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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)
8T5P
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SARS-CoV-2 ORF3a peptide in complex with TRAF3 TRAF domain
Descriptor: ORF3a protein, TNF receptor-associated factor 3
Authors:Busscher, B.M, Xiao, T.S.
Deposit date:2023-06-14
Release date:2023-11-29
Last modified:2023-12-06
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:SARS-CoV-2 ORF3a-Mediated NF-kappa B Activation Is Not Dependent on TRAF-Binding Sequence.
Viruses, 15, 2023
8T5Q
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SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain
Descriptor: DI(HYDROXYETHYL)ETHER, ORF3a protein, TETRAETHYLENE GLYCOL, ...
Authors:Busscher, B.M, Xiao, T.S.
Deposit date:2023-06-14
Release date:2023-11-29
Last modified:2023-12-06
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:SARS-CoV-2 ORF3a-Mediated NF-kappa B Activation Is Not Dependent on TRAF-Binding Sequence.
Viruses, 15, 2023
8UUL
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Prototypic SARS-CoV-2 spike (containing K417) in the closed 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:Geng, Q, Liu, B, Li, F.
Deposit date:2023-11-01
Release date:2023-11-29
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.
Elife, 12, 2023
8UUN
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Prototypic SARS-CoV-2 spike (containing V417) in the closed 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:Geng, Q, Liu, B, Li, F.
Deposit date:2023-11-01
Release date:2023-11-29
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.
Elife, 12, 2023
8WRH
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SARS-CoV-2 XBB.1.5.70 in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S2'
Authors:Feng, L.L, Feng, L.L.
Deposit date:2023-10-14
Release date:2023-11-29
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (3.08 Å)
Cite:Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8WRL
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XBB.1.5 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Feng, L.L, Feng, L.L.
Deposit date:2023-10-15
Release date:2023-11-29
Last modified:2024-06-19
Method:ELECTRON MICROSCOPY (3.36 Å)
Cite:Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
7YC2
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Crystal structure of auxiliary protein in complex with human protein
Descriptor: ORF, Protein zyg-11 homolog B
Authors:Gao, X, Cui, S.
Deposit date:2022-06-30
Release date:2023-12-06
Last modified:2024-06-19
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:SARS-CoV-2 ORF10 hijacking ubiquitination machinery reveals potential unique drug targeting sites
Acta Pharm Sin B, 2024
8HWS
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The complex structure of Omicron BA.4 RBD with BD604, S309, and S304
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, BD-604 Fab Heavy chain, BD-604 Fab Light chain, ...
Authors:He, Q.W, Xu, Z.P, Xie, Y.F.
Deposit date:2023-01-02
Release date:2023-12-06
Method:ELECTRON MICROSCOPY (2.36 Å)
Cite:An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB.
Cell Rep Med, 4, 2023
8HWT
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SARS-CoV-2 Omicron BA.2 RBD complexed with BD-604 and S304 Fab
Descriptor: BD-604 heavy chain, BD-604 light chain, S304 heavy chain, ...
Authors:He, Q.W, Xie, Y.
Deposit date:2023-01-02
Release date:2023-12-06
Method:ELECTRON MICROSCOPY (2.91 Å)
Cite:An updated atlas of antibody evasion by SARS-CoV-2 Omicron sub-variants including BQ.1.1 and XBB.
Cell Rep Med, 4, 2023
8UYS
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SARS-CoV-2 5' proximal stem-loop 5
Descriptor: SARS-CoV-2 RNA SL5 domain.
Authors:Kretsch, R.C, Xu, L, Zheludev, I.N, Zhou, X, Huang, R, Nye, G, Li, S, Zhang, K, Chiu, W, Das, R.
Deposit date:2023-11-14
Release date:2023-12-06
Last modified:2024-03-13
Method:ELECTRON MICROSCOPY (4.7 Å)
Cite:Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses.
Proc.Natl.Acad.Sci.USA, 121, 2024
8WRM
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XBB.1.5 spike protein in complex with ACE2
Descriptor: Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Feng, L.L, Feng, L.L.
Deposit date:2023-10-15
Release date:2023-12-06
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (4.34 Å)
Cite:Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8WRO
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XBB.1.5.10 spike protein in complex with ACE2
Descriptor: Processed angiotensin-converting enzyme 2, Spike glycoprotein,Spike glycoprotein,Spike glycoprotein,Fusion protein
Authors:Feng, L.L, Feng, L.L.
Deposit date:2023-10-15
Release date:2023-12-06
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8F2J
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Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain
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, ...
Authors:Sankhala, R.S, Joyce, M.G.
Deposit date:2022-11-08
Release date:2023-12-13
Method:X-RAY DIFFRACTION (3.16 Å)
Cite:Antibody Targeting of Conserved Sites of Vulnerability on the SARS-CoV-2 Spike Receptor-Binding Domain.
To Be Published
8FAH
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Crystal structure of SARS-CoV-2 receptor binding domain in complex with SARS-CoV-2 reactive human antibody CR3022
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CR3022 Fab heavy chain, CR3022 Fab light chain, ...
Authors:Sankhala, R.S, Jensen, J.L, Joyce, M.G.
Deposit date:2022-11-26
Release date:2023-12-13
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (4.22 Å)
Cite:Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Structure, 32, 2024
8K45
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A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nb4 nanobody, ...
Authors:Lu, Y, Gao, Y, Yao, H, Xu, W, Yang, H.
Deposit date:2023-07-17
Release date:2023-12-13
Method:ELECTRON MICROSCOPY (3.66 Å)
Cite:A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
MedComm (2020), 4, 2023
8K46
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A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains
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, Gao, Y, Yao, H, Xu, W, Yang, H.
Deposit date:2023-07-17
Release date:2023-12-13
Method:ELECTRON MICROSCOPY (3.37 Å)
Cite:A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
MedComm (2020), 4, 2023
8SGU
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Crystal structure of the SARS-CoV-2 receptor binding domain
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, GLYCEROL, ...
Authors:Sankhala, R.S, Jensen, J.L, Joyce, M.G.
Deposit date:2023-04-13
Release date:2023-12-13
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Structure, 32, 2024
8SMI
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Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, WRAIR-2123 Fab heavy chain, ...
Authors:Sankhala, R.S, Jensen, J.L, Joyce, M.G.
Deposit date:2023-04-26
Release date:2023-12-13
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Structure, 32, 2024
8WOX
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Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with rabbit ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
Authors:Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F.
Deposit date:2023-10-08
Release date:2023-12-13
Last modified:2024-02-28
Method:ELECTRON MICROSCOPY (2.75 Å)
Cite:Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
8WOY
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Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with rabbit ACE2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
Authors:Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F.
Deposit date:2023-10-08
Release date:2023-12-13
Last modified:2024-02-28
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
8WTD
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XBB.1.5.10 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S2'
Authors:Feng, L.L, Feng, L.L.
Deposit date:2023-10-18
Release date:2023-12-13
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (3.06 Å)
Cite:Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8WTJ
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XBB.1.5.70 spike protein in complex with ACE2
Descriptor: Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Feng, L.L, Feng, L.L.
Deposit date:2023-10-18
Release date:2023-12-13
Last modified:2024-03-20
Method:ELECTRON MICROSCOPY (4.64 Å)
Cite:Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding.
Plos Pathog., 19, 2023
8HPF
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Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with fab L4.65 and L5.34
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
Authors:Gao, G.F, Liu, S.
Deposit date:2022-12-12
Release date:2023-12-20
Last modified:2024-01-31
Method:ELECTRON MICROSCOPY (2.34 Å)
Cite:Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HPU
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Cryo-EM structure of SARS-CoV-2 Omicron BA.4 RBD in complex with fab L4.65 and L5.34
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2', fab L4.65, ...
Authors:Gao, G.F, Liu, S.
Deposit date:2022-12-13
Release date:2023-12-20
Last modified:2024-01-31
Method:ELECTRON MICROSCOPY (2.56 Å)
Cite:Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023
8HQ7
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Cryo-EM structure of SARS-CoV-2 Omicron Prototype RBD in complex with fab L4.65 and L5.34
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, fab L4.65, ...
Authors:Gao, G.F, Liu, S.
Deposit date:2022-12-13
Release date:2023-12-20
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine.
Cell Discov, 9, 2023

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PDB entries from 2024-07-17

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