Capsomer Dynamics and Stabilization in the T = 12 Marine Bacteriophage SIO-2 and Its Procapsid Studied by CryoEM

We report the subnanometer cryo-electron microscopy (cryoEM) reconstruction of a marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species with significant ecological importance, including the broadly antagonistic bacterium Vibrio sp. SWAT3. The three-dimensional structure of the 800 Å SIO-2, icosahedrally averaged head of the tailed particle revealed a T = 12 quasi-symmetry not previously described in a bacteriophage. Two morphologically distinct types of auxiliary proteins were also identified; one species bound to the surface of hexamers, and the other bound to pentamers. The secondary structure, evident in the electron density, shows that the major capsid protein has the HK97-like fold. The three-dimensional structure of the procapsid form, also presented here, has no “decoration” proteins and reveals a capsomer organization due to the constraints of the T = 12 symmetry. ► The SIO2 dsDNA bacteriophage displays T = 12 quasi-symmetry ► This places icosahedral symmetry constraints on subunit hexamers ► The restrictions are conspicuous in the procapsid where “hexamers” are skewed ► The balance of energetics required by stages of assembly and symmetry are discussed