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Yorodumi- PDB-1joc: EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1joc | ||||||
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Title | EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate | ||||||
Components | Early Endosomal Autoantigen 1 | ||||||
Keywords | MEMBRANE PROTEIN / FYVE domain / inositol 3-phosphate binding | ||||||
Function / homology | Function and homology information serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / axonal spine / chemical synaptic transmission, postsynaptic / vesicle fusion / modulation by host of viral process / GTP-dependent protein binding / early endosome to late endosome transport ...serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / axonal spine / chemical synaptic transmission, postsynaptic / vesicle fusion / modulation by host of viral process / GTP-dependent protein binding / early endosome to late endosome transport / Schaffer collateral - CA1 synapse / recycling endosome / endocytosis / early endosome membrane / postsynapse / early endosome / calmodulin binding / glutamatergic synapse / protein homodimerization activity / extracellular exosome / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Dumas, J.J. / Merithew, E. / Rajamani, D. / Hayes, S. / Lawe, D. / Corvera, S. / Lambright, D.G. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Multivalent endosome targeting by homodimeric EEA1. Authors: Dumas, J.J. / Merithew, E. / Sudharshan, E. / Rajamani, D. / Hayes, S. / Lawe, D. / Corvera, S. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1joc.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1joc.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 1joc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/1joc ftp://data.pdbj.org/pub/pdb/validation_reports/jo/1joc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14139.077 Da / Num. of mol.: 2 / Fragment: C-terminal domain, FYVE domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15075 #2: Chemical | ChemComp-ZN / #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: 2.42 Å3/Da / Density % sol: 49.15 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 11% PEG 4000, 50 mM HEPES, 60 mM ammonium acetate, 10% glycerol, and 1.5 mM Ins(1,3)P2, pH 7.0, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.28322, 1.28356, 1.23985 | ||||||||||||
Detector | Type: BRANDEIS - B1 / Detector: CCD / Date: Mar 20, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→20 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.221 / Stereochemistry target values: Engh & Huber Details: Residues 1287 and 1288 were missing from the electron density. | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.221 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.1 |