Fig 3. Secondary structure model for E. coli 16S rRNA.

This model was constrained by 16S rRNA consensus base pairs derived from SHAPE-based sequence alignment. Predicted pairs that exactly match the accepted covariation model [11] are shown with short black lines, and predicted pairs that match after modest local refolding are purple. Predicted pairs not in the covariation model are illustrated with blue lines. Covariation pairs not in the SHAPE-aligned structure are shown using red lines. E. coli SHAPE reactivities are shown by coloring of individual nucleotides (see scale). Areas with large-scale SHAPE-supported alternative folds are emphasized with cyan boxes. These areas (cyan) are illustrated on a structure model of the 16S ribosome [38] (bottom right) and cluster in the neck and decoding site. The inset is shown with an orientation that allows both h36 and the decoding site (h28 and h44) to be seen clearly.