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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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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: https://doi.org/10.1016/j.cell.2011.10.041
  • Primary Citation of Related Structures:  
    3UGO, 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 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


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor245Thermus aquaticusMutation(s): 0 
Find proteins for Q9EZJ8 (Thermus aquaticus)
Explore Q9EZJ8 
Go to UniProtKB:  Q9EZJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EZJ8
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
B, C
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.134α = 90
b = 86.134β = 90
c = 111.728γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-03-07
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description