Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation

Secondary structure of FMDV IRES. Domains are numbered 1–5 or H–L; a dot is positioned every 10 residues. RNA structure of the central domain is depicted according to RNA probing analysis (Fernández-Miragall and Martínez-Salas 2003). Underlined symbols depict the substitutions in RAAA motif (A₁₉₉AAAG₂₀₃) to CGCCC, in GNRA motif (G₁₇₈UAA₁₈₁) to GUAG or UACG; motif A (G₂₄₀CACG₂₄₄) to ACGGC; and motif B (G₂₄₇ACU₂₅₀) to CGGG. Transcript stem 3 encompasses residues 86–299 with 151–227 deleted.