8JH2
 
 | | RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome | | 分子名称: | DNA (218-MER), DNA (40-MER), DNA-directed RNA polymerase subunit, ... | | 著者 | Akatsu, M, Fujita, R, Ogasawara, M, Ehara, H, Kujirai, T, Takizawa, Y, Sekine, S, Kurumizaka, H. | | 登録日 | 2023-05-22 | | 公開日 | 2023-11-29 | | 最終更新日 | 2023-12-20 | | 実験手法 | ELECTRON MICROSCOPY (5.7 Å) | | 主引用文献 | Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
J.Biol.Chem., 299, 2023
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6JUL
 | | MsDpo4-DNA complex 1 | | 分子名称: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(P*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3'), DNA polymerase IV, ... | | 著者 | Nair, D.T, Johnson, M.K. | | 登録日 | 2019-04-15 | | 公開日 | 2020-02-19 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Nucleic Acids Res., 47, 2019
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6KBS
 | | Crystal structure of yedK in complex with ssDNA | | 分子名称: | DNA (5'-D(*CP*GP*GP*TP*CP*GP*AP*TP*TP*C)-3'), SOS response-associated protein | | 著者 | Wang, N, Bao, H, Huang, H. | | 登録日 | 2019-06-26 | | 公開日 | 2019-07-10 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.601 Å) | | 主引用文献 | Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.
Nucleic Acids Res., 47, 2019
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1TTD
 | | SOLUTION-STATE STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-SYN THYMINE CYCLOBUTANE DIMER | | 分子名称: | DNA (5'-D(*CP*TP*TP*AP*AP*TP*TP*CP*GP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*CP*GP*AP*AP*(TTD)P*AP*AP*G)-3') | | 著者 | Mcateer, K, Jing, Y, Kao, J, Taylor, J.-S, Kennedy, M.A. | | 登録日 | 1999-01-20 | | 公開日 | 1999-02-02 | | 最終更新日 | 2023-12-27 | | 実験手法 | SOLUTION NMR | | 主引用文献 | Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA.
J.Mol.Biol., 282, 1998
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3AV4
 | | Crystal structure of mouse DNA methyltransferase 1 | | 分子名称: | DNA (cytosine-5)-methyltransferase 1, ZINC ION | | 著者 | Takeshita, K, Suetake, I, Yamashita, E, Suga, M, Narita, H, Nakagawa, A, Tajima, S. | | 登録日 | 2011-02-22 | | 公開日 | 2011-05-04 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.75 Å) | | 主引用文献 | Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Proc.Natl.Acad.Sci.USA, 108, 2011
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5NSR
 | | Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex | | 分子名称: | DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... | | 著者 | Glyde, R, Ye, F.Z, Darbari, V.C, Zhang, N, Buck, M, Zhang, X.D. | | 登録日 | 2017-04-26 | | 公開日 | 2017-06-28 | | 最終更新日 | 2019-12-11 | | 実験手法 | ELECTRON MICROSCOPY (3.8 Å) | | 主引用文献 | Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.
Mol. Cell, 67, 2017
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7QXI
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4W9M
 | | AMPPNP bound Rad50 in complex with dsDNA | | 分子名称: | DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*CP*AP*CP*CP*GP*AP*CP*C)-3'), DNA (5'-D(*GP*GP*TP*CP*GP*GP*TP*GP*AP*CP*CP*GP*AP*CP*C)-3'), Exonuclease, ... | | 著者 | Rojowska, A, Lammens, K. | | 登録日 | 2014-08-27 | | 公開日 | 2015-01-14 | | 最終更新日 | 2024-05-08 | | 実験手法 | X-RAY DIFFRACTION (2.7 Å) | | 主引用文献 | Structure of the Rad50 DNA double-strand break repair protein in complex with DNA.
Embo J., 33, 2014
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5AWH
 | | Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex | | 分子名称: | DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3'), MAGNESIUM ION, RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'), ... | | 著者 | Miyoshi, T, Ito, K, Murakami, R, Uchiumi, T. | | 登録日 | 2015-07-03 | | 公開日 | 2016-07-06 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.
Nat Commun, 7, 2016
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1DUX
 | | ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING SURFACE AFFECT DNA-RECOGNITION | | 分子名称: | DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3'), DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3'), ETS-DOMAIN PROTEIN ELK-1 | | 著者 | Mo, Y, Vaessen, B, Johnston, K, Marmorstein, R. | | 登録日 | 2000-01-19 | | 公開日 | 2000-04-17 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA.
Nat.Struct.Biol., 7, 2000
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6KZA
 | | Crystal structure of the complex of the interaction domains of E. coli DnaB helicase and DnaC helicase loader | | 分子名称: | DNA replication protein DnaC, Replicative DNA helicase | | 著者 | Nagata, K, Okada, A, Ohtsuka, J, Ohkuri, T, Akama, Y, Sakiyama, Y, Miyazaki, E, Horita, S, Katayama, T, Ueda, T, Tanokura, M. | | 登録日 | 2019-09-23 | | 公開日 | 2019-11-20 | | 最終更新日 | 2024-03-27 | | 実験手法 | X-RAY DIFFRACTION (3.1 Å) | | 主引用文献 | Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding.
