2YGQ

WIF domain-epidermal growth factor (EGF)-like domains 1-3 of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.951 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.297 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Modular Mechanism of Wnt Signaling Inhibition by Wnt Inhibitory Factor 1

Malinauskas, T., Aricescu, A.R., Lu, W., Siebold, C., Jones, E.Y.

(2011) Nat.Struct.Mol.Biol. 18: 886

  • DOI: 10.1038/nsmb.2081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Wnt morphogens control embryonic development and homeostasis in adult tissues. In vertebrates the N-terminal WIF domain (WIF-1(WD)) of Wnt inhibitory factor 1 (WIF-1) binds Wnt ligands. Our crystal structure of WIF-1(WD) reveals a previously unidenti ...

    Wnt morphogens control embryonic development and homeostasis in adult tissues. In vertebrates the N-terminal WIF domain (WIF-1(WD)) of Wnt inhibitory factor 1 (WIF-1) binds Wnt ligands. Our crystal structure of WIF-1(WD) reveals a previously unidentified binding site for phospholipid; two acyl chains extend deep into the domain, and the head group is exposed to the surface. Biophysical and cellular assays indicate that there is a WIF-1(WD) Wnt-binding surface proximal to the lipid head group but also implicate the five epidermal growth factor (EGF)-like domains (EGFs I-V) in Wnt binding. The six-domain WIF-1 crystal structure shows that EGFs I-V are wrapped back, interfacing with WIF-1(WD) at EGF III. EGFs II-V contain a heparan sulfate proteoglycan (HSPG)-binding site, consistent with conserved positively charged residues on EGF IV. This combination of HSPG- and Wnt-binding properties suggests a modular model for the localization of WIF-1 and for signal inhibition within morphogen gradients.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WNT INHIBITORY FACTOR 1
A
324Homo sapiensMutation(s): 0 
Gene Names: WIF1
Find proteins for Q9Y5W5 (Homo sapiens)
Go to Gene View: WIF1
Go to UniProtKB:  Q9Y5W5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC
Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
PCF
Query on PCF
Download SDF File 
Download CCD File 
A
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
 Ligand Interaction
SCR
Query on SCR
Download SDF File 
Download CCD File 
A
SUCROSE OCTASULFATE
C12 H22 O35 S8
WEPNHBQBLCNOBB-UGDNZRGBSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.951 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.297 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 178.007α = 90.00
b = 178.007β = 90.00
c = 178.007γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2011-08-17
    Type: Database references