Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 36.99 kDa 
• Atom Count: 2780 
• Modelled Residue Count: 314 
• Deposited 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

• PDB DOI: 10.2210/pdb3SOQ/pdb

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


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

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:  
  3SOB, 3SOQ, 3SOV


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 6	A	318	Homo sapiens	Mutation(s): 0  Gene Names: LRP6
UniProt & NIH Common Fund Data Resources
Find proteins for O75581 (Homo sapiens) Explore O75581  Go to UniProtKB:  O75581
PHAROS:  O75581

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dickkopf-related protein 1	B [auth Z]	9	Homo sapiens	Mutation(s): 2  Gene Names: DKK1, UNQ492/PRO1008
UniProt & NIH Common Fund Data Resources
Find proteins for O94907 (Homo sapiens) Explore O94907  Go to UniProtKB:  O94907
PHAROS:  O94907

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC	D [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.32	α = 90
b = 46.976	β = 97.27
c = 68.722	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary