6AMB | pdb_00006amb

Crystal Structure of the Afadin RA1 domain in complex with HRAS

• PDB DOI: https://doi.org/10.2210/pdb6AMB/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-08-09 Released: 2017-11-01 
• Deposition Author(s): Smith, M.J., Ishiyama, N., Ikura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

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

• PubMed: 29062045 
• DOI: https://doi.org/10.1038/s41467-017-01326-5
• Primary Citation Related Structures: 
  6AMB


• 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 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.

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Organizational Affiliation: 
• Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada. [e-mail].
Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada. [e-mail].
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.
Institute of Pharmaceutical Biology, Goethe-University of Frankfurt, Frankfurt, 60323, Germany.
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada.
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 Pharmacology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada. [e-mail].
Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry, immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 31.46 kDa 
• Atom Count: 2,016 
• Modeled Residue Count: 249 
• Deposited Residue Count: 269 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	170	Homo sapiens	Mutation(s): 0  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Afadin	B	99	Mus musculus	Mutation(s): 0  Gene Names: Afdn, Af6, Mllt4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZQ1 (Mus musculus) Explore Q9QZQ1  Go to UniProtKB:  Q9QZQ1
IMPC:  MGI:1314653

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.239	α = 90
b = 57.152	β = 90
c = 73.329	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Smith, M.J., Ishiyama, N., Ikura, M.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description