+Open data
-Basic information
Entry | Database: PDB / ID: 4wee | ||||||
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Title | High-resolution structure of Synaptotagmin 1 C2A | ||||||
Components | Synaptotagmin-1 | ||||||
Keywords | METAL BINDING PROTEIN / synaptotagmin / C2 domain / Ca2+ / beta-sandwich | ||||||
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 / Resolution: 0.891 Å | ||||||
Authors | Sutton, R.B. / Fuson, K.L. | ||||||
Citation | Journal: To Be Published Title: High-resolution structure of Synaptotagmin 1 C2A Authors: Sutton, R.B. #1: Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold. Authors: Sutton, R.B. / Davletov, B.A. / Berghuis, A.M. / Sudhof, T.C. / Sprang, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wee.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wee.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/4wee ftp://data.pdbj.org/pub/pdb/validation_reports/we/4wee | HTTPS FTP |
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-Related structure data
Related structure data | 1rsyS S: Starting model for refinement |
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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: 16097.305 Da / Num. of mol.: 1 / Fragment: UNP residues 140-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Syt1 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21707 | ||||
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#2: Chemical | ChemComp-NA / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.5M ammonium sulfate, 1% PEG400 |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.81798 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81798 Å / Relative weight: 1 |
Reflection | Resolution: 0.7→50 Å / Num. obs: 97100 / % possible obs: 99.5 % / Redundancy: 7 % / Rsym value: 0.033 / Net I/av σ(I): 50 / Net I/σ(I): 50 |
Reflection shell | Resolution: 0.89→1.03 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1rsy Resolution: 0.891→19.781 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.77 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.891→19.781 Å
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Refine LS restraints |
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LS refinement shell |
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