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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 (4418)Repr. entries (1953)Latest entries (11)
7V82
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Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 1
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, ...
Authors:Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
Deposit date:2021-08-22
Release date:2021-10-06
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 1
To Be Published
7V86
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BU of 7v86 by Molmil
Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form
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, ...
Authors:Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
Deposit date:2021-08-22
Release date:2021-10-06
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form
To Be Published
7V8A
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Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2
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,Angiotensin-converting enzyme 2 (ACE2) ectodomain, ...
Authors:Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
Deposit date:2021-08-22
Release date:2021-10-06
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2
To Be Published
7V8C
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BU of 7v8c by Molmil
Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), Cleavable form, one RBD-up 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, Spike glycoprotein
Authors:Yang, T.J, Yu, P.Y, Chang, Y.C, Hsu, S.T.D.
Deposit date:2021-08-22
Release date:2021-10-06
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), Cleavable form, one RBD-up conformation
To Be Published
7D6I
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BU of 7d6i by Molmil
A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of GH12-Fab, Light chain of GH12-Fab, ...
Authors:Shi, R, Qi, J.X, Gao, G.F, Yan, J.H.
Deposit date:2020-09-30
Release date:2021-10-13
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.41 Å)
Cite:A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2
To Be Published
7E5R
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SARS-CoV-2 S trimer with three-antibody cocktail complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FC05 heavy chain, FC05 light chain, ...
Authors:Sun, Y, Wang, L, Wang, N, Feng, R, Wang, X.
Deposit date:2021-02-20
Release date:2021-10-13
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure-based development of three- and four-antibody cocktails against SARS-CoV-2 via multiple mechanisms.
Cell Res., 31, 2021
7P40
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P5C3 is a potent fab neutralizer
Descriptor: Spike glycoprotein, Variable Heavy Chain P5C3 (VH), Variable Light Chain P5C3 (VL)
Authors:perez, L.
Deposit date:2021-07-09
Release date:2021-10-13
Last modified:2023-04-12
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:A highly potent antibody effective against SARS-CoV-2 variants of concern.
Cell Rep, 37, 2021
7PHG
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MaP OF P5C3RBD Interface
Descriptor: Heavy ChaIn variable, Light ChaIn, Surface glycoprotein
Authors:Perez, L.
Deposit date:2021-08-17
Release date:2021-10-13
Last modified:2021-10-27
Method:ELECTRON MICROSCOPY (4.3 Å)
Cite:A highly potent antibody effective against SARS-CoV-2 variants of concern.
Cell Rep, 37, 2021
7RTD
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BU of 7rtd by Molmil
SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01
Descriptor: Beta-2-microglobulin, HLA class I antigen, Spike protein S1
Authors:Szeto, C, Nguyen, A.T, Gras, S.
Deposit date:2021-08-13
Release date:2021-10-13
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR.
Cells, 10, 2021
7RTR
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BU of 7rtr by Molmil
YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01
Descriptor: Beta-2-microglobulin, HLA class I antigen, SODIUM ION, ...
Authors:Szeto, C, Gras, S.
Deposit date:2021-08-14
Release date:2021-10-13
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR.
Cells, 10, 2021
7DTE
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BU of 7dte by Molmil
SARS-CoV-2 RdRP catalytic complex with T33-1 RNA
Descriptor: Non-structural protein 7, Non-structural protein 8, RNA (33-MER), ...
Authors:Wang, Q, Gong, P.
Deposit date:2021-01-04
Release date:2021-10-20
Last modified:2024-06-05
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Remdesivir overcomes the S861 roadblock in SARS-CoV-2 polymerase elongation complex.
Cell Rep, 37, 2021
7F2E
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BU of 7f2e by Molmil
SARS-CoV-2 nucleocapsid protein C-terminal domain (dodecamer)
Descriptor: Nucleoprotein, PHOSPHATE ION
Authors:Liu, C, Jiang, H.
Deposit date:2021-06-10
Release date:2021-10-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies.
