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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
8XYE
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BU of 8xye by Molmil
Crystal structure of SARS-CoV-2 BA.4 RBD and human ACE2
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Lan, J, Wang, C.H.
登録日2024-01-19
公開日2025-01-22
最終更新日2025-04-16
実験手法X-RAY DIFFRACTION (3.32 Å)
主引用文献Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage.
Virology, 600, 2024
8XYG
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BU of 8xyg by Molmil
Crystal structure of SARS-CoV-2 BQ.1.1 RBD and human ACE2
分子名称: Processed angiotensin-converting enzyme 2, Spike protein S1
著者Lan, J, Wang, C.H.
登録日2024-01-19
公開日2025-01-22
最終更新日2025-04-16
実験手法X-RAY DIFFRACTION (3.64 Å)
主引用文献Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage.
Virology, 600, 2024
8XYO
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BU of 8xyo by Molmil
Cryo-EM structure of CX1 receptor binding domain in complex with human ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Xu, Z.P, Li, L.J, Gu, Y.H, Qi, J.X, Gao, G.F.
登録日2024-01-20
公開日2025-01-22
実験手法ELECTRON MICROSCOPY (3.04 Å)
主引用文献Structural resemblances of bat-origin coronaviruses CX1 and BANAL-20-52 spikes provide further evidence on bat origination of SARS-CoV-2
To Be Published
8YZB
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BU of 8yzb by Molmil
BA.2.86 RBD protein in complex with ACE2.
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein,Fibritin,fusion protein
著者Wang, Y.J, Zhang, X, Sun, L.
登録日2024-04-06
公開日2025-01-22
実験手法ELECTRON MICROSCOPY (3.29 Å)
主引用文献Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.
Nat Commun, 15, 2024
8YZC
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BU of 8yzc by Molmil
Structure of BA.2.86 spike protein in complex with ACE2.
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Zang, X, Sun, L.
登録日2024-04-06
公開日2025-01-22
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.
Nat Commun, 15, 2024
8YZD
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BU of 8yzd by Molmil
Structure of JN.1 RBD protein in complex with ACE2.
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein,Fibritin,fusion protein
著者Wang, Y.J, Zhang, X, Sun, L.
登録日2024-04-06
公開日2025-01-22
実験手法ELECTRON MICROSCOPY (3.07 Å)
主引用文献Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.
Nat Commun, 15, 2024
8YZE
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BU of 8yze by Molmil
The JN.1 spike protein (S) in complex with ACE2.
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Zhang, X, Sun, L.
登録日2024-04-06
公開日2025-01-22
実験手法ELECTRON MICROSCOPY (3.06 Å)
主引用文献Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3.
Nat Commun, 15, 2024
9DNU
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BU of 9dnu by Molmil
SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13296
分子名称: 1,2-ETHANEDIOL, 2-methyl-5-[(1R,5S)-8-methyl-3,8-diazabicyclo[3.2.1]octan-3-yl]-N-{(1R)-1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}benzamide, ACETATE ION, ...
著者Ansari, A, Jadhav, P, Arnold, E, Ruiz, F.X, Wang, J.
登録日2024-09-18
公開日2025-01-22
最終更新日2025-02-26
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.
Nat Commun, 16, 2025
9DNV
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BU of 9dnv by Molmil
SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13308
分子名称: 2-methyl-5-[(1R,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]-N-{(1R)-1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}benzamide, ACETIC ACID, CHLORIDE ION, ...
著者Ansari, A, Jadhav, P, Arnold, E, Ruiz, F.X, Wang, J.
登録日2024-09-18
公開日2025-01-22
最終更新日2025-02-26
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.
Nat Commun, 16, 2025
9DO1
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BU of 9do1 by Molmil
SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13307
分子名称: 2-methyl-N-{(1R)-1-[(2M)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}-5-{[(2R)-1-methylpyrrolidin-2-yl]methoxy}benzamide, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
著者Ansari, A, Jadhav, P, Arnold, E, Ruiz, F.X, Wang, J.
登録日2024-09-18
公開日2025-01-22
最終更新日2025-02-26
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.
Nat Commun, 16, 2025
9DO3
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BU of 9do3 by Molmil
SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13317
分子名称: 1,2-ETHANEDIOL, 5-[(3S)-3,4-dimethylpiperazin-1-yl]-2-methyl-N-{(1R)-1-[(2M)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}benzamide, ACETATE ION, ...
著者Ansari, A, Jadhav, P, Arnold, E, Ruiz, F.X, Wang, J.
登録日2024-09-18
公開日2025-01-22
最終更新日2025-02-26
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.
Nat Commun, 16, 2025
9DO5
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BU of 9do5 by Molmil
SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun12665
分子名称: 5-[2-(dimethylamino)ethoxy]-N-{(1R)-1-[(2P)-2-{1-[2-(dimethylamino)-2-oxoethyl]-1H-pyrazol-4-yl}quinolin-4-yl]ethyl}-2-methylbenzamide, ACETATE ION, CHLORIDE ION, ...
著者Ansari, A, Jadhav, P, Arnold, E, Ruiz, F.X, Wang, J.
登録日2024-09-18
公開日2025-01-22
最終更新日2025-02-26
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.
Nat Commun, 16, 2025
9DOI
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BU of 9doi by Molmil
SARS-CoV-2 papain-like protease (PLpro) with inhibitor Jun13306
分子名称: 2-methyl-N-{(1S)-1-[(2P)-2-(1-methyl-1H-pyrazol-4-yl)quinolin-4-yl]ethyl}-5-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}benzamide, ACETATE ION, CHLORIDE ION, ...
著者Ansari, A, Jadhav, P, Arnold, E, Ruiz, F.X, Wang, J.
登録日2024-09-19
公開日2025-01-22
最終更新日2025-02-26
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Design of quinoline SARS-CoV-2 papain-like protease inhibitors as oral antiviral drug candidates.
Nat Commun, 16, 2025
9EXA
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BU of 9exa by Molmil
SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834
分子名称: 6-[[1-[4,6-dimethyl-5-(2-methylpropyl)pyrimidin-2-yl]piperidin-4-yl]-methyl-amino]-N-(2-pyrrolidin-1-ylethyl)pyridazine-4-carboxamide, Fab-B heavy chain, Fab-B light chain, ...
著者Debski-Antoniak, O.J, Hurdiss, D.L.
登録日2024-04-05
公開日2025-01-22
最終更新日2025-04-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献A coronavirus assembly inhibitor that targets the viral membrane protein.
Nature, 640, 2025
9JS4
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BU of 9js4 by Molmil
Cryo-EM structure of neutralizing antibody 8G3 in complex with BA.1 RBD
分子名称: Heavy chain of 8G3, Light chain of 8G3, Spike glycoprotein
著者Li, J, Li, H.
登録日2024-09-30
公開日2025-01-22
最終更新日2025-02-26
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Rapid restoration of potent neutralization activity against the latest Omicron variant JN.1 via AI rational design and antibody engineering.
Proc.Natl.Acad.Sci.USA, 122, 2025
8YZR
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BU of 8yzr by Molmil
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLL(EG.5.1)
分子名称: Beta-2-microglobulin, MHC class I antigen, Spike protein S1
著者Min, L, Liu, J.
登録日2024-04-08
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8YZW
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BU of 8yzw by Molmil
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRLF(BA.2.86)
分子名称: Beta-2-microglobulin, MHC class I antigen, Spike protein S2'
著者Liu, J, Tian, J.M, Shang, B.L.
登録日2024-04-08
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (2.36 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8YZZ
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BU of 8yzz by Molmil
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLF(Prototype)
分子名称: Beta-2-microglobulin, MHC class I antigen, Spike protein S1
著者Shang, B.L, Zhang, J.N, Tian, J.M, Liu, J.
登録日2024-04-08
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8Z05
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BU of 8z05 by Molmil
The structure of HLA-A*0201 complex with peptide from SARS-CoV-2 N222-230 LLLDRLNKL(BA.2.86/JN.1)
分子名称: Beta-2-microglobulin, HLA class I histocompatibility antigen, A alpha chain, ...
著者Zhang, J.N, Tian, J.M, Liu, J.
登録日2024-04-09
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (1.96 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8Z06
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BU of 8z06 by Molmil
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRSF(JN.1)
分子名称: Beta-2-microglobulin, MHC class I antigen, Spike protein S2'
著者Tian, J.M, Liu, J.
登録日2024-04-09
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (2.39 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8Z07
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BU of 8z07 by Molmil
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYRYRLF(Delta/BA.5.2)
分子名称: Beta-2-microglobulin, MHC class I antigen, Spike protein S2'
著者Yuechao, H, Liu, J.
登録日2024-04-09
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8Z08
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BU of 8z08 by Molmil
The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYQYRLF(BA.2.12.1)
分子名称: ASN-TYR-ASN-TYR-GLN-TYR-ARG-LEU-PHE, Beta-2-microglobulin, MHC class I antigen
著者Zhang, J.N, Liu, J.
登録日2024-04-09
公開日2025-01-29
最終更新日2025-05-28
実験手法X-RAY DIFFRACTION (2.01 Å)
主引用文献T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots.
Nat.Immunol., 26, 2025
8Z6R
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BU of 8z6r by Molmil
Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1.
分子名称: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Spike glycoprotein,Fibritin,Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-01-29
実験手法ELECTRON MICROSCOPY (2.87 Å)
主引用文献Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1.
To Be Published
8Z6T
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BU of 8z6t by Molmil
Structure of XBB.1.16 RBD in complex with antibody CYFN1006-1.
分子名称: CYFN1006-1 heavy chain, CYFN1006-1 ligth chain, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-01-29
実験手法ELECTRON MICROSCOPY (2.92 Å)
主引用文献Structure of XBB.1.16 RBD in complex with antibody CYFN1006-1.
To Be Published
8Z6X
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BU of 8z6x by Molmil
Structure of EG.5.1 RBD in complex with antibody CYFN1006-2.
分子名称: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-01-29
実験手法ELECTRON MICROSCOPY (2.96 Å)
主引用文献Structure of EG.5.1 RBD in complex with antibody CYFN1006-2.
To Be Published

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件を2025-07-09に公開中

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