7VMM
 
 | | Structure of recombinant RyR2 (EGTA dataset, class 1, closed state) | | Descriptor: | Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ZINC ION | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Nat Commun, 13, 2022
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7VML
 | | Structure of recombinant RyR2 (EGTA dataset, class 1&2, closed state) | | Descriptor: | Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ZINC ION | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Nat Commun, 13, 2022
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7VMN
 | | Structure of recombinant RyR2 (EGTA dataset, class 2, closed state) | | Descriptor: | Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ZINC ION | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Nat Commun, 13, 2022
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7VMS
 | | Structure of recombinant RyR2 mutant K4593A (Ca2+ dataset) | | Descriptor: | CALCIUM ION, Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ... | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2025-07-02 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations
Nat Commun, 13, 2022
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7VMO
 | | Structure of recombinant RyR2 (Ca2+ dataset, class 1, open state) | | Descriptor: | CALCIUM ION, Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ... | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-11-13 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Nat Commun, 13, 2022
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7VMP
 | | Structure of recombinant RyR2 (Ca2+ dataset, class 2, open state) | | Descriptor: | CALCIUM ION, Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ... | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-11-06 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Nat Commun, 13, 2022
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7VMR
 | | Structure of recombinant RyR2 mutant K4593A (EGTA dataset) | | Descriptor: | Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ZINC ION | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations.
Nat Commun, 13, 2022
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7VMQ
 | | Structure of recombinant RyR2 (Ca2+ dataset, class 3, open state) | | Descriptor: | CALCIUM ION, Peptidyl-prolyl cis-trans isomerase FKBP1B, Ryanodine receptor 2, ... | | Authors: | Kobayashi, T, Tsutsumi, A, Kurebayashi, N, Kodama, M, Kikkawa, M, Murayama, T, Ogawa, H. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-10 | | Last modified: | 2024-11-13 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations
Nat Commun, 13, 2022
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1J1U
 | | Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(Tyr) and L-tyrosine | | Descriptor: | MAGNESIUM ION, TYROSINE, Tyrosyl-tRNA synthetase, ... | | Authors: | Kobayashi, T, Nureki, O, Ishitani, R, Tukalo, M, Cusack, S, Sakamoto, K, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-17 | | Release date: | 2003-06-03 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion
NAT.STRUCT.BIOL., 10, 2003
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1VBM
 | | Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS | | Descriptor: | 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE, SULFATE ION, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-02-27 | | Release date: | 2005-01-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
J.Mol.Biol., 346, 2005
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1WQ4
 | | Escherichia coli tyrosyl-tRNA synthetase mutant complexed with L-tyrosine | | Descriptor: | TYROSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Nureki, O, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-20 | | Release date: | 2005-01-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1X8X
 | | Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine | | Descriptor: | SULFATE ION, TYROSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Takimura, T, Sekine, R, Kelly, V.P, Kamata, K, Sakamoto, K, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-08-19 | | Release date: | 2005-01-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural Snapshots of the KMSKS Loop Rearrangement for Amino Acid Activation by Bacterial Tyrosyl-tRNA Synthetase
J.MOL.BIOL., 346, 2005
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1VBN
 | | Escherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS | | Descriptor: | 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-02-27 | | Release date: | 2005-01-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1WQ3
 | | Escherichia coli tyrosyl-tRNA synthetase mutant complexed with 3-iodo-L-tyrosine | | Descriptor: | 3-IODO-TYROSINE, Tyrosyl-tRNA synthetase | | Authors: | Kobayashi, T, Sakamoto, K, Nureki, O, Takimura, T, Kamata, K, Sekine, R, Nishimura, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-20 | | Release date: | 2005-01-25 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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9J3U
 | | Crystal structure of tyrosine phenol-lyase in complex with 3,5-dihydroxybenzoic acid | | Descriptor: | 3,5-DIHYDROXYBENZOATE, POTASSIUM ION, Tyrosine phenol-lyase | | Authors: | Hara, K, Kobayashi, T, Ohishi, S, Hashimoto, H, Watanabe, K, Miyoshi, N. | | Deposit date: | 2024-08-08 | | Release date: | 2025-04-23 | | Last modified: | 2025-05-07 | | Method: | X-RAY DIFFRACTION (1.83 Å) | | Cite: | 3,5-Dihydroxybenzoic Acid as a Potent Inhibitor of Tyrosine Phenol-Lyase Decreases Fecal Phenol Levels in Mice.
J.Med.Chem., 68, 2025
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5A16
 | | Crystal structure of Fab4201 raised against Human Erythrocyte Anion Exchanger 1 | | Descriptor: | FAB4201 HEAVY CHAIN | | Authors: | Arakawa, T, Kobayashi-Yugiri, T, Alguel, Y, Weyand, S, Iwanari, H, Hatae, H, Iwata, M, Abe, Y, Hino, T, Ikeda-Suno, C, Kuma, H, Kang, D, Murata, T, Hamakubo, T, Cameron, A, Kobayashi, T, Hamasaki, N, Iwata, S. | | Deposit date: | 2015-04-28 | | Release date: | 2015-06-10 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal Structure of the Anion Exchanger Domain of Human Erythrocyte Band 3
Science, 350, 2015
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5H0Q
 | | Crystal structure of lipid binding protein Nakanori at 1.5A | | Descriptor: | Lipid binding protein | | Authors: | Makino, A, Abe, M, Ishitsuka, R, Murate, M, Kishimoto, T, Sakai, S, Hullin-Matsuda, F, Shimada, Y, Inaba, T, Miyatake, H, Tanaka, H, Kurahashi, A, Pack, C.G, Kasai, R.S, Kubo, S, Schieber, N.L, Dohmae, N, Tochio, N, Hagiwara, K, Sasaki, Y, Aida, Y, Fujimori, F, Kigawa, T, Nishikori, K, Parton, R.G, Kusumi, A, Sako, Y, Anderluh, G, Yamashita, M, Kobayashi, T, Greimel, P, Kobayashi, T. | | Deposit date: | 2016-10-06 | | Release date: | 2016-10-19 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (1.501 Å) | | Cite: | A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C
FASEB J., 31, 2017
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3VG9
 | | Crystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 2.7 A resolution | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a, DODECYL-BETA-D-MALTOSIDE, ... | | Authors: | Hino, T, Arakawa, T, Iwanari, H, Yurugi-Kobayashi, T, Ikeda-Suno, C, Nakada-Nakura, Y, Kusano-Arai, O, Weyand, S, Shimamura, T, Nomura, N, Cameron, A.D, Kobayashi, T, Hamakubo, T, Iwata, S, Murata, T. | | Deposit date: | 2011-08-04 | | Release date: | 2012-02-01 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody
Nature, 482, 2012
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3VGA
 | | Crystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 3.1 A resolution | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a, antibody fab fragment heavy chain, ... | | Authors: | Hino, T, Arakawa, T, Iwanari, H, Yurugi-Kobayashi, T, Ikeda-Suno, C, Nakada-Nakura, Y, Kusano-Arai, O, Weyand, S, Shimamura, T, Nomura, N, Cameron, A.D, Kobayashi, T, Hamakubo, T, Iwata, S, Murata, T. | | Deposit date: | 2011-08-04 | | Release date: | 2012-02-01 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody
Nature, 482, 2012
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4YZF
 | | Crystal structure of the anion exchanger domain of human erythrocyte Band 3 | | Descriptor: | 2,2'-ethane-1,2-diylbis{5-[(sulfanylmethyl)amino]benzenesulfonic acid}, Band 3 anion transport protein, FAB fragment of Immunoglobulin (IgG) molecule | | Authors: | Alguel, Y, Arakawa, T, Yugiri, T.K, Iwanari, H, Hatae, H, Iwata, M, Abe, Y, Hino, T, Suno, C.I, Kuma, H, Kang, D, Murata, T, Hamakubo, T, Cameron, A.D, Kobayashi, T, Hamasaki, N, Iwata, S. | | Deposit date: | 2015-03-25 | | Release date: | 2015-11-04 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Crystal structure of the anion exchanger domain of human erythrocyte band 3.
Science, 350, 2015
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3UON
 | | Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist | | Descriptor: | (3R)-1-azabicyclo[2.2.2]oct-3-yl hydroxy(diphenyl)acetate, CHLORIDE ION, Human M2 muscarinic acetylcholine, ... | | Authors: | Haga, K, Kruse, A.C, Asada, H, Yurugi-Kobayashi, T, Shiroishi, M, Zhang, C, Weis, W.I, Okada, T, Kobilka, B.K, Haga, T, Kobayashi, T. | | Deposit date: | 2011-11-16 | | Release date: | 2012-02-01 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist.
Nature, 482, 2012
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4X8Y
 | | Crystal structure of human PGRMC1 cytochrome b5-like domain | | Descriptor: | Membrane-associated progesterone receptor component 1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nakane, T, Yamamoto, T, Shimamura, T, Kobayashi, T, Kabe, Y, Suematsu, M. | | Deposit date: | 2014-12-11 | | Release date: | 2016-03-23 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance
Nat Commun, 7, 2016
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3RZE
 | | Structure of the human histamine H1 receptor in complex with doxepin | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (3E)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine, (3Z)-3-(dibenzo[b,e]oxepin-11(6H)-ylidene)-N,N-dimethylpropan-1-amine, ... | | Authors: | Shimamura, T, Han, G.W, Shiroishi, M, Weyand, S, Tsujimoto, H, Winter, G, Katritch, V, Abagyan, R, Cherezov, V, Liu, W, Kobayashi, T, Stevens, R, Iwata, S, GPCR Network (GPCR) | | Deposit date: | 2011-05-11 | | Release date: | 2011-06-15 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | Structure of the human histamine H1 receptor complex with doxepin.
Nature, 475, 2011
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3WVG
 | | Time-Resolved Crystal Structure of HindIII with 0sec soaking | | Descriptor: | DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3'), GLYCEROL, SODIUM ION, ... | | Authors: | Kawamura, T, Kobayashi, T, Watanabe, N. | | Deposit date: | 2014-05-21 | | Release date: | 2015-04-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Acta Crystallogr.,Sect.D, 71, 2015
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3WVK
 | | Time-Resolved Crystal Structure of HindIII with 230sec soaking | | Descriptor: | DNA (5'-D(*GP*CP*CP*A)-3'), DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3'), DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3'), ... | | Authors: | Kawamura, T, Kobayashi, T, Watanabe, N. | | Deposit date: | 2014-05-22 | | Release date: | 2015-04-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Acta Crystallogr.,Sect.D, 71, 2015
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