5GVC
 
 | | Human Topoisomerase IIIb topo domain | | Descriptor: | DNA topoisomerase 3-beta-1, MAGNESIUM ION | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S. | | Deposit date: | 2016-09-05 | | Release date: | 2017-06-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.436 Å) | | Cite: | Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
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5GVD
 | | Human TDRD3 DUF1767-OB domains | | Descriptor: | 1,2-ETHANEDIOL, MAGNESIUM ION, PHOSPHATE ION, ... | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S. | | Deposit date: | 2016-09-05 | | Release date: | 2017-06-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.623 Å) | | Cite: | Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
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5GVE
 | | Human TOP3B-TDRD3 complex | | Descriptor: | DNA topoisomerase 3-beta-1, MAGNESIUM ION, Tudor domain-containing protein 3 | | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Takahashi, T.S, Fukai, S. | | Deposit date: | 2016-09-05 | | Release date: | 2017-06-14 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.606 Å) | | Cite: | Structural basis of the interaction between Topoisomerase III beta and the TDRD3 auxiliary factor
Sci Rep, 7, 2017
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5H11
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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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1UDZ
 | | Isoleucyl-tRNA synthetase editing domain | | Descriptor: | Isoleucyl-tRNA synthetase | | Authors: | Fukunaga, R, Fukai, S, Ishitani, R, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-05-08 | | Release date: | 2004-03-23 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.
J.Biol.Chem., 279, 2004
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1UE0
 | | Isoleucyl-tRNA synthetase editing domain complexed with L-Valine | | Descriptor: | Isoleucyl-tRNA synthetase, VALINE | | Authors: | Fukunaga, R, Fukai, S, Ishitani, R, Nureki, O, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-05-08 | | Release date: | 2004-03-23 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.
J.Biol.Chem., 279, 2004
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4YFE
 | | Crystal structure of PTP delta Fn1-Fn2 | | Descriptor: | Receptor-type tyrosine-protein phosphatase delta | | Authors: | Yamagata, A, Fukai, S. | | Deposit date: | 2015-02-25 | | Release date: | 2015-05-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.972 Å) | | Cite: | Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
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4YH6
 | | Crystal structure of IL1RAPL1 ectodomain | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein-like 1, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Yamagata, A, Fukai, S. | | Deposit date: | 2015-02-27 | | Release date: | 2015-05-06 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
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4YFG
 | | Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor-type tyrosine-protein phosphatase delta | | Authors: | Yamagata, A, Fukai, S. | | Deposit date: | 2015-02-25 | | Release date: | 2015-05-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.491 Å) | | Cite: | Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
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4YFD
 | | Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein, Receptor-type tyrosine-protein phosphatase delta | | Authors: | Yamagata, A, Fukai, S. | | Deposit date: | 2015-02-25 | | Release date: | 2015-05-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.253 Å) | | Cite: | Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
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4YH7
 | | Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Interleukin-1 receptor accessory protein-like 1, ... | | Authors: | Yamagata, A, Fukai, S. | | Deposit date: | 2015-02-27 | | Release date: | 2015-05-06 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (4.4 Å) | | Cite: | Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation.
Nat Commun, 6, 2015
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1V2X
 | | TrmH | | Descriptor: | PHOSPHATE ION, S-ADENOSYLMETHIONINE, tRNA (Gm18) methyltransferase | | Authors: | Nureki, O, Watanabe, K, Fukai, S, Ishii, R, Endo, Y, Hori, H, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-17 | | Release date: | 2004-05-04 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme
STRUCTURE, 12, 2004
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7W86
 | | Crystal structure of the DYW domain of DYW1 | | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, GLYCEROL, ... | | Authors: | Sawada, Y, Shimizu, H, Toma-Fukai, S, Shimizu, T. | | Deposit date: | 2021-12-07 | | Release date: | 2022-12-14 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation.
Plant Cell, 35, 2023
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4Y61
 | | Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Receptor-type tyrosine-protein phosphatase delta, SLIT and NTRK-like protein 2 | | Authors: | Yamgata, A, Sato, Y, Goto-Ito, S, Uemura, T, Maeda, A, Shiroshima, T, Yoshida, T, Fukai, S. | | Deposit date: | 2015-02-12 | | Release date: | 2015-06-03 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.358 Å) | | Cite: | Structure of Slitrk2-PTP delta complex reveals mechanisms for splicing-dependent trans-synaptic adhesion.
