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 1.3 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

    Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK.,Protein Purification Facility, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.,Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; Protein Purification Facility, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.,Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.,Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università di Napoli Federico II, via S. Pansini 5, 80131 Naples, Italy.,Structural Biology Laboratory, Cancer Research UK, London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK. Electronic address: neil.mcdonald@cancer.org.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
  • Version 1.3: 2019-10-23
    Type: Data collection, Derived calculations, Other