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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
7FCP
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Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)
分子名称: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ...
著者Zheng, P, Jin, T.
登録日2021-07-15
公開日2022-06-15
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Ultrapotent neutralizing antibodies against SARS-CoV-2 with a high degree of mutation resistance.
J.Clin.Invest., 132, 2022
7FCQ
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Crystallographic structure of neutralizing antibody P14-44 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, P14-44 antibody Fab fragment heavy chain, ...
著者Zheng, P, Jin, T.
登録日2021-07-15
公開日2022-06-15
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.89 Å)
主引用文献Ultrapotent neutralizing antibodies against SARS-CoV-2 with a high degree of mutation resistance.
J.Clin.Invest., 132, 2022
7WHC
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Crystal structure of SARS-CoV-2 3CLpro catalytic domain
分子名称: 3C-like proteinase nsp5
著者Shin, D.H, Jo, S.R.
登録日2021-12-30
公開日2022-06-15
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.269 Å)
主引用文献Dimerization Tendency of 3CLpros of Human Coronaviruses Based on the X-ray Crystal Structure of the Catalytic Domain of SARS-CoV-2 3CLpro.
Int J Mol Sci, 23, 2022
7XIC
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S-ECD (Omicron) in complex with STS165
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Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2022-04-12
公開日2022-06-15
最終更新日2024-11-06
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants.
Iscience, 25, 2022
7XID
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S-ECD (Omicron) in complex with PD of ACE2
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 2, ...
著者Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
登録日2022-04-12
公開日2022-06-15
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants.
Iscience, 25, 2022
7XO5
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BU of 7xo5 by Molmil
SARS-CoV-2 Omicron BA.1 Variant Spike Trimer with one mouse ACE2 Bound
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Xu, Y, Wu, C, Liu, H, Yin, W, Xu, H.E.
登録日2022-05-01
公開日2022-06-15
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.13 Å)
主引用文献Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.
Cell Res., 32, 2022
7XO6
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SARS-CoV-2 Omicron BA.1 Variant RBD with mouse ACE2 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, Angiotensin-converting enzyme 2, ...
著者Xu, Y, Wu, C, Liu, H, Yin, W, Xu, H.E.
登録日2022-05-01
公開日2022-06-15
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.
Cell Res., 32, 2022
7XO9
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SARS-CoV-2 Omicron BA.2 Variant RBD complexed with human ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, CHLORIDE ION, ...
著者Xu, Y, Wu, C, Liu, H, Yin, W, Xu, H.E.
登録日2022-05-01
公開日2022-06-15
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.
Cell Res., 32, 2022
7XOA
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BU of 7xoa by Molmil
SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with one mouse ACE2 Bound
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Xu, Y, Wu, C, Liu, H, Yin, W, Xu, H.E.
登録日2022-05-01
公開日2022-06-15
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.
Cell Res., 32, 2022
7XOC
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BU of 7xoc by Molmil
SARS-CoV-2 Omicron BA.2 Variant RBD complexed with mouse ACE2
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 2, ...
著者Xu, Y, Wu, C, Liu, H, Yin, W, Xu, H.E.
登録日2022-05-01
公開日2022-06-15
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.
Cell Res., 32, 2022
7XOD
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SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three JMB2002 Fab 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, Heavy chain of JMB2002 Fab, ...
著者Xu, Y, Wu, C, Liu, H, Yin, W, Xu, H.E.
登録日2022-05-01
公開日2022-06-15
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.27 Å)
主引用文献Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins.
Cell Res., 32, 2022
7F3Q
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BU of 7f3q by Molmil
SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab
分子名称: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of A34-2 Fab, ...
著者Dou, Y, Wang, X, Liu, P, Lu, B, Wang, K.
登録日2021-06-16
公開日2022-06-22
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Development of neutralizing antibodies against SARS-CoV-2, using a high-throughput single-B-cell cloning method.
Antib Ther, 6, 2023
7F5R
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Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2
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, ...
著者Wang, X.Q, Ding, Q, Lan, J, Ren, W.L.
登録日2021-06-22
公開日2022-06-22
最終更新日2025-06-18
実験手法X-RAY DIFFRACTION (3.01 Å)
主引用文献Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption.
Plos Pathog., 17, 2021
7FC5
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Crystal structure of SARS-CoV-2 RBD and horse ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1
著者Wang, X.Q, Lan, J, Ge, J.W.
登録日2021-07-13
公開日2022-06-22
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.894 Å)
主引用文献Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2.
Structure, 30, 2022
7MB4
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp4/5 (P6-P1)
分子名称: 3C-like proteinase, THR-SER-ALA-VAL-LEU-GLN
著者Lockbaum, G.J, Schiffer, C.A.
登録日2021-03-31
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.83 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB5
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp5/6 (P6-P1)
分子名称: 3C-like proteinase, SER-GLY-VAL-THR-PHE-GLN
著者Lockbaum, G.J, Schiffer, C.A.
登録日2021-03-31
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB6
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp6/7 (P6-P1)
分子名称: 3C-like proteinase, LYS-VAL-ALA-THR-VAL-GLN
著者Lockbaum, G.J, Schiffer, C.A.
登録日2021-03-31
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.21 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB7
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp7/8 (P6-P1)
分子名称: 3C-like proteinase, ASN-ARG-ALA-THR-LEU-GLN
著者Lockbaum, G.J, Schiffer, C.A.
登録日2021-03-31
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.02 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB8
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp8/9 (P6-P1)
分子名称: 3C-like proteinase, SER-ALA-VAL-LYS-LEU-GLN
著者Lockbaum, G.J, Schiffer, C.A.
登録日2021-03-31
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.62 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB9
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp10/11 (P6-P1)
分子名称: 3C-like proteinase, ARG-GLU-PRO-MET-LEU-GLN
著者Lockbaum, G.J, Schiffer, C.A.
登録日2021-03-31
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.81 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T70
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 4/5
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, GLYCEROL, ...
著者Shaqra, A.M, Schiffer, C.A.
登録日2021-12-14
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T8M
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 5/6
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, GLYCEROL, ...
著者Shaqra, A.M, Schiffer, C.A.
登録日2021-12-16
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T8R
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 7/8
分子名称: 1,2-ETHANEDIOL, 3C-like proteinase, GLYCEROL, ...
著者Shaqra, A.M, Schiffer, C.A.
登録日2021-12-16
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T9Y
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 8/9
分子名称: 3C-like proteinase, GLYCEROL, Nonstructural protein 8/9
著者Shaqra, A.M, Schiffer, C.A.
登録日2021-12-20
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.18 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TA4
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 9/10
分子名称: 3C-like proteinase, Nonstructural protein 9/10
著者Shaqra, A.M, Schiffer, C.A.
登録日2021-12-20
公開日2022-06-22
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.78 Å)
主引用文献Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022

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件を2025-07-09に公開中

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