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Yorodumi- PDB-1x5z: Solution structure of the fibronectin type-III domain of human pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x5z | ||||||
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Title | Solution structure of the fibronectin type-III domain of human protein tyrosine phosphatase, receptor type, D isoform 4 variant | ||||||
Components | Receptor-type tyrosine-protein phosphatase delta | ||||||
Keywords | HYDROLASE / Fibronectin type III domain containing protein / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules / positive regulation of dendritic spine morphogenesis ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / Synaptic adhesion-like molecules / positive regulation of dendritic spine morphogenesis / negative regulation of receptor signaling pathway via JAK-STAT / phosphate-containing compound metabolic process / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / signaling receptor binding / glutamatergic synapse / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Saito, K. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the fibronectin type-III domain of human protein tyrosine phosphatase, receptor type, D isoform 4 variant Authors: Yoneyama, M. / Saito, K. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x5z.cif.gz | 664.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x5z.ent.gz | 557.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/1x5z ftp://data.pdbj.org/pub/pdb/validation_reports/x5/1x5z | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12272.406 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PTPRD / Plasmid: P050131-05 / References: UniProt: P23468, protein-tyrosine-phosphatase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.37mM fn3 domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |