Effect of the viral protease on the dynamics of bacteriophage HK97 maturation intermediates characterized by variance analysis of cryo EM particle ensembles

Cryo EM structures of maturation-intermediate Prohead I of bacteriophage HK97 with (PhIPro+PhIPro+) and without (PhIPro−PhIPro−) the viral protease packaged have been reported (Veesler et al., 2014). In spite of PhIPro+PhIPro+ containing an additional ∼100×24kD of protein, the two structures appeared identical although the two particles have substantially different biochemical properties, e.g., PhIPro−PhIPro− is less stable to disassembly conditions such as urea. Here the same cryo EM images are used to characterize the spatial heterogeneity of the particles at 17 Å resolution by variance analysis and show that PhIPro−PhIPro− has roughly twice the standard deviation of PhIPro+PhIPro+. Furthermore, the greatest differences in standard deviation are present in the region where the δ-domain, not seen in X-ray crystallographic structures or fully seen in cryo EM, is expected to be located. Thus presence of the protease appears to stabilize the δ-domain which the protease will eventually digest.