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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
7R12
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BU of 7r12 by Molmil
Dissociated S1 domain of Mink 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 (3.3 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R14
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BU of 7r14 by Molmil
Alpha Variant SARS-CoV-2 Spike with 1 Erect RBD
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 (3.4 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R16
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BU of 7r16 by Molmil
Beta Variant SARS-CoV-2 Spike with 1 Erect RBD
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
7R18
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BU of 7r18 by Molmil
Mink Variant SARS-CoV-2 Spike in Closed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
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 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R1B
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BU of 7r1b by Molmil
Mink Variant SARS-CoV-2 Spike with 1 Erect RBD
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 (2.8 Å)
主引用文献Evolution of the SARS-CoV-2 spike protein in the human host.
Nat Commun, 13, 2022
7R2V
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BU of 7r2v by Molmil
Structure of nsp14 from SARS-CoV-2 in complex with SAH
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, DI(HYDROXYETHYL)ETHER, Proofreading exoribonuclease nsp14, ...
著者Czarna, A, Plewka, J, Kresik, L, Matsuda, A, Abdulkarim, K, Robinson, C, OByrne, S, Cunningham, F, Georgiou, I, Pachota, M, Popowicz, G.M, Wyatt, P.G, Dubin, G, Pyrc, K.
登録日2022-02-06
公開日2022-03-09
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.53 Å)
主引用文献Refolding of lid subdomain of SARS-CoV-2 nsp14 upon nsp10 interaction releases exonuclease activity.
Structure, 30, 2022
7S5P
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BU of 7s5p by Molmil
Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody CS23
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CS23 Heavy chain, ...
著者Yuan, M, Wilson, I.A.
登録日2021-09-11
公開日2022-03-09
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.86 Å)
主引用文献SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.
Science, 375, 2022
7S5Q
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BU of 7s5q by Molmil
Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibodies CS44 and COVA1-16
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA1-16 Heavy chain, ...
著者Yuan, M, Wilson, I.A.
登録日2021-09-11
公開日2022-03-09
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.88 Å)
主引用文献SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.
Science, 375, 2022
7S5R
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BU of 7s5r by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibodies CV07-287 and COVA1-16
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA1-16 Heavy chain, ...
著者Yuan, M, Wilson, I.A.
登録日2021-09-11
公開日2022-03-09
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.45 Å)
主引用文献SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies.
Science, 375, 2022
7TGW
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BU of 7tgw by Molmil
Omicron spike at 3.0 A (open form)
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Ye, G, Liu, B, Li, F.
登録日2022-01-09
公開日2022-03-09
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain.
Nat Commun, 13, 2022
7TGY
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BU of 7tgy by Molmil
Prototypic SARS-CoV-2 G614 spike (closed form)
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Ye, G, Liu, B, Li, F.
登録日2022-01-09
公開日2022-03-09
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain.
Nat Commun, 13, 2022
7WP9
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BU of 7wp9 by Molmil
SARS-CoV-2 Omicron Variant SPIKE trimer, all 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Yin, W, Xu, Y, Xu, P, Cao, X, Wu, C, Gu, C, He, X, Wang, X, Huang, S, Yuan, Q, Wu, K, Hu, W, Huang, Z, Liu, J, Wang, Z, Jia, F, Xia, K, Liu, P, Wang, X, Song, B, Zheng, J, Jiang, H, Cheng, X, Jiang, Y, Deng, S, Xu, E.
登録日2022-01-23
公開日2022-03-09
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (2.56 Å)
主引用文献Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.
Science, 375, 2022
7WPC
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BU of 7wpc by Molmil
The second RBD of SARS-CoV-2 Omicron Variant in complexed with RBD-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Yin, W, Xu, Y, Xu, P, Cao, X, Wu, C, Gu, C, He, X, Wang, X, Huang, S, Yuan, Q, Wu, K, Hu, W, Huang, Z, Liu, J, Wang, Z, Jia, F, Xia, K, Liu, P, Wang, X, Song, B, Zheng, J, Jiang, H, Cheng, X, Jiang, Y, Deng, S, Xu, E.
登録日2022-01-23
公開日2022-03-09
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.57 Å)
主引用文献Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.
Science, 375, 2022
5SLD
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BU of 5sld by Molmil
PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z1246465616
分子名称: (2R)-3-(3,5-dimethyl-1,2-oxazol-4-yl)-N,N,2-trimethylpropanamide, PHOSPHATE ION, Proofreading exoribonuclease nsp14, ...
著者Imprachim, N, Yosaatmadja, Y, von-Delft, F, Bountra, C, Gileadi, O, Newman, J.A.
登録日2022-03-03
公開日2022-03-16
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.581 Å)
主引用文献PanDDA analysis group deposition
To Be Published
7MW2
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BU of 7mw2 by Molmil
Structure of the SARS-CoV-2 Spike trimer with all RBDs down in complex with the Fab fragment of human neutralizing antibody clone 6
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, Fab of antibody clone 6, ...
