5G1X

Crystal structure of Aurora-A kinase in complex with N-Myc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of N-Myc Binding by Aurora-A and its Destabilization by Kinase Inhibitors

Richards, M.Burgess, S.Poon, E.Carstensen, A.Eilers, M.Chesler, L.Bayliss, R.

(2016) Proc.Natl.Acad.Sci.USA 113: 13726

  • DOI: 10.1073/pnas.1610626113

  • PubMed Abstract: 
  • Myc family proteins promote cancer by inducing widespread changes in gene expression. Their rapid turnover by the ubiquitin-proteasome pathway is regulated through phosphorylation of Myc Box I and ubiquitination by the E3 ubiquitin ligase SCF <sup>Fb ...

    Myc family proteins promote cancer by inducing widespread changes in gene expression. Their rapid turnover by the ubiquitin-proteasome pathway is regulated through phosphorylation of Myc Box I and ubiquitination by the E3 ubiquitin ligase SCF FbxW7 However, N-Myc protein (the product of the MYCN oncogene) is stabilized in neuroblastoma by the protein kinase Aurora-A in a manner that is sensitive to certain Aurora-A-selective inhibitors. Here we identify a direct interaction between the catalytic domain of Aurora-A and a site flanking Myc Box I that also binds SCF FbxW7 We determined the crystal structure of the complex between Aurora-A and this region of N-Myc to 1.72-Å resolution. The structure indicates that the conformation of Aurora-A induced by compounds such as alisertib and CD532 is not compatible with the binding of N-Myc, explaining the activity of these compounds in neuroblastoma cells and providing a rational basis for the design of cancer therapeutics optimized for destabilization of the complex. We also propose a model for the stabilization mechanism in which binding to Aurora-A alters how N-Myc interacts with SCF FbxW7 to disfavor the generation of Lys48-linked polyubiquitin chains.


    Organizational Affiliation

    Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden National Health Service Trust, Belmont, Sutton, Surrey SM2 5NG, United Kingdom.,Department of Cancer Studies, University of Leicester, Leicester LE1 9HN, United Kingdom.,Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.,Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, 97074 Würzburg, Germany.,Astbury Centre for Structural and Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom; r.w.bayliss@leeds.ac.uk.,Cancer Research UK Leeds Centre, University of Leeds, Leeds LS2 9JT, United Kingdom.,Theodor Boveri Institute, University of Würzburg, 97074 Würzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AURORA KINASE A
A
285Homo sapiensMutation(s): 2 
Gene Names: AURKA (AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6)
EC: 2.7.11.1
Find proteins for O14965 (Homo sapiens)
Go to Gene View: AURKA
Go to UniProtKB:  O14965
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-MYC PROTO-ONCOGENE PROTEIN
B
63Homo sapiensMutation(s): 0 
Gene Names: MYCN (BHLHE37, NMYC)
Find proteins for P04198 (Homo sapiens)
Go to Gene View: MYCN
Go to UniProtKB:  P04198
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.176 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.520α = 90.00
b = 86.520β = 90.00
c = 92.210γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Structure summary
  • Version 1.2: 2016-12-14
    Type: Database references