1GE9
| SOLUTION STRUCTURE OF THE RIBOSOME RECYCLING FACTOR | Descriptor: | RIBOSOME RECYCLING FACTOR | Authors: | Yoshida, T, Uchiyama, S, Nakano, H, Kashimori, H, Kijima, H, Ohshima, T, Saihara, Y, Ishino, T, Shimahara, T, Yoshida, T, Yokose, K, Ohkubo, T, Kaji, A, Kobayashi, Y. | Deposit date: | 2000-10-19 | Release date: | 2001-05-16 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution structure of the ribosome recycling factor from Aquifex aeolicus. Biochemistry, 40, 2001
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5C2I
| Crystal structure of Anabaena sp. DyP-type peroxidese (AnaPX) | Descriptor: | 1,2-ETHANEDIOL, ACETIC ACID, Alr1585 protein, ... | Authors: | Yoshida, T, Amano, Y, Tsuge, H, Sugano, Y. | Deposit date: | 2015-06-16 | Release date: | 2015-12-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Anabaena sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers. Proteins, 84, 2016
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6KXX
| Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound A) | Descriptor: | 1-(4-chlorophenyl)-6-methyl-3-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | Authors: | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | Deposit date: | 2019-09-14 | Release date: | 2020-05-20 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives. Sci Rep, 10, 2020
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6KXY
| Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound B) | Descriptor: | 6-ethyl-1-(4-fluorophenyl)-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | Authors: | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | Deposit date: | 2019-09-14 | Release date: | 2020-05-20 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives. Sci Rep, 10, 2020
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6KLW
| Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with long stem | Descriptor: | CALCIUM ION, Iota toxin component Ia, Iota toxin component Ib | Authors: | Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H. | Deposit date: | 2019-07-30 | Release date: | 2020-01-15 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex. Nat.Struct.Mol.Biol., 27, 2020
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6KLX
| Pore structure of Iota toxin binding component (Ib) | Descriptor: | CALCIUM ION, Iota toxin component Ib | Authors: | Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H. | Deposit date: | 2019-07-30 | Release date: | 2020-01-15 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex. Nat.Struct.Mol.Biol., 27, 2020
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6KLO
| Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with short stem | Descriptor: | CALCIUM ION, Iota toxin component Ia, Iota toxin component Ib | Authors: | Yoshida, T, Yamada, T, Kawamoto, A, Mitsuoka, K, Iwasaki, K, Tsuge, H. | Deposit date: | 2019-07-30 | Release date: | 2020-01-15 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (2.8 Å) | Cite: | Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex. Nat.Struct.Mol.Biol., 27, 2020
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5ZJ4
| Guanine-specific ADP-ribosyltransferase | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, ADP-ribosyltransferase | Authors: | Yoshida, T, Tsuge, H. | Deposit date: | 2018-03-19 | Release date: | 2018-08-08 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.49739277 Å) | Cite: | Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP. J. Biol. Chem., 293, 2018
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5ZJ5
| Guanine-specific ADP-ribosyltransferase with NADH and GDP | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ADP-ribosyltransferase, GUANOSINE-5'-DIPHOSPHATE | Authors: | Yoshida, T, Tsuge, H. | Deposit date: | 2018-03-19 | Release date: | 2018-08-08 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.568112 Å) | Cite: | Substrate N2atom recognition mechanism in pierisin family DNA-targeting, guanine-specific ADP-ribosyltransferase ScARP. J. Biol. Chem., 293, 2018
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1AYG
| SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES | Descriptor: | CYTOCHROME C-552, HEME C | Authors: | Hasegawa, J, Yoshida, T, Yamazaki, T, Sambongi, Y, Yu, Y, Igarashi, Y, Kodama, T, Yamazaki, K, Hakusui, H, Kyogoku, Y, Kobayashi, Y. | Deposit date: | 1997-11-04 | Release date: | 1998-11-25 | Last modified: | 2022-02-16 | Method: | SOLUTION NMR | Cite: | Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy. Biochemistry, 37, 1998
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1GDH
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7W63
| Crystal structure of minor pilin TcpB from Vibrio cholerae | Descriptor: | SULFATE ION, Toxin-coregulated pilus biosynthesis protein B | Authors: | Oki, H, Kawahara, K, Iimori, M, Imoto, Y, Maruno, T, Uchiyama, S, Muroga, Y, Yoshida, A, Yoshida, T, Ohkubo, T, Matsuda, S, Iida, T, Nakamura, S. | Deposit date: | 2021-12-01 | Release date: | 2022-11-09 | Last modified: | 2022-11-16 | Method: | X-RAY DIFFRACTION (2.32 Å) | Cite: | Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor. Sci Adv, 8, 2022
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7W64
| Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with N-terminal peptide fragment of TcpF | Descriptor: | CALCIUM ION, CHLORIDE ION, PENTAETHYLENE GLYCOL, ... | Authors: | Oki, H, Kawahara, K, Iimori, M, Imoto, Y, Maruno, T, Uchiyama, S, Muroga, Y, Yoshida, A, Yoshida, T, Ohkubo, T, Matsuda, S, Iida, T, Nakamura, S. | Deposit date: | 2021-12-01 | Release date: | 2022-11-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor. Sci Adv, 8, 2022
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7W65
| Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with secreted protein TcpF | Descriptor: | Toxin coregulated pilus biosynthesis protein F, Toxin-coregulated pilus biosynthesis protein B | Authors: | Oki, H, Kawahara, K, Iimori, M, Imoto, Y, Maruno, T, Uchiyama, S, Muroga, Y, Yoshida, A, Yoshida, T, Ohkubo, T, Matsuda, S, Iida, T, Nakamura, S. | Deposit date: | 2021-12-01 | Release date: | 2022-11-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (4.05 Å) | Cite: | Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor. Sci Adv, 8, 2022
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2KTD
| Solution structure of mouse lipocalin-type prostaglandin D synthase / substrate analog (U-46619) complex | Descriptor: | (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid, Prostaglandin-H2 D-isomerase | Authors: | Shimamoto, S, Maruo, H, Yoshida, T, Kato, N, Ohkubo, T. | Deposit date: | 2010-01-27 | Release date: | 2011-02-02 | Last modified: | 2011-07-13 | Method: | SOLUTION NMR | Cite: | Solution Structure of Lipocalin-type Prostaglandin D synthase / Substrate analog complex reveals Open-Closed Conformational Change required for Substrate Recognition To be Published
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5H03
| Crystal structure of an ADP-ribosylating toxin BECa from C. perfringens | Descriptor: | Binary enterotoxin of Clostridium perfringens component a | Authors: | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | Deposit date: | 2016-10-03 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem.Biophys.Res.Commun., 480, 2016
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5H04
| Crystal structure of an ADP-ribosylating toxin BECa of a novel binary enterotoxin of C. perfringens with NADH | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Binary enterotoxin of Clostridium perfringens component a | Authors: | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | Deposit date: | 2016-10-03 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.825 Å) | Cite: | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem.Biophys.Res.Commun., 480, 2016
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2LAA
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2LAB
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1O5P
| Solution Structure of holo-Neocarzinostatin | Descriptor: | NEOCARZINOSTATIN-CHROMOPHORE, Neocarzinostatin | Authors: | Takashima, H, Ishino, T, Yoshida, T, Hasuda, K, Ohkubo, T, Kobayashi, Y. | Deposit date: | 2003-10-04 | Release date: | 2003-10-14 | Last modified: | 2023-12-27 | Method: | SOLUTION NMR | Cite: | Solution NMR Structure Investigation for Releasing Mechanism of Neocarzinostatin Chromophore from the Holoprotein J.Biol.Chem., 280, 2005
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1Q3S
| Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP) | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Thermosome alpha subunit | Authors: | Shomura, Y, Yoshida, T, Iizuka, R, Maruyama, T, Yohda, M, Miki, K. | Deposit date: | 2003-07-31 | Release date: | 2004-01-27 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. J.Mol.Biol., 335, 2004
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1Q2V
| Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form) | Descriptor: | SULFATE ION, Thermosome alpha subunit | Authors: | Shomura, Y, Yoshida, T, Iizuka, R, Yohda, M, Maruyama, T, Miki, K. | Deposit date: | 2003-07-26 | Release date: | 2004-01-27 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. J.Mol.Biol., 335, 2004
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1Q3R
| Crystal structure of the chaperonin from Thermococcus strain KS-1 (nucleotide-free form of single mutant) | Descriptor: | SULFATE ION, Thermosome alpha subunit | Authors: | Shomura, Y, Yoshida, T, Iizuka, R, Maruyama, T, Yohda, M, Miki, K. | Deposit date: | 2003-07-31 | Release date: | 2004-01-27 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. J.Mol.Biol., 335, 2004
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1Q3Q
| Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP) | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, Thermosome alpha subunit | Authors: | Shomura, Y, Yoshida, T, Iizuka, R, Maruyama, T, Yohda, M, Miki, K. | Deposit date: | 2003-07-31 | Release date: | 2004-01-27 | Last modified: | 2023-08-16 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. J.Mol.Biol., 335, 2004
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5GTT
| Crystal structure of C. perfringens iota-like enterotoxin CPILE-a | Descriptor: | 1,2-ETHANEDIOL, Binary enterotoxin of Clostridium perfringens component a | Authors: | Toniti, W, Yoshida, T, Tsurumura, T, Irikura, D, Tsuge, H. | Deposit date: | 2016-08-23 | Release date: | 2017-03-01 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.011 Å) | Cite: | Crystal structure and structure-based mutagenesis of actin-specific ADP-ribosylating toxin CPILE-a as novel enterotoxin PLoS ONE, 12, 2017
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