Fig. 2: Cryo-EM structures capture translocation and remodeling of σN-RI by the bEBP. | Nature Communications

Fig. 2: Cryo-EM structures capture translocation and remodeling of σN-RI by the bEBP.

From: Real-time capture of σN transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding

Fig. 2

a Overview of the merged, unsharpened cryo-EM map of the “open” ring state. Map density is colored according to the location of subunits, non-template (nt) and template (t) strands. The extent of visible map density for the DNA duplex is indicated by the colored letters at the top. b Helix 1 (H1) of σN-RI exhibits three turns in RPem (left) and RPem-bEBPADP-AlFx (middle), but a full turn is unfolded in the RPi1 intermediate (right). Residue P17 (red) located at the N-terminal end of H1 in RPem serves as visual indicator of helix changes. Regulatory interactions between σN-RI and the ELH remain intact (dotted circle; residues in magenta are mutation sites for bypass variants). Bases corresponding to the −11 position in dhsU are colored in yellow. c Comparison of the σN-RI:bEBP interaction between RPem- bEBPADP-AlFx (left) and RPi1 (right), illustrating the translocation of σN-RI by two residues. Every second residue in σN-RI starting with M1 up to Q11 is highlighted in red. M1 was not modeled for the open and closed ring structures.

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