PDB: 2862 resultsInfo pagesStatus searchChemie searchBIRD

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8X7K	Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Descriptor: DNA (143-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... Authors: Ai, H.S, Tong, Z.B, Deng, Z.H, Pan, M, Liu, L. Deposit date: 2023-11-24 Release date: 2024-08-07 Method: ELECTRON MICROSCOPY (3.27 Å) Cite: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168 Biorxiv, 2024
8X7I	Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Descriptor: DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... Authors: Ai, H.S, Tong, Z.B, Deng, Z.H, Pan, M, Liu, L. Deposit date: 2023-11-24 Release date: 2024-08-07 Method: ELECTRON MICROSCOPY (3.27 Å) Cite: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168 Biorxiv, 2024
2CRX	STRUCTURE OF THE HOLLIDAY JUNCTION INTERMEDIATE IN CRE-LOXP SITE-SPECIFIC RECOMBINATION Descriptor: DNA 35-MER, PROTEIN (CRE RECOMBINASE) Authors: Gopaul, D.N, Guo, F, Vanduyne, G.D. Deposit date: 1998-06-19 Release date: 1999-12-14 Last modified: 2023-08-23 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J., 17, 1998
8JND	The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Descriptor: DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-06-06 Release date: 2024-03-27 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (3.66 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
8JNE	The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Descriptor: DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-06-06 Release date: 2024-03-27 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (4.68 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
8XBV	The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the sticky end of the nucleosome Descriptor: DNA (5'-D(P*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*A)-3'), DNA (5'-D(P*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*G)-3'), DNA repair protein RAD51 homolog 1 Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-12-07 Release date: 2024-03-27 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (7.61 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
8XBY	The cryo-EM structure of the RAD51 L1 and L2 loops bound to the linker DNA with the blunt end of the nucleosome Descriptor: DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3'), DNA repair protein RAD51 homolog 1 Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-12-07 Release date: 2024-03-27 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (7.8 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
8XBU	The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Descriptor: DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-12-07 Release date: 2024-03-27 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (4.24 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
8XBX	The cryo-EM structure of the RAD51 L2 loop bound to the linker DNA with the blunt end of the nucleosome Descriptor: DNA (5'-D(P*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*CP*CP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*CP*GP*TP*T)-3'), DNA repair protein RAD51 homolog 1 Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-12-07 Release date: 2024-03-27 Last modified: 2024-04-17 Method: ELECTRON MICROSCOPY (4.36 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
8XBT	The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Descriptor: DNA (153-MER), DNA (156-MER), DNA repair protein RAD51 homolog 1, ... Authors: Shioi, T, Hatazawa, S, Ogasawara, M, Takizawa, Y, Kurumizaka, H. Deposit date: 2023-12-07 Release date: 2024-03-27 Last modified: 2024-05-08 Method: ELECTRON MICROSCOPY (4.12 Å) Cite: Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature, 628, 2024
3W03	XLF-XRCC4 complex Descriptor: DNA repair protein XRCC4, Non-homologous end-joining factor 1 Authors: Wu, Q, Ochi, T, Matak-Vinkovic, D, Robinson, C.V, Chirgadze, D.Y, Blundell, T.L. Deposit date: 2012-10-17 Release date: 2012-11-07 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (8.492 Å) Cite: Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions Biochem.Soc.Trans., 39, 2011
2R9A	Crystal structure of human XLF Descriptor: Non-homologous end-joining factor 1 Authors: Andres, S.N, Junop, M.S. Deposit date: 2007-09-12 Release date: 2008-01-01 Last modified: 2017-10-25 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Crystal Structure of Human XLF: A Twist in Nonhomologous DNA End-Joining Mol.Cell, 28
3RWR	Crystal structure of the human XRCC4-XLF complex Descriptor: DNA repair protein XRCC4, HEXATANTALUM DODECABROMIDE, Non-homologous end-joining factor 1 Authors: Andres, S.N, Junop, M.S. Deposit date: 2011-05-09 Release date: 2011-12-07 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (3.943 Å) Cite: Structure of human XLF-XRCC4: assembly of a functional DNA repair complex To be Published
