4F0A

Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of Wnt recognition by Frizzled.

Janda, C.Y.Waghray, D.Levin, A.M.Thomas, C.Garcia, K.C.

(2012) Science 337: 59-64

  • DOI: 10.1126/science.1222879

  • PubMed Abstract: 
  • Wnts are lipid-modified morphogens that play critical roles in development principally through engagement of Frizzled receptors. The 3.25 angstrom structure of Xenopus Wnt8 (XWnt8) in complex with mouse Frizzled-8 (Fz8) cysteine-rich domain (CRD) rev ...

    Wnts are lipid-modified morphogens that play critical roles in development principally through engagement of Frizzled receptors. The 3.25 angstrom structure of Xenopus Wnt8 (XWnt8) in complex with mouse Frizzled-8 (Fz8) cysteine-rich domain (CRD) reveals an unusual two-domain Wnt structure, not obviously related to known protein folds, resembling a "hand" with "thumb" and "index" fingers extended to grasp the Fz8-CRD at two distinct binding sites. One site is dominated by a palmitoleic acid lipid group projecting from serine 187 at the tip of Wnt's thumb into a deep groove in the Fz8-CRD. In the second binding site, the conserved tip of Wnt's "index finger" forms hydrophobic amino acid contacts with a depression on the opposite side of the Fz8-CRD. The conservation of amino acids in both interfaces appears to facilitate ligand-receptor cross-reactivity, which has important implications for understanding Wnt's functional pleiotropy and for developing Wnt-based drugs for cancer and regenerative medicine.


    Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Frizzled-8
A
132Mus musculusGene Names: Fzd8
Find proteins for Q61091 (Mus musculus)
Go to UniProtKB:  Q61091
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein Wnt-8
B
316Xenopus laevisGene Names: wnt8
Find proteins for P28026 (Xenopus laevis)
Go to UniProtKB:  P28026
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PAM
Query on PAM

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Download CCD File 
B
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 110.070α = 90.00
b = 110.070β = 90.00
c = 82.820γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SHARPphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-18
    Type: Database references
  • Version 1.2: 2013-09-25
    Type: Derived calculations, Non-polymer description
  • Version 1.3: 2013-10-09
    Type: Non-polymer description