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新型コロナウイルスの構造情報

このページの他言語版もあります: English简体中文繁體中文한국어
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
7SGU
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BU of 7sgu by Molmil
Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor
分子名称: 5-amino-N-(naphthalen-1-yl)pyridine-3-carboxamide, CHLORIDE ION, FORMIC ACID, ...
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2021-10-07
公開日2021-10-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.79 Å)
主引用文献Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder608 inhibitor
To Be Published
7SGV
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BU of 7sgv by Molmil
Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor
分子名称: CHLORIDE ION, N-(naphthalen-1-yl)pyridine-3-carboxamide, Papain-like protease, ...
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2021-10-07
公開日2021-10-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder630 inhibitor
To Be Published
7SGW
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BU of 7sgw by Molmil
Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor
分子名称: CHLORIDE ION, N-(naphthalen-1-yl)pyridine-3-carboxamide, Non-structural protein 3, ...
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2021-10-07
公開日2021-10-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Papain-Like Protease of SARS CoV-2 in complex with PLP_Snyder630 inhibitor
To Be Published
7SI9
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BU of 7si9 by Molmil
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with PF-07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase
著者Kovalevsky, A, Kneller, D.W, Coates, L.
登録日2021-10-12
公開日2021-10-20
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease
Nat Commun, 13, 2022
7V26
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BU of 7v26 by Molmil
XG005-bound SARS-CoV-2 S
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, XG005 Heavy chain, ...
著者Zhan, W.Q, Zhang, X, Sun, L, Chen, Z.G.
登録日2021-08-07
公開日2021-10-20
最終更新日2022-07-06
実験手法ELECTRON MICROSCOPY (3.85 Å)
主引用文献An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.
Protein Cell, 13, 2022
7V2A
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BU of 7v2a by Molmil
SARS-CoV-2 Spike trimer in complex with XG014 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, The heavy chain of XG014, ...
著者Wang, K, Wang, X, Pan, L.
登録日2021-08-07
公開日2021-10-20
最終更新日2022-07-06
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.
Protein Cell, 13, 2022
7N3K
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BU of 7n3k by Molmil
Oridonin-bound SARS-CoV-2 Nsp9
分子名称: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one, Non-structural protein 9, SULFATE ION
著者Littler, D.R, Gully, B.S, Rossjohn, J.
登録日2021-06-01
公開日2021-10-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein.
J.Biol.Chem., 297, 2021
7S3N
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BU of 7s3n by Molmil
SARS-CoV-2 S stem helix peptide bound to Fab22
分子名称: Fab22 Heavy Chain, Fab22 Light Chain, Spike glycoprotein
著者Goldsmith, J.A, McLellan, J.S.
登録日2021-09-07
公開日2021-10-27
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Stabilized coronavirus spike stem elicits a broadly protective antibody.
Cell Rep, 37, 2021
7VNU
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BU of 7vnu by Molmil
Crystal structure of the N-terminal domain of SARS-CoV-2 nucleocapsid protein
分子名称: ACETATE ION, Nucleoprotein
著者Zhou, R.J, Ni, X.C, Lei, J.
登録日2021-10-12
公開日2021-10-27
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2.
Commun Biol, 6, 2023
7DAT
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BU of 7dat by Molmil
The crystal structure of COVID-19 main protease treated by AF
分子名称: COVID-19 MAIN PROTEASE, GOLD ION
著者He, Z.S, He, B, Cao, P, Jiang, H.D, Gong, Y, Gao, X.Y.
登録日2020-10-18
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster.
Nano Today, 44, 2022
7DAU
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BU of 7dau by Molmil
The crystal structure of COVID-19 main protease treated by GA
分子名称: COVID-19 MAIN PROTEASE, GOLD ION
著者He, Z.S, He, B, Cao, P, Jiang, H.D, Gong, Y, Gao, X.Y.
登録日2020-10-18
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.72 Å)
主引用文献A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster.
Nano Today, 44, 2022
7DAV
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BU of 7dav by Molmil
The native crystal structure of COVID-19 main protease
分子名称: COVID-19 MAIN PROTEASE
著者He, Z.S, He, B, Cao, P, Jiang, H.D, Gong, Y, Gao, X.Y.
登録日2020-10-18
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.77 Å)
主引用文献A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster.
Nano Today, 44, 2022
7EKC
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BU of 7ekc by Molmil
Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed with 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, Angiotensin-converting enzyme 2, ...
著者Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
登録日2021-04-05
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.8 Å)
主引用文献Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKE
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BU of 7eke by Molmil
Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with human ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
著者Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
登録日2021-04-05
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.7 Å)
主引用文献Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKF
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BU of 7ekf by Molmil
Structure of SARS-CoV-2 Alpha variant spike receptor-binding domain complexed with 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, Angiotensin-converting enzyme 2, ...
著者Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
登録日2021-04-05
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKG
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BU of 7ekg by Molmil
Structure of SARS-CoV-2 Beta variant spike receptor-binding domain complexed with 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, Angiotensin-converting enzyme 2, ...
著者Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
登録日2021-04-05
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.63 Å)
主引用文献Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKH
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BU of 7ekh by Molmil
Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
著者Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
登録日2021-04-05
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7N5H
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BU of 7n5h by Molmil
Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 spike glycoprotein
分子名称: 2-36 Fab heavy chain, 2-36 Fab light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Casner, R.G, Cerutti, G, Shapiro, L.
登録日2021-06-05
公開日2021-11-03
最終更新日2022-11-16
実験手法ELECTRON MICROSCOPY (3.24 Å)
主引用文献A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses.
Emerg Microbes Infect, 11, 2022
7SBK
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BU of 7sbk by Molmil
Closed state of pre-fusion SARS-CoV-2 Delta variant spike protein
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2021-09-25
公開日2021-11-03
最終更新日2021-12-22
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7SBO
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BU of 7sbo by Molmil
One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant spike protein
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2021-09-25
公開日2021-11-03
最終更新日2021-12-22
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7SBP
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BU of 7sbp by Molmil
Closed state of pre-fusion SARS-CoV-2 Kappa variant spike protein
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2021-09-25
公開日2021-11-03
最終更新日2021-12-22
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7SBQ
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BU of 7sbq by Molmil
One RBD-up 1 of pre-fusion SARS-CoV-2 Kappa variant spike protein
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2021-09-25
公開日2021-11-03
最終更新日2021-12-22
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7SBR
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BU of 7sbr by Molmil
One RBD-up 2 of pre-fusion SARS-CoV-2 Kappa variant spike protein
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2021-09-25
公開日2021-11-03
最終更新日2021-12-22
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7SBS
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BU of 7sbs by Molmil
One RBD-up 1 of pre-fusion SARS-CoV-2 Gamma variant spike protein
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Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
登録日2021-09-25
公開日2021-11-03
最終更新日2021-12-22
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7VH8
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BU of 7vh8 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase, DIMETHYL SULFOXIDE
著者Zhao, Y, Zhang, Q, Yang, H, Rao, Z.
登録日2021-09-21
公開日2021-11-03
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.59 Å)
主引用文献Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332.
Protein Cell, 13, 2022

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