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Yorodumi- PDB-8dvm: Crystal structure of LRP6 E3E4 in complex with disulfide constrai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dvm | ||||||
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Title | Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.6 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / LRP6 / E3E4 / Wnt Signaling / Disulfide constrained peptide / Wnt agonism | ||||||
Function / homology | Function and homology information Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / kinase inhibitor activity / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / Wnt receptor activity ...Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / kinase inhibitor activity / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / Wnt receptor activity / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / Wnt-protein binding / 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 / 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 / Wnt signaling pathway / response to peptide hormone / positive regulation of DNA-binding transcription factor activity / cell-cell adhesion / early endosome membrane / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / chemical synaptic transmission / membrane raft / signaling receptor binding / neuronal cell body / synapse / positive regulation of DNA-templated transcription / 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 | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Thakur, A.K. / Liau, N.P.D. / Sudhamsu, J. / Hannoush, R.N. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Synthetic Multivalent Disulfide-Constrained Peptide Agonists Potentiate Wnt1/ beta-Catenin Signaling via LRP6 Coreceptor Clustering. Authors: Thakur, A.K. / Miller, S.E. / Liau, N.P.D. / Hwang, S. / Hansen, S. / de Sousa E Melo, F. / Sudhamsu, J. / Hannoush, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dvm.cif.gz | 285.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dvm.ent.gz | 225.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dvm_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8dvm_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8dvm_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 8dvm_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/8dvm ftp://data.pdbj.org/pub/pdb/validation_reports/dv/8dvm | HTTPS FTP |
-Related structure data
Related structure data | 8dvlC 8dvnC 4a0pS S: Starting model for refinement 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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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 71774.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LRP6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75581 |
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#2: Protein/peptide | Mass: 3470.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Sugars , 4 types, 5 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1212.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source | ||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
-Non-polymers , 4 types, 242 molecules
#7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-MES / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 100 mM MES pH 6.3, 12% PEG 20K |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.54 Å / Num. obs: 50517 / % possible obs: 98.71 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.68 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 6.7 % / Num. unique obs: 4407 / CC1/2: 0.451 / CC star: 0.788 / % possible all: 87.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A0P Resolution: 2→46.54 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.48 Å2 / Biso mean: 49.3589 Å2 / Biso min: 22.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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