8OMV | pdb_00008omv

Crystal structure of the constitutively active S117E/S181E mutant of human IKK2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.16 Å
  • R-Value Free: 
    0.299 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of IKK catalytic dimer docking to NF-kappa B substrates.

Li, C.Moro, S.Shostak, K.O'Reilly, F.J.Donzeau, M.Graziadei, A.McEwen, A.G.Desplancq, D.Poussin-Courmontagne, P.Bachelart, T.Fiskin, M.Berrodier, N.Pichard, S.Brillet, K.Orfanoudakis, G.Poterszman, A.Torbeev, V.Rappsilber, J.Davey, N.E.Chariot, A.Zanier, K.

(2024) Nat Commun 15: 7692-7692

  • DOI: https://doi.org/10.1038/s41467-024-52076-0
  • Primary Citation of Related Structures:  
    8OMV

  • PubMed Abstract: 

    The inhibitor of κB (IκB) kinase (IKK) is a central regulator of NF-κB signaling. All IKK complexes contain hetero- or homodimers of the catalytic IKKβ and/or IKKα subunits. Here, we identify a YDDΦxΦ motif, which is conserved in substrates of canonical (IκBα, IκBβ) and alternative (p100) NF-κB pathways, and which mediates docking to catalytic IKK dimers. We demonstrate a quantitative correlation between docking affinity and IKK activity related to IκBα phosphorylation/degradation. Furthermore, we show that phosphorylation of the motif's conserved tyrosine, an event previously reported to promote IκBα accumulation and inhibition of NF-κB gene expression, suppresses the docking interaction. Results from integrated structural analyzes indicate that the motif binds to a groove at the IKK dimer interface. Consistently, suppression of IKK dimerization also abolishes IκBα substrate binding. Finally, we show that an optimized bivalent motif peptide inhibits NF-κB signaling. This work unveils a function for IKKα/β dimerization in substrate motif recognition.


  • Organizational Affiliation
    • Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor of nuclear factor kappa-B kinase subunit beta
A, B, C, D, E
671Homo sapiensMutation(s): 2 
Gene Names: IKBKBIKKB
EC: 2.7.11.10 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O14920 (Homo sapiens)
Explore O14920 
Go to UniProtKB:  O14920
PHAROS:  O14920
GTEx:  ENSG00000104365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14920
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.16 Å
  • R-Value Free:  0.299 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.293α = 90
b = 136.802β = 91.45
c = 204.358γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Instruct-ERIC Center (Strasbourg Centre)FrancePID: 11382
Agence Nationale de la Recherche (ANR)FranceANR-13-JSV8-0004-01
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references, Structure summary