Fig. 2. Computational fitting of the VP5ud into the hexon and penton subunits. (A) Part of the 8.5 Å electron cryomicroscopy reconstruction of the HSV-1 B capsid. The penton capsomere is displayed in red, the hexon in blue and the triplex in green. The asymmetric unit of the HSV-1 nucleocapsid is enclosed by the white line. P, C and E represent the three types of hexons, the peripentonal, center and edge, respectively. (B) The crystal structure of VP5ud fitted into each of the positions it would be expected to occupy in the electron cryomicroscopy reconstruction of the HSV-1 capsid. The C_α backbones of the VP5uds are color coded yellow, red, green and blue depending on which capsomere (penton, central hexon, edge hexon or peripentonal hexon, respectively) they comprise. (C) Side view of the C_α trace of the VP5ud (magenta) modeled into the 8.5 Å electron cryomicroscopy density of a single hexon subunit. The blue density at the apical end of the VP5ud represents VP26. VP26 was delineated by calculating a difference map between the fitted VP5ud and a computationally isolated VP5 monomer from a hexon. (D) Side view of the C_α trace of the VP5ud (magenta) modeled into the 8.5 Å electron cryomicroscopy density of a single penton subunit, viewed from the same direction as in (A).