restriction
endonucleases that cleave RNA/DNA heteroduplexes bind
dsDNA in A-like conformation." Nucleic Acids
Res., 48, 6954-6969. doi:
10.1093/nar/gkaa403.
|
Avaii restriction endonuclease in complex with
partially cleaved dsDNA . SNAP output
|
|
6s6h
|
DNA binding protein |
X-ray (2.4 Å) |
Jalal ASB, Tran NT, Stevenson CE, Chan EW, Lo R, Tan
X, Noy A, Lawson DM, Le TBK |
(2020) "Diversification
of DNA-Binding Specificity by Permissive and
Specificity-Switching Mutations in the ParB/Noc Protein
Family." Cell Rep, 32,
107928. doi: 10.1016/j.celrep.2020.107928.
|
Crystal structure of the DNA binding domain of the
chromosome-partitioning protein parb complexed to the
centromeric pars site . SNAP output
|
|
6s85
|
DNA binding protein |
cryo-EM (4.2 Å) |
Kashammer L, Saathoff JH, Lammens K, Gut F, Bartho J,
Alt A, Kessler B, Hopfner KP |
(2019) "Mechanism
of DNA End Sensing and Processing by the Mre11-Rad50
Complex." Mol.Cell, 76,
382. doi: 10.1016/j.molcel.2019.07.035.
|
Cutting state of the e. coli mre11-rad50 (sbccd) head
complex bound to adp and dsDNA. . SNAP output
|
|
6sa0
|
transferase |
X-ray (2.209 Å) |
Brissett NC, Zabrady K, Plocinski P, Bianchi J,
Korycka-Machala M, Brzostek A, Dziadek J, Doherty AJ |
(2020) "Molecular
basis for DNA repair synthesis on short gaps by
mycobacterial Primase-Polymerase C." Nat
Commun, 11, 4196. doi: 10.1038/s41467-020-18012-8.
|
Ternary complex of prim-polc from mycobacterium
smegmatis with 2nt gapped DNA and upnhpp . SNAP output
|
|
6sa1
|
transferase |
X-ray (2.01 Å) |
Brissett NC, Zabrady K, Plocinski P, Bianchi J,
Korycka-Machala M, Brzostek A, Dziadek J, Doherty AJ |
(2020) "Molecular
basis for DNA repair synthesis on short gaps by
mycobacterial Primase-Polymerase C." Nat
Commun, 11, 4196. doi: 10.1038/s41467-020-18012-8.
|
Post catalytic complex of prim-polc from mycobacterium
smegmatis with gapped DNA and 3'-dutp . SNAP output
|
|
6sdg
|
transcription |
X-ray (2.96 Å) |
Kato H, Mutte SK, Suzuki H, Crespo I, Das S, Radoeva
T, Fontana M, Yoshitake Y, Hainiwa E, van den Berg W,
Lindhoud S, Ishizaki K, Hohlbein J, Borst JW, Boer DR,
Nishihama R, Kohchi T, Weijers D |
(2020) "Design
principles of a minimal auxin response system."
Nat.Plants, 6, 473-482. doi:
10.1038/s41477-020-0662-y.
|
Crystal structure of the DNA binding domain of m.
polymorpha auxin response factor 2 (mparf2) in complex
with high affinity DNA . SNAP output
|
|
6se0
|
nuclear protein |
cryo-EM (3.8 Å) |
Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M,
Sekulic N |
(2019) "CENP-C
unwraps the human CENP-A nucleosome through the H2A
C-terminal tail." Embo Rep.,
20, e48913. doi: 10.15252/embr.201948913.
|
Class 1 : cenp-a nucleosome . SNAP output
|
|
6se6
|
nuclear protein |
cryo-EM (3.5 Å) |
Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M,
Sekulic N |
(2019) "CENP-C
unwraps the human CENP-A nucleosome through the H2A
C-terminal tail." Embo Rep.,
20, e48913. doi: 10.15252/embr.201948913.
|
Class2 : cenp-a nucleosome in complex with cenp-c
central region . SNAP
output
|
|
6see
|
nuclear protein |
cryo-EM (4.2 Å) |
Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M,
Sekulic N |
(2019) "CENP-C
unwraps the human CENP-A nucleosome through the H2A
C-terminal tail." Embo Rep.,
20, e48913. doi: 10.15252/embr.201948913.
|
Class2a : cenp-a nucleosome in complex with cenp-c
central region . SNAP
output
|
|
6sef
|
nuclear protein |
cryo-EM (3.7 Å) |
Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M,
Sekulic N |
(2019) "CENP-C
unwraps the human CENP-A nucleosome through the H2A
C-terminal tail." Embo Rep.,
20, e48913. doi: 10.15252/embr.201948913.
|
Class2c : cenp-a nucleosome in complex with cenp-c
central region . SNAP
output
|
|
6seg
|
nuclear protein |
cryo-EM (3.1 Å) |
Ali-Ahmad A, Bilokapic S, Schafer IB, Halic M,
Sekulic N |
(2019) "CENP-C
unwraps the human CENP-A nucleosome through the H2A
C-terminal tail." Embo Rep.,
20, e48913. doi: 10.15252/embr.201948913.
|
Class1: cenp-a nucleosome in complex with cenp-c
central region . SNAP
output
|
|
6sei
|
DNA binding protein |
X-ray (2.69 Å) |
Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapinska M,
Nowotny M |
(2019) "Recognition
and processing of branched DNA substrates by Slx1-Slx4
nuclease." Nucleic Acids Res.,
47, 11681-11690. doi: 10.1093/nar/gkz842.
|
Recognition and processing of branched DNA substrates
by slx1-slx4 nuclease . SNAP output
|
|
6sjb
|
hydrolase |
cryo-EM (3.7 Å) |
Cheng K, Wilkinson M, Chaban Y, Wigley DB |
(2020) "A
conformational switch in response to Chi converts
RecBCD from phage destruction to DNA repair."
Nat.Struct.Mol.Biol., 27,
71-77. doi: 10.1038/s41594-019-0355-2.
|
cryo-EM structure of the recbcd chi recognised complex
. SNAP output
|
|
6sje
|
hydrolase |
cryo-EM (4.1 Å) |
Cheng K, Wilkinson M, Chaban Y, Wigley DB |
(2020) "A
conformational switch in response to Chi converts
RecBCD from phage destruction to DNA repair."
Nat.Struct.Mol.Biol., 27,
71-77. doi: 10.1038/s41594-019-0355-2.
|
cryo-EM structure of the recbcd chi
partially-recognised complex . SNAP output
|
|
6sjf
|
hydrolase |
cryo-EM (3.9 Å) |
Cheng K, Wilkinson M, Chaban Y, Wigley DB |
(2020) "A
conformational switch in response to Chi converts
RecBCD from phage destruction to DNA repair."
Nat.Struct.Mol.Biol., 27,
71-77. doi: 10.1038/s41594-019-0355-2.
|
cryo-EM structure of the recbcd chi unrecognised
complex . SNAP
output
|
|
6sjg
|
hydrolase |
cryo-EM (3.8 Å) |
Cheng K, Wilkinson M, Chaban Y, Wigley DB |
(2020) "A
conformational switch in response to Chi converts
RecBCD from phage destruction to DNA repair."
Nat.Struct.Mol.Biol., 27,
71-77. doi: 10.1038/s41594-019-0355-2.
|
cryo-EM structure of the recbcd no chi negative control
complex . SNAP
output
|
|
6skl
|
replication |
cryo-EM (3.7 Å) |
Baretic D, Jenkyn-Bedford M, Aria V, Cannone G,
Skehel M, Yeeles JTP |
(2020) "Cryo-EM
Structure of the Fork Protection Complex Bound to CMG
at a Replication Fork." Mol.Cell,
78, 926-940.e13. doi: 10.1016/j.molcel.2020.04.012.
|
cryo-EM structure of the cmg fork protection complex at
a replication fork - conformation 1 . SNAP output
|
|
6sko
|
replication |
cryo-EM (3.4 Å) |
Baretic D, Jenkyn-Bedford M, Aria V, Cannone G,
Skehel M, Yeeles JTP |
(2020) "Cryo-EM
Structure of the Fork Protection Complex Bound to CMG
at a Replication Fork." Mol.Cell,
78, 926-940.e13. doi: 10.1016/j.molcel.2020.04.012.
|
cryo-EM structure of the fork protection complex bound
to cmg at a replication fork - conformation 2 mcm
ctd:ssDNA . SNAP
output
|
|
6sxb
|
DNA binding protein |
cryo-EM (7.9 Å) |
Jones M, Beuron F, Borg A, Nans A, Earl CP, Briggs
DC, Snijders AP, Bowles M, Morris EP, Linch M, McDonald
NQ |
(2020) "Cryo-EM
structures of the XPF-ERCC1 endonuclease reveal how
DNA-junction engagement disrupts an auto-inhibited
conformation." Nat Commun,
11, 1120. doi: 10.1038/s41467-020-14856-2.
|
Xpf-ercc1 cryo-EM structure, DNA-bound form . SNAP output
|
|
6sy0
|
DNA binding protein |
X-ray (3.102 Å) |
Niederwieser I, Reiter D, Kantsadi A, Voss T,
Vakonakis I |
"Structural and functional analysis of the Plasmodium
falciparum SIP2 DNA binding domain." |
Structure of the plasmodium falciparum sip2 DNA-binding
ap2 tandem repeat in complex with two spe2 half-sites .
SNAP output
|
|
6t1f
|
DNA binding protein |
X-ray (2.9 Å) |
Jalal AS, Tran NT, Stevenson CE, Chimthanawala A,
Badrinarayanan A, Lawson DM, Le TB |
(2021) "A
CTP-dependent gating mechanism enables ParB spreading
on DNA." Elife, 10. doi:
10.7554/eLife.69676.
|
Crystal structure of the c-terminally truncated
chromosome-partitioning protein parb from caulobacter
crescentus complexed to the centromeric pars site .
SNAP output
|
|
6t21
|
hydrolase |
X-ray (2.07 Å) |
Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G,
Bochtler M |
(2019) "Crystal
structure of the EcoKMcrA N-terminal domain (NEco):
recognition of modified cytosine bases without
flipping." Nucleic Acids Res.,
47, 11943-11955. doi: 10.1093/nar/gkz1017.
|
N-terminal domain of ecokmcra restriction endonuclease
(neco) in complex with t5mcga target sequence .
SNAP output
|
|
6t22
|
hydrolase |
X-ray (2.21 Å) |
Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G,
Bochtler M |
(2019) "Crystal
structure of the EcoKMcrA N-terminal domain (NEco):
recognition of modified cytosine bases without
flipping." Nucleic Acids Res.,
47, 11943-11955. doi: 10.1093/nar/gkz1017.
|
N-terminal domain of ecokmcra restriction endonuclease
(neco) in complex with t5hmcga target sequence .
SNAP output
|
|
6t2u
|
hydrolase |
cryo-EM (3.6 Å) |
Cheng K, Wilkinson M, Chaban Y, Wigley DB |
(2020) "A
conformational switch in response to Chi converts
RecBCD from phage destruction to DNA repair."
Nat.Struct.Mol.Biol., 27,
71-77. doi: 10.1038/s41594-019-0355-2.
|
cryo-EM structure of the recbcd in complex with
chi-minus2 substrate . SNAP output
|
|
6t2v
|
hydrolase |
cryo-EM (3.8 Å) |
Cheng K, Wilkinson M, Chaban Y, Wigley DB |
(2020) "A
conformational switch in response to Chi converts
RecBCD from phage destruction to DNA repair."
Nat.Struct.Mol.Biol., 27,
71-77. doi: 10.1038/s41594-019-0355-2.
|
cryo-EM structure of the recbcd in complex with
chi-plus2 substrate . SNAP output
|
|
6t5t
|
DNA binding protein |
X-ray (1.7 Å) |
Golovinas E, Manakova E, Sasnauskas G, Zaremba M |
"Crystal structure of Archaeoglobus fulgidus
Argonaute protein with cognate DNA oligoduplex
5'-pATTGTGGCCACAAT." |
Crystal structure of archaeoglobus fulgidus argonaute
protein with cognate DNA oligoduplex 5'-pattgtggccacaat
. SNAP output
|
|
6t78
|
nuclear protein |
X-ray (2.504 Å) |
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer
P |
(2020) "Nucleosome-bound
SOX2 and SOX11 structures elucidate pioneer factor
function." Nature, 580,
669-672. doi: 10.1038/s41586-020-2195-y.
|
Structure of human sox11 transcription factor in
complex with a short DNA fragment . SNAP output
|
|
6t79
|
nuclear protein |
cryo-EM (3.2 Å) |
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer
P |
(2020) "Nucleosome-bound
SOX2 and SOX11 structures elucidate pioneer factor
function." Nature, 580,
669-672. doi: 10.1038/s41586-020-2195-y.
|
Structure of a human nucleosome at 3.2 Å resolution .
SNAP output
|
|
6t7a
|
nuclear protein |
cryo-EM (3.7 Å) |
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer
P |
(2020) "Nucleosome-bound
SOX2 and SOX11 structures elucidate pioneer factor
function." Nature, 580,
669-672. doi: 10.1038/s41586-020-2195-y.
|
Structure of human sox11 transcription factor in
complex with a nucleosome . SNAP output
|
|
6t7b
|
nuclear protein |
cryo-EM (5.1 Å) |
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer
P |
(2020) "Nucleosome-bound
SOX2 and SOX11 structures elucidate pioneer factor
function." Nature, 580,
669-672. doi: 10.1038/s41586-020-2195-y.
|
Structure of human sox2 transcription factor in complex
with a nucleosome . SNAP
output
|
|
6t7c
|
nuclear protein |
cryo-EM (4.0 Å) |
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer
P |
(2020) "Nucleosome-bound
SOX2 and SOX11 structures elucidate pioneer factor
function." Nature, 580,
669-672. doi: 10.1038/s41586-020-2195-y.
|
Structure of two copies of human sox11 transcription
factor in complex with a nucleosome . SNAP output
|
|
6t7d
|
nuclear protein |
cryo-EM (4.4 Å) |
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer
P |
(2020) "Nucleosome-bound
SOX2 and SOX11 structures elucidate pioneer factor
function." Nature, 580,
669-672. doi: 10.1038/s41586-020-2195-y.
|
Structure of human sox11 transcription factor in
complex with a nucleosome . SNAP output
|
|
6t8b
|
DNA binding protein |
cryo-EM (3.65 Å) |
Jean NL, Rutherford TJ, Lowe J |
(2020) "FtsK in
motion reveals its mechanism for double-stranded DNA
translocation." Proc.Natl.Acad.Sci.USA,
117, 14202-14208. doi: 10.1073/pnas.2001324117.
|
Ftsk motor domain with dsDNA, translocating state .
SNAP output
|
|
6t8g
|
DNA binding protein |
cryo-EM (4.34 Å) |
Jean NL, Rutherford TJ, Lowe J |
(2020) "FtsK in
motion reveals its mechanism for double-stranded DNA
translocation." Proc.Natl.Acad.Sci.USA,
117, 14202-14208. doi: 10.1073/pnas.2001324117.
|
Stalled ftsk motor domain bound to dsDNA . SNAP output
|
|
6t8h
|
replication |
cryo-EM (3.77 Å) |
Madru C, Henneke G, Raia P, Hugonneau-Beaufet I,
Pehau-Arnaudet G, England P, Lindahl E, Delarue M,
Carroni M, Sauguet L |
(2020) "Structural
basis for the increased processivity of D-family DNA
polymerases in complex with PCNA." Nat
Commun, 11, 1591. doi: 10.1038/s41467-020-15392-9.
|
cryo-EM structure of the DNA-bound pold-pcna processive
complex from p. abyssi . SNAP output
|
|
6t8o
|
DNA binding protein |
cryo-EM (3.99 Å) |
Jean NL, Rutherford TJ, Lowe J |
(2020) "FtsK in
motion reveals its mechanism for double-stranded DNA
translocation." Proc.Natl.Acad.Sci.USA,
117, 14202-14208. doi: 10.1073/pnas.2001324117.
|
Stalled ftsk motor domain bound to dsDNA end . SNAP output
|
|
6t90
|
transcription |
cryo-EM (3.05 Å) |
Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z,
Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR,
Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma
NH |
(2020) "Mechanisms
of OCT4-SOX2 motif readout on nucleosomes."
Science, 368, 1460-1465. doi:
10.1126/science.abb0074.
|
Oct4-sox2-bound nucleosome - shl-6 . SNAP output
|
|
6t93
|
transcription |
cryo-EM (3.49 Å) |
Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z,
Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR,
Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma
NH |
(2020) "Mechanisms
of OCT4-SOX2 motif readout on nucleosomes."
Science, 368, 1460-1465. doi:
10.1126/science.abb0074.
|
Nucleosome with oct4-sox2 motif at shl-6 . SNAP output
|
|
6t9l
|
gene regulation |
cryo-EM (3.6 Å) |
Wang H, Dienemann C, Stutzer A, Urlaub H, Cheung ACM,
Cramer P |
(2020) "Structure
of the transcription coactivator SAGA."
Nature, 577, 717-720. doi:
10.1038/s41586-020-1933-5.
|
Saga dub module bound to a ubiqitinated nucleosome .
SNAP output
|
|
6tbz
|
transcription |
X-ray (1.782 Å) |
Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C,
Freier R, Baginski B, Martin-Malpartida P, de Martin
Garrido N, Marquez JA, Cordeiro TN, Pluta R, Macias
MJ |
(2021) "Unveiling
the dimer/monomer propensities of Smad MH1-DNA
complexes." Comput Struct Biotechnol J,
19, 632-646. doi: 10.1016/j.csbj.2020.12.044.
|
Crystal structure of the mh1 domain of smad5-smad3
chimera construct bound to the ggcgc site . SNAP output
|
|
6tc9
|
DNA binding protein |
X-ray (2.175 Å) |
Landova B, Silhan J |
(2020) "Conformational
changes of DNA repair glycosylase MutM triggered by DNA
binding." Febs Lett.,
594, 3032-3044. doi: 10.1002/1873-3468.13876.
|
Crystal structure of mutm from neisseria meningitidis .
SNAP output
|
|
6tce
|
transcription |
X-ray (2.92 Å) |
Ruiz L, Kaczmarska Z, Gomes T, Aragon E, Torner C,
Freier R, Baginski B, Martin-Malpartida P, de Martin
Garrido N, Marquez JA, Cordeiro TN, Pluta R, Macias
MJ |
(2021) "Unveiling
the dimer/monomer propensities of Smad MH1-DNA
complexes." Comput Struct Biotechnol J,
19, 632-646. doi: 10.1016/j.csbj.2020.12.044.
|
Crystal structure of the ggct site-bound mh1 domain of
smad5 containing a gggs insertion in the loop1 .
SNAP output
|
|
6tda
|
DNA binding protein |
cryo-EM (15.0 Å) |
Wagner FR, Dienemann C, Wang H, Stutzer A, Tegunov D,
Urlaub H, Cramer P |
(2020) "Structure
of SWI/SNF chromatin remodeller RSC bound to a
nucleosome." Nature, 579,
448-451. doi: 10.1038/s41586-020-2088-0.
|
Structure of swi-snf chromatin remodeler rsc bound to a
nucleosome . SNAP
output
|
|
6ted
|
transcription |
cryo-EM (3.1 Å) |
Vos SM, Farnung L, Linden A, Urlaub H, Cramer P |
(2020) "Structure
of complete Pol II-DSIF-PAF-SPT6 transcription complex
reveals RTF1 allosteric activation."
Nat.Struct.Mol.Biol., 27,
668-677. doi: 10.1038/s41594-020-0437-1.
|
Structure of complete, activated transcription complex
pol ii-dsif-paf-spt6 uncovers allosteric elongation
activation by rtf1 . SNAP output
|
|
6tem
|
DNA binding protein |
cryo-EM (3.9 Å) |
Boopathi R, Danev R, Khoshouei M, Kale S, Nahata S,
Ramos L, Angelov D, Dimitrov S, Hamiche A, Petosa C,
Bednar J |
(2020) "Phase-plate
cryo-EM structure of the Widom 601 CENP-A nucleosome
core particle reveals differential flexibility of the
DNA ends." Nucleic Acids Res.,
48, 5735-5748. doi: 10.1093/nar/gkaa246.
|
Cenp-a nucleosome core particle with 145 base pairs of
the widom 601 sequence by cryo-EM . SNAP output
|
|
6tny
|
replication |
cryo-EM (3.08 Å) |
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N,
Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ,
Hamdan SM, De Biasio A |
(2020) "Structure
of the processive human Pol delta holoenzyme."
Nat Commun, 11, 1109. doi:
10.1038/s41467-020-14898-6.
|
Processive human polymerase delta holoenzyme . SNAP output
|
|
6tnz
|
replication |
cryo-EM (4.05 Å) |
Lancey C, Tehseen M, Raducanu VS, Rashid F, Merino N,
Ragan TJ, Savva CG, Zaher MS, Shirbini A, Blanco FJ,
Hamdan SM, De Biasio A |
(2020) "Structure
of the processive human Pol delta holoenzyme."
Nat Commun, 11, 1109. doi:
10.1038/s41467-020-14898-6.
|
Human polymerase delta-fen1-pcna toolbelt . SNAP output
|
|
6tps
|
transcription |
cryo-EM (3.54 Å) |
Pilsl M, Engel C |
(2020) "Structural
basis of RNA polymerase I pre-initiation complex
formation and promoter melting." Nat
Commun, 11, 1206. doi: 10.1038/s41467-020-15052-y.
|
Early intermediate RNA polymerase i pre-initiation
complex - eipic . SNAP
output
|
|
6tqn
|
transcription |
cryo-EM (3.8 Å) |
Huang YH, Hilal T, Loll B, Burger J, Mielke T,
Bottcher C, Said N, Wahl MC |
(2020) "Structure-Based
Mechanisms of a Molecular RNA Polymerase/Chaperone
Machine Required for Ribosome Biosynthesis."
Mol.Cell, 79, 1024-1036.e5.
doi: 10.1016/j.molcel.2020.08.010.
|
Rrn anti-termination complex without s4 . SNAP output
|
|
6tqo
|
transcription |
cryo-EM (3.8 Å) |
Huang YH, Hilal T, Loll B, Burger J, Mielke T,
Bottcher C, Said N, Wahl MC |
(2020) "Structure-Based
Mechanisms of a Molecular RNA Polymerase/Chaperone
Machine Required for Ribosome Biosynthesis."
Mol.Cell, 79, 1024-1036.e5.
doi: 10.1016/j.molcel.2020.08.010.
|
Rrn anti-termination complex . SNAP output
|
|
6tuo
|
DNA binding protein |
X-ray (1.8 Å) |
Golovinas E, Manakova E, Sasnauskas G, Zaremba M |
"Crystal structure of Archaeoglobus fulgidus
Argonaute protein with cognate DNA oligoduplex
5'-pATTGTACGTACAAT." |
Crystal structure of archaeoglobus fulgidus argonaute
protein with cognate DNA oligoduplex 5'-pattgtacgtacaat
. SNAP output
|
|
6tup
|
virus |
cryo-EM (3.2 Å) |
Tarafder AK, von Kugelgen A, Mellul AJ, Schulze U,
Aarts DGAL, Bharat TAM |
(2020) "Phage
liquid crystalline droplets form occlusive sheaths that
encapsulate and protect infectious rod-shaped
bacteria." Proc.Natl.Acad.Sci.USA,
117, 4724-4731. doi: 10.1073/pnas.1917726117.
|
cryo-EM structure of pf4 bacteriophage coat protein
with single-stranded DNA . SNAP output
|
|
6tuw
|
DNA binding protein |
X-ray (3.5 Å) |
Gonzalez-Corrochano R, Ruiz FM, Taylor NMI, Huecas S,
Drakulic S, Spinola-Amilibia M, Fernandez-Tornero C |
(2020) "The
crystal structure of human XPG, the xeroderma
pigmentosum group G endonuclease, provides insight into
nucleotide excision DNA repair." Nucleic Acids
Res., 48, 9943-9958. doi:
10.1093/nar/gkaa688.
|
Human xpg-DNA, complex 1 . SNAP output
|
|
6tux
|
DNA binding protein |
X-ray (3.1 Å) |
Gonzalez-Corrochano R, Ruiz FM, Taylor NMI, Huecas S,
Drakulic S, Spinola-Amilibia M, Fernandez-Tornero C |
(2020) "The
crystal structure of human XPG, the xeroderma
pigmentosum group G endonuclease, provides insight into
nucleotide excision DNA repair." Nucleic Acids
Res., 48, 9943-9958. doi:
10.1093/nar/gkaa688.
|
Human xpg-DNA, complex 2 . SNAP output
|
|
6tye
|
transcription |
X-ray (3.79 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Crystal structure of mtb sigma l transcription
initiation complex with 5 nt long RNA primer . SNAP output
|
|
6tyf
|
transcription |
X-ray (3.8 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Crystal structure of mtb sigma l transcription
initiation complex with 6 nt long RNA primer . SNAP output
|
|
6tyg
|
transcription |
X-ray (3.5 Å) |
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y |
(2020) "RNA
extension drives a stepwise displacement of an
initiation-factor structural module in initial
transcription." Proc.Natl.Acad.Sci.USA,
117, 5801-5809. doi: 10.1073/pnas.1920747117.
|
Crystal structure of mtb sigma l transcription
initiation complex with 9 nt long RNA primer . SNAP output
|
|
6u0m
|
replication-DNA |
cryo-EM (3.9 Å) |
Yuan Z, Georgescu R, Bai L, Zhang D, Li H, O'Donnell
ME |
(2020) "DNA unwinding mechanism of a eukaryotic
replicative CMG helicase." Nat Commun,
11, 688. doi: 10.1038/s41467-020-14577-6.
|
Structure of the s. cerevisiae replicative helicase cmg
in complex with a forked DNA . SNAP output
|
|
6u15
|
hydrolase |
X-ray (2.4 Å) |
Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat
AC |
(2019) "Excision
of 5-Carboxylcytosine by Thymine DNA Glycosylase."
J.Am.Chem.Soc., 141,
18851-18861. doi: 10.1021/jacs.9b10376.
|
Human thymine DNA glycosylase n140a mutant bound to DNA
with 2'-f-5-carboxyl-dc substrate analog . SNAP output
|
|
6u16
|
hydrolase |
X-ray (1.6 Å) |
Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat
AC |
(2019) "Excision
of 5-Carboxylcytosine by Thymine DNA Glycosylase."
J.Am.Chem.Soc., 141,
18851-18861. doi: 10.1021/jacs.9b10376.
|
Human thymine DNA glycosylase n140a mutant bound to DNA
with 5-carboxyl-dc substrate . SNAP output
|
|
6u17
|
hydrolase |
X-ray (1.55 Å) |
Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat
AC |
(2019) "Excision
of 5-Carboxylcytosine by Thymine DNA Glycosylase."
J.Am.Chem.Soc., 141,
18851-18861. doi: 10.1021/jacs.9b10376.
|
Human thymine DNA glycosylase bound to DNA with
2'-f-5-carboxyl-dc substrate analog . SNAP output
|
|
6u2o
|
transferase-DNA |
X-ray (2.3 Å) |
Ouzon-Shubeita H, Vilas CK, Lee S |
"Structures of the Mutagenic Bypass of the Major
Cisplatin-DNA Lesion by Human DNA Polymerase Beta Reveal
Insights into Cisplatin-Induced Mutagenesis." |
Structure of human DNA polymerase beta misinserting
dampnpp opposite the 5'g of the cisplatin pt-gg
intrastrand crosslink . SNAP output
|
|
6u6b
|
transferase-DNA |
X-ray (3.108 Å) |
Ouzon-Shubeita H, Vilas CK, Lee S |
(2020) "Structural
insights into the promutagenic bypass of the major
cisplatin-induced DNA lesion." Biochem.J.,
477, 937-951. doi: 10.1042/BCJ20190906.
|
Structure of human DNA polymerase beta misinserting
dampnpp opposite the 5'g of the cisplatin pt-gg
intrastrand crosslink with manganese in the active site
. SNAP output
|
|
6u6x
|
hydrolase |
X-ray (2.58 Å) |
Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z,
Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano
K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov
DN |
(2021) "Nucleic
acid binding by SAMHD1 contributes to the
antiretroviral activity and is enhanced by the GpsN
modification." Nat Commun,
12, 731. doi: 10.1038/s41467-021-21023-8.
|
Human samhd1 bound to
deoxyribo(c*g*c*c*t)-oligonucleotide . SNAP output
|
|
6u6z
|
hydrolase |
X-ray (2.1 Å) |
Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z,
Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano
K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov
DN |
(2021) "Nucleic
acid binding by SAMHD1 contributes to the
antiretroviral activity and is enhanced by the GpsN
modification." Nat Commun,
12, 731. doi: 10.1038/s41467-021-21023-8.
|
Human samhd1 bound to
deoxyribo(tg*ttca)-oligonucleotide . SNAP output
|
|
6u7t
|
hydrolase-DNA |
X-ray (2.0 Å) |
Russelburg LP, O'Shea Murray VL, Demir M, Knutsen KR,
Sehgal SL, Cao S, David SS, Horvath MP |
(2020) "Structural
Basis for Finding OG Lesions and Avoiding Undamaged G
by the DNA Glycosylase MutY." Acs
Chem.Biol., 15, 93-102. doi:
10.1021/acschembio.9b00639.
|
Muty adenine glycosylase bound to DNA containing a
transition state analog (1n) paired with d(8-oxo-g) .
SNAP output
|
|
6u81
|
DNA binding protein-DNA |
X-ray (2.34 Å) |
Klingler C, Ashley J, Shi K, Stiefvater A, Kyba M,
Sinnreich M, Aihara H, Kinter J |
(2020) "DNA
aptamers against the DUX4 protein reveal novel
therapeutic implications for FSHD." Faseb
J., 34, 4573-4590. doi: 10.1096/fj.201902696.
|
Crystal structure of the double homeodomain of dux4 in
complex with a DNA aptamer . SNAP output
|
|
6u82
|
DNA binding protein-DNA |
X-ray (3.21 Å) |
Klingler C, Ashley J, Shi K, Stiefvater A, Kyba M,
Sinnreich M, Aihara H, Kinter J |
(2020) "DNA
aptamers against the DUX4 protein reveal novel
therapeutic implications for FSHD." Faseb
J., 34, 4573-4590. doi: 10.1096/fj.201902696.
|
Crystal structure of the double homeodomain of dux4 in
complex with a DNA aptamer containing bulge and loop .
SNAP output
|
|
6u8p
|
transferase-DNA |
X-ray (3.05 Å) |
Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S,
Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H,
Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang
GG, Jeltsch A, Song J |
(2020) "Comprehensive
structure-function characterization of DNMT3B and
DNMT3A reveals distinctive de novo DNA methylation
mechanisms." Nat Commun,
11, 3355. doi: 10.1038/s41467-020-17109-4.
|
Crystal structure of dnmt3b-dnmt3l in complex with
cpgpa DNA . SNAP
output
|
|
6u8q
|
transferase-transferase inhibitor-DNA |
cryo-EM (4.67 Å) |
Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie
R |
(2020) "A
Peptide Derived from Lens Epithelium-Derived Growth
Factor Stimulates HIV-1 DNA Integration and Facilitates
Intasome Structural Studies." J.Mol.Biol.,
432, 2055-2066. doi: 10.1016/j.jmb.2020.01.040.
|
Cryoem structure of hiv-1 cleaved synaptic complex
(csc) intasome . SNAP
output
|
|
6u8v
|
transferase-DNA |
X-ray (3.0 Å) |
Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S,
Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H,
Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang
GG, Jeltsch A, Song J |
(2020) "Comprehensive
structure-function characterization of DNMT3B and
DNMT3A reveals distinctive de novo DNA methylation
mechanisms." Nat Commun,
11, 3355. doi: 10.1038/s41467-020-17109-4.
|
Crystal structure of dnmt3b-dnmt3l in complex with
cpgpt DNA . SNAP
output
|
|
6u8w
|
transferase-DNA |
X-ray (2.95 Å) |
Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S,
Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H,
Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang
GG, Jeltsch A, Song J |
(2020) "Comprehensive
structure-function characterization of DNMT3B and
DNMT3A reveals distinctive de novo DNA methylation
mechanisms." Nat Commun,
11, 3355. doi: 10.1038/s41467-020-17109-4.
