3IFU

The Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Leader Protease Nsp1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of porcine reproductive and respiratory syndrome virus leader protease Nsp1alpha

Sun, Y.Xue, F.Guo, Y.Ma, M.Hao, N.Zhang, X.C.Lou, Z.Li, X.Rao, Z.

(2009) J Virol 83: 10931-10940

  • DOI: 10.1128/JVI.02579-08
  • Primary Citation of Related Structures:  
    3IFU

  • PubMed Abstract: 
  • Porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV), a positive-strand RNA virus that belongs to the Arteriviridae family of Nidovirales, has been identified as the causative agent of PRRS. Nsp1alpha is the amino (N)-terminal protein in a polyprotein encoded by the PRRSV genome and is reported to be crucial for subgenomic mRNA synthesis, presumably by serving as a transcription factor ...

    Porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV), a positive-strand RNA virus that belongs to the Arteriviridae family of Nidovirales, has been identified as the causative agent of PRRS. Nsp1alpha is the amino (N)-terminal protein in a polyprotein encoded by the PRRSV genome and is reported to be crucial for subgenomic mRNA synthesis, presumably by serving as a transcription factor. Before functioning in transcription, nsp1alpha proteolytically releases itself from nsp1beta. However, the structural basis for the self-releasing and biological functions of nsp1alpha remains elusive. Here we report the crystal structure of nsp1alpha of PRRSV (strain XH-GD) in its naturally self-processed form. Nsp1alpha contains a ZF domain (which may be required for its biological function), a papain-like cysteine protease (PCP) domain with a zinc ion unexpectedly bound at the active site (which is essential for proteolytic self-release of nsp1alpha), and a carboxyl-terminal extension (which occupies the substrate binding site of the PCP domain). Furthermore, we determined the exact location of the nsp1alpha self-processing site at Cys-Ala-Met180 downward arrowAla-Asp-Val by use of crystallographic data and N-terminal amino acid sequencing. The crystal structure also suggested an in cis self-processing mechanism for nsp1alpha. Furthermore, nsp1alpha appears to have a dimeric architecture both in solution and as a crystal, with a hydrophilic groove on the molecular surface that may be related to nsp1alpha's biological function. Compared with existing structure and function data, our results suggest that PRRSV nsp1alpha functions differently from other reported viral leader proteases, such as that of foot-and-mouth disease.


    Organizational Affiliation

    Laboratory of Structural Biology, New Lifescience Building, Tsinghua University, Beijing 100084, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural proteinA180Porcine reproductive and respiratory syndrome virusMutation(s): 0 
Gene Names: ORF1a
Find proteins for B6VGX5 (Porcine reproductive and respiratory syndrome virus)
Explore B6VGX5 
Go to UniProtKB:  B6VGX5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51α = 90
b = 51β = 90
c = 154.6γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHELXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-04
    Changes: Data collection