2XRO
 
 | | Crystal structure of TtgV in complex with its DNA operator | | Descriptor: | HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGV, OSMIUM ION, TTGV OPERATOR DNA | | Authors: | Lu, D, Fillet, S, Meng, C, Alguel, Y, Kloppsteck, P, Bergeron, J, Krell, T, Gallegos, M.-T, Ramos, J, Zhang, X. | | Deposit date: | 2010-09-17 | | Release date: | 2010-12-01 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | 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, 2010
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7RBN
 | | Human DNA polymerase beta crosslinked complex, 20 min Ca to Mg exchange | | Descriptor: | 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), ... | | Authors: | Kumar, A. | | Deposit date: | 2021-07-06 | | Release date: | 2022-03-09 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Interlocking activities of DNA polymerase beta in the base excision repair pathway.
Proc.Natl.Acad.Sci.USA, 119, 2022
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8WPK
 | | Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with exgenous DNA | | Descriptor: | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA polymerase, DNA polymerase processivity factor, ... | | Authors: | Wang, X, Li, N, Gao, N. | | Deposit date: | 2023-10-10 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-27 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5.
Mol.Cell, 83, 2023
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8WPE
 | | Structure of monkeypox virus polymerase complex F8-A22-E4-H5 (tag-free A22) with exogenous DNA | | Descriptor: | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, A22R DNA polymerase processivity factor, DNA polymerase, ... | | Authors: | Wang, X, Li, N, Gao, N. | | Deposit date: | 2023-10-10 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-27 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5.
Mol.Cell, 83, 2023
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8WPP
 | | Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with endogenous DNA | | Descriptor: | A22R DNA polymerase processivity factor, DNA polymerase, E4R Uracil-DNA glycosylase, ... | | Authors: | Wang, X, Li, N, Gao, N. | | Deposit date: | 2023-10-10 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-27 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5.
Mol.Cell, 83, 2023
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8WPF
 | | Structure of monkeypox virus polymerase complex F8-A22-E4-H5 with exogenous DNA bearing one abasic site | | Descriptor: | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, A22R DNA polymerase processivity factor, DNA polymerase, ... | | Authors: | Wang, X, Li, N, Gao, N. | | Deposit date: | 2023-10-10 | | Release date: | 2023-11-29 | | Last modified: | 2023-12-27 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5.
Mol.Cell, 83, 2023
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5MCV
 | | New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LWC1) | | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, Cellular tumor antigen p53, ... | | Authors: | Golovenko, D, Rozenberg, H, Shakked, Z. | | Deposit date: | 2016-11-10 | | Release date: | 2018-06-13 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins.
Structure, 26, 2018
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8V5R
 | | Active conformation of DNA polymerase gamma bound to DNA | | Descriptor: | 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA polymerase subunit gamma-1, DNA polymerase subunit gamma-2, ... | | Authors: | Riccio, A.A, Krahn, J.M, Bouvette, J, Borgnia, J.M, Copeland, W.C. | | Deposit date: | 2023-11-30 | | Release date: | 2024-07-10 | | Last modified: | 2024-07-31 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis.
Nucleic Acids Res., 52, 2024
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3COQ
 | | Structural Basis for Dimerization in DNA Recognition by Gal4 | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*DAP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DAP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3'), DNA (5'-D(*DTP*DCP*DCP*DGP*DGP*DAP*DGP*DGP*DAP*DCP*DTP*DGP*DTP*DCP*DCP*DTP*DCP*DCP*DGP*DG)-3'), ... | | Authors: | Hong, M, Fitzgerald, M.X, Harper, S, Luo, C, Speicher, D.W. | | Deposit date: | 2008-03-29 | | Release date: | 2008-07-01 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for dimerization in DNA recognition by gal4.
Structure, 16, 2008
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7S9P
 | | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog | | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | | Authors: | Freudenthal, B.D, Ryan, B.J, Smith, M.R. | | Deposit date: | 2021-09-21 | | Release date: | 2022-08-03 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.
J.Am.Chem.Soc., 144, 2022
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7S9Q
 | | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dATP analog | | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... | | Authors: | Freudenthal, B.D, Ryan, B.J, Smith, M.R. | | Deposit date: | 2021-09-21 | | Release date: | 2022-08-03 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.
