PDB: 45817 件ウェブページステータス検索Chemie searchBIRD

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7Z5A	Crystal structure of the trapped complex of mouse Endonuclease VIII-LIKE 3 (mNEIL3) and hairpin DNA with 5'overhang 分子名称: DNA (5'-D(P*TP*TP*TP*(PED)P*AP*CP*GP*CP*GP*AP*AP*GP*CP*GP*TP*G)-3'), Endonuclease 8-like 3, ZINC ION 著者 Silhan, J, Huskova, A. 登録日 2022-03-08 公開日 2022-10-19 最終更新日 2024-01-31 実験手法 X-RAY DIFFRACTION (2.28 Å) 主引用文献 Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model. Nucleic Acids Res., 50, 2022
7Z03	Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and extended dsDNA 分子名称: ADENOSINE-5'-DIPHOSPHATE, DNA (39-MER), MAGNESIUM ION, ... 著者 Gut, F, Kaeshammer, L, Lammens, K, Bartho, J, van de Logt, E, Kessler, B, Hopfner, K.P. 登録日 2022-02-21 公開日 2022-08-17 最終更新日 2024-07-17 実験手法 ELECTRON MICROSCOPY (3.7 Å) 主引用文献 Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Mol.Cell, 82, 2022
7YZO	Endonuclease state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and dsDNA 分子名称: ADENOSINE-5'-DIPHOSPHATE, DNA (31-MER), MAGNESIUM ION, ... 著者 Gut, F, Kaeshammer, L, Lammens, K, Bartho, J, van de Logt, E, Kessler, B, Hopfner, K.P. 登録日 2022-02-21 公開日 2022-08-17 最終更新日 2024-07-17 実験手法 ELECTRON MICROSCOPY (3.4 Å) 主引用文献 Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Mol.Cell, 82, 2022
8PPU	Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches 分子名称: DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3'), DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(C7R)P*(PST)P*(PST)P*(PST))-3'), DNA polymerase II small subunit, ... 著者 Betancurt-Anzola, L, Martinez-Carranza, M, Zatopek, K.M, Gardner, A.F, Sauguet, L. 登録日 2023-07-10 公開日 2023-12-20 最終更新日 2023-12-27 実験手法 ELECTRON MICROSCOPY (3.02 Å) 主引用文献 Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun, 14, 2023
8PPV	Intermediate conformer of Pyrococcus abyssi DNA polymerase D (PolD) bound to a primer/template substrate containing three consecutive mismatches 分子名称: DNA (5'-D(*P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(G7P)P*(PST)P*(PST)P*(PST))-3'), DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3'), DNA polymerase II small subunit, ... 著者 Betancurt-Anzola, L, Martinez-Carranza, M, Zatopek, K.M, Gardner, A.F, Sauguet, L. 登録日 2023-07-10 公開日 2023-12-20 最終更新日 2023-12-27 実験手法 ELECTRON MICROSCOPY (3.02 Å) 主引用文献 Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun, 14, 2023
8PPT	Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing a mismatch 分子名称: DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3'), DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*GP*CP*TP*TP*T)-3'), DNA polymerase II small subunit, ... 著者 Betancurt-Anzola, L, Martinez-Carranza, M, Zatopek, K.M, Gardner, A.F, Sauguet, L. 登録日 2023-07-10 公開日 2023-12-20 最終更新日 2023-12-27 実験手法 ELECTRON MICROSCOPY (2.9 Å) 主引用文献 Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun, 14, 2023
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
7DTA	Solution structure of the C-clamp domain from human HDBP1 in complex with DNA 分子名称: DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3'), DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3'), SLC2A4 regulator, ... 著者 Duan, B, Xia, B. 登録日 2021-01-04 公開日 2021-07-21 最終更新日 2024-05-01 実験手法 SOLUTION NMR 主引用文献 Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains. J.Am.Chem.Soc., 143, 2021
4WX9	Crystal structure of Mycobacterium tuberculosis OGT in complex with DNA 分子名称: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'), GLYCEROL, ... 著者 Miggiano, R, Rossi, F, Garavaglia, S, Rizzi, M. 登録日 2014-11-13 公開日 2015-11-04 最終更新日 2024-01-10 実験手法 X-RAY DIFFRACTION (3 Å) 主引用文献 Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA. Biochem.J., 473, 2016
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
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
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
8PM4	Cryo-EM structure of the Cas12m-crRNA-target DNA complex 分子名称: DNA oligoduplex, non-target strand, chain D, ... 著者 Sasnauskas, G, Tamulaitiene, G, Karvelis, T, Bigelyte, G, Siksnys, V. 登録日 2023-06-28 公開日 2024-02-07 最終更新日 2024-04-24 実験手法 ELECTRON MICROSCOPY (2.93 Å) 主引用文献 Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing. Nucleic Acids Res., 52, 2024
