title: 3D domain swapping modulates the stability of members of an icosahedral virus group.
abstract: BACKGROUND
  Rice yellow mottle virus (RYMV) is a major pathogen that dramatically reduces rice production in many African countries. RYMV belongs to the genus sobemovirus, one group of plant viruses with icosahedral capsids and single-stranded, positive-sense RNA genomes.
  
  
  RESULTS
  The structure of RYMV was determined and refined to 2.8 A resolution by X-ray crystallography. The capsid contains 180 copies of the coat protein subunit arranged with T = 3 icosahedral symmetry. Each subunit adopts a jelly-roll beta sandwich fold. The RYMV capsid structure is similar to those of other sobemoviruses. When compared with these viruses, however, the betaA arm of the RYMV C subunit, which is a molecular switch that regulates 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 domain swapping and produces long-range interactions throughout the icosahedral surface lattice. Biochemical analysis supports the notion that 3D domain swapping increases the stability of RYMV.
  
  
  CONCLUSIONS
  The quasi-equivalent interactions between the RYMV proteins are regulated by the N-terminal ordered residues of the betaA arm, which functions as a molecular switch. Comparative analysis suggests that this molecular switch can also modulate the stability of the viral capsids.
authors.affiliation: Department of Molecular Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: C
authors.initials: C
authors.lastname: Qu
authors.forename: L
authors.initials: L
authors.lastname: Liljas
authors.forename: N
authors.initials: N
authors.lastname: Opalka
authors.forename: C
authors.initials: C
authors.lastname: Brugidou
authors.forename: M
authors.initials: M
authors.lastname: Yeager
authors.forename: R N
authors.initials: RN
authors.lastname: Beachy
authors.forename: C M
authors.initials: CM
authors.lastname: Fauquet
authors.forename: J E
authors.initials: JE
authors.lastname: Johnson
authors.forename: T
authors.initials: T
authors.lastname: Lin
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D002213:Capsid / Q000737:chemistry / Q000378:metabolism; D002852:Chromatography, Ion Exchange; D018360:Crystallography, X-Ray; D019281:Dimerization; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000821:virology*; D010942:Plant Viruses / Q000737:chemistry* / Q000378:metabolism; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012328:RNA Viruses / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D013816:Thermodynamics
chemical_list: D002118:Calcium