(A) View inside the RNAP active-site cleft where most of the β subunit has been removed (similar to Figure 2). The RNAP (β, light cyan; β’, light pink except the β’zipper, β’lid, and β’rudder are light magenta), Nun (green), and the na-scaffold (ntDNA, yellow; tDNA, dark grey; RNA, red) are shown in cartoon format except residues or nucleotides that interact with Nun are shown as CPK atoms. The RNAP active-site Mg2+-ion is shown as a yellow sphere. (B) Schematic illustrating in vivo action of Nun in the context of a λ nut TEC (carrying boxA and boxB RNA sequences) and Nus factors. The X-Nun/TEC structure determined here is contained within the dashed box (RNAP core, DNA template, Nun C-terminal segment). The N-terminal segment of Nun extends from the TEC, where the α-helical Nun-ARM interacts with the λ nut boxB RNA hairpin (Chattopadhyay et al., 1995; Faber et al., 2001), localizing Nun specifically to λ transcripts. Further upstream, the λ nut boxA RNA sequence interacts with NusB/E, and together with NusA/G stabilize the Nun/TEC complex and stimulate translocation arrest (Hung and Gottesman, 1995).