Fig. 2: Ap3G and Ap4G bound in de novo transcription initiation complexes.
From: Molecular insight into 5′ RNA capping with NpnNs by bacterial RNA polymerase
a, AS structure of de novo transcription initiation, where Ap3G guanine binds canonically in the i site and adenine binds noncanonically in the i − 1 site. CMPcPP is bound in a preinsertion position in the i + 1 site, stabilized by partially closed trigger loop. The DNA template strand is marked with respect to the putative +1 TSS site. The aspartate triad of the AS coordinates MgA. Conserved residues β/K838 and K846 reach toward the Ap3G α phosphate, β/H999 reaches toward the Ap3G β phosphate, β/Q567 reaches toward the Ap3G γ phosphate and β/Y998 points away from Ap3G. The distal adenine base pair with −1T is sandwiched between the i site base pair and −2G. Color coding as in Fig. 1. b, Cryo-EM density for Ap3G (gray) and template (blue). The proximal guanine base in the i site WC base pairs with template +1C. The distal adenine base in the i − 1 site rWC base pairs with template −1T. c, AS structure of de novo transcription initiation, where Ap4G guanine binds canonically in the i site and adenine binds noncanonically in the i − 1 site. The depiction is analogous to a. β′/D739 coordinates both MgA and MgB. Conserved residues β/K838 and K846 reach toward the Ap4G α phosphate, whereas conserved residues β/Q567 and β/H999 reach toward the Ap4G γ and δ phosphates; β/Y998 points toward the Ap4G δ phosphate. d, Cryo-EM density for Ap4G (gray) and template (blue). The proximal guanine base in the i site WC base pairs with template +1C. The cryo-EM density for the distal part of Ap4G is less well defined. The adenine base in the i − 1 site rWC base pairs with template −1T.
