Fig. 5. Proposed molecular mechanism for RafH action.

a Inhibition of the translation initiation factor binding by RafH. The pre-translation initiation structure SSU (PDB ID; 5LMT) docked into the ribosome RafH SSU complex structure. For clarity, only the RafH in ribbon (red) with 95% transparent surface, bS1 in ribbon (salmon) with 95% transparent surface, initiation complex factors: mRNA (navy blue), a-SD (gold), IF1 (cornflower blue), IF3 (cyan), and P- tRNA (dark olive green) are shown. A thumbnail is shown in the bottom right. b Protection of 16S rRNA from RNase degradation. The RafH (red) and bS1 (salmon) are shown in ribbon with a 95% transparent surface. 16S rRNA helices, h24, h28, h44, h45, aSD, and 3′ of 16S rRNA are shown in a ribbon with a ladder. The E-tRNA anticodon stem loop (hot pink) is shown in a ribbon with a 95% transparent surface. The RNase nucleolytic site predicted in E. coli 16S rRNA by ref. ¹⁵ and corresponding nucleotides in M. smegmatis 16S rRNA are shown in black with the scissors symbol. A thumbnail is shown in the bottom right. The 3′ to 5′ exonuclease RNase PH/RNase R is shown in an orange Pie shape. Its description in 2D is shown in Supplementary Fig. 12.