Extended Data Fig. 8: GTP bound in de novo transcription initiation complex; anti-scrunched template strand in the TC-empty complex.
From: Molecular insight into 5′ RNA capping with NpnNs by bacterial RNA polymerase
a, AS structure of de novo transcription initiation, where GTP binds canonically in the i site and CMPcPP is bound in a pre-insertion position in the i + 1 site, consistent with the trigger loop being only partially closed towards the AS. The DNA template strand is marked with respect to the +1 TSS site. The aspartate triad of the AS coordinates MgA and partially also MgB. Conserved residues are positioning the GTP phosphates, which themselves coordinate an additional MgC ion. b, Cryo-EM density for the GTP in the i site (transparent gray), base pairing with the template +1 C (transparent blue). c, When the AS is unoccupied, the template strand is antiscrunched by one nucleotide in respect to when the AS is occupied by GTP and CMPcPP (panel a). The template −2 G base is in line with the i − 1 site, the template −1 T base is in line with the i site and the template +1 C base is in line with the i + 1 site. The +2 G base is shifted over the bridge helix towards the downstream DNA duplex.
