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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 (5197)Repr. entries (2266)Latest entries (44)
8XKC
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The structure of HLA-A/Pep16
Descriptor: Beta-2-microglobulin, HLA class I heavy chain, Spike protein S1
Authors:Zhang, J.N, Yue, C, Liu, J.
Deposit date:2023-12-23
Release date:2024-07-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (2.18 Å)
Cite:Uncommon P1 Anchor-featured Viral T Cell Epitope Preference within HLA-A*2601 and HLA-A*0101 Individuals.
Immunohorizons, 8, 2024
8XKE
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The structure of HLA-A/14-3-D
Descriptor: Beta-2-microglobulin, GLU-VAL-ASP-ASN-ALA-THR-ARG-PHE-ALA-SER-VAL-TYR, HLA class I heavy chain
Authors:Zhang, J.N, Yue, C, Liu, J, Sun, Z.Y.
Deposit date:2023-12-23
Release date:2024-07-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Uncommon P1 Anchor-featured Viral T Cell Epitope Preference within HLA-A*2601 and HLA-A*0101 Individuals.
Immunohorizons, 8, 2024
8XKI
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A neutralizing nanobody VHH60 against wt SARS-CoV-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, Spike glycoprotein, ...
Authors:Lu, Y, Guo, H, Ji, X, Yang, H.
Deposit date:2023-12-23
Release date:2024-07-10
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:A broad neutralizing nanobody against SARS-CoV-2 engineered from an approved drug.
Cell Death Dis, 15, 2024
9AT4
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Crystal structure of SARS-CoV-2 3CL protease in complex with a methylbicyclo[2.2.1]heptane 2-pyrrolidone inhibitor
Descriptor: (1R,2S)-2-{[N-({[(2S)-1-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-{[N-({[(2S)-1-{[(1S,2S,4R)-bicyclo[2.2.1]heptan-2-yl]methyl}-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase nsp5, ...
Authors:Lovell, S, Cooper, A, Battaile, K.P, Dampalla, C.S, Groutas, W.C.
Deposit date:2024-02-26
Release date:2024-07-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.
J.Med.Chem., 67, 2024
8Q5Y
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cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23
Descriptor: Monoclonal antibody Mab 23 (Heavy Chain), Monoclonal antibody Mab 23 (Light chain), Spike glycoprotein
Authors:Hallberg, M, Das, H.
Deposit date:2023-08-10
Release date:2024-07-17
Last modified:2025-07-09
Method:ELECTRON MICROSCOPY (2.6 Å)
Cite:Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.
Nat Commun, 15, 2024
8THF
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SARS-CoV-2 BA.1 S-6P-no-RBD
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 protein S1,Spike glycoprotein
Authors:Bu, F, Li, F, Liu, B.
Deposit date:2023-07-15
Release date:2024-07-17
Last modified:2024-10-09
Method:ELECTRON MICROSCOPY (2.83 Å)
Cite:Universal subunit vaccine protects against multiple SARS-CoV-2 variants and SARS-CoV.
Npj Vaccines, 9, 2024
8XSE
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SARS-CoV-2 RBD + IMCAS-123 + IMCAS-72 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS-123 H chain, IMCAS-123 L chain, ...
Authors:Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
Deposit date:2024-01-09
Release date:2024-07-17
Last modified:2024-10-23
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSF
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SARS-CoV-2 RBD + IMCAS-364 + hACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, IMCAS-364 H chain, ...
Authors:Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
Deposit date:2024-01-09
Release date:2024-07-17
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.16 Å)
Cite:Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSI
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SARS-CoV-2 RBD + IMCAS-364 (Local Refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS-364 H chain, IMCAS-364 L chain, ...
Authors:Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
Deposit date:2024-01-09
Release date:2024-07-17
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (2.1 Å)
Cite:Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSJ
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SARS-CoV-2 Omicron BA.4 RBD + IMCAS-316 + 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:Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
Deposit date:2024-01-09
Release date:2024-07-17
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (2.61 Å)
Cite:Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8XSL
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BU of 8xsl by Molmil
SARS-CoV-2 spike + IMCAS-123
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, IMCAS-123 heavy chain, ...
Authors:Tong, Z, Cui, Y, Xie, Y, Tong, J, Gao, G.F, Qi, J.
Deposit date:2024-01-09
Release date:2024-07-17
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
8Y0Y
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BU of 8y0y by Molmil
Cryo-EM structure of the 123-316 scDb/PT-RBD complex
Descriptor: 123-316 scDb, 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Jia, G.W, Tong, Z, Tong, J.Y, Su, Z.M.
Deposit date:2024-01-23
Release date:2024-07-17
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.86 Å)
Cite:Deciphering a reliable synergistic bispecific strategy of rescuing antibodies for SARS-CoV-2 escape variants, including BA.2.86, EG.5.1, and JN.1.
Cell Rep, 43, 2024
9FZK
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BU of 9fzk by Molmil
SARS CoV-2 nsp10 in complex with theExoN domain from nsp14
Descriptor: Guanine-N7 methyltransferase nsp14, Non-structural protein 11, ZINC ION
Authors:Fisher, S.Z.
Deposit date:2024-07-05
Release date:2024-07-17
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:SARS CoV-2 nsp10 in complex with theExoN domain from nsp14
To Be Published
8UZE
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Crystal structure of chimeric bat coronavirus BANAL-20-236 RBD complexed with chimeric mouse ACE2
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Zhang, W, Shi, K, Aihara, H, Li, F.
Deposit date:2023-11-15
Release date:2024-07-24
Last modified:2025-02-05
Method:X-RAY DIFFRACTION (3.03 Å)
Cite:Structural basis for mouse receptor recognition by bat SARS2-like coronaviruses.
Proc.Natl.Acad.Sci.USA, 121, 2024
8VIF
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SARS-CoV-2 spike omicron (BA.1) ectodomain trimer in complex with SC27 Fab, local refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SC27 Fab heavy chain, SC27 Fab light chain, ...
Authors:Byrne, P.O, McLellan, J.S.
Deposit date:2024-01-04
Release date:2024-07-24
Last modified:2025-05-21
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.
Cell Rep Med, 5, 2024
8VKE
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SARS-CoV-2 spike omicron (BA.1) RBD ectodomain dimer-of-trimers in complex with SC27 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SC27 Fab heavy chain, SC27 Fab light chain, ...
Authors:Byrne, P.O, McLellan, J.S.
Deposit date:2024-01-09
Release date:2024-07-24
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.
Cell Rep Med, 5, 2024
8W4F
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SARS-CoV-2 spike protein in complex with a trivalent nanobody
Descriptor: Spike glycoprotein, Tribody
Authors:Jiang, X.Y, Qian, J.Q, Zhu, H.X, Qin, Q, Huang, Q.
Deposit date:2023-08-24
Release date:2024-07-24
Last modified:2024-11-20
Method:ELECTRON MICROSCOPY (4.2 Å)
Cite:Structure-guided design of a trivalent nanobody cluster targeting SARS-CoV-2 spike protein.
Int.J.Biol.Macromol., 256, 2024
8WDR
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Crystal structure of BQ.1.1 RBD 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:Li, W, Xie, Y.
Deposit date:2023-09-16
Release date:2024-07-24
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (3.47 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WDS
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Crystal structure of BF.7 RBD 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:Li, W, Xie, Y.
Deposit date:2023-09-16
Release date:2024-07-24
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WDY
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BU of 8wdy by Molmil
SARS-CoV-2 Omicron BQ.1.1 RBD 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Li, W, Xie, Y.
Deposit date:2023-09-16
Release date:2024-07-24
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (2.69 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WDZ
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BU of 8wdz by Molmil
SARS-CoV-2 Omicron BQ.1 RBD 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Li, W, Xie, Y.
Deposit date:2023-09-16
Release date:2024-07-24
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.71 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WE0
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BU of 8we0 by Molmil
SARS-CoV-2 Omicron XBB RBD complexed with human ACE2
Descriptor: 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, Angiotensin-converting enzyme 2, ...
Authors:Li, W, Xie, Y.
Deposit date:2023-09-16
Release date:2024-07-24
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WE1
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SARS-CoV-2 Omicron BF.7 RBD 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, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Li, W, Xie, Y.
Deposit date:2023-09-16
Release date:2024-07-24
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (2.47 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8WE4
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SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304
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:Li, W, Xie, Y.
Deposit date:2023-09-17
Release date:2024-07-24
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (2.91 Å)
Cite:Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Embo J., 43, 2024
8K9B
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SARS-CoV-2 spike protein in complex with one S2H5 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of S2H5 Fab, Light chain of S2H5 Fab, ...
Authors:Hong, Q, Cong, Y.
Deposit date:2023-07-31
Release date:2024-07-31
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (4.5 Å)
Cite:Molecular basis of SARS-CoV-2 immune evasion of NTD neutralizing antibodies.
Dian Zi Xian Wei Xue Bao, 2024

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