[English] 日本語
![](img/lk-miru.gif)
- PDB-7a17: Crystal structure of the 5-phosphatase domain of Synaptojanin1 bo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7a17 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody | ||||||||||||
![]() |
| ||||||||||||
![]() | HYDROLASE / Inositol polyphosphate 5-phosphatase / Phosphoinositide / Enzyme-substrate complex / Catalytic Mechanism / 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 | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 283 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 222.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 732.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 748.6 KB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 64.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a0vC ![]() 1i9yS ![]() 3mtcS ![]() 3n9vS ![]() 4cmnS ![]() 4nc2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
-Isoform 2 of Synaptojanin- ... , 2 types, 3 molecules ACE
#1: Protein | Mass: 39607.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#3: Protein | Mass: 39519.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Antibody , 3 types, 3 molecules BDF
#2: Antibody | Mass: 13031.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#4: Antibody | Mass: 13442.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Antibody | Mass: 13719.040 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 80 molecules ![](data/chem/img/IP9.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-IP9 / ( | ||||||
---|---|---|---|---|---|---|---|
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PO4 / #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% PEG 3350, 0.1 M sodium citrate pH 5.5, 13% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976246 Å / Relative weight: 1 |
Reflection | Resolution: 2.728→87.39 Å / Num. obs: 32151 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 43.28 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.148 / Rrim(I) all: 0.282 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.728→3.02 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2473 / CC1/2: 0.474 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1i9y, 3n9v, 3mtc, 4cmn, 4nc2 Resolution: 2.73→87.39 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.866 / SU B: 19.961 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.603 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→87.39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|