Fig. 3. Locations of general transcription factors and promoter DNA in the PIC.
(A) The PIC structure, sectioned to reveal the DNA in the center (cut surfaces are gray). The structure on the left side of Fig. 1A was rotated 60° counterclockwise about the vertical axis (left) or 120° clockwise (right). Subunits of TFIIE and TFIIH (core TFIIH and its Rad3 component, Ssl2, and TFIIK) are indicated. Atomic models of the TBP (green)-TFIIBC(red)-TATA-box complex (15) and TFIIA (cyan) (32) were fitted to the cryo-EM density and displayed as ribbon diagrams. The TATA box DNA was extended with straight B-form DNA with minor adjustments of the DNA path. (B) The underside of the G-lobe, viewed from bottom of left panel of (A) with the P-lobe removed. Atomic models of the Tfg1-Tfg2 dimerization domain (Tfg1 blue; Tfg2 magenta) and the winged helix (WH) domain of Tfg2 (navy blue) were located by protein-protein cross-linking and displayed as ribbon diagrams. (C) Schematic diagram of proximity relationships of promoter DNA (gray) and GTFs in the PIC. Positions in the DNA are numbered with respect to the first transcription start site of the HIS4 promoter. The TATA box spans positions from −63 to −56. Transcription bubble formed upon initial promoter melting is indicated by dashed box. Putative interactions are indicated by red shading.