6Q2N

Cryo-EM structure of RET/GFRa1/GDNF extracellular complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands.

Li, J.Shang, G.Chen, Y.J.Brautigam, C.A.Liou, J.Zhang, X.Bai, X.C.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.47650
  • Primary Citation of Related Structures:  
    6Q2J, 6Q2N, 6Q2O, 6Q2R, 6Q2S

  • PubMed Abstract: 

    RET is a receptor tyrosine kinase (RTK) that plays essential roles in development and has been implicated in several human diseases. Different from most of RTKs, RET requires not only its cognate ligands but also co-receptors for activation, the mechanisms of which remain unclear due to lack of high-resolution structures of the ligand/co-receptor/receptor complexes. Here, we report cryo-EM structures of the extracellular region ternary complexes of GDF15/GFRAL/RET, GDNF/GFRα1/RET, NRTN/GFRα2/RET and ARTN/GFRα3/RET. These structures reveal that all the four ligand/co-receptor pairs, while using different atomic interactions, induce a specific dimerization mode of RET that is poised to bring the two kinase domains into close proximity for cross-phosphorylation. The NRTN/GFRα2/RET dimeric complex further pack into a tetrameric assembly, which is shown by our cell-based assays to regulate the endocytosis of RET. Our analyses therefore reveal both the common mechanism and diversification in the activation of RET by different ligands.


  • Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glial cell line-derived neurotrophic factorA,
D [auth B]
134Homo sapiensMutation(s): 0 
Gene Names: GDNF
UniProt & NIH Common Fund Data Resources
Find proteins for P39905 (Homo sapiens)
Explore P39905 
Go to UniProtKB:  P39905
PHAROS:  P39905
GTEx:  ENSG00000168621 
Entity Groups  
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UniProt GroupP39905
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GDNF family receptor alpha-1B [auth C],
E [auth D]
412Homo sapiensMutation(s): 0 
Gene Names: GFRA1GDNFRARETL1TRNR1
UniProt & NIH Common Fund Data Resources
Find proteins for P56159 (Homo sapiens)
Explore P56159 
Go to UniProtKB:  P56159
PHAROS:  P56159
GTEx:  ENSG00000151892 
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UniProt GroupP56159
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase receptor RetC [auth E],
F
617Homo sapiensMutation(s): 0 
Gene Names: RETCDHF12CDHR16PTCRET51
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07949 (Homo sapiens)
Explore P07949 
Go to UniProtKB:  P07949
PHAROS:  P07949
GTEx:  ENSG00000165731 
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UniProt GroupP07949
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary