Figure 2. Translocation loop/RNA interactions.

(A) The Rho Q loops (left) and E1 β-hairpin loops (right) bind the nucleic acid backbone in a spiral staircase configuration. Both sets of nucleic acid binding loops are structured in a manner suggesting that they pull (arrows), rather than push, on the substrate to achieve a particular translocation polarity (5’→3’ for Rho vs. 3’→5’ for E1). The Rho Q loops for subunits A–E are shown (see key color key, panel B); subunit F, which does not contact the RNA, is removed for clarity. The E1 loops are colored similarly to those in Rho based on their position in the staircase. Nucleic acids are colored orange and illustrated as sticks on a cartoon backbone. The orientation of the Rho hexamer is similar to that shown in Figure 1B.

(B) The Rho R loops form a spiral staircase that engages the RNA phosphates. The R loops for all six subunit are colored (see key). The 5’ end of the RNA (orange and red sticks) projects out, toward the viewer. The side-chains of K326 (sticks), project into the center of the ring and interact with the RNA phosphate groups.

(C) Specific RNA contacts with the Q and R loops of subunits B and C (see color key, panel B). Backbone atoms and side-chains for the RNA-binding residues are shown as sticks. Dashed lines indicate hydrogen-bonds or salt bridges.