IRIS Explorer software for radial-depth cueing reovirus particles and other macromolecular structures determined by cryoelectron microscopy and image reconstruction

Structures of biological macromolecules deter-mined by transmission cryoelectron microscopy (cryo-TEM) and three-dimensional image recon-struction are often displayed as surface-shaded rep-resentations with depth cueing along the viewed direction (Z cueing). Depth cueing to indicate dis-tance from the center of virus particles (radial-depth cueing, or R cueing) has also been used. We have found that a style of R cueing in which color is applied in smooth or discontinuous gradients using the IRIS Explorer software is an informative tech-nique for displaying the structures of virus particles solved by cryo-TEM and image reconstruction. To develop and test these methods, we used existing cryo-TEM reconstructions of mammalian reovirus particles. The newly applied visualization tech-niques allowed us to discern several new structural features, including sites in the inner capsid through which the viral mRNAs may be extruded after they are synthesized by the reovirus transcriptase com-plexes. To demonstrate the broad utility of the meth-ods, we also applied them to cryo-TEM reconstruc-tions of human rhinovirus, native and swollen forms of cowpea chlorotic mottle virus, truncated core of pyruvate dehydrogenase complex from Saccharomy-ces cerevisiae, and flagellar filament of Salmonella typhimurium. We conclude that R cueing with color gradients is a useful tool for displaying virus par-ticles and other macromolecules analyzed by cryo-TEM and image reconstruction. r 1997 Academic Pres