7EAO
 
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7KEO
 | | Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment | | Descriptor: | PHOSPHATE ION, Synthetic antigen binding fragment, heavy chain, ... | | Authors: | Yu, Y, Zheng, Q, Erramilli, S, Pan, M, Kossiakoff, A, Liu, L, Zhao, M. | | Deposit date: | 2020-10-11 | | Release date: | 2021-07-28 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle.
Nat.Chem.Biol., 17, 2021
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2ZVO
 | | NEMO CoZi domain in complex with diubiquitin in C2 space group | | Descriptor: | NF-kappa-B essential modulator, UBC protein | | Authors: | Rahighi, S, Ikeda, F, Kawasaki, M, Akutsu, M, Suzuki, N, Kato, R, Kensche, T, Uejima, T, Bloor, S, Komander, D, Randow, F, Wakatsuki, S, Dikic, I. | | Deposit date: | 2008-11-12 | | Release date: | 2009-03-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation
Cell(Cambridge,Mass.), 136, 2009
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4XOL
 | | Observing the overall rocking motion of a protein in a crystal - Cubic Ubiquitin crystals. | | Descriptor: | Ubiquitin, ZINC ION | | Authors: | Coquelle, N, Peixiang, M, Schanda, P, Colletier, J.P. | | Deposit date: | 2015-01-16 | | Release date: | 2015-10-14 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.91 Å) | | Cite: | Observing the overall rocking motion of a protein in a crystal.
Nat Commun, 6, 2015
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5OE7
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5C7J
 | | CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT | | Descriptor: | E3 ubiquitin-protein ligase NEDD4, Polyubiquitin-C | | Authors: | Walker, J.R, Hu, J, Dong, A, Bountra, C, Edwards, A.M, Arrowsmith, C.H, Tong, Y, Structural Genomics Consortium (SGC) | | Deposit date: | 2015-06-24 | | Release date: | 2016-03-16 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Mol.Cell, 62, 2016
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2ZVN
 | | NEMO CoZi domain incomplex with diubiquitin in P212121 space group | | Descriptor: | NF-kappa-B essential modulator, UBC protein | | Authors: | Rahighi, S, Ikeda, F, Kawasaki, M, Akutsu, M, Suzuki, N, Kato, R, Kensche, T, Uejima, T, Bloor, S, Komander, D, Randow, F, Wakatsuki, S, Dikic, I. | | Deposit date: | 2008-11-12 | | Release date: | 2009-03-24 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation
Cell(Cambridge,Mass.), 136, 2009
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3EEC
 | | X-ray structure of human ubiquitin Cd(II) adduct | | Descriptor: | CADMIUM ION, Ubiquitin | | Authors: | Falini, G, Fermani, S, Tosi, G, Arnesano, F, Natile, G. | | Deposit date: | 2008-09-04 | | Release date: | 2009-03-10 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural probing of Zn(II), Cd(II) and Hg(II) binding to human ubiquitin.
Chem.Commun.(Camb.), 45, 2008
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3N30
 | | Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct | | Descriptor: | Ubiquitin, ZINC ION | | Authors: | Siliqi, D, Caliandro, R, Arnesano, F, Natile, G, Falini, G, Fermani, S, Belviso, B.D. | | Deposit date: | 2010-05-19 | | Release date: | 2011-01-12 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystallographic analysis of metal-ion binding to human ubiquitin.
Chemistry, 17, 2011
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5WQ4
 | | Crystal structure of OPTN and linear diubiquitin complex | | Descriptor: | Optineurin, ubiquitin | | Authors: | Li, F, Pan, L. | | Deposit date: | 2016-11-23 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural insights into the ubiquitin recognition by OPTN (optineurin) and its regulation by TBK1-mediated phosphorylation.
Autophagy, 14, 2018
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7MYF
 | | Ubiquitin variant UbV.k.1 in complex with Ube2k | | Descriptor: | Ubiquitin, Ubiquitin variant UbV.k.1, Ubiquitin-conjugating enzyme E2 K | | Authors: | Middleton, A.J, Day, C.L, Teyra, J, Sidhu, S.S. | | Deposit date: | 2021-05-21 | | Release date: | 2021-08-25 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Identification of Ubiquitin Variants That Inhibit the E2 Ubiquitin Conjugating Enzyme, Ube2k.
Acs Chem.Biol., 16, 2021
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5ZQ6
 | | SidE-Ubi-ADPr | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, SidE, Ubiquitin | | Authors: | Wang, Y, Gao, A, Gao, P. | | Deposit date: | 2018-04-17 | | Release date: | 2018-05-23 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.009 Å) | | Cite: | Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.
