2C5D

Structure of a minimal Gas6-Axl complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Basis for Gas6-Axl Signalling.

Sasaki, T.Knyazev, P.G.Clout, N.J.Cheburkin, Y.Goehring, W.Ullrich, A.Timpl, R.Hohenester, E.

(2006) EMBO J 25: 80

  • DOI: 10.1038/sj.emboj.7600912
  • Primary Citation of Related Structures:  
    2C5D

  • PubMed Abstract: 
  • Receptor tyrosine kinases of the Axl family are activated by the vitamin K-dependent protein Gas6. Axl signalling plays important roles in cancer, spermatogenesis, immunity, and platelet function. The crystal structure at 3.3 A resolution of a minimal human Gas6/Axl complex reveals an assembly of 2:2 stoichiometry, in which the two immunoglobulin-like domains of the Axl ectodomain are crosslinked by the first laminin G-like domain of Gas6, with no direct Axl/Axl or Gas6/Gas6 contacts ...

    Receptor tyrosine kinases of the Axl family are activated by the vitamin K-dependent protein Gas6. Axl signalling plays important roles in cancer, spermatogenesis, immunity, and platelet function. The crystal structure at 3.3 A resolution of a minimal human Gas6/Axl complex reveals an assembly of 2:2 stoichiometry, in which the two immunoglobulin-like domains of the Axl ectodomain are crosslinked by the first laminin G-like domain of Gas6, with no direct Axl/Axl or Gas6/Gas6 contacts. There are two distinct Gas6/Axl contacts of very different size, both featuring interactions between edge beta-strands. Structure-based mutagenesis, protein binding assays and receptor activation experiments demonstrate that both the major and minor Gas6 binding sites are required for productive transmembrane signalling. Gas6-mediated Axl dimerisation is likely to occur in two steps, with a high-affinity 1:1 Gas6/Axl complex forming first. Only the minor Gas6 binding site is highly conserved in the other Axl family receptors, Sky/Tyro3 and Mer. Specificity at the major contact is suggested to result from the segregation of charged and apolar residues to opposite faces of the newly formed beta-sheet.


    Related Citations: 
    • Crystal Structure of a C-Terminal Fragment of Growth Arrest-Specific Protein Gas6
      Sasaki, T., Knyazev, P.G., Cheburkin, Y., Goehring, W., Tisi, D., Ullrich, A., Timpl, R., Hohenester, E.
      (2002) J Biol Chem 277: 44164
    • Ligand Recognition and Homophilic Interactions in Tyro3
      Heiring, C., Dahlback, B., Muller, Y.A.
      (2004) J Biol Chem 279: 6952

    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GROWTH-ARREST-SPECIFIC PROTEIN 6 PRECURSORA, B422Homo 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
GTEx:  ENSG00000183087 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14393
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE RECEPTOR UFOC, D195Homo sapiensMutation(s): 0 
Gene Names: AXLUFO
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P30530 (Homo sapiens)
Explore P30530 
Go to UniProtKB:  P30530
PHAROS:  P30530
GTEx:  ENSG00000167601 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30530
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
I [auth C],
K [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 292.951α = 90
b = 292.951β = 90
c = 63.951γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary