SNAP output for PDB entry 1mvm [SNAP web server]

PDB-id

1mvm; SNAP-derived features in text and JSON formats; DNAproDB

Class

virus-DNA

Method

X-ray (3.5 Å)

Summary

Mvm(strain i), complex(viral coat-DNA), vp2, ph=7.5, t=4 degrees c

Reference

Llamas-Saiz AL, Agbandje-McKenna M, Wikoff WR, Bratton J, Tattersall P, Rossmann MG (1997): "Structure determination of minute virus of mice." Acta Crystallogr.,Sect.D, 53, 93-102. doi: 10.1107/S0907444996010566.

Abstract

The three-dimensional crystal structure of the single-stranded DNA-containing ('full') parvovirus, minute virus of mice (MVM), has been determined to 3.5 A resolution. Both full and empty particles of MVM were crystallized in the monoclinic space group C2 with cell dimensions of a = 448.7, b = 416.7, c = 305.3 A and beta = 95.8 degrees. Diffraction data were collected at the Cornell High Energy Synchrotron Source using an oscillation camera. The crystals have a pseudo higher R32 space group in which the particles are situated at two special positions with 32 point symmetry, separated by (1/2)c in the hexagonal setting. The self-rotation function showed that the particles are rotated with respect to each other by 60 degrees around the pseudo threefold axis. Subsequently, a more detailed analysis of the structure amplitudes demonstrated that the correct space-group symmetry is C2 as given above. Only one of the three twofold axes perpendicular to the threefold axis in the pseudo R32 space group is a 'true' crystallographic twofold axis; the other two are only 'local' non-crystallographic symmetry axes. The known canine parvovirus (CPV) structure was used as a phasing model to initiate real-space electron-density averaging phase improvement. The electron density was easily interpretable and clearly showed the amino-acid differences between MVM and CPV, although the final overall correlation coefficient was only 0.63. The structure of MVM has a large amount of icosahedrally ordered DNA, amounting to 22% of the viral genome, which is significantly more than that found in CPV.