8PWR	TINA-conjugated antiparallel DNA triplex 分子名称: DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3'), DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3'), DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3') 著者 Garavis, M, Edwards, P.J.B, Serrano-Chacon, I, Doluca, O, Filichev, V.V, Gonzalez, C. 登録日 2023-07-21 公開日 2024-01-17 最終更新日 2024-03-27 実験手法 SOLUTION NMR 主引用文献 Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex. Nucleic Acids Res., 52, 2024
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
6E93	Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 in complex with methylated DNA 分子名称: DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3'), ZINC ION, ... 著者 Hudson, N.O, Whitby, F.G, Buck-Koehntop, B.A. 登録日 2018-07-31 公開日 2018-11-07 最終更新日 2024-03-13 実験手法 X-RAY DIFFRACTION (1.747 Å) 主引用文献 Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J. Biol. Chem., 293, 2018
6E94	Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA 分子名称: DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3'), ZINC ION, ... 著者 Hudson, N.O, Whitby, F.G, Buck-Koehntop, B.A. 登録日 2018-07-31 公開日 2018-11-07 最終更新日 2024-03-13 実験手法 X-RAY DIFFRACTION (1.594 Å) 主引用文献 Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J. Biol. Chem., 293, 2018
5OND	RfaH from Escherichia coli in complex with ops DNA 分子名称: DNA (5'-D(*GP*CP*GP*GP*TP*AP*GP*TP*C)-3'), Transcription antitermination protein RfaH 著者 Zuber, P.K, Artsimovitch, I, Roesch, P, Knauer, S.H. 登録日 2017-08-03 公開日 2018-06-06 最終更新日 2024-01-17 実験手法 X-RAY DIFFRACTION (2.1 Å) 主引用文献 The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. Elife, 7, 2018
8I54	Lb2Cas12a RNA DNA complex 分子名称: DNA (25-MER), DNA (5'-D(*AP*GP*TP*GP*CP*TP*TP*TP*A)-3'), Lb2Cas12a, ... 著者 Li, J, Sivaraman, J, Satoru, M. 登録日 2023-01-24 公開日 2023-02-22 最終更新日 2024-07-03 実験手法 ELECTRON MICROSCOPY (3.95 Å) 主引用文献 Structures of apo Cas12a and its complex with crRNA and DNA reveal the dynamics of ternary complex formation and target DNA cleavage. Plos Biol., 21, 2023
4X0P	Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog 分子名称: 2',3'-dideoxyadenosine triphosphate, CALCIUM ION, DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3'), ... 著者 Zahn, K.E, Doublie, S. 登録日 2014-11-21 公開日 2015-03-18 最終更新日 2023-09-27 実験手法 X-RAY DIFFRACTION (3.911 Å) 主引用文献 Human DNA polymerase theta grasps the primer terminus to mediate DNA repair. Nat.Struct.Mol.Biol., 22, 2015
4X0Q	Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP 分子名称: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3'), DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3'), ... 著者 Zahn, K.E, Doublie, S. 登録日 2014-11-22 公開日 2015-03-18 最終更新日 2023-09-27 実験手法 X-RAY DIFFRACTION (3.9 Å) 主引用文献 Human DNA polymerase theta grasps the primer terminus to mediate DNA repair. Nat.Struct.Mol.Biol., 22, 2015
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
7YZP	Hairpin-bound state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and a DNA hairpin 分子名称: ADENOSINE-5'-DIPHOSPHATE, DNA hairpin (59-MER), MAGNESIUM ION, ... 著者 Gut, F, Kaeshammer, L, Lammens, K, Bartho, J, van de Logt, E, Kessler, B, Hopfner, K.P. 登録日 2022-02-21 公開日 2022-08-17 最終更新日 2024-07-17 実験手法 ELECTRON MICROSCOPY (4 Å) 主引用文献 Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Mol.Cell, 82, 2022
4WUH	Crystal structure of E. faecalis DNA binding domain LiaR wild type complexed with 22bp DNA 分子名称: DNA (5'-D(P*AP*AP*AP*TP*CP*G)-3'), DNA (5'-D(P*GP*GP*AP*CP*TP*TP*AP*AP*GP*AP*AP*CP*GP*AP*TP*TP*T)-3'), DNA (5'-D(P*TP*TP*CP*TP*TP*AP*AP*GP*TP*CP*C)-3'), ... 著者 Davlieva, M, Shamoo, Y. 登録日 2014-10-31 公開日 2015-05-06 最終更新日 2023-12-27 実験手法 X-RAY DIFFRACTION (2.294 Å) 主引用文献 A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin. Nucleic Acids Res., 43, 2015
7Z9P	The novel DNA binding mechanism of ridinilazole, a precision Clostridiodes difficile antibiotic 分子名称: DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G*(RID))-3'), Ridinilazole, SODIUM ION, ... 著者 Mason, S, Leonard, P.M. 登録日 2022-03-21 公開日 2023-03-29 最終更新日 2024-02-07 実験手法 X-RAY DIFFRACTION (2.2 Å) 主引用文献 The Novel DNA Binding Mechanism of Ridinilazole, a Precision Clostridiodes difficile Antibiotic. Antimicrob.Agents Chemother., 67, 2023

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