Fig. 6.

Structural homology between the corresponding RNA domains from different types of picornaviral IRESs. a Secondary structure of HAV IRES (type III IRES) dV based on the crystal structure obtained in this work. b Secondary structure of EMCV IRES (type II IRES) J–K domain based on the previously reported NMR structure (PDB code: 2NBX)²². c Secondary structure model of FMDV IRES (type II IRES) domain IV computed in silico. The computed model is based upon topological similarities observed between HAV dV and EMCV J–K domain and extensive homology between FMDV dIV and EMCV J–K domain and is consistent with previous biochemical probing results^{14, 16, 17, 33}. For facile comparison, important structural features and the corresponding nucleotides have analogous colors. Supplementary information provides detailed comparative structural analysis of HAV dV, EMCV J–K domain, and FMDV dIV (Supplementary Figs. 12–17). d, e Secondary structure models of type III and type II picornaviral IRESs, respectively with structurally homologous domains highlighted in red. f Available biochemical and bioinformatics data suggests that dV of type I picornaviral IRES also may form a three-way junction with the capacity to form a LPTL type structure (see Supplementary Fig. 18 for details)