+Open data
-Basic information
Entry | Database: PDB / ID: 5urz | |||||||||
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Title | Crystal structure of Frizzled 5 CRD in complex with BOG | |||||||||
Components | Frizzled-5 | |||||||||
Keywords | SIGNALING PROTEIN / Frizzled 5 / CRD | |||||||||
Function / homology | Function and homology information regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / cellular response to molecule of bacterial origin / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / chorionic trophoblast cell differentiation / embryonic camera-type eye morphogenesis / glandular epithelial cell maturation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 ...regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / cellular response to molecule of bacterial origin / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / chorionic trophoblast cell differentiation / embryonic camera-type eye morphogenesis / glandular epithelial cell maturation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / apoptotic process involved in morphogenesis / anterior/posterior axis specification, embryo / embryonic axis specification / Wnt receptor activity / regulation of mitophagy / non-canonical Wnt signaling pathway / intestinal epithelial cell maturation / Wnt-protein binding / branching involved in labyrinthine layer morphogenesis / Class B/2 (Secretin family receptors) / regulation of bicellular tight junction assembly / Disassembly of the destruction complex and recruitment of AXIN to the membrane / labyrinthine layer blood vessel development / positive regulation of protein targeting to mitochondrion / canonical Wnt signaling pathway / bicellular tight junction / synapse assembly / Regulation of FZD by ubiquitination / positive regulation of interleukin-1 beta production / Asymmetric localization of PCP proteins / G protein-coupled receptor activity / clathrin-coated endocytic vesicle membrane / neuron differentiation / positive regulation of T cell cytokine production / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / Ca2+ pathway / T cell differentiation in thymus / amyloid-beta binding / perikaryon / early endosome membrane / angiogenesis / axon / negative regulation of cell population proliferation / Golgi membrane / dendrite / synapse / lipid binding / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.202 Å | |||||||||
Authors | Mukund, S. / Nile, A.H. / Stanger, K. / Hannoush, R.N. / Wang, W. | |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding. Authors: Nile, A.H. / Mukund, S. / Stanger, K. / Wang, W. / 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 | 5urz.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5urz.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 5urz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/5urz ftp://data.pdbj.org/pub/pdb/validation_reports/ur/5urz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16769.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZD5, C2orf31 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13467 #2: Polysaccharide | alpha-L-fucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-BOG / | #4: Water | ChemComp-HOH / | |
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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: 3.05 Å3/Da / Density % sol: 59.73 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate tribasic dehydrate pH 5.5, 22% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 20901 / % possible obs: 99.9 % / Redundancy: 10.8 % / Net I/σ(I): 25.4 |
-Processing
Software |
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Refinement | Resolution: 2.202→29.556 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.76 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.202→29.556 Å
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Refine LS restraints |
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LS refinement shell |
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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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