|
Crystal structure of dnmt3b(k777a)-dnmt3l in complex
with cpgpt DNA . SNAP
output
|
|
6u8x
|
transferase-DNA |
X-ray (2.95 Å) |
Gao L, Emperle M, Guo Y, Grimm SA, Ren W, Adam S,
Uryu H, Zhang ZM, Chen D, Yin J, Dukatz M, Anteneh H,
Jurkowska RZ, Lu J, Wang Y, Bashtrykov P, Wade PA, Wang
GG, Jeltsch A, Song J |
(2020) "Comprehensive
structure-function characterization of DNMT3B and
DNMT3A reveals distinctive de novo DNA methylation
mechanisms." Nat Commun,
11, 3355. doi: 10.1038/s41467-020-17109-4.
|
Crystal structure of dnmt3b-dnmt3l in complex with
cpapg DNA . SNAP
output
|
|
6u90
|
transferase-DNA |
X-ray (3.0 Å) |
Gao L |
"Comprehensive structure-function characterization of
DNMT3B and DNMT3A reveals distinctive de novo DNA
methylation mechanisms." |
Crystal structure of dnmt3b(n779a)-dnmt3l in complex
with cpgpt DNA . SNAP
output
|
|
6u91
|
transferase-DNA |
X-ray (3.0 Å) |
Gao L |
"Comprehensive structure-function characterization of
DNMT3B and DNMT3A reveals distinctive de novo DNA
methylation mechanisms." |
Crystal structure of dnmt3b(q772r)-dnmt3l in complex
with cpgpt DNA . SNAP
output
|
|
6u9q
|
transcription-DNA |
X-ray (1.83 Å) |
Viennet T, Yin M, Jayaraj A, Kim W, Sun ZYJ, Fujiwara
Y, Zhang K, Seruggia D, Seo HS, Dhe-Paganon S, Orkin SH,
Arthanari H |
(2024) "Structural insights into the DNA-binding
mechanism of BCL11A: The integral role of ZnF6."
Structure. doi: 10.1016/j.str.2024.09.022.
|
Crystal structure analysis of DNA-bcl11a znf domain
complex . SNAP
output
|
|
6ubf
|
DNA binding protein-DNA |
X-ray (4.597 Å) |
Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y,
Liu L, Van Houten B, He C, Ansari A, Min JH |
(2015) "Kinetic
gating mechanism of DNA damage recognition by
Rad4/XPC." Nat Commun, 6,
5849. doi: 10.1038/ncomms6849.
|
Role of beta-hairpin motifs in the DNA duplex opening
by the rad4-xpc nucleotide excision repair complex .
SNAP output
|
|
6ueo
|
DNA binding protein-DNA |
X-ray (2.0 Å) |
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A,
Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon
GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan
R |
(2020) "DNA
mismatches reveal conformational penalties in
protein-DNA recognition." Nature,
587, 291-296. doi: 10.1038/s41586-020-2843-2.
|
Structure of a. thaliana tbp-ac mismatch DNA site .
SNAP output
|
|
6uep
|
DNA binding protein-DNA |
X-ray (2.05 Å) |
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A,
Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon
GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan
R |
(2020) "DNA
mismatches reveal conformational penalties in
protein-DNA recognition." Nature,
587, 291-296. doi: 10.1038/s41586-020-2843-2.
|
Structure of a. thaliana tbp bound to a DNA site with a
c-c mismatch . SNAP
output
|
|
6ueq
|
DNA binding protein-DNA |
X-ray (2.4 Å) |
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A,
Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon
GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan
R |
(2020) "DNA
mismatches reveal conformational penalties in
protein-DNA recognition." Nature,
587, 291-296. doi: 10.1038/s41586-020-2843-2.
|
Structure of tbp bound to c-c mismatch containing tata
site . SNAP output
|
|
6uer
|
DNA binding protein-DNA |
X-ray (2.5 Å) |
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A,
Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon
GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordan
R |
(2020) "DNA
mismatches reveal conformational penalties in
protein-DNA recognition." Nature,
587, 291-296. doi: 10.1038/s41586-020-2843-2.
|
Crystal form 2: structure of tbp bound to c-c mismatch
at ph 7 . SNAP
output
|
|
6ueu
|
replication |
X-ray (1.8 Å) |
Walsh AR, Beese LS, Wu EY |
"Structural basis for blockage of DNA synthesis by a
thymine dimer lesion in a high-fidelity DNA
polymerase." |
Crystal structure of bf DNA polymerase f710y mutant
bound to tetrahydrofuran and datp . SNAP output
|
|
6ug1
|
DNA binding protein-DNA |
X-ray (2.833 Å) |
Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C,
Ansari A, Broyde S, Min JH |
(2021) "Impact
of DNA sequences on DNA 'opening' by the Rad4/XPC
nucleotide excision repair complex." DNA Repair
(Amst), 107, 103194. doi:
10.1016/j.dnarep.2021.103194.
|
Sequence impact in DNA duplex opening by the rad4-xpc
nucleotide excision repair complex . SNAP output
|
|
6ugm
|
transferase-structural protein-DNA |
cryo-EM (3.7 Å) |
Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng
N |
(2019) "Structural
Basis of H2B Ubiquitination-Dependent H3K4 Methylation
by COMPASS." Mol.Cell,
76, 712. doi: 10.1016/j.molcel.2019.10.013.
|
Structural basis of compass ecm recognition of an
unmodified nucleosome . SNAP output
|
|
6uh5
|
transferase-structural protein-DNA |
cryo-EM (3.5 Å) |
Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng
N |
(2019) "Structural
Basis of H2B Ubiquitination-Dependent H3K4 Methylation
by COMPASS." Mol.Cell,
76, 712. doi: 10.1016/j.molcel.2019.10.013.
|
Structural basis of compass ecm recognition of the
h2bub nucleosome . SNAP
output
|
|
6ui2
|
DNA binding protein-DNA |
X-ray (2.35 Å) |
Koag MC, Jung H, Kou Y, Lee S |
(2019) "Bypass
of the Major Alkylative DNA Lesion by Human DNA
Polymerase eta." Molecules,
24. doi: 10.3390/molecules24213928.
|
Structure of human DNA polymerase eta complexed with
n7mg in the template base paired with incoming
non-hydrolyzable ctp . SNAP output
|
|
6uin
|
DNA binding protein-DNA |
X-ray (3.348 Å) |
Paul D, Mu H, Tavakoli A, Dai Q, Chen X, Chakraborty
S, He C, Ansari A, Broyde S, Min JH |
(2021) "Tethering-facilitated DNA 'opening' and
complementary roles of beta-hairpin motifs in the
Rad4/XPC DNA damage sensor protein." Nucleic Acids
Res., 48, 12348-12364. doi:
10.1093/nar/gkaa909.
|
Role of beta-hairpin motifs in the DNA duplex opening
by the rad4-xpc nucleotide excision repair complex .
SNAP output
|
|
6uir
|
viral protein |
X-ray (2.64 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 m184v reverse transcriptase-DNA complex with
(-)-ftc-tp . SNAP
output
|
|
6uis
|
viral protein |
X-ray (2.75 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 m184v reverse transcriptase-DNA complex with dctp
. SNAP output
|
|
6uit
|
viral protein |
X-ray (2.81 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 wild-type reverse transcriptase-DNA complex with
dctp . SNAP output
|
|
6ujx
|
viral protein |
X-ray (2.7 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 wild-type reverse transcriptase-DNA complex with
(-)-ftc-tp . SNAP
output
|
|
6ujy
|
viral protein |
X-ray (2.59 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 wild-type reverse transcriptase-DNA complex with
(-)-3tc-tp . SNAP
output
|
|
6ujz
|
viral protein-DNA |
X-ray (2.56 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 wild-type reverse transcriptase-DNA complex with
(+)-ftc-tp . SNAP
output
|
|
6uk0
|
viral protein |
X-ray (2.76 Å) |
Hung M, Tokarsky EJ, Lagpacan L, Zhang L, Suo Z,
Lansdon EB |
(2019) "Elucidating
molecular interactions ofL-nucleotides with HIV-1
reverse transcriptase and mechanism of M184V-caused
drug resistance." Commun Biol,
2, 469. doi: 10.1038/s42003-019-0706-x.
|
Hiv-1 m184v reverse transcriptase-DNA complex .
SNAP output
|
|
6uke
|
hydrolase-DNA |
X-ray (1.62 Å) |
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A,
Wilson GG, Roberts RJ, Cheng X |
(2020) "Structure
of HhaI endonuclease with cognate DNA at an atomic
resolution of 1.0 angstrom." Nucleic Acids
Res., 48, 1466-1478. doi:
10.1093/nar/gkz1195.
|
Hhai endonuclease in complex with iodine-labelled DNA .
SNAP output
|
|
6ukf
|
hydrolase-DNA |
X-ray (1.0 Å) |
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A,
Wilson GG, Roberts RJ, Cheng X |
(2020) "Structure
of HhaI endonuclease with cognate DNA at an atomic
resolution of 1.0 angstrom." Nucleic Acids
Res., 48, 1466-1478. doi:
10.1093/nar/gkz1195.
|
Hhai endonuclease in complex with DNA at 1 angstrom
resolution . SNAP
output
|
|
6ukg
|
hydrolase-DNA |
X-ray (1.16 Å) |
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A,
Wilson GG, Roberts RJ, Cheng X |
(2020) "Structure
of HhaI endonuclease with cognate DNA at an atomic
resolution of 1.0 angstrom." Nucleic Acids
Res., 48, 1466-1478. doi:
10.1093/nar/gkz1195.
|
Hhai endonuclease in complex with DNA in space group
p21 (ph 4.2) . SNAP
output
|
|
6ukh
|
hydrolase-DNA |
X-ray (2.82 Å) |
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A,
Wilson GG, Roberts RJ, Cheng X |
(2020) "Structure
of HhaI endonuclease with cognate DNA at an atomic
resolution of 1.0 angstrom." Nucleic Acids
Res., 48, 1466-1478. doi:
10.1093/nar/gkz1195.
|
Hhai endonuclease in complex with DNA in space group
p41212 (ph 6.0) . SNAP
output
|
|
6uki
|
hydrolase-DNA |
X-ray (2.7 Å) |
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A,
Wilson GG, Roberts RJ, Cheng X |
(2020) "Structure
of HhaI endonuclease with cognate DNA at an atomic
resolution of 1.0 angstrom." Nucleic Acids
Res., 48, 1466-1478. doi:
10.1093/nar/gkz1195.
|
Hhai endonuclease in complex with DNA in space group
p212121 (ph 6.0) . SNAP
output
|
|
6uok
|
transferase-DNA |
X-ray (2.55 Å) |
Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB,
Freudenthal BD |
(2020) "Molecular
and structural characterization of oxidized
ribonucleotide insertion into DNA by human DNA
polymerase beta." J.Biol.Chem.,
295, 1613-1622. doi: 10.1074/jbc.RA119.011569.
