3SOB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
antibody light chainL237Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Low-density lipoprotein receptor-related protein 6B316Homo sapiensMutation(s): 0 
Gene Names: LRP6
Find proteins for O75581 (Homo sapiens)
Explore O75581 
Go to UniProtKB:  O75581
NIH Common Fund Data Resources
PHAROS  O75581
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
antibody heavy chainH256Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.037α = 90
b = 83.363β = 111.8
c = 62.844γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2014-05-14
    Changes: Refinement description