COVID-19 featured content

This page is also available in: 日本語简体中文繁體中文 한국어

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 (4459)Repr. entries (1984)Latest entries (16)

7M71

SARS-CoV-2 Spike:5A6 Fab complex I focused refinement
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody 5A6 Fab heavy chain, Antibody 5A6 Fab light chain, ...
Authors:	Asarnow, D, Cheng, Y.
Deposit date:	2021-03-26
Release date:	2021-05-26
Last modified:	2021-06-23
Method:	ELECTRON MICROSCOPY (2.66 Å)
Cite:	Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia. Cell, 184, 2021

7M7B

SARS-CoV-2 Spike:Fab 3D11 complex focused refinement
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab 3D11 heavy chain, Antibody Fab 3D11 light chain, ...
Authors:	Asarnow, D, Cheng, Y.
Deposit date:	2021-03-27
Release date:	2021-05-26
Last modified:	2021-06-23
Method:	ELECTRON MICROSCOPY (2.95 Å)
Cite:	Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia. Cell, 184, 2021

7MKB

Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL
Descriptor:	Beta-2-microglobulin, GLYCEROL, MHC class I antigen, ...
Authors:	Nyovanie, S.T, Patskovsky, Y, Krogsgaard, M.
Deposit date:	2021-04-22
Release date:	2021-05-26
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	*Human leukocyte antigen A0201 in complex with SARS-CoV-2 epitope YLQPRTFLL** To be Published

7MKY

SARS-CoV-2 frameshifting pseudoknot RNA
Descriptor:	(4S)-2-METHYL-2,4-PENTANEDIOL, COBALT HEXAMMINE(III), MAGNESIUM ION, ...
Authors:	Jones, C.P, Ferre-D'Amare, A.R.
Deposit date:	2021-04-27
Release date:	2021-05-26
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.31 Å)
Cite:	Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot. Rna, 28, 2022

7MSW

Full length SARS-CoV-2 Nsp2
Descriptor:	Non-structural protein 2, ZINC ION
Authors:	QCRG Structural Biology Consortium
Deposit date:	2021-05-12
Release date:	2021-05-26
Last modified:	2024-05-29
Method:	ELECTRON MICROSCOPY (3.76 Å)
Cite:	CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. To Be Published

7MSX

SARS-CoV-2 Nsp2
Descriptor:	Non-structural protein 2, ZINC ION
Authors:	QCRG Structural Biology Consortium
Deposit date:	2021-05-12
Release date:	2021-05-26
Last modified:	2024-05-29
Method:	ELECTRON MICROSCOPY (3.15 Å)
Cite:	CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. To Be Published

7BAJ

Crystal structure of ligand-free SARS-CoV-2 main protease
Descriptor:	Main Protease
Authors:	Amporndanai, K, O'Neill, P.M, Hasnain, S.S.
Deposit date:	2020-12-15
Release date:	2021-06-02
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat Commun, 12, 2021

7BAK

Crystal structure of SARS-CoV-2 main protease treated with ebselen
Descriptor:	Main Protease, SELENIUM ATOM
Authors:	Amporndanai, K, O'Neill, P.M, Hasnain, S.S.
Deposit date:	2020-12-15
Release date:	2021-06-02
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (2.05 Å)
Cite:	Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat Commun, 12, 2021

7BAL

Crystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2
Descriptor:	Main Protease, SELENIUM ATOM
Authors:	Amporndanai, K, O'Neill, P.M, Hasnain, S.S.
Deposit date:	2020-12-15
Release date:	2021-06-02
Last modified:	2024-01-31
Method:	X-RAY DIFFRACTION (1.85 Å)
Cite:	Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives. Nat Commun, 12, 2021

7DZW

Apo spike protein from SARS-CoV2
Descriptor:	Spike glycoprotein
Authors:	Liu, Y, Soh, W.T, Li, S, Kishikawa, J, Hirose, M, Kato, T, Standley, D, Okada, M, Arase, H.
Deposit date:	2021-01-26
Release date:	2021-06-02
Last modified:	2024-03-27
Method:	ELECTRON MICROSCOPY (3.45 Å)
Cite:	An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies. Cell, 184, 2021

7DZX

Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 8D2
Descriptor:	Fab Heavy chain of enhancing antibody, Fab light chain of enhancing antibody, Spike glycoprotein
Authors:	Liu, Y, Soh, W.T, Li, S, Kishikawa, J, Hirose, M, Kato, T, Standley, D, Okada, M, Arase, H.
Deposit date:	2021-01-26
Release date:	2021-06-02
Last modified:	2024-03-27
Method:	ELECTRON MICROSCOPY (3.53 Å)
Cite:	An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies. Cell, 184, 2021

7DZY

Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490
Descriptor:	Fab Heavy chain of enhancing antibody 2490, Fab light chain of enhancing antibody 2490, Spike glycoprotein
Authors:	Liu, Y, Soh, W.T, Li, S, Kishikawa, J, Hirose, M, Kato, T, Standley, D, Okada, M, Arase, H.
Deposit date:	2021-01-26
Release date:	2021-06-02
Last modified:	2024-06-05
Method:	ELECTRON MICROSCOPY (3.6 Å)
Cite:	An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies. Cell, 184, 2021

