6GBI

Wnt signalling


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the Wnt signaling enhancer LYPD6 and its interactions with the Wnt coreceptor LRP6.

Zhao, Y.Ren, J.Lu, W.Harlos, K.Jones, E.Y.

(2018) FEBS Lett 592: 3152-3162

  • DOI: https://doi.org/10.1002/1873-3468.13212
  • Primary Citation of Related Structures:  
    6GBI

  • PubMed Abstract: 

    Ly6/urokinase-type plasminogen activator receptor (uPAR) (LU) domain containing 6 (LYPD6) is a Wnt signaling enhancer that promotes phosphorylation of the Wnt coreceptor low density lipoprotein receptor-related protein 6 (LRP6). It also binds the nicotinic acetylcholine receptor (nAChR). We report here the 1.25 Å resolution structure of the LYPD6 extracellular LU domain and map its interaction with LRP6 by mutagenesis and surface plasmon resonance. The LYPD6 LU structure reveals a 'trifingered protein domain' fold with the middle fingertip bearing an 'NxI' motif, a tripeptide motif associated with LRP5/6 binding by Wnt inhibitors. Of the Ly6 protein family members, only LYPD6 has an NxI motif. Since mutations in the LYPD6 NxI motif abolish or severely reduce interaction with LRP6, our results indicate its key role in the interaction of LYPD6 with LRP6.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ly6/PLAUR domain-containing protein 6104Homo sapiensMutation(s): 0 
Gene Names: LYPD6UNQ3023/PRO9821
UniProt & NIH Common Fund Data Resources
Find proteins for Q86Y78 (Homo sapiens)
Explore Q86Y78 
Go to UniProtKB:  Q86Y78
PHAROS:  Q86Y78
GTEx:  ENSG00000187123 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86Y78
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q86Y78-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.98α = 90
b = 61.98β = 90
c = 68.55γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
xia2data scaling
PHASERphasing
SHARPphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M000141/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary