4G0R

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

Summary for 4G0R

• Entry DOI: 10.2210/pdb4g0r/pdb
• Related: 4GBT
• Descriptor: Capsid protein VP1, DNA (5'-D(P*CP*TP*GP*AP*CP*TP*TP*CP*AP*A)-3'), 1,2-ETHANEDIOL, ... (8 entities in total)
• Functional Keywords: beta-barrel, ssdna binding, ssdna, icosahedral virus, virus, virus capsid protein, cell, virus-dna complex, virus/dna
• Biological source: H-1 parvovirus; More
• Cellular location: Virion (By similarity): P03136
• Total number of polymer chains: 2
• Total formula weight: 85030.73

Authors

Halder, S.,Agbandje-McKenna, M.,Nam, H.-J.,Govindasamy, L.,Vogel, M.,Dinsart, C.,Salome, N.,McKenna, R. (deposition date: 2012-07-09, release date: 2013-02-27, Last modification date: 2024-02-28)

Primary citation

Halder, S.,Nam, H.J.,Govindasamy, L.,Vogel, M.,Dinsart, C.,Salome, N.,McKenna, R.,Agbandje-McKenna, M.
Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids.
J.Virol., 87:5128-5140, 2013

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 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.

PubMed: 23449783
DOI: 10.1128/JVI.03416-12

Experimental method

X-RAY DIFFRACTION (2.7 Å)