3BRT

NEMO/IKK association domain structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of a NEMO/IKK-Associating Domain Reveals Architecture of the Interaction Site.

Rushe, M., Silvian, L., Bixler, S., Chen, L.L., Cheung, A., Bowes, S., Cuervo, H., Berkowitz, S., Zheng, T., Guckian, K., Pellegrini, M., Lugovskoy, A.

(2008) Structure 16: 798-808

  • DOI: 10.1016/j.str.2008.02.012
  • Primary Citation of Related Structures:  
    3BRT, 3BRV

  • PubMed Abstract: 

    • The phosphorylation of IkappaB by the IKK complex targets it for degradation and releases NF-kappaB for translocation into the nucleus to initiate the inflammatory response, cell proliferation, or cell differentiation. The IKK complex is composed of the catalytic IKKalpha/beta kinases and a regulatory protein, NF-kappaB essential modulator (NEMO; IKKgamma) ...

    The phosphorylation of IkappaB by the IKK complex targets it for degradation and releases NF-kappaB for translocation into the nucleus to initiate the inflammatory response, cell proliferation, or cell differentiation. The IKK complex is composed of the catalytic IKKalpha/beta kinases and a regulatory protein, NF-kappaB essential modulator (NEMO; IKKgamma). NEMO associates with the unphosphorylated IKK kinase C termini and activates the IKK complex's catalytic activity. However, detailed structural information about the NEMO/IKK interaction is lacking. In this study, we have identified the minimal requirements for NEMO and IKK kinase association using a variety of biophysical techniques and have solved two crystal structures of the minimal NEMO/IKK kinase associating domains. We demonstrate that the NEMO core domain is a dimer that binds two IKK fragments and identify energetic hot spots that can be exploited to inhibit IKK complex formation with a therapeutic agent.

    Organizational Affiliation: 

    Biogen Idec Inc., Cambridge, MA 02142, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inhibitor of nuclear factor kappa-B kinase subunit beta,Inhibitor of nuclear factor kappa-B kinase subunit alphaA, C47Homo sapiensMutation(s): 0 
Gene Names: IKBKB, IKKB
EC: 2.7.11.10 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15111 (Homo sapiens)
Explore O15111 
Go to UniProtKB:  O15111
PHAROS:  O15111
GTEx:  ENSG00000213341 
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 GroupsO14920O15111
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NF-kappa-B essential modulatorB, D68Homo sapiensMutation(s): 1 
Gene Names: IKBKG, FIP3, NEMO
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K9 (Homo sapiens)
Explore Q9Y6K9 
Go to UniProtKB:  Q9Y6K9
PHAROS:  Q9Y6K9
GTEx:  ENSG00000269335 
Entity Groups  
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UniProt GroupQ9Y6K9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.869α = 90
b = 105.556β = 90
c = 56.707γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-12-21 
  • Released Date: 2008-04-22 
    • Deposition Author(s): Silvian, L.F.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Advisory, Source and taxonomy
  • Version 1.3: 2021-10-20
    Changes: Advisory, Database references