Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 72.81 kDa 
• Atom Count: 5383 
• Modelled Residue Count: 609 
• Deposited Residue Count: 628 
• Unique protein chains: 1

4A0P

Crystal structure of LRP6P3E3P4E4

• PDB DOI: 10.2210/pdb4A0P/pdb

• Classification: SIGNALING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2011-09-11 Released: 2011-10-26 
• Deposition Author(s): Chen, S., Malinauskas, T., Aricescu, A.R., Siebold, C., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structural and Functional Studies of Lrp6 Ectodomain Reveal a Platform for Wnt Signaling.

Chen, S., Bubeck, D., Macdonald, B.T., Liang, W.X., Mao, J.H., Malinauskas, T., Llorca, O., Aricescu, A.R., Siebold, C., He, X., Jones, E.Y.

(2011) Dev Cell 21: 848

• PubMed: 22000855 
• DOI: 10.1016/j.devcel.2011.09.007
• Primary Citation of Related Structures:  
  4A0P


• PubMed Abstract: 
  

LDL-receptor-related protein 6 (LRP6), alongside Frizzled receptors, transduces Wnt signaling across the plasma membrane. The LRP6 ectodomain comprises four tandem β-propeller-EGF-like domain (PE) pairs that harbor binding sites for Wnt morphogens and their antagonists including Dickkopf 1 (Dkk1). To understand how these multiple interactions are integrated, we combined crystallographic analysis of the third and fourth PE pairs with electron microscopy (EM) to determine the complete ectodomain structure. An extensive inter-pair interface, conserved for the first-to-second and third-to-fourth PE interactions, contributes to a compact platform-like architecture, which is disrupted by mutations implicated in developmental diseases. EM reconstruction of the LRP6 platform bound to chaperone Mesd exemplifies a binding mode spanning PE pairs. Cellular and binding assays identify overlapping Wnt3a- and Dkk1-binding surfaces on the third PE pair, consistent with steric competition, but also suggest a model in which the platform structure supports an interplay of ligands through multiple interaction sites.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6	A	628	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	F [auth A], G [auth A], M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.815	α = 90
b = 42.699	β = 97.49
c = 119.879	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-11 
• Released Date: 2011-10-26 
Deposition Author(s): Chen, S., Malinauskas, T., Aricescu, A.R., Siebold, C., Jones, E.Y.

Revision History  

• Version 1.0: 2011-10-26
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary