Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions

Authors

Lucas Oliveira, CUNY Graduate CenterFollow
Ze Ye, CUNY Graduate Center
Al Katz, CUNY City College
Alexandra Alimova, CUNY City CollegeFollow
Hui Wei, CUNY City College
Gabor T. Herman, CUNY Graduate CenterFollow
Paul Gottlieb, CUNY City CollegeFollow

Document Type

Article

Publication Date

1-4-2018

Abstract

The 3-dimensional structure of the nucleocapsid (NC) of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2) are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC) is a dynamic structural intermediate where the P4 and P2 can attach and detach until held in place in mature NCs. During packaging, the PC expands to accommodate the RNA, and P2 translates from its original site near the inner 3-fold axis (20 sites) to the inner 5-fold axis (12 sites) with excess P2 positioned inside the central region of the NC.

Comments

This article was originally published in PLoS ONE, available at https://doi.org/10.1371/journal. pone.0188858.

This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License.