+Open data
-Basic information
Entry | Database: PDB / ID: 2z0o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of APPL1-BAR-PH 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: 2.58 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of APPL1-BAR-PH domain Authors: Murayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2z0o.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2z0o.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/2z0o ftp://data.pdbj.org/pub/pdb/validation_reports/z0/2z0o | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45002.203 Da / Num. of mol.: 1 / Fragment: residues 1-385 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PX061018-05 / Production host: cell-free protein synthesis (unknown) / References: UniProt: Q9UKG1 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.68 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG3350, 0.2M Ammonium acetate, 0.1M Bis-tris, 0.3M Non-Detergent Sulfo-betaine 195, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9792, 0.964, 0.97942 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.58→30.7 Å / Num. obs: 13536 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.1 | ||||||||||||
Reflection shell | Resolution: 2.58→2.67 Å / Rsym value: 0.17 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.58→30.7 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1036991.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.9513 Å2 / ksol: 0.37266 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→30.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.58→2.74 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|