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Yorodumi- PDB-4yh7: Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yh7 | |||||||||
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Title | Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1 | |||||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / Trans-synaptic complex / Synapse organizer / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information Interleukin-38 signaling / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / negative regulation of receptor signaling pathway via JAK-STAT ...Interleukin-38 signaling / trans-synaptic signaling / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / negative regulation of receptor signaling pathway via JAK-STAT / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of exocytosis / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of immune response / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / postsynaptic membrane / axon / signaling receptor binding / glutamatergic synapse / dendrite / cell surface / signal transduction / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å | |||||||||
Authors | Yamagata, A. / Fukai, S. | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation. Authors: Yamagata, A. / Yoshida, T. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Iwasawa-Okamoto, S. / Mori, H. / Mishina, M. / Fukai, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yh7.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yh7.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/4yh7 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yh7 | HTTPS FTP |
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-Related structure data
Related structure data | 4yfdC 4yfeC 4yfgC 4yh6C 5y32C 2djuS 2dlhS 4yfc 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 93559.461 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-854 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase | ||
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#2: Protein | Mass: 39816.277 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il1rapl1 / Cell line (production host): Freestyle 293-F / Production host: Homo sapiens (human) / References: UniProt: P59823 | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | ||
#5: Sugar | Sequence details | SEQUENCE OF THE CHAIN A WAS BASED ON ISOFORM 12 OF DATABASE UNP Q64487 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.39 Å3/Da / Density % sol: 77.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% PEG4000, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4.4→50 Å / Num. obs: 17618 / % possible obs: 95.6 % / Redundancy: 4.2 % / Rsym value: 0.072 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 4.4→4.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.2 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YFC, 2DJU, 2DLH Resolution: 4.4→39.09 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 37.84 / 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: 4.4→39.09 Å
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Refine LS restraints |
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LS refinement shell |
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