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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
8WRO
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BU of 8wro by Molmil
XBB.1.5.10 spike protein in complex with ACE2
分子名称: Processed angiotensin-converting enzyme 2, Spike glycoprotein,Spike glycoprotein,Spike glycoprotein,Fusion protein
著者Feng, L.L, Feng, L.L.
登録日2023-10-15
公開日2023-12-06
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.9 Å)
主引用文献Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8F2J
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BU of 8f2j by Molmil
Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain
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Sankhala, R.S, Joyce, M.G.
登録日2022-11-08
公開日2023-12-13
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (3.16 Å)
主引用文献Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.
To Be Published
8FAH
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BU of 8fah by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with SARS-CoV-2 reactive human antibody CR3022
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab heavy chain, CR3022 Fab light chain, ...
著者Sankhala, R.S, Jensen, J.L, Joyce, M.G.
登録日2022-11-26
公開日2023-12-13
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (4.22 Å)
主引用文献Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Structure, 32, 2024
8K45
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A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
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, Nb4 nanobody, ...
著者Lu, Y, Gao, Y, Yao, H, Xu, W, Yang, H.
登録日2023-07-17
公開日2023-12-13
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.66 Å)
主引用文献A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
MedComm (2020), 4, 2023
8K46
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A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
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Lu, Y, Gao, Y, Yao, H, Xu, W, Yang, H.
登録日2023-07-17
公開日2023-12-13
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.37 Å)
主引用文献A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
MedComm (2020), 4, 2023
8SGU
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Crystal structure of the SARS-CoV-2 receptor binding domain
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ...
著者Sankhala, R.S, Jensen, J.L, Joyce, M.G.
登録日2023-04-13
公開日2023-12-13
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (1.95 Å)
主引用文献Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Structure, 32, 2024
8SMI
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Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, WRAIR-2123 Fab heavy chain, ...
著者Sankhala, R.S, Jensen, J.L, Joyce, M.G.
登録日2023-04-26
公開日2023-12-13
最終更新日2024-10-30
実験手法X-RAY DIFFRACTION (3.5 Å)
主引用文献Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Structure, 32, 2024
8WOX
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BU of 8wox by Molmil
Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with rabbit ACE2 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F.
登録日2023-10-08
公開日2023-12-13
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (2.75 Å)
主引用文献Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
8WOY
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Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with rabbit ACE2 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F.
登録日2023-10-08
公開日2023-12-13
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (3.14 Å)
主引用文献Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
8WTD
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BU of 8wtd by Molmil
XBB.1.5.10 RBD in complex with ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S2'
著者Feng, L.L, Feng, L.L.
登録日2023-10-18
公開日2023-12-13
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (3.06 Å)
主引用文献Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8WTJ
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BU of 8wtj by Molmil
XBB.1.5.70 spike protein in complex with ACE2
分子名称: Processed angiotensin-converting enzyme 2, Spike glycoprotein
著者Feng, L.L, Feng, L.L.
登録日2023-10-18
公開日2023-12-13
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (4.64 Å)
主引用文献Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8HPF
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BU of 8hpf by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with fab L4.65 and L5.34
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
著者Gao, G.F, Liu, S.
登録日2022-12-12
公開日2023-12-20
最終更新日2024-11-13
実験手法ELECTRON MICROSCOPY (2.34 Å)
主引用文献Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HPU
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BU of 8hpu by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.4 RBD in complex with fab L4.65 and L5.34
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
著者Gao, G.F, Liu, S.
登録日2022-12-13
公開日2023-12-20
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (2.56 Å)
主引用文献Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HQ7
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BU of 8hq7 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron Prototype RBD in complex with fab L4.65 and L5.34
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, fab L4.65, ...
著者Gao, G.F, Liu, S.
登録日2022-12-13
公開日2023-12-20
最終更新日2024-10-30
実験手法ELECTRON MICROSCOPY (2.7 Å)
主引用文献Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HQI
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BU of 8hqi by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with inhibitor YH-53
分子名称: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
著者Li, W.W, Zhang, J, Li, J.
