Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

COVID-19 featured content

This page is also available in: 日本語简体中文繁體中文한국어
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 (5197)Repr. entries (2266)Latest entries (44)
9EWH
DownloadVisualize
BU of 9ewh by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Y109A
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A, Guenther, S.
Deposit date:2024-04-03
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EXB
DownloadVisualize
BU of 9exb by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain NTD
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A, Guenther, S.
Deposit date:2024-04-06
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9EZB
DownloadVisualize
BU of 9ezb by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P67S
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A, Guenther, S.
Deposit date:2024-04-11
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F5J
DownloadVisualize
BU of 9f5j by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant Q58I
Descriptor: CADMIUM ION, Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-04-29
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F5L
DownloadVisualize
BU of 9f5l by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant A119S
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-04-29
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2.363 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F7A
DownloadVisualize
BU of 9f7a by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
Descriptor: Nucleoprotein, ZINC ION
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-05-03
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F7C
DownloadVisualize
BU of 9f7c by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I
Descriptor: Nucleoprotein, ZINC ION
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-05-03
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F83
DownloadVisualize
BU of 9f83 by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A, Guenther, S.
Deposit date:2024-05-06
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9FBG
DownloadVisualize
BU of 9fbg by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P151S
Descriptor: Nucleoprotein
Authors:Dhamotharan, K, Schlundt, A.
Deposit date:2024-05-13
Release date:2024-11-20
Last modified:2024-12-18
Method:X-RAY DIFFRACTION (2.54 Å)
Cite:A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
8RJ7
DownloadVisualize
BU of 8rj7 by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 1.29, LYSINE, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2023-12-20
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
To Be Published
8YKN
DownloadVisualize
BU of 8ykn by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with X77
Descriptor: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide, Non-structural protein 11
Authors:Wang, J, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKP
DownloadVisualize
BU of 8ykp by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with X77
Descriptor: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
Authors:Zou, X.F, Zhang, J, Li, J.
Deposit date:2024-03-05
Release date:2024-11-27
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
9CRC
DownloadVisualize
BU of 9crc by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 3 closed RBDs
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:Ke, Z, Croll, T.I, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRE
DownloadVisualize
BU of 9cre by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 3 closed RBDs
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:Ke, Z, Croll, T.I, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRG
DownloadVisualize
BU of 9crg by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed RBDs
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:Ke, Z, Kotecha, A, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRH
DownloadVisualize
BU of 9crh by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs
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:Ke, Z, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRI
DownloadVisualize
BU of 9cri by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed RBDs
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:Ke, Z, Briggs, J.A.G.
Deposit date:2024-07-22
Release date:2024-11-27
Last modified:2024-12-25
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
8R6E
DownloadVisualize
BU of 8r6e by Molmil
SARS-CoV-2 Nucleocapsid dimerization domain
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
Authors:Fahoum, J, Wiener, R, Rouvinski, A, Isupov, M.N.
Deposit date:2023-11-22
Release date:2024-12-04
Method:X-RAY DIFFRACTION (1.53 Å)
Cite:SARS-CoV-2 Nucleocapsid dimerization domain
To Be Published
8RNE
DownloadVisualize
BU of 8rne by Molmil
HLA-E*01:03 in complex with SARS-CoV-2 Nsp13 peptide, VMPLSAPTL
Descriptor: Beta-2-microglobulin, HLA class I histocompatibility antigen, E alpha chain variant, ...
Authors:Sun, R, Achour, A, Sala, B.M, Sandalova, T.
Deposit date:2024-01-09
Release date:2024-12-04
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Plos Pathog., 20, 2024
8RNF
DownloadVisualize
BU of 8rnf by Molmil
HLA-E*01:03 in complex with SARS-CoV-2 Omicron Nsp13 peptide, VIPLSAPTL
Descriptor: Beta-2-microglobulin, HLA class I histocompatibility antigen, E alpha chain variant, ...
Authors:Sun, R, Achour, A, Sala, B.M, Sandalova, T.
Deposit date:2024-01-09
Release date:2024-12-04
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.872 Å)
Cite:Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Plos Pathog., 20, 2024
8USZ
DownloadVisualize
BU of 8usz by Molmil
Cryo-EM Structure of Full-Length Spike Protein of Omicron XBB.1.5
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:Huynh, K.W, Chang, J.S, Fennell, K.F, Che, Y, Wu, H.
Deposit date:2023-10-30
Release date:2024-12-04
Last modified:2025-05-21
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Preclinical characterization of the Omicron XBB.1.5-adapted BNT162b2 COVID-19 vaccine.
Npj Vaccines, 9, 2024
8XKO
DownloadVisualize
BU of 8xko by Molmil
CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Li, M, An, L, Hong, Y, Li, S, Zhang, K.
Deposit date:2023-12-23
Release date:2024-12-04
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.29 Å)
Cite:An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode.
Nat Commun, 15, 2024
8YX5
DownloadVisualize
BU of 8yx5 by Molmil
Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P35
Descriptor: 5-[(1~{R},5~{S})-3,6-diazabicyclo[3.1.1]heptan-3-yl]-2-methyl-~{N}-[1-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)cyclopropyl]benzamide, GLYCEROL, Papain-like protease nsp3, ...
Authors:Lu, Y, Shang, J.
Deposit date:2024-04-02
Release date:2024-12-04
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19.
Nat Commun, 15, 2024
9B82
DownloadVisualize
BU of 9b82 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-15 antibody heavy chain, COVA2-15 antibody light chain, ...
Authors:Yuan, M, Zhu, X, Wilson, I.A.
Deposit date:2024-03-28
Release date:2024-12-04
Last modified:2025-01-08
Method:X-RAY DIFFRACTION (3.38 Å)
Cite:Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy.
Plant Biotechnol J, 23, 2025
8RBY
DownloadVisualize
BU of 8rby by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3[N-MORPHOLINO]PROPANE SULFONIC ACID, Camel-derived nanobody 1.26, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2023-12-05
Release date:2024-12-11
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26
To Be Published

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon