ISDA

Deposition Date 2021-02-07

Release Date 2021-02-24

Last Version Date 2024-01-31

Entry Detail

PDB ID:

7NFV

Keywords:

HYDROLASE

Title:

Structure of SARS-CoV-2 Papain-like protease PLpro

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.42 Å

R-Value Free:

0.17

R-Value Work:

0.15

Space Group:

P 32 2 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Papain-like protease nsp3
Chain IDs:A (auth: AAA)
Chain Length:315
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTD1 Pfam ID:PF08715

Ligand Molecules

GOL

PO4

Primary Citation

Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.

Srinivasan, V, Brognaro, H, Prabhu, P.R, de Souza, E.E, Gunther, S, Reinke, P.Y.A, Lane, T.J, Ginn, H, Han, H, Ewert, W, Sprenger, J, Koua, F.H.M, Falke, S, Werner, N, Andaleeb, H, Ullah, N, Franca, B.A, Wang, M, Barra, A.L.C, Perbandt, M, Schwinzer, M, Schmidt, C, Brings, L, Lorenzen, K, Schubert, R, Machado, R.R.G, Candido, E.D, Oliveira, D.B.L, Durigon, E.L, Niebling, S, Garcia, A.S, Yefanov, O, Lieske, J, Gelisio, L, Domaracky, M, Middendorf, P, Groessler, M, Trost, F, Galchenkova, M, Mashhour, A.R, Saouane, S, Hakanpaa, J, Wolf, M, Alai, M.G, Turk, D, Pearson, A.R, Chapman, H.N, Hinrichs, W, Wrenger, C, Meents, A, Betzel, C.Show

Commun Biol 5 805 805 (2022)

PMID: 35953531 DOI: 10.1038/s42003-022-03737-7

Abstact

SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.

Legend

Protein

Chemical

Disease

Primary Citation of related structures