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. Author manuscript; available in PMC: 2009 Sep 22.
Published in final edited form as: Nat Struct Mol Biol. 2007 Dec 23;15(1):57–64. doi: 10.1038/nsmb1351

Figure 1. The P site domain of the Dicistroviridae intergenic region IRESes.

Figure 1

(a) Comparison of canonical initiation of protein synthesis compared with that driven by the Dicistroviridae IGR IRES RNA. The steps of initial ribosome recruitment and placement on the message are not shown. 40S subunit, yellow, 60S subunit, blue; tRNA, green; ribosome binding domain (regions 1 + 2) of the IRES, black; domain 3 of the IRES, red. Locations of the A, P and E sites are labeled. (b) Secondary structure of domain 3 from the CrPV IGR IRES. The orientation of this domain has been flipped relative to panel a to reflect how it generally is depicted in the literature. Nucleotides in lowercase are not included in our crystal construct. Gray-shaded boxes, nucleotides that are conserved in six or more of seven members of this IRES class (Supplementary Fig. 1). Dashed boxes, mutations that introduced a heavy atom binding site for obtaining crystallographic phase information (Supplementary Fig. 2). (c) Two views (90° rotation) of the crystal structure of domain 3 of the CrPV IGR IRES, colored to match the secondary structure of panel b. Nts 6203–6209 are not shown because their structure was affected by crystal packing (Supplementary Fig. 3).