6MI4

Structure of the I65M mutant of NEMO(51-112) with N- and C-terminal coiled-coil adaptors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The IKK-binding domain of NEMO is an irregular coiled coil with a dynamic binding interface.

Barczewski, A.H.Ragusa, M.J.Mierke, D.F.Pellegrini, M.

(2019) Sci Rep 9: 2950-2950

  • DOI: 10.1038/s41598-019-39588-2
  • Primary Citation of Related Structures:  
    6MI3, 6MI4

  • PubMed Abstract: 
  • NEMO is an essential component in the activation of the canonical NF-κB pathway and exerts its function by recruiting the IκB kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-κB mis-regulation, but a difficult endeavor because of the extensive protein-protein interface ...

    NEMO is an essential component in the activation of the canonical NF-κB pathway and exerts its function by recruiting the IκB kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-κB mis-regulation, but a difficult endeavor because of the extensive protein-protein interface. Here we report the high-resolution structure of the unbound IKKβ-binding domain of NEMO that will greatly facilitate the design of NEMO/IKK inhibitors. The structures of unbound NEMO show a closed conformation that partially occludes the three binding hot-spots and suggest a facile transition to an open state that can accommodate ligand binding. By fusing coiled-coil adaptors to the IKKβ-binding domain of NEMO, we succeeded in creating a protein with improved solution behavior, IKKβ-binding affinity and crystallization compatibility, which will enable the structural characterization of new NEMO/inhibitor complexes.


    Organizational Affiliation

    Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA. Maria.Pellegrini@Dartmouth.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NF-kB ESSENTIAL MODULATOR AB124Homo sapiensMutation(s): 0 
Gene Names: IKBKGFIP3NEMO
Find proteins for Q9Y6K9 (Homo sapiens)
Explore Q9Y6K9 
Go to UniProtKB:  Q9Y6K9
NIH Common Fund Data Resources
PHAROS:  Q9Y6K9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.407α = 90
b = 34.124β = 113.89
c = 77.416γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR03 AR066130
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM113132

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence