4KIK

Human IkB kinase beta

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Literature

Crystal Structure of a Human I kappa B Kinase beta Asymmetric Dimer.

Liu, S., Misquitta, Y.R., Olland, A., Johnson, M.A., Kelleher, K.S., Kriz, R., Lin, L.L., Stahl, M., Mosyak, L.

(2013) J Biol Chem 288: 22758-22767

  • DOI: 10.1074/jbc.M113.482596
  • Primary Citation of Related Structures:  
    4KIK

  • PubMed Abstract: 

    • Phosphorylation of inhibitor of nuclear transcription factor κB (IκB) by IκB kinase (IKK) triggers the degradation of IκB and migration of cytoplasmic κB to the nucleus where it promotes the transcription of its target genes. Activation of IKK is achieved by phosphorylation of its main subunit, IKKβ, at the activation loop sites ...

    Phosphorylation of inhibitor of nuclear transcription factor κB (IκB) by IκB kinase (IKK) triggers the degradation of IκB and migration of cytoplasmic κB to the nucleus where it promotes the transcription of its target genes. Activation of IKK is achieved by phosphorylation of its main subunit, IKKβ, at the activation loop sites. Here, we report the 2.8 Å resolution crystal structure of human IKKβ (hIKKβ), which is partially phosphorylated and bound to the staurosporine analog K252a. The hIKKβ protomer adopts a trimodular structure that closely resembles that from Xenopus laevis (xIKKβ): an N-terminal kinase domain (KD), a central ubiquitin-like domain (ULD), and a C-terminal scaffold/dimerization domain (SDD). Although hIKKβ and xIKKβ utilize a similar dimerization mode, their overall geometries are distinct. In contrast to the structure resembling closed shears reported previously for xIKKβ, hIKKβ exists as an open asymmetric dimer in which the two KDs are further apart, with one in an active and the other in an inactive conformation. Dimer interactions are limited to the C-terminal six-helix bundle that acts as a hinge between the two subunits. The observed domain movements in the structures of IKKβ may represent trans-phosphorylation steps that accompany IKKβ activation.

    Organizational Affiliation: 

    Structural Biology and Biophysics Group, Pfizer Worldwide Research, Groton, Connecticut 06340, USA. shenping.liu@pfizer.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inhibitor of nuclear factor kappa-B kinase subunit betaA677Homo 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 O14920 (Homo sapiens)
Explore O14920 
Go to UniProtKB:  O14920
PHAROS:  O14920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14920
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Inhibitor of nuclear factor kappa-B kinase subunit betaB677Homo 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 O14920 (Homo sapiens)
Explore O14920 
Go to UniProtKB:  O14920
PHAROS:  O14920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14920
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KSA
Query on KSA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		K-252A
C27 H21 N3 O5
KOZFSFOOLUUIGY-SOLYNIJKSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		A L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.954α = 90
b = 68.689β = 107.03
c = 107.401γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-05-02 
  • Released Date: 2013-06-26 
    • Deposition Author(s): Liu, S., Mosyak, L.

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references