Figure 4
From: Deep sequencing reveals global patterns of mRNA recruitment during translation initiation
Properties of Shine-Dalgarno (SD) interactions.
(a) Crystal structure of translation initiation complex (2QNH) illustrating the interactions between SD and anti-SD sequences near the 3′-end of the 16S rRNA as well as their relative position to the initiation codon AUG. The picture was generated using PyMOL (Version 0.98, DeLano Scientific LLC). (b) Illustration of the percentage of AGGAGG in N20U in the three initiation stages. (c) Illustration of the regional preference of AGGAGG in N20U in the three initiation stages. (d) Schematic illustration of the different complementary positions of the SD/anti-SD interactions near the 3′ end of the 16S rRNA. (e) Correlation of the relative preference of the eight 6-mers (as indicated in d) with their complementary positions at the 3′-end of 16S rRNA. The relative preference was calculated as the percentage of the KPMrelative of the target 6-mer compared with the maximum KPMrelative from the same selected library (see Fig. 3b and Supplementary Fig. 4a). (f) Illustration of the regional preference in N20U in 70SIC for those SD sequences complementary to different positions near the 3′ end of 16S rRNA.
