Crystallization and preliminary X-ray diffraction studies of Seneca Valley virus-001, a new member of the Picornaviridae family

Abstract

Seneca Valley Virus-001 (SVV-001) is a newly found species in the Picornaviridae family. SVV-001 is the first naturally occurring nonpathogenic picornavirus observed to mediate selective cytotoxicity towards tumor cells with neuroendocrine cancer features. The nonsegmented (+)ssRNA genome of SVV-001 shares closest sequence similarity to the genomes of the members of the Cardiovirus genus. However, based on the distinct characteristics of the genome organization and other biochemical properties, it has been suggested that SVV-001 represents a new genus, namely 'Senecavirus', in the Picornaviridae family. In order to understand the oncolytic properties of SVV-001, the native virus was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group R3, with unit-cell parameters (in the hexagonal setting) a = b = 311.5, c = 1526.4 A. Although the SVV crystals diffracted to better than 2.3 A resolution, the data quality is acceptable [I/sigma(I) > 2.0] to 2.6 A resolution. The unit-cell volume and the locked rotation-function analysis suggest that six particles could be accommodated in the unit cell, with two distinct sets of one third of a particle, each containing 20 protomers, occupying the crystallographic asymmetric unit. (ClinicalTrials.gov identifier NCT00314925)

Figures

Figure 1

(a) SDS–PAGE gel showing the purity of the SVV-001 sample used in crystallization trials. Lane 1 shows the molecular-weight markers (SeeBlue Pre-Stained marker from Invitrogen) and lane 2 shows bands corresponding to VP1, VP2, VP3 and VP4 of the purified SVV-001 sample. (b) An image of rhomboid-shaped crystals of SVV-001.

Figure 2

(a) A contour plot showing the threefold peaks relative to the unit-cell axis of the SVV-­001 crystals. A total of 46 784 large terms in the resolution range 20.0–5.0 Å with a radius of integration of 100 Å were used in the rotation-function calculation. (b) The locked rotation-function analysis illustrating the presence of signal in two resolution bins: one between 3.2 and 3.0 Å resolution (solid line) and the highest resolution bin between 2.4 and 2.3 Å (dotted line).