6M3X
 
 | | 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
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6M35
 | | 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
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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
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5GVI
 | | 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
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3WXG
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3WXE
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3WXF
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6JWI
 | | 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
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6JWH
 | | 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
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6JWJ
 | | 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
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3A9E
 | | 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
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3AJB
 | | 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
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1MCP
 | | PHOSPHOCHOLINE BINDING IMMUNOGLOBULIN FAB MC/PC603. AN X-RAY DIFFRACTION STUDY AT 2.7 ANGSTROMS | | Descriptor: | IGA-KAPPA MCPC603 FAB (HEAVY CHAIN), IGA-KAPPA MCPC603 FAB (LIGHT CHAIN), SULFATE ION | | Authors: | Satow, Y, Cohen, G.H, Padlan, E.A, Davies, D.R. | | Deposit date: | 1984-07-09 | | Release date: | 1985-01-02 | | Last modified: | 2023-07-26 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A.
J.Mol.Biol., 190, 1986
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2ZNV
 | | 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
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2ZNR
 | | 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
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2EQB
 | | 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
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2DZ7
 | | 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
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3A9J
 | | 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
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3A3G
 | | 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
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3A3B
 | | 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
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3B08
 | | 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
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3B0A
 | | 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
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3A1Q
 | | 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
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3A35
 | | 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
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3A9K
 | | 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
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