SNAP output for PDB entry 5nsr [SNAP web server]

PDB-id

5nsr; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription

Method

cryo-EM (3.8 Å)

Summary

cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex

Reference

Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X (2017): "Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation." Mol. Cell, 67, 106-116.e4. doi: 10.1016/j.molcel.2017.05.010.

Abstract

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ₅₄ factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ₅₄ interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ₅₄ that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.