3R0R

The 2.3 A structure of porcine circovirus 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.225 

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This is version 1.5 of the entry. See complete history


Literature

The 2.3-angstrom structure of porcine circovirus 2.

Khayat, R.Brunn, N.Speir, J.A.Hardham, J.M.Ankenbauer, R.G.Schneemann, A.Johnson, J.E.

(2011) J Virol 85: 7856-7862

  • DOI: https://doi.org/10.1128/JVI.00737-11
  • Primary Citation of Related Structures:  
    3R0R

  • PubMed Abstract: 

    Porcine circovirus 2 (PCV2) is a T=1 nonenveloped icosahedral virus that has had severe impact on the swine industry. Here we report the crystal structure of an N-terminally truncated PCV2 virus-like particle at 2.3-Å resolution, and the cryo-electron microscopy (cryo-EM) image reconstruction of a full-length PCV2 virus-like particle at 9.6-Å resolution. This is the first atomic structure of a circovirus. The crystal structure revealed that the capsid protein fold is a canonical viral jelly roll. The loops connecting the strands of the jelly roll define the limited features of the surface. Sulfate ions interacting with the surface and electrostatic potential calculations strongly suggest a heparan sulfate binding site that allows PCV2 to gain entry into the cell. The crystal structure also allowed previously determined epitopes of the capsid to be visualized. The cryo-EM image reconstruction showed that the location of the N terminus, absent in the crystal structure, is inside the capsid. As the N terminus was previously shown to be antigenic, it may externalize through viral "breathing."


  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. rkhayat@scripps.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Porcine circovirus 2 (PCV2) capsid protein226Porcine circovirus 2Mutation(s): 0 
Gene Names: capCapORF2cp
UniProt
Find proteins for Q805N7 (Porcine circovirus 2)
Explore Q805N7 
Go to UniProtKB:  Q805N7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ805N7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.612α = 90.01
b = 202.163β = 89.33
c = 230.975γ = 90.07
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Database references
  • Version 1.3: 2012-05-30
    Changes: Refinement description
  • Version 1.4: 2014-10-29
    Changes: Structure summary
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Derived calculations