5GJE

Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1

Matoba, K.Mihara, E.Tamura-Kawakami, K.Miyazaki, N.Maeda, S.Hirai, H.Thompson, S.Iwasaki, K.Takagi, J.

(2017) Cell Rep 18: 32-40

  • DOI: 10.1016/j.celrep.2016.12.017

  • PubMed Abstract: 
  • LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. Although multiple crystal structures are available ...

    LDL-receptor-related protein 6 (LRP6) is a single-pass membrane glycoprotein with a large modular ectodomain and forms a higher order signaling platform upon binding Wnt ligands on the cell surface. Although multiple crystal structures are available for fragments of the LRP6 ectodomain, we lack a consensus view on the overall molecular architecture of the full-length LRP6 and its dynamic aspects. Here, we used negative-stain electron microscopy to probe conformational states of the entire ectodomain of LRP6 in solution and found that the four-module ectodomain undergoes a large bending motion hinged at the junction between the second and the third modules. Importantly, the extent of inter-domain motion is modulated by evolutionarily conserved N-glycan chains proximal to the joint. We also found that the LRP6 ectodomain becomes highly compact upon complexation with the Wnt antagonist Dkk1, suggesting a potential role for the ectodomain conformational change in the regulation of receptor oligomerization and signaling.


    Organizational Affiliation

    Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.,Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan. Electronic address: takagi@protein.osaka-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low-density lipoprotein receptor-related protein 6
A
611Homo sapiensMutation(s): 0 
Gene Names: LRP6
Find proteins for O75581 (Homo sapiens)
Go to Gene View: LRP6
Go to UniProtKB:  O75581
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Low-density lipoprotein receptor-related protein 6
B
616Homo sapiensMutation(s): 1 
Gene Names: LRP6
Find proteins for O75581 (Homo sapiens)
Go to Gene View: LRP6
Go to UniProtKB:  O75581
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Dickkopf-related protein 1
C
85Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release