Sci Rep, 5, 2015
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3VU8
 | | Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue | | Descriptor: | Methionine--tRNA ligase, N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE, ZINC ION | | Authors: | Konno, M, Kato-Murayama, M, Toma-Fukai, S, Uchikawa, E, Nureki, O, Yokoyama, S. | | Deposit date: | 2012-06-22 | | Release date: | 2013-06-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases
To be Published
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1IT7
 | | Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine | | Descriptor: | Archaeosine tRNA-guanine transglycosylase, GUANINE, MAGNESIUM ION, ... | | Authors: | Ishitani, R, Nureki, O, Fukai, S, Kijimoto, T, Nameki, N, Watanabe, M, Kondo, H, Sekine, M, Okada, N, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-01-11 | | Release date: | 2002-05-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structure of archaeosine tRNA-guanine transglycosylase.
J.Mol.Biol., 318, 2002
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1IQ8
 | | Crystal Structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii | | Descriptor: | ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE, MAGNESIUM ION, ZINC ION | | Authors: | Ishitani, R, Nureki, O, Fukai, S, Kijimoto, T, Nameki, N, Watanabe, M, Kondo, H, Sekine, M, Okada, N, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-07-09 | | Release date: | 2002-05-22 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of archaeosine tRNA-guanine transglycosylase.
J.Mol.Biol., 318, 2002
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1IT8
 | | Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0 | | Descriptor: | 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE, MAGNESIUM ION, ZINC ION, ... | | Authors: | Ishitani, R, Nureki, O, Fukai, S, Kijimoto, T, Nameki, N, Watanabe, M, Kondo, H, Sekine, M, Okada, N, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-01-11 | | Release date: | 2002-05-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structure of archaeosine tRNA-guanine transglycosylase.
J.Mol.Biol., 318, 2002
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1HZD
 | | CRYSTAL STRUCTURE OF HUMAN AUH PROTEIN, AN RNA-BINDING HOMOLOGUE OF ENOYL-COA HYDRATASE | | Descriptor: | AU-BINDING PROTEIN/ENOYL-COA HYDRATASE | | Authors: | Kurimoto, K, Fukai, S, Nureki, O, Muto, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-01-24 | | Release date: | 2001-12-12 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase.
Structure, 9, 2001
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1IVO
 | | Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains. | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Epidermal Growth Factor Receptor, ... | | Authors: | Ogiso, H, Ishitani, R, Nureki, O, Fukai, S, Yamanaka, M, Kim, J.H, Saito, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-03-28 | | Release date: | 2002-10-16 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.
Cell(Cambridge,Mass.), 110, 2002
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1ILE
 | | ISOLEUCYL-TRNA SYNTHETASE | | Descriptor: | ISOLEUCYL-TRNA SYNTHETASE, ZINC ION | | Authors: | Nureki, O, Vassylyev, D.G, Tateno, M, Shimada, A, Nakama, T, Fukai, S, Konno, M, Schimmel, P, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1998-02-24 | | Release date: | 1999-04-13 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Enzyme structure with two catalytic sites for double-sieve selection of substrate.
Science, 280, 1998
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1KN0
 | | Crystal Structure of the human Rad52 protein | | Descriptor: | Rad52 | | Authors: | Kagawa, W, Kurumizaka, H, Ishitani, R, Fukai, S, Nureki, O, Shibata, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-12-18 | | Release date: | 2002-09-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form.
Mol.Cell, 10, 2002
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2YVX
 | | Crystal structure of magnesium transporter MgtE | | Descriptor: | MAGNESIUM ION, Mg2+ transporter MgtE | | Authors: | Hattori, M, Tanaka, Y, Fukai, S, Ishitani, R, Nureki, O. | | Deposit date: | 2007-04-18 | | Release date: | 2007-09-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Crystal structure of the MgtE Mg(2+) transporter
Nature, 448, 2007
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1VFG
 | | Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog | | Descriptor: | DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, RNA (75-MER), poly A polymerase | | Authors: | Tomita, K, Fukai, S, Ishitani, R, Ueda, T, Takeuchi, N, Vassylyev, D.G, Nureki, O, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-04-13 | | Release date: | 2004-08-10 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis for template-independent RNA polymerization.
Nature, 430, 2004
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