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

Structure. 2000 Oct 15;8(10):1095-103. doi: 10.1016/s0969-2126(00)00508-6.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Calcium / metabolism
  • Capsid / chemistry
  • Capsid / metabolism
  • Chromatography, Ion Exchange
  • Crystallography, X-Ray
  • Dimerization
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Oryza / virology*
  • Plant Viruses / chemistry*
  • Plant Viruses / metabolism
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • RNA Viruses / chemistry*
  • RNA Viruses / metabolism
  • Sequence Alignment
  • Thermodynamics


  • Calcium