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 7AB8 | pdb_00007ab8

Crystal structure of a GDNF-GFRalpha1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AB8

This is version 1.4 of the entry. See complete history. 

Literature

A two-site flexible clamp mechanism for RET-GDNF-GFR alpha 1 assembly reveals both conformational adaptation and strict geometric spacing.

Adams, S.E., Purkiss, A.G., Knowles, P.P., Nans, A., Briggs, D.C., Borg, A., Earl, C.P., Goodman, K.M., Nawrotek, A., Borg, A.J., McIntosh, P.B., Houghton, F.M., Kjaer, S., McDonald, N.Q.

(2021) Structure 29: 694

  • DOI: https://doi.org/10.1016/j.str.2020.12.012
  • Primary Citation Related Structures: 
    7AB8, 7AMK, 7AML

  • PubMed Abstract: 

    RET receptor tyrosine kinase plays vital developmental and neuroprotective roles in metazoans. GDNF family ligands (GFLs) when bound to cognate GFRα co-receptors recognize and activate RET stimulating its cytoplasmic kinase function. The principles for RET ligand-co-receptor recognition are incompletely understood. Here, we report a crystal structure of the cadherin-like module (CLD1-4) from zebrafish RET revealing interdomain flexibility between CLD2 and CLD3. Comparison with a cryo-electron microscopy structure of a ligand-engaged zebrafish RET ECD -GDNF-GFRα1a complex indicates conformational changes within a clade-specific CLD3 loop adjacent to the co-receptor. Our observations indicate that RET is a molecular clamp with a flexible calcium-dependent arm that adapts to different GFRα co-receptors, while its rigid arm recognizes a GFL dimer to align both membrane-proximal cysteine-rich domains. We also visualize linear arrays of RET ECD -GDNF-GFRα1a suggesting that a conserved contact stabilizes higher-order species. Our study reveals that ligand-co-receptor recognition by RET involves both receptor plasticity and strict spacing of receptor dimers by GFL ligands.


  • Organizational Affiliation: 
    • Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT London, UK.

Macromolecule Content 

  • Total Structure Weight: 35.91 kDa 
  • Atom Count: 2,736 
  • Modeled Residue Count: 307 
  • Deposited Residue Count: 307 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GDNF family receptor alpha209Danio rerioMutation(s): 0 
Gene Names: gfra1a, gfralpha1a
UniProt
Find proteins for Q98TT9 (Danio rerio)
Explore Q98TT9 
Go to UniProtKB:  Q98TT9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98TT9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Glial cell line-derived neurotrophic factor98Danio rerioMutation(s): 0 
Gene Names: gdnf
UniProt
Find proteins for Q98TU0 (Danio rerio)
Explore Q98TU0 
Go to UniProtKB:  Q98TU0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98TU0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.067α = 90
b = 55.544β = 90
c = 70.961γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata processing
Cootmodel building
STARANISOdata processing
PHASERphasing
DIALSdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited Kingdom10115

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary