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Yorodumi- PDB-5hjq: Crystal structure of the TBC domain of Skywalker/TBC1D24 from Dro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hjq | ||||||
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Title | Crystal structure of the TBC domain of Skywalker/TBC1D24 from Drosophila melanogaster in complex with inositol(1,4,5)triphosphate | ||||||
Components | LD10117p | ||||||
Keywords | SIGNALING PROTEIN / TBC / RabGAP | ||||||
Function / homology | Function and homology information synaptic vesicle endosomal processing / negative regulation of synaptic vesicle recycling / synaptic vesicle recycling via endosome / vesicle-mediated transport in synapse / neuromuscular synaptic transmission / negative regulation of neurotransmitter secretion / GTPase activator activity / neuromuscular junction / terminal bouton / synaptic vesicle membrane ...synaptic vesicle endosomal processing / negative regulation of synaptic vesicle recycling / synaptic vesicle recycling via endosome / vesicle-mediated transport in synapse / neuromuscular synaptic transmission / negative regulation of neurotransmitter secretion / GTPase activator activity / neuromuscular junction / terminal bouton / synaptic vesicle membrane / neuron projection development / chemical synaptic transmission / postsynapse / endosome membrane / lipid binding / synapse / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Fischer, B. / Paesmans, J. / Versees, W. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 Title: Skywalker-TBC1D24 has a lipid-binding pocket mutated in epilepsy and required for synaptic function. Authors: Fischer, B. / Luthy, K. / Paesmans, J. / De Koninck, C. / Maes, I. / Swerts, J. / Kuenen, S. / Uytterhoeven, V. / Verstreken, P. / Versees, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hjq.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hjq.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hjq_validation.pdf.gz | 842.1 KB | Display | wwPDB validaton report |
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Full document | 5hjq_full_validation.pdf.gz | 846.6 KB | Display | |
Data in XML | 5hjq_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 5hjq_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/5hjq ftp://data.pdbj.org/pub/pdb/validation_reports/hj/5hjq | HTTPS FTP |
-Related structure data
Related structure data | 5hjnSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43096.793 Da / Num. of mol.: 1 / Fragment: TBC domain, residues 1-353 Source method: isolated from a genetically manipulated source Details: Contains a N-terminal His-Tag / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sky, CG9339, Dmel_CG9339 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9VIH7 |
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#2: Chemical | ChemComp-I3P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 1500, sucinate/phosphate/glycine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.23 Å / Num. obs: 17353 / % possible obs: 99.4 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.18 |
Reflection shell | Resolution: 2.3→2.44 Å / Rmerge(I) obs: 0.802 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HJN Resolution: 2.3→39.23 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.23 Å
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Refine LS restraints |
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LS refinement shell |
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