6J74
| Complex of GGTaseIII and full-length Ykt6 | Descriptor: | Geranylgeranyl transferase type-2 subunit beta, PHOSPHATE ION, Protein prenyltransferase alpha subunit repeat-containing protein 1, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-16 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.212 Å) | Cite: | Complex of GGTaseIII and full-length Ykt6 To Be Published
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6J7F
| Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP | Descriptor: | DIPHOSPHATE, FARNESYL, GERAN-8-YL GERAN, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-18 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.883 Å) | Cite: | Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP To Be Published
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6IXG
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6J7X
| Complex of GGTaseIII, farnesyl-Ykt6, and GGPP | Descriptor: | FORMIC ACID, GERANYLGERANYL DIPHOSPHATE, Geranylgeranyl transferase type-2 subunit beta, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2019-01-18 | Release date: | 2020-01-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP To Be Published
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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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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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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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5XIT
| Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II | Descriptor: | E3 ubiquitin-protein ligase RNF168, GLYCEROL, PRASEODYMIUM ION, ... | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | Deposit date: | 2017-04-27 | Release date: | 2018-03-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Nat Commun, 9, 2018
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5XIS
| Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I | Descriptor: | E3 ubiquitin-protein ligase RNF168, MAGNESIUM ION, Ubiquitin-40S ribosomal protein S27a, ... | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | Deposit date: | 2017-04-27 | Release date: | 2018-03-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Nat Commun, 9, 2018
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5XIU
| Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin | Descriptor: | 1,2-ETHANEDIOL, E3 ubiquitin-protein ligase RNF168, Ubiquitin-40S ribosomal protein S27a | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | Deposit date: | 2017-04-27 | Release date: | 2018-03-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Nat Commun, 9, 2018
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5Y32
| Crystal structure of PTP delta Ig1-Ig2 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Yamagata, A, Fukai, S. | Deposit date: | 2017-07-27 | Release date: | 2017-08-16 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.701 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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5YDK
| Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form | Descriptor: | E3 ubiquitin-protein ligase RNF168, GLYCEROL, Ubiquitin-40S ribosomal protein S27a | Authors: | Takahashi, T.S, Sato, Y, Fukai, S. | Deposit date: | 2017-09-13 | Release date: | 2018-03-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.505 Å) | Cite: | Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168 Nat Commun, 9, 2018
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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: | 2023-06-28 | 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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5ZNM
| Colicin D Central Domain and C-terminal tRNase domain | Descriptor: | Colicin-D, GLYCEROL, SULFATE ION | Authors: | Chang, J.W, Sato, Y, Ogawa, T, Arakawa, T, Fukai, S, Fushinobu, S, Masaki, H. | Deposit date: | 2018-04-10 | Release date: | 2018-08-29 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell J. Biochem., 164, 2018
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5XWU
| Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2017-06-30 | Release date: | 2018-06-06 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (3.162 Å) | Cite: | Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation. Nat Commun, 9, 2018
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5XWS
| Crystal structure of SALM5 LRR-Ig | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Leucine-rich repeat and fibronectin type-III domain-containing protein 5 | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2017-06-30 | Release date: | 2018-06-06 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (3.084 Å) | Cite: | Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation. Nat Commun, 9, 2018
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5XWT
| Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Goto-Ito, S, Yamagata, A, Sato, Y, Fukai, S. | Deposit date: | 2017-06-30 | Release date: | 2018-06-06 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (4.178 Å) | Cite: | Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation. Nat Commun, 9, 2018
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3WWQ
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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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5XGC
| Crystal structure of SmgGDS-558 | Descriptor: | Rap1 GTPase-GDP dissociation stimulator 1 | Authors: | Shimizu, H, Toma-Fukai, S, Shimizu, T. | Deposit date: | 2017-04-13 | Release date: | 2017-06-28 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding J. Biol. Chem., 292, 2017
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5Y31
| Crystal structure of human LGI1-ADAM22 complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Disintegrin and metalloproteinase domain-containing protein 22, ... | Authors: | Yamagata, A, Fukai, S. | Deposit date: | 2017-07-27 | Release date: | 2018-05-02 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (7.125 Å) | Cite: | Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22. Nat Commun, 9, 2018
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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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5Y30
| Crystal structure of LGI1 LRR domain | Descriptor: | Leucine-rich glioma-inactivated protein 1 | Authors: | Yamagata, A, Fukai, S. | Deposit date: | 2017-07-27 | Release date: | 2018-05-02 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.781 Å) | Cite: | Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22. Nat Commun, 9, 2018
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5Y2Z
| Crystal structure of human LGI1 EPTP-ADAM22 complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Yamagata, A, Fukai, S. | Deposit date: | 2017-07-27 | Release date: | 2018-05-02 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.67 Å) | Cite: | Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22. Nat Commun, 9, 2018
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3VLC
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