PDBsum entry 5e18

Transcription/DNA/RNA

PDB id: 5e18

Contents

Protein chains

231 a.a.

1112 a.a.

1486 a.a.

94 a.a.

335 a.a.

DNA/RNA

Metals

_MG ×4

_ZN ×2

Waters ×26

References listed in PDB file

Key reference

• Title: Multiplexed protein-Dna cross-Linking: scrunching in transcription start site selection.
• Authors: J.T.Winkelman, I.O.Vvedenskaya, Y.Zhang, Y.Zhang, J.G.Bird, D.M.Taylor, R.L.Gourse, R.H.Ebright, B.E.Nickels.
• Ref.: Science, 2016, 351, 1090-1093. [DOI no: 10.1126/science.aad6881]
• PubMed id: 26941320

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.