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8ctg

Extracellular architecture of an engineered canonical Wnt signaling ternary complex

Method: ELECTRON MICROSCOPY Dmax: 129.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Frizzled-8

Mus musculus

UniProt Q61091

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 28–150 Not recorded Protein Wnt-8 × 1 （P28026） Low-density lipoprotein receptor-related protein 6 × 1 （O75581） PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE；3 s blotting before plunging Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8CTG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IJY CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 (MFZ8) Deposited 2001-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–155（128 aa） Fragment：CYSTEINE-RICH DOMAIN
Chain B 28–155（128 aa） Fragment：CYSTEINE-RICH DOMAIN
Mutation：N22E, N125E Mutation：N22E, N125E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；Ammonium Sulfate, Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.35 Å R-free 0.247
4F0A Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8 Deposited 2012-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–150（123 aa） Fragment：cysteine-rich domain, UNP residues 28-150
Not recorded PAM PALMITOLEIC ACID × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；4-10 % (w/v) PEG 400 15-25 mM Zinc acetate 100 mM Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.25 Å R-free 0.234
6AHY Wnt signaling complex Deposited 2018-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–159（132 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 1 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES-NaOH (pH 7.5), 0.1 M LiCl, 20%(v/v) Ethylene glycol, 7%(w/v) PEG 4000
Resolution 2.80 Å R-free 0.244
6AHY Wnt signaling complex Deposited 2018-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–159（132 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES-NaOH (pH 7.5), 0.1 M LiCl, 20%(v/v) Ethylene glycol, 7%(w/v) PEG 4000
Resolution 2.80 Å R-free 0.244
6AHY Wnt signaling complex Deposited 2018-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–159（132 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES-NaOH (pH 7.5), 0.1 M LiCl, 20%(v/v) Ethylene glycol, 7%(w/v) PEG 4000
Resolution 2.80 Å R-free 0.244
6TFB Carbamazepine binds Frizzled8 Deposited 2019-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–151（124 aa）
Not recorded GOL GLYCEROL × 2 N6W benzo[b][1]benzazepine-11-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 1.68 Å R-free 0.265
6TFB Carbamazepine binds Frizzled8 Deposited 2019-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–151（124 aa）
Not recorded GOL GLYCEROL × 1 N6W benzo[b][1]benzazepine-11-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 1.68 Å R-free 0.265
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FZD8_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–123； UniProt 28–150

Protein Wnt-8

Xenopus laevis

UniProt P28026

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 22–329 Not recorded Frizzled-8 × 1 （Q61091） Low-density lipoprotein receptor-related protein 6 × 1 （O75581） PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE；3 s blotting before plunging Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8CTG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4F0A Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8 Deposited 2012-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–338（316 aa） Fragment：UNP residues 23-338
Not recorded PAM PALMITOLEIC ACID × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；4-10 % (w/v) PEG 400 15-25 mM Zinc acetate 100 mM Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.25 Å R-free 0.234

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WNT8_XENLA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–309； UniProt 22–329

Low-density lipoprotein receptor-related protein 6

Homo sapiens

UniProt O75581

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 20–629 Not recorded Frizzled-8 × 1 （Q61091） Protein Wnt-8 × 1 （P28026） PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE；3 s blotting before plunging Resolution 3.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8CTG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
21KR A Wnt3a/Fzd8-CRD/LRP6-E3E4 complex with FKBP Deposited 2025-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 630–1245（616 aa）
Chain F 630–1245（616 aa）
Mutation：C715S Mutation：C715S No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
21KS A Wnt3a/Fzd8-CRD/LRP6-E3E4-LA complex with FKBP Deposited 2025-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 630–1370（741 aa）
Chain F 630–1370（741 aa）
Mutation：C840S Mutation：C840S No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.01 Å
21KT Wnt3a signalosome extracellular complex Deposited 2025-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain B 630–1245（616 aa）
Chain F 630–1245（616 aa）
Mutation：C715S Mutation：C715S No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.33 Å
3S2K Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6. Deposited 2011-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 630–1246（617 aa） Fragment：ectodomain repeats 3, 4 UNP residues 630-1246
Chain B 630–1246（617 aa） Fragment：ectodomain repeats 3, 4 UNP residues 630-1246
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；10-15% PEG3350, 100 mM Tris-Cl (pH 8.5), 100 mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.251
3S8V Crystal structure of LRP6-Dkk1 complex Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 629–1243（615 aa） Fragment：E3E4, residues 629-1243
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；20mM citric acid, 80mM Bis-tris propane pH 8.8, 19-20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.292
3S8V Crystal structure of LRP6-Dkk1 complex Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 629–1243（615 aa） Fragment：E3E4, residues 629-1243
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；20mM citric acid, 80mM Bis-tris propane pH 8.8, 19-20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.292
3S8Z Crystal structure of LRP6-E3E4 Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 629–1243（615 aa） Fragment：E3E4, residues 629-1243
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM ADA pH 6.5, 100mM MgCl2, 12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.282
3S94 Crystal structure of LRP6-E1E2 Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–630（611 aa） Fragment：E1E2, residues 20-630
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；80mM sodium citrate pH 5.5, 20-21% PEG3350, 40mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.296
3S94 Crystal structure of LRP6-E1E2 Deposited 2011-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 20–630（611 aa） Fragment：E1E2, residues 20-630
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；80mM sodium citrate pH 5.5, 20-21% PEG3350, 40mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.296
3SOB The structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB Deposited 2011-06-30 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 20–335（316 aa） Fragment：UNP residues 20-335
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M NaCl, 0.1 M Tris pH 8, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.90 Å R-free 0.212
3SOQ The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1 peptide Deposited 2011-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–326（307 aa） Fragment：UNP residues 20-335
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1 GOL GLYCEROL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.90 Å R-free 0.221
3SOV The structure of a beta propeller domain in complex with peptide S Deposited 2011-06-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–326（307 aa） Fragment：UNP residues 20-335
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FUC alpha-L-fucopyranose × 4 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M potassium thiocyanate and 30% (w/v) PEG MME 2000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.27 Å R-free 0.180
4A0P Crystal structure of LRP6P3E3P4E4 Deposited 2011-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 629–1244（616 aa） Fragment：P3E3P4E4, RESIDUES 629-1244
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.211
4DG6 Crystal structure of domains 1 and 2 of LRP6 Deposited 2012-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 20–635（616 aa） Fragment：UNP residues 20-635
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 5.9；292 K；20% PEG 8000, 20mM ammonium sulfate, pH 5.9, hanging drop, temperature 292K
Resolution 2.90 Å R-free 0.313
5AIR Structural analysis of mouse GSK3beta fused with LRP6 peptide. Deposited 2015-02-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1565–1575（11 aa） Fragment：;RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 ;
Chain B 1565–1575（11 aa） Fragment：;RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 ;
Not recorded MLI MALONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；200 MM SODIUM MALONATE, 20 % (V/V) PEG 3350, pH 7
Resolution 2.53 Å R-free 0.260
5FWW Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4) Deposited 2016-02-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 630–1246（617 aa） Fragment：PE3PE4, RESIDUES 630-1246
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20 %W/V PEG3350 0.2 M NA/K-PHOSPHATE, pH 7.5
Resolution 3.50 Å R-free 0.355
5GJE Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 Deposited 2016-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–630（611 aa） Fragment：UNP residues 20-630
Chain B 631–1246（616 aa） Fragment：UNP residues 631-1246
Mutation：V1062I PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
Resolution 21.00 Å
6H15 Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-B10 Deposited 2018-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 630–1244（615 aa）
Chain B 630–1244（615 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CL CHLORIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M sodium citrate, 0.2 M sodium acetate trihydrate pH 5.5, 10 % PEG w/v 4000
Resolution 2.60 Å R-free 0.247
6H16 Structure of LRP6 P3E3P4E4 in complex with VHH L-P2-D07 Deposited 2018-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 630–1244（615 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES pH 5.0, 10 % w/v PEG 6000
Resolution 2.90 Å R-free 0.252
6L6R Crystal structure of LRP6 E1E2-SOST complex Deposited 2019-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–630（610 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；301 K；PEG 8000, magnesium acetate, sodium citrate, HEPES
Resolution 3.80 Å R-free 0.256
6L6R Crystal structure of LRP6 E1E2-SOST complex Deposited 2019-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–630（610 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；301 K；PEG 8000, magnesium acetate, sodium citrate, HEPES
Resolution 3.80 Å R-free 0.256
7NAM LRP6_E1 in complex with Lr-EET-3.5 Deposited 2021-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–326（307 aa）
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% w/v PEG 3350, 0.2 M Na malate, pH 7.0
Resolution 1.60 Å R-free 0.193
8DVL Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.18 Deposited 2022-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 631–1253（623 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；0.1 M Bis-Tris 6.3, 18% PEG 10K
Resolution 2.50 Å R-free 0.245
8DVM Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.6 Deposited 2022-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 631–1253（623 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 14 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；100 mM MES pH 6.3, 12% PEG 20K
Resolution 2.00 Å R-free 0.221
8DVN Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.10 Deposited 2022-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 631–1253（623 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2 M KSCN
Resolution 2.53 Å R-free 0.246
8FFE Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide Deposited 2022-12-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 20–631（612 aa）
Not recorded GOL GLYCEROL × 7 NA SODIUM ION × 3 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；100 mM SPG (succinate/phosphate/glycine buffer), 25% PEG 1500
Resolution 1.72 Å R-free 0.231
8S7C Ternary Complex of Cachd1, FZD5 and LRP6 Deposited 2024-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 629–1244（616 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 4.5；296 K；0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5
Resolution 4.70 Å R-free 0.261
8S7C Ternary Complex of Cachd1, FZD5 and LRP6 Deposited 2024-02-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 629–1244（616 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 4.5；296 K；0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5
Resolution 4.70 Å R-free 0.261
8S7C Ternary Complex of Cachd1, FZD5 and LRP6 Deposited 2024-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 629–1244（616 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 4.5；296 K；0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5
Resolution 4.70 Å R-free 0.261
9FIW MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA Deposited 2024-05-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1516–1521（6 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Resolution 2.82 Å R-free 0.246
9FIX MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA Deposited 2024-05-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1516–1526（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Resolution 2.78 Å R-free 0.233
9FIY MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRHFA Deposited 2024-05-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1521–1526（6 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol
Resolution 2.88 Å R-free 0.242

