2E0Z
 
 | | Crystal structure of virus-like particle from Pyrococcus furiosus | | Descriptor: | Virus-like particle | | Authors: | Akita, F, Chong, K.T, Tanaka, H, Yamashita, E, Miyazaki, N, Nakaishi, Y, Namba, K, Ono, Y, Suzuki, M, Tsukihara, T, Nakagawa, A. | | Deposit date: | 2006-10-16 | | Release date: | 2007-04-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | The Crystal Structure of a Virus-like Particle from the Hyperthermophilic Archaeon Pyrococcus furiosus Provides Insight into the Evolution of Viruses
J.Mol.Biol., 368, 2007
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3VJJ
 | | Crystal Structure Analysis of the P9-1 | | Descriptor: | P9-1 | | Authors: | Akita, F, Higashiura, A, Suzuki, M, Tsukihara, T, Nakagawa, A, Omura, T. | | Deposit date: | 2011-10-24 | | Release date: | 2011-12-21 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus
J.Virol., 86, 2012
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6K33
 | | Structure of PSI-isiA supercomplex from Thermosynechococcus vulcanus | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Akita, F, Nagao, R, Kato, K, Shen, J.R, Miyazaki, N. | | Deposit date: | 2019-05-16 | | Release date: | 2020-05-20 | | Last modified: | 2020-05-27 | | Method: | ELECTRON MICROSCOPY (2.74 Å) | | Cite: | Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins.
Commun Biol, 3, 2020
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5ZZN
 | | Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus | | Descriptor: | (3R)-beta,beta-caroten-3-ol, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Nakajima, Y, Umena, Y, Nagao, R, Endo, K, Kobayashi, K, Akita, F, Suga, M, Wada, H, Noguchi, T, Shen, J.R. | | Deposit date: | 2018-06-03 | | Release date: | 2018-08-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.
J. Biol. Chem., 293, 2018
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4UB8
 | | Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | | Deposit date: | 2014-08-12 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015
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4UB6
 | | Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | | Deposit date: | 2014-08-12 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015
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7VD5
 | | Structure of C2S2M2-type PSII-FCPII supercomplex from diatom | | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ... | | Authors: | Nagao, R, Kato, K, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2021-09-06 | | Release date: | 2022-03-02 | | Last modified: | 2022-09-14 | | Method: | ELECTRON MICROSCOPY (2.5 Å) | | Cite: | Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Nat Commun, 13, 2022
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7VD6
 | | Structure of S1M1-type FCPII complex from diatom | | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, ... | | Authors: | Nagao, R, Kato, K, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2021-09-06 | | Release date: | 2022-03-02 | | Last modified: | 2022-09-14 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Nat Commun, 13, 2022
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7D1T
 | | Cryo-EM Structure of PSII at 1.95 angstrom resolution | | Descriptor: | (3R)-beta,beta-caroten-3-ol, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Kato, K, Miyazaki, N, Hamaguchi, T, Nakajima, Y, Akita, F, Yonekura, K, Shen, J.R. | | Deposit date: | 2020-09-15 | | Release date: | 2021-03-31 | | Last modified: | 2021-04-07 | | Method: | ELECTRON MICROSCOPY (1.95 Å) | | Cite: | High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.
Commun Biol, 4, 2021
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7D1U
 | | Cryo-EM Structure of PSII at 2.08 angstrom resolution | | Descriptor: | (3R)-beta,beta-caroten-3-ol, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Kato, K, Miyazaki, N, Hamaguchi, T, Nakajima, Y, Akita, F, Yonekura, K, Shen, J.R. | | Deposit date: | 2020-09-15 | | Release date: | 2021-03-31 | | Last modified: | 2021-04-07 | | Method: | ELECTRON MICROSCOPY (2.08 Å) | | Cite: | High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.
Commun Biol, 4, 2021
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7DR2
 | | Structure of GraFix PSI tetramer from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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7DR1
 | | Structure of Wild-type PSI monomer2 from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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7DR0
 | | Structure of Wild-type PSI monomer1 from Cyanophora paradoxa | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Akita, F, Miyazaki, N, Shen, J.R. | | Deposit date: | 2020-12-25 | | Release date: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes
Biorxiv, 2022
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7EDA
 | | Structure of monomeric photosystem II | | Descriptor: | (3R)-beta,beta-caroten-3-ol, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Yu, H, Hamaguchi, T, Nakajima, Y, Kato, K, kawakami, K, Akita, F, Yonekura, K, Shen, J.R. | | Deposit date: | 2021-03-15 | | Release date: | 2021-07-07 | | Last modified: | 2021-08-04 | | Method: | ELECTRON MICROSCOPY (2.78 Å) | | Cite: | Cryo-EM structure of monomeric photosystem II at 2.78 angstrom resolution reveals factors important for the formation of dimer.
