1S58

The structure of B19 parvovirus capsid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.2 of the entry. See complete history


Literature

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: 10.1073/pnas.0402992101
  • Primary Citation of Related Structures:  
    1S58

  • 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- ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B19 parvovirus capsidA554Human parvovirus B19Mutation(s): 0 
Gene Names: vp2
EC: 3.1.1.4
Find proteins for Q9PZT0 (Human parvovirus B19 (strain HV))
Explore Q9PZT0 
Go to UniProtKB:  Q9PZT0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
REFMACrefinement
ENVELOPEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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