Febs J., 289, 2022
7R95
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BU of 7r95 by Molmil
Membrane bound structure of HR1 domain of SARS-CoV-2 spike protein
Descriptor: Spike protein S2
Authors:Chiliveri, S.C, Bax, A.
Deposit date:2021-06-28
Release date:2021-10-20
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion.
Sci Adv, 7, 2021
7V26
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BU of 7v26 by Molmil
XG005-bound SARS-CoV-2 S
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, XG005 Heavy chain, ...
Authors:Zhan, W.Q, Zhang, X, Sun, L, Chen, Z.G.
Deposit date:2021-08-07
Release date:2021-10-20
Last modified:2022-07-06
Method:ELECTRON MICROSCOPY (3.85 Å)
Cite:An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.
Protein Cell, 13, 2022
7V2A
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BU of 7v2a by Molmil
SARS-CoV-2 Spike trimer in complex with XG014 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, The heavy chain of XG014, ...
Authors:Wang, K, Wang, X, Pan, L.
Deposit date:2021-08-07
Release date:2021-10-20
Last modified:2022-07-06
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:An ultrapotent pan-beta-coronavirus lineage B ( beta-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.
Protein Cell, 13, 2022
7S3N
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BU of 7s3n by Molmil
SARS-CoV-2 S stem helix peptide bound to Fab22
Descriptor: Fab22 Heavy Chain, Fab22 Light Chain, Spike glycoprotein
Authors:Goldsmith, J.A, McLellan, J.S.
Deposit date:2021-09-07
Release date:2021-10-27
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Stabilized coronavirus spike stem elicits a broadly protective antibody.
Cell Rep, 37, 2021
7VNU
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BU of 7vnu by Molmil
Crystal structure of the N-terminal domain of SARS-CoV-2 nucleocapsid protein
Descriptor: ACETATE ION, Nucleoprotein
Authors:Zhou, R.J, Ni, X.C, Lei, J.
Deposit date:2021-10-12
Release date:2021-10-27
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2.
Commun Biol, 6, 2023
7EKC
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BU of 7ekc by Molmil
Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed 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, Angiotensin-converting enzyme 2, ...
Authors:Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2021-04-05
Release date:2021-11-03
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKE
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BU of 7eke by Molmil
Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with human ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2021-04-05
Release date:2021-11-03
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKF
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BU of 7ekf by Molmil
Structure of SARS-CoV-2 Alpha variant spike receptor-binding domain complexed 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, Angiotensin-converting enzyme 2, ...
Authors:Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2021-04-05
Release date:2021-11-03
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKG
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BU of 7ekg by Molmil
Structure of SARS-CoV-2 Beta variant spike receptor-binding domain complexed 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, Angiotensin-converting enzyme 2, ...
Authors:Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2021-04-05
Release date:2021-11-03
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.63 Å)
Cite:Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7EKH
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Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Han, P.C, Su, C, Zhang, Y.F, Qi, J.X, Gao, G.F.
Deposit date:2021-04-05
Release date:2021-11-03
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants.
Nat Commun, 12, 2021
7N5H
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BU of 7n5h by Molmil
Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 spike glycoprotein
Descriptor: 2-36 Fab heavy chain, 2-36 Fab light chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Casner, R.G, Cerutti, G, Shapiro, L.
Deposit date:2021-06-05
Release date:2021-11-03
Last modified:2022-11-16
Method:ELECTRON MICROSCOPY (3.24 Å)
Cite:A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses.
Emerg Microbes Infect, 11, 2022
7SBO
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BU of 7sbo by Molmil
One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:2021-09-25
Release date:2021-11-03
Last modified:2021-12-22
Method:ELECTRON MICROSCOPY (3.44 Å)
Cite:Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021
7SBP
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BU of 7sbp by Molmil
Closed state of pre-fusion SARS-CoV-2 Kappa variant 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhang, J, Xiao, T.S, Cai, Y.F, Peng, H.Q, Volloch, S.R, Chen, B.
Deposit date:2021-09-25
Release date:2021-11-03
Last modified:2021-12-22
Method:ELECTRON MICROSCOPY (3.44 Å)
Cite:Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant.
Science, 374, 2021

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