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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
7KRO
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BU of 7kro by Molmil
Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - nsp13(2)-BTC
分子名称: ADENOSINE-5'-DIPHOSPHATE, ALUMINUM FLUORIDE, CHAPSO, ...
著者Chen, J, Malone, B, Campbell, E.A, Darst, S.A.
登録日2020-11-20
公開日2021-04-21
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.
Proc.Natl.Acad.Sci.USA, 118, 2021
7KRP
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BU of 7krp by Molmil
Structure of SARS-CoV-2 backtracked complex complex bound to nsp13 helicase - BTC (local refinement)
分子名称: ADENOSINE-5'-DIPHOSPHATE, CHAPSO, MAGNESIUM ION, ...
著者Chen, J, Malone, B, Campbell, E.A, Darst, S.A.
登録日2020-11-20
公開日2021-04-21
最終更新日2024-03-06
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.
Proc.Natl.Acad.Sci.USA, 118, 2021
7LGD
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BU of 7lgd by Molmil
HLA-B*07:02 in complex with SARS-CoV-2 nucleocapsid peptide N105-113
分子名称: Beta-2-microglobulin, CHLORIDE ION, HLA class I histocompatibility antigen, ...
著者Gras, S, Szeto, C, Chatzileontiadou, D.S.M.
登録日2021-01-20
公開日2021-04-21
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.88 Å)
主引用文献CD8 + T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses.
Immunity, 54, 2021
7B14
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BU of 7b14 by Molmil
Nanobody E bound to Spike-RBD in a localized reconstruction
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody against SARS-CoV-2, Spike protein S1
著者Hallberg, B.M, Das, H.
登録日2020-11-23
公開日2021-04-28
最終更新日2022-12-21
実験手法ELECTRON MICROSCOPY (3.79 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape
Science, 371, 2021
7B18
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BU of 7b18 by Molmil
SARS-CoV-spike bound to two neutralising nanobodies
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, Nanobody against SARS-CoV-2 VHH E, ...
著者Hallberg, B.M, Das, H.
登録日2020-11-24
公開日2021-04-28
実験手法ELECTRON MICROSCOPY (2.62 Å)
主引用文献Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Science, 371, 2021
7B62
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BU of 7b62 by Molmil
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
7NT9
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BU of 7nt9 by Molmil
Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed 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, 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 (3.36 Å)
主引用文献SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity.
Sci Adv, 7, 2021
7NTA
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BU of 7nta by Molmil
Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)
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 (3.5 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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BU of 7ntc by Molmil
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
7CAM
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BU of 7cam by Molmil
SARS-CoV-2 main protease (Mpro) apo structure (space group P212121)
分子名称: 3C-like proteinase
著者Wang, Y.C, Yang, C.S, Hou, M.H, Tsai, C.L, Chou, Y.Z, Chen, Y.
登録日2020-06-09
公開日2021-05-05
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.85 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
7CB7
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BU of 7cb7 by Molmil
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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BU of 7e23 by Molmil
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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BU of 7ldj by Molmil
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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BU of 7lw3 by Molmil
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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BU of 7lw4 by Molmil
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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BU of 7lx5 by Molmil
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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BU of 7m6e by Molmil
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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BU of 7m6f by Molmil
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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BU of 7m8k by Molmil
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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BU of 7mc5 by Molmil
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

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