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

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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factorA245Thermus aquaticusMutation(s): 0 
Gene Names: sigA
Find proteins for Q9EZJ8 (Thermus aquaticus)
Explore Q9EZJ8 
Go to UniProtKB:  Q9EZJ8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    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 CCD File 
    B, C
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • 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
    PHASERphasing
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

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