5U01

Cooperative DNA binding by two RelA dimers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor kappa B are not correlated.

Mulero, M.C.Huang, D.B.Nguyen, H.T.Wang, V.Y.Li, Y.Biswas, T.Ghosh, G.

(2017) J. Biol. Chem. 292: 18821-18830

  • DOI: 10.1074/jbc.M117.813980

  • PubMed Abstract: 
  • The nuclear factor kappa B (NF-κB) transcription factor family regulates genes involved in cell proliferation and inflammation. The promoters of these genes often contain NF-κB binding sites (κB sites) arranged in tandem. How NF-κB activates transcri ...

    The nuclear factor kappa B (NF-κB) transcription factor family regulates genes involved in cell proliferation and inflammation. The promoters of these genes often contain NF-κB binding sites (κB sites) arranged in tandem. How NF-κB activates transcription through these multiple sites is incompletely understood. We report here an X-ray crystal structure of homodimers comprising the RelA DNA binding domain containing the Rel homology region (RHR) in NF-κB bound to an E-selectin promoter fragment with tandem κB sites. This structure revealed that two dimers bind asymmetrically to the symmetrically arranged κB sites at which multiple cognate contacts between one dimer to the corresponding DNA are broken. Since simultaneous RelA RHR dimer binding to tandem sites in solution was anti-cooperative, we inferred that asymmetric RelA RHR binding with fewer contacts likely indicates a dissociative binding mode. We found that both κB sites are essential for reporter gene activation by full-length RelA homodimer, suggesting that dimers facilitate DNA binding to each other even though their stable co-occupation is not promoted. Promoter variants with altered spacing and orientation of tandem κB sites displayed unexpected reporter activities that were not explained by solution-binding pattern of RelA RHR. Remarkably, full-length RelA bound all DNAs with a weaker affinity and specificity. Moreover, the transactivation domain (AD) played a negative role in DNA binding. These observations suggest that other nuclear factors influence full-length RelA binding to DNA by neutralizing AD negative effect. We propose that DNA binding by NF-κB dimers is highly complex and modulated by facilitated association-dissociation processes.


    Organizational Affiliation

    University of California San Diego, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor p65
A, B, C, D
273Mus musculusGene Names: Rela (Nfkb3)
Find proteins for Q04207 (Mus musculus)
Go to UniProtKB:  Q04207
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (27-MER)F,E27Synthesium
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.910α = 90.00
b = 117.800β = 91.20
c = 70.810γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-11-22 
  • Released Date: 2017-09-27 
  • Deposition Author(s): Ghosh, G., Huang, D.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM 085490

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Database references