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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1NFT
 | | OVOTRANSFERRIN, N-TERMINAL LOBE, IRON LOADED OPEN FORM | | Descriptor: | FE (III) ION, NITRILOTRIACETIC ACID, PROTEIN (OVOTRANSFERRIN), ... | | Authors: | Mizutani, K, Yamashita, H, Kurokawa, H, Mikami, B, Hirose, M. | | Deposit date: | 1999-01-07 | | Release date: | 1999-01-13 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.
J.Biol.Chem., 274, 1999
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3VM5
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1IQ7
 | | Ovotransferrin, C-Terminal Lobe, Apo Form | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Ovotransferrin, SULFATE ION | | Authors: | Mizutani, K, Muralidhara, B.K, Yamashita, H, Tabata, S, Mikami, B, Hirose, M. | | Deposit date: | 2001-07-06 | | Release date: | 2001-11-28 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Anion-mediated Fe3+ release mechanism in ovotransferrin C-lobe: a structurally identified SO4(2-) binding site and its implications for the kinetic pathway.
J.Biol.Chem., 276, 2001
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1IEJ
 | | OVOTRANSFERRIN, N-TERMINAL LOBE, HOLO FORM, AT 1.65 A RESOLUTION | | Descriptor: | CARBONATE ION, FE (III) ION, OVOTRANSFERRIN | | Authors: | Mizutani, K, Mikami, B, Hirose, M. | | Deposit date: | 2001-04-10 | | Release date: | 2001-06-20 | | Last modified: | 2017-10-04 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Domain closure mechanism in transferrins: new viewpoints about the hinge structure and motion as deduced from high resolution crystal structures of ovotransferrin N-lobe.
J.Mol.Biol., 309, 2001
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3VUP
 | | Beta-1,4-mannanase from the common sea hare Aplysia kurodai | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Beta-1,4-mannanase, SULFATE ION | | Authors: | Mizutani, K, Tsuchiya, S, Toyoda, M, Nanbu, Y, Tominaga, K, Yuasa, K, Takahashi, N, Tsuji, A, Mikami, B. | | Deposit date: | 2012-07-04 | | Release date: | 2012-10-17 | | Method: | X-RAY DIFFRACTION (1.05 Å) | | Cite: | Structure of beta-1,4-mannanase from the common sea hare Aplysia kurodai at 1.05 A resolution.
Acta Crystallogr.,Sect.F, 68, 2012
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1V9F
 | | Crystal structure of catalytic domain of pseudouridine synthase RluD from Escherichia coli | | Descriptor: | PHOSPHATE ION, Ribosomal large subunit pseudouridine synthase D | | Authors: | Mizutani, K, Machida, Y, Unzai, S, Park, S.-Y, Tame, J.R.H. | | Deposit date: | 2004-01-26 | | Release date: | 2004-05-18 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli
Biochemistry, 43, 2004
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1TFA
 | | OVOTRANSFERRIN, N-TERMINAL LOBE, APO FORM | | Descriptor: | PROTEIN (OVOTRANSFERRIN), SULFATE ION | | Authors: | Mizutani, K, Yamashita, H, Mikami, B, Hirose, M. | | Deposit date: | 1999-01-07 | | Release date: | 1999-01-13 | | Last modified: | 2018-04-04 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.
J.Biol.Chem., 274, 1999
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3ABG
 | | X-ray Crystal Analysis of Bilirubin Oxidase from Myrothecium verrucaria at 2.3 angstrom Resolution using a Twin Crystal | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Bilirubin oxidase, COPPER (II) ION, ... | | Authors: | Mizutani, K, Toyoda, M, Sagara, K, Takahashi, N, Sato, A, Kamitaka, Y, Tsujimura, S, Nakanishi, Y, Sugiura, T, Yamaguchi, S, Kano, K, Mikami, B. | | Deposit date: | 2009-12-10 | | Release date: | 2010-08-18 | | Last modified: | 2023-07-26 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | X-ray analysis of bilirubin oxidase from Myrothecium verrucaria at 2.3 A resolution using a twinned crystal
Acta Crystallogr.,Sect.F, 66, 2010
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3AOU
 | | Structure of the Na+ unbound rotor ring modified with N,N f-Dicyclohexylcarbodiimide of the Na+-transporting V-ATPase | | Descriptor: | DICYCLOHEXYLUREA, UNDECYL-MALTOSIDE, V-type sodium ATPase subunit K | | Authors: | Mizutani, K, Yamamoto, M, Yamato, I, Kakinuma, Y, Shirouzu, M, Yokoyama, S, Iwata, S, Murata, T. | | Deposit date: | 2010-10-06 | | Release date: | 2011-08-17 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (3.14 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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2D3I
 | | Crystal Structure of Aluminum-Bound Ovotransferrin at 2.15 Angstrom Resolution | | Descriptor: | ALUMINUM ION, BICARBONATE ION, Ovotransferrin | | Authors: | Mizutani, K, Mikami, B, Aibara, S, Hirose, M. | | Deposit date: | 2005-09-28 | | Release date: | 2005-11-29 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Structure of aluminium-bound ovotransferrin at 2.15 Angstroms resolution.
