4G0R

Structural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids.

Halder, S.Nam, H.J.Govindasamy, L.Vogel, M.Dinsart, C.Salome, N.McKenna, R.Agbandje-McKenna, M.

(2013) J Virol 87: 5128-5140

  • DOI: 10.1128/JVI.03416-12
  • Primary Citation of Related Structures:  
    4G0R, 4GBT

  • PubMed Abstract: 
  • The structure of single-stranded DNA (ssDNA) packaging H-1 parvovirus (H-1PV), which is being developed as an antitumor gene delivery vector, has been determined for wild-type (wt) virions and noninfectious (empty) capsids to 2.7- and 3.2-Å resolution, respectively, using X-ray crystallography ...

    The structure of single-stranded DNA (ssDNA) packaging H-1 parvovirus (H-1PV), which is being developed as an antitumor gene delivery vector, has been determined for wild-type (wt) virions and noninfectious (empty) capsids to 2.7- and 3.2-Å resolution, respectively, using X-ray crystallography. The capsid viral protein (VP) structure consists of an α-helix and an eight-stranded anti-parallel β-barrel with large loop regions between the strands. The β-barrel and loops form the capsid core and surface, respectively. In the wt structure, 600 nucleotides are ordered in an interior DNA binding pocket of the capsid. This accounts for ∼12% of the H-1PV genome. The wt structure is identical to the empty capsid structure, except for side chain conformation variations at the nucleotide binding pocket. Comparison of the H-1PV nucleotides to those observed in canine parvovirus and minute virus of mice, two members of the genus Parvovirus, showed both similarity in structure and analogous interactions. This observation suggests a functional role, such as in capsid stability and/or ssDNA genome recognition for encapsulation. The VP structure differs from those of other parvoviruses in surface loop regions that control receptor binding, tissue tropism, pathogenicity, and antibody recognition, including VP sequences reported to determine tumor cell tropism for oncotropic rodent parvoviruses. These structures of H-1PV provide insight into structural features that dictate capsid stabilization following genome packaging and three-dimensional information applicable for rational design of tumor-targeted recombinant gene delivery vectors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1A735H-1 parvovirusMutation(s): 0 
UniProt
Find proteins for P03136 (Hamster parvovirus H1)
Explore P03136 
Go to UniProtKB:  P03136
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*TP*GP*AP*CP*TP*TP*CP*AP*A)-3')B [auth C]10H-1 parvovirus
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DC
    Query on DC

    Download Ideal Coordinates CCD File 
    F [auth A]2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
    C9 H14 N3 O7 P
    NCMVOABPESMRCP-SHYZEUOFSA-N
     Ligand Interaction
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A], E [auth A], H [auth A]1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

    Download Ideal Coordinates CCD File 
    J [auth A]CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    K [auth C], L [auth C]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    G [auth A], I [auth A]SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.217 
    • R-Value Work: 0.216 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 255.4α = 90
    b = 350.4β = 90.34
    c = 271.6γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    AMoREphasing
    CNSrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-02-27
      Type: Initial release
    • Version 1.1: 2013-04-24
      Changes: Database references