2GS9
| Crystal structure of TT1324 from Thermus thermophilis HB8 | Descriptor: | FORMIC ACID, Hypothetical protein TT1324, S-ADENOSYL-L-HOMOCYSTEINE | Authors: | Kamitori, S, Abe, A, Ebihara, A, Kanagawa, M, Nakagawa, N, Kuroishi, C, Agari, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-04-25 | Release date: | 2007-03-13 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structure of TT1324 from Thermus thermophilis HB8 To be Published
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5C2J
| Complex structure of the GAP domain of MgcRacGAP and Cdc42 | Descriptor: | ALUMINUM FLUORIDE, Cell division control protein 42 homolog, GUANOSINE-5'-DIPHOSPHATE, ... | Authors: | Murayama, K, Kato-Murayama, M, Hosaka, T, Kitamura, T, Yokoyama, S, Shirouzu, M. | Deposit date: | 2015-06-16 | Release date: | 2016-06-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural basis of G-protein target alternation of MgcRacGAP by phospholylation To Be Published
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3VUZ
| Crystal structure of histone methyltransferase SET7/9 in complex with AAM-1 | Descriptor: | 5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine, Histone-lysine N-methyltransferase SETD7 | Authors: | Niwa, H, Handa, N, Tomabechi, Y, Honda, K, Toyama, M, Ohsawa, N, Shirouzu, M, Kagechika, H, Hirano, T, Umehara, T, Yokoyama, S. | Deposit date: | 2012-07-10 | Release date: | 2013-03-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives Acta Crystallogr.,Sect.D, 69, 2013
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3VV0
| Crystal structure of histone methyltransferase SET7/9 in complex with DAAM-3 | Descriptor: | 5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]amino}-5'-deoxyadenosine, Histone-lysine N-methyltransferase SETD7 | Authors: | Niwa, H, Handa, N, Tomabechi, Y, Honda, K, Toyama, M, Ohsawa, N, Shirouzu, M, Kagechika, H, Hirano, T, Umehara, T, Yokoyama, S. | Deposit date: | 2012-07-10 | Release date: | 2013-03-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.001 Å) | Cite: | Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives Acta Crystallogr.,Sect.D, 69, 2013
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2RPR
| Solution structure of the fifth FLYWCH domain of FLYWCH-type zinc finger-containing protein 1 | Descriptor: | FLYWCH-type zinc finger-containing protein 1, ZINC ION | Authors: | Enomoto, M, Saito, K, Tochio, N, Kigawa, T, Yokoyama, S, Nameki, N. | Deposit date: | 2008-07-24 | Release date: | 2009-08-04 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution structure of the fifth FLYWCH domain of FLYWCH-type zinc finger-containing protein 1 To be Published
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3WF6
| Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine | Descriptor: | 4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine, Ribosomal protein S6 kinase beta-1, ZINC ION | Authors: | Niwa, H, Shirouzu, M, Yokoyama, S. | Deposit date: | 2013-07-17 | Release date: | 2014-08-06 | Last modified: | 2014-10-29 | Method: | X-RAY DIFFRACTION (2.031 Å) | Cite: | Crystal structures of the S6K1 kinase domain in complexes with inhibitors J.Struct.Funct.Genom., 15, 2014
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3WNC
| Crystal structure of EF-Pyl in complex with GDP | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Protein translation elongation factor 1A | Authors: | Yanagisawa, T, Ishii, R, Fukunaga, R, Sengoku, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2013-12-08 | Release date: | 2014-12-10 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | A SelB/EF-Tu/aIF2 gamma-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.). J. Struct. Funct. Genomics, 16, 2015
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2U2F
| SOLUTION STRUCTURE OF THE SECOND RNA-BINDING DOMAIN OF HU2AF65 | Descriptor: | PROTEIN (SPLICING FACTOR U2AF 65 KD SUBUNIT) | Authors: | Ito, T, Muto, Y, Green, M.R, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 1999-05-26 | Release date: | 1999-08-20 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)). EMBO J., 18, 1999
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3ECS
| Crystal structure of human eIF2B alpha | Descriptor: | CHLORIDE ION, SULFATE ION, Translation initiation factor eIF-2B subunit alpha | Authors: | Hiyama, T.B, Ito, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2008-09-01 | Release date: | 2009-09-01 | Last modified: | 2014-02-05 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | Crystal structure of the alpha subunit of human translation initiation factor 2B J.Mol.Biol., 392, 2009
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3WF7
| Crystal structure of S6K1 kinase domain in complex with a purine derivative 1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide | Descriptor: | 1-(9H-purin-6-yl)-N-[3-(trifluoromethyl)phenyl]piperidine-4-carboxamide, GLYCEROL, Ribosomal protein S6 kinase beta-1, ... | Authors: | Niwa, H, Shirouzu, M, Yokoyama, S. | Deposit date: | 2013-07-17 | Release date: | 2014-08-06 | Last modified: | 2014-10-29 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Crystal structures of the S6K1 kinase domain in complexes with inhibitors J.Struct.Funct.Genom., 15, 2014
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3WU5
| Reduced E.coli Lon Proteolytic domain | Descriptor: | Lon protease, SULFATE ION | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | Deposit date: | 2014-04-22 | Release date: | 2014-11-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.07 Å) | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis. Nat. Chem. Biol., 11, 2015
