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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
8OSX
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BU of 8osx by Molmil
SARS-CoV-2 nsp10-16 methyltransferase in complex with ATP
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D.
登録日2023-04-20
公開日2023-05-31
最終更新日2024-06-19
実験手法X-RAY DIFFRACTION (1.83 Å)
主引用文献Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16
To Be Published
7WT7
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BU of 7wt7 by Molmil
SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1)
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 Fab 9A8, ...
著者Wang, X, Wang, L.
登録日2022-02-04
公開日2023-06-07
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.
Cell Discov, 8, 2022
7WT8
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BU of 7wt8 by Molmil
SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 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, Heavy chain of Fab 9A8, ...
著者Wang, X, Wang, L.
登録日2022-02-04
公開日2023-06-07
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.
Cell Discov, 8, 2022
7WT9
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SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8
分子名称: Heavy chain of Fab 9A8, Light chain of Fab 9A8, Spike glycoprotein
著者Wang, X, Wang, L.
登録日2022-02-04
公開日2023-06-07
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD.
Cell Discov, 8, 2022
7Y6D
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BU of 7y6d by Molmil
Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed 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Xu, J, Song, Y, Li, S.
登録日2022-06-20
公開日2023-06-07
実験手法ELECTRON MICROSCOPY (4.39 Å)
主引用文献In situ architecture and membrane fusion of SARS-CoV-2 Delta variant.
Proc.Natl.Acad.Sci.USA, 120, 2023
8D4P
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BU of 8d4p by Molmil
Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10-90-3-C1
分子名称: 2-chloro-N-[(1R)-2-{[2-(3-fluorophenyl)ethyl]amino}-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]acetamide, 3C-like proteinase
著者Butler, S.G, Chen, Y, Wang, J.
登録日2022-06-02
公開日2023-06-07
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.04 Å)
主引用文献Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10-90-3-C1
To Be Published
8D55
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Closed state of SARS-CoV-2 BA.2 variant 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
登録日2022-06-04
公開日2023-06-07
最終更新日2023-07-26
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein.
Nat.Struct.Mol.Biol., 30, 2023
8D56
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One RBD-up state of SARS-CoV-2 BA.2 variant 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
登録日2022-06-04
公開日2023-06-07
最終更新日2023-07-26
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein.
Nat.Struct.Mol.Biol., 30, 2023
8D5A
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BU of 8d5a by Molmil
Middle state of SARS-CoV-2 BA.2 variant 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Zhang, J, Tang, W.C, Gao, H.L, Shi, W, Peng, H.Q, Volloch, S.R, Xiao, T.S, Chen, B.
登録日2022-06-04
公開日2023-06-07
最終更新日2023-07-26
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein.
Nat.Struct.Mol.Biol., 30, 2023
8SK4
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BU of 8sk4 by Molmil
Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors)
分子名称: 2-chloro-1-[(5R)-3-phenyl-5-(quinoxalin-5-yl)-4,5-dihydro-1H-pyrazol-1-yl]ethan-1-one, 3C-like proteinase nsp5, IMIDAZOLE
著者Knapp, M.S, Ornelas, E.
登録日2023-04-18
公開日2023-06-07
最終更新日2023-06-14
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors.
Chembiochem, 2023
8SKH
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BU of 8skh by Molmil
Co-structure of SARS-CoV-2 (COVID-19 with covalent pyrazoline based inhibitors
分子名称: 2-chloro-1-[(4R,5R)-3,4,5-triphenyl-4,5-dihydro-1H-pyrazol-1-yl]ethan-1-one, 3C-like proteinase nsp5
著者Knapp, M.S, Ornelas, E.
登録日2023-04-19
公開日2023-06-07
最終更新日2023-06-14
実験手法X-RAY DIFFRACTION (1.882 Å)
主引用文献Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors.
Chembiochem, 24, 2023
8A23
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BU of 8a23 by Molmil
Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383
分子名称: (2R,3R,4S,5R)-2-[4-azanyl-5-(2-quinolin-3-ylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-5-(hydroxymethyl)oxolane-3,4-diol, 2'-O-methyltransferase nsp16, GLYCEROL, ...
著者Hanigovsky, M, Krafcikova, P, Klima, M, Boura, E.
登録日2022-06-02
公開日2023-06-14
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383
To Be Published
8D34
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BU of 8d34 by Molmil
Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A
分子名称: Uridylate-specific endoribonuclease nsp15
著者Farraj, R.A, Edwards, R.A, Glover, J.N.M.
