3D domain swapping modulates the stability of members of an icosahedral virus group.
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.
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Department of Molecular Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Liljas
L
L
Opalka
N
N
Brugidou
C
C
Yeager
M
M
Beachy
R N
RN
Fauquet
C M
CM
Johnson
J E
JE
Lin
T
T
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
D002118:Calcium