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3WF5
| Crystal structure of S6K1 kinase domain in complex with a pyrazolopyrimidine derivative 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine | Descriptor: | 4-[4-(1H-benzimidazol-2-yl)piperidin-1-yl]-1H-pyrazolo[3,4-d]pyrimidine, Ribosomal protein S6 kinase beta-1, ZINC ION | Authors: | Niwa, H, Shirouzu, M, Yokoyama, S. | Deposit date: | 2013-07-17 | Release date: | 2014-08-06 | Last modified: | 2014-10-29 | Method: | X-RAY DIFFRACTION (2.099 Å) | Cite: | Crystal structures of the S6K1 kinase domain in complexes with inhibitors J.Struct.Funct.Genom., 15, 2014
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3WHE
| A new conserved neutralizing epitope at the globular head of hemagglutinin in H3N2 influenza viruses | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hemagglutinin, alpha-D-mannopyranose-(1-2)-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: | Fujii, Y, Sumida, T, Shirouzu, M, Yokoyama, S. | Deposit date: | 2013-08-25 | Release date: | 2014-04-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (4 Å) | Cite: | Conserved neutralizing epitope at globular head of hemagglutinin in H3N2 influenza viruses. J.Virol., 88, 2014
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3WU6
| Oxidized E.coli Lon Proteolytic domain | Descriptor: | Lon protease, SULFATE ION | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | Deposit date: | 2014-04-22 | Release date: | 2014-11-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis. Nat. Chem. Biol., 11, 2015
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3WE4
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3WCO
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3WCN
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5WXI
| EarP bound with dTDP-rhamnose (soaked) | Descriptor: | 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE, BETA-MERCAPTOETHANOL, EarP, ... | Authors: | Sengoku, T, Yokoyama, S, Yanagisawa, T. | Deposit date: | 2017-01-07 | Release date: | 2018-02-28 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP Nat. Chem. Biol., 14, 2018
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5WXJ
| Apo EarP | Descriptor: | BETA-MERCAPTOETHANOL, EarP, GLYCEROL, ... | Authors: | Sengoku, T, Yokoyama, S, Yanagisawa, T. | Deposit date: | 2017-01-07 | Release date: | 2018-02-28 | Last modified: | 2018-04-04 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP Nat. Chem. Biol., 14, 2018
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5YVA
| Structure of CaMKK2 in complex with CKI-010 | Descriptor: | 3-(1H-tetrazol-5-yl)-10lambda~6~-thioxanthene-9,10,10-trione, CHLORIDE ION, Calcium/calmodulin-dependent protein kinase kinase 2, ... | Authors: | Niwa, H, Handa, N, Yokoyama, S. | Deposit date: | 2017-11-24 | Release date: | 2018-12-05 | Last modified: | 2020-06-10 | Method: | X-RAY DIFFRACTION (2.574 Å) | Cite: | Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method. J.Mol.Graph.Model., 99, 2020
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5XHG
| Crystal structure of Trastuzumab Fab fragment bearing Ne-(o-azidobenzyloxycarbonyl)-L-lysine | Descriptor: | (2-azidophenyl)methyl hydrogen carbonate, 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, ... | Authors: | Kuratani, M, Yanagisawa, T, Sakamoto, K, Yokoyama, S. | Deposit date: | 2017-04-20 | Release date: | 2017-12-20 | Last modified: | 2019-12-25 | Method: | X-RAY DIFFRACTION (1.76 Å) | Cite: | Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes. Bioconjug. Chem., 28, 2017
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3WU3
| Reduced-form structure of E.coli Lon Proteolytic domain | Descriptor: | Lon protease, SULFATE ION | Authors: | Nishii, W, Kukimoto-Niino, M, Terada, T, Shirouzu, M, Muramatsu, T, Yokoyama, S. | Deposit date: | 2014-04-22 | Release date: | 2014-11-12 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.82 Å) | Cite: | A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis. Nat. Chem. Biol., 11, 2015
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2RS7
| Solution structure of the second dsRBD from RNA helicase A | Descriptor: | ATP-dependent RNA helicase A | Authors: | Nagata, T, Muto, Y, Tsuda, K, Inoue, M, Kigawa, T, Terada, T, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-11-29 | Release date: | 2012-03-14 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Solution structures of the double-stranded RNA-binding domains from RNA helicase A Proteins, 80, 2012
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2RUG
| Refined solution structure of the first RNA recognition motif domain in CPEB3 | Descriptor: | Cytoplasmic polyadenylation element-binding protein 3 | Authors: | Tsuda, K, Kuwasako, K, Nagata, T, Takahashi, M, Kigawa, T, Kobayashi, N, Guntert, P, Shirouzu, M, Yokoyama, S, Muto, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2014-04-15 | Release date: | 2014-09-17 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3. Proteins, 82, 2014
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2RS9
| Solution structure of the bromodomain of human BRPF1 in complex with histone H4K5ac peptide | Descriptor: | Acetylated lysine 5 of peptide from Histone H4, Peregrin | Authors: | Qin, X, Nagashima, T, Umehara, T, Hayashi, F, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-12-08 | Release date: | 2012-12-12 | Last modified: | 2023-11-15 | Method: | SOLUTION NMR | Cite: | Site-specific histone recognition by the bromodomain of Brpf1 and the role in MOZ/MORF histone acetyltransferase complexes To be Published
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