2V4H

NEMO CC2-LZ domain - 1D5 DARPin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Darpin-Assisted Crystallography of the Cc2-Lz Domain of Nemo Reveals a Coupling between Dimerization and Ubiquitin-Binding.

Grubisha, O.Kaminska, M.Duquerroy, S.Fontan, E.Cordier, F.Haouz, A.Raynal, B.Chiaravalli, J.Delepierre, M.Israel, A.Veron, M.Agou, F.

(2010) J.Mol.Biol. 395: 89

  • DOI: 10.1016/j.jmb.2009.10.018
  • Also Cited By: 4BWN

  • PubMed Abstract: 
  • NEMO is an integral part of the IkappaB kinase complex and serves as a molecular switch by which the NF-kappaB signaling pathway can be regulated. Oligomerization and polyubiquitin (poly-Ub) binding, mediated through the regulatory CC2-LZ domain, wer ...

    NEMO is an integral part of the IkappaB kinase complex and serves as a molecular switch by which the NF-kappaB signaling pathway can be regulated. Oligomerization and polyubiquitin (poly-Ub) binding, mediated through the regulatory CC2-LZ domain, were shown to be key features governing NEMO function, but the relationship between these two activities remains unclear. In this study, we solved the structure of this domain in complex with a designed ankyrin repeat protein, which helps its crystallization. We generated several NEMO mutants in this domain, including those associated with human diseases incontinentia pigmenti and immunodeficiency with or without anhidrotic ectodermal dysplasia. Analytical ultracentrifugation and thermal denaturation experiments were used to evaluate the dimerization properties of these mutants. A fluorescence-based assay was developed, as well, to quantify the interaction to monoubiquitin and poly-Ub chains. Moreover, the effect of these mutations was investigated for the full-length protein. We show that a proper folding of the ubiquitin-binding domain, termed NOA/UBAN/NUB, into a stable coiled-coil dimer is required but not sufficient for efficient interaction with poly-Ub. In addition, we show that binding to poly-Ub and, to a lesser extent, to monoubiquitin increases the stability of the NOA coiled-coil dimer. Collectively, these data provide structural insights into how several pathological mutations within and outside of the CC2-LZ's NOA ubiquitin binding site affect IkappaB kinase activation in the NF-kappaB signaling pathway.


    Related Citations: 
    • Inhibition of NF-kappaB Activation with Designed Ankyrin-Repeat Proteins Targeting the Ubiquitin-Binding/Oligomerization Domain of Nemo.
      Wyler, E.,Kaminska, M.,Coic, Y.,Baleux, F.,Veron, M.,Agou, F.
      (2007) Protein Sci. 16: 2013


    Organizational Affiliation

    Unité de Biochimie Structurale et Cellulaire, Institut Pasteur, CNRS, URA 2185, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NF-KAPPA-B ESSENTIAL MODULATOR
A, B
110Mus musculusGene Names: Ikbkg (Nemo)
Find proteins for O88522 (Mus musculus)
Go to UniProtKB:  O88522
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
1D5 DARPIN
C, D
136N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.020α = 90.00
b = 63.020β = 90.00
c = 436.917γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2016-12-21
    Type: Source and taxonomy, Structure summary