COVID-19 featured content

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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)

All entries (4406)Repr. entries (1944)Latest entries (19)

7QTJ

SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD up - 1-P2G3 and 1-P5C3 Fabs (Local)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, P2G3 Heavy Chain, P2G3 Light Chain, ...
Authors:	Ni, D, Lau, K, Turelli, P, Fenwick, C, Perez, L, Pojer, F, Stahlberg, H, Pantaleo, G, Trono, D.
Deposit date:	2022-01-14
Release date:	2022-08-03
Last modified:	2022-09-07
Method:	ELECTRON MICROSCOPY (4.01 Å)
Cite:	Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys. Nat Microbiol, 7, 2022

7QTK

SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, P2G3 Heavy Chain, P2G3 Light Chain, ...
Authors:	Ni, D, Lau, K, Turelli, P, Fenwick, C, Perez, L, Pojer, F, Stahlberg, H, Pantaleo, G, Trono, D.
Deposit date:	2022-01-14
Release date:	2022-08-03
Last modified:	2022-09-07
Method:	ELECTRON MICROSCOPY (3.84 Å)
Cite:	Patient-derived monoclonal antibody neutralizes SARS-CoV-2 Omicron variants and confers full protection in monkeys. Nat Microbiol, 7, 2022

7T7B

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing antibody ADI-62113 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ADI-62113 Fab heavy chain, ADI-62113 Fab light chain, ...
Authors:	Liu, H, Wilson, I.A.
Deposit date:	2021-12-14
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.59 Å)
Cite:	Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron. Commun Biol, 5, 2022

7TCQ

Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide
Descriptor:	Anti-SARS-CoV-2 antibody WS6 Fab heavy chain, Anti-SARS-CoV-2 antibody WS6 Fab light chain, DI(HYDROXYETHYL)ETHER, ...
Authors:	Zhou, T, Kwong, P.D.
Deposit date:	2021-12-28
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.02 Å)
Cite:	Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability. Structure, 30, 2022

7TUU

Structure of the SARS-CoV-2 main protease in complex with halicin
Descriptor:	3C-like proteinase nsp5, 5-nitro-1,3-thiazole
Authors:	Yang, K.S, Liu, W.R.
Deposit date:	2022-02-03
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.85 Å)
Cite:	Repurposing Halicin as a potent covalent inhibitor for the SARS-CoV-2 main protease. Curr Res Chem Biol, 2, 2022

7U09

Crystal Structure of C13B8 Fab in complex with SARS-CoV-2 S fusion peptide
Descriptor:	Heavy chain Fab C13B8, Light chain Fab C13B8, SARS-CoV-2 S fusion peptide
Authors:	Tortorici, M.A, Veesler, D.
Deposit date:	2022-02-17
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science, 377, 2022

7U0A

Crystal Structure of C77G12 Fab in complex with SARS-CoV-2 S fusion peptide
Descriptor:	CHLORIDE ION, Heavy chain Fab C77G12, Light chain Fab C77G12, ...
Authors:	Tortorici, M.A, Veesler, D.
Deposit date:	2022-02-17
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science, 377, 2022

7U0E

Crystal Structure of C13C9 Fab in complex with SARS-CoV-2 S fusion peptide
Descriptor:	Heavy chain Fab C13C9, Light chain Fab C13C9, SARS-CoV-2 S fusion peptide
Authors:	Tortorici, M.A, Veesler, D.
Deposit date:	2022-02-18
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science, 377, 2022

7VGR

SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab
Descriptor:	Membrane protein, YN7756_1 Fab heavy chain, YN7756_1 Fab light chain
Authors:	Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:	2021-09-18
Release date:	2022-08-03
Last modified:	2023-08-16
Method:	ELECTRON MICROSCOPY (2.7 Å)
Cite:	Structure of SARS-CoV-2 membrane protein essential for virus assembly. Nat Commun, 13, 2022

7VGS

SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
Descriptor:	Membrane protein, YN7717_9 Fab heavy chain, YN7717_9 Fab light chain
Authors:	Zhang, Z, Ohto, U, Shimizu, T.
Deposit date:	2021-09-18
Release date:	2022-08-03
Last modified:	2023-08-16
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	Structure of SARS-CoV-2 membrane protein essential for virus assembly. Nat Commun, 13, 2022

8DF5

SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab
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:	McCallum, M, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Snell, G, Veesler, D.
Deposit date:	2022-06-21
Release date:	2022-08-03
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.7 Å)
Cite:	Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution. Science, 377, 2022

8DT3

Cryo-EM structure of spike binding to Fab of neutralizing antibody (locally refined)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain Fab of SW186, Light chain Fab of SW186, ...
Authors:	Sun, P.C, Fang, Y, Bai, X.C, Chen, Z.J.
Deposit date:	2022-07-25
Release date:	2022-08-03
Last modified:	2022-11-09
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	An antibody that neutralizes SARS-CoV-1 and SARS-CoV-2 by binding to a conserved spike epitope outside the receptor binding motif. Sci Immunol, 7, 2022

7FJC

Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab
Descriptor:	P36-5D2 heavy chain, P36-5D2 light chain, Spike protein S1, ...
Authors:	Zhang, L.Q, Wang, X.Q, Shan, S.S, Lan, J.
Deposit date:	2021-08-03
Release date:	2022-08-10
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.96 Å)
Cite:	Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab To Be Published

7STR

Crystal Structure of Human Fab S24-1063 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2
Descriptor:	1,2-ETHANEDIOL, Fab S24-1063, Heavy chain, ...
Authors:	Kim, Y, Maltseva, N, Tesar, C, Jedrzejczak, R, Dugan, H, Stamper, C, Wilson, P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-11-15
Release date:	2022-08-10
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Iscience, 27, 2024

7STS

Crystal Structure of Human Fab S24-1379 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2
Descriptor:	Fab S24-1379, heavy chain, light chain, ...
Authors:	Kim, Y, Maltseva, N, Tesar, C, Jedrzejczak, R, Dugan, H, Stamper, C, Wilson, P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-11-15
Release date:	2022-08-10
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.16 Å)
Cite:	Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Iscience, 27, 2024

7SUE

Crystal Structure of Human Fab S24-188 in the complex with the N-teminal Domain of Nucleocapsid protein from SARS CoV-2
Descriptor:	Nucleoprotein, S24-188 Fab Heavy chain, S24-188 Fab Light chain
Authors:	Kim, Y, Maltseva, N, Tesar, C, Jedrzejczak, R, Dugan, H, Stamper, C, Wilson, P, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-11-17
Release date:	2022-08-10
Last modified:	2024-04-03
Method:	X-RAY DIFFRACTION (2.9 Å)
Cite:	Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Iscience, 27, 2024

7U0P

SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21F2
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:	Patel, A, Ortlund, E.
Deposit date:	2022-02-18
Release date:	2022-08-10
Last modified:	2023-02-22
Method:	ELECTRON MICROSCOPY (3.76 Å)
Cite:	Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Sci Adv, 8, 2022

7UPL

SARS-Cov2 Omicron varient S protein structure in complex with neutralizing monoclonal antibody 002-S21F2
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:	Patel, A, Ortlund, E.
Deposit date:	2022-04-15
Release date:	2022-08-10
Last modified:	2023-02-22
Method:	ELECTRON MICROSCOPY (4.1 Å)
Cite:	Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody. Sci Adv, 8, 2022

7V1T

A dual Inhibitor Against Main Protease
Descriptor:	3C-like proteinase, 5,8-bis(oxidanylidene)-7-[(2-piperazin-1-ylphenyl)amino]naphthalene-1-sulfonamide
Authors:	Yu, W.Y, Xiao, Y.B, Zhao, Y.C.
Deposit date:	2021-08-06
Release date:	2022-08-10
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.562 Å)
Cite:	SARS-CoV-2 Mpro complex with inhibitor To Be Published

7V20

CryoEM structure of del68-76/del679-688 prefusion-stabilized spike
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:	Du, S, Xiao, J.
Deposit date:	2021-08-07
Release date:	2022-08-10
Method:	ELECTRON MICROSCOPY (2.86 Å)
Cite:	CryoEM structure of del68-76/del679-688 prefusion-stabilized spike To Be Published

7V22

Local CryoEM structure del68-76/del679-688 prefusion-stabilized spike
Descriptor:	Spike glycoprotein
Authors:	Du, S, Xiao, J.
Deposit date:	2021-08-07
Release date:	2022-08-10
Method:	ELECTRON MICROSCOPY (3.38 Å)
Cite:	Local CryoEM structure del68-76/del679-688 prefusion-stabilized spike To Be Published

7V23

CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
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:	Du, S, Xiao, J.
Deposit date:	2021-08-07
Release date:	2022-08-10
Method:	ELECTRON MICROSCOPY (2.96 Å)
Cite:	CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9 To Be Published

7V24

Local CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9
Descriptor:	Spike glycoprotein, the heavy chain of N12-9 Fab, the lignt chain of N12-9 Fab
Authors:	Du, S, Xiao, J.
Deposit date:	2021-08-07
Release date:	2022-08-10
Method:	ELECTRON MICROSCOPY (3.29 Å)
Cite:	Local CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9 To Be Published

7V27

RBD/XG005 local refinement
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, XG005-VH, ...
Authors:	Zhan, W.Q, Zhang, X, Sun, L, Chen, Z.G.
Deposit date:	2021-08-07
Release date:	2022-08-10
Method:	ELECTRON MICROSCOPY (4.18 Å)
Cite:	RBD/XG005 local refinement To Be Published

7VOA

Crystal structure of SARS-CoV-2 RBD in complex with aRBD5
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, alpaca nanobody
Authors:	Ma, H, Zeng, W.H, Jin, T.C.
Deposit date:	2021-10-13
Release date:	2022-08-10
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron. Cell Res., 32, 2022

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