Acta Crystallogr.,Sect.D, 61, 2005
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7DQE
 | | Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, SULFATE ION, ... | | Authors: | Maruyama, S, Nakamoto, K, Suzuki, K, Mizutani, K, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Murata, T. | | Deposit date: | 2020-12-23 | | Release date: | 2021-12-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.694 Å) | | Cite: | The Combination of High-Speed AFM and X-ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-ATPase
To Be Published
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7DQD
 | | Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase | | Descriptor: | GLYCEROL, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | | Authors: | Maruyama, S, Suzuki, K, Mizutani, K, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Murata, T. | | Deposit date: | 2020-12-23 | | Release date: | 2021-12-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.383 Å) | | Cite: | The combination of high-speed AFM and X-ray crystallography reveals rotary catalysis
To Be Published
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7DQC
 | | Crystal structure of nucleotide-free mutant A(S23C)3B(N64C)3 complex from Enterococcus hirae V-ATPase | | Descriptor: | GLYCEROL, V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B | | Authors: | Maruyama, S, Suzuki, K, Mizutani, K, Imai, F.L, Ishizuka-Katsura, Y, Shirouzu, M, Murata, M. | | Deposit date: | 2020-12-23 | | Release date: | 2021-12-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.706 Å) | | Cite: | The combination of high-speed AFM and X-ray crystallography reveals rotary catalytic mechanism of shaftless V1-ATPase
To Be Published
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7FCI
 | | human NTCP in complex with YN69083 Fab | | Descriptor: | Fab Heavy chain, Fab Light chain, Sodium/bile acid cotransporter | | Authors: | Park, J.H, Iwamoto, M, Yun, J.H, Uchikubo-Kamo, T, Son, D, Jin, Z, Yoshida, H, Ohki, M, Ishimoto, N, Mizutani, K, Oshima, M, Muramatsu, M, Wakita, T, Shirouzu, M, Liu, K, Uemura, T, Nomura, N, Iwata, S, Watashi, K, Tame, J.R.H, Nishizawa, T, Lee, W, Park, S.Y. | | Deposit date: | 2021-07-14 | | Release date: | 2022-05-25 | | Last modified: | 2022-07-13 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural insights into the HBV receptor and bile acid transporter NTCP.
Nature, 606, 2022
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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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3VR2
 | | Crystal structure of nucleotide-free A3B3 complex from Enterococcus hirae V-ATPase [eA3B3] | | Descriptor: | V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B | | Authors: | Arai, S, Saijo, S, Suzuki, K, Mizutani, K, Kakinuma, Y, Ishizuka-Katsura, Y, Ohsawa, N, Terada, T, Shirouzu, M, Yokoyama, S, Iwata, S, Yamato, I, Murata, T. | | Deposit date: | 2012-04-03 | | Release date: | 2013-01-16 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Nature, 493, 2013
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3VR4
 | | Crystal structure of Enterococcus hirae V1-ATPase [eV1] | | Descriptor: | 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, GLYCEROL, ... | | Authors: | Saijo, S, Arai, S, Suzuki, K, Mizutani, K, Kakinuma, Y, Ishizuka-Katsura, Y, Ohsawa, N, Terada, T, Shirouzu, M, Yokoyama, S, Iwata, S, Yamato, I, Murata, T. | | Deposit date: | 2012-04-03 | | Release date: | 2013-01-16 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.172 Å) | | Cite: | Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Nature, 493, 2013
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3VR6
 | | Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1] | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, V-type sodium ATPase catalytic subunit A, ... | | Authors: | Arai, S, Saijo, S, Suzuki, K, Mizutani, K, Kakinuma, Y, Ishizuka-Katsura, Y, Ohsawa, N, Terada, T, Shirouzu, M, Yokoyama, S, Iwata, S, Yamato, I, Murata, T. | | Deposit date: | 2012-04-03 | | Release date: | 2013-01-16 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.68 Å) | | Cite: | Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Nature, 493, 2013
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3VR3
 | | Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3] | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, V-type sodium ATPase catalytic subunit A, ... | | Authors: | Arai, S, Saijo, S, Suzuki, K, Mizutani, K, Kakinuma, Y, Ishizuka-Katsura, Y, Ohsawa, N, Terada, T, Shirouzu, M, Yokoyama, S, Iwata, S, Yamato, I, Murata, T. | | Deposit date: | 2012-04-03 | | Release date: | 2013-01-16 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Nature, 493, 2013
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3VR5
 | | Crystal structure of nucleotide-free Enterococcus hirae V1-ATPase [eV1(L)] | | Descriptor: | V-type sodium ATPase catalytic subunit A, V-type sodium ATPase subunit B, V-type sodium ATPase subunit D, ... | | Authors: | Saijo, S, Arai, S, Suzuki, K, Mizutani, K, Kakinuma, Y, Ishizuka-Katsura, Y, Ohsawa, N, Terada, T, Shirouzu, M, Yokoyama, S, Iwata, S, Yamato, I, Murata, T. | | Deposit date: | 2012-04-03 | | Release date: | 2013-01-16 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (3.9 Å) | | Cite: | Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures
Nature, 493, 2013
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8XY0
 | | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR | | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, Endo-1,4-beta-xylanase A | | Authors: | Nakamura, T, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | | Deposit date: | 2024-01-19 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Sci Rep, 14, 2024
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8Y1M
 | | Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose. | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ... | | Authors: | Nakamura, T, Kuwata, K, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | | Deposit date: | 2024-01-25 | | Release date: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Sci Rep, 14, 2024
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