4OWF

Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Mechanism Underlying I kappa B Kinase Activation Mediated by the Linear Ubiquitin Chain Assembly Complex.

Fujita, H.Rahighi, S.Akita, M.Kato, R.Sasaki, Y.Wakatsuki, S.Iwai, K.

(2014) Mol.Cell.Biol. 34: 1322-1335

  • DOI: 10.1128/MCB.01538-13

  • PubMed Abstract: 
  • The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a compon ...

    The linear ubiquitin chain assembly complex (LUBAC) ligase, consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains. LUBAC-mediated linear polyubiquitination has been implicated in NF-κB activation. NEMO, a component of the IκB kinase (IKK) complex, is a substrate of LUBAC, but the precise molecular mechanism underlying linear chain-mediated NF-κB activation has not been fully elucidated. Here, we demonstrate that linearly polyubiquitinated NEMO activates IKK more potently than unanchored linear chains. In mutational analyses based on the crystal structure of the complex between the HOIP NZF1 and NEMO CC2-LZ domains, which are involved in the HOIP-NEMO interaction, NEMO mutations that impaired linear ubiquitin recognition activity and prevented recognition by LUBAC synergistically suppressed signal-induced NF-κB activation. HOIP NZF1 bound to NEMO and ubiquitin simultaneously, and HOIP NZF1 mutants defective in interaction with either NEMO or ubiquitin could not restore signal-induced NF-κB activation. Furthermore, linear chain-mediated activation of IKK2 involved homotypic interaction of the IKK2 kinase domain. Collectively, these results demonstrate that linear polyubiquitination of NEMO plays crucial roles in IKK activation and that this modification involves the HOIP NZF1 domain and recognition of NEMO-conjugated linear ubiquitin chains by NEMO on another IKK complex.


    Organizational Affiliation

    Cell Biology and Metabolism Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NF-kappa-B essential modulator
A, B
90Mus musculusGene Names: Ikbkg (Nemo)
Find proteins for O88522 (Mus musculus)
Go to UniProtKB:  O88522
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF31
G
30Homo sapiensGene Names: RNF31 (ZIBRA)
EC: 6.3.2.-
Find proteins for Q96EP0 (Homo sapiens)
Go to Gene View: RNF31
Go to UniProtKB:  Q96EP0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.259 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 81.410α = 90.00
b = 81.410β = 90.00
c = 74.501γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--
Japan Society for the Promotion of ScienceJapan--

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Other
  • Version 1.2: 2014-04-30
    Type: Database references
  • Version 1.3: 2016-03-16
    Type: Source and taxonomy
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence, Data collection, Derived calculations
  • Version 1.5: 2017-11-22
    Type: Refinement description