Fig. 5

Recognition by Mtb σ^L of σ^L-promoter -10 element: interactions with nontemplate strand positions “-12” through “-7”. For each promoter position, left subpanel shows DNA nucleotides in stick representation to highlight individual protein-nucleotide interactions, and right subpanel shows DNA nucleotide base moieties in space-filling representation to highlight protein-base steric complementarity. Yellow surfaces, solvent-accessible surfaces of Mtb σ^L σR2; gray surfaces, solvent-accessible surfaces of Mtb RNAP β subunit; dark blue surfaces, van der Waals surfaces of bases of σ^L-promoter -10 element; yellow ribbons, Mtb σ^L σR2 backbone; gray ribbons, Mtb RNAP β subunit backbone; yellow, yellow-blue, and yellow-red stick representations, σ^L carbon, nitrogen, and oxygen atoms, respectively; white, blue, red, and orange stick representations, DNA carbon, nitrogen, oxygen, and phosphorous atoms, respectively; blue dashed lines, H-bonds. Residues are numbered as in Mtb RNAP and σ^L, and, in parentheses, as in E. coli RNAP and σ⁷⁰. See Supplementary Fig. 4