Fig. 6: Effects of Rof on ρ conformation.
a, b Structural comparison of ρ subunit interactions in structures of open ρ bound to ATP (PDB ID: 6WA8)42 (a) and closed ρ bound to rut RNA (b). In the open hexamer conformation, residue R28 from one ρ protomer (ρD) is embedded in a pocket of the adjacent protomer (ρC), formed partially by α5. In the closed hexamer conformation, R28 is ejected from that pocket and substituted by K130 of the same protomer (ρc). Concomitantly, contacts between the N-terminal region of ρD and R128 of ρC are broken during ring closure (ρb an ρc in the closed hexamer). Rotation symbols, view relative to Fig. 5c. c Comparison of the NTD-CTD connectors (sticks) in open ρATP (top), the closed ρ-rut RNA complex (middle) and the open ρ6-ADP-Rof5 complex (bottom). Relative to open ρATP, the NTD-CTD connector (residues 127–140) in the closed ρ-rut RNA complex is re-aligned by one residue, most evident by the rearrangement of H140 towards the protomer interface. In the open ρ6-ADP-Rof5 structure, the NTD-CTD connector retains the register observed in the closed ρ-rut RNA complex. Rotation symbols in this and (d) views are relative to Fig. 2b. d Structural comparison of Q-loop conformations in open ρATP (top), the closed ρ-rut RNA complex (middle) and the open ρ6-ADP-Rof5 complex (bottom). In open ρATP, Q-loops adopt a conformation resulting in residues K283 (sticks) pointing towards the central axis of the ρ hexamer, where they could engage in initial contacts to SBS RNA. In the closed ρ-rut RNA complex, K283 residues are embedded in pockets formed in part by the Q-loops of the adjacent ρ protomers. In the open ρ6-ADP-Rof5 complex, the Q-loops adopt a conformation similar to that observed in the closed ρ-rut RNA complex.
