Preliminary crystallographic analysis of the major capsid protein P2 of the lipid-containing bacteriophage PM2

Abstract

PM2 (Corticoviridae) is a dsDNA bacteriophage which contains a lipid membrane beneath its icosahedral capsid. In this respect it resembles bacteriophage PRD1 (Tectiviridae), although it is not known whether the similarity extends to the detailed molecular architecture of the virus, for instance the fold of the major coat protein P2. Structural analysis of PM2 has been initiated and virus-derived P2 has been crystallized by sitting-nanodrop vapour diffusion. Crystals of P2 have been obtained in space group P2(1)2(1)2, with two trimers in the asymmetric unit and unit-cell parameters a = 171.1, b = 78.7, c = 130.1 A. The crystals diffract to 4 A resolution at the ESRF BM14 beamline (Grenoble, France) and the orientation of the non-crystallographic threefold axes, the spatial relationship between the two trimers and the packing of the trimers within the unit cell have been determined. The trimers form tightly packed layers consistent with the crystal morphology, possibly recapitulating aspects of the arrangement of subunits in the virus.

Figure 1

Self-rotation function and native Patterson. (a) Self-rotation function calculated using CNS (Brünger et al., 1998 ▶) in the resolution range 15–4.5 Å, integration radius 5–39 Å. Section at κ = 120° showing the threefold peak (9.4σ) aligned with one of the crystallographic 222 axes. Contours start at the 1σ level and increase in 1σ intervals. (b) Native Patterson map calculated using the CCP4 suite (Collaborative Computational Project, Number 4, 1994 ▶) in the resolution range 35–4 Å for a primitive orthorhombic lattice with unit-cell parameters a = 130.1, b = 78.7, c = 171.2 Å. Contours start at 3σ and increase in steps of 2σ. Left, section w = 0 showing the origin peak and that at (0.5, 0.49, 0) thought to arise from the pseudo-hexameric symmetry of P2 trimers. Right, section w = 0.5. A peak is evident at position (0.43, 0.5, 0.5). Prepared using the program GROPAT (R. Esnouf & D. I. Stuart, unpublished program).

Figure 2

Cartoon representation of trimer packing. The hexameric morphology of the P2 trimers is denoted by solid hexagons, while their underlying trimeric nature and orientation is denoted by black triangles. A and B label the two crystallographically independent trimers, which by application of crystallographic symmetry form a series of infinite and closely spaced planes. The lower left arrow corresponds to the Patterson vector (0.43, 0.5, 0.5), while the arrow at the upper right corresponds to the Patterson vector (0.5, 0.49, 0) and relates (by a 60° rotation) A and B trimers in the same plane.