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新型コロナウイルスの構造情報

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コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症(Novel Coronavirus disease 2019: COVID-19)の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)を理解し有効な薬を開発するため,関連するタンパク質の構造研究は既に始まっています。そして,解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため,新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは,同じ著者によるグループ登録のエントリーも全て区別し,すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており,アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは,今週公開された最も新しいエントリーです。


作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
8HHZ
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BU of 8hhz by Molmil
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
分子名称: IY-2A Fab heavy chain, IY-2A Fab light chain, Spike glycoprotein
著者Chen, X, Mohapatra, A, Wu, Y.-M.
登録日2022-11-17
公開日2023-02-01
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (4.28 Å)
主引用文献Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
7TPK
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BU of 7tpk by Molmil
SARS-CoV-2 E406W mutant RBD - Local Refinement
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1
著者Addetia, A, Veesler, D.
登録日2022-01-25
公開日2023-02-08
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献SARS-CoV-2 E406W mutant RBD - Local Refinement
To Be Published
7XWX
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BU of 7xwx by Molmil
Crystal structure of SARS-CoV-2 N-CTD
分子名称: Nucleoprotein, PHOSPHATE ION
著者Luan, X.D, Li, X.M, Li, Y.F.
登録日2022-05-27
公開日2023-02-08
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Sci Bull (Beijing), 67, 2022
7XWZ
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BU of 7xwz by Molmil
Crystal structure of SARS-CoV-2 N-NTD and dsRNA complex
分子名称: 1,2-ETHANEDIOL, GLYCEROL, Nucleoprotein, ...
著者Luan, X.D, Li, X.M, Li, Y.F.
登録日2022-05-27
公開日2023-02-08
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Sci Bull (Beijing), 67, 2022
7XX1
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BU of 7xx1 by Molmil
Crystal structure of SARS-CoV-2 N-NTD
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Nucleoprotein, ZINC ION
著者Luan, X.D, Li, X.M, Li, Y.F.
登録日2022-05-27
公開日2023-02-08
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Sci Bull (Beijing), 67, 2022
7YUE
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BU of 7yue by Molmil
Epitope-directed anti-SARS CoV 2 scFv engineered against the key spike protein region.
分子名称: Single chain variable Fragment, Spike protein S2
著者Kumar, U, Jaiswal, D, Gaur, V, Salunke, D.M.
登録日2022-08-17
公開日2023-02-08
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion.
Protein Sci., 32, 2023
8DM5
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BU of 8dm5 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with human ACE2
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, Processed angiotensin-converting enzyme 2, ...
著者Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
登録日2022-07-08
公開日2023-02-08
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.51 Å)
主引用文献Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023
8DM7
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BU of 8dm7 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2
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, Angiotensin-converting enzyme 2, ...
著者Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
登録日2022-07-08
公開日2023-02-08
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (2.49 Å)
主引用文献Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023
8DM9
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BU of 8dm9 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2
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, Angiotensin-converting enzyme 2, ...
著者Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
登録日2022-07-08
公開日2023-02-08
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.56 Å)
主引用文献Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023
8DQU
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BU of 8dqu by Molmil
Nanobody bound SARS-CoV-2 Nsp9
分子名称: Nanobody, Non-structural protein 9
著者Littler, D.R, Gully, B.S, Rossjohn, J.
登録日2022-07-20
公開日2023-02-08
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.45003185971 Å)
主引用文献Inside-out: Antibody-binding reveals potential folding hinge-points within the SARS-CoV-2 replication co-factor nsp9.
Plos One, 18, 2023
8EQJ
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BU of 8eqj by Molmil
Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like membrane environment, MSP1D1 nanodisc
分子名称: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, ORF3a protein
著者Miller, A.N, Houlihan, P.R, Matamala, E, Cabezas-Bratesco, D, Lee, G.Y, Cristofori-Armstrong, B, Dilan, T.L, Sanchez-Martinez, S, Matthies, D, Yan, R, Yu, Z, Ren, D, Brauchi, S.E, Clapham, D.E.
登録日2022-10-07
公開日2023-02-08
最終更新日2024-06-19
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins.
Elife, 12, 2023
8EQU
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BU of 8equ by Molmil
Structure of SARS-CoV-2 Orf3a in late endosome/lysosome-like environment, Saposin A nanodisc
分子名称: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, ORF3a protein, Saposin A, ...
著者Miller, A.N, Houlihan, P.R, Matamala, E, Cabezas-Bratesco, D, Lee, G.Y, Cristofori-Armstrong, B, Dilan, T.L, Sanchez-Martinez, S, Matthies, D, Yan, R, Yu, Z, Ren, D, Brauchi, S.E, Clapham, D.E.
登録日2022-10-09
公開日2023-02-08
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins.
Elife, 12, 2023
7WWI
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BU of 7wwi by Molmil
SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab in the class 1 conformation
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, 55A8 heavy chain, ...
著者Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
登録日2022-02-13
公開日2023-02-15
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab in the class 1 conformation
To Be Published
7WWK
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BU of 7wwk by Molmil
Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab
分子名称: 55A8 light chain, Spike glycoprotein
著者Guo, H, Gao, Y, Lu, Y, Yang, H, Ji, X.
登録日2022-02-13
公開日2023-02-15
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab
To Be Published
7Y7J
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BU of 7y7j by Molmil
SARS-CoV-2 S trimer in complex with 1F Fab
分子名称: 1F VH, 1F VL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhao, S, Liu, F, Yang, X, Zhong, G.
登録日2022-06-22
公開日2023-02-22
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献A core epitope targeting antibody of SARS-CoV-2.
Protein Cell, 14, 2023
7Y7K
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BU of 7y7k by Molmil
SARS-CoV-2 RBD in complex with 1F Fab
分子名称: 1F VH, 1F VL, Spike protein S1
著者Zhao, S, Liu, F, Yang, X, Zhong, G.
登録日2022-06-22
公開日2023-02-22
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (4.4 Å)
主引用文献A core epitope targeting antibody of SARS-CoV-2.
Protein Cell, 14, 2023
8C8P
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BU of 8c8p by Molmil
Structure of the SARS-CoV-2 spike glycoprotein in complex with the 10D12 heavy-chain-only antibody (local refinement)
分子名称: Heavy-chain-only antibody 10D12, Spike glycoprotein,SARS-CoV-2 spike glycoprotein
著者Serna Martin, I, Hurdiss, D.L.
登録日2023-01-20
公開日2023-02-22
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (4.1 Å)
主引用文献Avidity engineering of human heavy-chain-only antibodies mitigates neutralization resistance of SARS-CoV-2 variants.
Front Immunol, 14, 2023
7U0Q
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BU of 7u0q by Molmil
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-02
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, Spike glycoprotein, ...
著者Patel, A, Ortlund, E.
登録日2022-02-18
公開日2023-03-01
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.86 Å)
主引用文献Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response.
Structure, 31, 2023
7U0X
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BU of 7u0x by Molmil
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-13
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, Spike glycoprotein, ...
著者Patel, A, Ortlund, E.
登録日2022-02-19
公開日2023-03-01
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.82 Å)
主引用文献Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response.
Structure, 31, 2023
7WP6
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BU of 7wp6 by Molmil
Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies
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, 36H6 heavy chain, ...
著者Zheng, Q, Sun, H, Yuan, Q, Li, S, Xia, N.
登録日2022-01-23
公開日2023-03-01
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.81 Å)
主引用文献Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine.
Cell Host Microbe, 30, 2022
7X2H
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BU of 7x2h by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with 6-2C Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 6-2C H chain, 6-2C L chain, ...
著者Wang, X, Wang, Z.
登録日2022-02-25
公開日2023-03-01
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants.
Nat Commun, 14, 2023
7XCZ
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BU of 7xcz by Molmil
Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with BA7054 and BA7125 fab (local refinement)
分子名称: BA7054 fab, BA7125 fab, Spike glycoprotein
著者Liu, Z, Liu, S.
登録日2022-03-26
公開日2023-03-01
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Biparatopic antibody BA7208/7125 effectively neutralizes SARS-CoV-2 variants including Omicron BA.1-BA.5.
Cell Discov, 9, 2023
7XDA
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BU of 7xda by Molmil
Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with BA7208 and BA7125 fab (local refinement)
分子名称: BA7125 fab, BA7208 fab, Spike glycoprotein
著者Liu, Z, Liu, S, Liu, S.
登録日2022-03-26
公開日2023-03-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (2.98 Å)
主引用文献Biparatopic antibody BA7208/7125 effectively neutralizes SARS-CoV-2 variants including Omicron BA.1-BA.5.
Cell Discov, 9, 2023
7XDB
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BU of 7xdb by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron Spike protein in complex with BA7208 fab
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, BA7208 fab, ...
著者Liu, Z, Liu, S, Gao, Y.Z.
登録日2022-03-26
公開日2023-03-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (2.62 Å)
主引用文献Biparatopic antibody BA7208/7125 effectively neutralizes SARS-CoV-2 variants including Omicron BA.1-BA.5.
Cell Discov, 9, 2023
7XDK
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BU of 7xdk by Molmil
Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7054 and BA7125 fab
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, BA7054 fab, ...
著者Liu, Z, Lui, S, Gao, Y.
登録日2022-03-27
公開日2023-03-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Biparatopic antibody BA7208/7125 effectively neutralizes SARS-CoV-2 variants including Omicron BA.1-BA.5.
Cell Discov, 9, 2023

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件を2025-07-09に公開中

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