Fig. 5: Promoter escape and elongation complex formation during EcmrR-dependent transcription.

a Overall cryo-EM structure of RP_itc-5nt. The color schemes for Fig. 5a, b, d–f are the same as in Fig. 3. The 5’-end GTP in the nascent RNA transcript and three catalytic aspartate residues (β' D460, β' D462 and β' D464) in the polymerase active center are shown as sticks. The Mg²⁺ ions are shown as green spheres. Disordered nucleotides in the transcription bubble region are indicated as salmon and green circles for T-strand and NT-strand, respectively. b A close-up view of the 5-nt RNA transcript and σ_3.2 loop. The RNA 5’-end GTP and residues in the σ_3.2 loop acidic tip are shown as sticks. The σ_3.2 loop and RNA-DNA duplex are superimposed with their cryo-EM densities (blue surfaces) contoured at 4σ. c Comparison of the promoter DNA conformations in EcmrR-RP_itc-4nt and RP_itc-5nt. Disordered nucleotides in the transcription bubble region of RP_itc-5nt are indicated as violet filled circles. The −10 elements on NT-strands and −35 elements on T-strands in the two structures are highlighted and labeled. d Overall cryo-EM structure of RD_e1. e The 5’-end nucleotide (shown as sticks) of the 9-nt RNA transcript in RD_e structures reaches β' lid and is positioned at the entrance of RNA exit channel. f Overall cryo-EM structure of RD_e2. g Superimposition of RD_e2 with previously determined E. coli RD_e structure (PDB 6ALH).