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), 0.299 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8OMV

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 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.

Macromolecule Content 

  • Total Structure Weight: 387.04 kDa 
  • Atom Count: 25,125 
  • Modeled Residue Count: 3,111 
  • Deposited Residue Count: 3,355 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.16 Å
  • R-Value Free:  0.299 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.258 (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