8F2E

Crystal Structure of the CoV-Y domain of SARS-CoV-2 Nonstructural Protein 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3.

Li, Y.Pustovalova, Y.Shi, W.Gorbatyuk, O.Sreeramulu, S.Schwalbe, H.Hoch, J.C.Hao, B.

(2023) Sci Rep 13: 2890-2890

  • DOI: https://doi.org/10.1038/s41598-023-30045-9
  • Primary Citation of Related Structures:  
    8F2E

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030-3305, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease nsp3287Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.415α = 90
b = 109.415β = 90
c = 61.226γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135592

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description