6AMB

Crystal Structure of the Afadin RA1 domain in complex with HRAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Evolution of AF6-RAS association and its implications in mixed-lineage leukemia.

Smith, M.J.Ottoni, E.Ishiyama, N.Goudreault, M.Haman, A.Meyer, C.Tucholska, M.Gasmi-Seabrook, G.Menezes, S.Laister, R.C.Minden, M.D.Marschalek, R.Gingras, A.C.Hoang, T.Ikura, M.

(2017) Nat Commun 8: 1099-1099

  • DOI: 10.1038/s41467-017-01326-5

  • PubMed Abstract: 
  • Elucidation of activation mechanisms governing protein fusions is essential for therapeutic development. MLL undergoes rearrangement with numerous partners, including a recurrent translocation fusing the epigenetic regulator to a cytoplasmic RAS effe ...

    Elucidation of activation mechanisms governing protein fusions is essential for therapeutic development. MLL undergoes rearrangement with numerous partners, including a recurrent translocation fusing the epigenetic regulator to a cytoplasmic RAS effector, AF6/afadin. We show here that AF6 employs a non-canonical, evolutionarily conserved α-helix to bind RAS, unique to AF6 and the classical RASSF effectors. Further, all patients with MLL-AF6 translocations express fusion proteins missing only this helix from AF6, resulting in exposure of hydrophobic residues that induce dimerization. We provide evidence that oligomerization is the dominant mechanism driving oncogenesis from rare MLL translocation partners and employ our mechanistic understanding of MLL-AF6 to examine how dimers induce leukemia. Proteomic data resolve association of dimerized MLL with gene expression modulators, and inhibiting dimerization disrupts formation of these complexes while completely abrogating leukemogenesis in mice. Oncogenic gene translocations are thus selected under pressure from protein structure/function, underscoring the complex nature of chromosomal rearrangements.


    Organizational Affiliation

    Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada.,Department of Pharmacology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.,Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada. matthew.james.smith@umontreal.ca.,Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada. matthew.james.smith@umontreal.ca.,Institute of Pharmaceutical Biology, Goethe-University of Frankfurt, Frankfurt, 60323, Germany.,Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada.,Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada. mikura@uhnres.utoronto.ca.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada. mikura@uhnres.utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase HRas
A
170Homo sapiensMutation(s): 0 
Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Afadin
B
99Mus musculusMutation(s): 0 
Gene Names: Afdn (Af6, Mllt4)
Find proteins for Q9QZQ1 (Mus musculus)
Go to UniProtKB:  Q9QZQ1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.239α = 90.00
b = 57.152β = 90.00
c = 73.329γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references