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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
7WTG
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BU of 7wtg by Molmil
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv051
分子名称: Heavy chain of XGv051, Light chain of XGv051, Spike protein S1
著者Wang, X, Fu, W.
登録日2022-02-04
公開日2022-12-14
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages.
Cell Res., 32, 2022
7WTH
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BU of 7wth by Molmil
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv264
分子名称: Heavy chain of XGv264, Light chain of XGv264, Spike protein S1
著者Wang, X, Fu, W.
登録日2022-02-04
公開日2022-12-14
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages.
Cell Res., 32, 2022
7WTJ
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BU of 7wtj by Molmil
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286
分子名称: Heavy chain of XGv286, Light chain of XGv286, Spike protein S1
著者Wang, X, Fu, W.
登録日2022-02-04
公開日2022-12-14
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages.
Cell Res., 32, 2022
7WTK
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BU of 7wtk by Molmil
SARS-CoV-2 Omicron variant spike in complex with Fab XGv286
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 XGv286, ...
著者Wang, X, Fu, W.
登録日2022-02-04
公開日2022-12-14
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages.
Cell Res., 32, 2022
7X2M
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BU of 7x2m by Molmil
Crystal structure of nanobody 1-2C7 with SARS-CoV-2 RBD
分子名称: 1-2C7, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1
著者Wang, X.Q, Zhang, L.Q, Ren, Y.F, Li, M.X.
登録日2022-02-25
公開日2022-12-14
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses.
Nat Commun, 13, 2022
8GWG
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BU of 8gwg by Molmil
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
分子名称: GUANOSINE-5'-TRIPHOSPHATE, Helicase, Non-structural protein 7, ...
著者Yan, L.M, Huang, Y.C, Ge, J, Liu, Z.Y, Gao, Y, Rao, Z.H, Lou, Z.Y.
登録日2022-09-17
公開日2022-12-14
最終更新日2024-07-03
実験手法ELECTRON MICROSCOPY (3.37 Å)
主引用文献A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.
Cell, 185, 2022
8GWI
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BU of 8gwi by Molmil
A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors
分子名称: GUANOSINE-5'-TRIPHOSPHATE, Helicase, Non-structural protein 7, ...
著者Yan, L.M, Huang, Y.C, Ge, J, Liu, Z.Y, Gao, Y, Rao, Z.H, Lou, Z.Y.
登録日2022-09-17
公開日2022-12-14
最終更新日2024-07-03
実験手法ELECTRON MICROSCOPY (3.18 Å)
主引用文献A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.
Cell, 185, 2022
7T72
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BU of 7t72 by Molmil
Epitope-based selection of SARS-CoV-2 neutralizing antibodies from convalescent patients
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody heavy chain, Antibody light chain, ...
著者Langley, D.B, Christ, D, Rouet, R.
登録日2021-12-14
公開日2022-12-21
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (3.177 Å)
主引用文献Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.
Nat Commun, 14, 2023
7WD1
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BU of 7wd1 by Molmil
Crystal structure of R14 bound to SARS-CoV-2 RBD
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, R14, Spike protein S1, ...
著者Wang, Q.H, Gao, G.F, Qi, J.X, Su, C, Liu, H.H, Wu, L.L.
登録日2021-12-20
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Two pan-SARS-CoV-2 nanobodies and their multivalent derivatives effectively prevent Omicron infections in mice.
Cell Rep Med, 4, 2023
7WD2
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BU of 7wd2 by Molmil
Crystal structure of S43 bound to SARS-CoV-2 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Wang, Q.H, Gao, G.F, Qi, J.X, Su, C, Liu, H.H, Wu, L.L.
登録日2021-12-20
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.69 Å)
主引用文献Two pan-SARS-CoV-2 nanobodies and their multivalent derivatives effectively prevent Omicron infections in mice.
Cell Rep Med, 4, 2023
7WNM
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BU of 7wnm by Molmil
Structure of SARS-CoV-2 Gamma variant receptor-binding domain complexed with high affinity human ACE2 mutant (T27F,R273Q)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
著者Ma, R.Y, Han, P.C, Wang, Q.H, Han, P.
登録日2022-01-18
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献A binding-enhanced but enzymatic activity-eliminated human ACE2 efficiently neutralizes SARS-CoV-2 variants.
Signal Transduct Target Ther, 7, 2022
7WTI
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BU of 7wti by Molmil
SARS-CoV-2 Omicron variant spike in complex with Fab XGv264
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of XGv264, Light chain of XGv264, ...
著者Wang, X, Fu, W.
登録日2022-02-04
公開日2022-12-21
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages.
Cell Res., 32, 2022
7X2K
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BU of 7x2k by Molmil
Crystal structure of nanobody Nb70 with antibody 1F11 fab and SARS-CoV-2 RBD
分子名称: 1F11-H, 1F11-L, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Wang, X.Q, Zhang, L.Q, Ren, Y.F, Li, M.X.
登録日2022-02-25
公開日2022-12-21
最終更新日2023-06-28
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Broadly neutralizing and protective nanobodies against SARS-CoV-2 Omicron subvariants BA.1, BA.2, and BA.4/5 and diverse sarbecoviruses.
Nat Commun, 13, 2022
7XA7
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BU of 7xa7 by Molmil
Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Tang, L.F, Zhang, D, Han, P, Qi, J.X.
登録日2022-03-17
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.31 Å)
主引用文献Structural basis of SARS-CoV-2 and its variants binding to intermediate horseshoe bat ACE2.
Int J Biol Sci, 18, 2022
7XRS
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BU of 7xrs by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with inhibitor YH-53
分子名称: N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Replicase polyprotein 1a
著者Zhou, X.L, Zhong, F.L, Lin, C, Zeng, P, Zhang, J, Li, J.
登録日2022-05-11
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献Structural Basis for the Inhibition of Coronaviral Main Proteases by a Benzothiazole-Based Inhibitor.
Viruses, 14, 2022
8D47
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BU of 8d47 by Molmil
fp.006 Fab in complex with SARS-CoV-2 Fusion Peptide
分子名称: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, PHOSPHATE ION, ...
著者Abernathy, M.E, Barnes, C.O.
登録日2022-06-01
公開日2022-12-21
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein.
Sci Immunol, 8, 2023
8HDA
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BU of 8hda by Molmil
Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2
分子名称: Papain-like protease nsp3
著者Ni, X.C, Lei, J.
登録日2022-11-03
公開日2022-12-21
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2
To Be Published
7WCH
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BU of 7wch by Molmil
CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab
分子名称: SWA9H, SWA9L, Surface glycoprotein
著者Du, S, Xiao, J.Y.
登録日2021-12-20
公開日2022-12-28
実験手法ELECTRON MICROSCOPY (3.19 Å)
主引用文献CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab
To Be Published
7WCK
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BU of 7wck by Molmil
Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab
分子名称: SWA9H, SWA9L, Surface glycoprotein
著者Du, S, Xiao, J.Y.
登録日2021-12-20
公開日2022-12-28
実験手法ELECTRON MICROSCOPY (3.49 Å)
主引用文献Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab
To Be Published
7WCP
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BU of 7wcp by Molmil
CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
分子名称: SWC11H, SWC11L, Surface glycoprotein
著者Du, S, Xiao, J.Y.
登録日2021-12-20
公開日2022-12-28
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
To Be Published
7WCU
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BU of 7wcu by Molmil
Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
分子名称: SWC11H, SWC11L, Surface glycoprotein
著者Du, S, Xiao, J.Y.
登録日2021-12-20
公開日2022-12-28
実験手法ELECTRON MICROSCOPY (3.09 Å)
主引用文献Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
To Be Published
7YKJ
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BU of 7ykj by Molmil
Omicron RBDs bound with P3E6 Fab (one up and one down)
分子名称: P3E6 heavy chain, P3E6 light chain, Spike glycoprotein
著者Tang, B, Dang, S.
登録日2022-07-22
公開日2022-12-28
最終更新日2023-01-18
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.
Emerg Microbes Infect, 12, 2023
8AOU
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BU of 8aou by Molmil
Solution NMR structure of full-length Nsp1 from SARS-CoV-2.
分子名称: Host translation inhibitor nsp1
著者Wang, Y, Kirkpatrick, J.P, Carlomagno, T.
登録日2022-08-08
公開日2022-12-28
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2.
Structure, 31, 2023
7WGV
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BU of 7wgv by Molmil
SARS-CoV-2 spike glycoprotein trimer in closed 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, 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid, ...
著者Zhu, Y, Tai, L, Yin, G, Sun, F.
登録日2021-12-29
公開日2023-01-04
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies
Cell Discov, 8, 2022
7Y76
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BU of 7y76 by Molmil
SIT1-ACE2-BA.5 RBD
分子名称: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE, 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Shen, Y.P, Li, Y.N, Zhang, Y.Y, Yan, R.H.
登録日2022-06-21
公開日2023-01-04
最終更新日2023-02-08
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structures of ACE2-SIT1 recognized by Omicron variants of SARS-CoV-2.
Cell Discov, 8, 2022

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件を2024-07-17に公開中

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