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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
8F0H
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Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab 1H2 heavy chain, Antibody Fab 1H2 light chain, ...
Authors:Yu, X, Zyla, D, Hastie, K.M, Saphire, E.O.
Deposit date:2022-11-02
Release date:2023-05-03
Last modified:2024-11-20
Method:ELECTRON MICROSCOPY (3.18 Å)
Cite:Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Cell Rep, 42, 2023
8GS9
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SARS-CoV-2 BA.2 spike RBD in complex bound with VacBB-551
Descriptor: Heavy chain of VacBB-551, Light chain of VacBB-551, Spike glycoprotein
Authors:Liu, C.C, Ju, B, Shen, S.L, Zhang, Z.
Deposit date:2022-09-05
Release date:2023-05-03
Last modified:2024-11-06
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:Omicron BQ.1.1 and XBB.1 unprecedentedly escape broadly neutralizing antibodies elicited by prototype vaccination.
Cell Rep, 42, 2023
7XSA
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BU of 7xsa by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P2S-2E9 Fab
Descriptor: P2S-2E9 Heavy chain, P2S-2E9 Light chain, Spike protein S1
Authors:Wang, X, Wang, Z.
Deposit date:2022-05-13
Release date:2023-05-10
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
7XSB
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BU of 7xsb by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab
Descriptor: P5S-3B11 Heavy chain, P5S-3B11 Light chain, Spike protein S1
Authors:Wang, X, Wang, Z, Gao, M.
Deposit date:2022-05-13
Release date:2023-05-10
Last modified:2024-10-30
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8A99
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SARS Cov2 Spike in 1-up conformation complex with Fab47
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab47 (Heavy chain variable domain), ...
Authors:Hallberg, B.M, Das, H.
Deposit date:2022-06-28
Release date:2023-05-10
Last modified:2024-10-16
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies.
Immunity, 56, 2023
8H3M
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Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy chain, Spike glycoprotein
Authors:Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y.
Deposit date:2022-10-09
Release date:2023-05-10
Last modified:2024-11-13
Method:ELECTRON MICROSCOPY (2.48 Å)
Cite:Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
8H3N
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Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, MO1 heavy-chain, MO1 light chain, ...
Authors:Ishimaru, H, Nishimura, M, Sutandhio, S, Shigematsu, H, Kato, K, Hasegawa, N, Mori, Y.
Deposit date:2022-10-09
Release date:2023-05-10
Last modified:2024-10-09
Method:ELECTRON MICROSCOPY (2.73 Å)
Cite:Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants.
J.Virol., 97, 2023
8OT0
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SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA and glycine
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Falke, S.
Deposit date:2023-04-20
Release date:2023-05-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Elife, 2024
8OV1
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SARS-CoV-2 nsp10-16 methyltransferase in complex with ADP
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D.
Deposit date:2023-04-25
Release date:2023-05-10
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery
Elife, 2024
8BSE
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BU of 8bse by Molmil
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab
Descriptor: 1D1 FAB HEAVY CHAIN, 1D1 FAB LIGHT CHAIN, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ...
Authors:Welin, M, Kimbung, Y.R, Focht, D, Pisitkun, T.
Deposit date:2022-11-25
Release date:2023-05-17
Last modified:2024-10-09
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
Plos One, 18, 2023
8BSF
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BU of 8bsf by Molmil
CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3D2 FAB HEAVY CHAIN, 3D2 FAB LIGHT CHAIN, ...
Authors:Welin, M, Kimbung, Y.R, Focht, D, Pisitkun, T.
Deposit date:2022-11-25
Release date:2023-05-17
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Efficacy of the combination of monoclonal antibodies against the SARS-CoV-2 Beta and Delta variants.
Plos One, 18, 2023
8CSJ
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BU of 8csj by Molmil
Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein
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-(2-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Reddem, E.R, Shapiro, L.
Deposit date:2022-05-12
Release date:2023-05-17
Last modified:2025-06-04
Method:ELECTRON MICROSCOPY (3.53 Å)
Cite:Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein
To Be Published
8FWN
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BU of 8fwn by Molmil
Crystal structure of SARS-CoV-2 papain-like protease C111S mutant
Descriptor: ACETATE ION, CHLORIDE ION, GLYCEROL, ...