登録日2022-12-13
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor.
Acta Biochim.Biophys.Sin., 55, 2023
8HQJ
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BU of 8hqj by Molmil
Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53
分子名称: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
著者Zhou, X.L, Zhang, J, Li, J.
登録日2022-12-13
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor.
Acta Biochim.Biophys.Sin., 55, 2023
8HQT
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BU of 8hqt by Molmil
The complex structure of COPI cargo sorting module with SARS-CoV-2 Spike KxHxx sorting motif
分子名称: Coatomer subunit beta', SARS-CoV-2 Spike KxHxx motif
著者Ma, W.F, Nan, Y.N, Yang, M.R, Li, Y.Q.
登録日2022-12-14
公開日2023-12-20
最終更新日2025-01-29
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor.
Acta Pharm Sin B, 13, 2023
8HRD
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BU of 8hrd by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS74 Fab heavy chain, IMCAS74 Fab light chain, ...
著者Zhao, R.C, Wu, L.L, Han, P.
登録日2022-12-15
公開日2023-12-20
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.86 Å)
主引用文献Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
Proc.Natl.Acad.Sci.USA, 120, 2023
8HRI
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SARS-CoV-2 Delta variant spike protein
分子名称: Spike glycoprotein
著者Xu, J, Cheng, H, Liu, N, Wang, H.W.
登録日2022-12-15
公開日2023-12-20
最終更新日2025-01-01
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Self-assembled superstructure alleviates air-water interface effect in cryo-EM.
Nat Commun, 15, 2024
8HRL
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BU of 8hrl by Molmil
SARS-CoV-2 Delta S-RBD-ACE2
分子名称: Processed angiotensin-converting enzyme 2, Spike protein S1
著者Xu, J, Meng, F, Liu, N, Wang, H.W.
登録日2022-12-15
公開日2023-12-20
最終更新日2025-01-01
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Self-assembled superstructure alleviates air-water interface effect in cryo-EM.
Nat Commun, 15, 2024
8HSM
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BU of 8hsm by Molmil
CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67
分子名称: Beta-2-microglobulin, Ig-like domain-containing protein, PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
著者Wang, S.Q, Zhang, N.Z.
登録日2022-12-20
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation.
Commun Biol, 7, 2024
8HSO
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BU of 8hso by Molmil
CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.2 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
分子名称: Beta-2-microglobulin, Ig-like domain-containing protein, PHE-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
著者Wang, S.Q, Zhang, N.Z.
登録日2022-12-20
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation.
Commun Biol, 7, 2024
8HSW
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CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.1 ANGSTROM
分子名称: Beta-2-microglobulin, Ig-like domain-containing protein, THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
著者Wang, S.Q, Zhang, N.Z.
登録日2022-12-20
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (2.03 Å)
主引用文献Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation.
Commun Biol, 7, 2024
8HT1
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BU of 8ht1 by Molmil
CRYSTAL STRUCTURE OF A MUTANT MYLU-B-67 FOR 2.4 ANGSTROM, 52M 53Q 54Q 55P 56W DELETED
分子名称: Beta-2-microglobulin, Ig-like domain-containing protein, THR-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL
著者Wang, S.Q, Zhang, N.Z.
登録日2022-12-20
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation.
Commun Biol, 7, 2024
8HT9
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BU of 8ht9 by Molmil
CRYSTAL STRUCTURE OF BAT MHC CLASS I MYLU-B-67 FOR 2.2 ANGSTROM
分子名称: Beta-2-microglobulin, GLU-PRO-GLN-SER-ALA-PRO-HIS-GLY-VAL, Ig-like domain-containing protein
著者Wang, S.Q, Zhang, N.Z.
登録日2022-12-20
公開日2023-12-20
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation.
Commun Biol, 7, 2024

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件を2025-07-09に公開中

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