6L6R

Crystal structure of LRP6 E1E2-SOST complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains.

Kim, J., Han, W., Park, T., Kim, E.J., Bang, I., Lee, H.S., Jeong, Y., Roh, K., Kim, J., Kim, J.S., Kang, C., Seok, C., Han, J.-K., Choi, H.-J.

(2020) Nat Commun 11: 5357-5357

  • DOI: 10.1038/s41467-020-19155-4
  • Primary Citation of Related Structures:  
    6L6R

  • PubMed Abstract: 

    • Low-density lipoprotein receptor-related protein 6 (LRP6) is a coreceptor of the β-catenin-dependent Wnt signaling pathway. The LRP6 ectodomain binds Wnt proteins, as well as Wnt inhibitors such as sclerostin (SOST), which negatively regulates Wnt signaling in osteocytes ...

    Low-density lipoprotein receptor-related protein 6 (LRP6) is a coreceptor of the β-catenin-dependent Wnt signaling pathway. The LRP6 ectodomain binds Wnt proteins, as well as Wnt inhibitors such as sclerostin (SOST), which negatively regulates Wnt signaling in osteocytes. Although LRP6 ectodomain 1 (E1) is known to interact with SOST, several unresolved questions remain, such as the reason why SOST binds to LRP6 E1E2 with higher affinity than to the E1 domain alone. Here, we present the crystal structure of the LRP6 E1E2-SOST complex with two interaction sites in tandem. The unexpected additional binding site was identified between the C-terminus of SOST and the LRP6 E2 domain. This interaction was confirmed by in vitro binding and cell-based signaling assays. Its functional significance was further demonstrated in vivo using Xenopus laevis embryos. Our results provide insights into the inhibitory mechanism of SOST on Wnt signaling.

    Organizational Affiliation: 

    Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea. choihj@snu.ac.kr.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Low-density lipoprotein receptor-related protein 6A, B622Homo sapiensMutation(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
GTEx:  ENSG00000070018
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SclerostinC, D158Homo sapiensMutation(s): 0 
Gene Names: SOST, UNQ2976/PRO7455/PRO7476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQB4 (Homo sapiens)
Explore Q9BQB4 
Go to UniProtKB:  Q9BQB4
PHAROS:  Q9BQB4
GTEx:  ENSG00000167941
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, G2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF, H3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
 I [auth A], M [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
 L [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 J [auth A], K [auth A], N [auth B], O [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 252.792α = 90
b = 252.792β = 90
c = 86.286γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-10-29 
  • Released Date: 2020-10-28 
    • Deposition Author(s): Choi, H.-J., Kim, J.
Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2016R1A2B4013488
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2019M3E5D6063903

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references