J.Biochem., 167, 2020
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6L2N
 | | Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) complex | | 分子名称: | DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3'), RE_R_Pab1 domain-containing protein | | 著者 | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | | 登録日 | 2019-10-05 | | 公開日 | 2020-03-18 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2.45 Å) | | 主引用文献 | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res., 48, 2020
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6L2O
 | | Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) complex | | 分子名称: | DNA (5'-D(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G)-3'), RE_R_Pab1 domain-containing protein | | 著者 | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | | 登録日 | 2019-10-05 | | 公開日 | 2020-03-18 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res., 48, 2020
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5X6H
 | | Crystal Structure of SMAD5-MH1/GC-BRE DNA complex | | 分子名称: | DNA (5'-D(P*GP*TP*AP*TP*GP*GP*CP*GP*CP*CP*AP*TP*AP*C)-3'), Mothers against decapentaplegic homolog 5, ZINC ION | | 著者 | Chai, N, Wang, J, Wang, Z.X, Wu, J.W. | | 登録日 | 2017-02-22 | | 公開日 | 2017-03-15 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (3.1 Å) | | 主引用文献 | Structural basis for the Smad5 MH1 domain to recognize different DNA sequences.
Nucleic Acids Res., 43, 2015
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1DU0
 | | ENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX | | 分子名称: | DNA (5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3'), DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3'), ENGRAILED HOMEODOMAIN | | 著者 | Grant, R.A, Rould, M.A, Klemm, J.D, Pabo, C.O. | | 登録日 | 2000-01-13 | | 公開日 | 2000-07-31 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A.
Biochemistry, 39, 2000
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4WCG
 | | The binding mode of Cyprinid Herpesvirus3 ORF112-Zalpha to Z-DNA | | 分子名称: | DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3'), ORF112, SULFATE ION | | 著者 | Kus, K, Athanasiadis, A. | | 登録日 | 2014-09-04 | | 公開日 | 2015-11-18 | | 最終更新日 | 2024-01-10 | | 実験手法 | X-RAY DIFFRACTION (1.5 Å) | | 主引用文献 | 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, 2015
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6KKS
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8H40
 | | Cryo-EM structure of the transcription activation complex NtcA-TAC | | 分子名称: | DNA (125-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... | | 著者 | Han, S.J, Jiang, Y.L, You, L.L, Shen, L.Q, Wu, X.X, Yang, F, Kong, W.W, Chen, Z.P, Zhang, Y, Zhou, C.Z. | | 登録日 | 2022-10-09 | | 公開日 | 2023-10-04 | | 最終更新日 | 2024-02-28 | | 実験手法 | ELECTRON MICROSCOPY (3.6 Å) | | 主引用文献 | DNA looping mediates cooperative transcription activation.
Nat.Struct.Mol.Biol., 31, 2024
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8H3V
 | | Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC | | 分子名称: | DNA (125-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ... | | 著者 | Han, S.J, Jiang, Y.L, You, L.L, Shen, L.Q, Wu, X.X, Yang, F, Kong, W.W, Chen, Z.P, Zhang, Y, Zhou, C.Z. | | 登録日 | 2022-10-09 | | 公開日 | 2023-10-04 | | 最終更新日 | 2024-10-30 | | 実験手法 | ELECTRON MICROSCOPY (4.5 Å) | | 主引用文献 | DNA looping mediates cooperative transcription activation.
Nat.Struct.Mol.Biol., 31, 2024
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375D
 | | A NOVEL END-TO-END BINDING OF TWO NETROPSINS TO THE DNA DECAMER D(CCCCCIIIII)2 | | 分子名称: | DNA (5'-D(*CP*CP*CP*CP*CP*IP*IP*IP*IP*I)-3'), NETROPSIN | | 著者 | Chen, X, Rao, S.T, Sekar, K, Sundaralingam, M. | | 登録日 | 1998-01-14 | | 公開日 | 1998-12-02 | | 最終更新日 | 2024-02-21 | | 実験手法 | X-RAY DIFFRACTION (2.4 Å) | | 主引用文献 | A Novel End-to-End Binding of Two Netropsins to the DNA Decamers d(CCCCCIIIII) 2, d(CCCBr5CCIIIII)2, d(CBr5CCCCIIIII)2
Nucleic Acids Res., 26, 1998
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4X0P
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4X0Q
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309D
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1DSZ
 | | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | | 分子名称: | DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3'), RETINOIC ACID RECEPTOR ALPHA, ... | | 著者 | Rastinejad, F, Wagner, T, Zhao, Q, Khorasanizadeh, S. | | 登録日 | 2000-01-10 | | 公開日 | 2000-07-10 | | 最終更新日 | 2024-02-07 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.
EMBO J., 19, 2000
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8JH3
 | | RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome | | 分子名称: | DNA (198-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | 著者 | Akatsu, M, Fujita, R, Ogasawara, M, Ehara, H, Kujirai, T, Takizawa, Y, Sekine, S, Kurumizaka, H. | | 登録日 | 2023-05-22 | | 公開日 | 2023-11-29 | | 最終更新日 | 2023-12-20 | | 実験手法 | ELECTRON MICROSCOPY (3.7 Å) | | 主引用文献 | Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
J.Biol.Chem., 299, 2023
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