Secondary structure of the four smaller RNAs. These structures were created using the Saccharomyces cerevisiae LSU secondary structure as a guide. This was facilitated by structural alignments of the T. brucei small segments over the S. cerevisiae LSU crystallographic structure (PDBID 4V88) (Supplemental Table S5; Ben-Shem et al. 2011). In each case, there are no standard Watson–Crick stems created by interaction with another rRNA. This is in contrast to a comparison of the 5.8S, α, and β rRNAs where there are multiple shared stems that can contribute to holding these fragments together. Regions of interaction are marked with solid filled circles and a region number in the same color that is related to Tables 1–4. Missing regions and residues were not mapped due to a lack of structural counterpart in S cerevisiae. Red asterisks mark interacting regions that are a common feature within the T. brucei, L. donovani, and T. cruzi cryo-EM structures. T. brucei numbering system is used. (A) Eight interacting regions of the srRNA-I segment. Regions 2, 3, 5, and 7 are a common feature among the structures analyzed here (Table 1; Supplemental Table S1). Region 4 is not shown because this region is part of a small expansion segment (sES), marked in gray, which has no S. cerevisiae counterpart. (B) srRNA-II interacting regions 3–13. Regions 3, 4, 6, 7, 8, 9, 10, 11, and 13 are a common feature among the trypanosomatid structures (Table 2; Supplemental Table S2). (C) srRNA-III interacting regions. Only regions 3 and 4 are depicted due to structural incompatibility of this region (see discussion). Regions 1, 2, and 3 are a common feature among trypanosomatid structures (Table 3; Supplemental Table S3). (D) Interacting regions 1 to 7 in the srRNA-IV segment. Regions 1, 3, 5, 6, and 7 are a common feature among the structures analyzed here (Table 4; Supplemental Table S4).
