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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
5SSP
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BU of 5ssp by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166285 - (R,R) and (S,S) isomers
分子名称: (1R,2R)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid, (1S,2S)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-06-09
公開日2022-07-06
最終更新日2023-09-20
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
5SSQ
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BU of 5ssq by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166291
分子名称: 3-{[(1H-benzimidazole-5-carbonyl)amino]methyl}-1H-indole-2-carboxylic acid, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-06-09
公開日2022-07-06
最終更新日2023-09-20
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
5SSR
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BU of 5ssr by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5459166300
分子名称: 3-{[(2-hydroxy-1H-benzimidazole-5-carbonyl)amino]methyl}-1H-indole-2-carboxylic acid, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-06-09
公開日2022-07-06
最終更新日2023-09-20
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
7TUQ
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BU of 7tuq by Molmil
Crystal structure of BRD4 bromodomain 1 in complex with monoacetylated SARS-CoV-2 E
分子名称: Bromodomain-containing protein 4, Envelope small membrane protein
著者Vann, K.R, Kutateladze, T.G.
登録日2022-02-03
公開日2022-07-06
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.68 Å)
主引用文献Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection.
Structure, 30, 2022
7TV0
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BU of 7tv0 by Molmil
Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E
分子名称: Bromodomain-containing protein 4, Envelope small membrane protein
著者Vann, K.R, Holt, T.A, Kutateladze, T.G.
登録日2022-02-03
公開日2022-07-06
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection.
Structure, 30, 2022
7VBE
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BU of 7vbe by Molmil
1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0
分子名称: Nucleoprotein
著者Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
登録日2021-08-31
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.59 Å)
主引用文献1.6 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 5.0
To Be Published
7VBF
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BU of 7vbf by Molmil
1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5
分子名称: Nucleoprotein
著者Zhou, X.L, Zhong, F.L, Li, J, Zhang, J.
登録日2021-08-31
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献1.3 Angstrom Resolution Crystal Structure of SARS-CoV-2 Nucleocapsid dimerization domain, pH 8.5
To Be Published
7X1M
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BU of 7x1m by Molmil
The complex structure of Omicron BA.1 RBD with BD604, S309,and S304
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, BD-604 Fab heavy chain, BD-604 Fab light chain, ...
著者Huang, M, Xie, Y.F, Qi, J.X.
登録日2022-02-24
公開日2022-07-06
最終更新日2023-07-19
実験手法ELECTRON MICROSCOPY (2.74 Å)
主引用文献Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3.
Immunity, 55, 2022
7X6J
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BU of 7x6j by Molmil
SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3af
分子名称: 3C-like proteinase, quinoline-2-carboxylic acid
著者Su, H, Nie, T, Xie, H, Li, Z.W, Li, M.J, Xu, Y.
登録日2022-03-07
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination.
J.Med.Chem., 65, 2022
7X6K
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BU of 7x6k by Molmil
SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3w
分子名称: 1H-indole-2-carbaldehyde, 3C-like proteinase
著者Su, H, Nie, T, Xie, H, Li, Z.W, Li, M.J, Xu, Y.
登録日2022-03-07
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.34 Å)
主引用文献Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination.
J.Med.Chem., 65, 2022
7XAZ
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BU of 7xaz by Molmil
Crystal structure of Omicron BA.1.1 RBD complexed with hACE2
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, ...
著者Liao, H, Meng, Y, Li, W.
登録日2022-03-19
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1.
Cell, 185, 2022
7XB0
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BU of 7xb0 by Molmil
Crystal structure of Omicron BA.2 RBD complexed with hACE2
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, ...
著者Li, L, Liao, H, Meng, Y, Li, W.
登録日2022-03-19
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1.
Cell, 185, 2022
7XB1
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BU of 7xb1 by Molmil
Crystal structure of Omicron BA.3 RBD complexed with hACE2
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, ...
著者Li, W, Meng, Y, Liao, H.
登録日2022-03-19
公開日2022-07-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1.
Cell, 185, 2022
7Y42
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BU of 7y42 by Molmil
Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, RETINOIC ACID, Spike glycoprotein
著者Xiang, Y, Wang, L.
登録日2022-06-13
公開日2022-07-06
最終更新日2022-09-14
実験手法ELECTRON MICROSCOPY (3.45 Å)
主引用文献A Retinol Derivative Inhibits SARS-CoV-2 Infection by Interrupting Spike-Mediated Cellular Entry.
Mbio, 13, 2022
8CWU
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BU of 8cwu by Molmil
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21
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, Spike protein S1, VHH 1-21
著者Liu, H, Wilson, I.A.
登録日2022-05-19
公開日2022-07-06
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.71 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CWV
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BU of 8cwv by Molmil
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab
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, CC12.1 Fab heavy chain, CC12.1 Fab light chain, ...
著者Liu, H, Wilson, I.A.
登録日2022-05-19
公開日2022-07-06
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.51 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CXN
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BU of 8cxn by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, pan-sarbecovirus nanobody 2-57
著者Huang, W, Taylor, D.
登録日2022-05-22
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CXQ
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BU of 8cxq by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-22
分子名称: Spike glycoprotein, pan-sarbecovirus nanobody 1-22
著者Huang, W, Taylor, D.
登録日2022-05-22
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.3 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CY6
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BU of 8cy6 by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-65
分子名称: Spike glycoprotein, pan-sarbecovirus nanobody 2-65
著者Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CY7
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BU of 8cy7 by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34
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Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CY9
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BU of 8cy9 by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23
分子名称: Spike glycoprotein, pan-sarbecovirus nanobody 1-23
著者Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CYA
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BU of 8cya by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CYB
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BU of 8cyb by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8
分子名称: 1-deoxy-alpha-D-mannopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CYC
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BU of 8cyc by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34
分子名称: Spike glycoprotein, pan-sarbecovirus nanobody 2-34
著者Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022
8CYD
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BU of 8cyd by Molmil
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-45
分子名称: Spike glycoprotein, pan-sarbecovirus nanobody 2-45
著者Huang, W, Taylor, D.
登録日2022-05-23
公開日2022-07-06
最終更新日2022-07-13
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Superimmunity by pan-sarbecovirus nanobodies.
Cell Rep, 39, 2022

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件を2024-08-07に公開中

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