8F2E image
Entry Detail
PDB ID:
8F2E
Keywords:
Title:
Crystal Structure of the CoV-Y domain of SARS-CoV-2 Nonstructural Protein 3
Biological Source:
PDB Version:
Deposition Date:
2022-11-07
Release Date:
2023-03-08
Method Details:
Experimental Method:
Resolution:
2.43 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 65
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Papain-like protease nsp3
Chain IDs:A
Chain Length:287
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3.
Sci Rep 13 2890 2890 (2023)
PMID: 36801935 DOI: 10.1038/s41598-023-30045-9

Abstact

Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

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