5E18: 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)

Citation:
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.
PDB ID: 5E18Download
MMDB ID: 137270
PDB Deposition Date: 2015/9/29
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 3.3  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Biological Unit for 5E18: nonameric; determined by author and by software (PISA)
Molecular Components in 5E18
Label Count Molecule
Proteins (6 molecules)
2
DNA-directed RNA Polymerase Subunit Alpha
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta(Gene symbol: rpoB)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta'(Gene symbol: TTHA1812)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Omega(Gene symbol: rpoZ)
Molecule annotation
1
RNA Polymerase Sigma Factor Siga
Molecule annotation
Nucleotides(3 molecules)
1
DNA (5'-d(*cp*cp*t*gp*cp*ap*tp*cp*cp*gp*tp*gp*ap*gp*tp*cp*gp*ap*gp*gp*g)-3')
Molecule annotation
1
RNA (5'-r(*cp*cp*cp*up*cp*gp*a)-3')
Molecule annotation
1
DNA (28-mer)
Molecule annotation
Chemicals (6 molecules)
1
4
2
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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