(A) (Left) Overall view of RPo structure (similar to Figure 1B). The boxed area is magnified on the right. (Right) Magnified view showing the upstream ds/ss junction of the transcription bubble in RPo (the RNAP β subunit, which obscures the view, has been removed). RNAP is shown as a molecular surface, except side chains of key σA residues (R217, R220, W256, R288, R291) are shown (orange). The orthogonal directions of the ss nt- and t-strand DNA following the upstream ds/ss junction are denoted by black arrows. The dashed, curved line denotes the potential path of the t-strand −11 base from its position in the duplex DNA (base-paired to A−11(nt)) to its position in the structure. (B) Structure of Taq bound to the ss, nt-strand −10 element (PDB ID 3UGO) (Feklistov and Darst, 2011) showing the disposition of the universally conserved σA W-dyad (Taq σA W256/W257). Shown is the ss DNA from −14 to −7 (−10 element colored yellow), the (light orange) and the W-dyad (orange side chains with transparent CPK atoms). W256 makes an edge-on interaction with the face of W257, as observed in all other σ70/σA structures in many different contexts (Malhotra et al., 1996; Campbell et al., 2002; Vassylyev et al., 2002; Murakami et al., 2002a, 2002b; Feklistov and Darst, 2011; Zhang et al., 2012). (C) Disposition of the W-dyad in RPo (containing upstream ds/ss junction, shown schematically above). Only the nt-strand DNA from −14 to −7, the , and the W-dyad are shown (as in B). (D) Same view as (C). Superimposed is the simulated annealing omit map (grey mesh, 2Fo − Fc, contoured at 1σ), calculated from a model where the following segments of σA were completely removed (216–221, 255–258, and 287–292) and shown only within 2 Å of omitted atoms. (E) Similar view as (A) (right). Superimposed is the simulated annealing omit map (grey mesh, 2Fo − Fc, contoured at 1σ), calculated from a model where the following segments of σA were removed (216–221, 255–258, and 287–292) and shown only within 2 Å of omitted atoms. Clear Fourier density for σA Y217 and R288 is shown.