7MFU

Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain
Descriptor:	1,2-ETHANEDIOL, GLYCEROL, Spike protein S1, ...
Authors:	Jiang, J, Ahmad, J, Natarajan, K, Boyd, L.F, Margulies, D.H.
Deposit date:	2021-04-11
Release date:	2021-06-02
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem., 297, 2021

7N06

SARS-CoV-2 Nsp15 endoribonuclease post-cleavage state
Descriptor:	RNA (5'-R(APUP*A)-3'), Uridylate-specific endoribonuclease
Authors:	Frazier, M.N, Dillard, L.B, Krahn, J.M, Stanley, R.E.
Deposit date:	2021-05-25
Release date:	2021-06-02
Last modified:	2024-05-29
Method:	ELECTRON MICROSCOPY (2.2 Å)
Cite:	Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U. Nucleic Acids Res., 49, 2021

7N0G

CryoEm structure of SARS-CoV-2 spike protein (S-6P, 1-up) in complex with sybodies (Sb45)
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:	Jiang, J, Huang, R, Margulies, D.
Deposit date:	2021-05-25
Release date:	2021-06-02
Last modified:	2021-10-20
Method:	ELECTRON MICROSCOPY (3.02 Å)
Cite:	Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem., 297, 2021

7N0H

CryoEM structure of SARS-CoV-2 spike protein (S-6P, 2-up) in complex with sybodies (Sb45)
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:	Jiang, J, Huang, R, Margulies, D.
Deposit date:	2021-05-25
Release date:	2021-06-02
Last modified:	2021-10-20
Method:	ELECTRON MICROSCOPY (3.34 Å)
Cite:	Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction. J.Biol.Chem., 297, 2021

7N0R

Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody C2
Descriptor:	Nucleoprotein, SULFATE ION, Single-domain antibody C2
Authors:	Ye, Q, Corbett, K.D.
Deposit date:	2021-05-25
Release date:	2021-06-02
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (1.42 Å)
Cite:	Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Front Immunol, 12, 2021

7O7Y

Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)
Descriptor:	18S rRNA, 28S rRNA, 40S ribosomal protein S11, ...
Authors:	Bhatt, P.R, Scaiola, A, Leibundgut, M.A, Atkins, J.F, Ban, N.
Deposit date:	2021-04-14
Release date:	2021-06-02
Last modified:	2024-04-24
Method:	ELECTRON MICROSCOPY (2.2 Å)
Cite:	Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science, 372, 2021

7O7Z

Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)
Descriptor:	18S rRNA, 28S rRNA, 40S ribosomal protein S11, ...
Authors:	Bhatt, P.R, Scaiola, A, Leibundgut, M.A, Atkins, J.F, Ban, N.
Deposit date:	2021-04-14
Release date:	2021-06-02
Last modified:	2024-04-24
Method:	ELECTRON MICROSCOPY (2.4 Å)
Cite:	Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science, 372, 2021

7O80

Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site
Descriptor:	18S rRNA, 28S rRNA, 40S ribosomal protein S11, ...
Authors:	Bhatt, P.R, Scaiola, A, Leibundgut, M.A, Atkins, J.F, Ban, N.
Deposit date:	2021-04-14
Release date:	2021-06-02
Last modified:	2024-04-24
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science, 372, 2021

7O81

Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot
Descriptor:	18S rRNA, 28S rRNA, 40S ribosomal protein S11, ...
Authors:	Bhatt, P.R, Scaiola, A, Leibundgut, M.A, Atkins, J.F, Ban, N.
Deposit date:	2021-04-14
Release date:	2021-06-02
Last modified:	2024-04-24
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science, 372, 2021

5SA4

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z239136710
Descriptor:	N-(5-methyl-1H-pyrazol-3-yl)acetamide, Uridylate-specific endoribonuclease
Authors:	Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:	2021-05-19
Release date:	2021-06-09
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (2.046 Å)
Cite:	Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res., 2023

5SA5

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1530301542
Descriptor:	4-ethyl-2-(1H-imidazol-5-yl)-1,3-thiazole, CITRIC ACID, Uridylate-specific endoribonuclease
Authors:	Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:	2021-05-19
Release date:	2021-06-09
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (2.09 Å)
Cite:	Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res., 2023

5SA6

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2856434783
Descriptor:	N-benzyl-1-(4-fluorophenyl)methanamine, Uridylate-specific endoribonuclease
Authors:	Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:	2021-05-19
Release date:	2021-06-09
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (2.517 Å)
Cite:	Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res., 2023

5SA7

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1673618163
Descriptor:	4-amino-N-(2-hydroxyethyl)-N-methylbenzene-1-sulfonamide, Uridylate-specific endoribonuclease
Authors:	Godoy, A.S, Douangamath, A, Nakamura, A.M, Dias, A, Krojer, T, Noske, G.D, Gawiljuk, V.O, Fernandes, R.S, Fairhead, M, Powell, A, Dunnet, L, Aimon, A, Fearon, D, Brandao-Neto, J, Skyner, R, von Delft, F, Oliva, G.
Deposit date:	2021-05-19
Release date:	2021-06-09
Last modified:	2024-05-22
Method:	X-RAY DIFFRACTION (2.222 Å)
Cite:	Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res., 2023

<43 44 45 46 47 48 495051 52 53 54 55 56 57 58 >

Total results:	4459
Displayed results:	25
Sorted by:	Release date (from oldest)