Figure 2.

Overall view of the TBP/TFB_c/DNA complex. TBP is shown as a ribbon diagram with the N-terminal repeat colored red and the C-terminal repeat colored pink. TFB_c is shown as a ribbon diagram with the N-terminal cyclin repeat colored dark green and the C-terminal cyclin repeat colored green with the HTH highlighted in magenta. The DNA is shown as a stick drawing with the sense strand in cyan and the antisense strand in yellow. The TATA box is colored blue and orange. (A) View of the complex looking down the distorted double-helical axis of the TATA-box DNA. The upstream DNA is nearest the viewer. (B) View of the complex rotated from the orientation in A by 90° about the vertical axis. The arrow points in the direction of the start site of initiation. (C) View of the complex, highlighting the TFB_c/BRE interaction. (D) Stereo diagram of a (2F_o − F_c) electron-density map contoured at 1 rms deviation, showing contacts between TFB_c and the phosphate backbone of the BRE upstream of the TATA box. Red dots represent water molecules. (E) Same view as D with hydrogen bonds shown as dashed black lines. The phosphates are numbered with respect to the TATA-box sequence. Figures were created with bobscript (28) and raster-3d (29).