The three-dimensional structure of frozen-hydrated Nudaurelia capensis β Virus, a T = 4 insect Virus

Abstract

The three-dimensional structure of Nudaurelia capensis β virus (NβV) was reconstructed to 3.2-nm resolution from images of frozen-hydrated virions. The distinctly icosahedral capsid (∼40-nm diameter) contains 240 copies of a single 61-kDa protein subunit arranged with T = 4 lattice symmetry. The outer surface of unstained virions compares remarkably well with that previously observed in negatively stained specimens. Inspection of the density map, volume estimates, and model building experiments indicate that each subunit consists of two distinct domains. The large domain (∼40 kDa) has a cylindrical shape, ∼4-nm diameter by ∼4-nm high, and associates with two large domains of neighboring subunits to form a Y-shaped trimeric aggregate in the outer capsid surface. Four trimers make up each of the 20 planar faces of the capsid. Small domains (∼21 kDa) presumably associate at lower radii (∼13–16.5 nm) to form a contiguous, nonspherical shell. A T = 4 model, constructed from 80 trimers of the common β-barrel core motif (∼20 kDa) found in many of the smaller T = 3 and pseudo T = 3 viruses, fits the dimensions and features seen in the NβV reconstruction, suggesting that the contiguous shell of NβV may be formed by intersubunit contacts between small domains having that motif. The small (∼1800 kDa), ssRNA genome is loosely packed inside the capsid with a low average density.