3UGO

Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TACAAT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.096 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit.

Feklistov, A.Darst, S.A.

(2011) Cell 147: 1257-1269

  • DOI: 10.1016/j.cell.2011.10.041
  • Primary Citation of Related Structures:  3UGP

  • PubMed Abstract: 
  • The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA ...

    The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA bearing-10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A(-11) and T(-7), which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by σ. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.


    Organizational Affiliation

    The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. afeklistov@rockefeller.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor
A
245Thermus aquaticusGene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Go to UniProtKB:  Q9EZJ8
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*AP*CP*AP*AP*TP*GP*GP*G)-3'B,C11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.096 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: P 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.134α = 90.00
b = 86.134β = 90.00
c = 111.728γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
CBASSdata collection
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-03-07
    Type: Database references