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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 (4406)Repr. entries (1944)Latest entries (19)
8HC4
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BU of 8hc4 by Molmil
SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-32 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (3.54 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HC5
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BU of 8hc5 by Molmil
SARS-CoV-2 wildtype S1 in complex with YB9-258 Fab and R1-32 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of R1-32 Fab, Heavy chain of YB9-258 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (3.43 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HC6
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BU of 8hc6 by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258 Fab, focused refinement of Fab region
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of YB9-258 Fab, Light chain of YB9-258, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (4.69 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HC7
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BU of 8hc7 by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (6P) complex with YB9-258 Fab, focused refinement of RBD-dimer region
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain variable region of YB9-258, Light chain variable region of YB9-258, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (4.54 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HC8
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BU of 8hc8 by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-292 Fab, focused refinement of Fab region
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of YB13-292 Fab, Light chain of YB13-292 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (3.95 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HC9
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BU of 8hc9 by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (3 RBD down)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of YB13-292 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-08-02
Method:ELECTRON MICROSCOPY (6.03 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HCA
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BU of 8hca by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (1 RBD up)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of YB13-292 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (4.35 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
8HCB
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BU of 8hcb by Molmil
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (2 RBD up)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of YB13-292 Fab, ...
Authors:Liu, B, Gao, X, Chen, Q, Li, Z, Su, M, He, J, Xiong, X.
Deposit date:2022-11-01
Release date:2023-01-25
Last modified:2023-05-03
Method:ELECTRON MICROSCOPY (4.18 Å)
Cite:Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants.
Nat Commun, 14, 2023
7WRH
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BU of 7wrh by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse 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:Han, P, Xie, Y, Qi, J.
Deposit date:2022-01-26
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (2.66 Å)
Cite:Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s.
Cell Discov, 8, 2022
7WZO
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BU of 7wzo by Molmil
Crystal structure of the SARS-CoV-2 nucleocapsid protein N-terminal domain in complex with Ubl1
Descriptor: Nucleoprotein, nsp3
Authors:Ni, X.C, Zhou, R.J, Lei, J.
Deposit date:2022-02-18
Release date:2023-02-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.64 Å)
Cite:Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2.
Commun Biol, 6, 2023
7YCK
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BU of 7yck by Molmil
Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, FP-12A Fab heavy chain, FP-12A Fab light chain, ...
Authors:Nguyen, V.H.T, Chen, X.
Deposit date:2022-07-01
Release date:2023-02-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
7YCL
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BU of 7ycl by Molmil
Crystal structure of SARS-CoV-2 Spike RBD in complex with IS-9A Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, IS-9A Fab heavy chain, IS-9A Fab light chain, ...
Authors:Mohapatra, A, Chen, X.
Deposit date:2022-07-01
Release date:2023-02-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
7YCN
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BU of 7ycn by Molmil
Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, IY-2A Fab heavy chain, IY-2A Fab light chain, ...
Authors:Mohapatra, A, Chen, X.
Deposit date:2022-07-01
Release date:2023-02-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.85 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
8HHX
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BU of 8hhx by Molmil
SARS-CoV-2 Delta Spike in complex with FP-12A
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, FP-12A Fab heavy chain, ...
Authors:Chen, X, Wu, Y.-M.
Deposit date:2022-11-17
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (3.62 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
8HHY
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BU of 8hhy by Molmil
SARS-CoV-2 Delta Spike in complex with IS-9A
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, IS-9A Fab heavy chain, ...
Authors:Mohapatra, A, Wu, Y.-M.
Deposit date:2022-11-17
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (2.77 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
8HHZ
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BU of 8hhz by Molmil
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
Descriptor: IY-2A Fab heavy chain, IY-2A Fab light chain, Spike glycoprotein
Authors:Chen, X, Mohapatra, A, Wu, Y.-M.
Deposit date:2022-11-17
Release date:2023-02-01
Method:ELECTRON MICROSCOPY (4.28 Å)
Cite:Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun, 14, 2023
7TPK
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BU of 7tpk by Molmil
SARS-CoV-2 E406W mutant RBD - Local Refinement
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1
Authors:Addetia, A, Veesler, D.
Deposit date:2022-01-25
Release date:2023-02-08
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:SARS-CoV-2 E406W mutant RBD - Local Refinement
To Be Published
7XWX
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BU of 7xwx by Molmil
Crystal structure of SARS-CoV-2 N-CTD
Descriptor: Nucleoprotein, PHOSPHATE ION
Authors:Luan, X.D, Li, X.M, Li, Y.F.
Deposit date:2022-05-27
Release date:2023-02-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3 Å)
Cite:Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Sci Bull (Beijing), 67, 2022
7XWZ
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BU of 7xwz by Molmil
Crystal structure of SARS-CoV-2 N-NTD and dsRNA complex
Descriptor: 1,2-ETHANEDIOL, GLYCEROL, Nucleoprotein, ...
Authors:Luan, X.D, Li, X.M, Li, Y.F.
Deposit date:2022-05-27
Release date:2023-02-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Sci Bull (Beijing), 67, 2022
7XX1
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BU of 7xx1 by Molmil
Crystal structure of SARS-CoV-2 N-NTD
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Nucleoprotein, ZINC ION
Authors:Luan, X.D, Li, X.M, Li, Y.F.
Deposit date:2022-05-27
Release date:2023-02-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein.
Sci Bull (Beijing), 67, 2022
7YUE
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BU of 7yue by Molmil
Epitope-directed anti-SARS CoV 2 scFv engineered against the key spike protein region.
Descriptor: Single chain variable Fragment, Spike protein S2
Authors:Kumar, U, Jaiswal, D, Gaur, V, Salunke, D.M.
Deposit date:2022-08-17
Release date:2023-02-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Epitope-directed anti-SARS-CoV-2 scFv engineered against the key spike protein region could block membrane fusion.
Protein Sci., 32, 2023
8DM5
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BU of 8dm5 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex 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, Processed angiotensin-converting enzyme 2, ...
Authors:Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
Deposit date:2022-07-08
Release date:2023-02-08
Method:ELECTRON MICROSCOPY (2.51 Å)
Cite:Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023
8DM6
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BU of 8dm6 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
Deposit date:2022-07-08
Release date:2023-02-08
Method:ELECTRON MICROSCOPY (2.77 Å)
Cite:Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023
8DM7
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BU of 8dm7 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse 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:Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
Deposit date:2022-07-08
Release date:2023-02-08
Method:ELECTRON MICROSCOPY (2.49 Å)
Cite:Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023
8DM8
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BU of 8dm8 by Molmil
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 (focused refinement of RBD and ACE2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Zhu, X, Saville, J.W, Mannar, D, Berezuk, A.M, Cholak, S, Tuttle, K.S, Vahdatihassani, F, Subramaniam, S.
Deposit date:2022-07-08
Release date:2023-02-08
Method:ELECTRON MICROSCOPY (2.68 Å)
Cite:Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein.
Cell Rep, 42, 2023

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