Figure 6. The σ⁷⁰ W-dyad and 6S RNA.

(A) View of cryoEM density (blue mesh) showing RNA nucleotide A131 (yellow) in a duplex RNA base stack passing over the σ⁷⁰ W-dyad (absolutely conserved W433/W434). The Trp side chains maintain their edge-on conformation characteristic of σ⁷⁰ alone (Malhotra et al., 1996) when not interacting with the double-strand/single-strand fork at the upstream edge of the transcription bubble (Bae et al., 2015).

(B) Comparison of 6S RNA (left) and promoter DNA (right) interacting with the absolutely conserved σ⁷⁰ W-dyad (σ⁷⁰ W433/W434). Shown is only the ‘nt-strand’ of the RNA or DNA. Corresponding nucleotides A131/U135 of 6S RNA or conserved A_-11/T_-7 of the promoter -10 element (Shultzaberger et al., 2007) are colored yellow. In both the RNA and DNA complexes, U135/T_-7 is single-stranded and interacting with a pocket of σ⁷⁰ (Feklistov and Darst, 2011). In the promoter DNA structure, the critical A_-11 nucleotide is flipped out of the duplex base stack and σ⁷⁰-W433 takes its place, forming a ‘chair’ conformation with W434 to stabilize the upstream edge of the newly formed transcription bubble (Bae et al., 2015). A131 remains in the base stack and the W-dyad maintains the edge-on conformation characteristic of σ⁷⁰ alone (Feklistov and Darst, 2011). The 6S RNA is pre-melted (Figure 1A) and thus this interaction is dispensable.

See also Figure S6.