1KFA
| Crystal structure of Fab fragment complexed with gibberellin A4 | Descriptor: | GIBBERELLIN A4, monoclonal antibody heavy chain, monoclonal antibody light chain | Authors: | Murata, T, Fushinobu, S, Nakajima, M, Asami, O, Sassa, T, Wakagi, T, Yamaguchi, I. | Deposit date: | 2001-11-20 | Release date: | 2002-09-11 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment. Biochem.Biophys.Res.Commun., 293, 2002
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1YT6
| NMR structure of peptide SD | Descriptor: | peptide SD | Authors: | Murata, T, Hemmi, H, Nakamura, S, Shimizu, K, Suzuki, Y, Yamaguchi, I. | Deposit date: | 2005-02-10 | Release date: | 2005-09-27 | Last modified: | 2022-03-02 | Method: | SOLUTION NMR | Cite: | Structure, epitope mapping, and docking simulation of a gibberellin mimic peptide as a peptidyl mimotope for a hydrophobic ligand. Febs J., 272, 2005
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2BL2
| The membrane rotor of the V-type ATPase from Enterococcus hirae | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, SODIUM ION, UNDECYL-MALTOSIDE, ... | Authors: | Murata, T, Yamato, I, Kakinuma, Y, Leslie, A.G.W, Walker, J.E. | Deposit date: | 2005-02-25 | Release date: | 2005-04-05 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure of the Rotor of the Vacuolar-Type Na- ATPase from Enterococcus Hirae Science, 308, 2005
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2CYD
| Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, LITHIUM ION, UNDECYL-MALTOSIDE, ... | Authors: | Murata, T, Yamato, I, Kakinuma, Y, Shirouzu, M, Walker, J.E, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-07-06 | Release date: | 2006-06-27 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae To be Published
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2DB4
| Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, DICYCLOHEXYLUREA, SODIUM ION, ... | Authors: | Murata, T, Yamato, I, Kakinuma, Y, Shirouzu, M, Walker, J.E, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-12-15 | Release date: | 2006-12-05 | Last modified: | 2012-05-23 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structure of the rotor ring modified with N,N'-dicyclohexylcarbodiimide of the Na+-transporting vacuolar ATPase. Proc.Natl.Acad.Sci.USA, 108, 2011
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8Y6I
| P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in nanodisc | Descriptor: | 1,2-Distearoyl-sn-glycerophosphoethanolamine, ATP-dependent translocase ABCB1,mNeonGreen, CHOLESTEROL, ... | Authors: | Hamaguchi-Suzuki, N, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Anzai, N, Senda, T, Murata, T. | Deposit date: | 2024-02-02 | Release date: | 2024-04-17 | Method: | ELECTRON MICROSCOPY (2.54 Å) | Cite: | Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Biochem.Biophys.Res.Commun., 709, 2024
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8Y6H
| P-glycoprotein in complex with UIC2 Fab and triple elacridar molecules in LMNG detergent | Descriptor: | ATP-dependent translocase ABCB1,mNeonGreen, UIC2 Fab heavy chain, UIC2 Fab light chain, ... | Authors: | Hamaguchi-Suzuki, N, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Anzai, N, Senda, T, Murata, T. | Deposit date: | 2024-02-02 | Release date: | 2024-04-17 | Method: | ELECTRON MICROSCOPY (2.49 Å) | Cite: | Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Biochem.Biophys.Res.Commun., 709, 2024
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3O0R
| Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment | Descriptor: | CALCIUM ION, FE (III) ION, HEME C, ... | Authors: | Hino, T, Matsumoto, Y, Nagano, S, Sugimoto, H, Fukumori, Y, Murata, T, Iwata, S, Shiro, Y. | Deposit date: | 2010-07-20 | Release date: | 2010-12-29 | Last modified: | 2013-10-16 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structural basis of biological N2O generation by bacterial nitric oxide reductase Science, 330, 2010
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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: | 2015-11-18 | 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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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: | 2024-01-10 | 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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5KNC
| Crystal structure of the 3 ADP-bound V1 complex | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | Deposit date: | 2016-06-28 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.015 Å) | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor Nat Commun, 7, 2016
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5KNB
| Crystal structure of the 2 ADP-bound V1 complex | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | Deposit date: | 2016-06-28 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.251 Å) | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor Nat Commun, 7, 2016
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5KND
| Crystal structure of the Pi-bound V1 complex | Descriptor: | 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GLYCEROL, MAGNESIUM ION, ... | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | Deposit date: | 2016-06-28 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.888 Å) | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor Nat Commun, 7, 2016
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7W74
| Crystal structure of DTG rhodopsin from Pseudomonas putida | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Bacteriorhodopsin-like protein, ... | Authors: | Suzuki, K, Konno, M, Bagherzadeh, R, Inoue, K, Murata, T. | Deposit date: | 2021-12-03 | Release date: | 2022-02-23 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.84 Å) | Cite: | Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography. J.Biol.Chem., 298, 2022
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7VW7
| Crystal structure of the 2 ADP-AlF4-bound V1 complex | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, MAGNESIUM ION, ... | Authors: | Suzuki, K, Shekhar, M, Gupta, C, Singharoy, A, Murata, T. | Deposit date: | 2021-11-09 | Release date: | 2022-06-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.818 Å) | Cite: | Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations. Acs Cent.Sci., 8, 2022
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6KFQ
| Crystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus | Descriptor: | RETINAL, Rhodopsin, SULFATE ION, ... | Authors: | Suzuki, K, Akiyama, T, Hayashi, T, Yasuda, S, Kanehara, K, Kojima, K, Tanabe, M, Kato, R, Senda, T, Sudo, Y, Kinoshita, M, Murata, T. | Deposit date: | 2019-07-08 | Release date: | 2020-04-08 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained? J.Phys.Chem.B, 124, 2020
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5AZD
| Crystal structure of thermophilic rhodopsin. | Descriptor: | Bacteriorhodopsin | Authors: | Mizutani, K, Hashimoto, N, Tsukamoto, T, Yamashita, K, Yamamoto, M, Sudo, Y, Murata, T. | Deposit date: | 2015-09-30 | Release date: | 2016-04-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | X-ray crystallographic structure of thermophilic rhodopsin: implications for high thermal stability and optogenetic availability. To Be Published
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6IIE
| Crystal structure of human diacylglycerol kinase alpha EF-hand domains bound to Ca2+ | Descriptor: | CALCIUM ION, Diacylglycerol kinase alpha, GLYCEROL, ... | Authors: | Takahashi, D, Suzuki, K, Sakamoto, T, Iwamoto, T, Murata, T, Sakane, F. | Deposit date: | 2018-10-04 | Release date: | 2019-02-20 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.142 Å) | Cite: | Crystal structure and calcium-induced conformational changes of diacylglycerol kinase alpha EF-hand domains. Protein Sci., 28, 2019
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5ZE9
| Crystal structure of AMP-PNP bound mutant A3B3 complex from Enterococcus hirae V-ATPase | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, GLYCEROL, MAGNESIUM ION, ... | Authors: | Maruyama, S, Suzuki, K, Sasaki, H, Mizutani, K, Saito, Y, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Ichiro, Y, Murata, T. | Deposit date: | 2018-02-27 | Release date: | 2019-02-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.102 Å) | Cite: | Metastable asymmetrical structure of a shaftless V1motor. Sci Adv, 5, 2019
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7CN0
| Cryo-EM structure of K+-bound hERG channel | Descriptor: | POTASSIUM ION, potassium channel 1 | Authors: | Asai, T, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Senda, T, Murata, T. | Deposit date: | 2020-07-29 | Release date: | 2021-01-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Cryo-EM Structure of K + -Bound hERG Channel Complexed with the Blocker Astemizole. Structure, 29, 2021
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7CN1
| Cryo-EM structure of K+-bound hERG channel in the presence of astemizole | Descriptor: | POTASSIUM ION, potassium channel | Authors: | Asai, T, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Senda, T, Murata, T. | Deposit date: | 2020-07-29 | Release date: | 2021-01-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.7 Å) | Cite: | Cryo-EM Structure of K + -Bound hERG Channel Complexed with the Blocker Astemizole. Structure, 29, 2021
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5ZEA
| Crystal structure of the nucleotide-free mutant A3B3 | Descriptor: | GLYCEROL, V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B | Authors: | Maruyama, S, Suzuki, K, Mizutani, K, Saito, Y, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Ichiro, Y, Murata, T. | Deposit date: | 2018-02-27 | Release date: | 2019-02-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.384 Å) | Cite: | Metastable asymmetrical structure of a shaftless V1motor. Sci Adv, 5, 2019
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7DNS
| Crystal structure of domain-swapped dimer of H5_Fold-0 Elsa; de novo designed protein with an asymmetric all-alpha topology | Descriptor: | GLYCEROL, de novo designed protein | Authors: | Suzuki, K, Kobayashi, N, Murata, T, Sakuma, K, Kosugi, T, Koga, R, Koga, N. | Deposit date: | 2020-12-10 | Release date: | 2021-07-28 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.327 Å) | Cite: | Design of complicated all-alpha protein structures Nat.Struct.Mol.Biol., 2024
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2ZHK
| Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer (crystal 1) | Descriptor: | Galectin-9, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Nagae, M, Nishi, N, Murata, T, Usui, T, Nakamura, T, Wakatsuki, S, Kato, R. | Deposit date: | 2008-02-06 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology, 19, 2009
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2ZHL
| Crystal structure of human galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer (crystal 2) | Descriptor: | Galectin-9, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Authors: | Nagae, M, Nishi, N, Murata, T, Usui, T, Nakamura, T, Wakatsuki, S, Kato, R. | Deposit date: | 2008-02-06 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Structural analysis of the recognition mechanism of poly-N-acetyllactosamine by the human galectin-9 N-terminal carbohydrate recognition domain. Glycobiology, 19, 2009
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