6XNX	Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form) Descriptor: 12RSS integration strand DNA (55-MER), 12RSS signal top strand DNA (34-MER), 23RSS integration strand DNA (66-MER), ... Authors: Zhang, Y, Corbett, E, Wu, S, Schatz, D.G. Deposit date: 2020-07-05 Release date: 2020-08-26 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (2.7 Å) Cite: Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. Embo J., 39, 2020
6XNZ	Structure of RAG1 (R848M/E649V)-RAG2-DNA Target Capture Complex Descriptor: 12RSS integration strand (34-mer), 12RSS non-integration strand (34-mer), 23RSS integration strand (45-mer), ... Authors: Zhang, Y, Corbett, E, Wu, S, Schatz, D.G. Deposit date: 2020-07-05 Release date: 2020-08-26 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (3.8 Å) Cite: Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. Embo J., 39, 2020
6XNY	Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form) Descriptor: 12RSS integration strand (55-mer), 12RSS signal DNA top strand (34-mer), 23RSS integration strand (66-mer), ... Authors: Zhang, Y, Corbett, E, Wu, S, Schatz, D.G. Deposit date: 2020-07-05 Release date: 2020-08-26 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase. Embo J., 39, 2020
4WQO	Structure of VHL-EloB-EloC-Cul2 Descriptor: Cullin-2, Transcription elongation factor B polypeptide 1, Transcription elongation factor B polypeptide 2, ... Authors: Nguyen, H.C, Xiong, Y. Deposit date: 2014-10-22 Release date: 2015-03-04 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.2 Å) Cite: Insights into Cullin-RING E3 Ubiquitin Ligase Recruitment: Structure of the VHL-EloBC-Cul2 Complex. Structure, 23, 2015
7SHL	Structure of Xenopus laevis CRL2Lrr1 (State 2) Descriptor: CULLIN_2 domain-containing protein, Elongin-C, Lrr1, ... Authors: Zhou, H, Brown, A. Deposit date: 2021-10-09 Release date: 2021-12-08 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.5 Å) Cite: Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates. Nucleic Acids Res., 49, 2021
7SHK	Structure of Xenopus laevis CRL2Lrr1 (State 1) Descriptor: CULLIN_2 domain-containing protein, Elongin-C, Lrr1, ... Authors: Zhou, H, Brown, A. Deposit date: 2021-10-09 Release date: 2021-12-08 Last modified: 2024-06-05 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates. Nucleic Acids Res., 49, 2021
4WSN	Crystal structure of the COP9 signalosome, a P1 crystal form Descriptor: COP9 signalosome complex subunit 1, COP9 signalosome complex subunit 2, COP9 signalosome complex subunit 3, ... Authors: Bunker, R.D, Lingaraju, G.M, Thoma, N.H. Deposit date: 2014-10-28 Release date: 2015-12-23 Last modified: 2024-01-10 Method: X-RAY DIFFRACTION (5.5 Å) Cite: Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome. Nature, 531, 2016
8CIL	Crystal structure of Coxiella burnetii Fic protein 2 Descriptor: Fic family protein Authors: Hoepfner, D, Itzen, A, Pogenberg, V. Deposit date: 2023-02-10 Release date: 2023-11-15 Method: X-RAY DIFFRACTION (1.98 Å) Cite: The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3. Commun Biol, 6, 2023
8C06	Structure of Dimeric HECT E3 Ubiquitin Ligase UBR5 Descriptor: E3 ubiquitin-protein ligase UBR5, ZINC ION Authors: Hehl, L.A, Prabu, J.R, Schulman, B.A. Deposit date: 2022-12-16 Release date: 2023-08-23 Last modified: 2024-02-14 Method: ELECTRON MICROSCOPY (2.7 Å) Cite: Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5. Nat.Chem.Biol., 20, 2024
6OAB	Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 2 Descriptor: ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, Cell division control protein 48, ... Authors: Twomey, E.C, Ji, Z, Wales, T.E, Bodnar, N.O, Engen, J.R, Rapoport, T.A. Deposit date: 2019-03-15 Release date: 2019-07-03 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science, 365, 2019
7PMK	S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I) Descriptor: Cell division control protein 45,Cell division control protein 45, Chromosome segregation in meiosis protein 3, DNA helicase, ... Authors: Jenkyn-Bedford, M, Yeeles, J.T.P, Deegan, T.D. Deposit date: 2021-09-02 Release date: 2021-11-10 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature, 600, 2021
7PMN	S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) Descriptor: Cell division control protein 45,Cell division control protein 45, Chromosome segregation in meiosis protein 3, DNA polymerase alpha-binding protein, ... Authors: Jenkyn-Bedford, M, Yeeles, J.T.P, Deegan, T.D. Deposit date: 2021-09-02 Release date: 2021-11-10 Last modified: 2024-07-17 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: A conserved mechanism for regulating replisome disassembly in eukaryotes. Nature, 600, 2021

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