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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6JX3
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3WHR
| Crystal structure of gamma-glutamyltranspeptidase from Bacillus subtilis (crystal soaked for 3min. in acivicin soln. ) | Descriptor: | Gamma-glutamyltranspeptidase large chain, Gamma-glutamyltranspeptidase small chain | Authors: | Ida, T, Suzuki, H, Fukuyama, K, Hiratake, J, Wada, K. | Deposit date: | 2013-08-30 | Release date: | 2014-02-19 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.58 Å) | Cite: | Structure of Bacillus subtilis gamma-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue. Acta Crystallogr.,Sect.D, 70, 2014
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7OLG
| EB1 bound to MACF peptide | Descriptor: | 11MACF, Microtubule-associated protein RP/EB family member 1 | Authors: | Almeida, T.B, Barsukov, I.L. | Deposit date: | 2021-05-20 | Release date: | 2022-06-01 | Last modified: | 2024-06-19 | Method: | SOLUTION NMR | Cite: | EB1 bound to MACF peptide To Be Published
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8K2N
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8K2J
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8K2H
| Crystal structure of Group 2Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GalNAc-thiazoline | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Sumida, T, Fushinobu, S. | Deposit date: | 2023-07-12 | Release date: | 2024-04-24 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun, 15, 2024
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8K2K
| Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm in complex with GalNAc-thiazoline | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, CHLORIDE ION, GLYCEROL, ... | Authors: | Sumida, T, Fushinobu, S. | Deposit date: | 2023-07-12 | Release date: | 2024-04-24 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun, 15, 2024
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8K2F
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8K2I
| Crystal structure of Group 2 Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GlcNAc-thiazoline | Descriptor: | 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Sumida, T, Fushinobu, S. | Deposit date: | 2023-07-12 | Release date: | 2024-04-24 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun, 15, 2024
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8K2M
| Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaP2 from Paenibacillus sp. TS12 in complex with GalNAc-thiazoline | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, BROMIDE ION, Monosaccharide-releasing beta-N-acetylgalactosaminidase | Authors: | Sumida, T, Fushinobu, S. | Deposit date: | 2023-07-12 | Release date: | 2024-04-24 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Nat Commun, 15, 2024
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8K2L
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8K2G
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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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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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7FGJ
| The cross-reaction complex structure with VQILNK peptide and the tau antibody's Fab domain. | Descriptor: | CHLORIDE ION, Fab Heavy Chain, Fab Light Chain, ... | Authors: | Tsuchida, T, Tsuchiya, T, Miyamoto, K, In, Y, Minoura, K, Taniguchi, T, Ishida, T, Tomoo, K. | Deposit date: | 2021-07-27 | Release date: | 2022-07-27 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | The cross-reaction complex structure with VQILNK peptide and the antibody's Fab domain. To Be Published
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7FGL
| The complex structure of PHF core domain peptide of tau, VQIVYK, and antibody's Fab domain. | Descriptor: | AMMONIUM ION, Fab Heavy Chain, Fab Light Chain, ... | Authors: | Tsuchida, T, Tsuchiya, T, Miyamoto, K, In, Y, Minoura, K, Taniguchi, T, Ishida, T, Tomoo, K. | Deposit date: | 2021-07-27 | Release date: | 2022-07-27 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | The cross-reaction complex structure with VQIVYK of tau and the antibody's Fab domain. To Be Published
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7FGR
| The cross-reaction complex structure with VQIFNK peptide and the tau antibody's Fab domain. | Descriptor: | AMMONIUM ION, CHLORIDE ION, Fab Heavy Chain, ... | Authors: | Tsuchida, T, Tsuchiya, T, Miyamoto, K, In, Y, Minoura, K, Taniguchi, T, Ishida, T, Tomoo, K. | Deposit date: | 2021-07-27 | Release date: | 2022-07-27 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | The cross-reaction complex structure with VQIFNK peptide and the tau antibody's Fab domain. To Be Published
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7FGK
| The Fab antibody single structure against tau protein. | Descriptor: | Fab Heavy Chain, Fab Light Chain, GLYCEROL, ... | Authors: | Tsuchida, T, Susa, K, Kibiki, T, Tsuchiya, T, Miyamoto, K, In, Y, Minoura, K, Taniguchi, T, Ishida, T, Tomoo, K. | Deposit date: | 2021-07-27 | Release date: | 2022-07-27 | Last modified: | 2024-10-16 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | The free structure of the Fab domain of antibody that recognizes the PHF core region VQIINK in Tau protein. To Be Published
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7VTJ
| The cross-reaction complex structure with VQIIYK peptide and tau antibody's Fab domain. | Descriptor: | Heavy chain of Fab, Light chain of Fab, VQIIYK peptide | Authors: | Tsuchida, T, Fukuhara, N, Tsuchiya, T, Miyamoto, K, In, Y, Minoura, K, Taniguchi, Y, Ishida, T, Tomoo, K. | Deposit date: | 2021-10-29 | Release date: | 2022-11-02 | Last modified: | 2024-10-16 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | The cross-reaction complex structure with VQIIYK peptide and tau antibody's Fab domain. To Be Published
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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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3SUS
| Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with Gal-NAG-thiazoline | Descriptor: | (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol, Beta-hexosaminidase, SULFATE ION | Authors: | Sumida, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2011-07-11 | Release date: | 2012-06-06 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Gaining insight into the inhibition of glycoside hydrolase family 20 exo-beta-N-acetylhexosaminidases using a structural approach Org.Biomol.Chem., 10, 2012
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3SUW
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