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Yorodumi- PDB-1wgu: Solution Structure of the C-terminal Phosphotyrosine Interaction ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wgu | ||||||
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Title | Solution Structure of the C-terminal Phosphotyrosine Interaction Domain of APBB2 from Mouse | ||||||
Components | amyloid beta (A4) precursor protein-binding, family B, member 2 | ||||||
Keywords | PROTEIN BINDING / phosphotyrosine-interaction domain / amyloid disease / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of cell cycle phase transition / maintenance of lens transparency / smooth muscle contraction / extracellular matrix organization / axon guidance / neuron migration / amyloid-beta binding / early endosome / protein stabilization / positive regulation of apoptotic process ...negative regulation of cell cycle phase transition / maintenance of lens transparency / smooth muscle contraction / extracellular matrix organization / axon guidance / neuron migration / amyloid-beta binding / early endosome / protein stabilization / positive regulation of apoptotic process / regulation of DNA-templated transcription / negative regulation of apoptotic process / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, H. / Hayashi, F. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode Authors: Li, H. / Koshiba, S. / Hayashi, F. / Tochio, N. / Tomizawa, T. / Kasai, T. / Yabuki, T. / Motoda, Y. / Harada, T. / Watanabe, S. / Inoue, M. / Hayashizaki, Y. / Tanaka, A. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wgu.cif.gz | 781 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wgu.ent.gz | 655.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wgu_validation.pdf.gz | 344.8 KB | Display | wwPDB validaton report |
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Full document | 1wgu_full_validation.pdf.gz | 498.8 KB | Display | |
Data in XML | 1wgu_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 1wgu_validation.cif.gz | 73.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/1wgu ftp://data.pdbj.org/pub/pdb/validation_reports/wg/1wgu | HTTPS FTP |
-Related structure data
Related structure data | 2rozC 2yszC 2yt0C 2yt1C C: citing same article (ref.) |
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Similar structure data | |
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: 14750.546 Da / Num. of mol.: 1 / Fragment: Phosphotyrosine-Interaction Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1200015I07 / Plasmid: P031020-58 / References: UniProt: Q9DBR4 |
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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: 0.84mM phosphotyrosine-interaction domain U-13C, 15N; 20mM d-Tris-HCl (PH7.0); 100mM NaCl; 2mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 900 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 |