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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
7UAR
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BU of 7uar by Molmil
Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1717
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, C1717 Fab Heavy Chain, ...
著者Barnes, C.O.
登録日2022-03-13
公開日2022-04-27
最終更新日2022-06-22
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins.
Immunity, 55, 2022
7X7N
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BU of 7x7n by Molmil
3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5.
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, Synthetic peptide SIH-5
著者Khatri, B, Pramanick, I, Malladi, S.K, Rajmani, R.S, Kumar, S, Ghosh, P, Sengupta, N, Rahisuddin, R, Kumaran, S, Ringe, R.P, Varadarajan, R, Dutta, S, Chatterjee, J.
登録日2022-03-10
公開日2022-04-27
最終更新日2022-11-16
実験手法ELECTRON MICROSCOPY (4.47 Å)
主引用文献A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein.
Nat.Chem.Biol., 18, 2022
7RBU
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BU of 7rbu by Molmil
SARS-CoV-2 Spike in complex with PVI.V6-14 Fab
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, PVI.V6-14 Fab heavy chain, ...
著者Altomare, C.G, Bajic, G.
登録日2021-07-06
公開日2022-05-04
最終更新日2022-07-06
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain.
Mbio, 13, 2022
7RBV
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BU of 7rbv by Molmil
SARS-CoV-2 Spike in complex with PVI.V6-14 Fab
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, PVI.V6-14 Fab heavy chain, ...
著者Altomare, C.G, Bajic, G.
登録日2021-07-06
公開日2022-05-04
最終更新日2022-07-06
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain.
Mbio, 13, 2022
7U2D
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BU of 7u2d by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, ADG20 heavy chain, ADG20 light chain, ...
著者Zhu, X, Yuan, M, Wilson, I.A.
登録日2022-02-23
公開日2022-05-04
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.76 Å)
主引用文献A broad and potent neutralization epitope in SARS-related coronaviruses.
Proc.Natl.Acad.Sci.USA, 119, 2022
7U2E
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BU of 7u2e by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, ADI-55688 heavy chain, ADI-55688 light chain, ...
著者Yuan, M, Zhu, X, Wilson, I.A.
登録日2022-02-23
公開日2022-05-04
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (2.85 Å)
主引用文献A broad and potent neutralization epitope in SARS-related coronaviruses.
Proc.Natl.Acad.Sci.USA, 119, 2022
7URQ
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BU of 7urq by Molmil
Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 1
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, CITRIC ACID, COV11 Fab HEAVY CHAIN, ...
著者Tolbert, W.D, Pazgier, M.
登録日2022-04-22
公開日2022-05-04
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Front Immunol, 14, 2023
7URS
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BU of 7urs by Molmil
Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 2
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, COV11 Fab HEAVY CHAIN, ...
著者Tolbert, W.D, Pazgier, M.
登録日2022-04-22
公開日2022-05-04
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11.
Front Immunol, 14, 2023
7WE7
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BU of 7we7 by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv282
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 Fab 282, ...
著者Wang, X, Wang, L.
登録日2021-12-23
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WE8
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BU of 7we8 by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv265
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 Fab 265, ...
著者Wang, X, Wang, L.
登録日2021-12-23
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WE9
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BU of 7we9 by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv289
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, ...
著者Wang, X, Wang, L.
登録日2021-12-23
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WEA
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BU of 7wea by Molmil
SARS-CoV-2 Omicron variant spike protein in complex with two XGv347 binding to one close state RBD and one open state 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, ...
著者Wang, X, Wang, L.
登録日2021-12-23
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WEC
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BU of 7wec by Molmil
SARS-CoV-2 Omicron variant spike protein with three XGv347 Fabs binding to three closed state RBDs
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, ...
著者Wang, X, Wang, L.
登録日2021-12-23
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7WEF
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BU of 7wef by Molmil
SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv289
分子名称: Spike protein S1, The heavy chain of Fab XGv289, The light chain of Fab XGv289
著者Wang, X, Wang, L.