登録日2022-05-31
公開日2023-06-14
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.91 Å)
主引用文献Crystal Structure of SARS CoV-2 NSP15 Endroribonuclease H250A
To Be Published
8DT8
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BU of 8dt8 by Molmil
LM18/Nb136 bispecific tetra-nanobody immunoglobulin in complex with SARS-CoV-2-6P-Mut7 S protein (focused refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, LM18 nanobody, Nb136 nanobody, ...
著者Ozorowski, G, Turner, H.L, Ward, A.B.
登録日2022-07-25
公開日2023-06-14
実験手法ELECTRON MICROSCOPY (3.34 Å)
主引用文献Fully synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins.
Proc.Natl.Acad.Sci.USA, 120, 2023
8ELH
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BU of 8elh by Molmil
Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus
分子名称: ACETATE ION, Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, ...
著者Murdolo, L.D, Gras, S.
登録日2022-09-24
公開日2023-06-14
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.
Nature, 620, 2023
8EOO
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BU of 8eoo by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibodies WRAIR-2063 and WRAIR-2151
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
著者Jensen, J.L, Sankhala, R.S, Joyce, M.G.
登録日2022-10-03
公開日2023-06-14
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.77 Å)
主引用文献Targeting the Spike Receptor Binding Domain Class V Cryptic Epitope by an Antibody with Pan-Sarbecovirus Activity.
J.Virol., 97, 2023
8SXO
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BU of 8sxo by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant
分子名称: 3C-like proteinase nsp5
著者Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
登録日2023-05-23
公開日2023-06-14
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (2.76 Å)
主引用文献Crystal Structure of SARS-CoV-2 Main Protease (Mpro) H164I Mutant
To Be Published
7Y6L
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BU of 7y6l by Molmil
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab816
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Ab816 heavy chain, Ab816 light chain, ...
著者Uchikubo, T, Shirouzu, M.
登録日2022-06-21
公開日2023-06-21
最終更新日2023-09-13
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents.
Iscience, 26, 2023
7Y6N
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BU of 7y6n by Molmil
The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab803
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Ab803 heavy chain, Ab803 light chain, ...
著者Uchikubo, T, Shirouzu, M.
登録日2022-06-21
公開日2023-06-21
最終更新日2023-09-13
実験手法ELECTRON MICROSCOPY (4.4 Å)
主引用文献Potent neutralizing broad-spectrum antibody against SARS-CoV-2 generated from dual-antigen-specific B cells from convalescents.
Iscience, 26, 2023
8EPN
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BU of 8epn by Molmil
Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down 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, Spike glycoprotein, ...
著者Williams, J.A, Harshbarger, W.
登録日2022-10-06
公開日2023-06-21
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity.
Sci Adv, 9, 2023
8EPP
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BU of 8epp by Molmil
Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs in the open 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, Spike glycoprotein, ...
著者Williams, J.A, Harshbarger, W.
登録日2022-10-06
公開日2023-06-21
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity.
Sci Adv, 9, 2023
8EPQ
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BU of 8epq by Molmil
Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs exposed
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Williams, J.A, Harshbarger, W.
登録日2022-10-06
公開日2023-06-21
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity.
Sci Adv, 9, 2023
8HUR
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BU of 8hur by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with S217622
分子名称: 3C-like proteinase nsp5, 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Zhou, X.L, Zhang, J, Li, J.
登録日2022-12-24
公開日2023-06-21
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.64 Å)
主引用文献Structural basis for the inhibition of coronaviral main proteases by ensitrelvir.
Structure, 31, 2023
8HUV
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BU of 8huv by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with S217622
分子名称: 3C-like proteinase nsp5, 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Zeng, P, Zhang, J, Li, J.
登録日2022-12-24
公開日2023-06-21
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.97 Å)
主引用文献Structural basis for the inhibition of coronaviral main proteases by ensitrelvir.
Structure, 31, 2023
8HUW
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BU of 8huw by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with S217622
分子名称: 3C-like proteinase nsp5, 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Wang, J, Zhang, J, Li, J.
登録日2022-12-24
公開日2023-06-21
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.75 Å)
主引用文献Structural basis for the inhibition of coronaviral main proteases by ensitrelvir.
Structure, 31, 2023

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