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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
6ZLW
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BU of 6zlw by Molmil
SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-01
公開日2020-07-29
最終更新日2020-09-16
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZM7
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BU of 6zm7 by Molmil
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex
分子名称: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-01
公開日2020-07-29
最終更新日2020-09-16
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZN5
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BU of 6zn5 by Molmil
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-06
公開日2020-07-29
最終更新日2020-09-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZOK
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BU of 6zok by Molmil
SARS-CoV-2-Nsp1-40S complex, focused on body
分子名称: 18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
著者Schubert, K, Karousis, E.D, Jomaa, A, Scaiola, A, Echeverria, B, Gurzeler, L.-A, Leibundgut, M, Thiel, V, Muehlemann, O, Ban, N.
登録日2020-07-07
公開日2020-07-29
最終更新日2021-02-10
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
Nat.Struct.Mol.Biol., 27, 2020
6ZON
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BU of 6zon by Molmil
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-07
公開日2020-07-29
最終更新日2020-09-16
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZOW
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BU of 6zow by Molmil
SARS-CoV-2 spike in prefusion 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, DIMETHYL SULFOXIDE, ...
著者Martinez, M, Marabini, R, Carazo, J.M.
登録日2020-07-07
公開日2020-07-29
最終更新日2022-12-21
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.
Iucrj, 7, 2020
6ZP4
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BU of 6zp4 by Molmil
SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
分子名称: 18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-08
公開日2020-07-29
最終更新日2020-09-16
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZP5
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BU of 6zp5 by Molmil
SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up 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, DIMETHYL SULFOXIDE, ...
著者Martinez, M, Marabini, R, Carazo, J.M.
登録日2020-07-08
公開日2020-07-29
最終更新日2022-12-21
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.
Iucrj, 7, 2020
6ZP7
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BU of 6zp7 by Molmil
SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open 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, DIMETHYL SULFOXIDE, ...
著者Martinez, M, Marabini, R, Carazo, J.M.
登録日2020-07-08
公開日2020-07-29
最終更新日2022-12-21
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.
Iucrj, 7, 2020
6ZSL
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BU of 6zsl by Molmil
Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution
分子名称: PHOSPHATE ION, SARS-CoV-2 helicase NSP13, ZINC ION
著者Newman, J.A, Yosaatmadja, Y, Douangamath, A, Arrowsmith, C.H, von Delft, F, Edwards, A, Bountra, C, Gileadi, O.
登録日2020-07-15
公開日2020-07-29
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.94 Å)
主引用文献Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Nat Commun, 12, 2021
7C7P
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BU of 7c7p by Molmil
Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir
分子名称: (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase, CHLORIDE ION
著者Zeng, R, Qiao, J.X, Wang, Y.F, Li, Y.S, Yao, R, Yang, S.Y, Lei, J.
登録日2020-05-26
公開日2020-07-29
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.
Science, 371, 2021
7JFQ
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BU of 7jfq by Molmil
The crystal structure of 3CL MainPro of SARS-CoV-2 with de-oxidized C145
分子名称: 1,2-ETHANEDIOL, 3C-like proteinase, FORMIC ACID
著者Tan, K, Maltseva, N.I, Welk, L.F, Jedrzejczak, R.P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-07-17
公開日2020-07-29
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献The crystal structure of 3CL MainPro of SARS-CoV-2 with de-oxidized C145
To Be Published
6WC1
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BU of 6wc1 by Molmil
Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase
分子名称: SARS-coV-2 Non-structural protein 9, SULFATE ION
著者Littler, D.R, Gully, B.S, Rossjohn, J.
登録日2020-03-28
公開日2020-08-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase.
To Be Published
6ZWV
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BU of 6zwv by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs
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Ke, Z, Qu, K, Nakane, T, Xiong, X, Cortese, M, Zila, V, Scheres, S.H.W, Briggs, J.A.G.
登録日2020-07-28
公開日2020-08-05
最終更新日2020-12-30
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Structures and distributions of SARS-CoV-2 spike proteins on intact virions.
Nature, 588, 2020
7JIR
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BU of 7jir by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder457 inhibitor
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide, ACETATE ION, ...
著者Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-07-23
公開日2020-08-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.09 Å)
主引用文献Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Nat Commun, 12, 2021
7JIT
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BU of 7jit by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495 inhibitor
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ACETATE ION, ...
著者Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-07-23
公開日2020-08-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Nat Commun, 12, 2021
7JIV
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BU of 7jiv by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder530 inhibitor
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, ACETATE ION, ...
著者Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-07-23
公開日2020-08-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Nat Commun, 12, 2021
7JIW
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BU of 7jiw by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder530 inhibitor
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-(acryloylamino)-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide, CHLORIDE ION, ...
著者Osipiuk, J, Tesar, C, Endres, M, Lisnyak, V, Maki, S, Taylor, C, Zhang, Y, Zhou, Z, Azizi, S.A, Jones, K, Kathayat, R, Snyder, S.A, Dickinson, B.C, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2020-07-23
公開日2020-08-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Nat Commun, 12, 2021
6XLU
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BU of 6xlu by Molmil
Structure of SARS-CoV-2 spike at pH 4.0
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Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
登録日2020-06-29
公開日2020-08-12
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (2.4 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
6XM0
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BU of 6xm0 by Molmil
Consensus structure of SARS-CoV-2 spike at pH 5.5
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Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
登録日2020-06-29
公開日2020-08-12
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
6XM3
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BU of 6xm3 by Molmil
Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1
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Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
登録日2020-06-29
公開日2020-08-12
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
6XM4
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BU of 6xm4 by Molmil
Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 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, Spike glycoprotein
著者Zhou, T, Tsybovsky, Y, Olia, A, Kwong, P.D.
登録日2020-06-29
公開日2020-08-12
最終更新日2021-12-15
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Cell Host Microbe, 28, 2020
6ZME
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BU of 6zme by Molmil
SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex
分子名称: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
著者Thoms, M, Buschauer, R, Ameismeier, M, Denk, T, Kratzat, H, Mackens-Kiani, T, Cheng, J, Berninghausen, O, Becker, T, Beckmann, R.
登録日2020-07-02
公開日2020-08-12
最終更新日2020-09-16
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
Science, 369, 2020
6ZRT
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BU of 6zrt by Molmil
Crystal structure of SARS CoV2 main protease in complex with inhibitor Telaprevir
分子名称: (1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide, DIMETHYL SULFOXIDE, Main Protease
著者Oerlemans, R, Wang, W, Lunev, S, Domling, A, Groves, M.R.
登録日2020-07-14
公開日2020-08-12
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics.
Rsc Med Chem, 12, 2020
6ZRU
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BU of 6zru by Molmil
Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir
分子名称: DIMETHYL SULFOXIDE, Main Protease, boceprevir (bound form)
著者Oerlemans, R, Wang, W, Lunev, S, Domling, A, Groves, M.R.
登録日2020-07-14
公開日2020-08-12
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics.
Rsc Med Chem, 12, 2020

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