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 (4476)Repr. entries (1994)Latest entries (17)

8HLC

S protein of SARS-CoV-2 in complex with 3711
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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Zhang, Y.Y, Guo, Y.Y, Zhou, Q.
Deposit date:	2022-11-29
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	A SARS-CoV-2 Spike N-terminal domain neutralizing antibody targets on a glycans shielded silent face and inhibits virus entry via hindering the recognition of RBD and hACE2 To Be Published

8HLD

S protein of SARS-CoV-2 in complex with 26434
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:	Zhang, Y.Y, Guo, Y.Y, Zhou, Q.
Deposit date:	2022-11-29
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	A SARS-CoV-2 Spike N-terminal domain neutralizing antibody targets on a glycans shielded silent face and inhibits virus entry via hindering the recognition of RBD and hACE2 To Be Published

8K67

Crystal structure of SARS-CoV-2 3CLpro M165V mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (2.2 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K68

Crystal structure of SARS-CoV-2 3CLpro M49K mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6A

Crystal structure of SARS-CoV-2 3CLpro S301P mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6B

Crystal structure of SARS-CoV-2 3CLpro M49K/M165V mutant
Descriptor:	3C-like proteinase nsp5
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8K6D

Crystal structure of SARS-CoV-2 3CLpro M49K/S301P mutant in complex with WU-04
Descriptor:	3C-like proteinase nsp5, ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide
Authors:	Zhang, L.J, Hu, Q.
Deposit date:	2023-07-25
Release date:	2024-06-05
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04. Cell Discov, 10, 2024

8P5M

SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)
Descriptor:	Mab-23 (Heavy chain variable domain), Mab-23 (Light chain variable domain), Spike protein S1
Authors:	Das, H, Hallberg, B.M.
Deposit date:	2023-05-24
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab domains) To Be Published

8V4F

Model and map from local refinement of a CAB-A17 - Omicron Ba.1 spike complex
Descriptor:	CAB-A17 variable heavy-chain, CAB-A17 variable light chain, Spike protein S1
Authors:	Hallberg, B.M, Das, H.
Deposit date:	2023-11-29
Release date:	2024-06-05
Last modified:	2024-07-03
Method:	ELECTRON MICROSCOPY (2.68 Å)
Cite:	Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med, 5, 2024

8X0X

Crystal structure of JE-5C in complex with SARS-CoV-2 RBD
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of JE-5C Fab, Light chain of JE-5C Fab, ...
Authors:	Mohapatra, A, Chen, X.
Deposit date:	2023-11-06
Release date:	2024-06-05
Last modified:	2024-07-03
Method:	X-RAY DIFFRACTION (3.45 Å)
Cite:	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog., 20, 2024

8X0Y

Crystal structure of JM-1A in complex with SARS-CoV-2 RBD
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Heavy chain of JM-1A Fab, ...
Authors:	Mohapatra, A, Chen, X.
Deposit date:	2023-11-06
Release date:	2024-06-05
Last modified:	2024-07-03
Method:	X-RAY DIFFRACTION (1.94 Å)
Cite:	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog., 20, 2024

8YRO

SARS-CoV-2 Delta Spike in complex with JL-8C
Descriptor:	JL-8C Heavy Chain, JL-8C Light Chain, Spike glycoprotein
Authors:	Nguyen, V.H.T, Chen, X.
Deposit date:	2024-03-21
Release date:	2024-06-05
Last modified:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.27 Å)
Cite:	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog., 20, 2024

8YRP

SARS-CoV-2 Delta Spike in complex with JM-1A
Descriptor:	JM-1A Heavy Chain, JM-1A Light Chain, Spike glycoprotein
Authors:	Nguyen, V.H.T, Chen, X.
Deposit date:	2024-03-21
Release date:	2024-06-05
Last modified:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.64 Å)
Cite:	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog., 20, 2024

