Structures of T = 1 and T = 3 Particles of Cucumber Necrosis Virus: Evidence of Internal Scaffolding

Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus, of which tomato bushy stunt virus (TBSV) is the type member. The capsid protein for this group of viruses is composed of three major domains: the R domain, which interacts with the RNA genome: the S domain, which forms the tight capsid shell: and the protruding P domain, which extends ∼40 Å from the surface. Here, we present the cryo-transmission electron microscopy structures of both the T = 1 and T = 3 capsids to a resolution of ∼12 Å. The T = 3 capsid is essentially identical with that of TBSV, and the T = 1 particles are well described by the A subunit pentons from TBSV. Perhaps most notable is the fact that the T = 3 particles have an articulated internal structure with two major internal shells, while the internal core of the T = 1 particle is essentially disordered. These internal shells of the T = 3 capsid agree extremely well in both dimension and character with published neutron-scattering results. This structure, combined with mutagenesis results in the accompanying article, suggests that the R domain forms an internal icosahedral scaffold that may play a role in T = 3 capsid assembly. In addition, the N-terminal region has been shown to be involved in chloroplast targeting. Therefore, this region apparently has remarkably diverse functions that may be distributed unevenly among the quasi-equivalent A, B, and C subunits.