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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
8XKC
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The structure of HLA-A/Pep16
分子名称: Beta-2-microglobulin, HLA class I heavy chain, Spike protein S1
著者Zhang, J.N, Yue, C, Liu, J.
登録日2023-12-23
公開日2024-07-10
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (2.18 Å)
主引用文献Uncommon P1 Anchor-featured Viral T Cell Epitope Preference within HLA-A*2601 and HLA-A*0101 Individuals.
Immunohorizons, 8, 2024
8XKE
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BU of 8xke by Molmil
The structure of HLA-A/14-3-D
分子名称: Beta-2-microglobulin, GLU-VAL-ASP-ASN-ALA-THR-ARG-PHE-ALA-SER-VAL-TYR, HLA class I heavy chain
著者Zhang, J.N, Yue, C, Liu, J, Sun, Z.Y.
登録日2023-12-23
公開日2024-07-10
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.92 Å)
主引用文献Uncommon P1 Anchor-featured Viral T Cell Epitope Preference within HLA-A*2601 and HLA-A*0101 Individuals.
Immunohorizons, 8, 2024
8XKI
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A neutralizing nanobody VHH60 against wt SARS-CoV-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, Spike glycoprotein, ...
著者Lu, Y, Guo, H, Ji, X, Yang, H.
登録日2023-12-23
公開日2024-07-10
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug.
Cell Death Dis, 15, 2024
9AT4
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Crystal structure of SARS-CoV-2 3CL protease in complex with a methylbicyclo[2.2.1]heptane 2-pyrrolidone inhibitor
分子名称: (1R,2S)-2-{[N-({[(2S)-1-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-{[N-({[(2S)-1-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5, ...
著者Lovell, S, Cooper, A, Battaile, K.P, Dampalla, C.S, Groutas, W.C.
登録日2024-02-26
公開日2024-07-10
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.35 Å)
主引用文献Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.
J.Med.Chem., 67, 2024
8Q5Y
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cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23
分子名称: Monoclonal antibody Mab 23 (Heavy Chain), Monoclonal antibody Mab 23 (Light chain), Spike glycoprotein
著者Hallberg, M, Das, H.
登録日2023-08-10
公開日2024-07-17
最終更新日2025-07-09
実験手法ELECTRON MICROSCOPY (2.6 Å)
主引用文献Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.
Nat Commun, 15, 2024
8THF
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SARS-CoV-2 BA.1 S-6P-no-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 protein S1,Spike glycoprotein
著者Bu, F, Li, F, Liu, B.
登録日2023-07-15
公開日2024-07-17
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (2.83 Å)
主引用文献Universal subunit vaccine protects against multiple SARS-CoV-2 variants and SARS-CoV.
Npj Vaccines, 9, 2024
8XSE
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SARS-CoV-2 RBD + IMCAS-123 + IMCAS-72 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS-123 H chain, IMCAS-123 L chain, ...
著者Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
登録日2024-01-09
公開日2024-07-17
最終更新日2024-10-23
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSF
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SARS-CoV-2 RBD + IMCAS-364 + hACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, IMCAS-364 H chain, ...
著者Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
登録日2024-01-09
公開日2024-07-17
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.16 Å)
主引用文献Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSI
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BU of 8xsi by Molmil
SARS-CoV-2 RBD + IMCAS-364 (Local Refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS-364 H chain, IMCAS-364 L chain, ...
著者Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
登録日2024-01-09
公開日2024-07-17
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.1 Å)
主引用文献Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSJ
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BU of 8xsj by Molmil
SARS-CoV-2 Omicron BA.4 RBD + IMCAS-316 + 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Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
登録日2024-01-09
公開日2024-07-17
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (2.61 Å)
主引用文献Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSL
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BU of 8xsl by Molmil
SARS-CoV-2 spike + IMCAS-123
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, IMCAS-123 heavy chain, ...
著者Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
登録日2024-01-09
公開日2024-07-17
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8Y0Y
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BU of 8y0y by Molmil
Cryo-EM structure of the 123-316 scDb/PT-RBD complex
分子名称: 123-316 scDb, 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Jia, G.W, Tong, Z, Tong, J.Y, Su, Z.M.
登録日2024-01-23
公開日2024-07-17
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.86 Å)
主引用文献Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
9FZK
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BU of 9fzk by Molmil
SARS CoV-2 nsp10 in complex with theExoN domain from nsp14
分子名称: Guanine-N7 methyltransferase nsp14, Non-structural protein 11, ZINC ION
著者Fisher, S.Z.
登録日2024-07-05
公開日2024-07-17
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献SARS CoV-2 nsp10 in complex with theExoN domain from nsp14
To Be Published
8UZE
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BU of 8uze by Molmil
Crystal structure of chimeric bat coronavirus BANAL-20-236 RBD complexed with chimeric mouse ACE2
分子名称: 1,2-ETHANEDIOL, 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Zhang, W, Shi, K, Aihara, H, Li, F.
登録日2023-11-15
公開日2024-07-24
最終更新日2025-02-05
実験手法X-RAY DIFFRACTION (3.03 Å)
主引用文献Structural basis for mouse receptor recognition by bat SARS2-like coronaviruses.
Proc.Natl.Acad.Sci.USA, 121, 2024
8VIF
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BU of 8vif by Molmil
SARS-CoV-2 spike omicron (BA.1) ectodomain trimer in complex with SC27 Fab, local refinement
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, SC27 Fab heavy chain, SC27 Fab light chain, ...
著者Byrne, P.O, McLellan, J.S.
登録日2024-01-04
公開日2024-07-24
最終更新日2025-05-21
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.
Cell Rep Med, 5, 2024
8VKE
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BU of 8vke by Molmil
SARS-CoV-2 spike omicron (BA.1) RBD ectodomain dimer-of-trimers in complex with SC27 Fabs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, SC27 Fab heavy chain, SC27 Fab light chain, ...
著者Byrne, P.O, McLellan, J.S.
登録日2024-01-09
公開日2024-07-24
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.1 Å)
主引用文献Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.
Cell Rep Med, 5, 2024
8W4F
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SARS-CoV-2 spike protein in complex with a trivalent nanobody
分子名称: Spike glycoprotein, Tribody
著者Jiang, X.Y, Qian, J.Q, Zhu, H.X, Qin, Q, Huang, Q.
登録日2023-08-24
公開日2024-07-24
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (4.2 Å)
主引用文献Structure-guided design of a trivalent nanobody cluster targeting SARS-CoV-2 spike protein.
Int.J.Biol.Macromol., 256, 2024
8WDR
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Crystal structure of BQ.1.1 RBD complexed 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, Angiotensin-converting enzyme 2, ...
著者Li, W, Xie, Y.
登録日2023-09-16
公開日2024-07-24
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (3.47 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WDS
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Crystal structure of BF.7 RBD complexed 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, Angiotensin-converting enzyme 2, ...
著者Li, W, Xie, Y.
登録日2023-09-16
公開日2024-07-24
最終更新日2024-11-20
実験手法X-RAY DIFFRACTION (3.4 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WDY
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BU of 8wdy by Molmil
SARS-CoV-2 Omicron BQ.1.1 RBD complexed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Li, W, Xie, Y.
登録日2023-09-16
公開日2024-07-24
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (2.69 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WDZ
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BU of 8wdz by Molmil
SARS-CoV-2 Omicron BQ.1 RBD complexed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Li, W, Xie, Y.
登録日2023-09-16
公開日2024-07-24
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.71 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WE0
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BU of 8we0 by Molmil
SARS-CoV-2 Omicron XBB RBD complexed with human ACE2
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, Angiotensin-converting enzyme 2, ...
著者Li, W, Xie, Y.
登録日2023-09-16
公開日2024-07-24
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WE1
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BU of 8we1 by Molmil
SARS-CoV-2 Omicron BF.7 RBD complexed 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Li, W, Xie, Y.
登録日2023-09-16
公開日2024-07-24
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (2.47 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WE4
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SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304
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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Li, W, Xie, Y.
登録日2023-09-17
公開日2024-07-24
最終更新日2025-06-18
実験手法ELECTRON MICROSCOPY (2.91 Å)
主引用文献Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8K9B
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BU of 8k9b by Molmil
SARS-CoV-2 spike protein in complex with one S2H5 Fab
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of S2H5 Fab, Light chain of S2H5 Fab, ...
著者Hong, Q, Cong, Y.
登録日2023-07-31
公開日2024-07-31
最終更新日2025-07-02
実験手法ELECTRON MICROSCOPY (4.5 Å)
主引用文献Molecular basis of SARS-CoV-2 immune evasion of NTD neutralizing antibodies.
Dian Zi Xian Wei Xue Bao, 2024

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件を2025-07-09に公開中

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