crystal structure of the C-terminal domain of p100/NF-kB2

Experimental Data Snapshot

  • Resolution: 3.35 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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p100/I kappa B delta sequesters and inhibits NF-kappa B through kappaBsome formation.

Tao, Z.Fusco, A.Huang, D.B.Gupta, K.Young Kim, D.Ware, C.F.Van Duyne, G.D.Ghosh, G.

(2014) Proc Natl Acad Sci U S A 111: 15946-15951

  • DOI: https://doi.org/10.1073/pnas.1408552111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Degradation of I kappaB (κB) inhibitors is critical to activation of dimeric transcription factors of the NF-κB family. There are two types of IκB inhibitors: the prototypical IκBs (IκBα, IκBβ, and IκBε), which form low-molecular-weight (MW) IκB:NF-κB complexes that are highly stable, and the precursor IκBs (p105/IκBγ and p100/IκBδ), which form high-MW assemblies, thereby suppressing the activity of nearly half the cellular NF-κB [Savinova OV, Hoffmann A, Ghosh G (2009) Mol Cell 34(5):591-602]. The identity of these larger assemblies and their distinct roles in NF-κB inhibition are unknown. Using the X-ray crystal structure of the C-terminal domain of p100/IκBδ and functional analysis of structure-guided mutants, we show that p100/IκBδ forms high-MW (IκBδ)4:(NF-κB)4 complexes, referred to as kappaBsomes. These IκBδ-centric "kappaBsomes" are distinct from the 2:2 complexes formed by IκBγ. The stability of the IκBδ tetramer is enhanced upon association with NF-κB, and hence the high-MW assembly is essential for NF-κB inhibition. Furthermore, weakening of the IκBδ tetramer impairs both its association with NF-κB subunits and stimulus-dependent processing into p52. The unique ability of p100/IκBδ to stably interact with all NF-κB subunits by forming kappaBsomes demonstrates its importance in sequestering NF-κB subunits and releasing them as dictated by specific stimuli for developmental programs.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear factor NF-kappa-B p100 subunit359Homo sapiensMutation(s): 0 
Gene Names: NFKB2LYT10
UniProt & NIH Common Fund Data Resources
Find proteins for Q00653 (Homo sapiens)
Explore Q00653 
Go to UniProtKB:  Q00653
PHAROS:  Q00653
GTEx:  ENSG00000077150 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00653
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.35 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.67α = 90
b = 196.67β = 90
c = 68.46γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations