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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
7VX1
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BU of 7vx1 by Molmil
SARS-CoV-2 Beta variant spike protein in open state
分子名称: Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-11-24
最終更新日2022-03-16
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VX9
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BU of 7vx9 by Molmil
SARS-CoV-2 Kappa variant spike protein in complex wth ACE2, state C1
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-11-24
最終更新日2022-03-16
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VXA
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BU of 7vxa by Molmil
SARS-CoV-2 Kappa variant spike protein in complex with ACE2, state C2a
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-11-24
最終更新日2022-03-16
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7B0B
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BU of 7b0b by Molmil
Fab HbnC3t1p1_C6 bound to SARS-CoV-2 RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab heavy chain, IGK@ protein, ...
著者Borenstein-Katz, A, Diskin, R.
登録日2020-11-19
公開日2021-12-01
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.98 Å)
主引用文献Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants.
Immunity, 56, 2023
7DG6
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BU of 7dg6 by Molmil
Structure of SARS-Cov2-Mpro-1-302
分子名称: Replicase polyprotein 1ab
著者Fu, Z, Liu, M, Huang, H.
登録日2020-11-11
公開日2021-12-01
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Structure of SARS-CoV-2-Mpro-1-302
To Be Published
7RDY
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BU of 7rdy by Molmil
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - engaged class
分子名称: ADENOSINE-5'-DIPHOSPHATE, ALUMINUM FLUORIDE, CHAPSO, ...
著者Chen, J, Malone, B, Campbell, E.A, Darst, S.A.
登録日2021-07-12
公開日2021-12-01
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
Nat.Struct.Mol.Biol., 29, 2022
7RE0
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BU of 7re0 by Molmil
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - swiveled class
分子名称: ADENOSINE-5'-DIPHOSPHATE, ALUMINUM FLUORIDE, Helicase, ...
著者Chen, J, Malone, B, Campbell, E.A, Darst, S.A.
登録日2021-07-12
公開日2021-12-01
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
Nat.Struct.Mol.Biol., 29, 2022
7RE1
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BU of 7re1 by Molmil
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC (composite)
分子名称: ADENOSINE-5'-DIPHOSPHATE, ALUMINUM FLUORIDE, CHAPSO, ...
著者Chen, J, Malone, B, Campbell, E.A, Darst, S.A.
登録日2021-07-12
公開日2021-12-01
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.91 Å)
主引用文献Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
Nat.Struct.Mol.Biol., 29, 2022
7RE2
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BU of 7re2 by Molmil
SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(1)-RTC
分子名称: ADENOSINE-5'-DIPHOSPHATE, ALUMINUM FLUORIDE, CHAPSO, ...
著者Chen, J, Malone, B, Campbell, E.A, Darst, S.A.
登録日2021-07-12
公開日2021-12-01
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (3.17 Å)
主引用文献Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex.
Nat.Struct.Mol.Biol., 29, 2022
7VX4
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BU of 7vx4 by Molmil
ACE2-RBD in SARS-CoV-2 Beta variant S-ACE2 complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-12-01
最終更新日2022-03-16
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VX5
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BU of 7vx5 by Molmil
ACE2-RBD in SARS-CoV-2 Kappa variant S-ACE2 complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-12-01
最終更新日2022-03-16
実験手法ELECTRON MICROSCOPY (3.8 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VXD
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BU of 7vxd by Molmil
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 state
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-12-01
最終更新日2022-02-16
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VXE
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BU of 7vxe by Molmil
SARS-CoV-2 Kappa variant spike protein in open state
分子名称: Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-12-01
最終更新日2022-02-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7VXF
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BU of 7vxf by Molmil
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2B state
分子名称: Angiotensin-converting enzyme 2, Spike glycoprotein
著者Xu, C, Cong, Y.
登録日2021-11-12
公開日2021-12-01
最終更新日2022-02-16
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7DK2
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BU of 7dk2 by Molmil
Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, MW07 heavy chain, MW07 light chain, ...
著者Wang, J, Jiao, S, Wang, R, Zhang, J, Zhang, M, Wang, M, Chen, S.
登録日2020-11-22
公開日2021-12-08
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Architectural versatility of spike neutralization by a SARS-CoV-2 antibody
To Be Published
7NAB
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BU of 7nab by Molmil
Crystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide 1140-1165
分子名称: CITRIC ACID, CV3-25 Fab Heavy Chain, CV3-25 Fab Light Chain, ...
著者Chen, Y, Tolbert, W.D, Pazgier, M.
登録日2021-06-21
公開日2021-12-08
最終更新日2024-04-03
実験手法X-RAY DIFFRACTION (2.15 Å)
主引用文献Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern.
Cell Rep, 38, 2022
7SN0
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BU of 7sn0 by Molmil
Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2 from immunocompromised patient (d146*) in complex with human receptor ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Pan, J, Abraham, J, Clark, S.
登録日2021-10-27
公開日2021-12-08
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (3.08 Å)
主引用文献Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Science, 375, 2022
7SN2
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BU of 7sn2 by Molmil
Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Pan, J, Abraham, J, Yang, P, Shankar, S.
登録日2021-10-27
公開日2021-12-08
最終更新日2022-02-02
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Science, 375, 2022
7SN3
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BU of 7sn3 by Molmil
Structure of human SARS-CoV-2 spike glycoprotein trimer bound by neutralizing antibody C1C-A3 Fab (variable region)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Pan, J, Abraham, J, Shankar, S.
登録日2021-10-27
公開日2021-12-08
最終更新日2022-02-02
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain.
Science, 375, 2022
7DOI
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BU of 7doi by Molmil
Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir.
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Li, Z, Yu, X.
登録日2020-12-14
公開日2021-12-15
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
To Be Published
7DOK
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BU of 7dok by Molmil
Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir
分子名称: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
著者Li, Z, Yu, X.
登録日2020-12-14
公開日2021-12-15
最終更新日2024-06-05
実験手法ELECTRON MICROSCOPY (2.73 Å)
主引用文献Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
To Be Published
7FEM
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BU of 7fem by Molmil
SARS-CoV-2 B.1.1.7 S-ACE2 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, Angiotensin-converting enzyme 2, ...
著者Wen, Z.L, Zhu, Y, Sun, F.
登録日2021-07-21
公開日2021-12-15
実験手法ELECTRON MICROSCOPY (4.1 Å)
主引用文献Structure-based evidence for the enhanced transmissibility of the dominant SARS-CoV-2 B.1.1.7 variant (Alpha).
Cell Discov, 7, 2021
7FET
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BU of 7fet by Molmil
SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer
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Wen, Z.L, Zhu, Y, Sun, F.
登録日2021-07-21
公開日2021-12-15
実験手法ELECTRON MICROSCOPY (3.7 Å)
主引用文献Structure-based evidence for the enhanced transmissibility of the dominant SARS-CoV-2 B.1.1.7 variant (Alpha).
Cell Discov, 7, 2021
7PRY
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BU of 7pry by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with COVOX-45 and beta-6 Fabs
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, Beta-6 Fab heavy chain, Beta-6 Fab light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-09-22
公開日2021-12-15
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PRZ
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BU of 7prz by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-22 Fabs
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, Beta-22 Fab heavy chain, Beta-22 Fab light chain, ...
著者Zhou, D, Ren, J, Stuart, D.I.
登録日2021-09-22
公開日2021-12-15
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022

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件を2024-08-14に公開中

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