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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
8HZR
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BU of 8hzr by Molmil
Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF07321332
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
著者Zeng, X.Y, Zhang, J, Li, J.
登録日2023-01-09
公開日2024-01-17
最終更新日2025-07-09
実験手法X-RAY DIFFRACTION (1.92 Å)
主引用文献Evaluation of the Inhibition Potency of Nirmatrelvir against Main Protease Mutants of SARS-CoV-2 Variants.
Biochemistry, 62, 2023
8TM1
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BU of 8tm1 by Molmil
Antibody N3-1 bound to RBDs in the up and down conformations
分子名称: N3-1 Fab heavy chain, N3-1 Fab light chain, Spike glycoprotein
著者Hsieh, C.-L, McLellan, J.S.
登録日2023-07-27
公開日2024-01-17
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (2.79 Å)
主引用文献SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode.
Commun Biol, 6, 2023
8VCI
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BU of 8vci by Molmil
SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibranch Loop
分子名称: Frameshift Stimulatory Element with Upstream Multi-branch Loop
著者Peterson, J.M, Becker, S.T, O'Leary, C.A, Juneja, P, Yang, Y, Moss, W.N.
登録日2023-12-14
公開日2024-01-17
最終更新日2024-05-29
実験手法ELECTRON MICROSCOPY (6.1 Å)
主引用文献Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop.
Biochemistry, 63, 2024
8G72
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SARS-CoV-2 spike/Nb2 complex with 1 RBD up (local refinement at 5.6 A)
分子名称: Nanosota-2, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (5.6 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8G73
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SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 bound at 2.5 A
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, Nanosota-3, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8G74
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SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3
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, Nanosota-3, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8G75
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SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound
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, Nanosota-4, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8K3K
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BU of 8k3k by Molmil
The crystal structure of nanobody Nb4 in complex with receptor binding domain (RBD) of BA.1 Spike protein
分子名称: Nanobody Nb4, Spike protein S1
著者Wang, H.Y, Xu, W.Q.
登録日2023-07-16
公開日2024-01-24
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.43 Å)
主引用文献A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
MedComm (2020), 4, 2023
8U1G
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Prefusion-stabilized SARS-CoV-2 S2 subunit
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2
著者Hsieh, C.-L, McLellan, J.S.
登録日2023-08-31
公開日2024-01-24
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge.
Nat Commun, 15, 2024
8UH8
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Crystal structure of SARS-CoV-2 main protease E166V (Apo structure)
分子名称: ORF1a polyprotein
著者Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H.
登録日2023-10-07
公開日2024-01-24
最終更新日2025-02-19
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献An orally available P1'-5-fluorinated M pro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier.
Pnas Nexus, 4, 2025
8ENS
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BU of 8ens by Molmil
Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail hepta-peptide
分子名称: Coatomer subunit beta', spike tail hepta-peptide
著者Dey, D, Hasan, S.S.
登録日2022-09-30
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Nat Commun, 14, 2023
8ENW
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Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike tail heptapeptide.
分子名称: 1,2-ETHANEDIOL, Clientized spike tail peptide, Coatomer subunit beta'
著者Dey, D, Hasan, S.S.
登録日2022-09-30
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Nat Commun, 14, 2023
8ENX
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Crystal structure of beta'-COPI-WD40 domain Y33A mutant in complex with SARS-CoV-2 clientized spike tail heptapeptide.
分子名称: Clientized spike tail heptapeptide, Coatomer subunit beta'
著者Dey, D, Hasan, S.S.
登録日2022-09-30
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Nat Commun, 14, 2023
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
最終更新日2024-11-20
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
最終更新日2025-07-02
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2024-10-16
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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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
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (1.51 Å)
主引用文献Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor.
Acta Biochim.Biophys.Sin., 55, 2023
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
最終更新日2025-06-25
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2024-11-06
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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BU of 8kc2 by Molmil
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2024-10-23
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
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
最終更新日2024-11-06
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
最終更新日2024-10-16
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
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2024-11-20
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

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件を2025-07-09に公開中

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