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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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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7WMP
| Tail structure of Helicobacter pylori bacteriophage KHP30 | Descriptor: | Adaptor protein gp12, Nozzle protein gp25, Portal protein | Authors: | Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N. | Deposit date: | 2022-01-15 | Release date: | 2023-03-01 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Cryo-EM structure of Helicobacter pylori bacteriophage KHP30 To Be Published
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7X30
| Capsid structure of Staphylococcus jumbo bacteriophage S6 | Descriptor: | Hoc-like protein ORF90, Major structural protein ORF12 | Authors: | Koibuchi, W, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N. | Deposit date: | 2022-02-27 | Release date: | 2023-12-06 | Method: | ELECTRON MICROSCOPY (3.6 Å) | Cite: | Capsid structure of Staphylococcus jumbo bacteriophage S6 To Be Published
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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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1UF2
| The Atomic Structure of Rice dwarf Virus (RDV) | Descriptor: | Core protein P3, Outer capsid protein P8, Structural protein P7 | Authors: | Nakagawa, A, Miyazaki, N, Taka, J, Naitow, H, Ogawa, A, Fujimoto, Z, Mizuno, H, Higashi, T, Watanabe, Y, Omura, T, Cheng, R.H, Tsukihara, T. | Deposit date: | 2003-05-23 | Release date: | 2003-10-14 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (3.5 Å) | Cite: | The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure, 11, 2003
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6IUK
| Cryo-EM structure of Murine Norovirus capsid | Descriptor: | Major capsid protein VP1 | Authors: | Song, C, Miyazaki, N, Iwasaki, K, Katayama, K, Murata, K. | Deposit date: | 2018-11-28 | Release date: | 2020-02-26 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.5 Å) | Cite: | Dynamic rotation of the protruding domain enhances the infectivity of norovirus. Plos Pathog., 16, 2020
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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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6JO6
| Structure of the green algal photosystem I supercomplex with light-harvesting complex I | Descriptor: | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Miyazaki, N, Takahashi, Y. | Deposit date: | 2019-03-20 | Release date: | 2019-06-19 | Last modified: | 2019-06-26 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I. Nat.Plants, 5, 2019
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6JO5
| Structure of the green algal photosystem I supercomplex with light-harvesting complex I | Descriptor: | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | Authors: | Suga, M, Miyazaki, N, Takahashi, Y. | Deposit date: | 2019-03-20 | Release date: | 2019-06-19 | Last modified: | 2019-06-26 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I. Nat.Plants, 5, 2019
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6KNC
| PolD-PCNA-DNA (form B) | Descriptor: | DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ... | Authors: | Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y. | Deposit date: | 2019-08-05 | Release date: | 2020-08-05 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (9.3 Å) | Cite: | Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. Bmc Biol., 18, 2020
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6KNB
| PolD-PCNA-DNA (form A) | Descriptor: | DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ... | Authors: | Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y. | Deposit date: | 2019-08-05 | Release date: | 2020-08-05 | Last modified: | 2021-02-17 | Method: | ELECTRON MICROSCOPY (6.9 Å) | Cite: | Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. Bmc Biol., 18, 2020
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6LXV
| Cryo-EM structure of phosphoketolase from Bifidobacterium longum | Descriptor: | CALCIUM ION, Phosphoketolase, THIAMINE DIPHOSPHATE | Authors: | Nakata, K, Miyazaki, N, Yamaguchi, H, Hirose, M, Miyano, H, Mizukoshi, T, Kashiwagi, T, Iwasaki, K. | Deposit date: | 2020-02-12 | Release date: | 2021-02-17 | Last modified: | 2022-10-12 | Method: | ELECTRON MICROSCOPY (2.1 Å) | Cite: | High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis. J.Struct.Biol., 214, 2022
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3VKF
| Crystal Structure of Neurexin 1beta/Neuroligin 1 complex | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Neurexin-1-beta, ... | Authors: | Tanaka, H, Miyazaki, N, Nogi, T, Iwasaki, K, Takagi, J. | Deposit date: | 2011-11-15 | Release date: | 2012-08-01 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (3.3 Å) | Cite: | Higher-order architecture of cell adhesion mediated by polymorphic synaptic adhesion molecules neurexin and neuroligin. Cell Rep, 2, 2012
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5GJE
| Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Matoba, K, Mihara, E, Tamura-Kawakami, K, Hirai, H, Thompson, S, Iwasaki, K, Takagi, J. | Deposit date: | 2016-06-29 | Release date: | 2017-01-18 | Last modified: | 2020-07-29 | Method: | ELECTRON MICROSCOPY (21 Å) | Cite: | Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1 Cell Rep, 18, 2017
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5YKZ
| The crystal structure of Penaeus vannamei nodavirus P-domain (P21) | Descriptor: | Capsid protein | Authors: | Chen, N.C, Yoshimura, M, Lin, C.C, Guan, H.H, Chuankhayan, P, Chen, C.J. | Deposit date: | 2017-10-16 | Release date: | 2018-10-24 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.17 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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5YKV
| The crystal structure of Macrobrachium rosenbergii nodavirus P-domain | Descriptor: | Capsid protein | Authors: | Chen, N.C, Yoshimura, M, Lin, C.C, Guan, H.H, Chuankhayan, P, Chen, C.J. | Deposit date: | 2017-10-16 | Release date: | 2018-10-24 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.31 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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5YKU
| The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Zn ions | Descriptor: | Capsid protein, ZINC ION | Authors: | Chen, N.C, Yoshimura, M, Lin, C.C, Guan, H.H, Chuankhayan, P, Chen, C.J. | Deposit date: | 2017-10-16 | Release date: | 2018-10-24 | Last modified: | 2019-03-13 | Method: | X-RAY DIFFRACTION (1.39 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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5YL1
| T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368) | Descriptor: | CALCIUM ION, Capsid protein | Authors: | Chen, N.C, Yoshimura, M, Lin, C.C, Guan, H.H, Chuankhayan, P, Chen, C.J. | Deposit date: | 2017-10-16 | Release date: | 2018-12-12 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (3.12 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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7CEA
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7CEB
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2ZTN
| Hepatitis E virus ORF2 (Genotype 3) | Descriptor: | Capsid protein | Authors: | Yamashita, T, Unno, H, Mori, Y, Li, T.C, Takeda, N, Matsuura, Y. | Deposit date: | 2008-10-08 | Release date: | 2009-08-25 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.56 Å) | Cite: | Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure Proc.Natl.Acad.Sci.USA, 106, 2009
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5YL0
| The crystal structure of Penaeus vannamei nodavirus P-domain (P212121) | Descriptor: | Capsid protein | Authors: | Chen, N.C, Yoshimura, M, Lin, C.C, Guan, H.H, Chuankhayan, P, Chen, C.J. | Deposit date: | 2017-10-16 | Release date: | 2018-10-24 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.22 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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5YKX
| The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CADMIUM ION, Capsid protein, ... | Authors: | Chen, N.C, Yoshimura, M, Lin, C.C, Guan, H.H, Chuankhayan, P, Chen, C.J. | Deposit date: | 2017-10-16 | Release date: | 2018-10-24 | Last modified: | 2019-03-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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