PDB: 433 resultsInfo pagesStatus searchChemie searchBIRD

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7YW1	crystal structure of UBE2O Descriptor: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O Authors: Fu, Z, Zhu, W, Huang, H. Deposit date: 2022-08-20 Release date: 2023-08-30 Method: X-RAY DIFFRACTION (3.27 Å) Cite: crystal structure of UBE2O To Be Published
3SY2	Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7 Descriptor: E3 ubiquitin-protein ligase SopA, SULFATE ION, Ubiquitin-conjugating enzyme E2 L3 Authors: Diao, J, Lin, D.Y, Chen, J. Deposit date: 2011-07-15 Release date: 2012-01-25 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (3.27 Å) Cite: Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions. Proc.Natl.Acad.Sci.USA, 109, 2012
7LYB	Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Descriptor: BRCA1-associated RING domain protein 1, DNA (146-MER), DNA (147-MER), ... Authors: Hu, Q, Botuyan, M.V, Zhao, D, Cui, D, Mer, E, Mer, G. Deposit date: 2021-03-06 Release date: 2021-07-28 Last modified: 2021-09-01 Method: ELECTRON MICROSCOPY (3.28 Å) Cite: Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation. Nature, 596, 2021
4R8P	Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Descriptor: DNA (147-mer), E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3, ... Authors: McGinty, R.K, Henrici, R.C, Tan, S. Deposit date: 2014-09-02 Release date: 2014-11-05 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (3.2846 Å) Cite: Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature, 514, 2014
4DDG	Crystal structure of human OTUB1/UbcH5b~Ub/Ub Descriptor: Polyubiquitin-C, Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 Authors: Juang, Y.C, Sanches, M, Sicheri, F. Deposit date: 2012-01-18 Release date: 2012-02-22 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (3.2987 Å) Cite: OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function. Mol.Cell, 45, 2012
9B5L	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP) Descriptor: 4-aminobutanenitrile, ADENOSINE MONOPHOSPHATE, Polyubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
8SMW	Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Descriptor: DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... Authors: Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. Deposit date: 2023-04-26 Release date: 2024-01-17 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8SN1	Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Descriptor: DNA (147-MER), E3 ubiquitin-protein ligase RNF168, Histone H2A type 1-B/E, ... Authors: Hu, Q, Botuyan, M.V, Zhao, D, Cui, G, Mer, G. Deposit date: 2023-04-26 Release date: 2024-01-17 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8ATU	Cryo-EM structure of human BIRC6 Descriptor: Baculoviral IAP repeat-containing protein 6, ZINC ION Authors: Ehrmann, J.F, Grabarczyk, D.B, Clausen, T. Deposit date: 2022-08-24 Release date: 2023-02-15 Last modified: 2024-07-24 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex. Science, 379, 2023
3JVZ	E2~Ubiquitin-HECT Descriptor: E3 ubiquitin-protein ligase NEDD4-like, Ubiquitin, Ubiquitin-conjugating enzyme E2 D2 Authors: Souphron, J, Kamadurai, H.B, Schulman, B.A. Deposit date: 2009-09-17 Release date: 2010-01-12 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (3.3 Å) Cite: Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Mol.Cell, 36, 2009
7UN6	Complex of UBE2O with NAP1L1 Descriptor: (E3-independent) E2 ubiquitin-conjugating enzyme, Nucleosome assembly protein 1-like 1 Authors: Yip, M.C.J, Sedor, S.F, Shao, S. Deposit date: 2022-04-09 Release date: 2022-08-03 Last modified: 2024-02-14 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Mechanism of client selection by the protein quality-control factor UBE2O. Nat.Struct.Mol.Biol., 29, 2022
3SQV	Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7 Descriptor: GLYCEROL, SULFATE ION, Ubiquitin-conjugating enzyme E2 L3, ... Authors: Lin, D.Y, Chen, J. Deposit date: 2011-07-06 Release date: 2012-01-25 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (3.3 Å) Cite: Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions. Proc.Natl.Acad.Sci.USA, 109, 2012
