Figure 3.

Details of the specific interactions between TFB_c and the BRE. (A) Stereo diagram of the residues involved in sequence-specific contacts between TFB_c and the major groove of the DNA in the BRE. (B) Schematized representation of the protein/DNA interactions in the complex. The red and green boxes represent residues from TBP and TFB_c, respectively, that contact the DNA. The approximate locations of the β-strands of TBP are shown as pink stripes. Hydrogen bonds are shown as dashed lines, salt bridges are solid lines, and van der Waals contacts are shown as a solid line with a bar at the end or by a plain box overlaying the DNA site. The DNA is represented with circles, pentagons, and rectangles for the phosphates, ribose moieties, and bases, respectively. (C) Superposition of the C-terminal cyclin domains of TFB_c from the current and previous TBP/TFB_c/DNA complexes with the DNA. The current structure is shown in the same color scheme as in Fig. 2 with the −5 and −6 bases displayed. The previous structure of the archaeal complex (20) is shown as purple and dark blue for TFB_c and the DNA, respectively, with the +5 and +6 bases displayed. The HTH structural motif is shown in vivid color, while the rest of the C-terminal cyclin domain of TFB_c is shown in faded color. The surface of the major groove clearly forms a closer and more extensive contact with TFB_c in the current structure. (D) A side view of the superposition shown in C. The DNAs are displayed as tubes running through the phosphate backbone. The DNA in the current structure can be seen bending up toward TFB_c, allowing the protein to contact more of the major groove. Figures were created with bobscript (28), molscript (32), and raster-3d (29).