J.Am.Chem.Soc., 144, 2022
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5K5O
 | | Structure of AspA-26mer DNA complex | | Descriptor: | AspA, DNA (26-MER) | | Authors: | Schumacher, M. | | Deposit date: | 2016-05-23 | | Release date: | 2016-06-15 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Science, 349, 2015
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5K5R
 | | AspA-32mer DNA,crystal form 2 | | Descriptor: | AspA, DNA (32-MER), PHOSPHATE ION | | Authors: | Schumacher, M. | | Deposit date: | 2016-05-23 | | Release date: | 2016-06-15 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (3.09 Å) | | Cite: | Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Science, 349, 2015
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8SY5
 | | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dS-BTP base pair in the active site | | Descriptor: | 2-oxo-2-hydroadenosine 5'-(tetrahydrogen triphosphate), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Shan, Z, Lyumkis, D, Oh, J, Wang, D. | | Deposit date: | 2023-05-24 | | Release date: | 2023-12-27 | | Method: | ELECTRON MICROSCOPY (2.7 Å) | | Cite: | A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Nat Commun, 14, 2023
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8SY6
 | | E. coli DNA-directed RNA polymerase transcription elongation complex bound the unnatural dB-UTP base pair in the active site | | Descriptor: | 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Shan, Z, Lyumkis, D, Oh, J, Wang, D. | | Deposit date: | 2023-05-24 | | Release date: | 2023-12-27 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (3.28 Å) | | Cite: | A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
Nat Commun, 14, 2023
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8G9O
 | | Complete DNA elongation subcomplex of Xenopus laevis DNA polymerase alpha-primase | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA polymerase alpha catalytic subunit, DNA primase large subunit, ... | | Authors: | Mullins, E.A, Durie, C.L, Ohi, M.D, Chazin, W.J, Eichman, B.F. | | Deposit date: | 2023-02-21 | | Release date: | 2023-04-12 | | Last modified: | 2024-05-29 | | Method: | ELECTRON MICROSCOPY (4.4 Å) | | Cite: | A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase.
Nat.Struct.Mol.Biol., 31, 2024
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6UOL
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6UOK
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6UOM
 | | Y271G DNA polymerase beta ternary complex with templating adenine and incoming r8-oxo-GTP | | Descriptor: | 1,2-ETHANEDIOL, 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE, 8-OXO-GUANOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Smith, M.R, Freudenthal, B.D. | | Deposit date: | 2019-10-15 | | Release date: | 2020-01-08 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta.
J.Biol.Chem., 295, 2020
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8OJ7
 | | HSV-1 DNA polymerase-processivity factor complex in halted elongation state | | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (53-MER), DNA (67-MER), ... | | Authors: | Gustavsson, E, Grunewald, K, Elias, P, Hallberg, B.M. | | Deposit date: | 2023-03-24 | | Release date: | 2024-04-03 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (2.46 Å) | | Cite: | Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM.
Nucleic Acids Res., 52, 2024
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8OJA
 | | HSV-1 DNA polymerase-processivity factor complex in exonuclease state | | Descriptor: | CALCIUM ION, DNA (47-MER), DNA (68-MER), ... | | Authors: | Gustavsson, E, Grunewald, K, Elias, P, Hallberg, B.M. | | Deposit date: | 2023-03-24 | | Release date: | 2024-04-03 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (1.87 Å) | | Cite: | Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM.
Nucleic Acids Res., 52, 2024
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3D0A
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3W6V
 | | Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA | | Descriptor: | AdpA, DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*C)-3'), DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3') | | Authors: | Yao, M.D, Ohtsuka, J, Nagata, K, Miyazono, K, Ohnishi, Y, Tanokura, M. | | Deposit date: | 2013-02-22 | | Release date: | 2013-09-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | 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, 2013
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5N2E
 | | Structure of the E9 DNA polymerase from vaccinia virus | | Descriptor: | 2,3-DIHYDROXY-1,4-DITHIOBUTANE, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... | | Authors: | Tarbouriech, N, Burmeister, W.P, Iseni, F. | | Deposit date: | 2017-02-07 | | Release date: | 2017-11-29 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (2.74 Å) | | Cite: | The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.
Nat Commun, 8, 2017
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6VDD
 | | POL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP | | Descriptor: | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3'), DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... | | Authors: | Shuman, S, Goldgur, Y, Ghosh, S. | | Deposit date: | 2019-12-24 | | Release date: | 2020-02-12 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | 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, 2020
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