Determination and refinement of the canine parvovirus empty-capsid structure

The canine parvovirus (CPV) empty-capsid structure has been determined and refined to 3.0 Å resolution in the tetragonal space group P4₃2₁2 with cell dimensions a = b = 254.5 and c = 795.0 Å. The successful structure determination shows that reasonably good diffraction data were obtained in spite of the very long c axis. The structure was solved by molecular replacement using the electron density of CPV full particles in a monoclinic space group. The phases were refined by non-crystallographic symmetry averaging. The structure refinement was carried out by using the programs PROLSQ and X-PLOR. The final R factor for the structure that included 85 water molecules per icosahedral asymmetric unit was 21.1% for reflections between 6.0 and 3.0 Å resolution with an r.m.s. deviation of bond lengths of 0.020 Å from ideal values. The structure of CPV empty capsids showed conformational differences with respect to full capsids at a region where icosahedrally ordered DNA in full particles interacts with the capsid protein. It also confirmed the absence of density along the fivefold axis in the CPV empty-particle structure in contrast to the situation in CPV full particles.