The crystal structure of the Phi6 major capsid protein

Boura E.^1,2, Nemecek, D.^3,4, Plevka P.⁵ and Hurley J.H.²

¹Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Prague, CZ
²The National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
³Central European Institute of Technology, Department of Structural Biology, Brno, CZ
⁴National Institutes of Health, National Institute of Arthritis and Musculoskeletal andSkin Diseases , Bethesda, MD, USA
⁵Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907

Double-stranded RNA (dsRNA) viruses share several distinctive features, regardless of whether they infect mammals, fungi, or bacteria. Their genomes comprise multiple linear segments; the virions consist of up to three nested shells; the innermost capsid is icosahedrally symmetric with a nonequivalent packing of its subunits. Our goal was to device an atomic model of dsRNA virus maturation. In order to achieve that we have determined the crystal structure of its major capsid protein, P1, at 3.6 Å resolution. Self rotation function revealed that the P1 protein crystallized as one pentamer in the asymmetric unit. Thus, the structure was solved by molecular replacement using a cryo-electron map of a pentamer at 7 Å resolution as a search model and the phases were extended using non-crystallographic symmetry. The P1 subunit is shaped like a kite with sides of ~91 Å by 73 Å. The thickness varies between 14 Å and 38 Å at the edges, reaching 47 Å in the center. The fold is novel and mostly alpha helical. Fit of the crystal structure into high-resolution cryoEM map of the procapsid revealed conformational changes during virus maturation.