+Open data
-Basic information
Entry | Database: PDB / ID: 2ej8 | ||||||
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Title | Crystal structure of APPL1 PTB domain at 1.8A | ||||||
Components | DCC-interacting protein 13 alpha | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / regulation of glucose import / maintenance of synapse structure / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process ...negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / regulation of glucose import / maintenance of synapse structure / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process / regulation of toll-like receptor 4 signaling pathway / vesicle membrane / positive regulation of cytokine production involved in inflammatory response / early phagosome / Caspase activation via Dependence Receptors in the absence of ligand / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / phosphatidylserine binding / beta-tubulin binding / regulation of innate immune response / regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / ruffle / phosphatidylinositol binding / transforming growth factor beta receptor signaling pathway / positive regulation of glucose import / protein import into nucleus / presynapse / insulin receptor signaling pathway / cytoplasmic vesicle / early endosome membrane / postsynapse / early endosome / endosome membrane / endosome / cell cycle / glutamatergic synapse / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å | ||||||
Authors | Tanabe, H. / Hosaka, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of APPL1 PTB domain at 1.8A Authors: Tanabe, H. / Hosaka, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ej8.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ej8.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ej8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/2ej8 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/2ej8 | 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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Unit cell |
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-Components
#1: Protein | Mass: 18054.502 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: E.coli Cell-free expression system / Gene: APPL1 / References: UniProt: Q9UKG1 #2: Water | ChemComp-HOH / | |
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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: 2.04 Å3/Da / Density % sol: 39.61 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100mM Na Citrate, 10% PEG 3350, 15% Isopropanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 24816 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5652 % / Rmerge(I) obs: 0.104 / Rsym value: 0.103 / Net I/σ(I): 9.59801 |
Reflection shell | Resolution: 1.84→1.92 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.73783 / Num. unique all: 1784 / Rsym value: 0.331 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.075 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.; ANOMALOUS DATA WAS USED IN THE REFINEMENT. THE FRIEDEL PAIRS WERE USED FOR POHASING.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.701 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Total num. of bins used: 20 /
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