Loading
PDBj
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
9B0Y
DownloadVisualize
BU of 9b0y by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation
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:Singh, S, Hasan, S.S.
Deposit date:2024-03-12
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.32 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9BJ2
DownloadVisualize
BU of 9bj2 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C1533 Heavy Chain, C1533 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ3
DownloadVisualize
BU of 9bj3 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C1596 Fab Heavy Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ4
DownloadVisualize
BU of 9bj4 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C952
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C952 Heavy Chain, C952 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9CXE
DownloadVisualize
BU of 9cxe by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1
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:Singh, S, Hasan, S.S.
Deposit date:2024-07-31
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.48 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9I81
DownloadVisualize
BU of 9i81 by Molmil
SARS-CoV-2 RdRp bound to a stack of three HeE1-2Tyr molecules
Descriptor: N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine, Non-structural protein 7, Non-structural protein 8, ...
Authors:Kabinger, F, Doze, V, Schmitzova, J, Lidschreiber, M, Dienemann, C, Cramer, P.
Deposit date:2025-02-04
Release date:2025-03-05
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr.
Proc.Natl.Acad.Sci.USA, 122, 2025
8YK4
DownloadVisualize
BU of 8yk4 by Molmil
Structure of SARS-CoV-2 RBD and antibody NT-108
Descriptor: Spike protein S1, antibody NT-108, single chain Fv fragment
Authors:Anraku, Y, Kita, S, Onodera, T, Sato, A, Tadokoro, T, Adachi, Y, Ito, S, Suzuki, T, Sasaki, J, Shiwa, N, Iwata, N, Nagata, N, Kazuki, Y, Oshimura, M, Sasaki, M, Orba, Y, Suzuki, T, Sawa, H, Hashiguchi, T, Fukuhara, H, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-04
Release date:2025-03-12
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108
To Be Published
8YKG
DownloadVisualize
BU of 8ykg by Molmil
Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-up state)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-108 scFv, ...
Authors:Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-05
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.28 Å)
Cite:Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
8YKH
DownloadVisualize
BU of 8ykh by Molmil
Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-108 scFv, Spike glycoprotein
Authors:Anraku, Y, Kita, S, Onodera, T, Tadokoro, T, Ito, S, Adachi, Y, Kotaki, R, Suzuki, T, Hashiguchi, T, Takahashi, Y, Maenaka, K.
Deposit date:2024-03-05
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.27 Å)
Cite:Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108
To Be Published
9BLL
DownloadVisualize
BU of 9bll by Molmil
Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex
Descriptor: 1301B7 Heavy Chain, 1301B7 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Walter, M.R, Green, T.J.
Deposit date:2024-04-30
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (4.1 Å)
Cite:Potent neutralization by a RBD antibody with broad specificity for SARS-CoV-2 JN.1 and other variants.
Npj Viruses, 2, 2024
9CCI
DownloadVisualize
BU of 9cci by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, M39 Fab heavy chain, M39 Fab light chain, ...
Authors:Bajic, G, Jaiswal, D.
Deposit date:2024-06-21
Release date:2025-03-12
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (2.65 Å)
Cite:Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CCJ
DownloadVisualize
BU of 9ccj by Molmil
Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M2 Fab Heavy Chain, ...
Authors:Bajic, G, Civljak, A.
Deposit date:2024-06-21
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (2.37 Å)
Cite:Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines.
Biorxiv, 2024
9CGV
DownloadVisualize
BU of 9cgv by Molmil
SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1
Descriptor: MANGANESE (II) ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Osinski, A, Hernandez, G, Tagliabracci, V.S.
Deposit date:2024-07-01
Release date:2025-03-12
Last modified:2025-04-23
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.
J.Biol.Chem., 301, 2025
9J66
DownloadVisualize
BU of 9j66 by Molmil
Cryo-EM structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment CAV-C65 (local refinement)
Descriptor: CAV-C65 Heavy chain, CAV-C65 Light chain, Spike protein S1
Authors:Jing, X, Chen, Y, Gong, P.
Deposit date:2024-08-15
Release date:2025-03-12
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:IgA class switching enhances neutralizing potency against SARS-CoV-2 by increased antibody hinge flexibility.
