Fig. 3: Structures of EcmrR-RNAP-promoter initial transcribing complexes.
From: Structural visualization of transcription activated by a multidrug-sensing MerR family regulator
a Schematics of synthetic promoter DNA scaffolds and de novo synthesized RNA transcripts in EcmrR-RPitc-3nt. The two halves of the palindromic sequence recognized by EcmrR dimer are highlighted by medium blue and orange arrows, respectively. The transcription start site is indicated by a curved arrow. NT-strand, non-template strand; T-strand, template strand. b Schematics of synthetic promoter DNA scaffolds and de novo synthesized RNA transcripts in EcmrR-RPitc-4nt. c Overall cryo-EM structure of EcmrR-RPitc-3nt. 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. d Overall cryo-EM structure of EcmrR-RPitc-4nt. e Superimposition of RNA-DNA hybrid duplex and σ3.2 loop in EcmrR-RPitc-3nt (forest green) and EcmrR-RPitc-4nt (medium blue) illustrates the slight uplift of σ3.2 loop to avoid steric clashes when the length of RNA transcript reaches 4 nt.
