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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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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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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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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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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6AB5
| Cryo-EM structure of T=1 Penaeus vannamei nodavirus | Descriptor: | Capsid protein | Authors: | Chen, N.C, Miyazaki, N, Yoshimura, M, Guan, H.H, Lin, C.C, Iwasaki, K, Chen, C.J. | Deposit date: | 2018-07-20 | Release date: | 2019-03-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.7 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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6AB6
| Cryo-EM structure of T=3 Penaeus vannamei nodavirus | Descriptor: | CALCIUM ION, Capsid protein | Authors: | Chen, N.C, Miyazaki, N, Yoshimura, M, Guan, H.H, Lin, C.C, Iwasaki, K, Chen, C.J. | Deposit date: | 2018-07-20 | Release date: | 2019-03-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.5 Å) | Cite: | The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism. Commun Biol, 2, 2019
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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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7DOU
| Trimeric cement protein structure of Helicobacter pylori bacteriophage KHP40 | Descriptor: | Cement protein gp16 | Authors: | Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N. | Deposit date: | 2020-12-17 | Release date: | 2021-10-27 | Last modified: | 2022-02-23 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy. Structure, 30, 2022
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7DN2
| Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30 | Descriptor: | Cement protein gp15, Major structural protein ORF14 | Authors: | Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N. | Deposit date: | 2020-12-08 | Release date: | 2021-10-27 | Last modified: | 2022-02-23 | Method: | ELECTRON MICROSCOPY (2.7 Å) | Cite: | Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy. Structure, 30, 2022
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7F2P
| The head structure of Helicobacter pylori bacteriophage KHP40 | Descriptor: | Cement protein gp16, KHP40 MCP | Authors: | Kamiya, R, Uchiyama, J, Matsuzaki, S, Murata, K, Iwasaki, K, Miyazaki, N. | Deposit date: | 2021-06-13 | Release date: | 2021-10-27 | Last modified: | 2022-02-23 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy. Structure, 30, 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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7CEA
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7CEB
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6IKN
| Crystal structure of the GAS7 F-BAR domain | Descriptor: | Growth arrest-specific protein 7 | Authors: | Hanawa-Suetsugu, K, Itoh, Y, Kohda, D, Shimada, A, Suetsugu, S. | Deposit date: | 2018-10-16 | Release date: | 2019-10-16 | Last modified: | 2019-10-30 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7. Nat Commun, 10, 2019
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6IKO
| Crystal structure of mouse GAS7cb | Descriptor: | Growth arrest-specific protein 7 | Authors: | Hanawa-Suetsugu, K, Itoh, Y, Kohda, D, Shimada, A, Suetsugu, S. | Deposit date: | 2018-10-16 | Release date: | 2019-10-16 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.756 Å) | Cite: | Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7. Nat Commun, 10, 2019
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6IOL
| Cryo-EM structure of multidrug efflux pump MexAB-OprM (60 degree state) | Descriptor: | Multidrug resistance protein MexA, Multidrug resistance protein MexB, Outer membrane protein OprM | Authors: | Tsutsumi, K, Yonehara, R, Nakagawa, A, Yamashita, E. | Deposit date: | 2018-10-30 | Release date: | 2019-04-03 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.76 Å) | Cite: | Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism. Nat Commun, 10, 2019
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6IOK
| Cryo-EM structure of multidrug efflux pump MexAB-OprM (0 degree state) | Descriptor: | Multidrug resistance protein MexA, Multidrug resistance protein MexB, Outer membrane protein OprM | Authors: | Tsutsumi, K, Yonehara, R, Nakagawa, A, Yamashita, E. | Deposit date: | 2018-10-30 | Release date: | 2019-04-03 | Last modified: | 2019-04-17 | Method: | ELECTRON MICROSCOPY (3.64 Å) | Cite: | Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism. Nat Commun, 10, 2019
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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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