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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
8YF2
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BU of 8yf2 by Molmil
Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog 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Li, L.J, Luo, C.L, Qi, J.X, Gao, G.F.
登録日2024-02-23
公開日2024-10-23
最終更新日2025-04-30
実験手法ELECTRON MICROSCOPY (2.64 Å)
主引用文献Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Plos Pathog., 20, 2024
8YFT
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BU of 8yft by Molmil
Cryo-EM structure of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog 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Li, L.J, Luo, C.L, Qi, J.X, Gao, G.F.
登録日2024-02-25
公開日2024-10-23
最終更新日2025-04-30
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Plos Pathog., 20, 2024
9DW6
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BU of 9dw6 by Molmil
Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant in complex with peptide from human tRNA methyltransferase TRMT1
分子名称: 3C-like proteinase nsp5, CHLORIDE ION, GLYCEROL, ...
著者D'Oliviera, A, Mugridge, J.S.
登録日2024-10-08
公開日2024-10-23
最終更新日2025-01-22
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease.
Elife, 12, 2025
8RRN
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BU of 8rrn by Molmil
Crystal structure of the SARS-CoV-2 S RBD in complex with pT1616 Fab
分子名称: Spike protein S1, pT1616 Fab heavy chain, pT1616 Fab light chain
著者Hansen, G, Krey, T.
登録日2024-01-23
公開日2024-10-30
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (3.11 Å)
主引用文献A human monoclonal antibody neutralizing SARS-CoV-2 Omicron variants containing the L452R mutation.
J.Virol., 98, 2024
9GDY
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BU of 9gdy by Molmil
SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses
分子名称: Spike glycoprotein,Fibritin
著者Herreros, D, Mata, C.P, Noddings, C, Irene, D, Agard, D.A, Tsai, M.-D, Sorzano, C.O.S, Carazo, J.M.
登録日2024-08-06
公開日2024-10-30
最終更新日2025-05-07
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Nat Commun, 16, 2025
8U25
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BU of 8u25 by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant
分子名称: 3C-like proteinase
著者Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
登録日2023-09-05
公開日2024-11-06
最終更新日2025-02-12
実験手法X-RAY DIFFRACTION (2.23 Å)
主引用文献Distal protein-protein interactions contribute to nirmatrelvir resistance.
Nat Commun, 16, 2025
9CTU
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BU of 9ctu by Molmil
Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P
分子名称: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate, Membrane protein, POTASSIUM ION, ...
著者Dolan, K.A, Brohawn, S.G.
登録日2024-07-25
公開日2024-11-06
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Biorxiv, 2024
9CTW
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BU of 9ctw by Molmil
Cryo-EM structure of SARS-CoV-2 M (long conformation) in the presence of C1P
分子名称: Long conformation Fab heavy chain, Long conformation Fab light chain, Membrane protein
著者Dolan, K.A, Brohawn, S.G.
登録日2024-07-25
公開日2024-11-06
最終更新日2025-05-14
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Biorxiv, 2024
8R1Q
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BU of 8r1q by Molmil
SARS-CoV-2 Mpro (Omicron, P132H+T169S) in complex with alpha-ketoamide 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Sun, X, Ibrahim, M, Hilgenfeld, R.
登録日2023-11-02
公開日2024-11-13
最終更新日2025-04-09
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Hlife, 2, 2024
8TFD
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BU of 8tfd by Molmil
Crystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain
分子名称: 1,2-ETHANEDIOL, DNA aptamer, Nucleoprotein
著者Esler, M, Belica, C, Shi, K, Aihara, H.
登録日2023-07-10
公開日2024-11-13
最終更新日2024-12-11
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.
Nucleic Acids Res., 52, 2024
8WUR
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BU of 8wur by Molmil
Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with shikonin
分子名称: 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione, 3C-like proteinase nsp5
著者Zhao, Z.Y, Li, W.W, Zhang, J, Li, J.
登録日2023-10-21
公開日2024-11-13
実験手法X-RAY DIFFRACTION (2.08 Å)
主引用文献Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332.
Viruses, 16, 2023
8WYH
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BU of 8wyh by Molmil
The global map of Omicron Subvariants Spike with ACE2
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Yan, R.H, Wang, A.J, Yang, H.N.
登録日2023-10-31
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献The global map of Omicron Subvariants Spike with ACE2
To Be Published
8WYJ
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BU of 8wyj by Molmil
The global map of Omicron Subvariants Spike with two antibodies
分子名称: S309-HC, S309-KC, SA55-HC, ...
著者Yan, R.H, Wang, A.J, Yang, H.N.
登録日2023-10-31
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献The global map of Omicron Subvariants Spike with two antibodies
To Be Published
8XZ8
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BU of 8xz8 by Molmil
BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
著者Yue, C, Liu, P.
登録日2024-01-21
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.65 Å)
主引用文献BA.2.86 Spike in complex with bovine ACE2
To Be Published
8XZ9
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BU of 8xz9 by Molmil
BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Yue, C, Liu, P.
登録日2024-01-21
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.37 Å)
主引用文献BA.2.86 Spike in complex with bovine ACE2
To Be Published
8XZA
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BU of 8xza by Molmil
BA.2.86 Spike in complex with bovine ACE2 (Local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
著者Yue, C, Liu, P.
登録日2024-01-21
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (4.07 Å)
主引用文献BA.2.86 Spike in complex with bovine ACE2
To Be Published
8Y32
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BU of 8y32 by Molmil
BA.2.86-V483 RBD in complex with bACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
著者Yue, C, Liu, P.
登録日2024-01-28
公開日2024-11-13
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (4.13 Å)
主引用文献BA.2.86-V483 RBD in complex with bACE2
To Be Published
9F2H
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BU of 9f2h by Molmil
Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
分子名称: 1,2-ETHANEDIOL, 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine, Nucleoprotein, ...
著者Marquez-Monino, M.A, Gonzalez, B, Perez-Canadillas, J.M.
登録日2024-04-23
公開日2024-11-13
最終更新日2025-01-15
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.
Structure, 33, 2025
9C44
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BU of 9c44 by Molmil
SARS-CoV-2 S + S2L20
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, S2L20 Fab Heavy Chain Variable, ...
著者McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2024-06-03
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Design of customized coronavirus receptors.
Nature, 635, 2024
9C45
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BU of 9c45 by Molmil
SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region)
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, S2L20 Fab Heavy Chain Variable, ...
著者McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2024-06-03
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Design of customized coronavirus receptors.
Nature, 635, 2024
9CO6
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BU of 9co6 by Molmil
BA.5 spike/Nanosota-9 complex
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-9, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO7
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BU of 9co7 by Molmil
Local refinement of BA.5 spike/Nanosota-9 complex
分子名称: Nanosota-9, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.32 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO8
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BU of 9co8 by Molmil
JN.1 spike/Nanosota-9 complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-9, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (2.99 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO9
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BU of 9co9 by Molmil
Local refinement of JN.1 spike/Nanosota-9 complex
分子名称: Nanosota-9, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-07-16
公開日2024-11-20
最終更新日2024-12-11
実験手法ELECTRON MICROSCOPY (3.44 Å)
主引用文献Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9EVY
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BU of 9evy by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant E136D
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-04-02
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024

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件を2025-07-09に公開中

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