NF-kappaB p65 subunit dimerization domain homodimer

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.221 

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Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/I kappaB alpha complex formation

Huxford, T.Mishler, D.Phelps, C.B.Huang, D.-B.Sengchanthalangsy, L.L.Reeves, R.Hughes, C.A.Komives, E.A.Ghosh, G.

(2002) J Mol Biol 324: 587-597

  • DOI: https://doi.org/10.1016/s0022-2836(02)01149-x
  • Primary Citation of Related Structures:  
    1MY5, 1MY7

  • PubMed Abstract: 

    IkappaBalpha inhibits transcription factor NF-kappaB activity by specific binding to NF-kappaB heterodimers composed of p65 and p50 subunits. It binds with slightly lower affinity to p65 homodimers and with significantly lower affinity to homodimers of p50. We have employed a structure-based mutagenesis approach coupled with protein-protein interaction assays to determine the source of this dimer selectivity exhibited by IkappaBalpha. Mutation of amino acid residues in IkappaBalpha that contact NF-kappaB only marginally affects complex binding affinity, indicating a lack of hot spots in NF-kappaB/IkappaBalpha complex formation. Conversion of the weak binding NF-kappaB p50 homodimer into a high affinity binding partner of IkappaBalpha requires transfer of both the NLS polypeptide and amino acid residues Asn202 and Ser203 from the NF-kappaB p65 subunit. Involvement of Asn202 and Ser203 in complex formation is surprising as these amino acid residues occupy solvent exposed positions at a distance of 20A from IkappaBalpha in the crystal structures. However, the same amino acid residue positions have been genetically isolated as determinants of binding specificity in a homologous system in Drosophila. X-ray crystallographic and solvent accessibility experiments suggest that these solvent-exposed amino acid residues contribute to NF-kappaB/IkappaBalpha complex formation by modulating the NF-kappaB p65 subunit NLS polypeptide.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at San Diego, Mail Code 0359, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NF-kappaB p65 (RelA) subunit
A, B
114Mus musculusMutation(s): 0 
Gene Names: RELA
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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.348α = 90
b = 74.732β = 90
c = 109.147γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Refinement description