3T72

PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription Activation Sub-Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.33 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The Structure of a Transcription Activation Sub-Complex Reveals How Sigma-70 is Recruited to PhoB Promoters

Blanco, A.G., Canals, A., Bernues, J., Sola, M., Coll, M.

(2011) EMBO J 

  • DOI: 10.1038/emboj.2011.271
  • Primary Citation of Related Structures:  
    3T72

  • PubMed Abstract: 

    • PhoB is a two-component response regulator that activates transcription by interacting with the σ(70) subunit of the E. coli RNA polymerase in promoters in which the -35 σ(70)-recognition element is replaced by the pho box. The crystal structure of a transcription initiation subcomplex that includes the σ(4) domain of σ(70) fused with the RNA polymerase β subunit flap tip helix, the PhoB effector domain and the pho box DNA reveals how σ(4) recognizes the upstream pho box repeat ...

    PhoB is a two-component response regulator that activates transcription by interacting with the σ(70) subunit of the E. coli RNA polymerase in promoters in which the -35 σ(70)-recognition element is replaced by the pho box. The crystal structure of a transcription initiation subcomplex that includes the σ(4) domain of σ(70) fused with the RNA polymerase β subunit flap tip helix, the PhoB effector domain and the pho box DNA reveals how σ(4) recognizes the upstream pho box repeat. As with the -35 element, σ(4) achieves this recognition through the N-terminal portion of its DNA recognition helix, but contact with the DNA major groove is less extensive. Unexpectedly, the same recognition helix contacts the transactivation loop and helices α2 and α3 of PhoB. This result shows a simple and elegant mechanism for polymerase recruitment to pho box promoters in which the lost -35 element contacts are compensated by new ones with the activator. In addition, σ(4) is reoriented, thereby suggesting a remodelling mechanism for transcription initiation.

    Organizational Affiliation: 

    Institute for Research in Biomedicine, Barcelona Science Park, Spain.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphate regulon transcriptional regulatory protein phoB102Escherichia coli K-12Mutation(s): 0 
Gene Names: phoB, b0399, JW0389
UniProt
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AFJ5
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit betaWA [auth o], XA [auth q]99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoD, alt, b3067, JW3039, EKO11_4334, rpoB
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
Go to UniProtKB:  P00579
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
PHO BOX DNA (STRAND 1)26Escherichia coli
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
PHO BOX DNA (STRAND 2)26Escherichia coli
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.33 Å
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 277.3α = 90
b = 161.4β = 91.4
c = 260.1γ = 90
Software Package:
Software NamePurpose
DNAdata collection
SHELXSphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Derived calculations
  • Version 1.2: 2013-12-18
    Changes: Structure summary
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy