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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
8FWO
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BU of 8fwo by Molmil
Crystal structure of SARS-CoV-2 papain-like protease
分子名称: CHLORIDE ION, GLYCEROL, PHOSPHATE ION, ...
著者Bezerra, E.H.S, Soprano, A.S, Tonoli, C.C.C, Prado, P.F.V, da Silva, J.C, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
登録日2023-01-23
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Crystal structure of SARS-CoV-2 papain-like protease
To Be Published
8HP9
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BU of 8hp9 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 S-trimer in complex with fab L4.65 and L5.34
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
著者Gao, G.F, Liu, S.
登録日2022-12-12
公開日2024-01-31
実験手法ELECTRON MICROSCOPY (2.75 Å)
主引用文献Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HPQ
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BU of 8hpq by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
著者Gao, G.F, Liu, S.
登録日2022-12-12
公開日2024-01-31
実験手法ELECTRON MICROSCOPY (2.85 Å)
主引用文献Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HPV
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BU of 8hpv by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron Prototype S-trimer in complex with fab L4.65 and L5.34
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
著者Gao, G.F, Liu, S.
登録日2022-12-13
公開日2024-01-31
最終更新日2024-05-08
実験手法ELECTRON MICROSCOPY (2.65 Å)
主引用文献Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HQF
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BU of 8hqf by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with inhibitor YH-53
分子名称: N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, Non-structural protein 7
著者Zeng, P, Zhang, J, Li, J.
登録日2022-12-13
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.51 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with inhibitor YH-53
To Be Published
8I4H
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BU of 8i4h by Molmil
Omicron spike variant BA.1 with Bn03
分子名称: Bn03, Spike glycoprotein
著者Hao, A.H, Zhang, X, Chen, Z.G, Sun, L.
登録日2023-01-19
公開日2024-01-31
実験手法ELECTRON MICROSCOPY (3.81 Å)
主引用文献Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants.
Signal Transduct Target Ther, 8, 2023
8KA8
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BU of 8ka8 by Molmil
Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local 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, Angiotensin-converting enzyme, ...
著者Niu, S, Zhao, Z.N, Chai, Y, Gao, G.F.
登録日2023-08-02
公開日2024-01-31
最終更新日2024-03-27
実験手法ELECTRON MICROSCOPY (2.96 Å)
主引用文献Structural basis and analysis of hamster ACE2 binding to different SARS-CoV-2 spike RBDs.
J.Virol., 98, 2024
8KC2
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Cryo-EM structure of SARS-CoV-2 BA.3 RBD in complex with golden hamster ACE2 (local 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, Angiotensin-converting enzyme, ...
著者Niu, S, Zhao, Z.N, Chai, Y, Gao, G.F.
登録日2023-08-05
公開日2024-01-31
最終更新日2024-03-27
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Structural basis and analysis of hamster ACE2 binding to different SARS-CoV-2 spike RBDs.
J.Virol., 98, 2024
8PH4
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BU of 8ph4 by Molmil
Co-Crystal structure of the SARS-CoV2 main protease Nsp5 with an Uracil-carrying X77-like inhibitor
分子名称: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, MALONATE ION, ...
著者Barthel, T, Altincekic, N, Jores, N, Wollenhaupt, J, Weiss, M.S, Schwalbe, H.
登録日2023-06-18
公開日2024-01-31
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (1.69 Å)
主引用文献Targeting the Main Protease (M pro , nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.
Acs Chem.Biol., 19, 2024
8QPR
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BU of 8qpr by Molmil
SARS-CoV-2 S protein bound to human neutralising antibody UZGENT_G5
分子名称: 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, IgG heavy chain - FAB, ...
著者Remaut, H, Reiter, D, Vandenkerckhove, L, Acar, D.D, Witkowski, W, Gerlo, S.
登録日2023-10-03
公開日2024-01-31
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.
Ebiomedicine, 100, 2024
8QQ0
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BU of 8qq0 by Molmil
SARS-CoV-2 S protein bound to neutralising antibody UZGENT_A3
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Remaut, H, Reiter, D, Vandenkerckhove, L, Acar, D.D, Witkowski, W, Gerlo, S.
登録日2023-10-03
公開日2024-01-31
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted.
Ebiomedicine, 100, 2024
8C9L
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BU of 8c9l by Molmil
Crystal structure of SARS-CoV-2 Mpro-S144A mutant, free enzyme
分子名称: 3C-like proteinase nsp5
著者El Kilani, H, Ibrahim, M, Hilgenfeld, R.
登録日2023-01-23
公開日2024-02-07
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Crystal structure of SARS-CoV-2 Mpro-S144A mutant, free enzyme
To Be Published
8C9O
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BU of 8c9o by Molmil
Crystal structure of SARS-CoV-2 Mpro-S144A mutant in complex with 13b-K
分子名称: 3C-like proteinase nsp5, ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
著者Ibrahim, M, El Kilani, H, Hilgenfeld, R.
登録日2023-01-23
公開日2024-02-07
実験手法X-RAY DIFFRACTION (1.69 Å)
主引用文献Crystal structure of SARS-CoV-2 Mpro_S144A mutant in complex with 13b-K
To Be Published
8CBD
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BU of 8cbd by Molmil
SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, BA.4/5-1 heavy chain, BA.4/5-1 light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2023-01-25
公開日2024-02-07
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (3.52 Å)
主引用文献Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
Nat Commun, 15, 2024
8CBE
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BU of 8cbe by Molmil
SARS-CoV-2 Delta-RBD complexed with BA.4/5-2 and Beta-49 Fabs
分子名称: BA.4/5-2 heavy chain, BA.4/5-2 light chain, Beta-49 heavy chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2023-01-25
公開日2024-02-07
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (3.16 Å)
主引用文献Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
Nat Commun, 15, 2024
8CBF
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BU of 8cbf by Molmil
SARS-CoV-2 Delta-RBD complexed with Omi-42 and Beta-49 Fabs
分子名称: Beta-49 heavy chain, Beta-49 light chain, CHLORIDE ION, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2023-01-25
公開日2024-02-07
最終更新日2024-05-08
実験手法X-RAY DIFFRACTION (2.33 Å)
主引用文献Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
Nat Commun, 15, 2024
8DT9
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BU of 8dt9 by Molmil
Crystal Structure of SARS CoV-2 Mpro mutant L141R with Pfizer Intravenous Inhibitor PF-00835231
分子名称: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, ...
著者Shaqra, A.M, Schiffer, C.A.
登録日2022-07-25
公開日2024-02-07
最終更新日2024-04-24
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Contributions of Hyperactive Mutations in M pro from SARS-CoV-2 to Drug Resistance.
Acs Infect Dis., 10, 2024
8E4W
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BU of 8e4w by Molmil
Crystal Structure of SARS CoV-2 Mpro mutant N142P with Pfizer Intravenous Inhibitor PF-00835231
分子名称: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
著者Shaqra, A.M, Schiffer, C.A.
登録日2022-08-19
公開日2024-02-07
最終更新日2024-04-24
実験手法X-RAY DIFFRACTION (2.75 Å)
主引用文献Contributions of Hyperactive Mutations in M pro from SARS-CoV-2 to Drug Resistance.
Acs Infect Dis., 10, 2024
8E5C
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BU of 8e5c by Molmil
Crystal Structure of SARS CoV-2 Mpro mutant L50F with Nirmatrelvir captured in two conformational states
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 nsp5, CHLORIDE ION, ...
著者Shaqra, A.M, Schiffer, C.A.
登録日2022-08-20
公開日2024-02-07
最終更新日2024-04-24
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Contributions of Hyperactive Mutations in M pro from SARS-CoV-2 to Drug Resistance.
Acs Infect Dis., 10, 2024
8I9B
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BU of 8i9b by Molmil
S-ECD (Omicron BA.2.75) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2023-02-06
公開日2024-02-07
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published
8I9C
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BU of 8i9c by Molmil
S-ECD (Omicron BF.7) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2023-02-06
公開日2024-02-07
実験手法ELECTRON MICROSCOPY (3.85 Å)
主引用文献Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published
8I9D
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BU of 8i9d by Molmil
S-ECD (Omicron XBB.1) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2023-02-06
公開日2024-02-07
実験手法ELECTRON MICROSCOPY (3.95 Å)
主引用文献Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published
8I9E
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BU of 8i9e by Molmil
S-RBD(Omicron BA.3) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2023-02-06
公開日2024-02-07
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published
8I9F
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BU of 8i9f by Molmil
S-RBD (Omicron BA.2.75) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2023-02-06
公開日2024-02-07
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published
8I9G
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BU of 8i9g by Molmil
S-RBD (Omicron BF.7) in complex with PD of 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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2023-02-06
公開日2024-02-07
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published

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件を2024-07-10に公開中

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