Forum 09/22/2005

“Structure and Assembly of Large dsDNA Viruses and An Automated Program for 3D Image Reconstruction of Icosahedral Particles”

Xiaodong Yan – UCSD Chemistry Department

Cryo-electron microscopy and 3D image reconstructions of three viruses, Paramecium bursaria chlorella virus 1 (PBCV-1), Chilo iridescent virus (CIV) and Phaeocystis pouchetii virus (PpV01), revealed many characteristic features of these large, dsDNA, lipid-containing viruses. They all contain an icosahedral protein capsid shell (maximum diameter ranging from 185 to 220 nm) and an internal lipid bilayer. The protein shell is primarily composed of 12 pentameric capsomers and thousands of trimeric capsomers. In PBCV-1, CIV and PpV01 these capsomers are arranged on T=169d, 147 and 219 quasi-equivalent lattices, respectively. The capsomers in each virus are organized into 20 triangle- (trisymmetrons) and 12 pentagonal-shaped facets (pentasymmetrons). All of three viruses contain fiber-like structures that protrude above the capsid surface. These three viruses are the largest icosahedral viruses whose capsid structures have been determined in 3D from images of vitrified samples.  Striking similarities in the structures are consistent with a growing body of evidence that large, dsDNA viruses share a common evolutionary origin.  In response to the computational challenges inherent in reconstructing 3D structures of very large icosahedral complexes such as these dsDNA viruses, we have developed an automated procedure to refine and compute 3D reconstructions and also devised a simple way to create ab initio models of icosahedral particles for model-based search and refine procedures.  A brief introduction to these methods will be presented.