Fig. 5: Specific protein elements involved in mRNA binding.

a Electrostatic coulomb potential surface representation of the model shows a positively charged groove (blue) on mS39 that accommodates the mRNA. N-terminal loop of mS31 interacts with mS39. Y-N-C-Y motif and its interactions with mS39 residues are depicted as a schematic. Position of kink-2 is marked. b Interactions of the Y-N-C-Y motif with mS39 and density map (mesh). Protein mS31 has been removed for clarity. c Average percentage frequency of Y-N-C-Y motif (left) with +/− standard deviation for all mitochondrial mRNAs except ND6 (n = 12 biologically independent samples;; dark grey bar) and nuclear mRNAs (n = 1387 biologically independent samples; brown bar). P-value (‘****’ indicates p < 0.0001) calculated by Welch’s unpaired two-tailed t-test. Positions of the Y-N-C-Y motif in the mt-mRNAs are shown as discs (right) to depict its distribution along the mt-mRNA sequences. The total number of residues for each mt-mRNA is indicated. d Overview of uS5m showing a region of contact with mRNA. The polybasic stretch 111–124 along the mRNA is colored by electrostatic potential. Interacting residues between uS5m and mRNA are shown with the local density map. e Interactions of mS35 and uS9m with mRNA at the channel entry and the P-site. f, R46 and R48 of mS35 potentially interact with the mRNA backbone, and the density suggests flexibility of the side-chains. g uS9m forms stacking and hydrogen bonding interactions with mRNA position 15 via F54 and V55, respectively. h uS9m N-terminus (purple cartoon) adopts alternative conformations that result in mRNA channel blocked or open states regulating mRNA access to the SSU (gold surface).