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 (5197)Repr. entries (2266)Latest entries (44)

9B0Y

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 B07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)** To Be Published

8Z1H

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

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

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

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

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

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

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

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

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

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