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 (4138)Repr. entries (1841)Latest entries (14)

7C8V

Structure of sybody SR4 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
Authors:	Li, T, Yao, H, Cai, H, Qin, W, Li, D.
Deposit date:	2020-06-03
Release date:	2020-06-24
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.15 Å)
Cite:	A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Nat Commun, 12, 2021

7C8W

Structure of sybody MR17 in complex with the SARS-CoV-2 S receptor-binding domain (RBD)
Descriptor:	GLYCEROL, Spike protein S1, Synthetic nanobody MR17, ...
Authors:	Li, T, Cai, H, Yao, H, Qin, W, Li, D.
Deposit date:	2020-06-03
Release date:	2020-06-24
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.77 Å)
Cite:	A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Nat Commun, 12, 2021

7CAN

Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Receptor-binding domain (RBD)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Spike protein S1, ...
Authors:	Li, T, Yao, H, Cai, H, Qin, W, Li, D.
Deposit date:	2020-06-09
Release date:	2020-06-24
Last modified:	2023-11-29
Method:	X-RAY DIFFRACTION (2.94 Å)
Cite:	A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Nat Commun, 12, 2021

6XCM

Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)
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:	Barnes, C.O, Bjorkman, P.J.
Deposit date:	2020-06-08
Release date:	2020-07-01
Last modified:	2020-09-02
Method:	ELECTRON MICROSCOPY (3.42 Å)
Cite:	Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell, 182, 2020

6XE1

Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a potent neutralizing antibody, CV30 Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, CV30 Fab Heavy chain, CV30 Fab Kappa chain, ...
Authors:	Hurlburt, N.K, Pancera, M.
Deposit date:	2020-06-11
Release date:	2020-07-01
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.75 Å)
Cite:	Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation. Nat Commun, 11, 2020

6XIP

The 1.5 A Crystal Structure of the Co-factor Complex of NSP7 and the C-terminal Domain of NSP8 from SARS CoV-2
Descriptor:	1,2-ETHANEDIOL, Non-structural protein 7, Non-structural protein 8
Authors:	Wilamowski, M, Kim, Y, Jedrzejczak, R, Maltseva, N, Endres, M, Godzik, A, Michalska, K, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-06-20
Release date:	2020-07-01
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication. Biophys.J., 120, 2021

6Z97

Structure of the prefusion SARS-CoV-2 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, Spike glycoprotein,Fibritin
Authors:	Duyvesteyn, H.M.E, Ren, J, Zhao, Y, Zhou, D, Huo, J, Carrique, L, Malinauskas, T, Ruza, R.R, Shah, P.N.M, Fry, E.E, Owens, R, Stuart, D.I.
Deposit date:	2020-06-03
Release date:	2020-07-01
Last modified:	2020-09-23
Method:	ELECTRON MICROSCOPY (3.4 Å)
Cite:	Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. Cell Host Microbe, 28, 2020

6ZCO

Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2, crystal form II
Descriptor:	Nucleoprotein
Authors:	Zinzula, L, Basquin, J, Nagy, I, Bracher, A.
Deposit date:	2020-06-11
Release date:	2020-07-01
Last modified:	2024-01-24
Method:	X-RAY DIFFRACTION (1.361 Å)
Cite:	High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2. Biochem.Biophys.Res.Commun., 538, 2021

6ZDH

SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, EY6A heavy chain, ...
Authors:	Duyvesteyn, H.M.E, Zhou, D, Zhao, Y, Fry, E.E, Ren, J, Stuart, D.I.
Deposit date:	2020-06-14
Release date:	2020-07-01
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient. Nat.Struct.Mol.Biol., 27, 2020

6ZGE

Uncleavable Spike Protein of SARS-CoV-2 in Closed 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, Spike glycoprotein
Authors:	Wrobel, A.G, Benton, D.J, Rosenthal, P.B, Gamblin, S.J.
Deposit date:	2020-06-18
Release date:	2020-07-01
Last modified:	2020-09-16
Method:	ELECTRON MICROSCOPY (2.6 Å)
Cite:	SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat.Struct.Mol.Biol., 27, 2020

6ZGI

Furin Cleaved Spike Protein of SARS-CoV-2 in Closed 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, Spike glycoprotein
Authors:	Wrobel, A.G, Benton, D.J, Rosenthal, P.B, Gamblin, S.J.
Deposit date:	2020-06-18
Release date:	2020-07-01
Last modified:	2020-09-16
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat.Struct.Mol.Biol., 27, 2020

7C2L

S protein of SARS-CoV-2 in complex bound with 4A8
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:	Yan, R.H, Zhang, Y.Y, Guo, Y.Y, Li, Y.N, Xia, L, Zhou, Q.
Deposit date:	2020-05-08
Release date:	2020-07-01
Last modified:	2021-02-17
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science, 369, 2020

6XC2

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.1 heavy chain, CC12.1 light chain, ...
Authors:	Yuan, M, Liu, H, Wu, N.C, Zhu, X, Wilson, I.A.
Deposit date:	2020-06-08
Release date:	2020-07-08
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (3.112 Å)
Cite:	Structural basis of a shared antibody response to SARS-CoV-2. Science, 369, 2020

6XC3

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.1 and CR3022
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.1 heavy chain, CC12.1 light chain, ...
Authors:	Yuan, M, Liu, H, Wu, N.C, Zhu, X, Wilson, I.A.
Deposit date:	2020-06-08
Release date:	2020-07-08
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.698 Å)
Cite:	Structural basis of a shared antibody response to SARS-CoV-2. Science, 369, 2020

6XC4

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.3
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 heavy chain, CC12.3 light chain, ...
Authors:	Yuan, M, Liu, H, Wu, N.C, Zhu, X, Wilson, I.A.
Deposit date:	2020-06-08
Release date:	2020-07-08
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.341 Å)
Cite:	Structural basis of a shared antibody response to SARS-CoV-2. Science, 369, 2020

6XC7

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.3 and CR3022
Descriptor:	CC12.3 heavy chain, CC12.3 light chain, CR3022 heavy chain, ...
Authors:	Yuan, M, Liu, H, Wu, N.C, Zhu, X, Wilson, I.A.
Deposit date:	2020-06-08
Release date:	2020-07-08
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.883 Å)
Cite:	Structural basis of a shared antibody response to SARS-CoV-2. Science, 369, 2020

6ZFO

Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, EY6A heavy chain, EY6A light chain, ...
Authors:	Duyvesteyn, H.M.E, Zhou, D, Zhao, Y, Fry, E.E, Ren, J, Stuart, D.I.
Deposit date:	2020-06-17
Release date:	2020-07-08
Last modified:	2021-12-22
Method:	ELECTRON MICROSCOPY (4.4 Å)
Cite:	Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient. Nat.Struct.Mol.Biol., 27, 2020

6XEY

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-4
Descriptor:	2-4 Heavy Chain, 2-4 Light Chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:	Rapp, M, Shapiro, L, Ho, D.D.
Deposit date:	2020-06-14
Release date:	2020-07-22
Last modified:	2021-01-27
Method:	ELECTRON MICROSCOPY (3.25 Å)
Cite:	Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature, 584, 2020

6XR8

Distinct conformational states of SARS-CoV-2 spike protein
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:	Zhang, J, Cai, Y.F, Xiao, T.S, Peng, H.Q, Sterling, S.M, Walsh Jr, R.M, Rawson, S, Volloch, S.R, Chen, B.
Deposit date:	2020-07-11
Release date:	2020-07-22
Last modified:	2020-11-25
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Distinct conformational states of SARS-CoV-2 spike protein. Science, 369, 2020

6XS6

SARS-CoV-2 Spike D614G variant, minus RBD
Descriptor:	Spike glycoprotein
Authors:	Wang, X, Egri, S.B, Dudkina, N, Luban, J, Shen, K.
Deposit date:	2020-07-15
Release date:	2020-07-22
Last modified:	2020-11-11
Method:	ELECTRON MICROSCOPY (3.7 Å)
Cite:	Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell, 183, 2020

6ZOJ

SARS-CoV-2-Nsp1-40S complex, composite map
Descriptor:	18S ribosomal RNA, 40S ribosomal protein S10, 40S ribosomal protein S11, ...
Authors:	Schubert, K, Karousis, E.D, Jomaa, A, Scaiola, A, Echeverria, B, Gurzeler, L.-A, Leibundgut, M.L, Thiel, V, Muehlemann, O, Ban, N.
Deposit date:	2020-07-07
Release date:	2020-07-22
Last modified:	2021-02-10
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat.Struct.Mol.Biol., 27, 2020

6ZOX

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x2 disulphide-bond mutant, G413C, V987C, single Arg S1/S2 cleavage site)
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:	Xiong, X, Qu, K, Scheres, S.H.W, Briggs, J.A.G.
Deposit date:	2020-07-08
Release date:	2020-07-22
Last modified:	2021-06-02
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	A thermostable, closed SARS-CoV-2 spike protein trimer. Nat.Struct.Mol.Biol., 27, 2020

6ZOY

Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Closed 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, Spike glycoprotein
Authors:	Xiong, X, Qu, K, Scheres, S.H.W, Briggs, J.A.G.
Deposit date:	2020-07-08
Release date:	2020-07-22
Last modified:	2021-06-02
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	A thermostable, closed SARS-CoV-2 spike protein trimer. Nat.Struct.Mol.Biol., 27, 2020

6ZP0

Structure of SARS-CoV-2 Spike Protein Trimer (single Arg S1/S2 cleavage site) in Closed 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, Spike glycoprotein
Authors:	Xiong, X, Qu, K, Scheres, S.H.W, Briggs, J.A.G.
Deposit date:	2020-07-08
Release date:	2020-07-22
Last modified:	2021-06-02
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	A thermostable, closed SARS-CoV-2 spike protein trimer. Nat.Struct.Mol.Biol., 27, 2020

6ZP1

Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Closed 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, Spike glycoprotein
Authors:	Xiong, X, Qu, K, Scheres, S.H.W, Briggs, J.A.G.
Deposit date:	2020-07-08
Release date:	2020-07-22
Last modified:	2021-06-02
Method:	ELECTRON MICROSCOPY (3.3 Å)
Cite:	A thermostable, closed SARS-CoV-2 spike protein trimer. Nat.Struct.Mol.Biol., 27, 2020

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Displayed results:	25
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