27 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LRP6_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–612； UniProt 20–629

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8ctg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ctg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ctg
Deposition date deposition_date2022-05-14
Structure title titleExtracellular architecture of an engineered canonical Wnt signaling ternary complex
Keywords keywordssignaling complex, beta-catenin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.07 Å
Radius of gyration Rg (electron density) rg_electron40.06 Å
Forward intensity I(0) i0118950000.00
Molecular weight molecular_weight72268.0 kDa
Excluded volume excluded_volume83490 ų
Envelope volume envelope_volume164190 ų
Hydration-shell volume shell_volume35858 ų
Envelope diameter envelope_diameter131.5 Å
Shell Rg shell_rg43.71 Å
Envelope Rg envelope_rg38.43 Å
Shape Rg shape_rg39.93 Å
Total Rg total_rg40.61 Å
Total atoms total_atoms5100
Residues n_residues1006
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax129.3 Å
Rg (real space) rg_real40.14 Å
Rg uncertainty (real space) rg_real_error1.09 Å
I(0) (real space) i0_real1.1900e+08
I(0) uncertainty (real space) i0_real_error1.9430e+06
Rg (reciprocal space) rg_reciprocal40.07 Å
I(0) (reciprocal space) i0_reciprocal118900000.0000
Solution quality estimate total_estimate0.8640
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.0 Å
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.587
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6946000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.486
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8ctgC01
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily30 — TolB, C-terminal domain
Domain ID domain_id8ctgC02
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily30 — TolB, C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)