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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
9GRQ
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BU of 9grq by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-12
公開日2024-09-25
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8WKE
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BU of 8wke by Molmil
Sulfate-bound SARS-CoV-2 Nsp9
分子名称: Non-structural protein 9, SULFATE ION
著者Chen, P.J, Huang, H.Y, Hsiao, W.C, Huang, C.Y.
登録日2023-09-27
公開日2024-10-02
実験手法X-RAY DIFFRACTION (2.12 Å)
主引用文献Sulfate-bound SARS-CoV-2 Nsp9
To Be Published
8WSH
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BU of 8wsh by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=4.0
分子名称: Replicase polyprotein 1ab
著者Zhou, X.L, Jiang, H.H, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease ,pH=4.0
To Be Published
8WSJ
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BU of 8wsj by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=6.5
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=6.5
To Be Published
8WSK
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BU of 8wsk by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=8.5
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=8.5
To Be Published
9CSY
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BU of 9csy by Molmil
SARS-CoV-2 papain-like protease (PLpro) bound to PF-07957472
分子名称: 2-methyl-5-(4-methylpiperazin-1-yl)-N-{1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]cyclopropyl}benzamide, Papain-like protease, ZINC ION, ...
著者Mashalidis, E.H, Chang, J.S, Wu, H, Garnsey, M.
登録日2024-07-24
公開日2024-10-02
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.595 Å)
主引用文献Discovery of SARS-CoV-2 papain-like protease (PL pro ) inhibitors with efficacy in a murine infection model.
Sci Adv, 10, 2024
9GTF
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BU of 9gtf by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256190
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (2.28 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
9GUE
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BU of 9gue by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256189
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-19
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
9GUF
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BU of 9guf by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571106
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-19
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8K18
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BU of 8k18 by Molmil
Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
分子名称: Spike protein S1, ZCP4C9 heavy chain, ZCP4C9 light chain
著者Bingjie, T, Shangyu, D.
登録日2023-07-10
公開日2024-10-09
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.68 Å)
主引用文献Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
To Be Published
8K19
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BU of 8k19 by Molmil
Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
分子名称: Spike protein S1, ZCP3B4 heavy chain, ZCP3B4 light chain
著者Tang, B, Dang, S.
登録日2023-07-10
公開日2024-10-09
最終更新日2025-06-25
実験手法ELECTRON MICROSCOPY (3.88 Å)
主引用文献Ultrapotent class I neutralizing antibodies post Omicron breakthrough infection overcome broad SARS-CoV-2 escape variants.
Ebiomedicine, 108, 2024
8U4Y
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BU of 8u4y by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F Mutant
分子名称: 3C-like proteinase nsp5
著者Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
登録日2023-09-11
公開日2024-10-09
最終更新日2025-02-12
実験手法X-RAY DIFFRACTION (2.21 Å)
主引用文献Distal protein-protein interactions contribute to nirmatrelvir resistance.
Nat Commun, 16, 2025
8WXL
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BU of 8wxl by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
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Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2023-10-30
公開日2024-10-09
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (2.59 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUX
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BU of 8xux by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
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Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.22 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUY
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BU of 8xuy by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up state)
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, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.14 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XUZ
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BU of 8xuz by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state)
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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.05 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XV0
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BU of 8xv0 by Molmil
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
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, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XV1
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BU of 8xv1 by Molmil
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (down state)
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, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.05 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8XVM
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BU of 8xvm by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)
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, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-15
公開日2024-10-09
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.77 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
9IU1
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BU of 9iu1 by Molmil
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
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, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-07-20
公開日2024-10-09
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1.
Nat Commun, 15, 2024
8WPW
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BU of 8wpw by Molmil
Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CB6 fab mutant heavy chain, CB6 fab mutant light chain, ...
著者Su, C, Qi, J.X, Gao, G.F.
登録日2023-10-10
公開日2024-10-16
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.49 Å)
主引用文献An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
8WPY
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BU of 8wpy by Molmil
Cryo-EM structure of SARS-CoV-2 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
分子名称: CB6 fab mutant heavy chain, CB6 fab mutant light chain, S304 fab heavy chain, ...
著者Su, C, Qi, J.X, Gao, G.F.
登録日2023-10-10
公開日2024-10-16
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.02 Å)
主引用文献An improved design method enables the ineffective etesevimab broadly and efficiently against SARS-CoV-2 Omicron subvariants
To Be Published
9ATM
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BU of 9atm by Molmil
SARS-CoV-2 EG.5 RBD bound to the VIR-7229 and the S2H97 Fab fragments
分子名称: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2024-02-27
公開日2024-10-16
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU1
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BU of 9au1 by Molmil
SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ...
著者Rietz, T, Park, Y.J, Errico, J, Czudnochowski, N, Nix, J.C, Corti, D, Snell, G, Marco, A.D, Pinto, D, Cameroni, E, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D, Structural Genomics Consortium (SGC)
登録日2024-02-27
公開日2024-10-16
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (2.41 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
9AU2
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BU of 9au2 by Molmil
VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement)
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Tortorici, M.A, Park, Y.J, Veelser, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2024-02-28
公開日2024-10-16
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024

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件を2025-07-09に公開中

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