Figure 2. RNA binding and 3′-end recognition in the proximal site of Hfq. Left panels: Overview, with the protein as transparent surfaces (ring orientation as in Fig. 1D). Right panels: Zoom, with the protein as cartoon. (A) Dilated RNA conformation and an expelled 3′-end on SaHfq.²⁶ Hfq protomers are colored in white and gray and numbered clockwise for orientation. RNA is shown as sticks with a backbone cartoon that is colored with a gradient from light to dark blue to indicate the 5′-3′ direction. Nucleotides that reside in specific binding pockets are in red, the expelled terminal guanine is in dark blue. Dark blue spheres indicate conserved water molecules that, in the dilated conformation, contact the phosphates of the RNA backbone (hydrogen bonds dotted red). (B) Constricted RNA conformation on StHfq.²⁹ The constricted conformation allows the recognition of the 3′-end by H57 (residue and dotted hydrogen bond in lime). The conserved water molecules contact the ribose of the RNA backbone. (C) Mixed RNA conformation on EcHfq.³⁰ The irregular backbone alternates between the dilated and constricted conformations as illustrated by the contacts to the conserved waters. One of the uridines (dark blue) is expelled from its pocket, and another uridine (light blue) stabilizes the backbone conformation by a hydrogen bond (lime) to the last phosphate in the RNA chain. The 3′-hydroxyl group of the terminal adenine is recognized via a hydrogen bond to H57 (both in lime). The stabilizing Mg²⁺-ion and its coordination are also shown in lime, the remaining hydrogen bond network as dotted red lines.