+Open data
-Basic information
Entry | Database: PDB / ID: 2z0n | ||||||
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Title | Crystal structure of APPL1-BAR domain | ||||||
Components | DCC-interacting protein 13-alpha | ||||||
Keywords | SIGNALING PROTEIN / helix bundle / Cell cycle / Coiled coil / Endosome / Membrane / Nucleus / Phosphorylation / Structural Genomics / 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 / MAD / Resolution: 1.95 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Sakamoto, A. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of APPL1-BAR domain Authors: Murayama, K. / Kato-Murayama, M. / Sakamoto, A. / 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 | 2z0n.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z0n.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 2z0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z0n ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z0n | 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: 32708.053 Da / Num. of mol.: 1 / Fragment: reisdues 1-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKG1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 17.5% PEG3350, 0.2M Ammonium sulfate, 0.1M Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.979089, 0.979462, 0.964 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→50 Å / Num. obs: 19533 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 16.8 | ||||||||||||
Reflection shell | Resolution: 1.95→2.02 Å / Rsym value: 0.341 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→35.52 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1385109.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.905 Å2 / ksol: 0.375848 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→35.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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