Fig. 6: 3D variability analysis of the RNAP–HelD complex and a model for HelD-catalysed RNAP recycling. | Nature Communications

Fig. 6: 3D variability analysis of the RNAP–HelD complex and a model for HelD-catalysed RNAP recycling.

From: Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

Fig. 6

a, b Different orientations of the most distinct conformations determined by 3DVA. HelD is shown in solid colours with RNAP semi-transparent. The red conformation of HelD is matched to the pale green conformation of RNAP, and the purple HelD with the yellow RNAP. Orange arrows indicate the movement of the juxtaposed region of HelD, and cyan arrows regions of RNAP. Structural elements of RNAP referred to in the text are labelled as well as the up- (UP) and downstream (DOWN) sides of RNAP. c Model for HelD-catalysed recycling. HelD is shown in red, RNAP in white, DNA in purple (template) and pink (non-template), and RNA in orange. Clockwise from top left; HelD locates a stalled EC and binds with the SCA penetrating the secondary channel and the CA moving into position on the β’ clamp. The SCA is wedged deep within RNAP, and through conserved interactions with the 1 A torso domain, locks HelD in position. The contacts the CA makes with the β’ clamp, open the DNA-binding and RNA-exit channels to enable dissociation of nucleic acids from the EC, possibly assisted by interaction of the DNA with the positively-charged patch on the CA of HelD. HelD (and nucleic acid) dissociation is facilitated by the conformational changes facilitated by ATP binding/hydrolysis (ATP flash). Finally, core RNAP that has been released from the complex is free to enter a fresh round of transcription.

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