The highly basic nature of the P-site loop, its interaction with peptidyl-tRNA, and its proximity to 25S rRNA Helix 84 (H84) suggested that it might interact with either of these two RNA components depending on the occupancy status of the P-site. Changes in interactions between the P-site loop and local rRNA structures may in turn propagate outward to more distant regions of the ribosome. To test this, SHAPE (41) (42) (43) was employed to probe for structural alterations in selected regions of the 25S, 18S and 5S rRNAs due to either the L11B mutants or in wild-type ribosomes with occupied or unoccupied P-sites. Due to the large size and complex three-dimensional structure of the ribosome, the entire rRNA content was not examined. Rather, approximately one-third of the rRNA bases were interrogated, focusing on those bases closest to L11, the A-and P-sites, and the decoding center.