The NMR/Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

Omry Morag, School of Chemistry, Tel Aviv University, Tel-Aviv, Israel
Amir Goldbourt, School of Chemistry, Tel Aviv University, Tel-Aviv, Israel

Filamentous phage are elongated semi-flexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of approximately 1 micron and a diameter of ~7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using magic-angle spinning solid-state NMR experimental data together with Rosetta model building. The acquisition of many inter-subunit contacts between the sidechains of different capsid subunits facilitated the determination of the major coat protein structure as well as the symmetry of the entire assembly using a 5-start helix (including pentamer symmetry within the individual helical levels). The data are consistent with a rise of 16.6-16.7 Å and a tilt of 36.1-36.6° between consecutive pentamers. The coat protein subunit is mostly a-helical with an N-terminal type-II b-turn. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study non-crystalline, high-molecular weight molecular assemblies.