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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 (4406)Repr. entries (1944)Latest entries (19)
7SY1
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BU of 7sy1 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (global 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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (2.83 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY2
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BU of 7sy2 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (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, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY3
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Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2 ectodomain (global 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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (2.95 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY4
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BU of 7sy4 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2 ectodomain (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, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (3.35 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY5
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BU of 7sy5 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain bound to human ACE2 ectodomain (global 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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Last modified:2022-01-05
Method:ELECTRON MICROSCOPY (2.59 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY6
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BU of 7sy6 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain bound to human ACE2 ectodomain (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, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Method:ELECTRON MICROSCOPY (2.81 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY7
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BU of 7sy7 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain bound to human ACE2 ectodomain (global 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:Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Method:ELECTRON MICROSCOPY (2.81 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7SY8
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BU of 7sy8 by Molmil
Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain bound to human ACE2 ectodomain (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, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:2021-11-24
Release date:2021-12-29
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Cell Rep, 37, 2021
7T9J
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BU of 7t9j by Molmil
Cryo-EM structure of the SARS-CoV-2 Omicron 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, Tuttle, K.S, Subramaniam, S.
Deposit date:2021-12-19
Release date:2021-12-29
Last modified:2022-05-18
Method:ELECTRON MICROSCOPY (2.79 Å)
Cite:SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex.
Science, 375, 2022
7T9K
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BU of 7t9k by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron 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, Tuttle, K.S, Subramaniam, S.
Deposit date:2021-12-19
Release date:2021-12-29
Last modified:2022-05-18
Method:ELECTRON MICROSCOPY (2.45 Å)
Cite:SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex.
Science, 375, 2022
7T9L
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BU of 7t9l by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron 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, Tuttle, K.S, Subramaniam, S.
Deposit date:2021-12-19
Release date:2021-12-29
Last modified:2022-07-13
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex.
Science, 375, 2022
7T9W
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BU of 7t9w by Molmil
Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2
Descriptor: CHLORIDE ION, GLYCEROL, Papain-like protease nsp3
Authors:Stogios, P.J, Skarina, T, Di Leo, R, Savchenko, A, Joachimiak, A, Satchell, K.J.F, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:2021-12-20
Release date:2021-12-29
Last modified:2024-04-03
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2
To Be Published
7SPO
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BU of 7spo by Molmil
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ...
Authors:Shi, K, Aihara, H.
Deposit date:2021-11-02
Release date:2022-01-05
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography.
Nat Commun, 12, 2021
7SPP
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BU of 7spp by Molmil
Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 2C02
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:Shi, K, Aihara, H.
Deposit date:2021-11-02
Release date:2022-01-05
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:Mechanisms of SARS-CoV-2 neutralization by shark variable new antigen receptors elucidated through X-ray crystallography.
Nat Commun, 12, 2021
7SJS
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BU of 7sjs by Molmil
Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CC40.8
Descriptor: ACETATE ION, CC40.8 Fab heavy chain, CC40.8 Fab light chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2021-10-18
Release date:2022-01-12
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.612 Å)
Cite:A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection.
Sci Transl Med, 14, 2022
7TAS
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BU of 7tas by Molmil
SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (local refinement of the RBD and S2K146)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, S2K146 Fab heavy chain, S2K146 Fab light chain, ...
Authors:Park, Y.J, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2021-12-21
Release date:2022-01-12
Last modified:2022-02-09
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.
Science, 375, 2022
7TAT
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BU of 7tat by Molmil
SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (two receptor-binding domains open)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2K146 Fab heavy chain, ...
Authors:Park, Y.J, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2021-12-21
Release date:2022-01-12
Last modified:2022-02-09
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry.
Science, 375, 2022
7TB4
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BU of 7tb4 by Molmil
Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Surface glycoprotein
Authors:Zhou, T, Tsybovsky, T, Kwong, P.D.
Deposit date:2021-12-21
Release date:2022-01-12
Last modified:2022-01-19
Method:ELECTRON MICROSCOPY (3.29 Å)
Cite:Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants.
Biorxiv, 2021
7TE0
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BU of 7te0 by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor PF-07321332
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase
Authors:Yang, K.S, Liu, W.R.
Deposit date:2022-01-03
Release date:2022-01-12
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir.
J.Med.Chem., 65, 2022
7VXM
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BU of 7vxm by Molmil
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C3 state
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Xu, C, Cong, Y.
Deposit date:2021-11-12
Release date:2022-01-12
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Nat Commun, 12, 2021
7W92
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BU of 7w92 by Molmil
Open state of SARS-CoV-2 Delta variant spike protein
Descriptor: Spike glycoprotein
Authors:Cong, Y, Liu, C.X.
Deposit date:2021-12-09
Release date:2022-01-12
Last modified:2022-03-02
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W94
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BU of 7w94 by Molmil
Transition state of SARS-CoV-2 Delta variant spike protein
Descriptor: Spike glycoprotein
Authors:Cong, Y, Liu, C.X.
Deposit date:2021-12-09
Release date:2022-01-12
Last modified:2022-03-02
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W99
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BU of 7w99 by Molmil
SARS-CoV-2 Delta S-ACE2-C2a
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Cong, Y, Liu, C.X.
Deposit date:2021-12-09
Release date:2022-01-12
Last modified:2022-03-02
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W9B
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BU of 7w9b by Molmil
SARS-CoV-2 Delta S-ACE2-C2b
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Cong, Y, Liu, C.X.
Deposit date:2021-12-09
Release date:2022-01-12
Last modified:2022-03-02
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022
7W9C
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BU of 7w9c by Molmil
SARS-CoV-2 Delta S-ACE2-C3
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Cong, Y, Liu, C.X.
Deposit date:2021-12-09
Release date:2022-01-12
Last modified:2022-03-02
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Nat Commun, 13, 2022

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