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coronavirus
Coronavirus, 2020. Modified from the original illustration by David S. Goodsell@RCSB PDB

The recent outbreak of the Novel Coronavirus disease (COVID-19) is a serious threat to people all over the world. In order to understand and develop an effective drug against this virus (Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2), structural work on the related proteins has already started and the resultant entries are accumulating in the PDB. PDBj provides a portal page for the COVID-19 related entries for our users. New entries will be added simultaneously with the public release from the wwPDB.

An explanation article covering one of the proteins of this virus is available on the "Molecules of the Month" page below:

The tab "All entries" contains all PDB IDs, in case you want to check all independent entries, including group depositions by the same authors. The "Repr. entries" tab contains only representative PDB entries with the highest resolution, excluding duplicate entries with 100% amino acid sequence identitiy, even if they contain a different ligand. Finally, the "Latest entries" tab contains the latest entries released this week.

Created: 2020-10-28 (last edited: more than 1 year ago)2022-09-02
All entries (5527)Repr. entries (2333)Latest entries (8)
8XWR
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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
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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
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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
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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
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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
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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
Last modified:2025-09-03
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:CX1/BtSY2 and BANAL-20-52 exhibit broader receptor binding and higher affinities to multiple animal ACE2 orthologs than SARS-CoV-2 prototype.
J.Virol., 99, 2025
8YZC
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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
Last modified:2025-07-16
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
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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
Last modified:2025-07-23
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
Last modified:2025-07-23
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
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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
Last modified:2025-07-23
Method:ELECTRON MICROSCOPY (2.96 Å)
Cite:Structure of EG.5.1 RBD in complex with antibody CYFN1006-2.
To Be Published
9ARU
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BU of 9aru by Molmil
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
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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
9G9K
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CryoEM structure of Enterococcus italicus Csm-crRNA-CTR2 complex (4.3) bound to AMPNPP
Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (3.34 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8VUO
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Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE, ...
Authors:Misra, A, Rahisuddin, R, Gupta, Y.K.
Deposit date:2024-01-29
Release date:2025-02-05
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
To Be Published
8Z6A
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BU of 8z6a by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation
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, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-18
Release date:2025-02-05
Last modified:2025-07-23
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target.
Cell, 188, 2025
8Z7B
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BU of 8z7b by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-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, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-19
Release date:2025-02-05
Last modified:2025-07-23
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target.
Cell, 188, 2025

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