8YZ5

SARS-CoV-2 Delta Spike in complex with Fab of JE-5C
Descriptor:	Fab heavy chain of JE-5C, Fab light chain of JE-5C, Spike glycoprotein
Authors:	Chen, X, Wu, Y.-M.
Deposit date:	2024-04-06
Release date:	2024-06-05
Last modified:	2024-06-26
Method:	ELECTRON MICROSCOPY (3.93 Å)
Cite:	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog., 20, 2024

8YZ6

SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Fab heavy chain of JH-8B, ...
Authors:	Chen, X, Wu, Y.-M.
Deposit date:	2024-04-06
Release date:	2024-06-05
Last modified:	2024-06-26
Method:	ELECTRON MICROSCOPY (4.55 Å)
Cite:	The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog., 20, 2024

9FGR

SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, scFv76-77 single chain fragment
Authors:	Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:	2024-05-25
Release date:	2024-06-05
Method:	ELECTRON MICROSCOPY (4 Å)
Cite:	Structure of scFv76-77 in complex with SARS-CoV-2 Spike protein To Be Published

8JMM

Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution.
Descriptor:	7F3 Fv, GW01 Fv, Spike glycoprotein
Authors:	Hao, A, Mao, Q, Chen, Z, Huang, J, Sun, L.
Deposit date:	2023-06-05
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (3.75 Å)
Cite:	Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution. To Be Published

8JYS

SARS-CoV-2 Spike RBD (dimer) in complex with two 2S-1244 nanobodies
Descriptor:	IBT-CoV144 nanobody, Spike protein S1
Authors:	Yang, Y, Zhang, C.H.
Deposit date:	2023-07-03
Release date:	2024-06-12
Last modified:	2024-07-10
Method:	ELECTRON MICROSCOPY (4.5 Å)
Cite:	A novel nanobody broadly neutralizes SARS-CoV-2 via induction of spike trimer dimers conformation. Exploration (Beijing), 4, 2024

8UIR

SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16)
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:	Zhang, Q.E, Acharya, P.
Deposit date:	2023-10-10
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16) To Be Published

8UK1

SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer consensus (S-RRAR-Omicron-XBB.1.16)
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:	Zhang, Q.E, Acharya, P.
Deposit date:	2023-10-11
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer consensus (S-RRAR-Omicron-XBB.1.16) To Be Published

8XZD

The structure of fox ACE2 and Omicron BF.7 RBD complex
Descriptor:	Angiotensin-converting enzyme, Spike protein S1, ZINC ION
Authors:	sun, J.Q.
Deposit date:	2024-01-21
Release date:	2024-06-12
Last modified:	2024-07-24
Method:	ELECTRON MICROSCOPY (3.47 Å)
Cite:	The binding and structural basis of fox ACE2 to RBDs from different sarbecoviruses. Virol Sin, 2024

9AYW

SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5.1)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:	Zhang, Q.E, Acharya, P.
Deposit date:	2024-03-08
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5.1) To Be Published

9FGS

SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv41N (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Single Chain fragment scFv41N, Spike glycoprotein,Fibritin
Authors:	Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:	2024-05-25
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (4 Å)
Cite:	Structure of scFv41N in complex with SARS-CoV-2 Spike protein To Be Published

9FGT

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76 (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Single chain fragment scFv76, Spike glycoprotein,Fibritin
Authors:	Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:	2024-05-25
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (3.8 Å)
Cite:	Structure of scFv76 in complex with SARS-CoV-2 Omicron Spike protein To Be Published

9FGU

SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein,Fibritin, scFv76-77 single chain fragment
Authors:	Berlinguer, M, Chaves-Sanjuan, A, Milazzo, F.M, Minenkova, O, De Santis, R, Bolognesi, M.
Deposit date:	2024-05-25
Release date:	2024-06-12
Method:	ELECTRON MICROSCOPY (4.3 Å)
Cite:	Structure of scFv76-77 in complex with SARS-CoV-2 Omicron Spike protein To Be Published

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Total results:	1994
Displayed results:	25
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