Three-dimensional structure of physalis mottle virus: Implications for theviral assembly

The structure of the T = 3 single stranded RNA tymovirus, physalis mottle v irus (PhMV), has been determined to 3.8 Angstrom resolution. PhMV crystals belong to the rhombohedral space group R3, with one icosahedral particle in the unit cell leading to 20-fold non-crystallographic redundancy. Polyalan ine coordinates of the related turnip yellow mosaic virus (TYMV) with which PhMV coat protein shares 32% amino acid sequence identity were used for ob taining the initial phases. Extensive phase refinement by real space molecu lar replacement density averaging resulted in an electron density map that revealed density for most of the side-chains and for the 17 residues ordere d in PhMV, but not seen in TYMV, at the N terminus of the A subunits. The c ore secondary and tertiary structures of the subunits have a topology consi stent with the capsid proteins of other T = 3 plant viruses. The N-terminal arms of the A subunits, which constitute 12 pentamers at the icosahedral 5 -fold axes, have a conformation very different from the conformations obser ved in B and C subunits that constitute hexameric capsomers with near 6-fol d symmetry at the icosahedral 3-fold axes. An analysis of the interfacial c ontacts between protein subunits indicates that the hexamers are held more strongly than pentamers and hexamer-hexamer contacts are more extensive tha n pentamer-hexamer contacts. These observations suggest a plausible mechani sm for the formation of empty capsids, which might be initiated by a change in the conformation of the N-terminal arm of the A subunits. The structure also provides insights into immunological and mutagenesis results. Compari son of PhMV with the sobemovirus, sesbania mosaic virus reveals striking si milarities in the overall tertiary fold of the coat protein although the ca psid morphologies of these two viruses are very different. (C) 1999 Academi c Press.