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Yorodumi- PDB-4uzq: STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEO... -
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-Basic information
Entry | Database: PDB / ID: 4uzq | ||||||
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Title | STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A | ||||||
Components |
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Keywords | HYDROLASE / ESTERASE / EXTRACELLULAR / ALPHA/BETA HYDROLASE | ||||||
Function / homology | Function and homology information postsynapse assembly / positive regulation of excitatory synapse assembly / regulation of axon diameter / positive regulation of protein localization to presynapse / skeletal muscle satellite cell activation / asymmetric protein localization involved in cell fate determination / excitatory synapse assembly / cerebellar granule cell differentiation / lens fiber cell development / synaptic vesicle recycling ...postsynapse assembly / positive regulation of excitatory synapse assembly / regulation of axon diameter / positive regulation of protein localization to presynapse / skeletal muscle satellite cell activation / asymmetric protein localization involved in cell fate determination / excitatory synapse assembly / cerebellar granule cell differentiation / lens fiber cell development / synaptic vesicle recycling / WNT ligand biogenesis and trafficking / oviduct development / central nervous system vasculogenesis / cell proliferation in forebrain / uterus morphogenesis / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / secondary palate development / embryonic axis specification / somatic stem cell division / presynapse assembly / sex differentiation / positive regulation of epithelial cell proliferation involved in wound healing / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / stem cell development / establishment of blood-brain barrier / neurotransmitter secretion / phospholipase C activity / Release of Hh-Np from the secreting cell / dendritic spine morphogenesis / frizzled binding / regulation of bone mineralization / dorsal/ventral pattern formation / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / Class B/2 (Secretin family receptors) / positive regulation of synapse assembly / wound healing, spreading of epidermal cells / Wnt signaling pathway, planar cell polarity pathway / regulation of postsynapse organization / regulation of synaptic vesicle exocytosis / embryonic digit morphogenesis / cartilage condensation / establishment of cell polarity / negative regulation of Wnt signaling pathway / somatic stem cell population maintenance / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / cell fate commitment / canonical Wnt signaling pathway / chondrocyte differentiation / cellular response to transforming growth factor beta stimulus / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / axonogenesis / extracellular matrix / cytokine activity / positive regulation of JNK cascade / Post-translational protein phosphorylation / Schaffer collateral - CA1 synapse / bone development / negative regulation of canonical Wnt signaling pathway / neuron differentiation / Wnt signaling pathway / negative regulation of neurogenesis / Golgi lumen / response to estrogen / endocytic vesicle membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / presynapse / response to estradiol / angiogenesis / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / glutamatergic synapse / apoptotic process / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å | ||||||
Authors | Zebisch, M. / Jones, E.Y. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Notum Deacylates Wnt Proteins to Suppress Signalling Activity. Authors: Kakugawa, S. / Langton, P.F. / Zebisch, M. / Howell, S.A. / Chang, T. / Liu, Y. / Feizi, T. / Bineva, G. / O'Reilly, N. / Snijders, A.P. / Jones, E.Y. / Vincent, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uzq.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uzq.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 4uzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uzq_validation.pdf.gz | 521.9 KB | Display | wwPDB validaton report |
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Full document | 4uzq_full_validation.pdf.gz | 526 KB | Display | |
Data in XML | 4uzq_validation.xml.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uzq ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uzq | HTTPS FTP |
-Related structure data
Related structure data | 4uyuC 4uywC 4uyzC 4uz1C 4uz5C 4uz6C 4uz7C 4uz9C 4uzaC 4uzjC 4uzkC 4uzlC 4wbhC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 43974.547 Da / Num. of mol.: 1 / Fragment: RESIDUES 81-451 / Mutation: YES Source method: isolated from a genetically manipulated source Details: GLYCOSYLATED AT N96 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6P988, carboxylesterase |
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#2: Protein/peptide | Mass: 749.838 Da / Num. of mol.: 1 / Fragment: RESIDUES 202-209 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O00755 |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 311 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PAM / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | GAMMA-PALMITOLEOSequence details | C330S ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 3.0M NACL, 0.1 M CITRATE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.00,1.07 | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2014 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→60 Å / Num. obs: 64352 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.5→60.44 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.98 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.448 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→60.44 Å
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