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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
8UPX
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BU of 8upx by Molmil
Omicron-S-MERS-RBD
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 glycoprotein,SARS-CoV-2 omicron spike with MERS RBD
著者Bu, F, Li, F, Liu, B.
登録日2023-10-23
公開日2024-08-21
最終更新日2024-09-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Pan-beta-coronavirus subunit vaccine prevents SARS-CoV-2 Omicron, SARS-CoV, and MERS-CoV challenge.
J.Virol., 98, 2024
8YE4
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BU of 8ye4 by Molmil
The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF
分子名称: Beta-2-microglobulin, MHC class I antigen precusor, Spike protein S1, ...
著者Deng, S.S, Jin, T.C, Xu, Z.H, Wang, M.H.
登録日2024-02-21
公開日2024-08-21
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
J.Biol.Chem., 300, 2024
8ZHD
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BU of 8zhd by Molmil
SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs
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, Heavy chain of R1-26 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-10
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (3.41 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHE
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BU of 8zhe by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs
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, Heavy chain of R1-26 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-10
公開日2024-08-21
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHF
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BU of 8zhf by Molmil
SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate
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, Heavy chain of R1-26 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-10
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (5.26 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHG
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BU of 8zhg by Molmil
SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab region
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-26 Fab, Light chain of R1-26 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-10
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (3.51 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHH
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BU of 8zhh by Molmil
SARS-CoV-2 spike trimer (6P) in complex with two H18 Fabs
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-10
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (5.55 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHI
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BU of 8zhi by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (6.05 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHJ
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BU of 8zhj by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry)
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (8.45 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHK
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BU of 8zhk by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C3 symmetry)
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (6.3 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHL
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BU of 8zhl by Molmil
SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (3.96 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHM
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BU of 8zhm by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (3.39 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHN
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BU of 8zhn by Molmil
SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs (one RBD rotated)
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, Heavy chain of H18 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (4.12 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHO
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BU of 8zho by Molmil
SARS-CoV-2 S1 in complex with H18 and R1-32 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, Heavy chain of R1-32 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
実験手法ELECTRON MICROSCOPY (3.54 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZHP
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BU of 8zhp by Molmil
Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of H18 Fab, Heavy chain of R1-32 Fab, ...
著者Yan, Q, Gao, X, Liu, B, Hou, R, He, P, Li, Z, Chen, Q, Wang, J, He, J, Chen, L, Zhao, J, Xiong, X.
登録日2024-05-11
公開日2024-08-21
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.66 Å)
主引用文献Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants
To Be Published
8ZV9
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BU of 8zv9 by Molmil
Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF
分子名称: 1,2-ETHANEDIOL, Beta-2-microglobulin, MHC class I antigen, ...
著者Deng, S.S, Jin, T.C, Xu, Z.H, Wang, M.H.
登録日2024-06-11
公開日2024-08-21
最終更新日2024-08-28
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structural insights into immune escape at killer T cell epitope by SARS-CoV-2 Spike Y453F variants.
J.Biol.Chem., 300, 2024
9F9Y
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BU of 9f9y by Molmil
SARS-CoV-2 BA-2.87.1 Spike ectodomain
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 glycoprotein,Fibritin
著者Ren, J, Stuart, D.I, Duyvesteyn, H.M.E.
登録日2024-05-09
公開日2024-08-21
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike.
Structure, 32, 2024
8TY3
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BU of 8ty3 by Molmil
MI-31 ligand bound to SARS-CoV-2 Mpro
分子名称: (1S,3aR,6aS)-2-[(3,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-24
公開日2024-08-28
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献MI-31 bound to SARS-CoV-2 Mpro
To Be Published
8TY4
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BU of 8ty4 by Molmil
MI-30 bound to Mpro of SARS-CoV-2
分子名称: (1S,3aR,6aS)-2-[(2,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-24
公開日2024-08-28
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献MI-30 bound to SARS-CoV-2 Mpro
To Be Published
8TY5
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BU of 8ty5 by Molmil
MI-14 bound to Mpro of SARS-CoV-2
分子名称: (1R,2S,5S)-3-[(2,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-08-24
公開日2024-08-28
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献MI-14 bound to SARS-CoV-2 Mpro
To Be Published
8UG9
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BU of 8ug9 by Molmil
XBB.1.5 spike/Nb5 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-5, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-10-05
公開日2024-08-28
最終更新日2024-09-25
実験手法ELECTRON MICROSCOPY (3.49 Å)
主引用文献Dual-role epitope on SARS-CoV-2 spike enhances and neutralizes viral entry across different variants.
Plos Pathog., 20, 2024
8WTI
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BU of 8wti by Molmil
Crystal structure of the SARS-CoV-2 main protease in complex with 20j
分子名称: 3C-like proteinase nsp5, DI(HYDROXYETHYL)ETHER, SULFATE ION, ...
著者Zeng, R, Zhao, X, Yang, S.Y, Lei, J.
登録日2023-10-18
公開日2024-08-28
実験手法X-RAY DIFFRACTION (1.5 Å)
主引用文献Discovery of alpha-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups.
Bioorg.Chem., 143, 2024
9FEH
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BU of 9feh by Molmil
Crystal structure of SARS-CoV-2 nsp14 methyltransferase domain in complex with the STM957 inhibitor
分子名称: Transcription factor ETV6,Guanine-N7 methyltransferase nsp14, ZINC ION, ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-(2-pyridin-3-ylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-cyano-~{N}-ethyl-4-methoxy-benzenesulfonamide
著者Zilecka, E, Klima, M, Boura, E.
登録日2024-05-20
公開日2024-08-28
最終更新日2024-09-04
実験手法X-RAY DIFFRACTION (1.99 Å)
主引用文献Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39.
J Struct Biol X, 10, 2024
9FQ9
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BU of 9fq9 by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21110 (compound 29b in publication)
分子名称: (5-chloranylpyridin-3-yl) 4-ethoxy-2-fluoranyl-benzoate, BROMIDE ION, Non-structural protein 11
著者Strater, N, Claff, T, Sylvester, K, Oneto, A, Guetschow, M, Mueller, C.E.
登録日2024-06-19
公開日2024-08-28
最終更新日2024-09-25
実験手法X-RAY DIFFRACTION (1.25 Å)
主引用文献Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity.
J.Med.Chem., 67, 2024
9FQA
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BU of 9fqa by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21101 (compound 30b in publication)
分子名称: (5-chloranylpyridin-3-yl) 2-fluoranyl-4-phenylmethoxy-benzoate, BROMIDE ION, MAGNESIUM ION, ...
著者Strater, N, Claff, T, Sylvester, K, Oneto, A, Guetschow, M, Mueller, C.E.
登録日2024-06-14
公開日2024-08-28
最終更新日2024-09-25
実験手法X-RAY DIFFRACTION (1.47 Å)
主引用文献Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity.
J.Med.Chem., 67, 2024

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件を2024-10-16に公開中

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