Antiviral Res., 235, 2025
9N55
DownloadVisualize
BU of 9n55 by Molmil
X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
Descriptor: N-OCTANE, ORF9b protein
Authors:San Felipe, C.J, Fraser, J.S.
Deposit date:2025-02-03
Release date:2025-03-12
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
To Be Published
8UTC
DownloadVisualize
BU of 8utc by Molmil
HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
Descriptor: Beta-2-microglobulin, CHLORIDE ION, HLA class I histocompatibility antigen, ...
Authors:Oltean, N, Nyovanie, S, Hashem, A, Patskovska, L, Patskovsky, Y, Krogsgaard, M.
Deposit date:2023-10-30
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
To Be Published
8Z1H
DownloadVisualize
BU of 8z1h by Molmil
Crystal structure of SARS main protease in complex with PF-00835231
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Lin, C, Zhang, J, Li, J.
Deposit date:2024-04-11
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.61 Å)
Cite:Crystal structure of SARS main protease in complex with PF-00835231
To Be Published
9DJ8
DownloadVisualize
BU of 9dj8 by Molmil
RNA-nsp9 bound to the NiRAN domain of the E-RTC with an empty G-pocket
Descriptor: ADENOSINE MONOPHOSPHATE, Non-structural protein 9, RNA-directed RNA polymerase, ...
Authors:Small, G.I, Darst, S.A, Campbell, E.A.
Deposit date:2024-09-06
Release date:2025-03-19
Method:ELECTRON MICROSCOPY (2.58 Å)
Cite:Matters arising: There is no structure of the catalytic intermediate of GTP-mediated mRNA capping by the SARS-CoV-2 NiRAN domain, and thus the mechanism remains unknown
To Be Published
9L09
DownloadVisualize
BU of 9l09 by Molmil
SARS-CoV-2 C-RTC with 13-TP
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Huang, Y.C, Liang, L, Liu, Y.X, Yan, L.M, Lou, Z.Y, Rao, Z.H.
Deposit date:2024-12-12
Release date:2025-03-19
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Discovery of a 2'-a-Fluoro-2'-b-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent
J Med Chem, 68, 2025
9L6C
DownloadVisualize
BU of 9l6c by Molmil
Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of Fab ConD-852, Heavy chain of Fab P2C-1F11, ...
Authors:Zheng, Z, Bing, J, Congcong, L, Bing, Z.
Deposit date:2024-12-24
Release date:2025-03-19
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs
To Be Published
8ZYF
DownloadVisualize
BU of 8zyf by Molmil
Crystal structure of ZW2G10 Fab in complex with omicron RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ZW2G10 fab heavy chain, ...
Authors:Yuan, H.Y, Li, J.M.
Deposit date:2024-06-17
Release date:2025-03-26
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart.
Mol.Ther., 33, 2025
9GXE
DownloadVisualize
BU of 9gxe by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
Descriptor: 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
Deposit date:2024-09-30
Release date:2025-03-26
Method:ELECTRON MICROSCOPY (2.3 Å)
Cite:Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
To Be Published
9GXG
DownloadVisualize
BU of 9gxg by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
Descriptor: 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone, 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
Deposit date:2024-09-30
Release date:2025-03-26
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (1.92 Å)
Cite:Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
To Be Published
8YWE
DownloadVisualize
BU of 8ywe by Molmil
Local refinement of SARS-CoV-2 Omicron BA.2.86 S complexed with Abs G7-Fc
Descriptor: 7F3 scFv, GW01 scFv, Spike protein S1
Authors:Ma, Y, Liu, Q, Rehati, P, Zhang, Z.
Deposit date:2024-03-31
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (2.69 Å)
Cite:Impact of scFv Sequence and Position on the Functionality of Bispecific Antibodies against Omicron Variants EG.5 and BA.2.86
To Be Published
8ZFV
DownloadVisualize
BU of 8zfv by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
Descriptor: Ceftriaxone, DI(HYDROXYETHYL)ETHER, Nucleoprotein, ...
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2024-05-08
Release date:2025-04-02
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon