4OWF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.7 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: https://doi.org/10.1128/MCB.01538-13
  • Primary Citation of Related Structures:  
    4OWF

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NF-kappa-B essential modulator
A, B
90Mus musculusMutation(s): 0 
Gene Names: IkbkgNemo
EC: 6.3.2
UniProt
Find proteins for O88522 (Mus musculus)
Explore O88522 
Go to UniProtKB:  O88522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88522
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RNF31C [auth G]30Homo sapiensMutation(s): 0 
Gene Names: RNF31ZIBRA
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens)
Explore Q96EP0 
Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0
GTEx:  ENSG00000092098 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EP0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth G]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.41α = 90
b = 81.41β = 90
c = 74.501γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Other
  • Version 1.2: 2014-04-30
    Changes: Database references
  • Version 1.3: 2016-03-16
    Changes: Source and taxonomy
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.5: 2017-11-22
    Changes: Refinement description
  • Version 1.6: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.7: 2023-09-27
    Changes: Data collection, Database references, Refinement description