8OS6

Structure of a GFRA1/GDNF LICAM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Architecture and regulation of a GDNF-GFR alpha 1 synaptic adhesion assembly.

Houghton, F.M.Adams, S.E.Rios, A.S.Masino, L.Purkiss, A.G.Briggs, D.C.Ledda, F.McDonald, N.Q.

(2023) Nat Commun 14: 7551-7551

  • DOI: https://doi.org/10.1038/s41467-023-43148-8
  • Primary Citation of Related Structures:  
    8OS6

  • PubMed Abstract: 

    Glial-cell line derived neurotrophic factor (GDNF) bound to its co-receptor GFRα1 stimulates the RET receptor tyrosine kinase, promoting neuronal survival and neuroprotection. The GDNF-GFRα1 complex also supports synaptic cell adhesion independently of RET. Here, we describe the structure of a decameric GDNF-GFRα1 assembly determined by crystallography and electron microscopy, revealing two GFRα1 pentamers bridged by five GDNF dimers. We reconsitituted the assembly between adhering liposomes and used cryo-electron tomography to visualize how the complex fulfils its membrane adhesion function. The GFRα1:GFRα1 pentameric interface was further validated both in vitro by native PAGE and in cellulo by cell-clustering and dendritic spine assays. Finally, we provide biochemical and cell-based evidence that RET and heparan sulfate cooperate to prevent assembly of the adhesion complex by competing for the adhesion interface. Our results provide a mechanistic framework to understand GDNF-driven cell adhesion, its relationship to trophic signalling, and the central role played by GFRα1.


  • Organizational Affiliation

    Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GDNF family receptor alpha
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S
260Danio rerioMutation(s): 0 
Gene Names: gfralpha1azgc:110129gfra1a
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glial cell line-derived neurotrophic factor
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T
99Danio 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
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
U,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
V, W, X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth E]
EA [auth G]
FA [auth I]
GA [auth K]
CA [auth B],
DA [auth E],
EA [auth G],
FA [auth I],
GA [auth K],
HA [auth L],
IA [auth M],
JA [auth R],
KA [auth S],
LA [auth T]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.14α = 90
b = 170.044β = 96.17
c = 130.791γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomCC2068

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references