6OA9
| Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, 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 (3.9 Å) | Cite: | Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science, 365, 2019
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6OAA
| Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1 | 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 (4.1 Å) | Cite: | Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Science, 365, 2019
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3M91
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6EQI
| Structure of PINK1 bound to ubiquitin | Descriptor: | GLYCEROL, Nb696, Serine/threonine-protein kinase PINK1, ... | Authors: | Schubert, A.F, Gladkova, C, Pardon, E, Wagstaff, J.L, Freund, S.M.V, Steyaert, J, Maslen, S, Komander, D. | Deposit date: | 2017-10-13 | Release date: | 2017-11-08 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Structure of PINK1 in complex with its substrate ubiquitin. Nature, 552, 2017
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4JIO
| Bro1 V domain and ubiquitin | Descriptor: | BRO1, Ubiquitin | Authors: | Pashkova, N, Gakhar, L, Piper, R.C. | Deposit date: | 2013-03-06 | Release date: | 2013-06-19 | Last modified: | 2013-07-10 | Method: | X-RAY DIFFRACTION (3.6 Å) | Cite: | The yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes. Dev.Cell, 25, 2013
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4KBL
| Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism | Descriptor: | E3 ubiquitin-protein ligase ARIH1, ZINC ION | Authors: | Duda, D.M, Olszewski, J.L, Schulman, B.A. | Deposit date: | 2013-04-23 | Release date: | 2013-05-29 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Structure of HHARI, a RING-IBR-RING Ubiquitin Ligase: Autoinhibition of an Ariadne-Family E3 and Insights into Ligation Mechanism. Structure, 21, 2013
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7RBR
| The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Papain-like protease, ... | Authors: | Osipiuk, J, Tesar, C, Endres, M, Lanham, B.T, Wydorski, P, Fushman, D, Joachimiak, L, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID) | Deposit date: | 2021-07-06 | Release date: | 2021-09-29 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.88 Å) | Cite: | Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Nat Commun, 14, 2023
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8EFW
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8EFX
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2C7M
| Human Rabex-5 residues 1-74 in complex with Ubiquitin | Descriptor: | RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1, UBIQUITIN, ZINC ION | Authors: | Penengo, L, Mapelli, M, Murachelli, A.G, Confalioneri, S, Magri, L, Musacchio, A, Di Fiore, P.P, Polo, S, Schneider, T.R. | Deposit date: | 2005-11-25 | Release date: | 2006-02-15 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell, 124, 2006
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5B83
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2A7L
| Structure of the human hypothetical ubiquitin-conjugating enzyme, LOC55284 | Descriptor: | Hypothetical ubiquitin-conjugating enzyme LOC55284, SODIUM ION | Authors: | Walker, J.R, Avvakumov, G.V, Xue, S, Newman, E.M, Mackenzie, F, Weigelt, J, Sundstrom, M, Arrowsmith, C, Edwards, A, Bochkarev, A, Dhe-Paganon, S, Structural Genomics Consortium (SGC) | Deposit date: | 2005-07-05 | Release date: | 2005-09-06 | Last modified: | 2023-08-23 | Method: | X-RAY DIFFRACTION (1.82 Å) | Cite: | A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Mol Cell Proteomics, 11, 2012
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2C7N
| Human Rabex-5 residues 1-74 in complex with Ubiquitin | Descriptor: | RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1, UBIQUITIN, ZINC ION | Authors: | Penengo, L, Mapelli, M, Murachelli, A.G, Confalioneri, S, Magri, L, Musacchio, A, Di Fiore, P.P, Polo, S, Schneider, T.R. | Deposit date: | 2005-11-25 | Release date: | 2006-02-15 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal Structure of the Ubiquitin Binding Domains of Rabex-5 Reveals Two Modes of Interaction with Ubiquitin. Cell(Cambridge,Mass.), 124, 2006
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8CX9
| Structure of the SARS-COV2 PLpro (C111S) in complex with a dimeric Ubv that inhibits activity by an unusual allosteric mechanism | Descriptor: | BROMIDE ION, CHLORIDE ION, Papain-like protease nsp3, ... | Authors: | Singer, A.U, Slater, C.L, Patel, A, Russel, R, Mark, B.L, Sidhu, S.S. | Deposit date: | 2022-05-20 | Release date: | 2023-01-25 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3.5 Å) | Cite: | Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site. Plos Pathog., 18, 2022
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5YT6
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5HPK
| System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1 | Descriptor: | E3 ubiquitin-protein ligase NEDD4-like, Ubiquitin variant NL.1 | Authors: | Wu, K.-P, Mukherjee, M, Mercredi, P.Y, Schulman, B.A. | Deposit date: | 2016-01-20 | Release date: | 2016-03-16 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.431 Å) | Cite: | System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Mol.Cell, 62, 2016
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7S6O
| The crystal structure of Lys48-linked di-ubiquitin | Descriptor: | ACETATE ION, Ubiquitin | Authors: | Osipiuk, J, Tesar, C, Lanham, B.T, Wydorski, P, Fushman, D, Joachimiak, L, Joachimiak, A. | Deposit date: | 2021-09-14 | Release date: | 2021-09-22 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Nat Commun, 14, 2023
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6ZM3
| The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) essential for Leishmania amastigote differentiation | Descriptor: | Putative ubiquitin-conjugating enzyme e2, Ubiquitin-conjugating enzyme-like protein | Authors: | Burge, R.J, Dodson, E.J, Wilkinson, A.J, Mottram, J.C. | Deposit date: | 2020-07-01 | Release date: | 2020-07-22 | Last modified: | 2024-01-31 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. Plos Pathog., 16, 2020
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3VHT
| Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin | Descriptor: | Green fluorescent protein, Green fluorescent protein,ATPase WRNIP1, Ubiquitin, ... | Authors: | Suzuki, N, Wakatsuki, S, Kawasaki, M. | Deposit date: | 2011-09-06 | Release date: | 2012-10-10 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. Febs J., 2016
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5TTE
| Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester intermediate mimic | Descriptor: | E3 ubiquitin-protein ligase ARIH1, Ubiquitin-conjugating enzyme E2 L3, ZINC ION, ... | Authors: | Yuan, L, Lv, Z, Olsen, S.K. | Deposit date: | 2016-11-03 | Release date: | 2017-08-23 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (3.501 Å) | Cite: | Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI. Nat Commun, 8, 2017
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5DFL
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5N4W
| Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex | Descriptor: | Cullin-2, E3 ubiquitin-protein ligase RBX1, Elongin-B, ... | Authors: | Cardote, T.A.F, Gadd, M.S, Ciulli, A. | Deposit date: | 2017-02-11 | Release date: | 2017-06-07 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (3.9 Å) | Cite: | Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex. Structure, 25, 2017
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5O44
| Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages. | Descriptor: | MAGNESIUM ION, Polyubiquitin-B, SULFATE ION, ... | Authors: | Padala, P, Isupov, M.N, Wiener, R. | Deposit date: | 2017-05-26 | Release date: | 2017-11-08 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (3.14 Å) | Cite: | The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages. J. Mol. Biol., 429, 2017
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5HPL
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6NJ9
| Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex | Descriptor: | 601 DNA Strand 1, 601 DNA Strand 2, Histone H2A type 1, ... | Authors: | Worden, E.J, Hoffmann, N.A, Wolberger, C. | Deposit date: | 2019-01-02 | Release date: | 2019-02-20 | Last modified: | 2021-06-16 | Method: | ELECTRON MICROSCOPY (2.96 Å) | Cite: | Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L. Cell, 176, 2019
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