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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
7MY8
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BU of 7my8 by Molmil
Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles
分子名称: Spike protein S2
著者Koppisetti, R.K, Fulcher, Y.G, Van Doren, S.R.
登録日2021-05-20
公開日2021-08-18
最終更新日2024-10-23
実験手法SOLUTION NMR
主引用文献Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles.
J.Am.Chem.Soc., 143, 2021
7OZU
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BU of 7ozu by Molmil
SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with A
分子名称: Non-structural protein 7, Non-structural protein 8, Product RNA, ...
著者Kabinger, F, Stiller, C, Schmitzova, J, Dienemann, C, Kokic, G, Hillen, H.S, Hoebartner, C, Cramer, P.
登録日2021-06-28
公開日2021-08-18
最終更新日2024-07-17
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis.
Nat.Struct.Mol.Biol., 28, 2021
7OZV
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BU of 7ozv by Molmil
SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with G
分子名称: Non-structural protein 7, Non-structural protein 8, Product RNA, ...
著者Kabinger, F, Stiller, C, Schmitzova, J, Dienemann, C, Kokic, G, Hillen, H.S, Hoebartner, C, Cramer, P.
登録日2021-06-28
公開日2021-08-18
最終更新日2024-07-17
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis.
Nat.Struct.Mol.Biol., 28, 2021
7RQG
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BU of 7rqg by Molmil
Crystal structure of the Nsp3 Y3 domain from SARS-CoV-2
分子名称: Non-structural protein 3
著者Stogios, P.J, Skarina, T, Chang, C, Di Leo, R, Savchenko, A, Joachimiak, A, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2021-08-06
公開日2021-08-18
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (2.17 Å)
主引用文献Crystal structure of the Nsp3 Y3 domain from SARS-CoV-2
To Be Published
7EU2
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BU of 7eu2 by Molmil
Complex structure of HLA0201 with recognizing SARS-CoV-2 epitope S1
分子名称: Beta-2-microglobulin, MHC class I antigen, SARS-CoV-2 T-cell Epitope S1
著者Deng, S, Jin, T.
登録日2021-05-15
公開日2021-08-25
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.
Cell Rep, 36, 2021
7F4W
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BU of 7f4w by Molmil
Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4
分子名称: Beta-2-microglobulin, MHC class I antigen, SARS-CoV-2 T-cell Epitope pep4
著者Deng, S, Jin, T.
登録日2021-06-21
公開日2021-08-25
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.
Cell Rep, 36, 2021
7FDG
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BU of 7fdg by Molmil
SARS-COV-2 Spike RBDMACSp6 binding to hACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1
著者Wang, X, Cao, L.
登録日2021-07-16
公開日2021-08-25
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.69 Å)
主引用文献Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2.
Nat Commun, 12, 2021
7FDH
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BU of 7fdh by Molmil
SARS-COV-2 Spike RBDMACSp25 binding to hACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1
著者Wang, X, Cao, L.
登録日2021-07-16
公開日2021-08-25
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.72 Å)
主引用文献Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2.
Nat Commun, 12, 2021
7FDI
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BU of 7fdi by Molmil
SARS-COV-2 Spike RBDMACSp36 binding to hACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1
著者Wang, X, Cao, L.
登録日2021-07-16
公開日2021-08-25
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.12 Å)
主引用文献Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2.
Nat Commun, 12, 2021
7FDK
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BU of 7fdk by Molmil
SARS-COV-2 Spike RBDMACSp36 binding to mACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1
著者Wang, X, Cao, L.
登録日2021-07-16
公開日2021-08-25
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.69 Å)
主引用文献Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2.
Nat Commun, 12, 2021
7M2P
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BU of 7m2p by Molmil
Structure of the SARS-CoV-2 3CL protease in complex with inhibitor 18
分子名称: 3C-like proteinase, Inhibitor 18 in bound form
著者Yang, K, Li, L.
登録日2021-03-17
公開日2021-08-25
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Self-Masked Aldehyde Inhibitors: A Novel Strategy for Inhibiting Cysteine Proteases.
J.Med.Chem., 64, 2021
7E39
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BU of 7e39 by Molmil
SARS-CoV-2 spike in complex with the Ab4 neutralizing antibody (State 3)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy Chain of Ab4, Light Chain of Ab4, ...
著者Liu, C.
登録日2021-02-08
公開日2021-09-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Three epitope-distinct human antibodies from RenMab mice neutralize SARS-CoV-2 and cooperatively minimize the escape of mutants.
