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 (4559)Repr. entries (2032)Latest entries (12)

7Q9I

Beta-43 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-43 heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:	2021-11-12
Release date:	2021-12-15
Last modified:	2024-10-09
Method:	ELECTRON MICROSCOPY (4.9 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7Q9J

Beta-26 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-26 heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:	2021-11-12
Release date:	2021-12-15
Last modified:	2022-01-26
Method:	ELECTRON MICROSCOPY (4 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7Q9K

Beta-32 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-32 heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:	2021-11-12
Release date:	2021-12-15
Last modified:	2022-01-26
Method:	ELECTRON MICROSCOPY (4.5 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7Q9M

Beta-53 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-53 fab heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:	2021-11-12
Release date:	2021-12-15
Last modified:	2022-01-26
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7Q9P

Beta-06 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-06 heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:	2021-11-12
Release date:	2021-12-15
Last modified:	2024-10-16
Method:	ELECTRON MICROSCOPY (4.5 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7RPV

Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:	Chen, Y, Tolbert, D.W, Pazgier, M.
Deposit date:	2021-08-04
Release date:	2021-12-15
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (3.54 Å)
Cite:	Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities. Biorxiv, 2021

7FAE

S protein of SARS-CoV-2 in complex bound with P36-5D2(state2)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, P36-5D2 heavy chain, ...
Authors:	Zhang, L, Wang, X, Shan, S, Zhang, S.
Deposit date:	2021-07-06
Release date:	2021-12-22
Last modified:	2022-02-16
Method:	ELECTRON MICROSCOPY (3.65 Å)
Cite:	A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Front Immunol, 12, 2021

7Q0G

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-49 and FI-3A Fabs
Descriptor:	Beta-49 Fab heavy chain, Beta-49 Fab light chain, CHLORIDE ION, ...
Authors:	Zhou, D, Ren, J, Stuart, D.I.
Deposit date:	2021-10-14
Release date:	2021-12-22
Last modified:	2024-10-16
Method:	X-RAY DIFFRACTION (1.82 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7Q0H

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54
Descriptor:	Beta-50 Fab heavy chain, Beta-50 Fab light chain, Beta-54 Fab heavy chain, ...
Authors:	Zhou, D, Ren, J, Stuart, D.I.
Deposit date:	2021-10-14
Release date:	2021-12-22
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (3.65 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7Q0I

Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-43
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:	Zhou, D, Ren, J, Stuart, D.I.
Deposit date:	2021-10-14
Release date:	2021-12-22
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.39 Å)
Cite:	The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe, 30, 2022

7T46

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 8c
Descriptor:	(1R,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-1-hydroxy-2-{[N-({[7-(2-methylpropanoyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase
Authors:	Lovell, S, Liu, L, Battaile, K.P, Chamandi, S.D, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:	2021-12-09
Release date:	2021-12-22
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.45 Å)
Cite:	Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease. J.Med.Chem., 65, 2022

7VXC

SARS-CoV-2 Kappa variant spike protein in C3 state
Descriptor:	Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:	Xu, C, Cong, Y.
Deposit date:	2021-11-12
Release date:	2021-12-22
Last modified:	2022-02-16
Method:	ELECTRON MICROSCOPY (3.9 Å)
Cite:	Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM. Nat Commun, 12, 2021

7DQA

Cryo-EM structure of SARS-CoV2 RBD-ACE2 complex
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, CHLORIDE ION, ...
Authors:	Wang, J, Lan, J, Wang, X.Q, Wang, H.W.
Deposit date:	2020-12-22
Release date:	2021-12-29
Last modified:	2022-07-13
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM Biophys Rep, 7, 2022

7QIK

SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma
Descriptor:	14-3-3 protein sigma, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, BROMIDE ION, ...
Authors:	Sluchanko, N.N, Tugaeva, K.V, Smith, J.L.R, Antson, A.A.
Deposit date:	2021-12-15
Release date:	2021-12-29
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.01 Å)
Cite:	SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma To Be Published

7QIP

SARS-CoV-2 Nucleocapsid phosphopeptide 201-210 bound to human 14-3-3 sigma
Descriptor:	14-3-3 protein sigma, ARG-GLY-TPO-SER-PRO-ALA-ARG-MET, CHLORIDE ION
Authors:	Sluchanko, N.N, Tugaeva, K.V, Smith, J.L.R, Antson, A.A.
Deposit date:	2021-12-15
Release date:	2021-12-29
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.65 Å)
Cite:	SARS-CoV-2 Nucleocapsid phosphopeptide 193-200 bound to human 14-3-3 sigma To Be Published

7SXR

Cryo-EM structure of the SARS-CoV-2 D614G mutant spike protein ectodomain
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXS

Cryo-EM structure of the SARS-CoV-2 D614G,L452R mutant spike protein ectodomain
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2024-10-09
Method:	ELECTRON MICROSCOPY (2.64 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXT

Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (2.31 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXU

Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXV

Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (2.79 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXW

Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain
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:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2024-10-09
Method:	ELECTRON MICROSCOPY (2.85 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXX

Cryo-EM structure of the SARS-CoV-2 D614G mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (2.66 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SXZ

Cryo-EM structure of the SARS-CoV-2 D614G,L452R mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (2.61 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SY1

Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (2.83 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

7SY3

Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:	Zhu, X, Mannar, D, Saville, J.W, Srivastava, S.S, Berezuk, A.M, Zhou, S, Tuttle, K.S, Kim, A, Li, W, Dimitrov, D.S, Subramaniam, S.
Deposit date:	2021-11-24
Release date:	2021-12-29
Last modified:	2022-01-05
Method:	ELECTRON MICROSCOPY (2.95 Å)
Cite:	Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Cell Rep, 37, 2021

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Total results:	2032
Displayed results:	25
Sorted by:	Release date (from oldest)