The nsp1 protein of a new porcine coronavirus

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Structural and Biological Basis of Alphacoronavirus nsp1 Associated with Host Proliferation and Immune Evasion.

Shen, Z.Yang, Y.Yang, S.Zhang, G.Xiao, S.Fu, Z.F.Peng, G.

(2020) Viruses 12

  • DOI: https://doi.org/10.3390/v12080812
  • Primary Citation of Related Structures:  
    6LP9, 6LPA

  • PubMed Abstract: 

    Non-structural protein 1 (nsp1) is only characterized in alphacoronaviruses (α-CoVs) and betacoronaviruses (β-CoVs). There have been extensive researches on how the β-CoVs nsp1 regulates viral virulence by inhibiting host protein synthesis, but the regulatory mechanism of the α-CoVs nsp1 is still unclear. Here, we report the 2.1-Å full-length crystal structure of nsp1 in emerging porcine SADS-CoV and the 1.8-Å full-length crystal structure of nsp1 in the highly lethal cat FIPV. Although they belong to different subtypes of α-CoVs, these viruses all have a bucket-shaped fold composed of six β-sheets, similar to the crystal structure of PEDV and TGEV nsp1. Comparing the above four structures, we found that the structure of α-CoVs nsp1 in the same subtype was more conserved. We then selected mammalian cells that were treated with SADS-CoV and FIPV nsp1 for RNA sequencing analysis and found that nsp1 had a specific inhibitory effect on interferon (IFN) and cell cycle genes. Using the Renilla luciferase (Rluc) assay and Western blotting, we confirmed that seven representative α-CoVs nsp1s could significantly inhibit the phosphorylation of STAT1-S727 and interfere with the effect of IFN-I. Moreover, the cell cycle experiment confirmed that α-CoVs nsp1 could encourage host cells to stay in the G0/G1 phase. Based on these findings, we not only greatly improved the crystal structure data on α-CoVs nsp1, but we also speculated that α-CoVs nsp1 regulated host proliferation and immune evasion-related biological functions by inhibiting the synthesis of host proteins, thus creating an environment conducive to the virus.

  • Organizational Affiliation

    State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
sp1 protein
A, B
120Swine acute diarrhea syndrome coronavirusMutation(s): 0 
Gene Names: orf1abORF1ab
Find proteins for A0A2P1G738 (Swine acute diarrhea syndrome coronavirus)
Explore A0A2P1G738 
Go to UniProtKB:  A0A2P1G738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P1G738
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.831α = 90
b = 60.371β = 90
c = 84.005γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Advisory, Data collection, Database references, Refinement description