The multi-layered architecture of alphaviruses is built up with the registration of nucleocapsid (NC) proteins and envelope spike proteins across a lipid bilayer. At the surface of the NC, capsid proteins are organized as 42 capsomers such that the three tails from each spike complex bind three capsomers. Alphaviruses have been extensively studied using cryo-EM and X-ray crystallography at near-atomic resolution (see review by Sedzik et al.). This work involves averaging images of many isolated virions, and makes use of the symmetry of the particle. The study of assembly and budding of virus particles at the cell surface, however, requires structural determination of individual virions in situ. Electron tomography offers a means for such studies.

Small features are obscured in typical thin-section (ca. 50nm) TEM micrographs due to the projection in 2D of all the structures throughout the section thickness. However, slices thinner than lnm can easily be obtained from tomographic reconstructions. Thus, small structures such as capsomers can be seen, even in thick (>100nm) specimens (Fig. 1b).