Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 60.93 kDa 
• Atom Count: 4108 
• Modelled Residue Count: 523 
• Deposited Residue Count: 554 
• Unique protein chains: 1

1S58

The structure of B19 parvovirus capsid

• PDB DOI: 10.2210/pdb1S58/pdb

• Classification: VIRUS
• Organism(s): Human parvovirus B19
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2004-01-20 Released: 2004-08-17 
• Deposition Author(s): Kaufmann, B., Simpson, A.A., Rossmann, M.G.

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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 

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

• PubMed: 15289612 
• 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B19 parvovirus capsid	A	554	Human parvovirus B19	Mutation(s): 0  Gene Names: vp2 EC: 3.1.1.4
UniProt
Find proteins for Q9PZT0 (Human parvovirus B19 (strain HV)) Explore Q9PZT0  Go to UniProtKB:  Q9PZT0

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 = 351.393	α = 90
b = 351.393	β = 90
c = 351.393	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
ENVELOPE	model building
CNS	refinement
REFMAC	refinement
ENVELOPE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-20 
• Released Date: 2004-08-17 
Deposition Author(s): Kaufmann, B., Simpson, A.A., Rossmann, M.G.

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