3S8V

Crystal structure of LRP6-Dkk1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of the extracellular domain of LRP6 and its complex with DKK1.

Cheng, Z.Biechele, T.Wei, Z.Morrone, S.Moon, R.T.Wang, L.Xu, W.

(2011) Nat Struct Mol Biol 18: 1204-1210

  • DOI: 10.1038/nsmb.2139
  • Primary Citation of Related Structures:  
    3S94, 3S8V, 3S8Z

  • PubMed Abstract: 
  • Low-density-lipoprotein (LDL) receptor-related proteins 5 and 6 (LRP5/6) are Wnt co-receptors essential for Wnt/β-catenin signaling. Dickkopf 1 (DKK1) inhibits Wnt signaling by interacting with the extracellular domains of LRP5/6 and is a drug target for multiple diseases ...

    Low-density-lipoprotein (LDL) receptor-related proteins 5 and 6 (LRP5/6) are Wnt co-receptors essential for Wnt/β-catenin signaling. Dickkopf 1 (DKK1) inhibits Wnt signaling by interacting with the extracellular domains of LRP5/6 and is a drug target for multiple diseases. Here we present the crystal structures of a human LRP6-E3E4-DKK1 complex and the first and second halves of human LRP6's four propeller-epidermal growth factor (EGF) pairs (LRP6-E1E2 and LRP6-E3E4). Combined with EM analysis, these data demonstrate that LRP6-E1E2 and LRP6-E3E4 form two rigid structural blocks, with a short intervening hinge that restrains their relative orientation. The C-terminal domain of DKK1 (DKK1c) interacts with the top surface of the LRP6-E3 YWTD propeller and given their structural similarity, probably also that of the LRP6-E1 propeller, through conserved hydrophobic patches buttressed by a network of salt bridges and hydrogen bonds. Our work provides key insights for understanding LRP5/6 structure and the interaction of LRP5/6 with DKK, as well as for drug discovery.


    Organizational Affiliation

    Department of Biological Structure, University of Washington School of Medicine, Seattle, Washington, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Low-density lipoprotein receptor-related protein 6A, B623Homo 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dickkopf-related protein 1C [auth X]88Homo sapiensMutation(s): 0 
Gene Names: DKK1UNQ492/PRO1008
Find proteins for O94907 (Homo sapiens)
Explore O94907 
Go to UniProtKB:  O94907
NIH Common Fund Data Resources
PHAROS:  O94907
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.384α = 90
b = 105.05β = 90
c = 161.226γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-05-31 
  • Released Date: 2011-10-26 
  • Deposition Author(s): Cheng, Z., Xu, W.

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Database references