Figure 3. WhiB7 stabilizes σ^AD4 contacts with the −35 promoter element.

A. The W-RPo and RPo structures were superimposed by aligning α-carbon positions of σ^A, the CarD-CTD, and the RbpA-linker (root-mean-square deviation of 0.535 Å over 417 α-carbon atoms). The resulting DNA structures closely superimposed. WhiB7 is shown in faded pink to increase the clarity of σ^AD4. The disordered and unmodeled regions of the transcription bubble are indicated by spheres.

B. The sharpened (blue mesh) and local-resolution filtered (gray transparent surface) cryo-EM maps are show for RPo (top) and W-RPo (bottom), with the structures superimposed. The view shows a zoom-in of the boxed area in (A), reoriented as shown. Cryo-EM density for σ^AD4 contacts with the −35 promoter region in RPo is weak in the sharpened map, and density in the local-resolution filtered map disappears about six base-pairs upstream of the −35 motif. Cryo-EM density for the σ^AD4 contacts with the −35 promoter region in W-RPo is well-resolved and better connected in both the sharpened (blue mesh) and local-resolution filtered (light grey surface) maps, and density extends well upstream of the AT-rich DNA bound by the WhiB7 AT-hook. Maps were normalized in PyMOL and contoured at 4σ.