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Yorodumi- PDB-8ctg: Extracellular architecture of an engineered canonical Wnt signali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ctg | ||||||||||||
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Title | Extracellular architecture of an engineered canonical Wnt signaling ternary complex | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / signaling complex / beta-catenin | ||||||||||||
Function / homology | Function and homology information negative regulation of cardiac cell fate specification / Spemann organizer formation / neural crest cell fate commitment / Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Asymmetric localization of PCP proteins / neural crest formation / Signaling by RNF43 mutants / embryonic axis specification ...negative regulation of cardiac cell fate specification / Spemann organizer formation / neural crest cell fate commitment / Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Asymmetric localization of PCP proteins / neural crest formation / Signaling by RNF43 mutants / embryonic axis specification / kinase inhibitor activity / toxin transmembrane transporter activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / midbrain dopaminergic neuron differentiation / cellular response to cholesterol / negative regulation of protein serine/threonine kinase activity / dopaminergic neuron differentiation / frizzled binding / Wnt signalosome / neural crest cell differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / anterior/posterior axis specification / neuronal dense core vesicle / negative regulation of smooth muscle cell apoptotic process / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / Regulation of FZD by ubiquitination / TCF dependent signaling in response to WNT / protein localization to plasma membrane / G protein-coupled receptor activity / PDZ domain binding / positive regulation of DNA-binding transcription factor activity / Wnt signaling pathway / response to peptide hormone / cell-cell adhesion / endocytosis / cell-cell signaling / nervous system development / positive regulation of cytosolic calcium ion concentration / early endosome membrane / T cell differentiation in thymus / cytoplasmic vesicle / protease binding / chemical synaptic transmission / angiogenesis / collagen-containing extracellular matrix / positive regulation of protein phosphorylation / membrane raft / signaling receptor binding / neuronal cell body / ubiquitin protein ligase binding / synapse / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Xenopus laevis (African clawed frog) Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Tsutsumi, N. / Jude, K.M. / Garcia, K.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Structure of the Wnt-Frizzled-LRP6 initiation complex reveals the basis for coreceptor discrimination. Authors: Naotaka Tsutsumi / Sunhee Hwang / Deepa Waghray / Simon Hansen / Kevin M Jude / Nan Wang / Yi Miao / Caleb R Glassman / Nathanael A Caveney / Claudia Y Janda / Rami N Hannoush / K Christopher Garcia / Abstract: Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the ...Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the shared LRP5/6 coreceptors to initiate β-catenin signaling. The cryo-EM structure of a ternary initiation complex of an affinity-matured XWnt8-Frizzled8-LRP6 complex elucidates the basis of coreceptor discrimination by canonical Wnts by means of their N termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker "grafts" were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ctg.cif.gz | 157.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ctg.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ctg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ctg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ctg_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ctg_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 8ctg_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/8ctg ftp://data.pdbj.org/pub/pdb/validation_reports/ct/8ctg | HTTPS FTP |
-Related structure data
Related structure data | 26989MC 8ffeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 15061.343 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd8 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q61091 |
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#2: Protein | Mass: 36676.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: wnt8 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P28026 |
#3: Protein | Mass: 73384.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: O75581 |
#4: Chemical | ChemComp-PAM / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.13 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: haXWnt8-mFzd8CRD-hLRP6E1E2 | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 s blotting before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Calibrated magnification: 58680 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10077 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3840364 / Details: Particles include duplicates and junk. | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82235 Details: Model resolution is substantially lower and estimated to be ~10 angstrom based on the map-model FSC. Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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