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Yorodumi- PDB-5ccj: Crystal structure of the quintuple mutant of the synaptotagmin-1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ccj | ||||||
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Title | Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain | ||||||
Components | Synaptotagmin-1 | ||||||
Keywords | SIGNALING PROTEIN / Synaptotagmin1 / C2B domain | ||||||
Function / homology | Function and homology information synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / calcium ion sensor activity / spontaneous neurotransmitter secretion / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / dense core granule / GABA synthesis, release, reuptake and degradation / positive regulation of vesicle fusion / chromaffin granule membrane / Dopamine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / calcium-ion regulated exocytosis / neurotransmitter secretion / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / regulation of synaptic vesicle exocytosis / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / synaptic vesicle exocytosis / excitatory synapse / synaptic vesicle endocytosis / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / secretory granule / phospholipid binding / terminal bouton / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Zhou, Q. / Zhao, M. / Brunger, A.T. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. ...Authors: Zhou, Q. / Lai, Y. / Bacaj, T. / Zhao, M. / Lyubimov, A.Y. / Uervirojnangkoorn, M. / Zeldin, O.B. / Brewster, A.S. / Sauter, N.K. / Cohen, A.E. / Soltis, S.M. / Alonso-Mori, R. / Chollet, M. / Lemke, H.T. / Pfuetzner, R.A. / Choi, U.B. / Weis, W.I. / Diao, J. / Sudhof, T.C. / Brunger, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ccj.cif.gz | 301.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ccj.ent.gz | 247.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ccj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/5ccj ftp://data.pdbj.org/pub/pdb/validation_reports/cc/5ccj | HTTPS FTP |
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-Related structure data
Related structure data | 5ccgC 5cchC 5cciC 1uowS 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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Unit cell |
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-Components
#1: Protein | Mass: 17017.801 Da / Num. of mol.: 4 / Fragment: UNP residues 271-421 / Mutation: R281A, E295A, Y338W, R398A, R399A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #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: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 98593 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 19.69 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.99 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 2.34 / % possible all: 98.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UOW Resolution: 1.65→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.21 / Stereochemistry target values: ML
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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: 27.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.0053 Å / Origin y: -1.7077 Å / Origin z: -17.8569 Å
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Refinement TLS group | Selection details: ALL |