Extended Data Fig. 12: Structure of the Initiation Complex (IC).

a, The mRNA can be traced all the way from the mS39 docking platform, through the channel entry formed by uS5m-uS9m, A-site, P-site (pairing with tRNA^Met), and E-site (contacting uS7m). The mRNA residues at the E-site correspond to the 5′ untranslated region (UTR) that fits with a purine in the position −1, and pyrimidines in the positions −2 and −3. Out of all the mitochondrial mRNAs, only two, namely those of COX1 and ND4, have the fitting residues, CUG and CCA, respectively. For the position −1, the density fits better with G than A, due to the differences in amino group locations 2 vs 6. In addition, in the start codon, the density supports AUG over AUA, and +4 fits pyrimidine, which is also present in COX1. Therefore, the cryo-EM map singles out COX1 as an enriched mRNA, associated with the resolved translation initiation complex. Structurally, the three 5′ UTR residues in the E-site are stacked with their bases against each other and against Gly164 and Gly165 of uS7m, whereas a configuration of one or two UTR residues would not stack with uS7m in this region. The specific enrichment of the COX1 mRNA complex most likely represents the most stable variant of the pool of translation initiation complexes charged with mRNA that was trapped in our structure. b, Comparison with a reconstituted monosome complex. In addition to similar relative location of mtIF2 and mS37, a weak density that fits the C-terminal domain (CTD) of bL12m is observed next to the G-domain of mtIF2 (density shown as mesh). The bL12m CTD is also present in the complete initiation complex.