4DPV

PARVOVIRUS/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Canine parvovirus capsid structure, analyzed at 2.9 A resolution.

Xie, Q.Chapman, M.S.

(1996) J.Mol.Biol. 264: 497-520

  • DOI: 10.1006/jmbi.1996.0657

  • PubMed Abstract: 
  • The DNA-containing capsid of canine parvovirus (CPV) is analyzed following atomic refinement at 2.9 A resolution. The capsid contains 60 copies of the capsid protein related by icosahedral symmetry. The atomic model has been extended from the first r ...

    The DNA-containing capsid of canine parvovirus (CPV) is analyzed following atomic refinement at 2.9 A resolution. The capsid contains 60 copies of the capsid protein related by icosahedral symmetry. The atomic model has been extended from the first residue (Gly37) of the unrefined 3.25 A structure towards the N terminus. The electron density shows that approximately 87% of the capsid proteins have N termini on the inside of the capsid, but for approximately 13%, the polypeptide starts on the outside and runs through one of the pores surrounding each 5-fold axis, explaining apparently conflicting antigenic data. Analysis of potential hydrogen bonds reveals approximately 50% more secondary structure than previously apparent. Most of the additional secondary structure are in the 71 and 221 residue-long loop insertions between beta-strands E and F and G and H, forming subunit-bridging sheets that likely add specificity to assembly interactions. Structural analysis of the extensive subunit interactions around the 3-fold axes shows that assembly is a multistep process with loops intertwining following initial contact. Estimated free energies of association suggest that the formation of 3 and 5-fold contacts likely takes precedence over 2-fold interactions. Energies for initial association into trimers or pentamers would be similar, but the intertwining of loops about the 3-fold axis adds an additional large activation barrier to dissociation. Analysis of the surfaces of the assembled capsid shows a surprising lack of basic amino acids that might have been expected to interact with the negatively charged phosphoribose backbone of the DNA. Instead, uncharged polar and van der Waal's interactions predominate in the packaging of single-stranded DNA into the capsid.


    Related Citations: 
    • Preliminary X-Ray Crystallographic Analysis of Canine Parvovirus Crystals
      Luo, M.,Tsao, J.,Rossmann, M.G.,Basak, S.,Compans, R.W.
      (1988) J.Mol.Biol. 200: 209
    • Restrained Real-Space Macromolecular Atomic Refinement Using a New Resolution- Dependent Electron Density Function
      Chapman, M.S.
      (1995) Acta Crystallogr.,Sect.A 51: 69
    • Structure Determination of Monoclinic Canine Parvovirus
      Tsao, J.,Chapman, M.S.,Wu, H.,Agbandje, M.,Keller, W.,Rossmann, M.G.
      (1992) Acta Crystallogr.,Sect.B 48: 75
    • Structural Refinement of the DNA-Containing Capsid of Canine Parvovirus Using a New Restrained Real Space Method
      Chapman, M.S.,Rossmann, M.G.
      (1996) Acta Crystallogr.,Sect.D 52: 129
    • Single-Stranded DNA-Protein Interactions in Canine Parvovirus
      Chapman, M.S.,Rossmann, M.G.
      (1995) Structure 3: 151
    • Structure, Sequence, and Function Correlations Among Parvoviruses
      Chapman, M.S.,Rossmann, M.G.
      (1993) Virology 194: 491
    • Ab Initio Phase Determination for Spherical Viruses: Parameter Determination for Spherical-Shell Models
      Chapman, M.S.,Tsao, J.,Rossmann, M.G.
      (1992) Acta Crystallogr.,Sect.A 48: 301
    • The Three-Dimensional Structure of Canine Parvovirus and its Functional Implications
      Tsao, J.,Chapman, M.S.,Agbandje, M.,Keller, W.,Smith, K.,Wu, H.,Luo, M.,Smith, T.J.,Rossmann, M.G.,Compans, R.W.,al., et
      (1991) Science 251: 1456


    Organizational Affiliation

    Department of Chemistry, Florida State University, Tallahassee 32306-3015, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PARVOVIRUS COAT PROTEIN)
Z
584Canine parvovirustype 2Mutation(s): 0 
Find proteins for P17455 (Canine parvovirustype 2)
Go to UniProtKB:  P17455
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')N11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
N, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 263.210α = 90.00
b = 349.010β = 90.82
c = 267.320γ = 90.00
Software Package:
Software NamePurpose
PURDUEdata reduction
TNTrefinement
PURDUEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance