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COVID-19特辑

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冠状病毒
冠状病毒,2020. 由David S. Goodsell @ RCSB PDB原图修改

最近爆发的新型冠状病毒传染病(Novel Coronavirus disease 2019: COVID-19)对全世界的人们都构成了严重威胁。 为了尽早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以开发出有效的抗病毒药物,已经有很多科研人員开始了相关蛋白结构的研究,并且将所获得的结构数据存储于PDB。 PDBj为用户提供了COVID-19相关数据一览的门户页面,并将于每周三更新当日新发布的相关数据。

有关该病毒蛋白质的解说,请参见下面的“当月的分子”页面。

“所有结构”标签的页面则逐一罗列了所有的结构数据,包括由同一研究组提交的系列数据群。 “代表性结构”标签的页面精选具有相同氨基酸序列的结构数据中的高分辨率数据,不重复选择具同一氨基酸序列的数据,即使该数据可能包含不同配体。 “最新条目”标签内包含本周新更新数据。


Created: 2020-09-03 (last edited: more than 1 year ago)2020-12-02
9C2H
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BU of 9c2h by Molmil
SARS-CoV-2 Nucleocapsid Dimerization Domain bound to Fab-NP1E9 and Fab-NP3B4
Descriptor: Antibody Fab NP1-E9 Heavy Chain (variable region), Antibody Fab NP1-E9 Light Chain (variable region), Antibody Fab NP3-B4 Heavy Chain (variable region), ...
Authors:Landeras-Bueno, S, Hariharan, C, Diaz Avalos, R, Ollmann Saphire, E.
Deposit date:2024-05-31
Release date:2025-05-14
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome
To Be Published
9F7P
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BU of 9f7p by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S mutant
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MALONATE ION, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7R
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BU of 9f7r by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S mutant
Descriptor: GLYCEROL, PHOSPHATE ION, Replicase polyprotein 1ab, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7S
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BU of 9f7s by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MALONATE ION, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
To Be Published
9F7U
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BU of 9f7u by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
Descriptor: CHLORIDE ION, GLYCEROL, MALONIC ACID, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-05
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
To Be Published
9LVR
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BU of 9lvr by Molmil
Crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, 6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Unoh, Y, Hirai, K, Uehara, S, Kawashima, S, Nobori, H, Sato, J, Shibayama, H, Hori, A, Nakahara, K, Kurahashi, K, Takamatsu, M, Yamamoto, S, Zhang, O, Tanimura, M, Dodo, R, Maruyama, Y, Sawa, H, Watari, R, Miyano, T, Kato, T, Sato, T, Tachibana, Y.
Deposit date:2025-02-12
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19
To Be Published
9FCM
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BU of 9fcm by Molmil
Single-domain antibody binding the SARS-COV2 S2
Descriptor: CHLORIDE ION, Single-domain antibody R3DC23, Spike protein S2'
Authors:Vann Molle, I, Remaut, H.
Deposit date:2024-05-15
Release date:2025-05-21
Last modified:2025-06-11
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base.
Nat Commun, 16, 2025
9UJ2
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BU of 9uj2 by Molmil
14-3-3 zeta chimera with the S202R peptide of SARS-CoV-2 N (residues 200-213)
Descriptor: 1,2-ETHANEDIOL, 14-3-3 protein zeta/delta,Peptide from Nucleoprotein, DI(HYDROXYETHYL)ETHER
Authors:Boyko, K.M, Matyuta, I.O, Minyaev, M.E, Perfilova, K.V, Sluchanko, N.N.
Deposit date:2025-04-16
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness.
Biochem.Biophys.Res.Commun., 767, 2025
9ELE
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BU of 9ele by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 RBD in complex with human ACE2 (local refinement of RBD and hACE2)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (3.16 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELF
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BU of 9elf by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.88 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELG
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BU of 9elg by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike RBD and NTD (local refinement of RBD and NTD)
Descriptor: 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
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (3.71 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELH
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BU of 9elh by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (one RBD up state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELI
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BU of 9eli by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (closed state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.82 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELO
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BU of 9elo by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (closed state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.74 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELQ
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BU of 9elq by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (closed state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-05-28
Method:ELECTRON MICROSCOPY (2.64 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9HH5
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BU of 9hh5 by Molmil
Crystal Structure of nsp15 Endoribonuclease from SARS CoV-2 in Complex with Sepantronium (YM-155)
Descriptor: 1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Nsp15 - Uridylate-specific endoribonuclease, ...
Authors:Chatziefthymiou, S.D, Kolbe, M, Hakanpaeae, J, Labahn, J, Windshuegel, B.
Deposit date:2024-11-21
Release date:2025-05-28
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.
Protein Sci., 34, 2025
9HH6
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BU of 9hh6 by Molmil
Crystal Structure of Nsp15 Endoribonuclease from SARS CoV-2 in Complex with TAS-103
Descriptor: 1,2-ETHANEDIOL, 6-[2-(dimethylamino)ethylamino]-3-oxidanyl-indeno[2,1-c]quinolin-7-one, ORF1ab polyprotein, ...
Authors:Chatziefthymiou, S.D, Kolbe, M, Hakanpaeae, J, Labahn, J, Windshuegel, B.
Deposit date:2024-11-21
Release date:2025-05-28
Method:SOLUTION SCATTERING (2 Å), X-RAY DIFFRACTION
Cite:Identification, validation, and characterization of approved and investigational drugs interfering with the SARS-CoV-2 endoribonuclease Nsp15.
Protein Sci., 34, 2025
9IZB
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BU of 9izb by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with TMP1
Descriptor: 3C-like proteinase nsp5, TMP1
Authors:Deng, X.Y, Zeng, R, Yang, S.Y, Lei, J.
Deposit date:2024-08-01
Release date:2025-05-28
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structure of SARS-CoV-2 main protease in complex with TMP1
To Be Published
9ELK
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BU of 9elk by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (closed state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.82 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELL
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BU of 9ell by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (one RBD up state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ELM
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BU of 9elm by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (closed state)
Descriptor: 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, ...
Authors:Feng, Z, Huang, J, Ward, A.B.
Deposit date:2024-12-04
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (2.68 Å)
Cite:Structure of SARS-CoV-2 KP.3.1.1 Spike Protein
To Be Published
9ML4
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BU of 9ml4 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-A10 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-A10 heavy chain, M8b-A10 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML5
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BU of 9ml5 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-B8 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML6
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BU of 9ml6 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C9 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C9 heavy chain, M8b-C9 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML7
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BU of 9ml7 by Molmil
Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C10 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C10 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025

238582

数据于2025-07-09公开中

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