› 5gje

Electron Microscopy
21Å resolution

Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1

Released:
DOI: 10.2210/pdb5gje/pdb
PDB entry 5gje coloured by chain, front view.
PDB entry 5gje coloured by chain, side view.
PDB entry 5gje coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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
Cell Rep 18 32-40 (2017)
PMID: 28052259
Related structures: EMD-9501

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131058 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Low-density lipoprotein receptor-related protein 6 Chain: A
Molecule details ›
Chain: A
Length: 611 amino acids
Theoretical weight: 69.03 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: O75581 (Residues: 20-630; Coverage: 38%)
Gene name: LRP6
Sequence domains:
Low-density lipoprotein receptor-related protein 6 Chain: B
Molecule details ›
Chain: B
Length: 616 amino acids
Theoretical weight: 69.81 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O75581 (Residues: 631-1246; Coverage: 39%)
Gene name: LRP6
Sequence domains:
Dickkopf-related protein 1 Chain: C
Molecule details ›
Chain: C
Length: 85 amino acids
Theoretical weight: 9.61 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O94907 (Residues: 182-266; Coverage: 36%)
Gene names: DKK1, UNQ492/PRO1008
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand PO4 2 x PO4
Ligand NAG 3 x NAG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 21Å
Relevant EMDB volumes: EMD-9501
Expression systems:
  • Cricetulus griseus
  • Spodoptera frugiperda

Quick links

Citations

13 review citations

Rationale for targeting the Wnt signalling modulator Dickkopf-1 for oncology.
Kagey et al. (2017)
12 more

5 mentions without citation

Identifying Drug Targets in Pancreatic Ductal Adenocarcinoma Through Machine Learning, Analyzing Biomolecular Networks, and Structural Modeling.
Yan et al. (2020)
4 more