Ordered duplex RNA controls capsid architecture in an icosahedral animal virus

Small spherical viruses are among the simplest replicating systems in biology, yet the factors affecting their assembly, stability and disassembly are still poorly understood. A molecular switch is required for the assembly of icosahedral virus particles containing more than 60 identical subunits because strict symmetry cannot be maintained in subunit packing. All previously reported viruses with this type of structure use a portion of the capsid protein to regulate interactions between chemically equivalent but structurally distinct interfaces. We have investigated the T = 3 quasiequivalent nodaviruses, which are small non-enveloped viruses with a single-stranded RNA genome that infect insects, mice and fish. They undergo a well-characterized series of steps in assembly and maturation, which in some respects are similar to the picornaviruses, despite their different capsid architecture. Here we report the X-ray structure of Flock House virus at 3.0 A resolution, which reveals an ordered RNA duplex of 20 nucleotides and a protein segment that control the subunit interactions in this animal virus. The RNA interacts with a helical protein domain of the subunit that lies inside the capsid shell. One of the helices that binds the RNA is part of a 44-amino-acid polypeptide which is autocatalytically cleaved from the initial subunit translation product after virion assembly. The structure indicates that RNA associated with the cleaved polypeptide may be important in the infection process.