2V4H

NEMO CC2-LZ domain - 1D5 DARPin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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
  • Primary Citation of Related Structures:  
    2V4H

  • 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, were shown to be key features governing NEMO function, but the relationship between these two activities remains unclear ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NF-KAPPA-B ESSENTIAL MODULATORA, B110Mus musculusMutation(s): 0 
Gene Names: IkbkgNemo
UniProt
Find proteins for O88522 (Mus musculus)
Explore O88522 
Go to UniProtKB:  O88522
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
1D5 DARPINC, D136synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.02α = 90
b = 63.02β = 90
c = 436.917γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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