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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 ach ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inhibitor of nuclear factor kappa-B kinase subunit beta
A
677Homo sapiensMutation(s): 0 
Gene Names: IKBKB (IKKB)
EC: 2.7.11.10
Find proteins for O14920 (Homo sapiens)
Go to Gene View: IKBKB
Go to UniProtKB:  O14920
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Inhibitor of nuclear factor kappa-B kinase subunit beta
B
677Homo sapiensMutation(s): 0 
Gene Names: IKBKB (IKKB)
EC: 2.7.11.10
Find proteins for O14920 (Homo sapiens)
Go to Gene View: IKBKB
Go to UniProtKB:  O14920
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KSA
Query on KSA

Download SDF File 
Download CCD File 
A, B
K-252A
C27 H21 N3 O5
KOZFSFOOLUUIGY-SOLYNIJKSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 110.954α = 90.00
b = 68.689β = 107.03
c = 107.401γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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