The structure of B19 parvovirus capsid

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.313 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


The structure of human parvovirus B19.

Kaufmann, B.Simpson, A.A.Rossmann, M.G.

(2004) Proc Natl Acad Sci U S A 101: 11628-11633

  • DOI: https://doi.org/10.1073/pnas.0402992101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human parvovirus B19 is the only parvovirus known to be a human pathogen. The structure of recombinant B19-like particles has been determined to approximately 3.5-A resolution by x-ray crystallography and, to our knowledge, represents the first near-atomic structure of an Erythrovirus. The polypeptide fold of the major capsid protein VP2 is a "jelly roll" with a beta-barrel motif similar to that found in many icosahedral viruses. The large loops connecting the strands of the beta-barrel form surface features that differentiate B19 from other parvoviruses. Although B19 VP2 has only 26% sequence identity to VP3 of adeno-associated virus, 72% of the C(alpha) atoms can be aligned structurally with a rms deviation of 1.8 A. Both viruses require an integrin as a coreceptor, and conserved surface features suggest a common receptor-binding region.

  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B19 parvovirus capsid554Human parvovirus B19Mutation(s): 0 
Gene Names: vp2
Find proteins for Q9PZT0 (Human parvovirus B19 (strain HV))
Explore Q9PZT0 
Go to UniProtKB:  Q9PZT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PZT0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.313 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 351.393α = 90
b = 351.393β = 90
c = 351.393γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
ENVELOPEmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2024-04-03
    Changes: Data collection, Refinement description