Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 622.99 kDa 
• Atom Count: 39026 
• Residue Count: 4814 
• Unique protein chains: 1

3QA8

Crystal Structure of inhibitor of kappa B kinase beta

• DOI: 10.2210/pdb3QA8/pdb

• Classification: IMMUNE SYSTEM, SIGNALING PROTEIN
• Organism(s): Xenopus laevis
• Mutation(s): Yes 


• Deposited: 2011-01-10 Released: 2011-04-06 
• Deposition Author(s): Xu, G., Lo, Y.C., Li, Q., Napolitano, G., Wu, X., Jiang, X., Dreano, M., Karin, M., Wu, H.

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Experimental Data Snapshot

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

Literature

Crystal structure of inhibitor of kappaB kinase beta.

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

(2011) Nature 

• PubMed: 21423167 
• DOI: 10.1038/nature09853
• Primary Citation of Related Structures:  
  3RZF, 3QA8


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MGC80376 protein	A, B, C, D, E, F, G, H	676	Xenopus laevis	Mutation(s): 2  Gene Names: ikbkb.L, ikbkb, MGC80376 EC: 2.7.11.10
Find proteins for Q6INT1 (Xenopus laevis) Explore Q6INT1  Go to UniProtKB:  Q6INT1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.344 
• R-Value Work: 0.308 
• R-Value Observed: 0.310 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.17	α = 71.28
b = 140.339	β = 79.56
c = 161.167	γ = 86.04

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-10 
• Released Date: 2011-04-06 
Deposition Author(s): Xu, G., Lo, Y.C., Li, Q., Napolitano, G., Wu, X., Jiang, X., Dreano, M., Karin, M., Wu, H.

Revision History 

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance