COVID-19特辑

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)

所有结构 (5519)代表性结构 (2329)最新条目 (113)

8XCH

SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation.
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, Helicase, MAGNESIUM ION, ...
Authors:	Yan, L, Lou, Z.
Deposit date:	2023-12-09
Release date:	2025-06-11
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Structural basis for template-product RNA duplex unwinding by SARS-CoV-2 helicase To Be Published

8ZPQ

Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
Descriptor:	70fab-H, 70fab-L, Spike protein S1
Authors:	Wu, Y, Gao, F.
Deposit date:	2024-05-31
Release date:	2025-06-11
Method:	X-RAY DIFFRACTION (2.75 Å)
Cite:	Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab To Be Published

8ZQ8

SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
Descriptor:	3C-like proteinase nsp5, CG-1039
Authors:	Chen, X, Hou, K, Tang, X.
Deposit date:	2024-06-01
Release date:	2025-06-11
Method:	X-RAY DIFFRACTION (1.77 Å)
Cite:	SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039 To Be Published

8ZT9

The Crystal structure of mol066 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor:	3C-like proteinase, 6-[(6-chloranyl-2-propan-2-yl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione, GLYCEROL
Authors:	Yan, M, Zhang, H.
Deposit date:	2024-06-06
Release date:	2025-06-11
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities. Bioorg.Chem., 154, 2025

8ZUC

The Crystal structure of mol080 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor:	3C-like proteinase, 6-[[6-chloranyl-2-(3-methylbutyl)indazol-5-yl]amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione
Authors:	Yan, M, Zhang, H.
Deposit date:	2024-06-08
Release date:	2025-06-11
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities. Bioorg.Chem., 154, 2025

9FC2

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.
Descriptor:	1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, ...
Authors:	Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:	2024-05-15
Release date:	2025-06-11
Method:	X-RAY DIFFRACTION (1.21 Å)
Cite:	Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants. Mabs, 17, 2025

9GUB

SARS-CoV-2 Mac1 in complex with MCD-628
Descriptor:	(2~{S})-3-(1~{H}-indol-3-yl)-2-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylamino)propanoic acid, Papain-like protease nsp3
Authors:	Duong, M, Paakkonen, J, Lehtio, L.
Deposit date:	2024-09-19
Release date:	2025-06-11
Last modified:	2025-06-25
Method:	X-RAY DIFFRACTION (1.1 Å)
Cite:	Identification of a series of pyrrolo-pyrimidine-based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication. Mbio, 16, 2025

9NPX

SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosomal subunit (local refinement of the 40S body)
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
Authors:	Gen, R, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:	2025-03-11
Release date:	2025-06-11
Last modified:	2025-07-30
Method:	ELECTRON MICROSCOPY (2.1 Å)
Cite:	SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals. Cell Rep, 44, 2025

9C7X

Crystal structure of SARS-CoV-2 antibody 1H06 in complex with a HR2 peptide
Descriptor:	Heavy Chain of SARS-CoV-2 antibody 1H06, Light Chain of SARS-CoV-2 antibody 1H06, Spike protein S2'
Authors:	Van Wazer, D.J, Zhou, T, Kwong, P.D.
Deposit date:	2024-06-11
Release date:	2025-06-18
Method:	X-RAY DIFFRACTION (1.96 Å)
Cite:	SARS-CoV-2 Peptide Immunization in Mice Elicits Broadly Neutralizing Antibodies Targeting Cryptic S2 Helical-Stem Epitope To Be Published

9EEI

Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor GC376
Descriptor:	3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:	Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:	2024-11-19
Release date:	2025-06-18
Method:	X-RAY DIFFRACTION (2.76 Å)
Cite:	Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease. Sci Adv, 11, 2025

9IKZ

SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-
Descriptor:	BERYLLIUM TRIFLUORIDE ION, GUANOSINE-5'-DIPHOSPHATE, Helicase nsp13, ...
Authors:	Yan, L.M, Huang, Y.C, Liu, Y.X, Rao, Z.H, Lou, Z.Y.
Deposit date:	2024-06-29
Release date:	2025-06-18
Last modified:	2025-07-23
Method:	ELECTRON MICROSCOPY (3.14 Å)
Cite:	Substrate selection and transition reveal the mechanism for RNA capping catalyzed by SARS-CoV-2 NiRAN To Be Published

9VAO

Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
Descriptor:	GLYCEROL, PHOSPHATE ION, Papain-like protease nsp3, ...
Authors:	Arya, R, Ganesh, J, Prashar, V, Kumar, M.
Deposit date:	2025-06-03
Release date:	2025-06-18
Method:	X-RAY DIFFRACTION (1.82 Å)
Cite:	Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2 To Be Published

9CPP

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-17 and CC12.3
Descriptor:	CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3.19 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPQ

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-44 and CC12.3
Descriptor:	CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (2.88 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPR

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3.1 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPS

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3.03 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPT

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-92 and CC12.3
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3.51 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPU

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0304 and CC12.3
Descriptor:	C03-0304 Fab heavy chain, C03-0304 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPV

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0614 and CC12.3
Descriptor:	C03-0614 Fab heavy chain, C03-0614 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPW

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-1036 and CC12.3
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C11-1036 Fab heavy chain, C11-1036 Fab light chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3.1 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPX

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0138 and CC12.3
Descriptor:	C03-0138 Fab heavy chain, C03-0138 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9CPY

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-0860 and CC12.3
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, C11-0860 Fab heavy chain, C11-0860 Fab light chain, ...
Authors:	Feng, Z, Wilson, I.A.
Deposit date:	2024-07-18
Release date:	2025-06-25
Last modified:	2025-08-06
Method:	X-RAY DIFFRACTION (3.1 Å)
Cite:	In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med., 222, 2025

9P0F

Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2
Descriptor:	Non-structural protein 4, SODIUM ION
Authors:	Minasov, G, Shuvalova, L, Brunzelle, J.S, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:	2025-06-06
Release date:	2025-06-25
Method:	X-RAY DIFFRACTION (2.35 Å)
Cite:	Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2 To Be Published

9CFE

Cryo-EM Local Refinement of Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein RBD
Descriptor:	Spike protein S1, heavy chain, light chain
Authors:	Casner, R.G, Shapiro, L.
Deposit date:	2024-06-27
Release date:	2025-07-02
Last modified:	2025-10-01
Method:	ELECTRON MICROSCOPY (3.03 Å)
Cite:	Optimizing a human monoclonal antibody for better neutralization of SARS-CoV-2. Nat Commun, 16, 2025

9CFF

Cryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 HK.3 RBD
Descriptor:	Spike protein S1, heavy chain, light chain
Authors:	Casner, R.G, Shapiro, L.
Deposit date:	2024-06-27
Release date:	2025-07-02
Last modified:	2025-10-01
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Optimizing a human monoclonal antibody for better neutralization of SARS-CoV-2. Nat Commun, 16, 2025

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