6XTZ

Structure of Dally-like protein in complex with O-palmitoleoyl serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Glypicans shield the Wnt lipid moiety to enable signalling at a distance.

McGough, I.J.Vecchia, L.Bishop, B.Malinauskas, T.Beckett, K.Joshi, D.O'Reilly, N.Siebold, C.Jones, E.Y.Vincent, J.P.

(2020) Nature 

  • DOI: 10.1038/s41586-020-2498-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A relatively small number of proteins have been suggested to act as morphogens-signalling molecules that spread within tissues to organize tissue repair and the specification of cell fate during development. Among them are Wnt proteins, which carry a ...

    A relatively small number of proteins have been suggested to act as morphogens-signalling molecules that spread within tissues to organize tissue repair and the specification of cell fate during development. Among them are Wnt proteins, which carry a palmitoleate moiety that is essential for signalling activity 1-3 . How a hydrophobic lipoprotein can spread in the aqueous extracellular space is unknown. Several mechanisms, such as those involving lipoprotein particles, exosomes or a specific chaperone, have been proposed to overcome this so-called Wnt solubility problem 4-6 . Here we provide evidence against these models and show that the Wnt lipid is shielded by the core domain of a subclass of glypicans defined by the Dally-like protein (Dlp). Structural analysis shows that, in the presence of palmitoleoylated peptides, these glypicans change conformation to create a hydrophobic space. Thus, glypicans of the Dlp family protect the lipid of Wnt proteins from the aqueous environment and serve as a reservoir from which Wnt proteins can be handed over to signalling receptors.


    Organizational Affiliation

    The Francis Crick Institute, London, UK. jp.vincent@crick.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dally-like, isoform AA555Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for Q9VUG1 (Drosophila melanogaster)
Explore Q9VUG1 
Go to UniProtKB:  Q9VUG1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O18
Query on O18

Download CCD File 
A
[(2~{S})-2-azanyl-3-oxidanylidene-propyl] (~{Z})-hexadec-9-enoate
C19 H35 N O3
BUNQZTJOMDSTRU-JTHGQSKGSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.691α = 90
b = 77.38β = 90
c = 118.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001204
European Union (EU)European Union294523
European Union (EU)European Union647278
Cancer Research UKUnited KingdomC375/A17721
Cancer Research UKUnited KingdomC20724/A26752
Wellcome TrustUnited Kingdom102164/B/13/Z
Wellcome TrustUnited Kingdom203141/Z/16/Z

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references