7VEB
 
 | | Phycocyanin rod structure of cyanobacterial phycobilisome | | 分子名称: | C-phycocyanin alpha subunit, C-phycocyanin beta subunit, PHYCOCYANOBILIN, ... | | 著者 | Kawakami, K, Hamaguchi, T, Hirose, Y, Kosumi, D, Miyata, M, Kamiya, N, Yonekura, K. | | 登録日 | 2021-09-08 | | 公開日 | 2022-06-15 | | 最終更新日 | 2022-08-17 | | 実験手法 | ELECTRON MICROSCOPY (4.2 Å) | | 主引用文献 | Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Nat Commun, 13, 2022
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7VEA
 | | Pentacylindrical allophycocyanin core from Thermosynechococcus vulcanus | | 分子名称: | Allophycocyanin alpha chain, Allophycocyanin beta chain, PHYCOCYANOBILIN, ... | | 著者 | Kawakami, K, Hamaguchi, T, Hirose, Y, Kosumi, D, Miyata, M, Kamiya, N, Yonekura, K. | | 登録日 | 2021-09-08 | | 公開日 | 2022-06-22 | | 最終更新日 | 2022-08-17 | | 実験手法 | ELECTRON MICROSCOPY (3.7 Å) | | 主引用文献 | Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Nat Commun, 13, 2022
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3A0B
 | | Crystal structure of Br-substituted Photosystem II complex | | 分子名称: | (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE, ... | | 著者 | Kawakami, K, Umena, Y, Kamiya, N, Shen, J.-R. | | 登録日 | 2009-03-16 | | 公開日 | 2009-05-19 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (3.7 Å) | | 主引用文献 | Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography
Proc.Natl.Acad.Sci.USA, 106, 2009
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3A0H
 | | Crystal structure of I-substituted Photosystem II complex | | 分子名称: | (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE, ... | | 著者 | Kawakami, K, Umena, Y, Kamiya, N, Shen, J.-R. | | 登録日 | 2009-03-17 | | 公開日 | 2009-05-19 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (4 Å) | | 主引用文献 | Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography
Proc.Natl.Acad.Sci.USA, 106, 2009
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7COY
 | | Structure of the far-red light utilizing photosystem I of Acaryochloris marina | | 分子名称: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, CHLOROPHYLL D, ... | | 著者 | Kawakami, K, Yonekura, K, Hamaguchi, T, Kashino, Y, Shinzawa-Itoh, K, Inoue-Kashino, N, Itoh, S, Ifuku, K, Yamashita, E. | | 登録日 | 2020-08-05 | | 公開日 | 2021-03-31 | | 最終更新日 | 2021-05-05 | | 実験手法 | ELECTRON MICROSCOPY (2.5 Å) | | 主引用文献 | Structure of the far-red light utilizing photosystem I of Acaryochloris marina.
Nat Commun, 12, 2021
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8J5A
 | | Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A) | | 分子名称: | Ferritin heavy chain, SODIUM ION | | 著者 | Kawakami, K, Maki-Yonekura, S, Hamaguchi, T, Takaba, K, Yonekura, K. | | 登録日 | 2023-04-21 | | 公開日 | 2023-07-12 | | 最終更新日 | 2024-07-03 | | 実験手法 | ELECTRON MICROSCOPY (1.19 Å) | | 主引用文献 | Measurement of charges and chemical bonding in a cryo-EM structure.
Commun Chem, 6, 2023
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8WEY
 | | PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137) | | 分子名称: | (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R} )-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, BETA-CAROTENE, ... | | 著者 | Kato, K, Hamaguchi, T, Nakajima, Y, Kawakami, K, Yonekura, K, Shen, J.R, Nagao, R. | | 登録日 | 2023-09-19 | | 公開日 | 2024-02-14 | | 最終更新日 | 2024-03-13 | | 実験手法 | ELECTRON MICROSCOPY (1.92 Å) | | 主引用文献 | The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.
Proc.Natl.Acad.Sci.USA, 121, 2024
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5GJE
 | | Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 | | 分子名称: | 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, ... | | 著者 | Matoba, K, Mihara, E, Tamura-Kawakami, K, Hirai, H, Thompson, S, Iwasaki, K, Takagi, J. | | 登録日 | 2016-06-29 | | 公開日 | 2017-01-18 | | 最終更新日 | 2020-07-29 | | 実験手法 | ELECTRON MICROSCOPY (21 Å) | | 主引用文献 | 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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4IL6
 | | Structure of Sr-substituted photosystem II | | 分子名称: | 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, ... | | 著者 | Koua, F.H.M, Umena, Y, Kawakami, K, Kamiya, N, Shen, J.R. | | 登録日 | 2012-12-29 | | 公開日 | 2013-03-06 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation
Proc.Natl.Acad.Sci.USA, 110, 2013
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5H2F
 | | Crystal structure of the PsbM-deletion mutant of photosystem II | | 分子名称: | (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, ... | | 著者 | Uto, S, Kawakami, K, Umena, Y, Iwai, M, Ikeuchi, M, Shen, J.R, Kamiya, N. | | 登録日 | 2016-10-15 | | 公開日 | 2017-03-22 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II.
Faraday Discuss., 198, 2017
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7EDA
 | | Structure of monomeric photosystem II | | 分子名称: | (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, ... | | 著者 | Yu, H, Hamaguchi, T, Nakajima, Y, Kato, K, kawakami, K, Akita, F, Yonekura, K, Shen, J.R. | | 登録日 | 2021-03-15 | | 公開日 | 2021-07-07 | | 最終更新日 | 2021-08-04 | | 実験手法 | ELECTRON MICROSCOPY (2.78 Å) | | 主引用文献 | 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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7F4V
 | | Cryo-EM structure of a primordial cyanobacterial photosystem I | | 分子名称: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | 著者 | Kato, K, Hamaguchi, T, Nagao, R, Kawakami, K, Yonekura, K, Shen, J.R. | | 登録日 | 2021-06-21 | | 公開日 | 2022-04-06 | | 実験手法 | ELECTRON MICROSCOPY (2.04 Å) | | 主引用文献 | Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI
Biorxiv, 2022
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3WKL
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3WKM
 | | The periplasmic PDZ tandem fragment of the RseP homologue from Aquifex aeolicus in complex with the Fab fragment | | 分子名称: | MOUSE IGG1-KAPPA FAB (HEAVY CHAIN), MOUSE IGG1-KAPPA FAB (LIGHT CHAIN), Putative zinc metalloprotease aq_1964 | | 著者 | Nogi, T, Tabata, S, Tamura-kawakami, K, Takagi, J. | | 登録日 | 2013-10-28 | | 公開日 | 2013-12-18 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | A Structure-Based Model of Substrate Discrimination by a Noncanonical PDZ Tandem in the Intramembrane-Cleaving Protease RseP
Structure, 22, 2013
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3WU2
 | | Crystal structure analysis of Photosystem II complex | | 分子名称: | (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, ... | | 著者 | Umena, Y, Kawakami, K, Shen, J.R, Kamiya, N. | | 登録日 | 2014-04-21 | | 公開日 | 2014-09-03 | | 最終更新日 | 2020-07-29 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A
Nature, 473, 2011
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7Y3F
 | | Structure of the Anabaena PSI-monomer-IsiA supercomplex | | 分子名称: | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, BETA-CAROTENE, ... | | 著者 | Nagao, R, Kato, K, Hamaguchi, T, Kawakami, K, Yonekura, K, Shen, J.R. | | 登録日 | 2022-06-10 | | 公開日 | 2023-03-01 | | 最終更新日 | 2024-05-08 | | 実験手法 | ELECTRON MICROSCOPY (2.62 Å) | | 主引用文献 | Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120.
Nat Commun, 14, 2023
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3Q3K
 | | Factor Xa in complex with a phenylenediamine derivative | | 分子名称: | Activated factor Xa heavy chain, CALCIUM ION, Factor X light chain, ... | | 著者 | Suzuki, M, Imai, E. | | 登録日 | 2010-12-22 | | 公開日 | 2011-12-28 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Design, synthesis and SAR of novel ethylenediamine and phenylenediamine derivatives as factor Xa inhibitors.
Bioorg.Med.Chem.Lett., 21, 2011
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6LZ9
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8IC0
 | | Cryo-EM structure of CXCL8 bound C-X-C chemokine receptor 1 in complex with Gi heterotrimer | | 分子名称: | C-X-C chemokine receptor type 1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... | | 著者 | Ishimoto, N, Park, J.H, Park, S.Y. | | 登録日 | 2023-02-10 | | 公開日 | 2023-07-19 | | 実験手法 | ELECTRON MICROSCOPY (3.41 Å) | | 主引用文献 | Structural basis of CXC chemokine receptor 1 ligand binding and activation.
Nat Commun, 14, 2023
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3T1F
 | | Crystal structure of the mouse CD1d-Glc-DAG-s2 complex | | 分子名称: | (2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | 著者 | Girardi, E, Zajonc, D.M. | | 登録日 | 2011-07-21 | | 公開日 | 2011-09-21 | | 最終更新日 | 2020-07-29 | | 実験手法 | X-RAY DIFFRACTION (1.7 Å) | | 主引用文献 | Invariant natural killer T cells recognize glycolipids from pathogenic Gram-positive bacteria.
Nat.Immunol., 12, 2011
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5V2C
 | | RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX | | 分子名称: | 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, ... | | 著者 | Wang, J, Wiwczar, J.M, Brudvig, G.W. | | 登録日 | 2017-03-03 | | 公開日 | 2017-08-30 | | 最終更新日 | 2023-10-04 | | 実験手法 | X-RAY DIFFRACTION (1.9 Å) | | 主引用文献 | Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria.
Photosyn. Res., 134, 2017
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4YUU
 | | Crystal structure of oxygen-evolving photosystem II from a red alga | | 分子名称: | 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, ... | | 著者 | Ago, H, Shen, J.-R. | | 登録日 | 2015-03-19 | | 公開日 | 2016-01-20 | | 最終更新日 | 2020-02-05 | | 実験手法 | X-RAY DIFFRACTION (2.7700038 Å) | | 主引用文献 | Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga
J.Biol.Chem., 291, 2016
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8GW8
 | | the human PTH1 receptor bound to an intracellular biased agonist | | 分子名称: | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, ... | | 著者 | Kobayashi, K, Kusakizako, T, Okamoto, H.H, Nureki, O. | | 登録日 | 2022-09-16 | | 公開日 | 2023-06-14 | | 最終更新日 | 2023-09-27 | | 実験手法 | ELECTRON MICROSCOPY (2.9 Å) | | 主引用文献 | Class B1 GPCR activation by an intracellular agonist.
Nature, 618, 2023
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5XCX
 | | Crystal structure of TS2/16 Fv-clasp fragment | | 分子名称: | 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID, GLYCEROL, PHOSPHATE ION, ... | | 著者 | Arimori, T, Takagi, J. | | 登録日 | 2017-03-23 | | 公開日 | 2017-10-04 | | 最終更新日 | 2017-10-18 | | 実験手法 | X-RAY DIFFRACTION (2.04 Å) | | 主引用文献 | Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability
Structure, 25, 2017
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5XCQ
 | | Crystal structure of P20.1 Fv-clasp fragment with its antigen peptide | | 分子名称: | C8 peptide, SULFATE ION, VH-SARAH(Y35C)chimera, ... | | 著者 | Arimori, T, Takagi, J. | | 登録日 | 2017-03-23 | | 公開日 | 2017-10-04 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.313 Å) | | 主引用文献 | Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability
Structure, 25, 2017
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