Fig. 5.

Comparison of three-way junction structures of analogous RNA domains within picornaviral IRESs. Three-dimensional structure of the three-way junction, corresponding A_L motif and overall secondary structure of HAV dV (a–c), EMCV J–K domain (d–f) and FMDV dIV (g–i), respectively. Based on the structural homology with EMCV J–K domain, a model of the FMDV dIV structure was computed in silico using the FARFAR and stepwise Monte Carlo Rosetta protocols^{55, 56}. For facile comparison, important structural features and the corresponding nucleotides are colored analogously in all figures. Solid and hollow circles depict canonical and non-canonical base-pairing interactions, respectively, and solid orange bars indicate tertiary interactions