PDB: 1507 resultsInfo pagesStatus searchChemie searchBIRD

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5VZW	TRIM23 RING domain in complex with UbcH5-Ub Descriptor: E3 ubiquitin-protein ligase TRIM23, Ubiquitin, Ubiquitin-conjugating enzyme E2 D2, ... Authors: Pornillos, O, Dawidziak, D. Deposit date: 2017-05-29 Release date: 2017-08-09 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.278 Å) Cite: Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase. Proteins, 85, 2017
8OO0	Chaetomium thermophilum Methionine Aminopeptidase 2 autoproteolysis product at the 80S ribosome Descriptor: 18S rRNA, 28S rRNA, 40S ribosomal protein S0, ... Authors: Klein, M.A, Wild, K, Kisonaite, M, Sinning, I. Deposit date: 2023-04-04 Release date: 2024-02-21 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: Methionine aminopeptidase 2 and its autoproteolysis product have different binding sites on the ribosome. Nat Commun, 15, 2024
8OJ5	60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Descriptor: 28S rRNA, 5.8S rRNA, 5S rRNA, ... Authors: Penchev, I, DaRosa, P.A, Peter, J.J, Kulathu, Y, Becker, T, Beckmann, R, Kopito, R. Deposit date: 2023-03-23 Release date: 2024-02-21 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (2.9 Å) Cite: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature, 627, 2024
8OHD	60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Descriptor: 28S rRNA, 5.8S rRNA, 5S rRNA, ... Authors: Penchev, I, DaRosa, P.A, Becker, T, Beckmann, R, Kopito, R. Deposit date: 2023-03-21 Release date: 2024-02-21 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (3.1 Å) Cite: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature, 627, 2024
8OJ8	60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) Descriptor: 28S rRNA, 5.8S rRNA, 5S rRNA, ... Authors: Penchev, I, DaRosa, P.A, Becker, T, Beckmann, R, Kopito, R. Deposit date: 2023-03-24 Release date: 2024-02-21 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature, 627, 2024
8OJ0	60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Descriptor: 28S rRNA, 5.8S rRNA, 5S rRNA, ... Authors: Penchev, I, DaRosa, P.A, Becker, T, Beckmann, R, Kopito, R. Deposit date: 2023-03-23 Release date: 2024-02-21 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature, 627, 2024
5Z56	cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom. Descriptor: 116 kDa U5 small nuclear ribonucleoprotein component, BUD13 homolog, Cell division cycle 5-like protein, ... Authors: Zhang, X, Yan, C, Zhan, X, Li, L, Lei, J, Shi, Y. Deposit date: 2018-01-17 Release date: 2018-09-19 Last modified: 2020-10-14 Method: ELECTRON MICROSCOPY (5.1 Å) Cite: Structure of the human activated spliceosome in three conformational states. Cell Res., 28, 2018
6KFP	Crystal structure of MavC ternary complex Descriptor: MavC, Ubiquitin-40S ribosomal protein S27a, Ubiquitin-conjugating enzyme E2 N Authors: Mu, Y, Wang, Y, Han, Y, Li, D, Feng, Y. Deposit date: 2019-07-08 Release date: 2020-04-01 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.92 Å) Cite: Structural insights into the mechanism and inhibition of transglutaminase-induced ubiquitination by the Legionella effector MavC. Nat Commun, 11, 2020
6KIV	Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Descriptor: DNA (145-MER), Histone H2A, Histone H2B 1.1, ... Authors: Huang, J, Xue, H, Yao, T. Deposit date: 2019-07-20 Release date: 2019-09-11 Last modified: 2024-03-27 Method: ELECTRON MICROSCOPY (4 Å) Cite: Structural basis of nucleosome recognition and modification by MLL methyltransferases. Nature, 573, 2019
5Z58	Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom. Descriptor: 116 kDa U5 small nuclear ribonucleoprotein component, BUD13 homolog, Cell division cycle 5-like protein, ... Authors: Zhang, X, Yan, C, Zhan, X, Li, L, Lei, J, Shi, Y. Deposit date: 2018-01-17 Release date: 2018-09-19 Last modified: 2020-10-14 Method: ELECTRON MICROSCOPY (4.9 Å) Cite: Structure of the human activated spliceosome in three conformational states. Cell Res., 28, 2018
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
5Z57	Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom Descriptor: 116 kDa U5 small nuclear ribonucleoprotein component, ALANINE, BUD13 homolog, ... Authors: Zhang, X, Yan, C, Zhan, X, Li, L, Lei, J, Shi, Y. Deposit date: 2018-01-17 Release date: 2018-09-19 Last modified: 2020-10-14 Method: ELECTRON MICROSCOPY (6.5 Å) Cite: Structure of the human activated spliceosome in three conformational states. Cell Res., 28, 2018
2IZV	CRYSTAL STRUCTURE OF SOCS-4 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 2.55A RESOLUTION Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, SODIUM ION, ... Authors: Debreczeni, J.E, Bullock, A, Papagrigoriou, E, Turnbull, A, Pike, A.C.W, Gorrec, F, von Delft, F, Sundstrom, M, Arrowsmith, C, Weigelt, J, Edwards, A, Knapp, S. Deposit date: 2006-07-26 Release date: 2006-08-02 Last modified: 2023-12-13 Method: X-RAY DIFFRACTION (2.55 Å) Cite: Structure of the SOCS4-ElonginB/C complex reveals a distinct SOCS box interface and the molecular basis for SOCS-dependent EGFR degradation. Structure, 15, 2007
