4UX8

RET recognition of GDNF-GFRalpha1 ligand by a composite binding site promotes membrane-proximal self-association


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ret Recognition of Gdnf-Gfralpha1 Ligand by a Composite Binding Site Promotes Membrane-Proximal Self-Association.

Goodman, K.M.Kjaer, S.Beuron, F.Knowles, P.P.Nawrotek, A.Burns, E.M.Purkiss, A.G.George, R.Santoro, M.Morris, E.P.Mcdonald, N.Q.

(2014) Cell Rep. 8: 1894

  • DOI: 10.1016/j.celrep.2014.08.040

  • PubMed Abstract: 
  • The RET receptor tyrosine kinase is essential to vertebrate development and implicated in multiple human diseases. RET binds a cell surface bipartite ligand comprising a GDNF family ligand and a GFRα coreceptor, resulting in RET transmembrane signali ...

    The RET receptor tyrosine kinase is essential to vertebrate development and implicated in multiple human diseases. RET binds a cell surface bipartite ligand comprising a GDNF family ligand and a GFRα coreceptor, resulting in RET transmembrane signaling. We present a hybrid structural model, derived from electron microscopy (EM) and low-angle X-ray scattering (SAXS) data, of the RET extracellular domain (RET(ECD)), GDNF, and GFRα1 ternary complex, defining the basis for ligand recognition. RET(ECD) envelopes the dimeric ligand complex through a composite binding site comprising four discrete contact sites. The GFRα1-mediated contacts are crucial, particularly close to the invariant RET calcium-binding site, whereas few direct contacts are made by GDNF, explaining how distinct ligand/coreceptor pairs are accommodated. The RET(ECD) cysteine-rich domain (CRD) contacts both ligand components and makes homotypic membrane-proximal interactions occluding three different antibody epitopes. Coupling of these CRD-mediated interactions suggests models for ligand-induced RET activation and ligand-independent oncogenic deregulation.


    Organizational Affiliation

    Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
A, B
607Homo sapiensMutation(s): 2 
Gene Names: RET (CDHF12, CDHR16, PTC, RET51)
EC: 2.7.10.1
Find proteins for P07949 (Homo sapiens)
Go to Gene View: RET
Go to UniProtKB:  P07949
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GDNF FAMILY RECEPTOR ALPHA-1
C, E
463Rattus norvegicusMutation(s): 0 
Gene Names: Gfra1 (Gdnfra, Retl1, Trnr1)
Find proteins for Q62997 (Rattus norvegicus)
Go to UniProtKB:  Q62997
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR
D, F
134Homo sapiensMutation(s): 0 
Gene Names: GDNF
Find proteins for P39905 (Homo sapiens)
Go to Gene View: GDNF
Go to UniProtKB:  P39905
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection