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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
7JMO
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-04
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-04 heavy chain, COVA2-04 light chain, ...
著者Wu, N.C, Yuan, M, Liu, H, Zhu, X, Wilson, I.A.
登録日2020-08-02
公開日2020-08-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.359 Å)
主引用文献An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.
Cell Rep, 33, 2020
7JMP
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-39 heavy chain, COVA2-39 light chain, ...
著者Wu, N.C, Yuan, M, Liu, H, Zhu, X, Wilson, I.A.
登録日2020-08-02
公開日2020-08-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.712 Å)
主引用文献An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.
Cell Rep, 33, 2020
7JRN
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Crystal structure of the wild type SARS-CoV-2 papain-like protease (PLPro) with inhibitor GRL0617
分子名称: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide, Non-structural protein 3, SULFATE ION, ...
著者Sacco, M, Ma, C, Wang, J, Chen, Y.
登録日2020-08-12
公開日2020-08-26
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.48 Å)
主引用文献Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay.
Acs Cent.Sci., 7, 2021
7JTL
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Structure of SARS-CoV-2 ORF8 accessory protein
分子名称: ORF8 protein, SODIUM ION
著者Flower, T.G, Buffalo, C.Z, Hooy, R.M, Allaire, M, Ren, X, Hurley, J.H.
登録日2020-08-18
公開日2020-08-26
最終更新日2021-02-10
実験手法X-RAY DIFFRACTION (2.04 Å)
主引用文献Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein.
Proc.Natl.Acad.Sci.USA, 118, 2021
6XF5
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BU of 6xf5 by Molmil
Cryo-EM structure of a biotinylated SARS-CoV-2 spike probe in the prefusion state (RBDs down)
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Cerutti, G, Gorman, J, Kwong, P.D, Shapiro, L.
登録日2020-06-15
公開日2020-09-02
最終更新日2020-12-02
実験手法ELECTRON MICROSCOPY (3.45 Å)
主引用文献Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes.
SSRN, 2020
6ZH9
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Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2)
分子名称: CR3022 Light chain, CR3022 heavy, Nanobody H11-H4, ...
著者Naismith, J.H, Mikolajek, H, Le Bas, A.
登録日2020-06-21
公開日2020-09-02
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (3.31 Å)
主引用文献Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2.
Nat.Struct.Mol.Biol., 27, 2020
7C2Q
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The crystal structure of COVID-19 main protease in the apo state
分子名称: 3C-like proteinase
著者Zhou, X.L, Zhong, F.L, Lin, C, Hu, X.H, Zhou, H, Wang, Q.S, Li, j, Zhang, J.
登録日2020-05-08
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献Structure of SARS-CoV-2 main protease in the apo state.
Sci China Life Sci, 64, 2021
7C2Y
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The crystal structure of COVID-2019 main protease in the apo state
分子名称: 3C-like proteinase
著者Zhou, X.L, Zhong, F.L, Lin, C, Zhou, H, Hu, X.H, Wang, Q.S, Li, J, Zhang, J.
登録日2020-05-10
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.91 Å)
主引用文献COVID-2019 main protease in the apo state
To Be Published
7C8D
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BU of 7c8d by Molmil
Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
分子名称: Angiotensin-converting enzyme 2, Spike protein S1, ZINC ION
著者Gao, G.F, Wang, Q.H, Wu, L.l.
登録日2020-05-29
公開日2020-09-02
最終更新日2020-12-02
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2.
Cell Discov, 6, 2020
7CBT
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BU of 7cbt by Molmil
The crystal structure of SARS-CoV-2 main protease in complex with GC376
分子名称: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase
著者Shi, Y, Peng, G.
登録日2020-06-13
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.346 Å)
主引用文献The preclinical inhibitor GS441524 in combination with GC376 efficaciously inhibited the proliferation of SARS-CoV-2 in the mouse respiratory tract.
Emerg Microbes Infect, 10, 2021
7CDZ
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BU of 7cdz by Molmil
Crystal structure of 2019-nCoV nucleocapsid N-terminal domain (NTD) protein
分子名称: Nucleoprotein
著者Peng, Y, Song, H, Qi, J, Gao, G.F.
登録日2020-06-21
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structures of the SARS-CoV-2 nucleocapsid and their perspectives for drug design.
Embo J., 39, 2020
7CJD
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BU of 7cjd by Molmil
Crystal structure of the SARS-CoV-2 PLpro C111S mutant
分子名称: 1,2-ETHANEDIOL, Non-structural protein 3, ZINC ION
著者Gao, X, Cui, S.
登録日2020-07-10
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.501 Å)
主引用文献Crystal structure of SARS-CoV-2 papain-like protease.
Acta Pharm Sin B, 11, 2021
7CJM
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SARS CoV-2 PLpro in complex with GRL0617
分子名称: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide, Non-structural protein 3, ZINC ION
著者Fu, Z, Huang, H.
登録日2020-07-11
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery.
Nat Commun, 12, 2021
7CMD
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BU of 7cmd by Molmil
Crystal structure of the SARS-CoV-2 PLpro with GRL0617
分子名称: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide, Non-structural protein 3, ZINC ION
著者Gao, X, Cui, S.
登録日2020-07-27
公開日2020-09-02
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.59 Å)
主引用文献Crystal structure of SARS-CoV-2 papain-like protease.
Acta Pharm Sin B, 11, 2021
7CTT
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BU of 7ctt by Molmil
Cryo-EM structure of Favipiravir bound to replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state.
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Peng, Q, Peng, R, Shi, Y.
登録日2020-08-20
公開日2020-09-02
最終更新日2021-09-15
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural Basis of SARS-CoV-2 Polymerase Inhibition by Favipiravir.
Innovation (N Y), 2, 2021
7A5R
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BU of 7a5r by Molmil
Complex of SARS-CoV-2 spike and CR3022 Fab (Non-Uniform Refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab Heavy Chain, CR3022 Fab Light Chain, ...
著者Wrobel, A.G, Benton, D.J, Rosenthal, P.B, Gamblin, S.J.
登録日2020-08-21
公開日2020-09-16
最終更新日2020-11-04
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein.
Nat Commun, 11, 2020
7A5S
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Complex of SARS-CoV-2 spike and CR3022 Fab (Homogeneous Refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab Heavy Chain, CR3022 Fab Light Chain, ...
著者Wrobel, A.G, Benton, D.J, Rosenthal, P.B, Gamblin, S.J.
登録日2020-08-21
公開日2020-09-16
最終更新日2020-11-04
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein.
Nat Commun, 11, 2020
7A91
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BU of 7a91 by Molmil
Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
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, Rosenthal, P.B, Gamblin, S.J.
登録日2020-09-01
公開日2020-09-16
最終更新日2020-12-16
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Nature, 588, 2020
7A94
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SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound
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, Rosenthal, P.B, Gamblin, S.J.
登録日2020-09-01
公開日2020-09-16
最終更新日2020-12-16
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
Nature, 588, 2020
7CH4
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Crystal structure of the SARS-CoV-2 S RBD in complex with BD-604 Fab
分子名称: BD-604 Fab H, BD-604 Fab L, Spike protein S1
著者Du, S, Xiao, J.Y.
登録日2020-07-05
公開日2020-09-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.15 Å)
主引用文献Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020
7CH5
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Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab
分子名称: BD-629 Fab H, BD-629 Fab L, Spike protein S1
著者Du, S, Xiao, J.Y.
登録日2020-07-05
公開日2020-09-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020
7CHB
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BU of 7chb by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BD-236 Fab heavy chain, BD-236 Fab light chain, ...
著者Xiao, J, Zhu, Q.
登録日2020-07-05
公開日2020-09-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020
7CHC
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Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab and BD-368-2 Fab
分子名称: BD-368-2 Fab H, BD-368-2 Fab L, BD-629 Fab H, ...
著者Du, S, Xiao, J.Y.
登録日2020-07-05
公開日2020-09-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.71 Å)
主引用文献Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020
7CHE
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BU of 7che by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab and BD-368-2 Fab
分子名称: BD-236 Fab heavy chain, BD-236 Fab light chain, BD-368-2 Fab heavy chain, ...
著者Xiao, J, Zhu, Q.
登録日2020-07-05
公開日2020-09-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.416 Å)
主引用文献Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020
7CHF
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BU of 7chf by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab
分子名称: BD-368-2 Fab heavy chain, BD-368-2 Fab light chain, BD-604 Fab heavy chain, ...
著者Xiao, J, Zhu, Q.
登録日2020-07-05
公開日2020-09-16
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.674 Å)
主引用文献Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.
Cell, 183, 2020

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