Cryo-EM Reconstruction of the Bacteriophage phi6 Procapsid at Near-Atomic Resolution Shows Conformational Changes in dsRNA Virus Maturation

Nemecek, D.,^1,2 Boura, E.,^3,4 Wu, W.,² Cheng, N.,² Qiao, J.,⁵ Mindich, L.⁵ Heyman, B.,² and Steven, A.C.²

¹Central European Institute of Technology, Department of Structural Biology, Brno, CZ

²National Institutes of Health, National Institute of Arthritis and Musculoskeletal and
Skin Diseases , Bethesda, MD, USA

³Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, CZ

⁴The National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA

⁵University of Medicine and Dentistry of New Jersey, Department of Microbiology, NJ, USA

Bacteriophage phi6 is the type member of dsRNA bacterial viruses that share many structural and mechanistic features with other dsRNA viruses regardless if they infect mammals or fungi. The mature virion consists of multiple concentric shells that enclose the segmented dsRNA genome, viral RNA polymerase and other accessory proteins. The genome is replicated inside the innermost icosahedral capsid with a non-equivalent packing of 120 subunits. The inner capsid of phi6 is first assembled as the precursor procapsid that undergoes major conformational changes as it matures. We have determined the procapsid structure by cryo-electron microscopy at 4.5 Å resolution and compared the crystal structure of the major capsid protein (P1) with its two conformers in the procapsid shell (P1_A and P1_B). The P1_A and P1_B subunits exhibit distinct conformations from each other and from the crystal structure. The P1_A’s fit snugly together and comprise inverted 5-fold vertices with a central channel wide enough (~20 Å) for translocation of ssRNA. The P1_B’s bind to the outer rim of the P1_A vertex and connect 12 vertices into the procapsid shell. In maturation, the P1 subunits pivot mostly as rigid bodies and interlock into an almost spherical shell in a stepwise manner that controls packaging of the tripartite genome. These observations have also implications for interaction of P1 subunits with the viral RNA polymerase and for regulation of packaging and replication of the segmented genome.