2V5E

The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of the Glial Cell Line-Derived Neurotrophic Factor-Coreceptor Complex: Insights Into Ret Signaling and Heparin Binding.

Parkash, V.Leppanen, V.-M.Virtanen, H.Jurvansuu, J.-M.Bespalov, M.M.Sidorova, Y.A.Runeberg-Roos, P.Saarma, M.Goldman, A.

(2008) J.Biol.Chem. 283: 35164

  • DOI: 10.1074/jbc.M802543200

  • PubMed Abstract: 
  • Glial cell line-derived neurotrophic factor (GDNF), a neuronal survival factor, binds its co-receptor GDNF family receptor alpha1 (GFR alpha 1) in a 2:2 ratio and signals through the receptor tyrosine kinase RET. We have solved the GDNF(2).GFR alpha ...

    Glial cell line-derived neurotrophic factor (GDNF), a neuronal survival factor, binds its co-receptor GDNF family receptor alpha1 (GFR alpha 1) in a 2:2 ratio and signals through the receptor tyrosine kinase RET. We have solved the GDNF(2).GFR alpha 1(2) complex structure at 2.35 A resolution in the presence of a heparin mimic, sucrose octasulfate. The structure of our GDNF(2).GFR alpha 1(2) complex and the previously published artemin(2).GFR alpha 3(2) complex are unlike in three ways. First, we have experimentally identified residues that differ in the ligand-GFR alpha interface between the two structures, in particular ones that buttress the key conserved Arg(GFR alpha)-Glu(ligand)-Arg(GFR alpha) interaction. Second, the flexible GDNF ligand "finger" loops fit differently into the GFR alphas, which are rigid. Third, and we believe most importantly, the quaternary structure of the two tetramers is dissimilar, because the angle between the two GDNF monomers is different. This suggests that the RET-RET interaction differs in different ligand(2)-co-receptor(2)-RET(2) heterohexamer complexes. Consistent with this, we showed that GDNF(2).GFR alpha1(2) and artemin(2).GFR alpha 3(2) signal differently in a mitogen-activated protein kinase assay. Furthermore, we have shown by mutagenesis and enzyme-linked immunosorbent assays of RET phosphorylation that RET probably interacts with GFR alpha 1 residues Arg-190, Lys-194, Arg-197, Gln-198, Lys-202, Arg-257, Arg-259, Glu-323, and Asp-324 upon both domains 2 and 3. Interestingly, in our structure, sucrose octasulfate also binds to the Arg(190)-Lys(202) region in GFR alpha 1 domain 2. This may explain how GDNF.GFR alpha 1 can mediate cell adhesion and how heparin might inhibit GDNF signaling through RET.


    Organizational Affiliation

    Institute of Biotechnology, University of Helsinki, Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GDNF FAMILY RECEPTOR ALPHA-1
A
200Rattus norvegicusMutation(s): 0 
Gene Names: Gfra1 (Gdnfra, Retl1, Trnr1)
Find proteins for Q62997 (Rattus norvegicus)
Go to UniProtKB:  Q62997
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR
B
101Homo sapiensMutation(s): 0 
Gene Names: GDNF
Find proteins for P39905 (Homo sapiens)
Go to Gene View: GDNF
Go to UniProtKB:  P39905
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SCR
Query on SCR

Download SDF File 
Download CCD File 
A
SUCROSE OCTASULFATE
C12 H22 O35 S8
WEPNHBQBLCNOBB-UGDNZRGBSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.900α = 90.00
b = 75.700β = 91.90
c = 105.500γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance