Fig. 7: Electron density of the AR9 nvRNAP-DNA interacting regions.

a, b Composite omit X-ray electron density and cryo-EM map of the promoter binding pocket with refined atomic models. The X-ray and cryo-EM maps are contoured at 1.5 and 5.0 std dev above the mean, respectively. The carbon atoms are colored as in Fig. 2a. V206, which is critical for U specificity, is colored cyan. c A fragment of composite omit X-ray electron density that is interpreted in terms of non-template strand nucleotides that are (fortuitously) partially complementary to the template strand promoter sequence. The X-ray map is contoured at 1.5 std dev above the mean. The carbon atoms are colored as in Fig. 2a. Residues Y246 and S245 that affect recognition of dsDNA template are colored forest green. d, e Composite omit X-ray electron density and cryo-EM map of gp226 CTD in the AR9 nvRNAP promoter complex. The cryo-EM and X-ray maps are contoured at 1.0 and 2.0 std dev above the mean, respectively. The ds segment of the downstream oligonucleotide belonging to a neighboring unit cell is shown in the X-ray map (see Supplementary Fig. 2c). The cryo-EM map of the upstream oligonucleotide is of insufficient quality for model building and its atomic model has been copied from the AR9 nvRNAP-Pro-Xray structure for illustration purposes only. Proteins are colored as in Fig. 2a. The pseudo-⁻³⁵element binding motif is colored light green.