5UI5

Crystal structure of Aquifex aeolicus sigmaN bound to promoter DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Aquifex aeolicus sigma (N) bound to promoter DNA and the structure of sigma (N)-holoenzyme.

Campbell, E.A.Kamath, S.Rajashankar, K.R.Wu, M.Darst, S.A.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E1805-E1814

  • DOI: 10.1073/pnas.1619464114
  • Primary Citation of Related Structures:  5UI8

  • PubMed Abstract: 
  • The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by spec ...

    The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σN fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σN The structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σN that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σN in blocking transcription activity and in maintaining the activator sensitivity of σN.


    Organizational Affiliation

    Laboratory for Molecular Biophysics, The Rockefeller University, New York, NY 10065.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoN
I, V
342Aquifex aeolicus (strain VF5)Gene Names: rpoN
Find proteins for O66858 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66858
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (31-MER)A,N31Aquifex aeolicus
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (30-MER)B,O31Aquifex aeolicus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.289 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 99.921α = 90.00
b = 99.921β = 90.00
c = 123.300γ = 120.00
Software Package:
Software NamePurpose
autoSHARPphasing
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1 R35 GM118130

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references
  • Version 1.2: 2017-03-22
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence