Figure 2. Asymmetric reconstruction of free Φ29 virions.

A) A central section of an asymmetric reconstruction of Φ29 as determined by subtomogram averaging. No rotational symmetry was applied to the portal and tail assembly, which includes the lower collar, appendages, tail knob and tail tip protein. B) A side view of the surface rendering of a Φ29 virion. C) Surface rendering with crystal structures for the gp8.5 head fiber (PDB 3QC7), gp12* appendages (PDB 3GQ7), and gp13 tail tip protein (PDB 3CSQ) manually docked. In surface renderings and crystal models, head fibers are shown in light blue, the capsid in darker blue, appendages in oranges and yellow, and the tail is shown as a gradient from blue to green, terminating with the tail knob and tip protein. D) A cross-section of the asymmetric reconstruction clearly shows five head fibers (outside of the larger circle), twelve appendages (A1–A12, defined by the larger circle) and the tail knob (TK, defined by the smaller circle). E) A bottom view shows the five head fibers; the twelve appendages are displayed in either an extended (yellow) or down (orange) orientation. F) Two class averages show appendages with the gp12* crystal structures docked into both extended (right panel) and down conformations (left panel).