5E17

T. thermophilus transcription initiation complex having a RRR discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 7 (RPo-GGG-7)

Summary for 5E17

• Entry DOI: 10.2210/pdb5e17/pdb
• Related: 5E18
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (11 entities in total)
• Functional Keywords: dna, single-stranded, dna-directed rna polymerases, gene expression regulation, bacterial, promoter regions, protein conformation, sigma factor, thermus thermophilus, transcription initiation, start site selection, promoter escape, initial transcript, abortive product, sigma finger, transcription-dna-rna complex, transcription/dna/rna
• Biological source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); More
• Cellular location: Cytoplasm : Q5SKW1
• Total number of polymer chains: 9
• Total formula weight: 446134.96

Authors

Zhang, Y.,Ebright, R.H. (deposition date: 2015-09-29, release date: 2016-03-09, Last modification date: 2024-11-20)

Primary citation

Winkelman, J.T.,Vvedenskaya, I.O.,Zhang, Y.,Zhang, Y.,Bird, J.G.,Taylor, D.M.,Gourse, R.L.,Ebright, R.H.,Nickels, B.E.
Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.
Science, 351:1090-1093, 2016

PubMed 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.

PubMed: 26941320
DOI: 10.1126/science.aad6881

Experimental method

X-RAY DIFFRACTION (3.2 Å)