5URY

Crystal structure of Frizzled 5 CRD in complex with PAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.098 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding.

Nile, A.H.Mukund, S.Stanger, K.Wang, W.Hannoush, R.N.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 4147-4152

  • DOI: 10.1073/pnas.1618293114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to overactive Wnt signaling in subsets of pancreatic, ovarian, ...

    Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to overactive Wnt signaling in subsets of pancreatic, ovarian, gastric, and colorectal tumors. Despite the progress in biochemical understanding of Wnt-FZD receptor interactions, the molecular basis for recognition of Wnt cis -unsaturated fatty acyl groups by the cysteine-rich domain (CRD) of FZD receptors remains elusive. Here, we determined a crystal structure of human FZD7 CRD unexpectedly bound to a 24-carbon fatty acid. We also report a crystal structure of human FZD5 CRD bound to C16:1 cis -Δ9 unsaturated fatty acid. Both structures reveal a dimeric arrangement of the CRD. The lipid-binding groove exhibits flexibility and spans both monomers, adopting a U-shaped geometry that accommodates the fatty acid. Re-evaluation of the published mouse FZD8 CRD structure reveals that it also shares the same architecture as FZD5 and FZD7 CRDs. Our results define a common molecular mechanism for recognition of the cis -unsaturated fatty acyl group, a necessary posttranslational modification of Wnts, by multiple FZD receptors. The fatty acid bridges two CRD monomers, implying that Wnt binding mediates FZD receptor dimerization. Our data uncover possibilities for the arrangement of Wnt-FZD CRD complexes and shed structural insights that could aide in the identification of pharmacological strategies to modulate FZD receptor function.


    Organizational Affiliation

    Department of Structural Biology, Genentech, South San Francisco, CA 94080.,Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080.,Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080; hannoush.rami@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Frizzled-5
A, B
146Homo sapiensMutation(s): 0 
Gene Names: FZD5 (C2orf31)
Find proteins for Q13467 (Homo sapiens)
Go to Gene View: FZD5
Go to UniProtKB:  Q13467
Small Molecules
Ligands 3 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
PAM
Query on PAM

Download SDF File 
Download CCD File 
A, B
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-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: 2.098 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.170 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.412α = 90.00
b = 123.412β = 90.00
c = 46.951γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release