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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
8YF2
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BU of 8yf2 by Molmil
Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog ACE2 (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, ...
Authors:Li, L.J, Luo, C.L, Qi, J.X, Gao, G.F.
Deposit date:2024-02-23
Release date:2024-10-23
Last modified:2025-04-30
Method:ELECTRON MICROSCOPY (2.64 Å)
Cite:Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Plos Pathog., 20, 2024
8YFT
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BU of 8yft by Molmil
Cryo-EM structure of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog ACE2 (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, ...
Authors:Li, L.J, Luo, C.L, Qi, J.X, Gao, G.F.
Deposit date:2024-02-25
Release date:2024-10-23
Last modified:2025-04-30
Method:ELECTRON MICROSCOPY (3.16 Å)
Cite:Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Plos Pathog., 20, 2024
9DW6
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BU of 9dw6 by Molmil
Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant in complex with peptide from human tRNA methyltransferase TRMT1
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, GLYCEROL, ...
Authors:D'Oliviera, A, Mugridge, J.S.
Deposit date:2024-10-08
Release date:2024-10-23
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease.
Elife, 12, 2025
8RRN
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BU of 8rrn by Molmil
Crystal structure of the SARS-CoV-2 S RBD in complex with pT1616 Fab
Descriptor: Spike protein S1, pT1616 Fab heavy chain, pT1616 Fab light chain
Authors:Hansen, G, Krey, T.
Deposit date:2024-01-23
Release date:2024-10-30
Last modified:2025-01-01
Method:X-RAY DIFFRACTION (3.11 Å)
Cite:A human monoclonal antibody neutralizing SARS-CoV-2 Omicron variants containing the L452R mutation.
J.Virol., 98, 2024
9GDY
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BU of 9gdy by Molmil
SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses
Descriptor: Spike glycoprotein,Fibritin
Authors:Herreros, D, Mata, C.P, Noddings, C, Irene, D, Agard, D.A, Tsai, M.-D, Sorzano, C.O.S, Carazo, J.M.
Deposit date:2024-08-06
Release date:2024-10-30
Last modified:2025-05-07
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Nat Commun, 16, 2025
8U25
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BU of 8u25 by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant
Descriptor: 3C-like proteinase
Authors:Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
Deposit date:2023-09-05
Release date:2024-11-06
Last modified:2025-02-12
Method:X-RAY DIFFRACTION (2.23 Å)
Cite:Distal protein-protein interactions contribute to nirmatrelvir resistance.
Nat Commun, 16, 2025
9CTU
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BU of 9ctu by Molmil
Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P
Descriptor: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate, Membrane protein, POTASSIUM ION, ...
Authors:Dolan, K.A, Brohawn, S.G.
Deposit date:2024-07-25
Release date:2024-11-06
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Biorxiv, 2024
9CTW
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BU of 9ctw by Molmil
Cryo-EM structure of SARS-CoV-2 M (long conformation) in the presence of C1P
Descriptor: Long conformation Fab heavy chain, Long conformation Fab light chain, Membrane protein
Authors:Dolan, K.A, Brohawn, S.G.
Deposit date:2024-07-25
Release date:2024-11-06
Last modified:2025-05-14
Method:ELECTRON MICROSCOPY (3.01 Å)
Cite:Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Biorxiv, 2024
8R1Q
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BU of 8r1q by Molmil
SARS-CoV-2 Mpro (Omicron, P132H+T169S) in complex with alpha-ketoamide 13b-K
Descriptor: 3C-like proteinase nsp5, ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
Authors:Sun, X, Ibrahim, M, Hilgenfeld, R.
Deposit date:2023-11-02
Release date:2024-11-13
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Hlife, 2, 2024
8TFD
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BU of 8tfd by Molmil
Crystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain
Descriptor: 1,2-ETHANEDIOL, DNA aptamer, Nucleoprotein
Authors:Esler, M, Belica, C, Shi, K, Aihara, H.
Deposit date:2023-07-10
Release date:2024-11-13
Last modified:2024-12-11
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.
Nucleic Acids Res., 52, 2024
8WUR
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BU of 8wur by Molmil
Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with shikonin
Descriptor: 2-[(1R)-4-methyl-1-oxidanyl-pent-3-enyl]-5,8-bis(oxidanyl)naphthalene-1,4-dione, 3C-like proteinase nsp5
Authors:Zhao, Z.Y, Li, W.W, Zhang, J, Li, J.
Deposit date:2023-10-21
Release date:2024-11-13
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332.
Viruses, 16, 2023
8WYH
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BU of 8wyh by Molmil
The global map of Omicron Subvariants Spike with ACE2
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Yan, R.H, Wang, A.J, Yang, H.N.
Deposit date:2023-10-31
Release date:2024-11-13
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3 Å)
Cite:The global map of Omicron Subvariants Spike with ACE2
To Be Published
8WYJ
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BU of 8wyj by Molmil
The global map of Omicron Subvariants Spike with two antibodies
Descriptor: S309-HC, S309-KC, SA55-HC, ...
Authors:Yan, R.H, Wang, A.J, Yang, H.N.
Deposit date:2023-10-31
Release date:2024-11-13
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:The global map of Omicron Subvariants Spike with two antibodies
To Be Published
8XZ8
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BU of 8xz8 by Molmil
BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
Authors:Yue, C, Liu, P.
Deposit date:2024-01-21
Release date:2024-11-13
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3.65 Å)
Cite:BA.2.86 Spike in complex with bovine ACE2
To Be Published
8XZ9
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BU of 8xz9 by Molmil
BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein, ...
Authors:Yue, C, Liu, P.
Deposit date:2024-01-21
Release date:2024-11-13
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (3.37 Å)
Cite:BA.2.86 Spike in complex with bovine ACE2
To Be Published
8XZA
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BU of 8xza by Molmil
BA.2.86 Spike in complex with bovine ACE2 (Local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
Authors:Yue, C, Liu, P.
Deposit date:2024-01-21
Release date:2024-11-13
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (4.07 Å)
Cite:BA.2.86 Spike in complex with bovine ACE2
To Be Published
8Y32
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BU of 8y32 by Molmil
BA.2.86-V483 RBD in complex with bACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, CHLORIDE ION, ...
Authors:Yue, C, Liu, P.
Deposit date:2024-01-28
Release date:2024-11-13
Last modified:2024-11-27
Method:ELECTRON MICROSCOPY (4.13 Å)
Cite:BA.2.86-V483 RBD in complex with bACE2
To Be Published
9F2H
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BU of 9f2h by Molmil
Crystal structure of SARS-CoV-2 N-protein C-terminal domain in complex with riluzole
Descriptor: 1,2-ETHANEDIOL, 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine, Nucleoprotein, ...
Authors:Marquez-Monino, M.A, Gonzalez, B, Perez-Canadillas, J.M.
Deposit date:2024-04-23
Release date:2024-11-13
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.
Structure, 33, 2025
9C44
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BU of 9c44 by Molmil
SARS-CoV-2 S + S2L20
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 Fab Heavy Chain Variable, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2024-06-03
Release date:2024-11-20
Last modified:2024-12-11
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Design of customized coronavirus receptors.
Nature, 635, 2024
9C45
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BU of 9c45 by Molmil
SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, S2L20 Fab Heavy Chain Variable, ...
Authors:McCallum, M, Veesler, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2024-06-03
Release date:2024-11-20
Last modified:2024-12-11
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Design of customized coronavirus receptors.
Nature, 635, 2024
9CO6
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BU of 9co6 by Molmil
BA.5 spike/Nanosota-9 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, Nanosota-9, ...
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-07-16
Release date:2024-11-20
Last modified:2024-12-11
Method:ELECTRON MICROSCOPY (3.01 Å)
Cite:Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO7
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BU of 9co7 by Molmil
Local refinement of BA.5 spike/Nanosota-9 complex
Descriptor: Nanosota-9, Spike glycoprotein
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-07-16
Release date:2024-11-20
Last modified:2024-12-11
Method:ELECTRON MICROSCOPY (3.32 Å)
Cite:Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO8
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BU of 9co8 by Molmil
JN.1 spike/Nanosota-9 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-9, Spike glycoprotein
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-07-16
Release date:2024-11-20
Last modified:2024-12-11
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9CO9
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BU of 9co9 by Molmil
Local refinement of JN.1 spike/Nanosota-9 complex
Descriptor: Nanosota-9, Spike glycoprotein
Authors:Ye, G, Bu, F, Liu, B, Li, F.
Deposit date:2024-07-16
Release date:2024-11-20
Last modified:2024-12-11
Method:ELECTRON MICROSCOPY (3.44 Å)
Cite:Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate.
Plos Pathog., 20, 2024
9EVY
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BU of 9evy by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant E136D
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A, Guenther, S.
Deposit date:2024-04-02
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024

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