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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
8AZC
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BU of 8azc by Molmil
Structure of SARS-CoV-2 NSP3 macrodomain in the apo form
分子名称: 3[N-MORPHOLINO]PROPANE SULFONIC ACID, CHLORIDE ION, Papain-like protease nsp3
著者Sander, S, Tidow, H, Fliegert, R, Sandmann, M.
登録日2022-09-05
公開日2023-09-13
最終更新日2024-09-18
実験手法X-RAY DIFFRACTION (0.93 Å)
主引用文献Structure of SARS-CoV-2 NSP3 macrodomain in the apo form
To Be Published
8F0I
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BU of 8f0i by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody COVA309-22
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA309-22 heavy chain, COVA309-22 light chain, ...
著者Yuan, M, Wilson, I.A.
登録日2022-11-03
公開日2023-09-13
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (3.7 Å)
主引用文献Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual.
Iscience, 26, 2023
8U2X
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BU of 8u2x by Molmil
Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2 (H235A mutant)
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, Uridylate-specific endoribonuclease nsp15
著者Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2023-09-06
公開日2023-09-13
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2 (H235A mutant)
To be published
7YR4
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BU of 7yr4 by Molmil
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(interface)
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Wang, L.
登録日2022-08-08
公開日2023-09-20
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (4.12 Å)
主引用文献BA.2.75 in complex with ACE2
To Be Published
8CQ1
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BU of 8cq1 by Molmil
Stem-Loop 4 of the 5'-UTR of the SARS-CoV2 genomic RNA
分子名称: 5_SL4
著者Duchardt-Ferner, E, Voegele, J.
登録日2023-03-03
公開日2023-09-20
最終更新日2023-11-22
実験手法SOLUTION NMR
主引用文献High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR.
Nucleic Acids Res., 51, 2023
8EDF
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BU of 8edf by Molmil
Bovine Fab SKD in complex with Sars COV-2 receptor binding domain
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, SKD Fab Light chain, SKD Fab heavy chain, ...
著者Stanfield, R.L, Wilson, I.A.
登録日2022-09-04
公開日2023-09-20
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (3.4 Å)
主引用文献The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8GVD
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BU of 8gvd by Molmil
SARS-CoV-2 Mpro in complex with D-4-38
分子名称: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE, 3C-like proteinase nsp5
著者Liu, M, Huang, H.
登録日2022-09-14
公開日2023-09-20
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献SARS-CoV-2 Mpro in complex with D-4-38
To Be Published
8GWJ
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BU of 8gwj by Molmil
SARS CoV-2 Mpro 1-302 C145A in complex with peptide 7
分子名称: Replicase polyprotein 1ab, VAL-LYS-LEU-GLN-ALA-VAL-PHE-ARG
著者Liu, M, Huang, H.
登録日2022-09-17
公開日2023-09-20
実験手法X-RAY DIFFRACTION (2.9 Å)
主引用文献SARS CoV-2 Mpro 1-302 C145A in complex with peptide 7
To Be Published
8DD6
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BU of 8dd6 by Molmil
SARS-CoV-2 Main Protease (Mpro) H163A Mutant in Complex with GC376
分子名称: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, DIMETHYL SULFOXIDE, ORF1a polyprotein
著者Tran, N, McLeod, M.J, Kalyaanamoorthy, S, Ganesan, A, Holyoak, T.
登録日2022-06-17
公開日2023-09-27
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease.
Nat Commun, 14, 2023
8P99
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SARS-CoV-2 S-protein:D614G mutant in 1-up 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, Spike protein S1,Spike glycoprotein
著者Adhav, A, Forcada-Nadal, A, Marco-Marin, C, Lopez-Redondo, M.L, Llacer, J.L.
登録日2023-06-05
公開日2023-09-27
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献C-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein.
J.Med.Chem., 66, 2023
7UKL
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BU of 7ukl by Molmil
Cryo-EM structure of Antibody 12-16 in complex with prefusion SARS-CoV-2 Spike glycoprotein
分子名称: 12-16 Fab Heavy Chain, 12-16 Fab Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Casner, R.G, Shapiro, L.
登録日2022-04-01
公開日2023-10-04
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.09 Å)
主引用文献Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking.
Immunity, 56, 2023
7UKM
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BU of 7ukm by Molmil
Cryo-EM structure of Antibody 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein
分子名称: 12-19 Fab Heavy Chain, 12-19 Fab Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Casner, R.G, Shapiro, L.
登録日2022-04-01
公開日2023-10-04
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Structure and Neutralization of two quaternary SARS-CoV-2 omicron antibodies
To Be Published
8CRF
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BU of 8crf by Molmil
Crystal structure of N-terminal SARS-CoV-2 nsp1 in complex with fragment hit 5E11 refined against anomalous diffraction data
分子名称: Host translation inhibitor nsp1, ~{N}-methyl-1-(4-thiophen-2-ylphenyl)methanamine
著者Ma, S, Mykhaylyk, V, Pinotsis, N, Bowler, M.W, Kozielski, F.
登録日2023-03-08
公開日2023-10-04
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献High-Confidence Placement of Fragments into Electron Density Using Anomalous Diffraction-A Case Study Using Hits Targeting SARS-CoV-2 Non-Structural Protein 1.
Int J Mol Sci, 24, 2023
8FXC
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BU of 8fxc by Molmil
SARS-CoV-2 BQ.1.1 spike RBD bound to the human ACE2 ectodomain and the S309 neutralizing antibody Fab fragment
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, S309 Heavy chain, ...
著者Park, Y.J, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2023-01-24
公開日2023-10-04
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Neutralization, effector function and immune imprinting of Omicron variants.
Nature, 621, 2023
8I3S
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BU of 8i3s by Molmil
Local CryoEM structure of the SARS-CoV-2 S6P in complex with 7B3 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain od Fab 7B3, Light chain of Fab 7B3, ...
著者Li, Z, Yu, F, Cao, S, ZHao, H.
登録日2023-01-17
公開日2023-10-04
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Broadly neutralizing antibodies derived from the earliest COVID-19 convalescents protect mice from SARS-CoV-2 variants challenge.
Signal Transduct Target Ther, 8, 2023
8I3U
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BU of 8i3u by Molmil
Local CryoEM structure of the SARS-CoV-2 S6P in complex with 14B1 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab 14B1, Light chain of Fab 14B1, ...
著者Li, Z, Yu, F, Cao, S.
登録日2023-01-18
公開日2023-10-04
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Broadly neutralizing antibodies derived from the earliest COVID-19 convalescents protect mice from SARS-CoV-2 variants challenge.
Signal Transduct Target Ther, 8, 2023
8EQF
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BU of 8eqf by Molmil
cryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibody STI-9167
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab heavy chain, Fab light chain, ...
著者Bajic, G.
登録日2022-10-07
公開日2023-10-11
最終更新日2025-05-21
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献An in vitro experimental pipeline to characterize the epitope of a SARS-CoV-2 neutralizing antibody.
Mbio, 15, 2024
8H3G
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BU of 8h3g by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Enstrelvir
分子名称: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, GLYCEROL
著者Wang, H, Lin, M, Duan, Y, Zhang, X, Zhou, H, Bian, Q, Liu, X, Rao, Z, Yang, H.
登録日2022-10-08
公開日2023-10-11
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.46 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H3L
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Enstrelvir
分子名称: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
著者Wang, H, Lin, M, Duan, Y, Zhang, X, Zhou, H, Bian, Q, Liu, X, Rao, Z, Yang, H.
登録日2022-10-08
公開日2023-10-11
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H4Y
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BU of 8h4y by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) F140L Mutant in Complex with Inhibitor Nirmatrelvir
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Lin, M, Liu, X.
登録日2022-10-11
公開日2023-10-11
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H51
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BU of 8h51 by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir
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Lin, M, Liu, X.
登録日2022-10-11
公開日2023-10-11
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.18 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H57
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BU of 8h57 by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) A193P Mutant in Complex with Inhibitor Nirmatrelvir
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Lin, M, Liu, X.
登録日2022-10-12
公開日2023-10-11
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H5F
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BU of 8h5f by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor Nirmatrelvir
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Lin, M, Liu, X.
登録日2022-10-13
公開日2023-10-11
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.79 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H6I
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The crystal structure of SARS-CoV-2 3C-like protease Double Mutant (L50F and E166V) in complex with a traditional Chinese Medicine Inhibitors
分子名称: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one, 3C-like proteinase nsp5
著者Lin, M, Liu, X.
登録日2022-10-17
公開日2023-10-11
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023
8H7K
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SARS-CoV-2 Mpro Double Mutant (H41A and T21I) in complex with nsp4/5 peptidyl substrate
分子名称: 3C-like proteinase nsp5, nsp4/5 peptidyl substrate
著者Lin, M, Liu, X.
登録日2022-10-20
公開日2023-10-11
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Nature, 622, 2023

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件を2025-07-09に公開中

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