RESOLUTION OF SPACE-GROUP AMBIGUITY AND THE STRUCTURE DETERMINATION OF NODAMURA VIRUS TO 3.3 ANGSTROM RESOLUTION FROM PSEUDO-R32 (MONOCLINIC) CRYSTALS

Monoclinic crystals of nodamura virus (NOV) have two virus molecules p er asymmetric unit. Packing analysis reveals a pseudo-rhombohedral (ps eudo-C2, monoclinic) arrangement of particles in the actual P2(1) spac e group (a = 562.1, b = 354.1, c = 612.8 Angstrom, beta = 110.9 degree s). The R32 symmetry is broken rotationally and translationally. The p seudo-symmetry of the unit cell results in three possible monoclinic o rigins and also restrains the four particles in the unit cell to simil ar orientations. NOV particles deviate by less than 3 degrees from the ideal orientations, causing overlap of peaks in the rotation function and the generation of peaks that were not interpretable as particle s ymmetry elements. The space-group ambiguity was resolved by analysing the relationship between the particle orientations determined by high- resolution rotation functions and the attenuation of peak heights in n ative Patterson maps. Particles were centered less than 1 Angstrom fro m the R32 special positions. Three different approaches were required to identify the correct particle center. Following the solutions of th e rotation and translation problems, phases were computed using the co ordinates of flock house virus (FHV), another member of this virus fam ily. The phases were improved by real-space molecular averaging with a 120-fold non-crystallographic symmetry and by solvent flattening with a spherical mask. The final model for the NOV structure was built usi ng the 3.3 Angstrom averaged map. While the overall subunit structure was very similar to that of other nodaviruses, FHV and black beetle vi rus, NOV showed distinct structural features near particle threefold a nd quasi-threefold axes and at the protein-RNA interfaces that are con sistent with phenotype differences among the related viruses.