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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphate regulon transcriptional regulatory protein phoB
A, B, E, F, I, J, M, N, R, S, V, W, Z, 1, 4, 5, 8, 9, c, d, g, h, k, l
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: phoB
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFJ5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta
o, q
99Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD), rpoD (alt)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Entity ID: 2
MoleculeChainsLengthOrganism
PHO BOX DNA (STRAND 1)C,G,K,O,T,X,2,6,a,e,i,m26Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
PHO BOX DNA (STRAND 2)D,H,L,P,U,Y,3,7,b,f,j,n26Escherichia coli
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 = 277.300α = 90.00
b = 161.400β = 91.40
c = 260.100γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHELXSphasing
DNAdata collection
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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