2ZR2
 
 | | Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with ATP | | Descriptor: | ADENOSINE MONOPHOSPHATE, SULFATE ION, Seryl-tRNA synthetase | | Authors: | Itoh, Y, Sekine, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2008-08-22 | | Release date: | 2008-09-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
Rna Biol., 5, 2008
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3ADC
 | | Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 2) | | Descriptor: | L-seryl-tRNA(Sec) kinase, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | | Authors: | Itoh, Y, Chiba, S, Sekine, S, Yokoyama, S. | | Deposit date: | 2010-01-18 | | Release date: | 2010-07-28 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
Mol.Cell, 39, 2010
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3ADB
 | | Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 1) | | Descriptor: | L-seryl-tRNA(Sec) kinase, MAGNESIUM ION, PHOSPHATE ION, ... | | Authors: | Itoh, Y, Chiba, S, Sekine, S, Yokoyama, S. | | Deposit date: | 2010-01-18 | | Release date: | 2010-07-28 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
Mol.Cell, 39, 2010
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3ADD
 | | Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 3) | | Descriptor: | L-seryl-tRNA(Sec) kinase, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | | Authors: | Itoh, Y, Chiba, S, Sekine, S, Yokoyama, S. | | Deposit date: | 2010-01-18 | | Release date: | 2010-07-28 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
Mol.Cell, 39, 2010
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7Y4N
 | | Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos | | Descriptor: | Growth factor receptor-bound protein 2 | | Authors: | Pooppadi, M.S, Ikeya, T, Sugasawa, H, Watanabe, R, Mishima, M, Inomata, K, Ito, Y. | | Deposit date: | 2022-06-15 | | Release date: | 2022-08-31 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos.
Biochem.Biophys.Res.Commun., 625, 2022
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2E4E
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1AA3
 | | C-TERMINAL DOMAIN OF THE E. COLI RECA, NMR, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | RECA | | Authors: | Aihara, H, Ito, Y, Kurumizaka, H, Terada, T, Yokoyama, S, Shibata, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1997-01-22 | | Release date: | 1997-07-23 | | Last modified: | 2024-04-10 | | Method: | SOLUTION NMR | | Cite: | An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing.
J.Mol.Biol., 274, 1997
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1B22
 | | RAD51 (N-TERMINAL DOMAIN) | | Descriptor: | DNA REPAIR PROTEIN RAD51 | | Authors: | Aihara, H, Ito, Y, Kurumizaka, H, Yokoyama, S, Shibata, T, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1998-12-04 | | Release date: | 1999-12-03 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
J.Mol.Biol., 290, 1999
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1X3U
 | | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot | | Descriptor: | Transcriptional regulatory protein fixJ | | Authors: | Kurashima-Ito, K, Kasai, Y, Hosono, K, Tamura, K, Oue, S, Isogai, M, Ito, Y, Nakamura, H, Shiro, Y. | | Deposit date: | 2005-05-10 | | Release date: | 2006-05-02 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter
Biochemistry, 44, 2005
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5ZCZ
 | | Solution structure of the T. Thermophilus HB8 TTHA1718 protein in living eukaryotic cells by in-cell NMR spectroscopy | | Descriptor: | Heavy metal binding protein | | Authors: | Tanaka, T, Teppei, I, Kamoshida, H, Mishima, M, Shirakawa, M, Guentert, P, Ito, Y. | | Deposit date: | 2018-02-22 | | Release date: | 2019-08-21 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.
Angew.Chem.Int.Ed.Engl., 58, 2019
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5ZD0
 | | Solution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy | | Descriptor: | ubiquitin | | Authors: | Tanaka, T, Ikeya, T, Kamoshida, H, Mishima, M, Shirakawa, M, Guentert, P, Ito, Y. | | Deposit date: | 2018-02-22 | | Release date: | 2019-08-21 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.
Angew.Chem.Int.Ed.Engl., 58, 2019
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5Z4B
 | | GB1 structure determination in living eukaryotic cells by in-cell NMR spectroscopy | | Descriptor: | Protein LG | | Authors: | Tanaka, T, Teppei, I, Kamoshida, H, Mishima, M, Shirakawa, M, Guentert, P, Ito, Y. | | Deposit date: | 2018-01-10 | | Release date: | 2019-01-23 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.