著者Hu, Y, Xiong, Y.
登録日2021-05-15
公開日2022-03-16
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (2.97 Å)
主引用文献Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.
Nat Commun, 13, 2022
7MW3
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BU of 7mw3 by Molmil
Structure of the SARS-CoV-2 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody clone 6
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-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Hu, Y, Xiong, Y.
登録日2021-05-15
公開日2022-03-16
最終更新日2025-05-14
実験手法ELECTRON MICROSCOPY (3.15 Å)
主引用文献Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.
Nat Commun, 13, 2022
7MW5
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BU of 7mw5 by Molmil
Structure of the SARS-CoV-2 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody clone 2
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, Fab of antibody clone 2, ...
著者Hu, Y, Xiong, Y.
登録日2021-05-15
公開日2022-03-16
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.42 Å)
主引用文献Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.
Nat Commun, 13, 2022
7MW6
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BU of 7mw6 by Molmil
Structure of the SARS-CoV-2 Spike trimer with three RBDs up in complex with the Fab fragment of human neutralizing antibody clone 2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-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Hu, Y, Xiong, Y.
登録日2021-05-15
公開日2022-03-16
最終更新日2025-05-14
実験手法ELECTRON MICROSCOPY (3.22 Å)
主引用文献Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.
Nat Commun, 13, 2022
7OWX
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BU of 7owx by Molmil
Structure of coiled-coil tetramer from SARS-CoV-2 spike stalk region
分子名称: 1,2-ETHANEDIOL, Spike protein S2, ZINC ION
著者Zivic, Z, Hadzi, S.
登録日2021-06-21
公開日2022-03-16
最終更新日2024-06-19
実験手法X-RAY DIFFRACTION (1.929 Å)
主引用文献Structural polymorphism of coiled-coils from the stalk domain of SARS-CoV-2 spike protein.
Faseb J., 36, 2022
7RNW
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BU of 7rnw by Molmil
SARS-CoV-2 Main Protease in complex with a cyclic peptide inhibitor
分子名称: 3C-like proteinase, ACE-DTY-LEU-GLN-TYR-ALA-VAL-LEU-ARG-HIS-LYS-ARG-ARG-GLU-SEC
著者Frkic, R.L, Jackson, C.J.
登録日2021-07-30
公開日2022-03-16
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Antiviral cyclic peptides targeting the main protease of SARS-CoV-2.
Chem Sci, 13, 2022
7SUO
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BU of 7suo by Molmil
Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein
分子名称: Nucleoprotein, Ras GTPase-activating protein-binding protein 1
著者Biswal, M, Lu, J, Song, J.
登録日2021-11-17
公開日2022-03-16
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献SARS-CoV-2 Nucleocapsid Protein Targets a Conserved Surface Groove of the NTF2-like Domain of G3BP1.
J.Mol.Biol., 434, 2022
7TEY
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BU of 7tey by Molmil
Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein
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Zhu, X, Saville, J.W, Mannar, D, Srivastava, S.S, Berezuk, A.M, Demers, J.P, Zhou, S, Tuttle, K.S, Subramaniam, S.
登録日2022-01-06
公開日2022-03-16
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (2.25 Å)
主引用文献Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants.
Nat Commun, 13, 2022
7THM
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BU of 7thm by Molmil
SARS-CoV-2 nsp12/7/8 complex with a native N-terminus nsp9
分子名称: MANGANESE (II) ION, Non-structural protein 7, Non-structural protein 8, ...
著者Osinski, A, Tagliabracci, V.S, Chen, Z, Li, Y.
登録日2022-01-11
公開日2022-03-16
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.18 Å)
主引用文献The mechanism of RNA capping by SARS-CoV-2.
Nature, 609, 2022
7WPF
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BU of 7wpf by Molmil
SARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 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, Anti-Fab nanobody, ...
著者Yin, W, Xu, Y, Xu, P, Cao, X, Wu, C, Gu, C, He, X, Wang, X, Huang, S, Yuan, Q, Wu, K, Hu, W, Huang, Z, Liu, J, Wang, Z, Jia, F, Xia, K, Liu, P, Wang, X, Song, B, Zheng, J, Jiang, H, Cheng, X, Jiang, Y, Deng, S.J, Xu, H.E.
登録日2022-01-23
公開日2022-03-16
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (2.92 Å)
主引用文献Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody.
Science, 375, 2022
7WUE
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BU of 7wue by Molmil
Crystal structure of SARS-CoV-2 Receptor Binding Domain in complex with the monoclonal antibody m31A7
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Mohapatra, A.
登録日2022-02-08
公開日2022-03-16
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models.
Sci Transl Med, 14, 2022

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件を2025-07-09に公開中

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