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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
7SY5
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Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain bound to human ACE2 ectodomain (global 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, Processed angiotensin-converting enzyme 2, ...
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
登録日2021-11-24
公開日2021-12-29
最終更新日2022-01-05
実験手法ELECTRON MICROSCOPY (2.59 Å)
主引用文献Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY7
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BU of 7sy7 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain bound to human ACE2 ectodomain (global 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, Processed angiotensin-converting enzyme 2, ...
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
登録日2021-11-24
公開日2021-12-29
実験手法ELECTRON MICROSCOPY (2.81 Å)
主引用文献Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7T9J
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Cryo-EM structure of the SARS-CoV-2 Omicron spike 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Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Tuttle, K.S, Subramaniam, S.
登録日2021-12-19
公開日2021-12-29
最終更新日2022-05-18
実験手法ELECTRON MICROSCOPY (2.79 Å)
主引用文献SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex.
Science, 375, 2022
7T9K
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BU of 7t9k by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with human 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, Processed angiotensin-converting enzyme 2, ...
著者Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Tuttle, K.S, Subramaniam, S.
登録日2021-12-19
公開日2021-12-29
最終更新日2022-05-18
実験手法ELECTRON MICROSCOPY (2.45 Å)
主引用文献SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex.
Science, 375, 2022
7T9W
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BU of 7t9w by Molmil
Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2
分子名称: CHLORIDE ION, GLYCEROL, Papain-like protease nsp3
著者Stogios, P.J, Skarina, T, Di Leo, R, Savchenko, A, Joachimiak, A, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
登録日2021-12-20
公開日2021-12-29
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2
To Be Published
7SPO
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Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ...
著者Shi, K, Aihara, H.
登録日2021-11-02
公開日2022-01-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.92 Å)
主引用文献Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography.
Nat Commun, 12, 2021
7SPP
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BU of 7spp by Molmil
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 2C02
分子名称: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
著者Shi, K, Aihara, H.
登録日2021-11-02
公開日2022-01-05
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.96 Å)
主引用文献Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography.
Nat Commun, 12, 2021
7SJS
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BU of 7sjs by Molmil
Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CC40.8
分子名称: ACETATE ION, CC40.8 Fab heavy chain, CC40.8 Fab light chain, ...
著者Yuan, M, Wilson, I.A.
登録日2021-10-18
公開日2022-01-12
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.612 Å)
主引用文献A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection.
Sci Transl Med, 14, 2022
7TAS
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BU of 7tas by Molmil
SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (local refinement of the RBD and S2K146)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, S2K146 Fab heavy chain, S2K146 Fab light chain, ...
著者Park, Y.J, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
登録日2021-12-21
公開日2022-01-12
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.
Science, 375, 2022
7TAT
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BU of 7tat by Molmil
SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (two receptor-binding domains open)
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, S2K146 Fab heavy chain, ...
著者Park, Y.J, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2021-12-21
公開日2022-01-12
最終更新日2022-02-09
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.
Science, 375, 2022
7TB4
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BU of 7tb4 by Molmil
Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern
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, Surface glycoprotein
著者Zhou, T, Tsybovsky, T, Kwong, P.D.
登録日2021-12-21
公開日2022-01-12
最終更新日2022-01-19
実験手法ELECTRON MICROSCOPY (3.29 Å)
主引用文献Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants.
Biorxiv, 2021
7W92
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BU of 7w92 by Molmil
Open state of SARS-CoV-2 Delta variant spike protein
分子名称: Spike glycoprotein
著者Cong, Y, Liu, C.X.
登録日2021-12-09
公開日2022-01-12
最終更新日2022-03-02
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W9C
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BU of 7w9c by Molmil
SARS-CoV-2 Delta S-ACE2-C3
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Cong, Y, Liu, C.X.
登録日2021-12-09
公開日2022-01-12
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W9E
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BU of 7w9e by Molmil
SARS-CoV-2 Delta S-8D3
分子名称: Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain, Spike glycoprotein, The light chain of 8D3 fab
著者Cong, Y, Liu, C.X.
登録日2021-12-09
公開日2022-01-12
最終更新日2022-03-02
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W9F
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BU of 7w9f by Molmil
SARS-CoV-2 Delta S-RBD-8D3
分子名称: Spike protein S1, The heavy chain of 8D3, The light chain of 8D3
著者Cong, Y, Liu, C.X.
登録日2021-12-09
公開日2022-01-12
最終更新日2022-03-02
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7DVP
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BU of 7dvp by Molmil
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp4|5 peptidyl substrate
分子名称: 3C-like proteinase, nsp4/5 peptidyl substrate
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-01-14
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.69 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7DVW
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BU of 7dvw by Molmil
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp5|6 peptidyl substrate
分子名称: 3C-like proteinase, DIMETHYL SULFOXIDE, nsp5/6 peptidyl substrate
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-01-15
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.49 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7DVX
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BU of 7dvx by Molmil
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp6|7 peptidyl substrate
分子名称: 3C-like proteinase, nsp6/7 peptidyl substrate
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-01-15
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7DVY
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BU of 7dvy by Molmil
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp9|10 peptidyl substrate
分子名称: 3C-like proteinase, nsp9/10 peptidyl substrate
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-01-15
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7DW0
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BU of 7dw0 by Molmil
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp14|15 peptidyl substrate
分子名称: 3C-like proteinase, nsp14/15 peptidyl substrate
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-01-15
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.81 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7DW6
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BU of 7dw6 by Molmil
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp15|16 peptidyl substrate
分子名称: 3C-like proteinase, nsp15/16 peptidyl substrate
著者Liu, X, Zhao, Y, Yang, H, Rao, Z.
登録日2021-01-15
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 119, 2022
7F5F
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BU of 7f5f by Molmil
SARS-CoV-2 ORF8 S84
分子名称: CALCIUM ION, ORF8 protein
著者Chen, S, Zhou, Z, Chen, X.
登録日2021-06-22
公開日2022-01-19
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.62 Å)
主引用文献Crystal Structures of Bat and Human Coronavirus ORF8 Protein Ig-Like Domain Provide Insights Into the Diversity of Immune Responses.
Front Immunol, 12, 2021
7MSQ
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BU of 7msq by Molmil
Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)
分子名称: AB-3467 Fab Heavy Chain, AB-3467 Fab Light Chain, CHLORIDE ION, ...
著者Langley, D.B, Christ, D.
登録日2021-05-12
公開日2022-01-19
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (2.29 Å)
主引用文献Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability.
Immunity, 54, 2021
7PKU
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BU of 7pku by Molmil
Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a
分子名称: 3C-like proteinase, Nucleoprotein
著者Bessa, L.M, Guseva, S, Camacho-Zarco, A.R, Salvi, N, Blackledge, M.
登録日2021-08-26
公開日2022-01-19
最終更新日2024-06-19
実験手法SOLUTION NMR
主引用文献The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a.
Sci Adv, 8, 2022
7QNW
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BU of 7qnw by Molmil
The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Beta-55 heavy chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-12-23
公開日2022-01-19
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.
Cell, 185, 2022

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件を2024-10-16に公開中

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