登録日2021-12-23
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.
Nature, 603, 2022
7Z3Z
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BU of 7z3z by Molmil
Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid 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, STEARIC ACID, ...
著者Duyvesteyn, H.M.E, Carrique, L, Ren, J, Stuart, D.I, Fry, E.E.
登録日2022-03-03
公開日2022-05-04
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer
bioRxiv, 2020
7S6I
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BU of 7s6i by Molmil
SARS-CoV-2-6P-Mut2 S protein
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
著者Ozorowski, G, Torres, J.L, Ward, A.B.
登録日2021-09-14
公開日2022-05-11
最終更新日2022-05-25
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7S6J
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BU of 7s6j by Molmil
J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 1)
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, J08 fragment antigen binding heavy chain variable domain, ...
著者Ozorowski, G, Torres, J.L, Ward, A.B.
登録日2021-09-14
公開日2022-05-11
最終更新日2022-05-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7S6K
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BU of 7s6k by Molmil
J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 2)
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, J08 fragment antigen binding heavy chain variable domain, ...
著者Ozorowski, G, Torres, J.L, Ward, A.B.
登録日2021-09-14
公開日2022-05-11
最終更新日2022-05-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7S6L
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BU of 7s6l by Molmil
J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (conformation 3)
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, J08 fragment antigen binding heavy chain variable domain, ...
著者Ozorowski, G, Torres, J.L, Ward, A.B.
登録日2021-09-14
公開日2022-05-11
最終更新日2022-05-25
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7SBU
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BU of 7sbu by Molmil
Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a highly potent antibody J08 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, J08 Fab heavy chain, ...
著者Liu, H, Wilson, I.A.
登録日2021-09-25
公開日2022-05-11
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.53 Å)
主引用文献Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody.
Proc.Natl.Acad.Sci.USA, 119, 2022
7UV5
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BU of 7uv5 by Molmil
The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin
分子名称: 1,2-ETHANEDIOL, Papain-like protease nsp3, Ubiquitin, ...
著者Osipiuk, J, Tesar, C, Endres, M, Lanham, B.T, Wydorski, P, Fushman, D, Joachimiak, L, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2022-04-29
公開日2022-05-11
最終更新日2023-10-25
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.
Nat Commun, 14, 2023
7WHI
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BU of 7whi by Molmil
The state 2 complex structure of Omicron spike with Bn03 (2-up RBD, 4 nanobodies)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Bn03_nano1, Bn03_nano2, ...
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2021-12-30
公開日2022-05-11
実験手法ELECTRON MICROSCOPY (2.93 Å)
主引用文献Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody.
Cell, 185, 2022
7WHK
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BU of 7whk by Molmil
The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Bn03_nano1, Bn03_nano2, ...
著者Zhan, W.Q, Zhang, X, Chen, Z.G, Sun, L.
登録日2021-12-30
公開日2022-05-11
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody.
Cell, 185, 2022
7X9E
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BU of 7x9e by Molmil
Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide
分子名称: 76E1 Fab Heavy Chain, 76E1 Fab Light Chain, Spike peptide
著者Chen, X, Zhang, T, Ding, J, Sun, X, Sun, B.
登録日2022-03-15
公開日2022-05-11
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2.
Nat Microbiol, 7, 2022
7EPX
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BU of 7epx by Molmil
S protein of SARS-CoV-2 in complex with GW01
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, ...
著者Shen, Y.P, Zhang, Y.Y, Yan, R.H, Li, Y.N, Zhou, Q.
登録日2021-04-28
公開日2022-05-18
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Novel sarbecovirus bispecific neutralizing antibodies with exceptional breadth and potency against currently circulating SARS-CoV-2 variants and sarbecoviruses.
Cell Discov, 8, 2022

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件を2024-07-17に公開中

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