Figure 6. Structural role of the σ_3.2-loop.

(Left) Overall view of RPo structure, colored as in Figure 1 except σ^A is orange. The RNAP β and β′ subunits are transparent to reveal the RNAP active site Mg²⁺ (yellow sphere) and the nucleic acids held inside the RNAP active site channel. The ss nt-strand DNA is omitted for clarity. The boxed area is magnified on the right. (Right) Magnified view showing a cross-section of the RNAP active site channel. For clarity, the RNAP β, β′, and ${\mathrm{\sigma }}_2^{\text{A}}$ domains are shown mostly as outlined shapes, with β transparent. The ss t-strand DNA (−11 to −4) is directed towards the RNAP active site through a tunnel between the σ_3.2-loop and the β1-lobe. The 4-nt RNA transcript (−3 to +1) contacts the distal tip of the σ_3.2-loop. Further elongation of the RNA would require displacement of the σ_3.2-loop.

DOI: http://dx.doi.org/10.7554/eLife.08504.017