Cell Discov, 7, 2021
7E3B
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BU of 7e3b by Molmil
SARS-Cov-2 spike in complex with the Ab5 neutralizing antibody (focused refinement on Fab-RBD)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy Chain of Ab5, Light Chain of Ab5, ...
著者Liu, C.
登録日2021-02-08
公開日2021-09-01
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献Three epitope-distinct human antibodies from RenMab mice neutralize SARS-CoV-2 and cooperatively minimize the escape of mutants.
Cell Discov, 7, 2021
7E3C
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BU of 7e3c by Molmil
SARS-CoV-2 spike in complex with the Ab1 neutralizing antibody (focused refinement on Fab-RBD)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Ab1, Light chain of Ab1, ...
著者Liu, C.
登録日2021-02-08
公開日2021-09-01
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献Three epitope-distinct human antibodies from RenMab mice neutralize SARS-CoV-2 and cooperatively minimize the escape of mutants.
Cell Discov, 7, 2021
7EDG
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BU of 7edg by Molmil
Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 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, Spike glycoprotein, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Wu, H.C, Hsu, S.T.D.
登録日2021-03-16
公開日2021-09-01
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function.
Nat.Struct.Mol.Biol., 28, 2021
7EDJ
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BU of 7edj by Molmil
Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain
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 (ACE2) ectodomain, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Wu, H.C, Hsu, S.T.D.
登録日2021-03-16
公開日2021-09-01
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function.
Nat.Struct.Mol.Biol., 28, 2021
7EH5
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BU of 7eh5 by Molmil
Cryo-EM structure of SARS-CoV-2 S-D614G variant in complex with neutralizing antibodies, RBD-chAb15 and RBD-chAb45
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, RBD-chAb15, ...
著者Yang, T.J, Yu, P.Y, Chang, Y.C, Wu, H.C, Hsu, S.T.D.
登録日2021-03-28
公開日2021-09-01
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function.
Nat.Struct.Mol.Biol., 28, 2021
7F2B
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BU of 7f2b by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain at 2.0A resolution
分子名称: CHLORIDE ION, Nucleoprotein, PHOSPHATE ION
著者Liu, C, Chen, Y.W.
登録日2021-06-10
公開日2021-09-01
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies.
Febs J., 289, 2022
7L7D
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BU of 7l7d by Molmil
Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
著者Dong, J, Crowe, J.E.
登録日2020-12-28
公開日2021-09-01
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail.
Nat Microbiol, 6, 2021
7L7E
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BU of 7l7e by Molmil
Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibodies AZD8895 and AZD1061
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, PHOSPHATE ION, Spike protein S1, ...
著者Dong, J, Crowe, J.E.
登録日2020-12-28
公開日2021-09-01
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail.
Nat Microbiol, 6, 2021
7RW2
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BU of 7rw2 by Molmil
Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein
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, 5-7 heavy chain, ...
著者Cerutti, G, Shapiro, L.
登録日2021-08-19
公開日2021-09-01
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain.
Cell Rep, 37, 2021
7E5O
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BU of 7e5o by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-193 Heavy chain, NT-193 Light chain, ...
著者Kita, S, Onodera, T, Adachi, Y, Moriayma, S, Nomura, T, Tadokoro, T, Anraku, Y, Yumoto, K, Tian, C, Fukuhara, H, Suzuki, T, Tonouchi, K, Sasaki, J, Sun, L, Hashiguchi, T, Takahashi, Y, Maenaka, K.
登録日2021-02-19
公開日2021-09-08
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献A SARS-CoV-2 antibody broadly neutralizes SARS-related coronaviruses and variants by coordinated recognition of a virus-vulnerable site.
Immunity, 54, 2021
7EY0
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BU of 7ey0 by Molmil
Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-813 Fab and BD-744 Fab
分子名称: BD-744H, BD-744L, BD-813H, ...
著者Du, S, Xiao, J.
登録日2021-05-29
公開日2021-09-08
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants.
Cell Res., 31, 2021
7EY4
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BU of 7ey4 by Molmil
Local CryoEM of the SARS-CoV-2 S6PV2 in complex with BD-667
分子名称: BD-667 H, BD-667 L, Spike glycoprotein, ...
著者Liu, P.L.
登録日2021-05-29
公開日2021-09-08
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.69 Å)
主引用文献Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants.
Cell Res., 31, 2021
7EY5
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BU of 7ey5 by Molmil
Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab
分子名称: BD-771H, BD-771L, BD-821H, ...
著者Zhang, Z.Y.
登録日2021-05-29
公開日2021-09-08
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants.
Cell Res., 31, 2021

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件を2025-07-09に公開中

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