7ZAV

GPC3-Unc5D octamer structure and role in cell migration


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

GPC3-Unc5 receptor complex structure and role in cell migration.

Akkermans, O.Delloye-Bourgeois, C.Peregrina, C.Carrasquero-Ordaz, M.Kokolaki, M.Berbeira-Santana, M.Chavent, M.Reynaud, F.Raj, R.Agirre, J.Aksu, M.White, E.S.Lowe, E.Ben Amar, D.Zaballa, S.Huo, J.Pakos, I.McCubbin, P.T.N.Comoletti, D.Owens, R.J.Robinson, C.V.Castellani, V.Del Toro, D.Seiradake, E.

(2022) Cell 185: 3931-3949.e26

  • DOI: https://doi.org/10.1016/j.cell.2022.09.025
  • Primary Citation of Related Structures:  
    7ZA1, 7ZA2, 7ZA3, 7ZAV, 7ZAW

  • PubMed Abstract: 

    Neural migration is a critical step during brain development that requires the interactions of cell-surface guidance receptors. Cancer cells often hijack these mechanisms to disseminate. Here, we reveal crystal structures of Uncoordinated-5 receptor D (Unc5D) in complex with morphogen receptor glypican-3 (GPC3), forming an octameric glycoprotein complex. In the complex, four Unc5D molecules pack into an antiparallel bundle, flanked by four GPC3 molecules. Central glycan-glycan interactions are formed by N-linked glycans emanating from GPC3 (N241 in human) and C-mannosylated tryptophans of the Unc5D thrombospondin-like domains. MD simulations, mass spectrometry and structure-based mutants validate the crystallographic data. Anti-GPC3 nanobodies enhance or weaken Unc5-GPC3 binding and, together with mutant proteins, show that Unc5/GPC3 guide migrating pyramidal neurons in the mouse cortex, and cancer cells in an embryonic xenograft neuroblastoma model. The results demonstrate a conserved structural mechanism of cell guidance, where finely balanced Unc5-GPC3 interactions regulate cell migration.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glypican-3464Mus musculusMutation(s): 0 
Gene Names: Gpc3
UniProt
Find proteins for Q8CFZ4 (Mus musculus)
Explore Q8CFZ4 
Go to UniProtKB:  Q8CFZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CFZ4
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q8CFZ4-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.488α = 90
b = 100.488β = 90
c = 90.62γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom202827/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary