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)

7W9E

SARS-CoV-2 Delta S-8D3
Descriptor:	Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain, Spike glycoprotein, The light chain of 8D3 fab
Authors:	Cong, Y, Liu, C.X.
Deposit date:	2021-12-09
Release date:	2022-01-12
Last modified:	2022-03-02
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Nat Commun, 13, 2022

7W9F

SARS-CoV-2 Delta S-RBD-8D3
Descriptor:	Spike protein S1, The heavy chain of 8D3, The light chain of 8D3
Authors:	Cong, Y, Liu, C.X.
Deposit date:	2021-12-09
Release date:	2022-01-12
Last modified:	2022-03-02
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Nat Commun, 13, 2022

7DVP

SARS-CoV-2 Mpro mutant (H41A) in complex with nsp4\|5 peptidyl substrate
Descriptor:	3C-like proteinase, nsp4/5 peptidyl substrate
Authors:	Liu, X, Zhao, Y, Yang, H, Rao, Z.
Deposit date:	2021-01-14
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.69 Å)
Cite:	Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 119, 2022

7DVW

SARS-CoV-2 Mpro mutant (H41A) in complex with nsp5\|6 peptidyl substrate
Descriptor:	3C-like proteinase, DIMETHYL SULFOXIDE, nsp5/6 peptidyl substrate
Authors:	Liu, X, Zhao, Y, Yang, H, Rao, Z.
Deposit date:	2021-01-15
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.49 Å)
Cite:	Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 119, 2022

7DVX

SARS-CoV-2 Mpro mutant (H41A) in complex with nsp6\|7 peptidyl substrate
Descriptor:	3C-like proteinase, nsp6/7 peptidyl substrate
Authors:	Liu, X, Zhao, Y, Yang, H, Rao, Z.
Deposit date:	2021-01-15
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 119, 2022

7DVY

SARS-CoV-2 Mpro mutant (H41A) in complex with nsp9\|10 peptidyl substrate
Descriptor:	3C-like proteinase, nsp9/10 peptidyl substrate
Authors:	Liu, X, Zhao, Y, Yang, H, Rao, Z.
Deposit date:	2021-01-15
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 119, 2022

7DW0

SARS-CoV-2 Mpro mutant (H41A) in complex with nsp14\|15 peptidyl substrate
Descriptor:	3C-like proteinase, nsp14/15 peptidyl substrate
Authors:	Liu, X, Zhao, Y, Yang, H, Rao, Z.
Deposit date:	2021-01-15
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.81 Å)
Cite:	Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 119, 2022

7DW6

SARS-CoV-2 Mpro mutant (H41A) in complex with nsp15\|16 peptidyl substrate
Descriptor:	3C-like proteinase, nsp15/16 peptidyl substrate
Authors:	Liu, X, Zhao, Y, Yang, H, Rao, Z.
Deposit date:	2021-01-15
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Proc.Natl.Acad.Sci.USA, 119, 2022

7F5F

SARS-CoV-2 ORF8 S84
Descriptor:	CALCIUM ION, ORF8 protein
Authors:	Chen, S, Zhou, Z, Chen, X.
Deposit date:	2021-06-22
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.62 Å)
Cite:	Crystal Structures of Bat and Human Coronavirus ORF8 Protein Ig-Like Domain Provide Insights Into the Diversity of Immune Responses. Front Immunol, 12, 2021

7MSQ

Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)
Descriptor:	AB-3467 Fab Heavy Chain, AB-3467 Fab Light Chain, CHLORIDE ION, ...
Authors:	Langley, D.B, Christ, D.
Deposit date:	2021-05-12
Release date:	2022-01-19
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.29 Å)
Cite:	Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability. Immunity, 54, 2021

7PKU

Structure of SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a
Descriptor:	3C-like proteinase, Nucleoprotein
Authors:	Bessa, L.M, Guseva, S, Camacho-Zarco, A.R, Salvi, N, Blackledge, M.
Deposit date:	2021-08-26
Release date:	2022-01-19
Last modified:	2024-06-19
Method:	SOLUTION NMR
Cite:	The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. Sci Adv, 8, 2022

7QNW

The receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with Beta-55 and EY6A Fabs
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, Beta-55 heavy chain, ...
Authors:	Zhou, D, Ren, J, Stuart, D.I.
Deposit date:	2021-12-23
Release date:	2022-01-19
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.4 Å)
Cite:	SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell, 185, 2022

