9CP0 | pdb_00009cp0

Crystal structure of the porcine astrovirus 4 capsid spike domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.362 (Depositor), 0.361 (DCC) 
  • R-Value Work: 
    0.316 (Depositor), 0.316 (DCC) 
  • R-Value Observed: 
    0.318 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure and Antigenicity of the Porcine Astrovirus 4 Capsid Spike.

Haley, D.J.Lanning, S.Henricson, K.E.Mardirossian, A.A.Cirillo, I.Rahe, M.C.DuBois, R.M.

(2024) Viruses 16

  • DOI: https://doi.org/10.3390/v16101596
  • Primary Citation Related Structures: 
    9CP0

  • PubMed Abstract: 

    Porcine astrovirus 4 (PoAstV4) has been recently associated with respiratory disease in pigs. In order to understand the scope of PoAstV4 infections and to support the development of a vaccine to combat PoAstV4 disease in pigs, we designed and produced a recombinant PoAstV4 capsid spike protein for use as an antigen in serological assays and for potential future use as a vaccine antigen. Structural prediction of the full-length PoAstV4 capsid protein guided the design of the recombinant PoAstV4 capsid spike domain expression plasmid. The recombinant PoAstV4 capsid spike was expressed in Escherichia coli , purified by affinity and size-exclusion chromatography, and its crystal structure was determined at 1.85 Å resolution, enabling structural comparisons to other animal and human astrovirus capsid spike structures. The recombinant PoAstV4 capsid spike protein was also used as an antigen for the successful development of a serological assay to detect PoAstV4 antibodies, demonstrating that the recombinant PoAstV4 capsid spike retains antigenic epitopes found on the native PoAstV4 capsid. These studies lay a foundation for seroprevalence studies and the development of a PoAstV4 vaccine for swine.


  • Organizational Affiliation
    • Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

Macromolecule Content 

  • Total Structure Weight: 108.61 kDa 
  • Atom Count: 7,411 
  • Modeled Residue Count: 911 
  • Deposited Residue Count: 988 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike proteinA [auth B],
B [auth C],
C [auth D],
D [auth A]
247Porcine astrovirus 4Mutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.362 (Depositor), 0.361 (DCC) 
  • R-Value Work:  0.316 (Depositor), 0.316 (DCC) 
  • R-Value Observed: 0.318 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.386α = 74.54
b = 66.211β = 81.67
c = 87.752γ = 78.61
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI44090

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references