Authors:Bezerra, E.H.S, Soprano, A.S, Tonoli, C.C.C, Prado, P.F.V, da Silva, J.C, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
Deposit date:2023-01-23
Release date:2023-05-17
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structure of SARS-CoV-2 papain-like protease C111S mutant
To Be Published
8HN6
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BU of 8hn6 by Molmil
Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
Descriptor: Heavy chain of monoclonal antibody 3G10, Light chain of monoclonal antibody 3G10, Spike protein S1
Authors:Qi, J, Chen, Y.
Deposit date:2022-12-07
Release date:2023-05-17
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Front Immunol, 14, 2023
8HN7
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BU of 8hn7 by Molmil
Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of monoclonal antibody 3C11, Light chain of monoclonal antibody 3C11, ...
Authors:Qi, J, Chen, Y.
Deposit date:2022-12-07
Release date:2023-05-17
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (3 Å)
Cite:Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.
Front Immunol, 14, 2023
8IF2
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BU of 8if2 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor 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:Kimura, K, Suzuki, T, Hashiguchi, T.
Deposit date:2023-02-17
Release date:2023-05-17
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (2.78 Å)
Cite:Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant.
Nat Commun, 14, 2023
7XSC
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BU of 7xsc by Molmil
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-2B10
Descriptor: P5S-2B10 Heavy chain, P5S-2B10 Light chain, Spike protein S1
Authors:Wang, X, Wang, Z, Lin, Z.
Deposit date:2022-05-13
Release date:2023-05-24
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.88 Å)
Cite:Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol., 24, 2023
8CWI
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BU of 8cwi by Molmil
Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Heavy chain of Fab arm of antibody 10G4, ...
Authors:Langley, D.B, Christ, D.
Deposit date:2022-05-19
Release date:2023-05-24
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.873 Å)
Cite:Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.
Proc.Natl.Acad.Sci.USA, 122, 2025
8CWK
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BU of 8cwk by Molmil
Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Heavy chain of Fab arm of antibody 10G4, ...
Authors:Langley, D.B, Christ, D.
Deposit date:2022-05-19
Release date:2023-05-24
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (2.368 Å)
Cite:Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.
Proc.Natl.Acad.Sci.USA, 122, 2025
8DNN
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BU of 8dnn by Molmil
Crystal structure of neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 80 FAB HEAVY CHAIN, 80 FAB LIGHT CHAIN, ...
Authors:Muthuraman, K, Kucharska, I, Ivanochko, D, Julien, J.P.
Deposit date:2022-07-11
Release date:2023-05-24
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (3.12 Å)
Cite:A multi-specific, multi-affinity antibody platform neutralizes sarbecoviruses and confers protection against SARS-CoV-2 in vivo.
Sci Transl Med, 15, 2023
8GB5
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BU of 8gb5 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9
Descriptor: 25F9 Heavy chain, 25F9 Light chain, BICINE, ...
Authors:Yuan, M, Zhu, X, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-12-25
Method:X-RAY DIFFRACTION (3.35 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB6
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BU of 8gb6 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 21B6
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, 21B6 Heavy chain, 21B6 Light chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-11-13
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB7
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BU of 8gb7 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 20A7
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 20A7 Heavy chain, 20A7 Light chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.57 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8GB8
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BU of 8gb8 by Molmil
Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 20A7 Heavy chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-02-24
Release date:2023-05-24
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine.
Sci Transl Med, 15, 2023
8ILC
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BU of 8ilc by Molmil
Crystal structure of Se-Met CoV-Y domain of Nsp3 in SARS-CoV-2
Descriptor: CHLORIDE ION, Papain-like protease nsp3, SULFATE ION
Authors:Wang, K, Nan, J, Lei, J.
Deposit date:2023-03-03
Release date:2023-05-24
Last modified:2024-10-23
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:The CoV-Y domain of SARS-CoV-2 Nsp3 interacts with BRAP to stimulate NF-kappa B signaling and induce host inflammatory responses.
Int.J.Biol.Macromol., 280, 2024

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