7QNX

The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with Beta-55 and EY6A Fabs
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-55 heavy chain, Beta-55 light chain, ...
Authors:	Zhou, D, Ren, J, Stuart, D.I.
Deposit date:	2021-12-23
Release date:	2022-01-19
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.92 Å)
Cite:	SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell, 185, 2022

7QNY

The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with COVOX-58 and COVOX-158 Fabs
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, COVOX-158 heavy chain, COVOX-158 light chain, ...
Authors:	Zhou, D, Ren, J, Stuart, D.I.
Deposit date:	2021-12-23
Release date:	2022-01-19
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.84 Å)
Cite:	SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell, 185, 2022

7QO7

SARS-CoV-2 S Omicron Spike B.1.1.529
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:	Ni, D, Lau, K, Turelli, P, Beckert, B, Nazarov, S, Pojer, F, Myasnikov, A, Stahlberg, H, Trono, D.
Deposit date:	2021-12-23
Release date:	2022-01-19
Method:	ELECTRON MICROSCOPY (3.02 Å)
Cite:	Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion Biorxiv, 2021

7THH

SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein
Descriptor:	1,2-ETHANEDIOL, CHLORIDE ION, HEXAETHYLENE GLYCOL, ...
Authors:	Osipiuk, J, Jedrzejczak, R, Endres, M, Wydorski, P, Joachimiak, L, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2022-01-11
Release date:	2022-01-19
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.32 Å)
Cite:	SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein to be published

7VPH

Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98
Descriptor:	Isoform 3 of Nuclear pore complex protein Nup98-Nup96, ORF6 protein, mRNA export factor
Authors:	Li, T, Guo, H, Yang, T, Wen, Y, Ji, X.
Deposit date:	2021-10-17
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.8 Å)
Cite:	Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export. Front Mol Biosci, 8, 2021

7WBL

Cryo-EM structure of human ACE2 complexed with SARS-CoV-2 Omicron RBD
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:	Liu, S, Gao, F.G.
Deposit date:	2021-12-17
Release date:	2022-01-19
Last modified:	2022-03-02
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell, 185, 2022

7WBP

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor 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:	Qi, J, Han, P.
Deposit date:	2021-12-17
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell, 185, 2022

7WBQ

Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike glycoprotein in complex with its receptor 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:	Qi, J, Han, P.
Deposit date:	2021-12-17
Release date:	2022-01-19
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (3.34 Å)
Cite:	Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2. Cell, 185, 2022

7EJL

Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein
Descriptor:	9-mer peptide from the HCoV spike protein, Beta-2-microglobulin, MHC class I antigen
Authors:	Murayama, K, Kato-Murayama, M, Shirouzu, M.
Deposit date:	2021-04-02
Release date:	2022-01-26
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (1.89 Å)
Cite:	Identification of TCR repertoires in functionally competent cytotoxic T cells cross-reactive to SARS-CoV-2. Commun Biol, 4, 2021

7FCD

Structure of the SARS-CoV-2 A372T spike glycoprotein (open)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:	Wang, X, Zhang, S.
Deposit date:	2021-07-14
Release date:	2022-01-26
Last modified:	2022-03-16
Method:	ELECTRON MICROSCOPY (3.9 Å)
Cite:	Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2. Cell Res., 32, 2022

7FCE

Structure of the SARS-CoV-2 A372T spike glycoprotein (closed)
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:	Wang, X, Zhang, S.
Deposit date:	2021-07-14
Release date:	2022-01-26
Last modified:	2022-03-16
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2. Cell Res., 32, 2022

7NWX

SARS-COV2 NSP5 in the presence of Zn2+
Descriptor:	Replicase polyprotein 1a, ZINC ION
Authors:	Calderone, V, Grifagni, D, Cantini, F, Fragai, M, Banci, L.
Deposit date:	2021-03-17
Release date:	2022-01-26
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design. Chem.Commun.(Camb.), 57, 2021

7NXH

Structure of SARS-CoV2 NSP5 (3C-like proteinase) determined in-house
Descriptor:	3C-like proteinase
Authors:	Calderone, V, Grifagni, D, Cantini, F, Fragai, M, Banci, L.
Deposit date:	2021-03-18
Release date:	2022-01-26
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.1 Å)
Cite:	SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design. Chem.Commun.(Camb.), 57, 2021

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