8OS6 | pdb_00008os6

Structure of a GFRA1/GDNF LICAM complex

PDB DOI: https://doi.org/10.2210/pdb8OS6/pdb

Classification: CELL ADHESION
Organism(s): Danio rerio
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-04-18 Released: 2023-11-29
Deposition Author(s): Houghton, F.M., Adams, S.E., Briggs, D.C., McDonald, N.Q.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free:
0.283 (Depositor), 0.253 (DCC)
R-Value Work:
0.244 (Depositor), 0.245 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 37985758 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-43148-8
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 411.87 kDa
Atom Count: 23,825
Modeled Residue Count: 3,001
Deposited Residue Count: 3,590
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDNF family receptor alpha	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S	260	Danio rerio	Mutation(s): 0 Gene Names: gfralpha1a, zgc:110129, gfra1a
UniProt
Find proteins for Q98TT9 (Danio rerio) Explore Q98TT9 Go to UniProtKB: Q98TT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q98TT9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain E Focus chain G Focus chain I Focus chain K Focus chain M Focus chain O Focus chain S
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glial cell line-derived neurotrophic factor	B, D, F, H, J B, D, F, H, J, L, N, P, R, T	99	Danio rerio	Mutation(s): 0 Gene Names: gdnf
UniProt
Find proteins for Q98TU0 (Danio rerio) Explore Q98TU0 Go to UniProtKB: Q98TU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q98TU0
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D Focus chain F Focus chain H Focus chain J Focus chain L Focus chain N Focus chain P Focus chain R Focus chain T
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], U, Y, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain U Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain U Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	3		N-Glycosylation	Interactions Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain LA [auth T] SDF format, chain KA [auth S] SDF format, chain JA [auth R] SDF format, chain IA [auth M] SDF format, chain HA [auth L] SDF format, chain GA [auth K] SDF format, chain FA [auth I] SDF format, chain EA [auth G] SDF format, chain DA [auth E] SDF format, chain CA [auth B] MOL2 format, chain LA [auth T] MOL2 format, chain KA [auth S] MOL2 format, chain JA [auth R] MOL2 format, chain IA [auth M] MOL2 format, chain HA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain FA [auth I] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth B] mmCIF format, chain LA [auth T] mmCIF format, chain KA [auth S] mmCIF format, chain JA [auth R] mmCIF format, chain IA [auth M] mmCIF format, chain HA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain FA [auth I] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth B]	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		Interactions Focus chain CA [auth B] Focus chain DA [auth E] Focus chain EA [auth G] Focus chain FA [auth I] Focus chain GA [auth K] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain JA [auth R] Focus chain KA [auth S] Focus chain LA [auth T] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth E] Focus chain EA [auth G] Focus chain FA [auth I] Focus chain GA [auth K] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain JA [auth R] Focus chain KA [auth S] Focus chain LA [auth T]