3D domain swapping modulates the stability of members of an icosahedral virus group

Background: Rice yellow mottle virus (RYMV) is a major pathogen that dramat ically reduces rice production in many African countries. RYMV belongs to t he genus sobemovirus, one group of plant viruses with icosahedral capsids a nd single-stranded, positive-sense RNA genomes. Results: The structure of RYMV was determined and refined to 2.8 Angstrom r esolution by X-ray crystallography. The capsid contains 180 copies of the c oat protein subunit arranged with T = 3 icosahedral symmetry. Each subunit adopts a jelly-roll p sandwich fold. The RYMV capsid structure is similar t o those of other sobemoviruses. When compared with these viruses, however, the PA arm of the RYMV C subunit, which is a molecular switch that regulate s quasi-equivalent subunit interactions, is swapped with the 2-fold-related betaA arm to a similar, noncovalent bonding environment. This exchange of identical structural elements across a symmetry axis is categorized as 3D d omain swapping and produces long-range interactions throughout the icosahed ral surface lattice. Biochemical analysis supports the notion that 3D domai n swapping increases the stability of RYMV. Conclusions: The quasi-equivalent interactions between the RYMV proteins ar e regulated by the N-terminal ordered residues of the betaA arm, which func tions as a molecular switch. Comparative analysis suggests that this molecu lar switch can also modulate the stability of the viral capsids.