Cell, 173, 2018
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5C7M
 | | CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT | | Descriptor: | E3 ubiquitin-protein ligase Itchy homolog, Polyubiquitin-C | | Authors: | Walker, J.R, Hu, J, Dong, A, Wernimont, A, Zhang, W, Sidhu, S, Bountra, C, Edwards, A.M, Arrowsmith, C.H, Tong, Y, Structural Genomics Consortium (SGC) | | Deposit date: | 2015-06-24 | | Release date: | 2016-03-16 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (3.03 Å) | | Cite: | System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes.
Mol.Cell, 62, 2016
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4BOZ
 | | Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin | | Descriptor: | GLYCEROL, UBIQUITIN THIOESTERASE OTU1, UBIQUITIN-C | | Authors: | Mevissen, T.E.T, Hospenthal, M.K, Geurink, P.P, Elliott, P.R, Akutsu, M, Arnaudo, N, Ekkebus, R, Kulathu, Y, Wauer, T, El Oualid, F, Freund, S.M.V, Ovaa, H, Komander, D. | | Deposit date: | 2013-05-22 | | Release date: | 2013-07-17 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (3.03 Å) | | Cite: | Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis.
Cell(Cambridge,Mass.), 154, 2013
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8EB0
 | | RNF216/E2-Ub/Ub transthiolation complex | | Descriptor: | E3 ubiquitin-protein ligase RNF216, SULFATE ION, Ubiquitin, ... | | Authors: | Cotton, T.R, Wang, X.S, Lechtenberg, B.C. | | Deposit date: | 2022-08-30 | | Release date: | 2023-01-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3.03 Å) | | Cite: | The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family.
Nat Commun, 14, 2023
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8EAZ
 | | HOIL-1/E2-Ub/Ub transthiolation complex | | Descriptor: | RanBP-type and C3HC4-type zinc finger-containing protein 1, Ubiquitin, Ubiquitin-conjugating enzyme E2 L3, ... | | Authors: | Wang, X.S, Cotton, T.R, Lechtenberg, B.C. | | Deposit date: | 2022-08-30 | | Release date: | 2023-01-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3.08 Å) | | Cite: | The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family.
Nat Commun, 14, 2023
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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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4LCD
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7K6Q
 | | Active state Dot1 bound to the H4K16ac nucleosome | | Descriptor: | DNA (146-MER), Histone H2A type 1, Histone H2B 1.1, ... | | Authors: | Valencia-Sanchez, M.I, De Ioannes, P.E, Miao, W, Truong, D.M, Lee, R, Armache, J.-P, Boeke, J.D, Armache, K.-J. | | Deposit date: | 2020-09-21 | | Release date: | 2021-02-10 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.
Science, 371, 2021
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3JW0
 | | E2~Ubiquitin-HECT | | Descriptor: | E3 ubiquitin-protein ligase NEDD4-like, Ubiquitin, Ubiquitin-conjugating enzyme E2 D2 | | Authors: | Kamadurai, H.B, Schulman, B.A. | | Deposit date: | 2009-09-17 | | Release date: | 2010-01-12 | | Last modified: | 2021-10-13 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex.
Mol.Cell, 36, 2009
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4DHZ
 | | The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub | | Descriptor: | Ubiquitin, Ubiquitin aldehyde, Ubiquitin thioesterase otubain-like, ... | | Authors: | Wiener, R, Zhang, X, Wang, T, Wolberger, C. | | Deposit date: | 2012-01-30 | | Release date: | 2012-02-22 | | Last modified: | 2017-11-15 | | Method: | X-RAY DIFFRACTION (3.11 Å) | | Cite: | The mechanism of OTUB1-mediated inhibition of ubiquitination.
Nature, 483, 2012
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6W9D
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8SVF
 | | BAP1/ASXL1 bound to the H2AK119Ub Nucleosome | | Descriptor: | DNA/RNA (187-MER), DNA/RNA (327-MER), Histone H2A type 1, ... | | Authors: | Thomas, J.F, Valencia-Sanchez, M.I, Armache, K.-J. | | Deposit date: | 2023-05-16 | | Release date: | 2023-08-30 | | Last modified: | 2024-02-14 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.
Sci Adv, 9, 2023
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7EB9
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7K6P
 | | Active state Dot1 bound to the unacetylated H4 nucleosome | | Descriptor: | DNA (146-MER), Histone H2A type 1, Histone H2B 1.1, ... | | Authors: | Valencia-Sanchez, M.I, De Ioannes, P.E, Miao, W, Truong, D.M, Lee, R, Armache, J.-P, Boeke, J.D, Armache, K.-J. | | Deposit date: | 2020-09-21 | | Release date: | 2021-02-10 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.
Science, 371, 2021
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