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Yorodumi- PDB-5bq8: Crystal structure of Norrin, a Wnt signalling activator, Crystal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bq8 | ||||||||||||
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Title | Crystal structure of Norrin, a Wnt signalling activator, Crystal Form II | ||||||||||||
Components | (Norrin) x 3 | ||||||||||||
Keywords | SIGNALING PROTEIN / Wnt signalling pathway / Norrie disease protein / cystine-knot like growth factor / ligand for Frizzled 4 receptor | ||||||||||||
Function / homology | Function and homology information retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / ubiquitin-dependent endocytosis / retina layer formation / retinal pigment epithelium development ...retina blood vessel maintenance / cone retinal bipolar cell differentiation / Norrin signaling pathway / extracellular matrix-cell signaling / re-entry into mitotic cell cycle / retinal blood vessel morphogenesis / retinal rod cell differentiation / ubiquitin-dependent endocytosis / retina layer formation / retinal pigment epithelium development / establishment of blood-retinal barrier / glycine metabolic process / microglial cell proliferation / endothelial cell differentiation / dendritic spine development / establishment of blood-brain barrier / vacuole organization / protein targeting to lysosome / microglia differentiation / frizzled binding / lens development in camera-type eye / exploration behavior / optic nerve development / smoothened signaling pathway / retinal ganglion cell axon guidance / action potential / decidualization / response to axon injury / canonical Wnt signaling pathway / blood vessel remodeling / tricarboxylic acid cycle / visual perception / glutathione metabolic process / transforming growth factor beta receptor signaling pathway / cytokine activity / mitotic cell cycle / nervous system development / cellular response to hypoxia / angiogenesis / collagen-containing extracellular matrix / neuron apoptotic process / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / inflammatory response / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Chang, T.-H. / Hsieh, F.-L. / Harlos, K. / Jones, E.Y. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Elife / Year: 2015 Title: Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan. Authors: Chang, T.H. / Hsieh, F.L. / Zebisch, M. / Harlos, K. / Elegheert, J. / Jones, E.Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bq8.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bq8.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 5bq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/5bq8 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/5bq8 | HTTPS FTP |
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-Related structure data
Related structure data | 5bpbC 5bpqC 5bpuSC 5bqbC 5bqcC 5bqeC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 4 molecules ACBD
#1: Protein | Mass: 13668.798 Da / Num. of mol.: 2 / Fragment: UNP residues 25-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604 #2: Protein | | Mass: 13695.845 Da / Num. of mol.: 1 / Fragment: UNP residues 25-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604 #3: Protein | | Mass: 13722.891 Da / Num. of mol.: 1 / Fragment: UNP residues 25-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NDP, EVR2 / Plasmid: Plasmid / Details (production host): pHLIgK-STR-8H-SUMO-1D4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q00604 |
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-Non-polymers , 3 types, 126 molecules
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 sodium acetate, pH 5.0, 5% PGA-LM, 4% PEG2000MME, 24% PEG550MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.65 Å / Num. obs: 36272 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.289 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BPU Resolution: 2→33.65 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.27 / 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→33.65 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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