Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 157.57 kDa 
• Atom Count: 10613 
• Modelled Residue Count: 1298 
• Deposited Residue Count: 1355 
• Unique protein chains: 2

3S2K

Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6.

• DOI: 10.2210/pdb3S2K/pdb

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


• Deposited: 2011-05-16 Released: 2011-11-02 
• Deposition Author(s): Ahn, V.E., Chu, M.L.-H., Choi, H.-J., Tran, D., Abo, A., Weis, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Structural Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6.

Ahn, V.E., Chu, M.L., Choi, H.J., Tran, D., Abo, A., Weis, W.I.

(2011) Dev Cell 21: 862-873

• PubMed: 22000856 
• DOI: 10.1016/j.devcel.2011.09.003
• Primary Citation of Related Structures:  
  3S2K


• PubMed Abstract: 
  

LDL receptor-related proteins 5 and 6 (LRP5/6) are coreceptors for Wnt growth factors, and also bind Dkk proteins, secreted inhibitors of Wnt signaling. The LRP5/6 ectodomain contains four β-propeller/EGF-like domain repeats. The first two repeats, LRP6(1-2), bind to several Wnt variants, whereas LRP6(3-4) binds other Wnts. We present the crystal structure of the Dkk1 C-terminal domain bound to LRP6(3-4), and show that the Dkk1 N-terminal domain binds to LRP6(1-2), demonstrating that a single Dkk1 molecule can bind to both portions of the LRP6 ectodomain and thereby inhibit different Wnts. Small-angle X-ray scattering analysis of LRP6(1-4) bound to a noninhibitory antibody fragment or to full-length Dkk1 shows that in both cases the ectodomain adopts a curved conformation that places the first three repeats at a similar height relative to the membrane. Thus, Wnts bound to either portion of the LRP6 ectodomain likely bear a similar spatial relationship to Frizzled coreceptors.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 6	A, B	629	Homo sapiens	Mutation(s): 0  Gene Names: LRP6
Find proteins for O75581 (Homo sapiens) Explore O75581  Go to UniProtKB:  O75581
NIH Common Fund Data Resources
PHAROS:  O75581 GTEx:  ENSG00000070018

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dickkopf-related protein 1	C	97	Homo sapiens	Mutation(s): 0  Gene Names: DKK1, UNQ492/PRO1008
Find proteins for O94907 (Homo sapiens) Explore O94907  Go to UniProtKB:  O94907
NIH Common Fund Data Resources
PHAROS:  O94907 GTEx:  ENSG00000107984

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.043	α = 90
b = 108.014	β = 90
c = 173.12	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-16 
• Released Date: 2011-11-02 
Deposition Author(s): Ahn, V.E., Chu, M.L.-H., Choi, H.-J., Tran, D., Abo, A., Weis, W.I.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2011-12-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary