1K3V | pdb_00001k3v

Porcine Parvovirus Capsid

• PDB DOI: https://doi.org/10.2210/pdb1K3V/pdb

• Classification: VIRUS
• Organism(s): Porcine parvovirus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2001-10-04 Released: 2001-10-24 
• Deposition Author(s): Simpson, A.A., Hebert, B., Sullivan, G.M., Parrish, C.R., Zadori, Z., Tijssen, P., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.283 (Depositor) 
• R-Value Work: 
  0.286 (Depositor) 
• R-Value Observed: 
  0.283 (Depositor) 

Starting Model: experimental

Literature

The structure of porcine parvovirus: comparison with related viruses.

Simpson, A.A., Hebert, B., Sullivan, G.M., Parrish, C.R., Zadori, Z., Tijssen, P., Rossmann, M.G.

(2002) J Mol Biology 315: 1189-1198

• PubMed: 11827486 
• DOI: https://doi.org/10.1006/jmbi.2001.5319
• Primary Citation Related Structures: 
  1K3V


• PubMed Abstract: 
  

  The structure of baculovirus-expressed porcine parvovirus (PPV) capsids was solved using X-ray crystallography and was found to be similar to the related canine parvovirus (CPV) and minute virus of mice (MVM). The PPV capsid protein has 57 % and 49 % amino acid sequence identity with CPV and MVM, respectively, but the degree of conservation of surface-exposed residues is lower than average. Consequently, most of the structural differences are on the surface and are the probable cause of the known variability in antigenicity and host range. The NADL-2 and Kresse strains of PPV have distinct tissue tropisms and pathogenicity, which are mediated by one or more of the amino acid residues 381, 386, and 436. These residues are on or near the surface of the virus capsid, where they are likely to be associated with virus-cell interactions.

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Organizational Affiliation: 
• Department of Biological Sciences, Lilly Hall of Life Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 64.41 kDa 
• Atom Count: 4,306 
• Modeled Residue Count: 542 
• Deposited Residue Count: 579 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein VP2	A	579	Porcine parvovirus	Mutation(s): 0  Gene Names: VP2
UniProt
Find proteins for P18546 (Porcine parvovirus (strain NADL-2)) Explore P18546  Go to UniProtKB:  P18546

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.283 (Depositor) 
• R-Value Work:  0.286 (Depositor) 
• R-Value Observed: 0.283 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 442.49	α = 90
b = 443.05	β = 90
c = 251.31	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-24 
Deposition Author(s): Simpson, A.A., Hebert, B., Sullivan, G.M., Parrish, C.R., Zadori, Z., Tijssen, P., Rossmann, M.G.

Revision History  

• Version 1.0: 2001-10-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description