2JT4	Solution Structure of the Sla1 SH3-3-Ubiquitin Complex Descriptor: Cytoskeleton assembly control protein SLA1, Ubiquitin Authors: He, Y, Radhakrishnan, I. Deposit date: 2007-07-18 Release date: 2007-09-25 Last modified: 2024-05-29 Method: SOLUTION NMR Cite: Structural Basis for Ubiquitin Recognition by SH3 Domains J.Mol.Biol., 373, 2007
2LZ6	Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications Descriptor: CD2-associated protein, Ubiquitin Authors: Ortega-Roldan, J, Azuaga, A, Blackledge, M, Van Nuland, N. Deposit date: 2012-09-24 Release date: 2013-10-02 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Distinct Ubiquitin Binding Modes Exhibited by SH3 Domains: Molecular Determinants and Functional Implications. Plos One, 8, 2013
2KJH	NMR based structural model of the UBCH8-UBIQUITIN complex Descriptor: Ubiquitin, Ubiquitin/ISG15-conjugating enzyme E2 L6 Authors: Serniwka, S.A, Shaw, G.S. Deposit date: 2009-05-28 Release date: 2009-12-08 Last modified: 2021-10-13 Method: SOLUTION NMR Cite: The structure of the UbcH8-ubiquitin complex shows a unique ubiquitin interaction site. Biochemistry, 48, 2009
2KNB	Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain Descriptor: E3 ubiquitin-protein ligase parkin, Endophilin-A1 Authors: Trempe, J, Guennadi, K, Edna, C.M, Kalle, G. Deposit date: 2009-08-20 Release date: 2009-12-22 Last modified: 2024-05-01 Method: SOLUTION NMR Cite: SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination. Mol.Cell, 36, 2009
2NVU	Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex Descriptor: ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera, ... Authors: Huang, D.T, Hunt, H.W, Zhuang, M, Ohi, M.D, Holton, J.M, Schulman, B.A. Deposit date: 2006-11-13 Release date: 2007-01-30 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature, 445, 2007
2GMI	Mms2/Ubc13~Ubiquitin Descriptor: Ubiquitin, Ubiquitin-conjugating enzyme E2 13, Ubiquitin-conjugating enzyme variant MMS2 Authors: Wolberger, C, Eddins, M.J, Carlile, C.M, Gomez, K.G, Pickart, C.M. Deposit date: 2006-04-06 Release date: 2006-09-19 Last modified: 2023-08-30 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation. Nat.Struct.Mol.Biol., 13, 2006
8C83	Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex Descriptor: 18S ribosomal RNA, 40S ribosomal protein S0-A, 40S ribosomal protein S11-A, ... Authors: Ikeuchi, K, Buschauer, R, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R. Deposit date: 2023-01-18 Release date: 2023-05-24 Method: ELECTRON MICROSCOPY (3 Å) Cite: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nat Commun, 14, 2023
8CAH	Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex Descriptor: 18S ribosomal RNA, 40S ribosomal protein S0-A, 40S ribosomal protein S1-A, ... Authors: Ikeuchi, K, Buschauer, R, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R. Deposit date: 2023-01-24 Release date: 2023-05-24 Method: ELECTRON MICROSCOPY (3 Å) Cite: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nat Commun, 14, 2023
8CAS	Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial) Descriptor: 18S ribosomal RNA, 40S ribosomal protein S0-A, 40S ribosomal protein S1-A, ... Authors: Ikeuchi, K, Buschauer, R, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R. Deposit date: 2023-01-24 Release date: 2023-05-24 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Nat Commun, 14, 2023
8CH6	Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex). Descriptor: 116 kDa U5 small nuclear ribonucleoprotein component, BUD13 homolog, Cell division cycle 5-like protein, ... Authors: Cretu, C, Schmitzova, J, Pena, V. Deposit date: 2023-02-07 Release date: 2023-05-10 Last modified: 2023-06-14 Method: ELECTRON MICROSCOPY (5.9 Å) Cite: Structural basis of catalytic activation in human splicing. Nature, 617, 2023
8C3A	Crystal structure of ailanthone bound to the Candida albicans 80S ribosome Descriptor: 18S, 25S, 3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose, ... Authors: Kolosova, O, Zgadzay, Y, Yusupov, M. Deposit date: 2022-12-23 Release date: 2024-01-10 Last modified: 2024-01-17 Method: X-RAY DIFFRACTION (3 Å) Cite: New crystal system to promote screening for new eukaryotic inhibitors To Be Published
8DAW	Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) Descriptor: ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 48, ... Authors: Lee, H.G, Lima, C.D. Deposit date: 2022-06-14 Release date: 2022-11-30 Last modified: 2023-01-11 Method: ELECTRON MICROSCOPY (3.6 Å) Cite: SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA, 120, 2023

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