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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
7WK5
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BU of 7wk5 by Molmil
Cryo-EM structure of Omicron S-ACE2, C2 state
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Han, W.Y, Wang, Y.F.
登録日2022-01-08
公開日2022-02-02
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.66 Å)
主引用文献Molecular basis of SARS-CoV-2 Omicron variant receptor engagement and antibody evasion and neutralization
Biorxiv, 2022
7WK6
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BU of 7wk6 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron spike protein with human ACE2 (focus refinement on RBD-1/ACE2)
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Han, W.Y, Wang, Y.F.
登録日2022-01-08
公開日2022-02-02
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.67 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron
Nature, 604, 2022
7WK9
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SARS-CoV-2 Omicron open state spike protein in complex with S3H3 Fab
分子名称: Heavy chain of S3H3 Fab, Light chain of S3H3 Fab, Spike glycoprotein
著者Hong, Q, Cong, Y.
登録日2022-01-08
公開日2022-02-02
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.48 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
5SBF
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BU of 5sbf by Molmil
PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NendoU
分子名称: CITRIC ACID, Uridylate-specific endoribonuclease
著者Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
登録日2021-07-23
公開日2022-02-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.64 Å)
主引用文献Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.
Nucleic Acids Res., 51, 2023
7LHQ
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BU of 7lhq by Molmil
Solution structure of SARS-CoV-2 nonstructural protein 7 at pH 7.0
分子名称: Non-structural protein 7
著者Lee, Y, Tonelli, M, Anderson, T.K, Kirchdoerfer, R.N, Henzler-Wildman, K, Lee, W.
登録日2021-01-26
公開日2022-02-09
最終更新日2024-05-15
実験手法SOLUTION NMR
主引用文献pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7
Biorxiv, 2021
7TOV
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BU of 7tov by Molmil
Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; consensus state D2
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Gobeil, S, Acharya, P.
登録日2022-01-24
公開日2022-02-09
最終更新日2025-06-04
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7ED5
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BU of 7ed5 by Molmil
A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Shannon, A, Fattorini, V, Sama, B, Selisko, B, Feracci, M, Falcou, C, Gauffre, P, El Kazzi, P, Delpal, A, Decroly, E, Alvarez, K, Eydoux, C, Guillemot, J.-C, Moussa, A, Good, S, Colla, P, Lin, K, Sommadossi, J.-P, Zhu, Y.X, Yan, X.D, Shi, H, Ferron, F, Canard, B.
登録日2021-03-15
公開日2022-02-16
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (2.98 Å)
主引用文献A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase.
Nat Commun, 13, 2022
7TF8
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SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)
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Stalls, V, Acharya, P.
登録日2022-01-06
公開日2022-02-16
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.36 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7THE
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Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interface
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, DH1042 Fab Heavy Chain, DH1042 Fab Light Chain, ...
著者May, A.J, Manne, K, Acharya, P.
登録日2022-01-10
公開日2022-02-16
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.87 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7THT
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BU of 7tht by Molmil
CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042
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, DH1042 heavy chain, ...
著者Manne, K, May, A, Acharya, P.
登録日2022-01-12
公開日2022-02-16
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.42 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7TNW
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Structural and functional impact by SARS-CoV-2 Omicron spike mutations
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2022-01-21
公開日2022-02-16
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural and functional impact by SARS-CoV-2 Omicron spike mutations.
Cell Rep, 39, 2022
7TOW
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BU of 7tow by Molmil
Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide
分子名称: CALCIUM ION, DH1058 Fab Light chain, DH1058 Fab heavy chain, ...
著者Gobeil, S, Acharya, P.
登録日2022-01-24
公開日2022-02-16
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献Structural diversity of the SARS-CoV-2 Omicron spike.
Mol.Cell, 82, 2022
7Q0A
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BU of 7q0a by Molmil
SARS-CoV-2 Spike ectodomain with Fab FI3A
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, FI3A fab Light chain, ...
著者Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
登録日2021-10-14
公開日2022-02-23
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (4.8 Å)
主引用文献Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2.
Theranostics, 12, 2022
7TP3
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2
分子名称: CACODYLATE ION, K288.2 heavy chain, K288.2 light chain, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2022-01-24
公開日2022-02-23
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.33 Å)
主引用文献Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.
Sci Transl Med, 14, 2022
7TP4
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K398.22
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, K398.22 heavy chain, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2022-01-24
公開日2022-02-23
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.
Sci Transl Med, 14, 2022
7TX0
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Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43 crystal form)
分子名称: Non-structural protein 3, [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
著者Correy, G.J, Fraser, J.S.
登録日2022-02-07
公開日2022-02-23
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (0.84 Å)
主引用文献Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43 crystal form)
To Be Published
7TX4
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Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P21 crystal form)
分子名称: Papain-like protease nsp3
著者Correy, G.J, Fraser, J.S, Kovalevsky, A.
登録日2022-02-07
公開日2022-02-23
最終更新日2023-10-25
実験手法NEUTRON DIFFRACTION (1.9 Å), X-RAY DIFFRACTION
主引用文献The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.
Sci Adv, 8, 2022
7R10
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Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Benton, D.J, Wrobel, A.G, Gamblin, S.J.
登録日2022-02-02
公開日2022-03-02
最終更新日2025-07-09
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R1A
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BU of 7r1a by Molmil
Furin Cleaved Alpha Variant SARS-CoV-2 Spike in complex with 3 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Benton, D.J, Wrobel, A.G, Gamblin, S.J.
登録日2022-02-02
公開日2022-03-02
最終更新日2025-07-09
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7THK
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BU of 7thk by Molmil
Cryo-EM structure of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Cerutti, G, Shapiro, L.
登録日2022-01-11
公開日2022-03-02
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.11 Å)
主引用文献Cryo-EM structure of the SARS-CoV-2 Omicron spike.
Cell Rep, 38, 2022
7VYR
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BU of 7vyr by Molmil
Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment
分子名称: D27 heavy chain, D27 light chain, Spike protein S1
著者Jeong, B.-S, Oh, B.-H.
登録日2021-11-15
公開日2022-03-02
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants.
Mabs, 14, 2022
7YWR
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BU of 7ywr by Molmil
NMR structure of the N-terminal domain of Nsp8 from SARS-CoV-2
分子名称: ORF1a polyprotein
著者Mompean, M, Laurents, D.V, Pantoja-Uceda, D, Trevino, M.A.
登録日2022-02-14
公開日2022-03-02
最終更新日2025-01-15
実験手法SOLUTION NMR
主引用文献SARS-CoV-2 Nsp8 N-terminal domain folds autonomously and binds dsRNA.
Nucleic Acids Res., 51, 2023
7E9O
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BU of 7e9o by Molmil
Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(3 up RBDs, state2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 35B5 Fab, Light chain of 35B5 Fab, ...
著者Wang, X.F, Zhu, Y.Q.
登録日2021-03-04
公開日2022-03-09
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (3.41 Å)
主引用文献A potent human monoclonal antibody with pan-neutralizing activities directly dislocates S trimer of SARS-CoV-2 through binding both up and down forms of RBD
Signal Transduct Target Ther, 7, 2022
7R0Z
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BU of 7r0z by Molmil
Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Benton, D.J, Wrobel, A.G, Gamblin, S.J.
登録日2022-02-02
公開日2022-03-09
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R11
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BU of 7r11 by Molmil
Dissociated S1 domain of Beta Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Benton, D.J, Wrobel, A.G, Gamblin, S.J.
登録日2022-02-02
公開日2022-03-09
最終更新日2025-07-09
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022

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件を2025-07-09に公開中

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