3QA8 | pdb_00003qa8

Crystal Structure of inhibitor of kappa B kinase beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.344 (Depositor) 
  • R-Value Work: 
    0.308 (Depositor) 
  • R-Value Observed: 
    0.310 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3QA8

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of inhibitor of kappa B kinase beta.

Xu, G.Lo, Y.C.Li, Q.Napolitano, G.Wu, X.Jiang, X.Dreano, M.Karin, M.Wu, H.

(2011) Nature 472: 325-330

  • DOI: https://doi.org/10.1038/nature09853
  • Primary Citation Related Structures: 
    3QA8, 3RZF

  • PubMed Abstract: 

    Inhibitor of κB (IκB) kinase (IKK) phosphorylates IκB proteins, leading to their degradation and the liberation of nuclear factor κB for gene transcription. Here we report the crystal structure of IKKβ in complex with an inhibitor, at a resolution of 3.6 Å. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, α-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix-loop-helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with IκBα that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKKβ dimerization, but dimerization per se is not important for maintaining IKKβ activity and instead is required for IKKβ activation. Other IKK family members, IKKα, TBK1 and IKK-i, may have a similar trimodular architecture and function.


  • Organizational Affiliation
    • Department of Biochemistry, Weill Cornell Medical College, New York, New York 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 622.99 kDa 
  • Atom Count: 39,026 
  • Modeled Residue Count: 4,814 
  • Deposited Residue Count: 5,408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MGC80376 protein
A, B, C, D, E
A, B, C, D, E, F, G, H
676Xenopus laevisMutation(s): 2 
EC: 2.7.11.10
UniProt
Find proteins for Q6INT1 (Xenopus laevis)
Explore Q6INT1 
Go to UniProtKB:  Q6INT1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6INT1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.344 (Depositor) 
  • R-Value Work:  0.308 (Depositor) 
  • R-Value Observed: 0.310 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.17α = 71.28
b = 140.339β = 79.56
c = 161.167γ = 86.04
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-07-26
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Data collection