SNAP output for PDB entry 5e18 [SNAP web server]

PDB-id

5e18; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA-RNA

Method

X-ray (3.3 Å)

Summary

T. thermophilus transcription initiation complex having a yyy discriminator sequence and a nontemplate-strand length corresponding to tss selection at position 8 (rpo-ccc-8)

Reference

Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE (2016): "Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection." Science, 351, 1090-1093. doi: 10.1126/science.aad6881.

Abstract

In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.