6Q2S

Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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 ...

    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 Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,ArteminA,
D [auth B]		235Saccharomyces cerevisiae, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: SMT3, ARTN, EVN
UniProt & NIH Common Fund Data Resources
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12306
Find proteins for Q5T4W7 (Homo sapiens)
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Go to UniProtKB:  Q5T4W7
PHAROS:  Q5T4W7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ5T4W7Q12306
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GDNF family receptor alpha-3B [auth C],
E [auth D]		342Homo sapiensMutation(s): 0 
Gene Names: GFRA3, UNQ339/PRO538/PRO3664
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Find proteins for O60609 (Homo sapiens)
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PHAROS:  O60609
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UniProt GroupO60609
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase receptor RetC [auth E],
F		617Homo sapiensMutation(s): 0 
Gene Names: RET, CDHF12, CDHR16, PTC, RET51
EC: 2.7.10.1
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Find proteins for P07949 (Homo sapiens)
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PHAROS:  P07949
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UniProt GroupP07949
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
G [auth C],
H [auth E],
I [auth E],
J [auth E],
K [auth E],
G [auth C],
H [auth E],
I [auth E],
J [auth E],
K [auth E],
L [auth E],
M [auth E],
R [auth D],
S [auth F],
T [auth F],
U [auth F],
V [auth F],
W [auth F],
X [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CA (Subject of Investigation/LOI)
Query on CA
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
N [auth E],
O [auth E],
P [auth E],
AA [auth F],
BA [auth F],
N [auth E],
O [auth E],
P [auth E],
Q [auth E],
Y [auth F],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary