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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
7B62
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Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, BILIVERDINE IX ALPHA, DI(HYDROXYETHYL)ETHER, ...
著者Pye, V.E, Rosa, A, Roustan, C, Cherepanov, P.
登録日2020-12-07
公開日2021-04-28
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.82 Å)
主引用文献SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.
Sci Adv, 7, 2021
7NTC
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Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab
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, BILIVERDINE IX ALPHA, ...
著者Rosa, A, Pye, V.E, Nans, A, Cherepanov, P.
登録日2021-03-09
公開日2021-04-28
最終更新日2021-06-09
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.
Sci Adv, 7, 2021
7CB7
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1.7A resolution structure of SARS-CoV-2 main protease (Mpro) in complex with broad-spectrum coronavirus protease inhibitor GC376
分子名称: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, ...
著者Wang, Y.C, Yang, C.S, Hou, M.H, Tsai, C.L, Chou, Y.Z, Chen, Y, Hung, M.C.
登録日2020-06-10
公開日2021-05-05
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.69 Å)
主引用文献Structural basis of SARS-CoV-2 main protease inhibition by a broad-spectrum anti-coronaviral drug.
Am J Cancer Res, 10, 2020
7E23
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SARS-CoV-2 spike in complex with the CA521 neutralizing antibody Fab (focused refinement on Fab-RBD)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CA521 Heavy Chain, CA521 Light Chain, ...
著者Liu, C, Song, D, Dou, C.
登録日2021-02-04
公開日2021-05-05
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structure and function analysis of a potent human neutralizing antibody CA521 FALA against SARS-CoV-2.
Commun Biol, 4, 2021
7LDJ
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SARS-CoV-2 receptor binding domain in complex with WNb-2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody 2, ...
著者Pymm, P, Dietrich, M.H, Tan, L.L, Adair, A, Tham, W.H.
登録日2021-01-13
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.36 Å)
主引用文献SARS-CoV-2 receptor binding domain in complex with WNb-2
Proc.Natl.Acad.Sci.USA, 2021
7LW3
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Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of Cap-1 analog (m7GpppAmU) and SAH
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Gupta, Y.K, Viswanathan, T, Misra, A, Qi, S.
登録日2021-02-27
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide.
Nat Commun, 12, 2021
7LW4
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Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH)
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Gupta, Y.K, Viswanathan, T, Misra, A, Qi, S.
登録日2021-02-27
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide.
Nat Commun, 12, 2021
7LX5
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The SARS-CoV-2 spike protein receptor binding domain bound to neutralizing nanobodies WNb 2 and WNb 10
分子名称: Spike glycoprotein, WNb 10, WNb 2
著者Pymm, P, Glukhova, A, Tham, W.-H.
登録日2021-03-03
公開日2021-05-05
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice.
Proc.Natl.Acad.Sci.USA, 118, 2021
7M6D
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BU of 7m6d by Molmil
Structure of the SARS-CoV-2 RBD in complex with neutralizing antibodies BG4-25 and CR3022
分子名称: BG4-25 Fab Heavy Chain, BG4-25 Fab Light Chain, CR3022 Fab Heavy Chain, ...
著者Barnes, C.O, Bjorkman, P.J.
登録日2021-03-25
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Cell, 184, 2021
7M6E
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Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG10-19
分子名称: 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, BG10-19 Fab Heavy Chain, ...
著者Barnes, C.O, Bjorkman, P.J.
登録日2021-03-25
公開日2021-05-05
最終更新日2021-06-23
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Cell, 184, 2021
7M6F
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Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22
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, BG1-22 Fab Heavy Chain, ...
著者Barnes, C.O, Bjorkman, P.J.
登録日2021-03-25
公開日2021-05-05
最終更新日2021-06-23
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Cell, 184, 2021
7M6G
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BU of 7m6g by Molmil
Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG7-15
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, BG7-15 Fab Heavy Chain, ...
著者Barnes, C.O, Bjorkman, P.J.
登録日2021-03-25
公開日2021-05-05
最終更新日2021-06-23
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Cell, 184, 2021
7M6H
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BU of 7m6h by Molmil
Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG7-20
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, BG7-20 Fab Heavy Chain, BG7-20 Fab Light Chain, ...
著者Barnes, C.O, Bjorkman, P.J.
登録日2021-03-25
公開日2021-05-05
最終更新日2021-06-23
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Cell, 184, 2021
7M6I
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BU of 7m6i by Molmil
Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG1-24
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, BG1-24 Fab Heavy Chain, ...
著者Barnes, C.O, Bjorkman, P.J.
登録日2021-03-25
公開日2021-05-05
最終更新日2021-06-23
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV.
