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 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    4RA0

  • 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 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 ...

    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

    1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2] Department of Chemical Engineering, Stanford University, Stanford, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest-specific protein 6A, B401Homo sapiensMutation(s): 0 
Gene Names: GAS6AXLLG
UniProt & NIH Common Fund Data Resources
Find proteins for Q14393 (Homo sapiens)
Explore Q14393 
Go to UniProtKB:  Q14393
PHAROS:  Q14393
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase receptor UFOC, D195Homo sapiensMutation(s): 0 
Gene Names: AXLUFO
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P30530 (Homo sapiens)
Explore P30530 
Go to UniProtKB:  P30530
PHAROS:  P30530
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.37α = 90
b = 112.37β = 90
c = 361.26γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary