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5GVI
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BU of 5gvi by Molmil
Zebrafish USP30 in complex with Lys6-linked diubiquitin
Descriptor: Ubiquitin carboxyl-terminal hydrolase 30, ZINC ION, ubiquitin
Authors:Sato, Y, Fukai, S.
Deposit date:2016-09-05
Release date:2017-09-13
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30
Nat. Struct. Mol. Biol., 24, 2017
3A9E
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BU of 3a9e by Molmil
Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha heterodimer ligand binding domains
Descriptor: (2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid, 13-mer (LXXLL motif) from Nuclear receptor coactivator 2, RETINOIC ACID, ...
Authors:Sato, Y, Duclaud, S, Peluso-Iltis, C, Poussin, P, Moras, D, Rochel, N, Structural Proteomics in Europe (SPINE)
Deposit date:2009-10-24
Release date:2010-10-06
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:The Phantom Effect of the Rexinoid LG100754: structural and functional insights
Plos One, 5, 2010
2ZNV
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BU of 2znv by Molmil
Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer
Descriptor: 1,2-ETHANEDIOL, AMSH-like protease, Ubiquitin, ...
Authors:Sato, Y, Azusa, Y, Yamagata, A, Mimura, H, Wang, X, Yamashita, M, Ookata, K, Nureki, O, Iwai, K, Komada, M, Fukai, S.
Deposit date:2008-05-01
Release date:2008-09-02
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains
Nature, 455, 2008
2ZNR
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BU of 2znr by Molmil
Crystal structure of the DUB domain of human AMSH-LP
Descriptor: 1,2-ETHANEDIOL, AMSH-like protease, PRASEODYMIUM ION, ...
Authors:Sato, Y, Azusa, Y, Yamagata, A, Mimura, H, Wang, X, Yamashita, M, Ookata, K, Nureki, O, Iwai, K, Komada, M, Fukai, S.
Deposit date:2008-05-01
Release date:2008-09-02
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains
Nature, 455, 2008
3AJB
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BU of 3ajb by Molmil
Crystal Structure of human Pex3p in complex with N-terminal Pex19p peptide
Descriptor: Peroxisomal biogenesis factor 19, Peroxisomal biogenesis factor 3
Authors:Sato, Y, Shibata, H, Nakatsu, T, Kato, H.
Deposit date:2010-05-27
Release date:2010-12-22
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p
Embo J., 29, 2010
6JWI
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BU of 6jwi by Molmil
Yeast Npl4 in complex with Lys48-linked diubiquitin
Descriptor: BICINE, Nuclear protein localization protein 4, Ubiqutin, ...
Authors:Sato, Y, Fukai, S.
Deposit date:2019-04-20
Release date:2019-12-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
Nat Commun, 10, 2019
6JWJ
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BU of 6jwj by Molmil
Npl4 in complex with Ufd1
Descriptor: GLYCEROL, Nuclear protein localization protein 4, Peptide from Ubiquitin fusion degradation protein 1, ...
Authors:Sato, Y, Fukai, S.
Deposit date:2019-04-20
Release date:2019-12-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
Nat Commun, 10, 2019
6JWH
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BU of 6jwh by Molmil
Yeast Npl4 zinc finger, MPN and CTD domains
Descriptor: GLYCEROL, Nuclear protein localization protein 4, ZINC ION
Authors:Sato, Y, Fukai, S.
Deposit date:2019-04-20
Release date:2019-12-25
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.72000253 Å)
Cite:Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
Nat Commun, 10, 2019
3WXG
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BU of 3wxg by Molmil
Crystal structure of CYLD USP domain (C596A) in complex with Lys63-linked diubiquitin
Descriptor: Ubiquitin, Uncharacterized protein
Authors:Sato, Y, Fukai, S.
Deposit date:2014-07-30
Release date:2015-02-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Nat.Struct.Mol.Biol., 22, 2015
3WXE
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BU of 3wxe by Molmil
Crystal structure of CYLD USP domain (C596S) in complex with Met1-linked diubiquitin
Descriptor: Ubiquitin, Uncharacterized protein
Authors:Sato, Y, Fukai, S.
Deposit date:2014-07-30
Release date:2015-02-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Nat.Struct.Mol.Biol., 22, 2015
3A9J
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BU of 3a9j by Molmil
Crystal structure of the mouse TAB2-NZF in complex with Lys63-linked di-ubiquitin
Descriptor: Mitogen-activated protein kinase kinase kinase 7-interacting protein 2, Ubiquitin, ZINC ION
Authors:Sato, Y, Yoshikawa, A, Yamashita, M, Yamagata, A, Fukai, S.
Deposit date:2009-10-29
Release date:2009-12-08
Last modified:2021-11-10
Method:X-RAY DIFFRACTION (1.18 Å)
Cite:Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3
Embo J., 28, 2009
3A3G
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BU of 3a3g by Molmil
Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine
Descriptor: 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol, Lumazine protein
Authors:Sato, Y.
Deposit date:2009-06-12
Release date:2009-11-10
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and FMN, at high resolution
J.Bacteriol., 192, 2009
3A3B
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BU of 3a3b by Molmil
Crystal structure of LumP complexed with flavin mononucleotide
Descriptor: FLAVIN MONONUCLEOTIDE, Lumazine protein, RIBOFLAVIN
Authors:Sato, Y.
Deposit date:2009-06-11
Release date:2009-11-10
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and FMN, at high resolution
J.Bacteriol., 192, 2009
3WXF
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BU of 3wxf by Molmil
Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin
Descriptor: SULFATE ION, Ubiquitin, Uncharacterized protein
Authors:Sato, Y, Fukai, S.
Deposit date:2014-07-30
Release date:2015-02-11
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity.
Nat.Struct.Mol.Biol., 22, 2015
3A1Q
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BU of 3a1q by Molmil
Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin
Descriptor: Ubiquitin, Ubiquitin interaction motif-containing protein 1
Authors:Sato, Y, Yoshikawa, A, Mimura, H, Yamashita, M, Yamagata, A, Fukai, S.
Deposit date:2009-04-21
Release date:2009-07-21
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80
Embo J., 28, 2009
3A35
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BU of 3a35 by Molmil
Crystal structure of LumP complexed with riboflavin
Descriptor: Lumazine protein, RIBOFLAVIN
Authors:Sato, Y.
Deposit date:2009-06-09
Release date:2009-11-10
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.421 Å)
Cite:Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl-8-(1'-D-ribityl) lumazine and its analogues, riboflavin and FMN, at high resolution
J.Bacteriol., 192, 2009
3A9K
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BU of 3a9k by Molmil
Crystal structure of the mouse TAB3-NZF in complex with Lys63-linked di-ubiquitin
Descriptor: Mitogen-activated protein kinase kinase kinase 7-interacting protein 3, Ubiquitin, ZINC ION
Authors:Sato, Y, Yoshikawa, A, Yamashita, M, Yamagata, A, Fukai, S.
Deposit date:2009-10-29
Release date:2009-12-08
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3
Embo J., 28, 2009
3B0A
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BU of 3b0a by Molmil
Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin
Descriptor: Polyubiquitin-C, RanBP-type and C3HC4-type zinc finger-containing protein 1, TRIS(HYDROXYETHYL)AMINOMETHANE, ...
Authors:Sato, Y, Fujita, H, Yoshikawa, A, Yamashita, M, Yamagata, A, Kaiser, S.E, Iwai, K, Fukai, S.
Deposit date:2011-06-07
Release date:2011-12-14
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Proc.Natl.Acad.Sci.USA, 108, 2011
3B08
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BU of 3b08 by Molmil
Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin
Descriptor: Polyubiquitin-C, RanBP-type and C3HC4-type zinc finger-containing protein 1, ZINC ION, ...
Authors:Sato, Y, Fujita, H, Yoshikawa, A, Yamashita, M, Yamagata, A, Kaiser, S.E, Iwai, K, Fukai, S.
Deposit date:2011-06-07
Release date:2011-12-14
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.701 Å)
Cite:Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex
Proc.Natl.Acad.Sci.USA, 108, 2011
6M3X
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BU of 6m3x by Molmil
Cryo-EM structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Descriptor: FE (III) ION, Sulfur oxygenase/reductase
Authors:Sato, Y, Adachi, N, Moriya, T, Arakawa, T, Kawasaki, M, Yamada, C, Senda, T, Fushinobu, S.
Deposit date:2020-03-04
Release date:2020-07-15
Last modified:2024-03-27
Method:ELECTRON MICROSCOPY (2.24 Å)
Cite:Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase fromSulfurisphaera tokodaii.
J Struct Biol X, 4, 2020
6M35
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BU of 6m35 by Molmil
Crystal structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Descriptor: FE (III) ION, GLYCEROL, SULFATE ION, ...
Authors:Sato, Y, Yabuki, T, Arakawa, T, Yamada, C, Fushinobu, S, Wakagi, T.
Deposit date:2020-03-02
Release date:2020-07-15
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase fromSulfurisphaera tokodaii.
J Struct Biol X, 4, 2020
3VON
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BU of 3von by Molmil
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
2DZ7
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BU of 2dz7 by Molmil
DNA Octaplex Formation with an I-Motif of A-Quartets: The Revised Crystal Structure of d(GCGAAAGC)
Descriptor: DNA (5'-D(*DGP*DCP*DGP*DAP*DAP*DAP*DGP*DC)-3'), MAGNESIUM ION
Authors:Sato, Y, Mitomi, K, Sumani, T, Kondo, J, Takenaka, A.
Deposit date:2006-09-21
Release date:2007-08-14
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC)
J.Biochem.(Tokyo), 140, 2006
2EQB
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BU of 2eqb by Molmil
Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex
Descriptor: PHOSPHATE ION, Rab guanine nucleotide exchange factor SEC2, Ras-related protein SEC4
Authors:Sato, Y, Fukai, S, Ishitani, R, Nureki, O.
Deposit date:2007-03-30
Release date:2007-05-22
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state
Proc.Natl.Acad.Sci.Usa, 104, 2007
4NIK
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BU of 4nik by Molmil
Structure of human Gankyrin in complex to the single chain antibody F5
Descriptor: 26S proteasome non-ATPase regulatory subunit 10, Single-chain Fv fragment antibody
Authors:Sato, Y, Weiss, E, Rochel, N.
Deposit date:2013-11-06
Release date:2014-09-10
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Restricted diversity of antigen binding residues of antibodies revealed by computational alanine scanning of 227 antibody-antigen complexes
J.Mol.Biol., 426, 2014

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