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Yorodumi- PDB-1wj1: Solution structure of phosphotyrosine interaction domain of mouse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wj1 | ||||||
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Title | Solution structure of phosphotyrosine interaction domain of mouse Numb protein | ||||||
Components | Numb protein | ||||||
Keywords | SIGNALING PROTEIN / PTB / PID domain / Numb protein / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information neuroblast division in subventricular zone / regulation of postsynapse assembly / Degradation of GLI1 by the proteasome / lateral ventricle development / Hedgehog 'on' state / Recycling pathway of L1 / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization ...neuroblast division in subventricular zone / regulation of postsynapse assembly / Degradation of GLI1 by the proteasome / lateral ventricle development / Hedgehog 'on' state / Recycling pathway of L1 / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization / positive regulation of dendrite morphogenesis / clathrin-coated vesicle / positive regulation of neurogenesis / regulation of neuron differentiation / neuroblast proliferation / clathrin-coated pit / forebrain development / axonogenesis / beta-catenin binding / apical part of cell / nervous system development / cytoplasmic vesicle / basolateral plasma membrane / dendritic spine / postsynaptic density / early endosome / endosome membrane / positive regulation of cell migration / cadherin binding / glutamatergic synapse / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Sato, M. / Tomizawa, T. / Koshiba, S. / Tochio, N. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of phosphotyrosine interaction domain of mouse Numb protein Authors: Sato, M. / Tomizawa, T. / Koshiba, S. / Tochio, N. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 700 | SHEET AUTHOR DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wj1.cif.gz | 928.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wj1.ent.gz | 775.1 KB | Display | PDB format |
PDBx/mmJSON format | 1wj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wj1_validation.pdf.gz | 344.5 KB | Display | wwPDB validaton report |
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Full document | 1wj1_full_validation.pdf.gz | 523.9 KB | Display | |
Data in XML | 1wj1_validation.xml.gz | 73.1 KB | Display | |
Data in CIF | 1wj1_validation.cif.gz | 90.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/1wj1 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/1wj1 | HTTPS FTP |
-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: 17226.615 Da / Num. of mol.: 1 / Fragment: PID domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1200002O22 / Plasmid: P031020-52 / References: UniProt: Q9QZS3 |
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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: 1.3mM PID domain U-15N,13C; 20mM phosphate buffer NA; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-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: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |