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- PDB-1joc: EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-di... -
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Open data
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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 | ||||||
![]() | Early Endosomal Autoantigen 1 | ||||||
![]() | MEMBRANE PROTEIN / FYVE domain / inositol 3-phosphate binding | ||||||
Function / homology | ![]() serine-pyruvate aminotransferase complex / synaptic vesicle to endosome fusion / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / chemical synaptic transmission, postsynaptic / axonal spine / modulation by host of viral process / vesicle fusion / 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 / chemical synaptic transmission, postsynaptic / axonal spine / modulation by host of viral process / vesicle fusion / 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 / zinc ion binding / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dumas, J.J. / Merithew, E. / Rajamani, D. / Hayes, S. / Lawe, D. / Corvera, S. / Lambright, D.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.4 KB | Display | ![]() |
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Full document | ![]() | 497 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||
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: ![]() 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: ![]() | |||||||||||||||
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 |