PDB: 433 resultsInfo pagesStatus searchChemie searchBIRD

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3VON	Crystalstructure of the ubiquitin protease Descriptor: Ubiquitin thioesterase OTUB1, Ubiquitin-conjugating enzyme E2 N, Ubiquitin-conjugating enzyme E2 variant 2 Authors: Sato, Y, Fukai, S. Deposit date: 2012-01-30 Release date: 2012-05-30 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (3.15 Å) Cite: Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13. J.Biol.Chem., 287, 2012
9B5K	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (Ub(A)/ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, Large ribosomal subunit protein eL40B, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.16 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5T	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.16 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
3L1Z	Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme Descriptor: Ubiquitin conjugation factor E4 B, Ubiquitin-conjugating enzyme E2 D3 Authors: Benirschke, R, Thompson, J.R, Mer, G. Deposit date: 2009-12-14 Release date: 2010-05-05 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (3.17 Å) Cite: Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4. Structure, 18, 2010
6ZHU	Yeast Uba1 in complex with Ubc3 and ATP Descriptor: ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Ubiquitin-activating enzyme E1 1, ... Authors: Misra, M, Schindelin, H. Deposit date: 2020-06-23 Release date: 2022-01-12 Last modified: 2024-01-24 Method: X-RAY DIFFRACTION (3.18 Å) Cite: ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system To Be Published
9B5O	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from consensus Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.19 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
6W9D	RNF12 RING domain in complex with a Ube2d2~Ub conjugate Descriptor: E3 ubiquitin-protein ligase RLIM, IODIDE ION, Ubiquitin, ... Authors: Middleton, A.J, Day, C.L. Deposit date: 2020-03-22 Release date: 2020-05-20 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (3.19 Å) Cite: The RING Domain of RING Finger 12 Efficiently Builds Degradative Ubiquitin Chains. J.Mol.Biol., 432, 2020
8SMX	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 2) 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 (3.2 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8SMY	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 3) 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 (3.2 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8SMZ	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 4) 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 (3.2 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8SN0	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 5) 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 (3.2 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8QAT	Cryo-EM structure of Fts-Hook3-FHIP1B at 3.2 A resolution. Descriptor: AKT-interacting protein, FHF complex subunit HOOK-interacting protein 1B, Protein Hook homolog 3 Authors: Abid Ali, F, Carter, A.P. Deposit date: 2023-08-23 Release date: 2024-09-04 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: KIF1C activates and extends dynein movement through the FHF cargo adaptor To Be Published
8UPF	Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c 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: 2023-10-22 Release date: 2024-01-17 Last modified: 2024-03-20 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell, 84, 2024
8BTL	Crystal structure of a complex between the E2 conjugating enzyme UBE2A and the E3 ligase module from UBR4 Descriptor: Ubiquitin conjugating enzyme E2 A, ZINC ION, cDNA FLJ12511 fis, ... Authors: Virdee, S, Mabbitt, P.D, Barnsby-Greer, L. Deposit date: 2022-11-29 Release date: 2023-12-13 Last modified: 2024-04-17 Method: X-RAY DIFFRACTION (3.2 Å) Cite: UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4. Nat.Struct.Mol.Biol., 31, 2024
8SE9	Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2) 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 (3.2 Å) Cite: Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Nat Commun, 14, 2023
7W75	Crystal structure of the K. lactis Bre1 RBD in complex with Rad6, crystal form I Descriptor: E3 ubiquitin-protein ligase BRE1, Ubiquitin-conjugating enzyme E2 2 Authors: Shi, M, Zhao, J, Xiang, S. Deposit date: 2021-12-03 Release date: 2023-03-29 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (3.2 Å) Cite: Structural basis for the Rad6 activation by the Bre1 N-terminal domain. Elife, 12, 2023
5ZBU	Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Descriptor: E3 ubiquitin-protein ligase RNF13, Ubiquitin, Ubiquitin-conjugating enzyme E2 D2, ... Authors: Datta, A.B, Sarkar, S. Deposit date: 2018-02-12 Release date: 2019-02-27 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (3.2 Å) Cite: Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub To Be Published
8E2K	Cryo-EM structure of BIRC6/HtrA2-S306A Descriptor: Baculoviral IAP repeat-containing protein 6, Serine protease HTRA2, mitochondrial Authors: Hunkeler, M, Fischer, E.S. Deposit date: 2022-08-15 Release date: 2023-02-15 Last modified: 2024-06-12 Method: ELECTRON MICROSCOPY (3.21 Å) Cite: Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases. Science, 379, 2023
9B55	Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1 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 (3.23 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
4BWF	Pex4p-Pex22p disulphide bond mutant Descriptor: 1,2-ETHANEDIOL, PEROXISOME ASSEMBLY PROTEIN 22, UBIQUITIN-CONJUGATING ENZYME E2-21 KDA Authors: Williams, C, van den Berg, M, Stanley, W.A, Wilmanns, M, Distel, B. Deposit date: 2013-07-01 Release date: 2013-07-17 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (3.23 Å) Cite: A Disulphide Bond in the E2 Enzyme Pex4P Modulates Ubiquitin-Conjugating Activity Sci.Rep., 3, 2013
8SEB	Cryo-EM structure of a single loaded human UBA7-UBE2L6-ISG15 adenylate complex 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 (3.24 Å) Cite: Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Nat Commun, 14, 2023
5UDH	HHARI/ARIH1-UBCH7~Ubiquitin Descriptor: E3 ubiquitin-protein ligase ARIH1, Ubiquitin C variant, Ubiquitin-conjugating enzyme E2 L3, ... Authors: Miller, D.J, Schulman, B.A. Deposit date: 2016-12-27 Release date: 2017-06-14 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (3.24 Å) Cite: Structural Studies of HHARI/UbcH7Ub Reveal Unique E2Ub Conformational Restriction by RBR RING1. Structure, 25, 2017
2Y9P	Pex4p-Pex22p mutant II structure Descriptor: PEROXISOME ASSEMBLY PROTEIN 22, UBIQUITIN-CONJUGATING ENZYME E2-21 KDA Authors: Williams, C, van den Berg, M, Panjikar, S, Distel, B, Wilmanns, M. Deposit date: 2011-02-16 Release date: 2012-02-29 Last modified: 2023-12-20 Method: X-RAY DIFFRACTION (3.25 Å) Cite: Pex4P-Pex22P Structure To be Published
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
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

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