Volume 3, Issue 4, Pages 487-493 (April 1999) The Structural Basis for Terminator Recognition by the Rho Transcription Termination Factor  Cynthia E. Bogden, Deborah Fass, Nick Bergman, Matthew D. Nichols, James M. Berger  Molecular Cell  Volume 3, Issue 4, Pages 487-493 (April 1999) DOI: 10.1016/S1097-2765(00)80476-1

Figure 1 Structure of Rho13N Bound to RNA (a) Experimental electron density map superposed on a ball-and-stick model of the refined RNA. The map was generated using phases from the 3-fold-averaged poly-serine molecular replacement solution and the observed structure factors. Gold contours are at 1.0 σ and cyan at 2.5 σ. (b) Refined 2Fo − Fc, model-phased map of the same region. Gold contours are at 1.3 σ. (c) Front view of the secondary structure of Rho13N monomer (green) shown with bound oligoribocytidine (ball-and-stick) in the OB-fold cleft. The cleft is formed on the surface of strands β2 and β3, with the β1–β2 and β4–β5 loops forming parts of the lower and upper walls, respectively. Helices and strands are labeled. (d) View as in (c), rotated 90° about the vertical axis ([a] and [b] generated by BOBSCRIPT and RASTER3D [Merritt and Murphy 1994; Esnouf 1997]; (c) and (d) generated by RIBBONS [Carson 1991]). Molecular Cell 1999 3, 487-493DOI: (10.1016/S1097-2765(00)80476-1)

Figure 2 Specific Interactions of Rho13N with Its Target RNA (a) The RNA moiety (blue sticks) is shown on a surface representation of the Rho13N C-terminal subdomain. The Cα path of Rho13N is marked by a gold coil, while residues and atoms that interact directly with the RNA are colored black and labeled. (b) Stereo view of the environment around the first RNA cytosine. A Van der Waals dot surface is drawn about the protein atoms. Hydrogen bonds are indicated by dashed lines. (c) Stereo view of the Watson/Crick-like recognition of the hydrogen bond donor/acceptor groups of the second RNA cytosine by Arg-66 and Asp-78; the cytidine base stacks on the ring of Phe-64. The orientation of these side chains with respect to the cytosine base is tilted slightly, analogous to a “propeller twist.” (d) Stereo view of a DNA C·G base pair (from PDB accession number 126D [Goodsell et al. 1993]); the cytosine base is stacked on the ring of a second cytosine (figure generated by RIBBONS [Carson 1991]). Molecular Cell 1999 3, 487-493DOI: (10.1016/S1097-2765(00)80476-1)

Figure 3 Binding of a Single RNA by Two Rho13N Protomers (a) View of two Rho13N molecules complexed to rC9 as packed in the crystal lattice. The two molecules are separated by a single base spacer. (b) Hypothetical reorientation of the two protomers seen in (a), generated by rotating one protomer and bound ligand about the free phosphodiester bond of the spacer nucleotide. (c) View as in (b), rotated 90° about the horizontal axis. Molecular Cell 1999 3, 487-493DOI: (10.1016/S1097-2765(00)80476-1)

Figure 4 Model for Rho Function Rho protein is a symmetric molecule with six low-activity (a6) ATP-binding sites (1). Pairing of N-terminal domains on closely spaced sites within the terminator RNA converts the hexamer to a “trimer of dimers” (Aa)3 state, “priming” three ATP-binding sites (decreasing Km) for ATP (2). Upon binding of RNA in the secondary site of Rho (shown here in the interior of the C-terminal ATPase domains, by analogy to other hexameric helicases [Egelman et al. 1995; Richardson 1996; Yu et al. 1996a]), the primed ATP-binding sites become active (A*), vmax increases, and turnover ensues (3). Note that the suggestion of three different ATP-binding states is not unlike that already observed in the F1 ATPase (Abrahams et al. 1994). The combination of primary sites, secondary sites, and spacer regions is expected to include the 70–80 nucleotides bound by the enzyme (Bear et al. 1988). Rho may remain tethered to the primary RNA-binding sites throughout the termination event while tracking via the secondary RNA interactions to the site of the paused polymerase (Faus and Richardson 1990; Steinmetz and Platt 1994). As it is yet unclear how the RNA may enter the interior of the molecule, two possibilities are shown. The direction of movement of the RNA into the molecule via secondary site interactions is indicated by a small green arrow in both cases. Molecular Cell 1999 3, 487-493DOI: (10.1016/S1097-2765(00)80476-1)