Cooperative DNA binding by two RelA dimers

  • Classification: TRANSCRIPTION/DNA
  • Organism(s): Mus musculus, Synthesium
  • Mutation(s): No 

  • Deposited: 2016-11-22 Released: 2017-09-27 
  • Deposition Author(s): Ghosh, G., Huang, D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1074/jbc.M117.813980
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The nuclear factor κB (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. Because 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 the solution-binding pattern of RelA-RHR. Remarkably, full-length RelA bound all DNAs with a weaker affinity and specificity. Moreover, the transactivation domain played a negative role in DNA binding. These observations suggest that other nuclear factors influence full-length RelA binding to DNA by neutralizing the transactivation domain negative effect. We propose that DNA binding by NF-κB dimers is highly complex and modulated by facilitated association-dissociation processes.

  • Organizational Affiliation

    From the Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 and.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor p65
A, B, C, D
273Mus musculusMutation(s): 0 
Find proteins for Q04207 (Mus musculus)
Explore Q04207 
Go to UniProtKB:  Q04207
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04207
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (27-MER)E [auth F],
F [auth E]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.91α = 90
b = 117.8β = 91.2
c = 70.81γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM 085490

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description