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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
7X7T
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BU of 7x7t by Molmil
Cryo-EM structure of SARS-CoV-2 spike protein in complex with three nAbs X01, X10 and X17
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, X01 heavy chain, ...
著者Sun, H, Liu, L, Zheng, Q, Li, S, Zhang, T, Xia, N.
登録日2022-03-10
公開日2022-08-17
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.48 Å)
主引用文献The neutralizing breadth of antibodies targeting diverse conserved epitopes between SARS-CoV and SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7X7U
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Cryo-EM structure of SARS-CoV-2 Delta variant spike protein in complex with three nAbs X01, X10 and X17
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, X01 heavy chain, ...
著者Sun, H, Liu, L, Zhang, T, Zheng, Q, Li, S, Xia, N.
登録日2022-03-10
公開日2022-08-17
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.77 Å)
主引用文献The neutralizing breadth of antibodies targeting diverse conserved epitopes between SARS-CoV and SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7Y9N
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an engineered 5-helix bundle derived from SARS-CoV-2 S2 in complex with HR2P
分子名称: SARS-coV-2 S2 subunit, Spike protein S2',5HB-H2
著者Lu, G.W, Lin, X, Guo, L.Y, Lin, S.
登録日2022-06-25
公開日2022-08-17
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.885 Å)
主引用文献An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry.
Emerg Microbes Infect, 11, 2022
7ZBU
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CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3-[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid, P008_60 antibody, ...
著者Rosa, A, Pye, V.E, Cronin, N, Cherepanov, P.
登録日2022-03-24
公開日2022-08-17
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (4.31 Å)
主引用文献A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination.
Cell Rep, 40, 2022
7RU1
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SARS-CoV-2-6P-Mut7 S protein (C3 symmetry)
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Ozorowski, G, Turner, H.L, Ward, A.B.
登録日2021-08-16
公開日2022-08-24
最終更新日2025-06-04
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways.
Iscience, 25, 2022
7RU4
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CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (RBD/Fv local refinement)
分子名称: 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, CC6.33 IgG heavy chain Fv, ...
著者Ozorowski, G, Turner, H.L, Ward, A.B.
登録日2021-08-16
公開日2022-08-24
最終更新日2025-06-04
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways.
Iscience, 25, 2022
7RU5
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CC6.30 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (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, CC6.30 Fab heavy chain Fv, ...
著者Ozorowski, G, Turner, H.L, Ward, A.B.
登録日2021-08-16
公開日2022-08-24
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways.
Iscience, 25, 2022
7RU8
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CC6.30 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (RBD/Fv local 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, CC6.30 Fab Kappa chain Fv, ...
著者Ozorowski, G, Turner, H.L, Ward, A.B.
登録日2021-08-16
公開日2022-08-24
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways.
Iscience, 25, 2022
7T3M
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SARS-CoV-2 S (Spike Glycoprotein) D614G with Three (3) RBDs Up, Bound to Antibody 2-7 scFv, composite map
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, Antibody 2-7 scFv, ...
著者Byrne, P.O, McLellan, J.S.
登録日2021-12-08
公開日2022-08-24
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern.
Nat Commun, 13, 2022
7T67
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SARS-CoV-2 S (Spike Glycoprotein) D614G with One(1) RBD Up
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Byrne, P.O, McLellan, J.S.
登録日2021-12-13
公開日2022-08-24
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern.
Nat Commun, 13, 2022
7YDI
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SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD region
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-32, Light chain of R1-32, ...
著者Liu, B, Gao, X, Li, Z, Chen, X, He, J, Chen, L, Xiong, X.
登録日2022-07-04
公開日2022-08-24
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.98 Å)
主引用文献SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.
Nat Microbiol, 7, 2022
7YE9
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SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs
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, Heavy chain of R1-32 Fab, ...
著者Liu, B, Gao, X, Li, Z, Chen, X, He, J, Chen, L, Xiong, X.
登録日2022-07-05
公開日2022-08-24
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (4.17 Å)
主引用文献SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.
Nat Microbiol, 7, 2022
7YEG
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BU of 7yeg by Molmil
SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 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Liu, B, Gao, X, Li, Z, Chen, X, He, J, Chen, L, Xiong, X.
登録日2022-07-05
公開日2022-08-24
最終更新日2025-03-12
実験手法ELECTRON MICROSCOPY (3.73 Å)
主引用文献SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope.
Nat Microbiol, 7, 2022
8DAD
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SARS-CoV-2 receptor binding domain in complex with AZ090 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, AZ090 Fab Heavy Chain, AZ090 Fab Light Chain, ...
著者Zong, S, Wang, Z, Gaebler, C, Nussenzweig, M.
登録日2022-06-13
公開日2022-08-24
最終更新日2025-05-14
実験手法ELECTRON MICROSCOPY (3.85 Å)
主引用文献SARS-CoV-2 receptor binding domain in complex with AZ090 Fab
To Be Published
8DI5
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Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with VH domain F6 (focused refinement of RBD and VH F6)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, VH F6
著者Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Subramaniam, S.
登録日2022-06-28
公開日2022-08-24
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.04 Å)
主引用文献Potent and broad neutralization of SARS-CoV-2 variants of concern (VOCs) including omicron sub-lineages BA.1 and BA.2 by biparatopic human VH domains.
Iscience, 25, 2022
8DOY
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BU of 8doy by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198
分子名称: 2-(2-METHOXYETHOXY)ETHANOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 3C-like proteinase nsp5, ...
著者Bulut, H, Hayashi, H, Tsuji, K, Kuwata, N, Das, D, Tamamura, H, Mitsuya, H.
登録日2022-07-14
公開日2022-08-24
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.59 Å)
主引用文献Potent and biostable inhibitors of the main protease of SARS-CoV-2.
Iscience, 25, 2022
8DZ9
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Crystal Structure of SARS-CoV-2 Main protease G143S mutant in complex with Nirmatrelvir
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者Noske, G.D, Oliva, G, Godoy, A.S.
登録日2022-08-06
公開日2022-08-24
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (1.664 Å)
主引用文献Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.
J.Biol.Chem., 299, 2023
8E1Y
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Crystal Structure of SARS-CoV-2 Main protease A193S mutant in complex with Nirmatrelvir
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者Noske, G.D, Oliva, G, Godoy, A.S.
登録日2022-08-11
公開日2022-08-24
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.48 Å)
主引用文献Structural basis of nirmatrelvir and ensitrelvir activity against naturally occurring polymorphisms of the SARS-CoV-2 main protease.
J.Biol.Chem., 299, 2023
7VBD
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BU of 7vbd by Molmil
Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0
分子名称: Nucleoprotein
著者Zeng, P, Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
登録日2021-08-31
公開日2022-08-31
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0
To Be Published
7WBZ
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Crystal structure of the SARS-Cov-2 RBD in complex with Fab 2303
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2303 heavy chain, 2303 light chain, ...
著者Xiang, Y, Ma, B.
登録日2021-12-17
公開日2022-08-31
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.42 Å)
主引用文献Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies.
Commun Biol, 5, 2022
7XCH
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BU of 7xch by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with human ACE2 ectodomain (two-RBD-up state)
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Gao, G.F, Qi, J.X, Zhao, Z.N, Liu, S, Xie, Y.F.
登録日2022-03-24
公開日2022-08-31
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7XCI
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BU of 7xci by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with human ACE2 ectodomain (local 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, Processed angiotensin-converting enzyme 2, ...
著者Gao, G.F, Qi, J.X, Zhao, Z.N, Liu, S, Xie, Y.F.
登録日2022-03-24
公開日2022-08-31
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7XCK
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Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement)
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, S309 heavy chain, S309 light chain, ...
著者Gao, G.F, Qi, J.X, Zhao, Z.N, Xie, Y.F, Liu, S.
登録日2022-03-24
公開日2022-08-31
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7XCP
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Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 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, Heavy chain of 304 Fab, ...
著者Zhao, Z, Qi, J, Gao, F.G.
登録日2022-03-24
公開日2022-08-31
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.05 Å)
主引用文献Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7YA1
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Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (local 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Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
登録日2022-06-27
公開日2022-08-31
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.11 Å)
主引用文献Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape.
Nat Commun, 13, 2022

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