Cell, 184, 2021
7M7W
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BU of 7m7w by Molmil
Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Monoclonal antibody S2H97 Fab heavy chain, Monoclonal antibody S2H97 Fab light chain, ...
著者Snell, G, Czudnochowski, N, Croll, T.I, Nix, J.C, Corti, D, Cameroni, E, Pinto, D, Beltramello, M.
登録日2021-03-29
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.65 Å)
主引用文献SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.
Nature, 597, 2021
7M8K
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Cryo-EM structure of Brazil (P.1) SARS-CoV-2 spike glycoprotein variant in the prefusion state (1 RBD up)
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Casner, R.G, Cerutti, G, Shapiro, L, Ho, D.D.
登録日2021-03-29
公開日2021-05-05
最終更新日2021-05-26
実験手法ELECTRON MICROSCOPY
主引用文献Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization.
Cell Host Microbe, 29, 2021
7MC5
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Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex
分子名称: 1,2-ETHANEDIOL, CHLORIDE ION, L(+)-TARTARIC ACID, ...
著者Moeller, N.M, Shi, K, Banerjee, S, Yin, L, Aihara, H.
登録日2021-04-01
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.64 Å)
主引用文献Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.
Proc.Natl.Acad.Sci.USA, 119, 2022
7MC6
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Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion
分子名称: 1,2-ETHANEDIOL, CHLORIDE ION, MAGNESIUM ION, ...
著者Moeller, N.M, Shi, K, Banerjee, S, Yin, L, Aihara, H.
登録日2021-04-01
公開日2021-05-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.
Proc.Natl.Acad.Sci.USA, 119, 2022
7B27
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RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Surface glycoprotein, neutralizing nanobody NM1230
著者Ostertag, E, Zocher, G, Stehle, T.
登録日2020-11-26
公開日2021-05-12
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.902 Å)
主引用文献NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies.
Embo Rep., 22, 2021
7DHG
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BU of 7dhg by Molmil
Crystal structure of SARS-CoV-2 Orf9b complex with human TOM70
分子名称: Mitochondrial import receptor subunit TOM70, ORF9b protein
著者Gao, X, Zhu, K, Qin, B, Olieric, V, Wang, M, Cui, S.
登録日2020-11-14
公開日2021-05-12
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Crystal structure of SARS-CoV-2 Orf9b in complex with human TOM70 suggests unusual virus-host interactions.
Nat Commun, 12, 2021
7M3I
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BU of 7m3i by Molmil
Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CV2-75 Fab Heavy chain, CV2-75 Fab Light chain, ...
著者Hurlburt, N.K, Pancera, M.
登録日2021-03-18
公開日2021-05-12
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects.
Cell Rep, 36, 2021
7MF1
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 47D1
分子名称: 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, 47D1 Fab heavy chain, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2021-04-08
公開日2021-05-12
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.092 Å)
主引用文献Diverse immunoglobulin gene usage and convergent epitope targeting in neutralizing antibody responses to SARS-CoV-2.
Cell Rep, 35, 2021
7MJG
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BU of 7mjg by Molmil
Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein 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, Spike glycoprotein
著者Zhu, X, Mannar, D, Srivastava, S.S, Berezuk, A.M, Demers, J.P, Saville, J.W, Leopold, K, Li, W, Dimitrov, D.S, Tuttle, K.S, Zhou, S, Chittori, S, Subramaniam, S.
登録日2021-04-20
公開日2021-05-12
実験手法ELECTRON MICROSCOPY (2.81 Å)
主引用文献Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies.
Plos Biol., 19, 2021
7MJH
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BU of 7mjh by Molmil
Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8
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Zhu, X, Mannar, D, Srivastava, S.S, Berezuk, A.M, Demers, J.P, Saville, J.W, Leopold, K, Li, W, Dimitrov, D.S, Tuttle, K.S, Zhou, S, Chittori, S, Subramaniam, S.
登録日2021-04-20
公開日2021-05-12
実験手法ELECTRON MICROSCOPY (2.66 Å)
主引用文献Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies.
Plos Biol., 19, 2021
7MJK
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Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 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, Fab ab1 Heavy Chain, ...
著者Zhu, X, Mannar, D, Srivastava, S.S, Berezuk, A.M, Demers, J.P, Saville, J.W, Leopold, K, Li, W, Dimitrov, D.S, Tuttle, K.S, Zhou, S, Chittori, S, Subramaniam, S.
登録日2021-04-20
公開日2021-05-12
実験手法ELECTRON MICROSCOPY (2.73 Å)
主引用文献Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies.
Plos Biol., 19, 2021

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