Fig. 1.

Secondary structure of the IAPV IGR IRES. Pseudoknots PKI, PKII, and PKIII; stem loops SLIII, SLIV, and SLV and loop L1.1; and the variable loop region (VLR) are indicated. The PKI domain comprises a three-way junction involving helices P3.1 (green), P3.2 (purple), and P3.3 (blue). The IAPV IRES can mediate translation of ORFx in the +1 reading frame, which overlaps the viral structural protein coding region. IRES-mediated translation in the 0 and +1 frames starts from the GGC glycine and GCG alanine codons, respectively. Translation of the +1 frame ORFx is directed by a U6562/G6618 base pair adjacent to PKI (red nucleotides). Conserved nucleotides within the type II IGR IRESs are shown in capital letters.