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Yorodumi- PDB-5un6: Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset -
+Open data
-Basic information
Entry | Database: PDB / ID: 5un6 | ||||||
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Title | Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset | ||||||
Components |
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Keywords | SIGNALING PROTEIN/DE NOVO PROTEIN / SIGNALING PROTEIN-DE NOVO PROTEIN complex | ||||||
Function / homology | Function and homology information Wnt-Frizzled-LRP5/6 complex / Signaling by RNF43 mutants / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / neuronal dense core vesicle / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins ...Wnt-Frizzled-LRP5/6 complex / Signaling by RNF43 mutants / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / Class B/2 (Secretin family receptors) / neuronal dense core vesicle / canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / PDZ domain binding / G protein-coupled receptor activity / neuron differentiation / T cell differentiation in thymus / angiogenesis / positive regulation of protein phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Janda, C.Y. / Garcia, K.C. / Jude, K.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2017 Title: Surrogate Wnt agonists that phenocopy canonical Wnt and beta-catenin signalling. Authors: Janda, C.Y. / Dang, L.T. / You, C. / Chang, J. / de Lau, W. / Zhong, Z.A. / Yan, K.S. / Marecic, O. / Siepe, D. / Li, X. / Moody, J.D. / Williams, B.O. / Clevers, H. / Piehler, J. / Baker, D. ...Authors: Janda, C.Y. / Dang, L.T. / You, C. / Chang, J. / de Lau, W. / Zhong, Z.A. / Yan, K.S. / Marecic, O. / Siepe, D. / Li, X. / Moody, J.D. / Williams, B.O. / Clevers, H. / Piehler, J. / Baker, D. / Kuo, C.J. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5un6.cif.gz | 169.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5un6.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 5un6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5un6_validation.pdf.gz | 478.9 KB | Display | wwPDB validaton report |
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Full document | 5un6_full_validation.pdf.gz | 481.8 KB | Display | |
Data in XML | 5un6_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 5un6_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/5un6 ftp://data.pdbj.org/pub/pdb/validation_reports/un/5un6 | HTTPS FTP |
-Related structure data
Related structure data | 5un5C 4f0aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 14961.150 Da / Num. of mol.: 4 / Fragment: UNP residues 28-150 / Mutation: Q22N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZD8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H461 #2: Protein | Mass: 13824.968 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
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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: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% PEG 3000, 0.1 M Sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K Details: the diffraction images at the SBGrid databank. DOI is 10.15785/SBGRID/422 |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→38.76 Å / Num. obs: 17882 / % possible obs: 99.81 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rsym value: 0.115 / Net I/σ(I): 12.88 |
Reflection shell | Resolution: 3.2→3.418 Å / Num. unique obs: 800 / CC1/2: 0.829 / Rsym value: 0.601 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F0A, calculated model of B12 Resolution: 3.2→19.816 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.816 Å
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Refine LS restraints |
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LS refinement shell |
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