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- PDB-7a0v: Crystal structure of the 5-phosphatase domain of Synaptojanin1 in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a0v | ||||||||||||
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Title | Crystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody | ||||||||||||
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![]() | HYDROLASE / Inositol polyphosphate 5-phosphatase / Phosphoinositide / Parkinson's disease / Epilepsy | ||||||||||||
Function / homology | ![]() positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / clathrin coat of coated pit ...positive regulation of endosome organization / phosphatidylinositol phosphate 5-phosphatase activity / phosphatidylinositol-4-phosphate phosphatase activity / phosphatidylinositol phosphate 4-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / clathrin coat of coated pit / synaptic vesicle uncoating / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / membrane coat / phosphatidylinositol dephosphorylation / membrane organization / vesicle membrane / phosphatidylinositol biosynthetic process / neurotransmitter transport / synaptic vesicle priming / synaptic vesicle transport / Synthesis of IP3 and IP4 in the cytosol / Synthesis of PIPs at the plasma membrane / synaptic vesicle endocytosis / learning / synaptic membrane / terminal bouton / SH3 domain binding / presynapse / Clathrin-mediated endocytosis / perinuclear region of cytoplasm / RNA binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Paesmans, J. / Galicia, C. / Martin, E. / Versees, W. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations. Authors: Paesmans, J. / Martin, E. / Deckers, B. / Berghmans, M. / Sethi, R. / Loeys, Y. / Pardon, E. / Steyaert, J. / Verstreken, P. / Galicia, C. / Versees, W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 287.4 KB | Display | ![]() |
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PDB format | ![]() | 226.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.2 KB | Display | ![]() |
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Full document | ![]() | 508.3 KB | Display | |
Data in XML | ![]() | 50.4 KB | Display | |
Data in CIF | ![]() | 69.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a17C ![]() 1i9yS ![]() 3mtcS ![]() 3n9vS ![]() 4cmnS ![]() 4nc2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Antibody , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 39866.387 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 14559.901 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 369 molecules ![](data/chem/img/PO4.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 15% PEG 4000, 0.1 M sodium citrate pH 5, 10% 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980105 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→86.81 Å / Num. obs: 53823 / % possible obs: 92.3 % / Redundancy: 7 % / Biso Wilson estimate: 38.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.43 Å / Num. unique obs: 1511 / CC1/2: 0.512 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 Resolution: 2.3→86.81 Å / SU ML: 0.3193 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8898 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→86.81 Å
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Refine LS restraints |
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LS refinement shell |
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