3SOQ

The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Wnt antagonists bind through a short peptide to the first beta-propeller domain of LRP5/6.

Bourhis, E.Wang, W.Tam, C.Hwang, J.Zhang, Y.Spittler, D.Huang, O.W.Gong, Y.Estevez, A.Zilberleyb, I.Rouge, L.Chiu, C.Wu, Y.Costa, M.Hannoush, R.N.Franke, Y.Cochran, A.G.

(2011) Structure 19: 1433-1442

  • DOI: 10.1016/j.str.2011.07.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Wnt pathway inhibitors DKK1 and sclerostin (SOST) are important therapeutic targets in diseases involving bone loss or damage. It has been appreciated that Wnt coreceptors LRP5/6 are also important, as human missense mutations that result in bone ...

    The Wnt pathway inhibitors DKK1 and sclerostin (SOST) are important therapeutic targets in diseases involving bone loss or damage. It has been appreciated that Wnt coreceptors LRP5/6 are also important, as human missense mutations that result in bone overgrowth (bone mineral density, or BMD, mutations) cluster to the E1 propeller domain of LRP5. Here, we report a crystal structure of LRP6 E1 bound to an antibody, revealing that the E1 domain is a peptide recognition module. Remarkably, the consensus E1 binding sequence is a close match to a conserved tripeptide motif present in all Wnt inhibitors that bind LRP5/6. We show that this motif is important for DKK1 and SOST binding to LRP6 and for inhibitory function, providing a detailed structural explanation for the effect of the BMD mutations.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech Research and Early Development, 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low-density lipoprotein receptor-related protein 6
A
318Homo sapiensMutation(s): 0 
Gene Names: LRP6
Find proteins for O75581 (Homo sapiens)
Go to Gene View: LRP6
Go to UniProtKB:  O75581
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dickkopf-related protein 1
Z
9Homo sapiensMutation(s): 0 
Gene Names: DKK1
Find proteins for O94907 (Homo sapiens)
Go to Gene View: DKK1
Go to UniProtKB:  O94907
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
Z
NON-POLYMERH2 N

--

ACE
Query on ACE
Z
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.320α = 90.00
b = 46.976β = 97.27
c = 68.722γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references