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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 (4559)Repr. entries (2032)Latest entries (12)
7XCI
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Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with human ACE2 ectodomain (local refinement)
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:Gao, G.F, Qi, J.X, Zhao, Z.N, Liu, S, Xie, Y.F.
Deposit date:2022-03-24
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7XCK
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Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, S309 heavy chain, S309 light chain, ...
Authors:Gao, G.F, Qi, J.X, Zhao, Z.N, Xie, Y.F, Liu, S.
Deposit date:2022-03-24
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7XCP
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Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 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, Heavy chain of 304 Fab, ...
Authors:Zhao, Z, Qi, J, Gao, F.G.
Deposit date:2022-03-24
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (3.05 Å)
Cite:Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape
Nat Commun, 13, 2022
7YA1
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Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (local refinement)
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:Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2022-06-27
Release date:2022-08-31
Last modified:2022-09-07
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape.
Nat Commun, 13, 2022
7YAD
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Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, S309 neutralizing antibody heavy chain, S309 neutralizing antibody light chain, ...
Authors:Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, F.
Deposit date:2022-06-27
Release date:2022-08-31
Last modified:2022-09-07
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape.
Nat Commun, 13, 2022
8DDI
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166N Mutant
Descriptor: 3C-like proteinase nsp5
Authors:Lewandowski, E.M, Jacobs, L.M.C, Chen, Y.
Deposit date:2022-06-18
Release date:2022-08-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations.
Plos Pathog., 19, 2023
8DDM
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166R Mutant in Complex with Inhibitor GC376
Descriptor: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5
Authors:Lewandowski, E.M, Chen, Y.
Deposit date:2022-06-18
Release date:2022-08-31
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.78 Å)
Cite:A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations.
Plos Pathog., 19, 2023
8DLI
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Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike 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, Spike glycoprotein
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.56 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLJ
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Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) 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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.91 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLL
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Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike 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, Spike glycoprotein
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.56 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLM
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Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) 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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.89 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLO
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BU of 8dlo by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike 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, Spike glycoprotein
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.25 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLP
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BU of 8dlp by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.64 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLR
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Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of NTD and 4-8)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 4-8 heavy chain, Fab 4-8 light chain, ...
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.51 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLS
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BU of 8dls by Molmil
Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab 4A8 heavy chain, ...
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLT
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Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike 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, Spike glycoprotein
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.4 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLV
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Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLW
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Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with Fab S2M11
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab S2M11 heavy chain, ...
Authors:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.16 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLX
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BU of 8dlx by Molmil
Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6
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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.45 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DLZ
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BU of 8dlz by Molmil
Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6
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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Subramaniam, S.
Deposit date:2022-07-08
Release date:2022-08-31
Method:ELECTRON MICROSCOPY (2.57 Å)
Cite:SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Nat Commun, 13, 2022
8DV1
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BU of 8dv1 by Molmil
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain, Spike glycoprotein
Authors:QCRG Structural Biology Consortium, Remesh, S.G, Merz, G.E, Brilot, A.F, Chio, U, Verba, K.A.
Deposit date:2022-07-27
Release date:2022-08-31
Last modified:2023-03-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.
Structure, 31, 2023
8DV2
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BU of 8dv2 by Molmil
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion, Spike glycoprotein
Authors:QCRG Structural Biology Consortium, Remesh, S.G, Merz, G.E, Brilot, A.F, Chio, U, Verba, K.A.
Deposit date:2022-07-27
Release date:2022-08-31
Last modified:2023-03-15
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.
Structure, 31, 2023
8DZH
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BU of 8dzh by Molmil
Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody MB.02
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:Hu, Y, Xiong, Y.
Deposit date:2022-08-07
Release date:2022-08-31
Last modified:2023-11-15
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.
Signal Transduct Target Ther, 8, 2023
7TW9
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Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to Sinefungin
Descriptor: DI(HYDROXYETHYL)ETHER, ETHANOL, METHANOL, ...
Authors:Kottur, J, Aggarwal, A.K.
Deposit date:2022-02-06
Release date:2022-09-07
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.41 Å)
Cite:High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.
Nat.Struct.Mol.Biol., 29, 2022
8CZI
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BU of 8czi by Molmil
Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with extended HR2
Descriptor: Scaffolded Spike protein S2' HR1, Spike protein S2' HR2
Authors:Yang, K, Brunger, A.T.
Deposit date:2022-05-24
Release date:2022-09-07
Last modified:2024-06-12
Method:ELECTRON MICROSCOPY (2.22 Å)
Cite:Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein.
Proc.Natl.Acad.Sci.USA, 119, 2022

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