|
Y271g DNA polymerase beta substrate complex with
templating cytosine and incoming r8-oxo-gtp . SNAP output
|
|
6uol
|
transferase-DNA |
X-ray (1.936 Å) |
Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB,
Freudenthal BD |
(2020) "Molecular
and structural characterization of oxidized
ribonucleotide insertion into DNA by human DNA
polymerase beta." J.Biol.Chem.,
295, 1613-1622. doi: 10.1074/jbc.RA119.011569.
|
Y271g DNA polymerase beta substrate complex with a
templating cytosine and incoming rgtp . SNAP output
|
|
6uom
|
transferase-DNA |
X-ray (2.05 Å) |
Smith MR, Alnajjar KS, Hoitsma NM, Sweasy JB,
Freudenthal BD |
(2020) "Molecular
and structural characterization of oxidized
ribonucleotide insertion into DNA by human DNA
polymerase beta." J.Biol.Chem.,
295, 1613-1622. doi: 10.1074/jbc.RA119.011569.
|
Y271g DNA polymerase beta ternary complex with
templating adenine and incoming r8-oxo-gtp . SNAP output
|
|
6uph
|
cell cycle |
cryo-EM (2.7 Å) |
Migl D, Kschonsak M, Arthur CP, Khin Y, Harrison SC,
Ciferri C, Dimitrova YN |
(2020) "Cryoelectron
Microscopy Structure of a Yeast Centromeric Nucleosome
at 2.7 angstrom Resolution." Structure,
28, 363-370.e3. doi: 10.1016/j.str.2019.12.002.
|
Structure of a yeast centromeric nucleosome at 2.7
angstrom resolution . SNAP output
|
|
6upk
|
transcription-DNA |
cryo-EM (4.9 Å) |
Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z,
Carragher B, Potter CS, D'Arcy S, Luger K |
(2020) "FACT
caught in the act of manipulating the nucleosome."
Nature, 577, 426-431. doi:
10.1038/s41586-019-1820-0.
|
Structure of fact_subnucleosome complex 1 . SNAP output
|
|
6upl
|
transcription-DNA |
cryo-EM (7.4 Å) |
Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z,
Carragher B, Potter CS, D'Arcy S, Luger K |
(2020) "FACT
caught in the act of manipulating the nucleosome."
Nature, 577, 426-431. doi:
10.1038/s41586-019-1820-0.
|
Structure of fact_subnucleosome complex 2 . SNAP output
|
|
6upx
|
transcription-RNA-DNA |
X-ray (3.4 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with
5-guanidinohydantoin lesion in state 1 . SNAP output
|
|
6upy
|
transcription-RNA-DNA |
X-ray (3.4 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with
5-guanidinohydantoin lesion in state 2e . SNAP output
|
|
6upz
|
transcription-RNA-DNA |
X-ray (3.1 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with
5-guanidinohydantoin lesion in state 3 . SNAP output
|
|
6uq0
|
transcription-RNA-DNA |
X-ray (3.56 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with
5-guanidinohydantoin lesion in state 4 . SNAP output
|
|
6uq1
|
transcription-DNA-RNA |
X-ray (3.6 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with
5-guanidinohydantoin lesion in state 6 . SNAP output
|
|
6uq2
|
transcription-RNA-DNA |
X-ray (3.2 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with dg in state 1
. SNAP output
|
|
6uq3
|
transcription-RNA-DNA |
X-ray (3.47 Å) |
Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang
D |
(2020) "RNA
polymerase II stalls on oxidative DNA damage via a
torsion-latch mechanism involving lone pair-pi and
CH-pi interactions."
Proc.Natl.Acad.Sci.USA, 117,
9338-9348. doi: 10.1073/pnas.1919904117.
|
RNA polymerase ii elongation complex with
5-guanidinohydantoin lesion in state 5 . SNAP output
|
|
6uqi
|
transferase-DNA |
X-ray (2.5 Å) |
Jung H, Lee S |
"Crystal structure of Q38A human DNA polymerase eta
bound with 8-oxoadenine (oxoA) and non-hydrolyzable dGTP
analog (dGTP*)." |
Crystal structure of q38a human DNA polymerase eta
bound with 8-oxoadenine (oxoa) and non-hydrolyzable
dgtp analog (dgtp*) . SNAP output
|
|
6ur2
|
replication-DNA |
X-ray (2.27 Å) |
Lelyveld VS, Zhang W, Szostak JW |
(2020) "Synthesis
of phosphoramidate-linked DNA by a modified DNA
polymerase." Proc.Natl.Acad.Sci.USA,
117, 7276-7283. doi: 10.1073/pnas.1922400117.
|
DNA polymerase i large fragment from bacillus
stearothermophilus with DNA template and primer
containing an n3'-> p5' linkage . SNAP output
|
|
6ur4
|
replication-DNA |
X-ray (2.25 Å) |
Lelyveld VS, Zhang W, Szostak JW |
(2020) "Synthesis
of phosphoramidate-linked DNA by a modified DNA
polymerase." Proc.Natl.Acad.Sci.USA,
117, 7276-7283. doi: 10.1073/pnas.1922400117.
|
DNA polymerase i large fragment from bacillus
stearothermophilus with DNA template and 3'-amino
primer . SNAP output
|
|
6ur9
|
replication-DNA |
X-ray (2.1 Å) |
Lelyveld VS, Zhang W, Szostak JW |
(2020) "Synthesis
of phosphoramidate-linked DNA by a modified DNA
polymerase." Proc.Natl.Acad.Sci.USA,
117, 7276-7283. doi: 10.1073/pnas.1922400117.
|
DNA polymerase i large fragment from bacillus
stearothermophilus with DNA template, dideoxy primer,
3'-amino-ddgtp (ngtp), and ca2+ . SNAP output
|
|
6us5
|
replication-DNA |
X-ray (2.25 Å) |
Lelyveld VS, Zhang W, Szostak JW |
(2020) "Synthesis
of phosphoramidate-linked DNA by a modified DNA
polymerase." Proc.Natl.Acad.Sci.USA,
117, 7276-7283. doi: 10.1073/pnas.1922400117.
|
DNA polymerase i large fragment from bacillus
stearothermophilus with DNA template, 3'-amino primer,
dgpnhpp analog, and mn2+ . SNAP output
|
|
6usj
|
DNA binding protein-DNA |
cryo-EM (10.5 Å) |
Gaullier G, Roberts G, Muthurajan UM, Bowerman S,
Rudolph J, Mahadevan J, Jha A, Rae PS, Luger K |
(2020) "Bridging
of nucleosome-proximal DNA double-strand breaks by
PARP2 enhances its interaction with HPF1." Plos
One, 15, e0240932. doi: 10.1371/journal.pone.0240932.
|
Structure of two nucleosomes bridged by human parp2 .
SNAP output
|
|
6uso
|
nuclear protein, transferase-RNA-DNA |
X-ray (2.54 Å) |
Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang
TH, Opresko PL, Freudenthal BD |
(2020) "Mechanisms
of nucleotide selection by telomerase."
Elife, 9. doi: 10.7554/eLife.55438.
|
Telomerase reverse transcriptase prenucleotide binary
complex, tert:DNA . SNAP
output
|
|
6usp
|
nuclear protein, transferase-RNA-DNA |
X-ray (3.56 Å) |
Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang
TH, Opresko PL, Freudenthal BD |
(2020) "Mechanisms
of nucleotide selection by telomerase."
Elife, 9. doi: 10.7554/eLife.55438.
|
Telomerase reverse transcriptase product complex,
tert:DNA . SNAP
output
|
|
6usq
|
nuclear protein, transferase-RNA-DNA |
X-ray (3.62 Å) |
Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang
TH, Opresko PL, Freudenthal BD |
(2020) "Mechanisms
of nucleotide selection by telomerase."
Elife, 9. doi: 10.7554/eLife.55438.
|
Telomerase reverse transcriptase binary complex with
y256a mutation, tert:DNA . SNAP output
|
|
6usr
|
nuclear protein, transferase-RNA-DNA |
X-ray (2.93 Å) |
Schaich MA, Sanford SL, Welfer GA, Johnson SA, Khoang
TH, Opresko PL, Freudenthal BD |
(2020) "Mechanisms
of nucleotide selection by telomerase."
Elife, 9. doi: 10.7554/eLife.55438.
|
Telomerase reverse transcriptase ternary complex,
tert:DNA:dgpcpp . SNAP
output
|
|
6utv
|
transcription, transferase-DNA-RNA |
X-ray (3.45 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
6-nt RNA ("fresh" crystal soaked with ctp, utp, gtp,
and ddatp for 150 seconds) . SNAP output
|
|
6utw
|
transcription, transferase-DNA-RNA |
X-ray (3.854 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
4-nt RNA ("fresh" crystal) . SNAP output
|
|
6utx
|
transcription, transferase-DNA |
X-ray (4.05 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with
an empty bubble ("old" crystal) . SNAP output
|
|
6uty
|
transcription, transferase-DNA |
X-ray (4.15 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
mismatching ctp ("old" crystal soaked with ctp for 30
minutes) . SNAP
output
|
|
6utz
|
transcription, transferase-DNA-RNA |
X-ray (3.803 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
6-nt RNA ("fresh" crystal soaked with ctp and utp for
30 minutes) . SNAP
output
|
|
6uu0
|
transcription, transferase-DNA-RNA |
X-ray (3.9 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
3-nt RNA and a mismatching gtp ("fresh" crystal soaked
with gtp for 1 hour) . SNAP output
|
|
6uu1
|
transcription, transferase-DNA-RNA |
X-ray (4.097 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
4-nt RNA and a ctp ("fresh" crystal soaked with ctp,
gtp, and ddttp for 30 minutes) . SNAP output
|
|
6uu2
|
transcription, transferase-DNA-RNA |
X-ray (4.404 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with
3-nt RNA ("old" crystal soaked with gtp and atp for 30
minutes) . SNAP
output
|
|
6uu3
|
transcription, transferase-DNA-RNA |
X-ray (4.002 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
4-nt RNA and a ctp ("old" crystal soaked with gtp, atp,
ctp, and ddttp for 30 minutes) . SNAP output
|
|
6uu4
|
transcription, transferase-DNA-RNA |
X-ray (4.305 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
3-nt RNA ("old" crystal soaked with gtp and
dinucleotide gpa for 30 minutes) . SNAP output
|
|
6uu5
|
transcription, transferase-DNA-RNA |
X-ray (5.403 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
6-nt RNA ("old" crystal soaked with gtp, utp, ctp, and
dinucleotide gpa for 30 minutes) . SNAP output
|
|
6uu6
|
transcription, transferase-DNA-RNA |
X-ray (4.201 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
4-nt RNA and a utp ("old" crystal soaked with utp,
ddctp, and dinucleotide apg for 30 minutes) . SNAP output
|
|
6uu7
|
transcription, transferase-RNA |
X-ray (4.4 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
6-nt RNA and an ntp ("old" crystal soaked with utp,
ctp, ddgtp, and dinucleotide apg for 30 minutes) .
SNAP output
|
|
6uu8
|
transcription, transferase-DNA-RNA |
X-ray (4.4 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli mutant sigma-s transcription initiation complex
with a 7-nt RNA ("fresh" mutant crystal soaked with
gtp, utp, and ctp for 30 minutes) . SNAP output
|
|
6uu9
|
transcription, transferase-DNA-RNA |
X-ray (5.4 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli mutant sigma-s transcription initiation complex
with an 8-nt RNA ("fresh" mutant crystal soaked with
gtp, utp, ctp, and ddatp for 30 minutes) . SNAP output
|
|
6uua
|
transcription, transferase-DNA |
X-ray (4.002 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
mismatching ctp ("fresh" crystal soaked with ctp for 2
hours) . SNAP output
|
|
6uub
|
transcription, transferase-DNA |
X-ray (3.955 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
mismatching utp ("fresh" crystal soaked with utp for 2
hours) . SNAP output
|
|
6uuc
|
transcription, transferase-DNA-RNA |
X-ray (4.096 Å) |
Zuo Y, De S, Feng Y, Steitz TA |
(2020) "Structural
Insights into Transcription Initiation from De Novo RNA
Synthesis to Transitioning into Elongation."
Iscience, 23, 101445. doi:
10.1016/j.isci.2020.101445.
|
E. coli sigma-s transcription initiation complex with a
3-nt RNA and a mismatching atp ("fresh" crystal soaked
with atp for 2 hours) . SNAP output
|
|
6uvn
|
hydrolase-RNA |
cryo-EM (3.1 Å) |
Li Z, Zhang H, Xiao R, Chang L |
(2020) "Cryo-EM
structure of a type I-F CRISPR RNA guided surveillance
complex bound to transposition protein TniQ."
Cell Res., 30, 179-181. doi:
10.1038/s41422-019-0268-y.
|
Cryoem structure of vccascasde-tniq complex . SNAP output
|
|
6uvw
|
DNA binding protein-DNA |
X-ray (2.551 Å) |
Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard
BL |
(2020) "Optimization
of Protein Thermostability and Exploitation of
Recognition Behavior to Engineer Altered Protein-DNA
Recognition." Structure,
28, 760-775.e8. doi: 10.1016/j.str.2020.04.009.
|
Engineered variant of i-onui meganuclease with improved
thermostability . SNAP
output
|
|
6uw0
|
DNA binding protein-DNA |
X-ray (2.72 Å) |
Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard
BL |
(2020) "Optimization
of Protein Thermostability and Exploitation of
Recognition Behavior to Engineer Altered Protein-DNA
Recognition." Structure,
28, 760-775.e8. doi: 10.1016/j.str.2020.04.009.
|
Engineered variant of i-onui meganuclease with improved
thermostability and fully altered specificity targeting
cholera toxin a subunit . SNAP output
|
|
6uwg
|
DNA binding protein-DNA |
X-ray (2.22 Å) |
Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard
BL |
(2020) "Optimization
of Protein Thermostability and Exploitation of
Recognition Behavior to Engineer Altered Protein-DNA
Recognition." Structure,
28, 760-775.e8. doi: 10.1016/j.str.2020.04.009.
|
Engineered variant of i-onui meganuclease with improved
thermostability and e178d mutation at catalytic site .
SNAP output
|
|
6uwh
|
DNA binding protein-DNA |
X-ray (2.299 Å) |
Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard
BL |
(2020) "Optimization
of Protein Thermostability and Exploitation of
Recognition Behavior to Engineer Altered Protein-DNA
Recognition." Structure,
28, 760-775.e8. doi: 10.1016/j.str.2020.04.009.
|
Intermediate engineered variant of i-onui meganuclease
with improved thermostability and partially altered
specificity . SNAP
output
|
|
6uwj
|
DNA binding protein-DNA |
X-ray (1.852 Å) |
Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard
BL |
(2020) "Optimization
of Protein Thermostability and Exploitation of
Recognition Behavior to Engineer Altered Protein-DNA
Recognition." Structure,
28, 760-775.e8. doi: 10.1016/j.str.2020.04.009.
|
Intermediate engineered variant of i-onui meganuclease
with improved thermostability and partially altered
specificity . SNAP
output
|
|
6uwk
|
DNA binding protein-DNA |
X-ray (2.533 Å) |
Lambert AR, Hallinan JP, Werther R, Glow D, Stoddard
BL |
(2020) "Optimization
of Protein Thermostability and Exploitation of
Recognition Behavior to Engineer Altered Protein-DNA
Recognition." Structure,
28, 760-775.e8. doi: 10.1016/j.str.2020.04.009.
|
Engineered variant of i-onui meganuclease with improved
stability and fully altered specificity targeting human
chromosome 11 trans integration site . SNAP output
|
|
6uxw
|
transcription-DNA |
cryo-EM (8.96 Å) |
Han Y, Reyes AA, Malik S, He Y |
(2020) "Cryo-EM
structure of SWI/SNF complex bound to a
nucleosome." Nature, 579,
452-455. doi: 10.1038/s41586-020-2087-1.
|
Swi-snf nucleosome complex with adp-befx . SNAP output
|
|
6uz7
|
ribosome |
cryo-EM (3.6 Å) |
Huang BY, Fernandez IS |
(2020) "Long-range
interdomain communications in eIF5B regulate GTP
hydrolysis and translation initiation."
Proc.Natl.Acad.Sci.USA, 117,
1429-1437. doi: 10.1073/pnas.1916436117.
|
K.lactis 80s ribosome with p-pe trna and eif5b .
SNAP output
|
|
6v0v
|
recombination-DNA |
cryo-EM (3.61 Å) |
Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W,
Gellert M |
(2020) "Cutting
antiparallel DNA strands in a single active site."
Nat.Struct.Mol.Biol., 27,
119-126. doi: 10.1038/s41594-019-0363-2.
|
cryo-EM structure of mouse wt rag1-2 nfc complex (dna0)
. SNAP output
|
|
6v10
|
virus |
cryo-EM (3.77 Å) |
Mietzsch M, Barnes C, Hull JA, Chipman P, Xie J,
Bhattacharya N, Sousa D, McKenna R, Gao G,
Agbandje-McKenna M |
(2020) "Comparative
Analysis of the Capsid Structures of AAVrh.10,
AAVrh.39, and AAV8." J.Virol.,
94. doi: 10.1128/JVI.01769-19.
|
Genome-containing aav8 particles . SNAP output
|
|
6v1g
|
virus |
cryo-EM (2.98 Å) |
Mietzsch M, Barnes C, Hull JA, Chipman P, Xie J,
Bhattacharya N, Sousa D, McKenna R, Gao G,
Agbandje-McKenna M |
(2020) "Comparative
Analysis of the Capsid Structures of AAVrh.10,
AAVrh.39, and AAV8." J.Virol.,
94. doi: 10.1128/JVI.01769-19.
|
Genome-containing aavrh.10 . SNAP output
|
|
6v1z
|
virus |
cryo-EM (3.58 Å) |
Mietzsch M, Barnes C, Hull JA, Chipman P, Xie J,
Bhattacharya N, Sousa D, McKenna R, Gao G,
Agbandje-McKenna M |
(2020) "Comparative
Analysis of the Capsid Structures of AAVrh.10,
AAVrh.39, and AAV8." J.Virol.,
94. doi: 10.1128/JVI.01769-19.
|
Genome-containing aavrh.39 particles . SNAP output
|
|
6v2k
|
nuclear protein-DNA |
X-ray (2.6 Å) |
Hirano R, Arimura Y, Kujirai T, Shibata M, Okuda A,
Morishima K, Inoue R, Sugiyama M, Kurumizaka H |
(2021) "Histone
variant H2A.B-H2B dimers are spontaneously exchanged
with canonical H2A-H2B in the nucleosome."
Commun Biol, 4, 191. doi:
10.1038/s42003-021-01707-z.
|
The nucleosome structure after h2a-h2b exchange .
SNAP output
|
|
6v3k
|
viral protein-DNA |
cryo-EM (3.4 Å) |
Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins
D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke Jr
TR, Craigie R, Lyumkis D |
(2020) "Structural
basis for strand-transfer inhibitor binding to HIV
intasomes." Science, 367,
810-814. doi: 10.1126/science.aay8015.
|
Structure of hiv cleaved synaptic complex (csc)
intasome bound with magnesium and insti xz419 (compound
4c) . SNAP output
|
|
6v5k
|
transferase |
X-ray (2.69 Å) |
Jung H, Lee S |
"Crystal structure of human DNA polymerase eta
complexed with N7-nitrogen half-mustard guanine (NHMG)
and dCTP*." |
Crystal structure of human DNA polymerase eta complexed
with n7-nitrogen half-mustard guanine (nhmg) and dctp*
. SNAP output
|
|
6v7b
|
virus |
cryo-EM (3.4 Å) |
Wang F, Baquero DP, Su Z, Osinski T, Prangishvili D,
Egelman EH, Krupovic M |
(2020) "Structure
of a filamentous virus uncovers familial ties within
the archaeal virosphere." Virus Evol,
6, veaa023. doi: 10.1093/ve/veaa023.
|
cryo-EM reconstruction of pyrobaculum filamentous virus
2 (pfv2) . SNAP
output
|
|
6v8u
|
DNA binding protein |
X-ray (2.103 Å) |
Nikolova EN, Stanfield RL, Dyson HJ, Wright PE |
(2020) "A
Conformational Switch in the Zinc Finger Protein Kaiso
Mediates Differential Readout of Specific and
Methylated DNA Sequences." Biochemistry,
59, 1909-1926. doi: 10.1021/acs.biochem.0c00253.
|
Kaiso (zbtb33) zinc finger DNA binding domain in
complex with a modified kaiso binding sequence (kbs) .
SNAP output
|
|
6v92
|
gene regulation-DNA |
cryo-EM (20.0 Å) |
Patel AB, Moore CM, Greber BJ, Luo J, Zukin SA,
Ranish J, Nogales E |
(2019) "Architecture
of the chromatin remodeler RSC and insights into its
nucleosome engagement." Elife,
8. doi: 10.7554/eLife.54449.
|
Rsc-ncp . SNAP
output
|
|
6v93
|
DNA binding protein |
cryo-EM (3.1 Å) |
Malik R, Kopylov M, Gomez-Llorente Y, Jain R, Johnson
RE, Prakash L, Prakash S, Ubarretxena-Belandia I,
Aggarwal AK |
(2020) "Structure
and mechanism of B-family DNA polymerase zeta
specialized for translesion DNA synthesis."
Nat.Struct.Mol.Biol., 27,
913-924. doi: 10.1038/s41594-020-0476-7.
|
Structure of DNA polymerase zeta-DNA-dntp ternary
complex . SNAP
output
|
|
6vaa
|
DNA binding protein-DNA |
cryo-EM (3.4 Å) |
Wang R, Wang S, Dhar A, Peralta C, Pavletich NP |
(2020) "DNA
clamp function of the monoubiquitinated Fanconi anaemia
ID complex." Nature, 580,
278-282. doi: 10.1038/s41586-020-2110-6.
|
Structure of the fanconi anemia id complex bound to icl
DNA . SNAP output
|
|
6vae
|
DNA binding protein-DNA |
cryo-EM (3.6 Å) |
Wang R, Wang S, Dhar A, Peralta C, Pavletich NP |
(2020) "DNA
clamp function of the monoubiquitinated Fanconi anaemia
ID complex." Nature, 580,
278-282. doi: 10.1038/s41586-020-2110-6.
|
Mono-ubiquitinated fanconi anemia id complex bound to
icl DNA . SNAP
output
|
|
6vaf
|
DNA binding protein-DNA |
cryo-EM (3.9 Å) |
Wang R, Wang S, Dhar A, Peralta C, Pavletich NP |
(2020) "DNA
clamp function of the monoubiquitinated Fanconi anaemia
ID complex." Nature, 580,
278-282. doi: 10.1038/s41586-020-2110-6.
|
Structure of mono-ubiquitinated fancd2 bound to
non-ubiquitinated fanci and to DNA . SNAP output
|
|
6vbw
|
immune system |
cryo-EM (3.2 Å) |
Jia N, Xie W, de la Cruz MJ, Eng ET, Patel DJ |
(2020) "Structure-function
insights into the initial step of DNA integration by a
CRISPR-Cas-Transposon complex." Cell Res.,
30, 182-184. doi: 10.1038/s41422-019-0272-2.
|
cryo-EM structure of cascade-tniq-dsDNA ternary complex
. SNAP output
|
|
6vcs
|
DNA binding protein-DNA |
X-ray (1.7 Å) |
Dong C, Tempel W, Bountra C, Edwards AM, Arrowsmith
CH, Min J, Structural Genomics Consortium (SGC) |
"SRA domain of UHRF1 in complex with DNA." |
Sra domain of uhrf1 in complex with DNA . SNAP output
|
|
6vdd
|
transferase-DNA |
X-ray (1.9 Å) |
Ghosh S, Goldgur Y, Shuman S |
(2020) "Mycobacterial
DNA polymerase I: activities and crystal structures of
the POL domain as apoenzyme and in complex with a DNA
primer-template and of the full-length FEN/EXO-POL
enzyme." Nucleic Acids Res.,
48, 3165-3180. doi: 10.1093/nar/gkaa075.
|
Pol domain of pol1 from m. smegmatis complex with DNA
primer-template and dntp . SNAP output
|
|
6vdk
|
transferase-DNA |
cryo-EM (4.5 Å) |
Li M, Chen X, Wang H, Jurado KA, Engelman AN, Craigie
R |
(2020) "A
Peptide Derived from Lens Epithelium-Derived Growth
Factor Stimulates HIV-1 DNA Integration and Facilitates
Intasome Structural Studies." J.Mol.Biol.,
432, 2055-2066. doi: 10.1016/j.jmb.2020.01.040.
|
Cryoem structure of hiv-1 conserved intasome core .
SNAP output
|
|
6ven
|
transferase-structural protein-DNA |
cryo-EM (3.37 Å) |
Worden EJ, Zhang X, Wolberger C |
(2020) "Structural
basis for COMPASS recognition of an H2B-ubiquitinated
nucleosome." Elife, 9.
doi: 10.7554/eLife.53199.
|
Yeast compass in complex with a ubiquitinated
nucleosome . SNAP
output
|
|
6vez
|
replication |
X-ray (1.875 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Pre-Catalytic
Ternary Complex, 20 mM Ca2+ (60 min)." |
DNA polymerase mu, 8-oxorgtp:at pre-catalytic ternary
complex, 20 mm ca2+ (60 min) . SNAP output
|
|
6vf0
|
replication |
X-ray (1.58 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Reaction State
Ternary Complex, 50 mM Mg2+ (30 min)." |
DNA polymerase mu, 8-oxorgtp:at reaction state ternary
complex, 50 mm mg2+ (30 min) . SNAP output
|
|
6vf1
|
replication |
X-ray (1.68 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Product State
Ternary Complex, 50 mM Mg2+ (120 min)." |
DNA polymerase mu, 8-oxorgtp:at product state ternary
complex, 50 mm mg2+ (120 min) . SNAP output
|
|
6vf2
|
replication |
X-ray (1.6 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Product State
Ternary Complex, 50 mM Mg2+ (960 min)." |
DNA polymerase mu, 8-oxorgtp:at product state ternary
complex, 50 mm mg2+ (960 min) . SNAP output
|
|
6vf3
|
replication |
X-ray (1.521 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Ground State Ternary
Complex, 50 mM Mn2+ (15 min)." |
DNA polymerase mu, 8-oxorgtp:at ground state ternary
complex, 50 mm mn2+ (15 min) . SNAP output
|
|
6vf4
|
replication |
X-ray (1.75 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Reaction State
Ternary Complex, 50 mM Mn2+ (30 min)." |
DNA polymerase mu, 8-oxorgtp:at reaction state ternary
complex, 50 mm mn2+ (30 min) . SNAP output
|
|
6vf5
|
replication |
X-ray (1.6 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Product State
Ternary Complex, 50 mM Mn2+ (120 min)." |
DNA polymerase mu, 8-oxorgtp:at product state ternary
complex, 50 mm mn2+ (120 min) . SNAP output
|
|
6vf6
|
replication |
X-ray (1.69 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:At Product State
Ternary Complex, 50 mM Mn2+ (960 min)." |
DNA polymerase mu, 8-oxorgtp:at product state ternary
complex, 50 mm mn2+ (960 min) . SNAP output
|
|
6vf7
|
replication |
X-ray (1.871 Å) |
Jamsen JA, Sassa A, Beard WA, Wilson SH |
"DNA Polymerase Mu, 8-oxodGTP:At Ground State Ternary
Complex, 50 mM Mn2+ (15 min)." |
DNA polymerase mu, 8-oxodgtp:at ground state ternary
complex, 50 mm mn2+ (15 min) . SNAP output
|
|
6vf8
|
replication |
X-ray (1.7 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:Ct Pre-Catalytic
Ternary Complex, 20 mM Ca2+ (120 min)." |
DNA polymerase mu, 8-oxorgtp:ct pre-catalytic ternary
complex, 20 mm ca2+ (120 min) . SNAP output
|
|
6vf9
|
replication |
X-ray (1.56 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:Ct Ternary Complex, 50
mM Mg2+ (2160 min)." |
DNA polymerase mu, 8-oxorgtp:ct ternary complex, 50 mm
mg2+ (2160 min) . SNAP
output
|
|
6vfa
|
replication |
X-ray (1.76 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:Ct Ground State Ternary
Complex, 50 mM Mn2+ (15 min)." |
DNA polymerase mu, 8-oxorgtp:ct ground state ternary
complex, 50 mm mn2+ (15 min) . SNAP output
|
|
6vfb
|
replication |
X-ray (1.55 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:Ct Reaction State
Ternary Complex, 50 mM Mn2+ (960 min)." |
DNA polymerase mu, 8-oxorgtp:ct reaction state ternary
complex, 50 mm mn2+ (960 min) . SNAP output
|
|
6vfc
|
replication |
X-ray (1.59 Å) |
Jamsen JA, Sassa A, Shock DD, Beard WA, Wilson
SH |
"DNA Polymerase Mu, 8-oxorGTP:Ct Product State
Ternary Complex, 50 mM Mn2+ (2160 min)." |
DNA polymerase mu, 8-oxorgtp:ct product state ternary
complex, 50 mm mn2+ (2160 min) . SNAP output
|
|
6vg2
|
transcription |
X-ray (3.9 Å) |
Hou C, Mandal A, Rohr J, Tsodikov OV |
(2021) "Allosteric
interference in oncogenic FLI1 and ERG transactions by
mithramycins." Structure,
29, 404-412.e4. doi: 10.1016/j.str.2020.11.012.
|
Crystal structure of the DNA binding domain of human
transcription factor fli1 in complex with 16-mer DNA
cagaggatgtggcttc . SNAP
output
|
|
6vg6
|
transferase-DNA |
X-ray (3.08 Å) |
Jung H, Lee S |
(2020) "Promutagenic
bypass of 7,8-dihydro-8-oxoadenine by translesion
synthesis DNA polymerase Dpo4."
Biochem.J., 477, 2859-2871.
doi: 10.1042/BCJ20200449.
|
Crystal structure of dpo4 with 8-oxoadenine (oxoa) and
dgtp* . SNAP output
|
|
6vg8
|
transcription |
X-ray (4.31 Å) |
Hou C, Mandal A, Rohr J, Tsodikov OV |
(2021) "Allosteric
interference in oncogenic FLI1 and ERG transactions by
mithramycins." Structure,
29, 404-412.e4. doi: 10.1016/j.str.2020.11.012.
|
Crystal structure of the DNA binding domains of human
fli1 and runx2 in complex with 16-mer DNA
cagaggatgtggcttc . SNAP
output
|
|
6vgd
|
transcription |
X-ray (4.2 Å) |
Hou C, Mandal A, Rohr J, Tsodikov OV |
(2021) "Allosteric
interference in oncogenic FLI1 and ERG transactions by
mithramycins." Structure,
29, 404-412.e4. doi: 10.1016/j.str.2020.11.012.
|
Crystal structure of the DNA binding domain (dbd) of
human fli1 and the complex of the dbd of human runx2
with core binding factor beta (cbfb), in complex with
16mer DNA cagaggatgtggcttc . SNAP output
|
|
6vge
|
transcription |
X-ray (4.25 Å) |
Hou C, Mandal A, Rohr J, Tsodikov OV |
(2021) "Allosteric
interference in oncogenic FLI1 and ERG transactions by
mithramycins." Structure,
29, 404-412.e4. doi: 10.1016/j.str.2020.11.012.
|
Crystal structure of the DNA binding domains of human
transcription factor erg, human runx2 bound to core
binding factor beta (cbfb), in complex with 16mer DNA
cagaggatgtggcttc . SNAP
output
|
|
6vgg
|
transcription |
X-ray (4.31 Å) |
Hou C, Mandal A, Rohr J, Tsodikov OV |
(2021) "Allosteric
interference in oncogenic FLI1 and ERG transactions by
mithramycins." Structure,
29, 404-412.e4. doi: 10.1016/j.str.2020.11.012.
|
Crystal structure of the DNA binding domains of human
transcription factor erg, human runx2 bound to core
binding factor beta (cbfb), and mithramycin, in complex
with 16mer DNA cagaggatgtggcttc . SNAP output
|
|
6vgm
|
transferase |
X-ray (2.84 Å) |
Jung H, Lee S |
(2020) "Promutagenic
bypass of 7,8-dihydro-8-oxoadenine by translesion
synthesis DNA polymerase Dpo4."
