+Open data
-Basic information
Entry | Database: PDB / ID: 5c5b | ||||||
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Title | Crystal Structure of Human APPL BAR-PH Heterodimer | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / heterodimer | ||||||
Function / homology | Function and homology information negative regulation of cellular response to insulin stimulus / positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / early phagosome membrane / negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of fatty acid oxidation / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / cold acclimation ...negative regulation of cellular response to insulin stimulus / positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / early phagosome membrane / negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of fatty acid oxidation / positive regulation of macropinocytosis / adiponectin-activated signaling pathway / macropinosome / regulation of fibroblast migration / cold acclimation / negative regulation of neural precursor cell proliferation / maintenance of synapse structure / regulation of glucose import / protein kinase B binding / signaling / positive regulation of melanin biosynthetic process / regulation of toll-like receptor 4 signaling pathway / positive regulation of phagocytosis, engulfment / vesicle membrane / negative regulation of glucose import / positive regulation of cytokine production involved in inflammatory response / early phagosome / Caspase activation via Dependence Receptors in the absence of ligand / regulation of innate immune response / cellular response to hepatocyte growth factor stimulus / intracellular vesicle / phosphatidylserine binding / beta-tubulin binding / diet induced thermogenesis / regulation of G1/S transition of mitotic cell cycle / negative regulation of cytokine production involved in inflammatory response / regulation of protein localization to plasma membrane / ruffle / phosphatidylinositol binding / transforming growth factor beta receptor signaling pathway / positive regulation of glucose import / ruffle membrane / negative regulation of neurogenesis / protein import into nucleus / glucose homeostasis / presynapse / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / cytoplasmic vesicle / early endosome membrane / postsynapse / protein homotetramerization / vesicle / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Chen, Y.J. / Chen, B. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Human APPL BAR-PH Heterodimer Authors: Chen, Y.J. / Chen, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c5b.cif.gz | 289.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c5b.ent.gz | 233.6 KB | Display | PDB format |
PDBx/mmJSON format | 5c5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/5c5b ftp://data.pdbj.org/pub/pdb/validation_reports/c5/5c5b | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 42966.359 Da / Num. of mol.: 2 / Fragment: BAR-PH domain, UNP residues 5-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APPL1, APPL, DIP13A, KIAA1428 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKG1 #2: Protein | Mass: 42434.359 Da / Num. of mol.: 2 / Fragment: UNP residues 1-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APPL2, DIP13B / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NEU8 #3: Chemical | #4: 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: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M disodium hydrogen phosphate, 18% (w/v) PEG3350, 100 mM HEPES, and 1 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 28, 2009 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 46308 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.89 |
Reflection shell | Mean I/σ(I) obs: 1.72 / % possible all: 90.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.077 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.14 Å2 / Biso mean: 68.2411 Å2 / Biso min: 21.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→49.077 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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