+Open data
-Basic information
Entry | Database: PDB / ID: 2elb | ||||||
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Title | Crystal Structure of the BAR-PH domain of human APPL1 | ||||||
Components | Adapter protein containing PH domain, PTB domain and leucine zipper motif 1 | ||||||
Keywords | PROTEIN BINDING / APPL / BAR domain / PH domain | ||||||
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: 2.6 Å | ||||||
Authors | Li, J. / Mao, X. / Dong, L.Q. / Liu, F. / Tong, L. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Crystal Structures of the BAR-PH and PTB Domains of Human APPL1 Authors: Li, J. / Mao, X. / Dong, L.Q. / Liu, F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2elb.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2elb.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 2elb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/2elb ftp://data.pdbj.org/pub/pdb/validation_reports/el/2elb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 45987.117 Da / Num. of mol.: 1 / Fragment: The BAR-PH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKG1 |
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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: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES (pH 7.5), 22% (w/v) polyacrylic acid 5100, 20mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 22741 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 27.5853 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 5.94 / Num. unique all: 2267 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→29.84 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 594181.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.6318 Å2 / ksol: 0.304871 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
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Xplor file |
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