7CCS
 
 | | Consensus mutated xCT-CD98hc complex | | Descriptor: | 4F2 cell-surface antigen heavy chain, Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System | | Authors: | Oda, K, Lee, Y, Takemoto, M, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2020-06-17 | | Release date: | 2020-12-09 | | Last modified: | 2020-12-16 | | Method: | ELECTRON MICROSCOPY (6.2 Å) | | Cite: | Consensus mutagenesis approach improves the thermal stability of system x c - transporter, xCT, and enables cryo-EM analyses.
Protein Sci., 29, 2020
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3QHN
 | | Crystal analysis of the complex structure, E201A-cellotetraose, of endocellulase from pyrococcus horikoshii | | Descriptor: | 458aa long hypothetical endo-1,4-beta-glucanase, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose | | Authors: | Kim, H.-W, Ishikawa, K. | | Deposit date: | 2011-01-26 | | Release date: | 2012-02-01 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Functional analysis of hyperthermophilic endocellulase from Pyrococcus horikoshii by crystallographic snapshots
Biochem.J., 437, 2011
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6IK5
 | | Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with galactose | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-galactosidase, ... | | Authors: | Matsuyama, K, Nakae, S, Igarashi, K, Tada, T, Ishimaru, M. | | Deposit date: | 2018-10-15 | | Release date: | 2018-11-28 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Substrate-recognition mechanism of tomato beta-galactosidase 4 using X-ray crystallography and docking simulation.
Planta, 252, 2020
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1LKJ
 | | NMR Structure of Apo Calmodulin from Yeast Saccharomyces cerevisiae | | Descriptor: | Calmodulin | | Authors: | Ishida, H, Nakashima, K, Kumaki, Y, Nakata, M, Hikichi, K, Yazawa, M. | | Deposit date: | 2002-04-25 | | Release date: | 2003-04-29 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | The solution structure of apocalmodulin from Saccharomyces cerevisiae implies a mechanism for its unique Ca2+ binding property.
Biochemistry, 41, 2002
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7FBH
 | | geranyl pyrophosphate C6-methyltransferase BezA | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BezA, ... | | Authors: | Tsutsumi, H, Moriwaki, Y, Terada, T, Shimizu, K, Katsuyama, Y, Ohnishi, Y. | | Deposit date: | 2021-07-10 | | Release date: | 2021-12-01 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase.
Angew.Chem.Int.Ed.Engl., 61, 2022
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7FBO
 | | geranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, BezA, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Tsutsumi, H, Moriwaki, Y, Terada, T, Shimizu, K, Katsuyama, Y, Ohnishi, Y. | | Deposit date: | 2021-07-12 | | Release date: | 2021-12-01 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase.
Angew.Chem.Int.Ed.Engl., 61, 2022
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7CBD
 | | Catalytic domain of Cellulomonas fimi Cel6B | | Descriptor: | Exoglucanase A | | Authors: | Nakamura, A, Ishiwata, D, Visootsat, A, Uchiyama, T, Mizutani, K, Kaneko, S, Murata, T, Igarashi, K, Iino, R. | | Deposit date: | 2020-06-12 | | Release date: | 2020-08-26 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases.
J.Biol.Chem., 295, 2020
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6IJE
 | | Crystal structure of the type VI amidase immunity (Tai4) from Agrobacterium tumefaciens | | Descriptor: | 1,2-ETHANEDIOL, Tai4 | | Authors: | Fukuhara, S, Nakane, T, Yamashita, K, Ishii, R, Ishitani, R, Nureki, O. | | Deposit date: | 2018-10-09 | | Release date: | 2018-12-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.
Acta Crystallogr F Struct Biol Commun, 74, 2018
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1ISE
 | | Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly | | Descriptor: | Ribosome Recycling Factor | | Authors: | Nakano, H, Yoshida, T, Oka, S, Uchiyama, S, Nishina, K, Ohkubo, T, Kato, H, Yamagata, Y, Kobayashi, Y. | | Deposit date: | 2001-11-30 | | Release date: | 2003-10-07 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly
To be Published
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8W7N
 | | Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis | | Descriptor: | Pesticidal crystal protein Cry1Aa, UNKNOWN ATOM OR ION | | Authors: | Tanaka, J, Abe, S, Hayakawa, T, Kojima, M, Yamashita, K, Hirata, K, Ueno, T. | | Deposit date: | 2023-08-31 | | Release date: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis.
Biochem.Biophys.Res.Commun., 685, 2023
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8WY1
 | | The structure of cyclization domain in cyclic beta-1,2-glucan synthase from Thermoanaerobacter italicus | | Descriptor: | Glycosyltransferase 36 | | Authors: | Tanaka, N, Saito, R, Kobayashi, K, Nakai, H, Kamo, S, Kuramochi, K, Taguchi, H, Nakajima, M, Masaike, T. | | Deposit date: | 2023-10-30 | | Release date: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (3.9 Å) | | Cite: | Functional and structural analysis of a cyclization domain in a cyclic beta-1,2-glucan synthase.
Appl.Microbiol.Biotechnol., 108, 2024
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8H87
 | | Cryo-EM structure of the potassium-selective channelrhodopsin HcKCR2 in lipid nanodisc | | Descriptor: | (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, HcKCR2, PALMITIC ACID, ... | | Authors: | Tajima, S, Kim, Y, Yamashita, K, Fukuda, M, Deisseroth, K, Kato, H.E. | | Deposit date: | 2022-10-21 | | Release date: | 2023-09-06 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (2.53 Å) | | Cite: | Structural basis for ion selectivity in potassium-selective channelrhodopsins.
Cell, 186, 2023
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8H86
 | | Cryo-EM structure of the potassium-selective channelrhodopsin HcKCR1 in lipid nanodisc | | Descriptor: | (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, HcKCR1, PALMITIC ACID, ... | | Authors: | Tajima, S, Kim, Y, Yamashita, K, Fukuda, M, Deisseroth, K, Kato, H.E. | | Deposit date: | 2022-10-21 | | Release date: | 2023-09-06 | | Last modified: | 2024-10-23 | | Method: | ELECTRON MICROSCOPY (2.56 Å) | | Cite: | Structural basis for ion selectivity in potassium-selective channelrhodopsins.
Cell, 186, 2023
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8IU0
 | | Cryo-EM structure of the potassium-selective channelrhodopsin HcKCR1 H225F mutant in lipid nanodisc | | Descriptor: | (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, HcKCR1, PALMITIC ACID, ... | | Authors: | Tajima, S, Kim, Y, Nakamura, S, Yamashita, K, Fukuda, M, Deisseroth, K, Kato, H.E. | | Deposit date: | 2023-03-23 | | Release date: | 2023-09-06 | | Last modified: | 2024-05-01 | | Method: | ELECTRON MICROSCOPY (2.66 Å) | | Cite: | Structural basis for ion selectivity in potassium-selective channelrhodopsins.
Cell, 186, 2023
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6IJF
 | | Crystal structure of the type VI effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens | | Descriptor: | PENTAETHYLENE GLYCOL, SULFATE ION, Tae4, ... | | Authors: | Fukuhara, S, Nakane, T, Yamashita, K, Ishii, R, Ishitani, R, Nureki, O. | | Deposit date: | 2018-10-09 | | Release date: | 2018-12-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.
Acta Crystallogr F Struct Biol Commun, 74, 2018
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3A57
 | | Crystal structure of Thermostable Direct Hemolysin | | Descriptor: | Thermostable direct hemolysin 2 | | Authors: | Hashimoto, H, Yanagihara, I, Nakahira, K, Hamada, D, Ikegami, T, Mayanagi, K, Kaieda, S, Fukui, T, Ohnishi, K, Kajiyama, S, Yamane, T, Ikeguchi, M, Honda, T, Shimizu, T, Sato, M. | | Deposit date: | 2009-08-03 | | Release date: | 2010-03-31 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin
J.Biol.Chem., 285, 2010
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5GX3
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 6.9 MGy (6th measurement) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | Authors: | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | Deposit date: | 2016-09-15 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX5
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 26 MGy (23rd measurement) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | Authors: | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | Deposit date: | 2016-09-15 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX2
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 3.4 MGy (3rd measurement) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | Authors: | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | Deposit date: | 2016-09-15 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GX1
 | | Luciferin-regenerating enzyme collected with serial synchrotron rotational crystallography with accumulated dose of 1.1 MGy (1st measurement) | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ... | | Authors: | Hasegawa, K, Yamashita, K, Murai, T, Nuemket, N, Hirata, K, Ueno, G, Ago, H, Nakatsu, T, Kumasaka, T, Yamamoto, M. | | Deposit date: | 2016-09-15 | | Release date: | 2017-01-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography
J Synchrotron Radiat, 24, 2017
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5GQI
 | | Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala194 | | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | | Deposit date: | 2016-08-07 | | Release date: | 2017-02-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
ACS Nano, 11, 2017
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5GQL
 | | Crystal structure of Wild Type Cypovirus Polyhedra | | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... | | Authors: | Abe, S, Tabe, H, Ijiri, H, Yamashita, K, Hirata, K, Mori, H, Ueno, T. | | Deposit date: | 2016-08-07 | | Release date: | 2017-02-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells
ACS Nano, 11, 2017
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7VPK
 | | Cryo-EM structure of the human ATP13A2 (SPM-bound E2P state) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BERYLLIUM TRIFLUORIDE ION, MAGNESIUM ION, ... | | Authors: | Tomita, A, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-10-17 | | Release date: | 2021-12-29 | | Last modified: | 2024-10-16 | | Method: | ELECTRON MICROSCOPY (3.92 Å) | | Cite: | Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2.
Mol.Cell, 81, 2021
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7VPI
 | | Cryo-EM structure of the human ATP13A2 (E1-ATP state) | | Descriptor: | MAGNESIUM ION, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, Polyamine-transporting ATPase 13A2 | | Authors: | Tomita, A, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-10-17 | | Release date: | 2021-12-29 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2.
Mol.Cell, 81, 2021
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7VPL
 | | Cryo-EM structure of the human ATP13A2 (SPM-bound E2Pi state) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, MAGNESIUM ION, Polyamine-transporting ATPase 13A2, ... | | Authors: | Tomita, A, Yamashita, K, Nishizawa, T, Nureki, O. | | Deposit date: | 2021-10-17 | | Release date: | 2021-12-29 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Cryo-EM reveals mechanistic insights into lipid-facilitated polyamine export by human ATP13A2.
Mol.Cell, 81, 2021
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