Biochem.J., 477, 2859-2871.
doi: 10.1042/BCJ20200449.
|
Crystal structure of dpo4 with 8-oxoadenine (oxoa) and
dttp* . SNAP output
|
|
6vjw
|
transferase |
X-ray (2.02 Å) |
Ouzon-Shubeita H, Jung H, Lee MH, Koag MC, Lee S |
(2020) "Catalytic
mechanism of the mismatch-specific DNA glycosylase
methyl-CpG-binding domain 4." Biochem.J.,
477, 1601-1612. doi: 10.1042/BCJ20200125.
|
Crystal structure of wt hmbd4 complexed with t:g
mismatch DNA . SNAP
output
|
|
6vkp
|
transferase-DNA |
X-ray (2.54 Å) |
Jung H, Lee S |
(2021) "Insights
into the mismatch discrimination mechanism of Y-family
DNA polymerase Dpo4." Biochem.J.,
478, 1769-1781. doi: 10.1042/BCJ20210162.
|
Crystal structure of dpo4 extension past 8-oxoadenine
(oxoa) and dg . SNAP
output
|
|
6vnp
|
transferase-DNA |
X-ray (2.42 Å) |
Jung H, Lee S |
"Crystal structure of DPO4 extension past
8-oxoadenine (oxoA) and dT." |
Crystal structure of dpo4 extension past 8-oxoadenine
(oxoa) and dt . SNAP
output
|
|
6voy
|
DNA binding protein-DNA |
cryo-EM (3.7 Å) |
Bhatt V, Shi K, Salamango DJ, Moeller NH, Pandey KK,
Bera S, Bohl TE, Kurniawan F, Orellana K, Zhang W,
Grandgenett DP, Harris RS, Sundborger-Lunna AC, Aihara
H |
(2020) "Structural
basis of host protein hijacking in human T-cell
leukemia virus integration." Nat Commun,
11, 3121. doi: 10.1038/s41467-020-16963-6.
|
cryo-EM structure of htlv-1 instasome . SNAP output
|
|
6vpc
|
DNA binding protein-DNA-RNA |
cryo-EM (3.2 Å) |
Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E,
Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA |
(2020) "DNA
capture by a CRISPR-Cas9-guided adenine base
editor." Science, 369,
566-571. doi: 10.1126/science.abb1390.
|
Structure of the spcas9 DNA adenine base editor - abe8e
. SNAP output
|
|
6vrd
|
hydrolase-RNA |
X-ray (1.299 Å) |
Cho Y-J, Butler D |
"Crystal structure of RNase H/RNA/PS-ASO complex at
an atomic level." |
Crystal structure of rnase h-RNA-ps-aso complex at an
atomic level . SNAP
output
|
|
6vtx
|
DNA binding protein-DNA |
X-ray (2.14 Å) |
Sharma R, Choi KJ, Quan MD, Sharma S, Sankaran B,
Park H, LaGrone A, Kim JJ, MacKenzie KR, Ferreon ACM, Kim
C, Ferreon JC |
(2021) "Liquid
condensation of reprogramming factor KLF4 with DNA
provides a mechanism for chromatin organization."
Nat Commun, 12, 5579. doi:
10.1038/s41467-021-25761-7.
|
Crystal structure of human klf4 zinc finger DNA binding
domain in complex with nanog DNA . SNAP output
|
|
6vu3
|
ribosome |
cryo-EM (3.7 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
cryo-EM structure of escherichia coli
transcription-translation complex a (ttc-a) containing
mrna with a 12 nt long spacer . SNAP output
|
|
6vug
|
protein binding |
X-ray (3.0 Å) |
Chesterman C, Arnold E |
(2021) "Co-crystallization
with diabodies: A case study for the introduction of
synthetic symmetry." Structure,
29, 598-605.e3. doi: 10.1016/j.str.2021.02.001.
|
Diabody bound to a reverse transcriptase aptamer
complex . SNAP
output
|
|
6vvs
|
transcription,transferase-DNA-antibiotic |
X-ray (3.112 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Crystal structure of a mycobacterium smegmatis RNA
polymerase transcription initiation complex with
antibiotic sorangicin . SNAP output
|
|
6vvt
|
transcription,transferase-DNA-antibiotic |
X-ray (2.901 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Crystal structure of a mycobacterium smegmatis
transcription initiation complex with
rifampicin-resistant RNA polymerase and antibiotic
sorangicin . SNAP
output
|
|
6vvv
|
transcription,transferase-DNA |
X-ray (3.2 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Crystal structure of a mycobacterium smegmatis
transcription initiation complex with
rifampicin-resistant RNA polymerase . SNAP output
|
|
6vvx
|
transcription,transferase-DNA-antibiotic |
cryo-EM (3.39 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Mycobacterium tuberculosis wt rnap transcription
initiation intermediate structure with sorangicin .
SNAP output
|
|
6vvy
|
transcription,transferase-DNA-antibiotic |
cryo-EM (3.42 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Mycobacterium tuberculosis wt rnap transcription open
promoter complex with sorangicin . SNAP output
|
|
6vvz
|
transcription,transferase-DNA-antibiotic |
cryo-EM (3.72 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Mycobacterium tuberculosis rnap s456l mutant
transcription initiation intermediate structure with
sorangicin . SNAP
output
|
|
6vw0
|
transcription,transferase-DNA |
cryo-EM (3.59 Å) |
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA,
Herrmann J, Muller R, Mooney R, Landick R, Darst SA,
Campbell EA |
(2020) "The
antibiotic sorangicin A inhibits promoter DNA unwinding
in a Mycobacterium tuberculosis rifampicin-resistant
RNA polymerase." Proc.Natl.Acad.Sci.USA,
117, 30423-30432. doi: 10.1073/pnas.2013706117.
|
Mycobacterium tuberculosis rnap s456l mutant open
promoter complex . SNAP
output
|
|
6vyp
|
nuclear protein-DNA |
X-ray (4.99 Å) |
Kim SA, Zhu J, Yennawar N, Eek P, Tan S |
(2020) "Crystal
Structure of the LSD1/CoREST Histone Demethylase Bound
to Its Nucleosome Substrate." Mol.Cell,
78, 903. doi: 10.1016/j.molcel.2020.04.019.
|
Crystal structure of the lsd1-corest histone
demethylase bound to its nucleosome substrate .
SNAP output
|
|
6vyq
|
ribosome,transcription-translation |
cryo-EM (3.7 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex a1
(ttc-a1) containing an 15 nt long mrna spacer, nusg,
and fmet-trnas at e-site and p-site . SNAP output
|
|
6vyr
|
ribosome,transcription-translation |
cryo-EM (3.8 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex a1
(ttc-a1) containing an 18 nt long mrna spacer, nusg,
and fmet-trnas at e-site and p-site . SNAP output
|
|
6vys
|
ribosome,transcription-translation |
cryo-EM (3.7 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex a1
(ttc-a1) containing a 21 nt long mrna spacer, nusg, and
fmet-trnas at e-site and p-site . SNAP output
|
|
6vyt
|
ribosome,transcription-translation |
cryo-EM (14.0 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex a2
(ttc-a2) containing a 15 nt long mrna spacer, nusg, and
fmet-trnas at p-site and e-site . SNAP output
|
|
6vyu
|
ribosome,transcription-translation |
cryo-EM (7.0 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex c2
(ttc-c2) containing a 27 nt long mrna spacer . SNAP output
|
|
6vyw
|
ribosome,transcription-translation |
cryo-EM (7.0 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex c3
(ttc-c3) containing mrna with a 27 nt long spacer,
nusg, and fmet-trnas at e-site and p-site . SNAP output
|
|
6vyx
|
ribosome-transcription-translation |
cryo-EM (9.9 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex c4
(ttc-c4) containing mrna with a 21 nt long spacer,
transcription factor nusg, and fmet-trnas at p-site and
e-site . SNAP output
|
|
6vyy
|
ribosome,transcription-translation |
cryo-EM (9.9 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex c5
(ttc-c5) containing mrna with a 21 nt long spacer,
nusg, and fmet-trnas at e-site and p-site . SNAP output
|
|
6vyz
|
ribosome,transcription-translation |
cryo-EM (9.9 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex c6
(ttc-c6) containing mrna with a 21 nt long spacer,
nusa, and fmet-trnas at e-site and p-site . SNAP output
|
|
6vz2
|
ribosome,transcription-translation |
cryo-EM (10.0 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex d1
(ttc-d1) containing mrna with a 27 nt long spacer,
nusg, and fmet-trnas at e-site and p-site . SNAP output
|
|
6vz3
|
ribosome,transcription-translation |
cryo-EM (8.9 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex d2
(ttc-d2) containing mrna with a 27 nt long spacer .
SNAP output
|
|
6vz4
|
motor protein |
cryo-EM (3.9 Å) |
Baker RW, Reimer JM, Carman PJ, Turegun B, Arakawa T,
Dominguez R, Leschziner AE |
(2021) "Structural
insights into assembly and function of the RSC
chromatin remodeling complex."
Nat.Struct.Mol.Biol., 28,
71-80. doi: 10.1038/s41594-020-00528-8.
|
cryo-EM structure of sth1-arp7-arp9-rtt102 bound to the
nucleosome in adp beryllium fluoride state . SNAP output
|
|
6vz5
|
ribosome,transcription-translation |
cryo-EM (8.9 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex d3
(ttc-d3) containing mrna with a 21 nt long spacer,
nusg, and fmet-trnas at e-site and p-site . SNAP output
|
|
6vz7
|
ribosome |
cryo-EM (7.0 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex c1
(ttc-c1) containing a 27 nt long mrna spacer, nusg, and
fmet-trnas at p-site and e-site . SNAP output
|
|
6vzj
|
ribosome |
cryo-EM (4.1 Å) |
Wang C, Molodtsov V, Firlar E, Kaelber JT, Blaha G,
Su M, Ebright RH |
(2020) "Structural
basis of transcription-translation coupling."
Science, 369, 1359-1365. doi:
10.1126/science.abb5317.
|
Escherichia coli transcription-translation complex a1
(ttc-a1) containing mrna with a 15 nt long spacer,
fmet-trnas at e-site and p-site, and lacking
transcription factor nusg . SNAP output
|
|
6w0m
|
lyase-DNA |
X-ray (2.37 Å) |
Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus
M, Nam K, Verdine GL |
(2020) "The
trajectory of intrahelical lesion recognition and
extrusion by the human 8-oxoguanine DNA
glycosylase." Nat Commun,
11, 4437. doi: 10.1038/s41467-020-18290-2.
|
Human 8-oxoguanine glycosylase crosslinked with oxog
lesion containing DNA . SNAP output
|
|
6w0q
|
DNA binding protein-DNA |
X-ray (1.89 Å) |
Whitaker AM, Stark WJ, Flynn TS, Freudenthal BD |
(2020) "Molecular
and structural characterization of disease-associated
APE1 polymorphisms." DNA Repair (Amst.)</ |