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Yorodumi- PDB-5xwu: Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xwu | |||||||||
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Title | Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig | |||||||||
Components |
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Keywords | CELL ADHESION / synaptic orgnizers | |||||||||
Function / homology | Function and homology information : / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of synapse assembly ...: / Receptor-type tyrosine-protein phosphatases / trans-synaptic signaling / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / dephosphorylation / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron differentiation / presynaptic membrane / receptor complex / signaling receptor binding / glutamatergic synapse / cell surface Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.162 Å | |||||||||
Authors | Goto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation. Authors: Goto-Ito, S. / Yamagata, A. / Sato, Y. / Uemura, T. / Shiroshima, T. / Maeda, A. / Imai, A. / Mori, H. / Yoshida, T. / Fukai, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xwu.cif.gz | 253.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xwu.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xwu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5xwu_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5xwu_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 5xwu_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/5xwu ftp://data.pdbj.org/pub/pdb/validation_reports/xw/5xwu | HTTPS FTP |
-Related 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: 34432.973 Da / Num. of mol.: 2 / Fragment: UNP residues 20-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase #2: Protein | Mass: 40254.949 Da / Num. of mol.: 2 / Fragment: UNP residues 32-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrfn1, Salm2, Semo1 / Production host: Homo sapiens (human) / References: UniProt: Q2WF71 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Chemical | |
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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: 4.04 Å3/Da / Density % sol: 69.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 7% PEG 20000, 0.1M MES (pH 6.0) |
-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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→50 Å / Num. obs: 41658 / % possible obs: 99.8 % / Redundancy: 9.6 % / Net I/σ(I): 7.48 |
-Processing
Software |
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Refinement | Resolution: 3.162→48.71 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.84 / 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: 3.162→48.71 Å
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Refine LS restraints |
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LS refinement shell |
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