8ATM	Structure of the giant inhibitor of apoptosis, BIRC6 (composite map) Descriptor: Baculoviral IAP repeat-containing protein 6 Authors: Dietz, L, Elliott, P.R. Deposit date: 2022-08-23 Release date: 2023-03-08 Last modified: 2024-07-24 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Structural basis for SMAC-mediated antagonism of caspase inhibition by the giant ubiquitin ligase BIRC6. Science, 379, 2023
9B5B	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 7 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.31 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
7P47	Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic Descriptor: E3 SUMO-protein ligase MMS21, SUMO-conjugating enzyme UBC9, Structural maintenance of chromosomes protein 5, ... Authors: Lascorz, J, Varejao, N, Reverter, D. Deposit date: 2021-07-09 Release date: 2021-11-24 Last modified: 2024-01-31 Method: X-RAY DIFFRACTION (3.314 Å) Cite: Structural basis for the E3 ligase activity enhancement of yeast Nse2 by SUMO-interacting motifs. Nat Commun, 12, 2021
9B56	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 2 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.35 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
7MEX	Structure of yeast Ubr1 in complex with Ubc2 and N-degron Descriptor: E3 ubiquitin-protein ligase UBR1, N-degron, Ubiquitin, ... Authors: Pan, M, Zheng, Q, Wang, T, Liang, L, Yu, Y, Liu, L, Zhao, M. Deposit date: 2021-04-08 Release date: 2021-11-24 Last modified: 2024-05-29 Method: ELECTRON MICROSCOPY (3.35 Å) Cite: Structural insights into Ubr1-mediated N-degron polyubiquitination. Nature, 600, 2021
9B57	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 3 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.37 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
8SV8	Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex from a composite map Descriptor: ADENOSINE MONOPHOSPHATE, Ubiquitin-like modifier-activating enzyme 7, Ubiquitin-like protein ISG15, ... Authors: Afsar, M, Jia, L, Ruben, E.A, Olsen, S.K. Deposit date: 2023-05-15 Release date: 2023-10-11 Method: ELECTRON MICROSCOPY (3.38 Å) Cite: Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Nat Commun, 14, 2023
9B58	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4 Descriptor: 4-aminobutanenitrile, E3 ubiquitin-protein ligase pub2, Ubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.39 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
8X7J	Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Descriptor: DNA (144-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 (3.39 Å) Cite: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168 Biorxiv, 2024
8PJN	Catalytic module of human CTLH E3 ligase bound to multiphosphorylated UBE2H~ubiquitin Descriptor: E3 ubiquitin-protein transferase MAEA, E3 ubiquitin-protein transferase RMND5A, Ubiquitin, ... Authors: Chrustowicz, J, Sherpa, D, Prabu, R.J, Schulman, B.A. Deposit date: 2023-06-23 Release date: 2024-01-03 Last modified: 2024-01-31 Method: ELECTRON MICROSCOPY (3.4 Å) Cite: Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies. Mol.Cell, 84, 2024
3OJ4	Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Descriptor: Tumor necrosis factor alpha-induced protein 3, Ubiquitin, Ubiquitin-conjugating enzyme E2 D1, ... Authors: Bosanac, I, Hymowitz, S.G. Deposit date: 2010-08-20 Release date: 2010-12-08 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (3.4 Å) Cite: Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB Signaling Mol.Cell, 40, 2010
8SEA	Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 1) Descriptor: ADENOSINE MONOPHOSPHATE, Ubiquitin-like modifier-activating enzyme 7, Ubiquitin-like protein ISG15, ... Authors: Afsar, M, Jia, L, Ruben, E.A, Olsen, S.K. Deposit date: 2023-04-08 Release date: 2023-10-11 Method: ELECTRON MICROSCOPY (3.4 Å) Cite: Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Nat Commun, 14, 2023
3EB6	Structure of the cIAP2 RING domain bound to UbcH5b Descriptor: Baculoviral IAP repeat-containing protein 3, Ubiquitin-conjugating enzyme E2 D2, ZINC ION Authors: Mace, P.D, Linke, K, Schumacher, F.-R, Smith, C.A, Day, C.L. Deposit date: 2008-08-27 Release date: 2008-09-09 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (3.4 Å) Cite: Structures of the cIAP2 RING Domain Reveal Conformational Changes Associated with Ubiquitin-conjugating Enzyme (E2) Recruitment. J.Biol.Chem., 283, 2008

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