4RA0

An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.

Kariolis, M.S.Miao, Y.R.Jones, D.S.Kapur, S.Mathews, I.I.Giaccia, A.J.Cochran, J.R.

(2014) Nat.Chem.Biol. 10: 977-983

  • DOI: 10.1038/nchembio.1636

  • PubMed Abstract: 
  • Aberrant signaling through the Axl receptor tyrosine kinase has been associated with a myriad of human diseases, most notably metastatic cancer, identifying Axl and its ligand Gas6 as important therapeutic targets. Using rational and combinatorial ap ...

    Aberrant signaling through the Axl receptor tyrosine kinase has been associated with a myriad of human diseases, most notably metastatic cancer, identifying Axl and its ligand Gas6 as important therapeutic targets. Using rational and combinatorial approaches, we engineered an Axl 'decoy receptor' that binds Gas6 with high affinity and inhibits its function, offering an alternative approach from drug discovery efforts that directly target Axl. Four mutations within this high-affinity Axl variant caused structural alterations in side chains across the Gas6-Axl binding interface, stabilizing a conformational change on Gas6. When reformatted as an Fc fusion, the engineered decoy receptor bound Gas6 with femtomolar affinity, an 80-fold improvement compared to binding of the wild-type Axl receptor, allowing effective sequestration of Gas6 and specific abrogation of Axl signaling. Moreover, increased Gas6 binding affinity was critical and correlative with the ability of decoy receptors to potently inhibit metastasis and disease progression in vivo.


    Organizational Affiliation

    Department of Bioengineering, Stanford University, Stanford, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth arrest-specific protein 6
A, B
401Homo sapiensMutation(s): 0 
Gene Names: GAS6 (AXLLG)
Find proteins for Q14393 (Homo sapiens)
Go to Gene View: GAS6
Go to UniProtKB:  Q14393
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase receptor UFO
C, D
195Homo sapiensMutation(s): 0 
Gene Names: AXL (UFO)
EC: 2.7.10.1
Find proteins for P30530 (Homo sapiens)
Go to Gene View: AXL
Go to UniProtKB:  P30530
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.370α = 90.00
b = 112.370β = 90.00
c = 361.260γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references