2ZVN

NEMO CoZi domain incomplex with diubiquitin in P212121 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation

Rahighi, S.Ikeda, F.Kawasaki, M.Akutsu, M.Suzuki, N.Kato, R.Kensche, T.Uejima, T.Bloor, S.Komander, D.Randow, F.Wakatsuki, S.Dikic, I.

(2009) Cell 136: 1098-1109

  • DOI: https://doi.org/10.1016/j.cell.2009.03.007
  • Primary Citation of Related Structures:  
    2ZVN, 2ZVO, 3F89

  • PubMed Abstract: 

    Activation of nuclear factor-kappaB (NF-kappaB), a key mediator of inducible transcription in immunity, requires binding of NF-kappaB essential modulator (NEMO) to ubiquitinated substrates. Here, we report that the UBAN (ubiquitin binding in ABIN and NEMO) motif of NEMO selectively binds linear (head-to-tail) ubiquitin chains. Crystal structures of the UBAN motif revealed a parallel coiled-coil dimer that formed a heterotetrameric complex with two linear diubiquitin molecules. The UBAN dimer contacted all four ubiquitin moieties, and the integrity of each binding site was required for efficient NF-kappaB activation. Binding occurred via a surface on the proximal ubiquitin moiety and the canonical Ile44 surface on the distal one, thereby providing specificity for linear chain recognition. Residues of NEMO involved in binding linear ubiquitin chains are required for NF-kappaB activation by TNF-alpha and other agonists, providing an explanation for the detrimental effect of NEMO mutations in patients suffering from X-linked ectodermal dysplasia and immunodeficiency.


  • Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBC proteinA,
B [auth G],
E [auth C],
F [auth E]
154Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NF-kappa-B essential modulatorC [auth B],
D,
G [auth F],
H
87Mus musculusMutation(s): 0 
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.195α = 90
b = 141.288β = 90
c = 144.179γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references