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. Author manuscript; available in PMC: 2022 Jul 15.
Published in final edited form as: Mol Cell. 2021 Jun 24;81(14):2875–2886.e5. doi: 10.1016/j.molcel.2021.05.017

Figure 2. Structures of Mtb CarD-RbpA-EσA-DNA complexes with and without WhiB7.

Figure 2.

A. Overall structures of W-RPo, W-RPc, and RPo on the whiB7 promoter. Core RNAP and RbpA are shown as transparent surfaces. CarD, WhiB7 and σA are rendered in cartoon and the DNAs are shown as molecular surfaces. Each feature is colored as labeled in the key on the bottom right. Middle inset, W-RPo (blue) aligned to W-RPc (colored by key) by WhiB7 to show that the disposition of WhiB7 to the β’ subunit is the same between structures.

B. Structure of RPo on the AP3 promoter (Boyaci et al., 2019a). The upstream DNA corresponding the AT-rich motif of the whiB7 promoter is colored yellow to emphasize the upstream DNA trajectory.

C. Alignment of σAD4 from structures in (A) and (B) shows the trajectories of the upstream DNA in the different structures. Left: The presence of WhiB7 stabilizes the DNA at least 14 bps upstream of the −35 element (pink and grey versus purple). Right: The upstream trajectory of the whiB7 promoter, in the presence of WhiB7, differs from that of RPo with the AP3 promoter (pale green); WhiB7 would clash with the upstream DNA of RPo with the AP3 promoter.