Biochim Biophys Acta Bioenerg, 1862, 2021
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6KMX
 | | Structure of PSI from H. hongdechloris grown under far-red light condition | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Shen, J.R, Miyazaki, N, Akita, F. | | Deposit date: | 2019-08-01 | | Release date: | 2020-01-15 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (2.41 Å) | | Cite: | Structural basis for the adaptation and function of chlorophyll f in photosystem I.
Nat Commun, 11, 2020
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6KMW
 | | Structure of PSI from H. hongdechloris grown under white light condition | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Shen, J.R, Miyazaki, N, Akita, F. | | Deposit date: | 2019-08-01 | | Release date: | 2020-01-15 | | Last modified: | 2024-03-27 | | Method: | ELECTRON MICROSCOPY (2.35 Å) | | Cite: | Structural basis for the adaptation and function of chlorophyll f in photosystem I.
Nat Commun, 11, 2020
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6J3Z
 | | Structure of C2S1M1-type PSII-FCPII supercomplex from diatom | | Descriptor: | (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Nagao, R, Kato, K, Shen, J.R, Miyazaki, N, Akita, F. | | Deposit date: | 2019-01-07 | | Release date: | 2019-08-07 | | Last modified: | 2019-11-06 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.
Nat.Plants, 5, 2019
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6J3Y
 | | Structure of C2S2-type PSII-FCPII supercomplex from diatom | | Descriptor: | (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Nagao, R, Kato, K, Shen, J.R, Miyazaki, N, Akita, F. | | Deposit date: | 2019-01-07 | | Release date: | 2019-08-07 | | Last modified: | 2019-11-06 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.
Nat.Plants, 5, 2019
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6J40
 | | Structure of C2S2M2-type PSII-FCPII supercomplex from diatom | | Descriptor: | (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Nagao, R, Kato, K, Shen, J.R, Miyazaki, N, Akita, F. | | Deposit date: | 2019-01-07 | | Release date: | 2019-08-07 | | Last modified: | 2019-11-06 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.
Nat.Plants, 5, 2019
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6JEO
 | | Structure of PSI tetramer from Anabaena | | Descriptor: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | Authors: | Kato, K, Nagao, R, Shen, J.R, Miyazaki, N, Akita, F. | | Deposit date: | 2019-02-06 | | Release date: | 2019-11-13 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy.
Nat Commun, 10, 2019
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6L4T
 | | Structure of the peripheral FCPI from diatom | | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Nagao, R, Kato, K, Miyazaki, N, Akita, F, Shen, J.R. | | Deposit date: | 2019-10-21 | | Release date: | 2020-05-20 | | Method: | ELECTRON MICROSCOPY (2.6 Å) | | Cite: | Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom
Nat Commun, 2020
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6L4U
 | | Structure of the PSI-FCPI supercomplex from diatom | | Descriptor: | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, ... | | Authors: | Nagao, R, Kato, K, Miyazaki, N, Akita, F, Shen, J.R. | | Deposit date: | 2019-10-21 | | Release date: | 2020-05-20 | | Method: | ELECTRON MICROSCOPY (2.4 Å) | | Cite: | Structure of photosystem I-light-harvesting supercomplex from a red-lineage diatom
Nat Commun, 2020
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3WHO
 | | X-ray-Crystallographic Structure of an RNase Po1 Exhibiting Anti-tumor Activity | | Descriptor: | Guanyl-specific ribonuclease Po1 | | Authors: | Kobayashi, H, Katsurtani, T, Hara, Y, Motoyoshi, N, Itagaki, T, Akita, F, Higashiura, A, Yamada, Y, Suzuki, M, Inokuchi, N. | | Deposit date: | 2013-08-30 | | Release date: | 2014-07-02 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | X-ray crystallographic structure of RNase Po1 that exhibits anti-tumor activity.
Biol.Pharm.Bull., 37, 2014
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5WS5
 | | Native XFEL structure of photosystem II (preflash dark dataset) | | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Shen, J.R. | | Deposit date: | 2016-12-05 | | Release date: | 2017-03-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.
Nature, 543, 2017
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5WS6
 | | Native XFEL structure of Photosystem II (preflash two-flash dataset | | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Shen, J.R. | | Deposit date: | 2016-12-05 | | Release date: | 2017-03-15 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.
Nature, 543, 2017
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