Fig. 4. DNA interaction with RNAP in the presence of TFEα.

a Close-up view of the DNA binding channel of the RNAP–TFEα–DNA complex is shown with the cryo-EM density map (yellow and transparent) of DNA. DNA is shown as a stick model (template DNA, dark green; non-template DNA, light green). Template DNA strand (tDNA), downstream double-stranded DNA (dDNA) and transcription start site (+1) are indicated. Mg²⁺ bound at the active site of RNAP and bridge helix (BH) are depicted. b The structures of the RNAP–TFEα binary (red) and the RNAP–TFEα–DNA ternary (green) complexes are superimposed. The conformational changes of the clamp and stalk by DNA positioning in the ternary complex are indicated. c Conformational change of TFEα upon RNAP binding DNA. The ZRD of TFEα was used as a reference to superimpose the RNAP and TFEα in the binary (color) and ternary complexes (light gray), revealing movement of the eWHD of TFEα together with the RNAP clamp indicated by an arrow. d Close-up view of the RNAP lobe and TFEα wing interaction. Amino acid residues involved in the RNAP lobe and TFEα wing interaction are depicted as stick models and indicated. Surface exposed aromatic residues (W75 and Y77) of TFEα involved in the DNA interaction are also indicated.