Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36988.32 
• Atom Count: 2514 
• Residue Count: 327 
• Unique protein chains: 2

3SOQ

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

• DOI: 10.2210/pdb3SOQ/pdb

• Classification: PROTEIN BINDING/Antagonist
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2011-06-30 Released: 2011-09-21 
• Deposition Author(s): Wang, W., Bourhis, E., Zhang, Y., Rouge, L., Wu, Y., Franke, Y., Cochran, A.G.

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Experimental Data Snapshot

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

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

• PubMed: 21944579 
• DOI: 10.1016/j.str.2011.07.005
• Primary Citation of Related Structures:  
  3SOV, 3SOB


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Low-density lipoprotein receptor-related protein 6	A	318	Homo sapiens	Mutation(s): 0  Gene Names: LRP6
Find proteins for O75581 (Homo sapiens) Go to Gene View: LRP6 Go to UniProtKB:  O75581

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Dickkopf-related protein 1	Z	9	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
FUC	A	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	Z	NON-POLYMER	H2 N		--
ACE	Z	NON-POLYMER	C2 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 = 103.320	α = 90.00
b = 46.976	β = 97.27
c = 68.722	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-30 
• Released Date: 2011-09-21 
• Deposition Author(s): Wang, W., Bourhis, E., Zhang, Y., Rouge, L., Wu, Y., Franke, Y., Cochran, A.G.

Revision History 

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