Refined structure of Desmodium yellow mottle tymovirus at 2.7 angstrom resolution

Desmodium yellow mottle virus is a 28 nm diameter, T = 3 icosahedral plant virus of the tymovirus group. Its structure has been solved to a resolution of 2.7 Angstrom using X-ray diffraction analysis based on molecular replac ement and phase extension methods. The final R value was 0.151 (R-free = 0. 159) for 134,454 independent reflections. The folding of the polypeptide ba ckbone is nearly identical with that of turnip yellow mosaic virus, as is t he arrangement of subunits in the virus capsid. However, a major difference in the disposition of the amino-terminal ends of the subunits was observed . In turnip yellow mosaic virus, those from the B and C subunits comprising the hexameric capsomeres formed an annulus about the interior of the capso mere, while the corresponding N termini of the pentameric capsomere A subun its were not visible at all in electron density maps. In Desmodium yellow m ottle tymovirus, amino termini from the A and B subunits combine to form th e annuli, thereby resulting in a much strengthened association between the two types of capsomeres and an, apparently, more stable capsid. The first 1 3 residues of the C subunit were invisible in electron density maps. Two or dered fragments of single-stranded RNA, seven and two nucleotides in length , were observed. The ordered water structure of the virus particle was deli neated and required 95 solvent molecules per protein subunit. (C) 2000 Acad emic Press.