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 (5197)代表性结构 (2266)最新条目 (44)

9IUQ

KP.2 RBD in complex with ACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:	Feng, L.L.
Deposit date:	2024-07-22
Release date:	2025-01-15
Last modified:	2025-06-25
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2. Cell Discov, 10, 2024

9IUU

JN.1 RBD with Q493E in complex with ACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, CHLORIDE ION, ...
Authors:	Feng, L.L.
Deposit date:	2024-07-22
Release date:	2025-01-15
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.29 Å)
Cite:	Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2. Cell Discov, 10, 2024

9JJ7

The crystal structure of SARS-CoV-2 NSP5 in complex with eIF4G2
Descriptor:	3C-like proteinase nsp5, Eukaryotic translation initiation factor 4 gamma 2
Authors:	Yan, X, Jin, Z, Wang, Y, Zhang, J.
Deposit date:	2024-09-13
Release date:	2025-01-15
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Coronavirus NSP5 is an Evolutionarily Conserved Inhibitor of Host Translation To Be Published

8XAL

Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with 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, Angiotensin-converting enzyme 2,Green fluorescent protein (Fragment), ...
Authors:	Hsu, H.F, Wu, M.H, Chang, Y.C, Hsu, S.T.D.
Deposit date:	2023-12-04
Release date:	2025-01-22
Last modified:	2025-07-02
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody. JCI Insight, 9, 2024

8XWR

Crystal structure of SARS-CoV-2 3CLpro-T21I/L50F double mutant with its peptidyl substrate
Descriptor:	3C-like proteinase nsp5, cleaved N-terminal product of nsp5/6 substrate peptide
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2024-01-16
Release date:	2025-01-22
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Crystal structure of SARS-CoV-2 3CLpro-T21I/L50F double mutant with its peptidyl substrate To Be Published

8XWT

Crystal structure of SARS-CoV-2 3CLpro-L50F mutant with its peptidyl substrate
Descriptor:	3C-like proteinase nsp5, CYS-SER-GLY-VAL-THR-PHE-GLN-SER-ALA-VAL-LYS-ARG-THR-ILE
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2024-01-16
Release date:	2025-01-22
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Crystal structure of SARS-CoV-2 3CLpro-L50F mutant with its peptidyl substrate To Be Published

8XY9

Crystal structure of SARS-CoV-2 BF.7 RBD and human ACE2 complex
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:	Lan, J, Wang, C.H.
Deposit date:	2024-01-19
Release date:	2025-01-22
Last modified:	2025-04-16
Method:	X-RAY DIFFRACTION (3.64 Å)
Cite:	Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage. Virology, 600, 2024

8XYE

Crystal structure of SARS-CoV-2 BA.4 RBD and 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:	Lan, J, Wang, C.H.
Deposit date:	2024-01-19
Release date:	2025-01-22
Last modified:	2025-04-16
Method:	X-RAY DIFFRACTION (3.32 Å)
Cite:	Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage. Virology, 600, 2024

8XYG

Crystal structure of SARS-CoV-2 BQ.1.1 RBD and human ACE2
Descriptor:	Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:	Lan, J, Wang, C.H.
Deposit date:	2024-01-19
Release date:	2025-01-22
Last modified:	2025-04-16
Method:	X-RAY DIFFRACTION (3.64 Å)
Cite:	Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage. Virology, 600, 2024

8XYO

Cryo-EM structure of CX1 receptor binding domain in complex with human ACE2
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein, ...
Authors:	Xu, Z.P, Li, L.J, Gu, Y.H, Qi, J.X, Gao, G.F.
Deposit date:	2024-01-20
Release date:	2025-01-22
Method:	ELECTRON MICROSCOPY (3.04 Å)
Cite:	Structural resemblances of bat-origin coronaviruses CX1 and BANAL-20-52 spikes provide further evidence on bat origination of SARS-CoV-2 To Be Published

8YZC

Structure of BA.2.86 spike protein in complex with ACE2.
Descriptor:	Angiotensin-converting enzyme 2, Spike glycoprotein,Fibritin,Expression Tag
Authors:	Wang, Y.J, Zang, X, Sun, L.
Deposit date:	2024-04-06
Release date:	2025-01-22
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3. Nat Commun, 15, 2024

8YZE

The JN.1 spike protein (S) in complex with ACE2.
Descriptor:	Angiotensin-converting enzyme 2, Spike glycoprotein,Fibritin,Expression Tag
Authors:	Wang, Y.J, Zhang, X, Sun, L.
Deposit date:	2024-04-06
Release date:	2025-01-22
Method:	ELECTRON MICROSCOPY (3.06 Å)
Cite:	Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3. Nat Commun, 15, 2024

9EXA

SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834
Descriptor:	6-[[1-[4,6-dimethyl-5-(2-methylpropyl)pyrimidin-2-yl]piperidin-4-yl]-methyl-amino]-N-(2-pyrrolidin-1-ylethyl)pyridazine-4-carboxamide, Fab-B heavy chain, Fab-B light chain, ...
Authors:	Debski-Antoniak, O.J, Hurdiss, D.L.
Deposit date:	2024-04-05
Release date:	2025-01-22
Last modified:	2025-04-16
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	A coronavirus assembly inhibitor that targets the viral membrane protein. Nature, 640, 2025

9JS4

Cryo-EM structure of neutralizing antibody 8G3 in complex with BA.1 RBD
Descriptor:	Heavy chain of 8G3, Light chain of 8G3, Spike glycoprotein
Authors:	Li, J, Li, H.
Deposit date:	2024-09-30
Release date:	2025-01-22
Last modified:	2025-02-26
Method:	ELECTRON MICROSCOPY (3.8 Å)
Cite:	Rapid restoration of potent neutralization activity against the latest Omicron variant JN.1 via AI rational design and antibody engineering. Proc.Natl.Acad.Sci.USA, 122, 2025

8YZR

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLL(EG.5.1)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, Spike protein S1
Authors:	Min, L, Liu, J.
Deposit date:	2024-04-08
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8YZW

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRLF(BA.2.86)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, Spike protein S2'
Authors:	Liu, J, Tian, J.M, Shang, B.L.
Deposit date:	2024-04-08
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (2.36 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8YZZ

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLF(Prototype)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, Spike protein S1
Authors:	Shang, B.L, Zhang, J.N, Tian, J.M, Liu, J.
Deposit date:	2024-04-08
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (1.88 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8Z05

The structure of HLA-A*0201 complex with peptide from SARS-CoV-2 N222-230 LLLDRLNKL(BA.2.86/JN.1)
Descriptor:	Beta-2-microglobulin, HLA class I histocompatibility antigen, A alpha chain, ...
Authors:	Zhang, J.N, Tian, J.M, Liu, J.
Deposit date:	2024-04-09
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (1.96 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8Z06

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRSF(JN.1)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, Spike protein S2'
Authors:	Tian, J.M, Liu, J.
Deposit date:	2024-04-09
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (2.39 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8Z07

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYRYRLF(Delta/BA.5.2)
Descriptor:	Beta-2-microglobulin, MHC class I antigen, Spike protein S2'
Authors:	Yuechao, H, Liu, J.
Deposit date:	2024-04-09
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8Z08

The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYQYRLF(BA.2.12.1)
Descriptor:	ASN-TYR-ASN-TYR-GLN-TYR-ARG-LEU-PHE, Beta-2-microglobulin, MHC class I antigen
Authors:	Zhang, J.N, Liu, J.
Deposit date:	2024-04-09
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	X-RAY DIFFRACTION (2.01 Å)
Cite:	T cell immune evasion by SARS-CoV-2 JN.1 escapees targeting two cytotoxic T cell epitope hotspots. Nat.Immunol., 26, 2025

8Z6R

Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1.
Descriptor:	CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Spike glycoprotein,Fibritin,Spike glycoprotein,Fibritin,Expression Tag
Authors:	Wang, Y.J, Sun, L.
Deposit date:	2024-04-19
Release date:	2025-01-29
Method:	ELECTRON MICROSCOPY (2.87 Å)
Cite:	Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1. To Be Published

8Z6X

Structure of EG.5.1 RBD in complex with antibody CYFN1006-2.
Descriptor:	CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:	Wang, Y.J, Sun, L.
Deposit date:	2024-04-19
Release date:	2025-01-29
Method:	ELECTRON MICROSCOPY (2.96 Å)
Cite:	Structure of EG.5.1 RBD in complex with antibody CYFN1006-2. To Be Published

9ARU

COVA2-15 fragment antigen binding in complex with SARS-CoV-2 6P-mut7 S protein
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-15 heavy chain variable region, ...
Authors:	Ozorowski, G, Turner, H.L, Ward, A.B.
Deposit date:	2024-02-23
Release date:	2025-01-29
Last modified:	2025-05-28
Method:	ELECTRON MICROSCOPY (3.9 Å)
Cite:	Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy. Plant Biotechnol J, 23, 2025

9G9I

CryoEM structure of Enterococcus italicus Csm-crRNA-CTR2 complex bound to pNppA3 and AMPNPP
Descriptor:	CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:	Jungfer, K, Jinek, M.
Deposit date:	2024-07-25
Release date:	2025-01-29
Method:	ELECTRON MICROSCOPY (3.31 Å)
Cite:	Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes. Nucleic Acids Res., 53, 2025

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