3JSV

Crystal structure of mouse NEMO CoZi in complex with Lys63-linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.250 

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This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin

Yoshikawa, A.Sato, Y.Yamashita, M.Mimura, H.Yamagata, A.Fukai, S.

(2009) Febs Lett. 583: 3317-3322

  • DOI: 10.1016/j.febslet.2009.09.028

  • PubMed Abstract: 
  • NEMO is essential for activation of the NF-kappaB signaling pathway, which is regulated by ubiquitination of proteins. The C-terminal leucine zipper of NEMO and its adjacent coiled-coil region (CC2-LZ) reportedly bind to linear ubiquitin chains with ...

    NEMO is essential for activation of the NF-kappaB signaling pathway, which is regulated by ubiquitination of proteins. The C-terminal leucine zipper of NEMO and its adjacent coiled-coil region (CC2-LZ) reportedly bind to linear ubiquitin chains with 1 microM affinity and to Lys 63-linked chains with 100 microM affinity. Here we report the crystal structure of the CC2-LZ region of mouse NEMO in complex with Lys 63-linked di-ubiquitin (K63-Ub(2)) at 2.7A resolution. The ubiquitin-binding region consists of a 130A-long helix and forms a parallel coiled-coil dimer. The Ile 44-centered hydrophobic patch of ubiquitin is recognized in the middle of the NEMO ubiquitin-binding region. NEMO interacts with each K63-Ub(2)via a single ubiquitin-binding site, consistent with low affinity binding with K63-Ub(2).


    Organizational Affiliation

    Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
77Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NF-kappa-B essential modulator
C, D
94Mus musculusMutation(s): 0 
Gene Names: Ikbkg (Nemo)
Find proteins for O88522 (Mus musculus)
Go to UniProtKB:  O88522
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.380α = 90.00
b = 45.870β = 99.83
c = 83.290γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance