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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
7ENF
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Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30
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 Fab30, ...
著者Wang, X.F, Zhu, Y.Q.
登録日2021-04-16
公開日2022-04-06
最終更新日2022-09-21
実験手法ELECTRON MICROSCOPY (2.76 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
7ENG
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BU of 7eng by Molmil
Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30 (local refinement of the RBD and Fab30)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab30, Light chain of Fab30, ...
著者Wang, X.F, Zhu, Y.Q.
登録日2021-04-16
公開日2022-04-06
最終更新日2022-09-21
実験手法ELECTRON MICROSCOPY (3.59 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
7RZQ
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BU of 7rzq by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex
分子名称: SARS-CoV-2 HR1 linked to a scaffold,Spike protein S2', Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2021-08-27
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.09 Å)
主引用文献Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Proc.Natl.Acad.Sci.USA, 119, 2022
7RZR
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Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with D936Y mutation
分子名称: SARS-CoV-2 HR1 D936Y linked to a scaffold,Spike protein S2', Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2021-08-27
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.27 Å)
主引用文献Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Proc.Natl.Acad.Sci.USA, 119, 2022
7RZS
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BU of 7rzs by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with L938F mutation
分子名称: SARS-CoV-2 HR1 L938F linked to a scaffold,Spike protein S2', Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2021-08-27
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.52 Å)
主引用文献Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Proc.Natl.Acad.Sci.USA, 119, 2022
7RZT
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BU of 7rzt by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with S940F mutation
分子名称: SARS-CoV-2 HR1 S940F linked to a scaffold,Spike protein S2', Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2021-08-27
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.35 Å)
主引用文献Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Proc.Natl.Acad.Sci.USA, 119, 2022
7RZU
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BU of 7rzu by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with A942S mutation
分子名称: SARS-CoV-2 HR1 A942S linked to a scaffold,Spike protein S2', Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2021-08-27
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.3 Å)
主引用文献Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Proc.Natl.Acad.Sci.USA, 119, 2022
7RZV
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BU of 7rzv by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with V1176F mutation
分子名称: SARS-CoV-2 HR1 linked to a scaffold,Spike protein S2', Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2021-08-27
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.11 Å)
主引用文献Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Proc.Natl.Acad.Sci.USA, 119, 2022
7TIK
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BU of 7tik by Molmil
Structure of the SARS-CoV-2 Omicron spike post-fusion bundle
分子名称: Ferritin, Dps family protein and Spike protein S2' chimera, Spike protein S2'
著者Yang, K, Brunger, A.T.
登録日2022-01-13
公開日2022-04-06
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.4 Å)
主引用文献Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor.
Proc.Natl.Acad.Sci.USA, 120, 2023
7VAH
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BU of 7vah by Molmil
The crystal structure of COVID-19 main protease in H41A mutation
分子名称: 3C-like proteinase
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-08-29
公開日2022-04-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.491 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7VLP
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BU of 7vlp by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P1211
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, Replicase polyprotein 1a
著者Zhou, X.L, Zhong, F.L, Lin, C, Li, J, Zhang, J.
登録日2021-10-05
公開日2022-04-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.50251932385 Å)
主引用文献Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332.
J.Virol., 96, 2022
7VLQ
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BU of 7vlq by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with PF07321332 in spacegroup P212121
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
著者Zhou, X.L, Zhong, F.L, Lin, C, Zhang, J, Li, J.
登録日2021-10-05
公開日2022-04-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.93910601486 Å)
主引用文献Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate PF-07321332.
J.Virol., 96, 2022
7VTH
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BU of 7vth by Molmil
The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
分子名称: 2-[4-[[4-[bis(fluoranyl)methoxy]-2-methyl-phenyl]amino]-2,6-bis(oxidanylidene)-3-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazin-1-yl]-N-methyl-ethanamide, 3C-like proteinase
著者Yamamoto, S, Tachibana, Y.
登録日2021-10-29
公開日2022-04-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.
J.Med.Chem., 65, 2022
7VU6
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The crystal structure of SARS-CoV-2 3CL protease in complex with compound 3
分子名称: 3C-like proteinase, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
著者Yamamoto, S, Yamane, J, Tachibana, Y.
登録日2021-11-01
公開日2022-04-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.
J.Med.Chem., 65, 2022
7WVP
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Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C2 state
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Han, W.Y, Wang, Y.F.
登録日2022-02-10
公開日2022-04-06
最終更新日2022-05-04
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
7WVQ
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BU of 7wvq by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C3 state
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Han, W.Y, Wang, Y.F.
登録日2022-02-10
公開日2022-04-06
最終更新日2022-05-04
実験手法ELECTRON MICROSCOPY (4.04 Å)
主引用文献Molecular basis of receptor binding and antibody neutralization of Omicron.
Nature, 604, 2022
7EJY
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Complex Structure of antibody BD-503 and RBD of COVID-19
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy Chain of BD-503, Light Chain of BD-503, ...
著者Xu, H, Wang, B, Zhao, T.N, Su, X.D.
登録日2021-04-03
公開日2022-04-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.04 Å)
主引用文献Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.
Cell Res., 31, 2021
7EJZ
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BU of 7ejz by Molmil
Complex Structure of antibody BD-503 and RBD-S477N of COVID-19
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy Chain of BD-503, Light Chain of BD-503, ...
著者Xu, H, Wang, B, Zhao, T.N, Su, X.D.
登録日2021-04-03
公開日2022-04-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3.63 Å)
主引用文献Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.
Cell Res., 31, 2021
7EK0
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BU of 7ek0 by Molmil
Complex Structure of antibody BD-503 and RBD-N501Y of COVID-19
分子名称: Heavy Chain of BD-503, Light Chain of BD-503, Spike protein S1
著者Xu, H, Wang, B, Zhao, T.N, Su, X.D.
登録日2021-04-03
公開日2022-04-13
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.
Cell Res., 31, 2021
7FJO
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BU of 7fjo by Molmil
Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with three T6 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, T6 heavy chain, ...
著者Wang, X, Zhang, L, Zhang, S, Liang, Q.
登録日2021-08-04
公開日2022-04-13
実験手法ELECTRON MICROSCOPY (3.34 Å)
主引用文献RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants.
Iscience, 25, 2022
7O05
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BU of 7o05 by Molmil
Crystal structure of SARS-CoV-2 N-CTD
分子名称: Nucleoprotein
著者Ciges-Tomas, J.R, Vilar, M.
登録日2021-03-25
公開日2022-04-13
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.
Commun Biol, 5, 2022
7O35
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BU of 7o35 by Molmil
Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I)
分子名称: GUANOSINE-5'-TRIPHOSPHATE, Nucleoprotein
著者Ciges-Tomas, J.R, Vilar, M.
登録日2021-04-01
公開日2022-04-13
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.
Commun Biol, 5, 2022
7O36
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BU of 7o36 by Molmil
Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (II)
分子名称: GLYCEROL, GUANOSINE-5'-TRIPHOSPHATE, Nucleoprotein
著者Ciges-Tomas, J.R, Vilar, M.
登録日2021-04-01
公開日2022-04-13
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Identification of a guanine-specific pocket in the protein N of SARS-CoV-2.
Commun Biol, 5, 2022
7RAQ
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BU of 7raq by Molmil
Crystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem helix peptide
分子名称: CV3-25 Fab Heavy Chain, CV3-25 Fab Light Chain, GLYCEROL, ...
著者Hurlburt, N.K, Pancera, M.
登録日2021-07-02
公開日2022-04-13
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.
Commun Biol, 5, 2022
7T01
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BU of 7t01 by Molmil
SARS-CoV-2 S-RBD + Fab 54042-4
分子名称: 54042-4 Fab - Heavy Chain, 54042-4 Fab - Light Chain, Spike protein S1
著者Johnson, N.V, Mclellan, J.S.
登録日2021-11-29
公開日2022-04-13
実験手法ELECTRON MICROSCOPY (2.69 Å)
主引用文献Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition.
Cell Rep, 37, 2021

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