Angew.Chem.Int.Ed.Engl., 58, 2019
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8J4C
 | | YeeE(TsuA)-YeeD(TsuB) complex for thiosulfate uptake | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Spirochaeta thermophila YeeE(TsuA)-YeeD(TsuB),UPF0033 domain-containing protein, SirA-like domain-containing protein (chimera), ... | | Authors: | Ikei, M, Miyazaki, R, Monden, K, Naito, Y, Takeuchi, A, Takahashi, Y.S, Tanaka, Y, Ichikawa, M, Tsukazaki, T. | | Deposit date: | 2023-04-19 | | Release date: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (3.34 Å) | | Cite: | Structure and function of YeeE-YeeD complex for sophisticated thiosulfate uptake
To Be Published
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8J12
 | | Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex | | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (247-MER), ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-12 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (3.08 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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8J1J
 | | Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (38-MER), MAGNESIUM ION, RNA (118-MER), ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-13 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (2.91 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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8J3R
 | | Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA | | Descriptor: | DNA (37-MER), DNA (38-MER), MAGNESIUM ION, ... | | Authors: | Hino, T, Omura, N.S, Nakagawa, R, Togashi, T, Takeda, N.S, Hiramoto, T, Tasaka, S, Hirano, H, Tokuyama, T, Uosaki, H, Ishiguro, H, Yamano, H, Ozaki, Y, Motooka, D, Mori, H, Kirita, Y, Kise, Y, Itoh, Y, Matoba, S, Aburatani, H, Yachie, N, Siksnys, V, Ohmori, T, Hoshino, A, Nureki, O. | | Deposit date: | 2023-04-18 | | Release date: | 2023-09-27 | | Method: | ELECTRON MICROSCOPY (2.95 Å) | | Cite: | Minimal and most efficient genome editing Cas enzyme
To Be Published
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5WTQ
 | | Crystal structure of human proteasome-assembling chaperone PAC4 | | Descriptor: | CHLORIDE ION, NICKEL (II) ION, Proteasome assembly chaperone 4 | | Authors: | Kurimoto, E, Satoh, T, Ito, Y, Ishihara, E, Tanaka, K, Kato, K. | | Deposit date: | 2016-12-13 | | Release date: | 2017-03-22 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation
Protein Sci., 26, 2017
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1WLC
 | | Congerin II Y16S/T88I double mutant | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Congerin II | | Authors: | Shionyu-Mitsuyama, C, Ito, Y, Konno, A, Miwa, Y, Ogawa, T, Muramoto, K, Shirai, T. | | Deposit date: | 2004-06-22 | | Release date: | 2005-06-07 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | In vitro evolutionary thermostabilization of congerin II: a limited reproduction of natural protein evolution by artificial selection pressure
J.Mol.Biol., 347, 2005
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1WLD
 | | Congerin II T88I single mutant | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CONGERIN II, beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | | Authors: | Shionyu-Mitsuyama, C, Ito, Y, Konno, A, Miwa, Y, Ogawa, T, Muramoto, K, Shirai, T. | | Deposit date: | 2004-06-22 | | Release date: | 2005-06-07 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | In vitro evolutionary thermostabilization of congerin II: a limited reproduction of natural protein evolution by artificial selection pressure
J.Mol.Biol., 347, 2005
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1WLW
 | | Congerin II Y16S single mutant | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Congerin II, beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose | | Authors: | Shionyu-Mitsuyama, C, Ito, Y, Konno, A, Miwa, Y, Ogawa, T, Muramoto, K, Shirai, T. | | Deposit date: | 2004-06-30 | | Release date: | 2005-06-07 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | In vitro evolutionary thermostabilization of congerin II: a limited reproduction of natural protein evolution by artificial selection pressure
J.Mol.Biol., 347, 2005
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2N9L
 | | 1H, 13C, and 15N Chemical Shift Assignments for in-cell GB1 | | Descriptor: | Immunoglobulin G-binding protein G | | Authors: | Ikeya, T, Hanashima, T, Hosoya, S, Shimazaki, M, Ikeda, S, Mishima, M, Guentert, P, Ito, Y. | | Deposit date: | 2015-11-30 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Improved in-cell structure determination of proteins at near-physiological concentration
Sci Rep, 6, 2016
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2N9K
 | | 1H, 13C, and 15N Chemical Shift Assignments for in vitro GB1 | | Descriptor: | Immunoglobulin G-binding protein G | | Authors: | Ikeya, T, Hanashima, T, Hosoya, S, Shimazaki, M, Ikeda, S, Mishima, M, Guentert, P, Ito, Y. | | Deposit date: | 2015-11-26 | | Release date: | 2016-12-28 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Improved in-cell structure determination of proteins at near-physiological concentration
Sci Rep, 6, 2016
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8QNN
 | | Crystal structure of a Class A beta-lactamase from Nocardia cyriacigeorgica | | Descriptor: | Beta-lactamase, CITRATE ANION | | Authors: | Feuillard, J, Couston, J, Benito, Y, Hodille, E, Dumitrescu, O, Blaise, M. | | Deposit date: | 2023-09-27 | | Release date: | 2024-01-17 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | Biochemical and structural characterization of a class A beta-lactamase from Nocardia cyriacigeorgica.
Acta Crystallogr.,Sect.F, 80, 2024
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5Y5N
 | | Crystal structure of human Sirtuin 2 in complex with a selective inhibitor | | Descriptor: | 2-[[3-(2-phenylethoxy)phenyl]amino]benzamide, NAD-dependent protein deacetylase sirtuin-2, ZINC ION | | Authors: | Mellini, P, Itoh, Y, Tsumoto, H, Li, Y, Suzuki, M, Tokuda, N, Kakizawa, T, Miura, Y, Takeuchi, J, Lahtela-Kakkonen, M, Suzuki, T. | | Deposit date: | 2017-08-09 | | Release date: | 2017-09-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Potent mechanism-based sirtuin-2-selective inhibition by anin situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD+-binding site.
Chem Sci, 8, 2017
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8AU4
 | | Structural insights reveal a heterotetramer between oncogenic K-Ras4BG12V and Rgl2, a RalA/B activator | | Descriptor: | Ral guanine nucleotide dissociation stimulator-like 2 | | Authors: | Tariq, M, Ikeya, T, Togashi, N, Fairall, L, Alejo, C.B, Kamei, S, Alonso, B.R, Campillo, M.A.M, Hudson, A, Ito, Y, Schwabe, J, Dominguez, C, Tanaka, K. | | Deposit date: | 2022-08-25 | | Release date: | 2023-08-23 | | Last modified: | 2023-10-25 | | Method: | SOLUTION NMR | | Cite: | Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator.
Life Sci Alliance, 7, 2024
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