4UX8

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    4UX8

  • 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 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 ...

    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; 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RETA, B607Homo sapiensMutation(s): 2 
Gene Names: RETCDHF12CDHR16PTCRET51
EC: 2.7.10.1
Find proteins for P07949 (Homo sapiens)
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PHAROS:  P07949
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GDNF FAMILY RECEPTOR ALPHA-1C, E463Rattus norvegicusMutation(s): 0 
Gene Names: Gfra1GdnfraRetl1Trnr1
Find proteins for Q62997 (Rattus norvegicus)
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Go to UniProtKB:  Q62997
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTORD, F134Homo sapiensMutation(s): 0 
Gene Names: GDNF
Find proteins for P39905 (Homo sapiens)
Explore P39905 
Go to UniProtKB:  P39905
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PHAROS:  P39905
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Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, H2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 24.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Data collection
  • Version 1.3: 2019-10-23
    Changes: Data collection, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary