SNAP output for PDB entry 6bjs [SNAP web server]

PDB-id

6bjs; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA-RNA

Method

cryo-EM (5.5 Å)

Summary

Cryoem structure of e.coli his pause elongation complex without pause hairpin

Reference

Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R (2018): "RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing." Mol. Cell, 69, 802-815.e1. doi: 10.1016/j.molcel.2018.01.018.

Abstract

Sequence-specific pausing by RNA polymerase (RNAP) during transcription plays crucial and diverse roles in gene expression. In bacteria, RNA structures are thought to fold within the RNA exit channel of the RNAP and can increase pause lifetimes significantly. The biophysical mechanism of pausing is uncertain. We used single-particle cryo-EM to determine structures of paused complexes, including a 3.8-Å structure of an RNA hairpin-stabilized, paused RNAP that coordinates RNA folding in the his operon attenuation control region of E. coli. The structures revealed a half-translocated pause state (RNA post-translocated, DNA pre-translocated) that can explain transcriptional pausing and a global conformational change of RNAP that allosterically inhibits trigger loop folding and can explain pause hairpin action. Pause hairpin interactions with the RNAP RNA exit channel suggest how RNAP guides the formation of nascent RNA structures.