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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
7E3K
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Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants
分子名称: 13G9 heavy chain, 13G9 light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Guo, H, Li, T, Liu, F, Gao, Y, Ji, X, Yang, H.
登録日2021-02-09
公開日2021-09-15
最終更新日2022-03-02
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants.
Nat Commun, 12, 2021
7E3L
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Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 58G6 heavy chain, 58G6 light chain, ...
著者Guo, H, Li, T, Liu, F, Gao, Y, Ji, X, Yang, H.
登録日2021-02-09
公開日2021-09-15
最終更新日2022-03-02
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants.
Nat Commun, 12, 2021
7E3O
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody nCoV617
分子名称: Spike protein S1, nCoV617 Heigh Chain, nCoV617 Light Chain
著者Chen, S.D, Yang, M.
登録日2021-02-09
公開日2021-09-15
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.51 Å)
主引用文献Structural Basis of a Human Neutralizing Antibody Specific to the SARS-CoV-2 Spike Protein Receptor-Binding Domain.
Microbiol Spectr, 9, 2021
7LQ7
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV503 and COVA1-16
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA1-16 heavy chain, COVA1-16 light chain, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2021-02-13
公開日2021-09-15
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.4 Å)
主引用文献Bispecific antibodies targeting distinct regions of the spike protein potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 13, 2021
7MTC
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Structure of freshly purified SARS-CoV-2 S2P spike at pH 7.4
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Tsybovsky, Y, Olia, A.S, Kwong, P.D.
登録日2021-05-13
公開日2021-09-15
最終更新日2021-10-13
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity.
J.Biol.Chem., 297, 2021
7MTD
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BU of 7mtd by Molmil
Structure of aged SARS-CoV-2 S2P spike at pH 7.4
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Tsybovsky, Y, Olia, A.S, Kwong, P.D.
登録日2021-05-13
公開日2021-09-15
最終更新日2021-10-13
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity.
J.Biol.Chem., 297, 2021
7MTE
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Structure of SARS-CoV-2 S2P spike at pH 7.4 refolded by low-pH treatment
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Tsybovsky, Y, Olia, A.S, Kwong, P.D.
登録日2021-05-13
公開日2021-09-15
最終更新日2021-10-13
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity.
J.Biol.Chem., 297, 2021
7S3K
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Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530718726
分子名称: 2-(5-chloro-2-methoxyphenyl)-N-(isoquinolin-4-yl)acetamide, 3C-like proteinase
著者Kovalevsky, A, Kneller, D.W, Coates, L.
登録日2021-09-07
公開日2021-09-15
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.
Acs Pharmacol Transl Sci, 5, 2022
7S3S
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Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724813
分子名称: 2-(3-chlorophenyl)-N-(isoquinolin-4-yl)acetamide, 3C-like proteinase
著者Kovalevsky, A, Kneller, D.W, Coates, L.
登録日2021-09-08
公開日2021-09-15
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.
Acs Pharmacol Transl Sci, 5, 2022
7S4B
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BU of 7s4b by Molmil
Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724963
分子名称: (2R)-2-(3-fluorophenyl)-N-(isoquinolin-4-yl)propanamide, 3C-like proteinase
著者Kovalevsky, A, Kneller, D.W, Coates, L.
登録日2021-09-08
公開日2021-09-15
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.
Acs Pharmacol Transl Sci, 5, 2022
7EIZ
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Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading
分子名称: Helicase, MAGNESIUM ION, Non-structural protein 10, ...
著者Yan, L, Yang, Y.X, Li, M.Y, Zhang, Y, Zheng, L.T, Ge, J, Huang, Y.C, Liu, Z.Y, Wang, T, Gao, S, Zhang, R, Huang, Y.Y, Guddat, L.W, Gao, Y, Rao, Z.H, Lou, Z.Y.
登録日2021-04-01
公開日2021-09-22
最終更新日2023-07-26
実験手法ELECTRON MICROSCOPY
主引用文献Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading
Cell, 184, 2021
7KN3
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Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-B8 Fab
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, S-B8 Fab heavy chain, ...
著者Liu, H, Zhu, X, Wilson, I.A.
登録日2020-11-04
公開日2021-09-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.251 Å)
主引用文献Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago.
Adv Sci, 9, 2022
7KN4
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Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-E6 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, S-E6 Fab heavy chain, S-E6 Fab light chain, ...
著者Liu, H, Wilson, I.A.
登録日2020-11-04
公開日2021-09-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Neutralizing Antibodies to SARS-CoV-2 Selected from a Human Antibody Library Constructed Decades Ago.
Adv Sci, 9, 2022
7L8I
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BU of 7l8i by Molmil
SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21)
分子名称: 3C-like proteinase, 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER
著者Lockbaum, G.J, Henes, M, Lee, J.M, Timm, J, Nalivaika, E.A, Yilmaz, N.K, Thompson, P.R, Schiffer, C.A.
登録日2020-12-31
公開日2021-09-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode.
Biochemistry, 60, 2021
7L8J
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SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212)
分子名称: 3C-like proteinase, 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER
著者Lockbaum, G.J, Henes, M, Lee, J.M, Timm, J, Nalivaika, E.A, Yilmaz, N.K, Thompson, P.R, Schiffer, C.A.
登録日2020-12-31
公開日2021-09-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.45 Å)
主引用文献Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode.
Biochemistry, 60, 2021
7RKU
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Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, C022 Antibody Fab Heavy Chain, C022 Antibody Fab Light Chain, ...
著者Jette, C.A, Bjorkman, P.J, Barnes, C.O.
登録日2021-07-22
公開日2021-09-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Cell Rep, 36, 2021
7RKV
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Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C118 (State 1)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, C118 Fab Heavy Chain, C118 Fab Light Chain, ...
著者Barnes, C.O, Jette, C.A, Bjorkman, P.J.
登録日2021-07-22
公開日2021-09-22
最終更新日2021-10-13
実験手法ELECTRON MICROSCOPY (3.45 Å)
主引用文献Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies.
Cell Rep, 36, 2021
7S4S
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BU of 7s4s by Molmil
Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, CoV11 heavy chain, ...
著者Tolbert, W.D, Pazgier, M.
登録日2021-09-09
公開日2021-09-22
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Front Immunol, 14, 2023
7D64
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The crystal structure of SARS-CoV-2 3CLpro with Zinc
分子名称: 3C-like proteinase, ZINC ION
著者Mao, Z.W, Xia, W, Tao, X.
登録日2020-09-29
公開日2021-09-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.45011599532 Å)
主引用文献Inhibition of SARS-CoV-2 replication by zinc gluconate in combination with hinokitiol.
J.Inorg.Biochem., 231, 2022
7DHX
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BU of 7dhx by Molmil
Crystal structure of SARS-CoV-2 RBD binding to pangolin ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ZINC ION, ...
著者Wang, Q.H, Qi, J.X, Wu, L.L.
登録日2020-11-17
公開日2021-09-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Molecular basis of pangolin ACE2 engaged by COVID-19 virus
Chin.Sci.Bull., 66, 2021
7FG2
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BU of 7fg2 by Molmil
Minor cryo-EM structure of S protein trimer of SARS-CoV2 with K-874A VHH, composite map
分子名称: K-874A VHH, Spike glycoprotein
著者Song, C, Murata, K, Katayama, K.
登録日2021-07-25
公開日2021-09-29
最終更新日2022-03-23
実験手法ELECTRON MICROSCOPY (4.4 Å)
主引用文献Nasal delivery of single-domain antibody improves symptoms of SARS-CoV-2 infection in an animal model.
Plos Pathog., 17, 2021
7FG3
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BU of 7fg3 by Molmil
Major cryo-EM structure of S protein trimer of SARS-CoV2 with K-874, composite map
分子名称: K-874A VHH, Spike glycoprotein
著者Song, C, Katayama, K, Murata, K.
登録日2021-07-25
公開日2021-09-29
最終更新日2022-03-23
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Nasal delivery of single-domain antibody improves symptoms of SARS-CoV-2 infection in an animal model.
Plos Pathog., 17, 2021
7FG7
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Cryo-EM structure of S protein trimer of SARS-CoV2
分子名称: Spike glycoprotein
著者Song, C, Murata, K, Katayama, K.
登録日2021-07-26
公開日2021-09-29
最終更新日2022-03-23
実験手法ELECTRON MICROSCOPY (6.9 Å)
主引用文献Nasal delivery of single-domain antibody improves symptoms of SARS-CoV-2 infection in an animal model.
Plos Pathog., 17, 2021
7K9H
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BU of 7k9h by Molmil
SARS-CoV-2 Spike in complex with neutralizing Fab 2B04 (one up, two 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, 2B04 heavy chain, ...
著者Errico, J.M, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-09-29
公開日2021-09-29
最終更新日2021-11-10
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD.
Cell Rep, 37, 2021
7K9I
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SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2B04 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2B04 heavy chain, 2B04 light chain, ...
著者Errico, J.M, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-09-29
公開日2021-09-29
最終更新日2021-11-10
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD.
Cell Rep, 37, 2021

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