L11 mutants promote local and distant changes in rRNA structure. (A) 1M7 SHAPE modification of wild-type and mutant salt washed ribosomes show opposite effects of solvent accessibility on H84 bases C2675-A2679 in mutants 51-4A and 54-7A relative to wild type. DMSO lanes are unmodified controls. Sequencing ladder is shown to the left. (B) PyMol generated image of H84′s protected/deprotected bases (black with gray surface) in mutants 51-4A and 54-7A respectively, for salt-washed empty ribosomes. P-site tRNA is added for reference. Blue spheres mark amino acids changed to alanines in 51-4A, red for 54-7A, purple is mutated in both. (C) Changes in H84 accessibility upon binding of P-site tRNA. Ac-Phe-tRNA^Phe was pre-bound to salt washed ribosomes along with poly(U) and complexes were probed with 1M7 or DMSO controls. In both wild type and 54-7A base C2675 became more deprotected with tRNA bound to the P-site while bases A2676-A2679 show increased protection. 51-4A’s level of protection is unchanged. (D) Differences observed, in both treated and untreated lanes, of natural stops between wild-type and mutant strains in the terminal loop of 25S rRNA Helix 88 (A2779, A2780), and in Expansion Segment 31 (G2531, G2534). (E) Two-dimensional structure of yeast 25S rRNA showing locations of bases showing changes in reactivity. H84 gray highlighted bases protected/deprotected relative to wild-type in empty salt-washed ribosomes in the 51-4A and 54-7A mutants, respectively. Open circled bases indicate sites of decreased innate lability (C2531, G2534) in ES31 for both 51-4A and 54-7A, or increased natural lability (A2779-A2780) in H88 for the 51-4A mutant.