SNAP output for PDB entry 5vt0 [SNAP web server]

PDB-id

5vt0; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-RNA

Method

cryo-EM (3.78 Å)

Summary

Escherichia coli 6s RNA derivative in complex with escherichia coli RNA polymerase sigma70-holoenzyme

Reference

Chen J, Wassarman KM, Feng S, Leon K, Feklistov A, Winkelman JT, Li Z, Walz T, Campbell EA, Darst SA (2017): "6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase." Mol. Cell, 68, 388-397.e6. doi: 10.1016/j.molcel.2017.09.006.

Abstract

Noncoding RNAs (ncRNAs) regulate gene expression in all organisms. Bacterial 6S RNAs globally regulate transcription by binding RNA polymerase (RNAP) holoenzyme and competing with promoter DNA. Escherichia coli (Eco) 6S RNA interacts specifically with the housekeeping σ₇₀-holoenzyme (Eσ₇₀) and plays a key role in the transcriptional reprogramming upon shifts between exponential and stationary phase. Inhibition is relieved upon 6S RNA-templated RNA synthesis. We report here the 3.8 Å resolution structure of a complex between 6S RNA and Eσ₇₀ determined by single-particle cryo-electron microscopy and validation of the structure using footprinting and crosslinking approaches. Duplex RNA segments have A-form C3' endo sugar puckers but widened major groove widths, giving the RNA an overall architecture that mimics B-form promoter DNA. Our results help explain the specificity of Eco 6S RNA for Eσ₇₀ and show how an ncRNA can mimic B-form DNA to directly regulate transcription by the DNA-dependent RNAP.