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Open data
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Basic information
Entry | Database: PDB / ID: 6u4w | ||||||
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Title | 1.4 A structure of a pathogenic human Syt 1 C2B (D366E) | ||||||
![]() | Synaptotagmin-1 | ||||||
![]() | EXOCYTOSIS / C2 domain / C2B / Greek Key / Baker-Gordon syndrome | ||||||
Function / homology | ![]() clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / 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 / Acetylcholine Neurotransmitter Release Cycle ...clathrin-sculpted acetylcholine transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / 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 / Acetylcholine Neurotransmitter Release Cycle / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / clathrin-sculpted monoamine transport vesicle membrane / dense core granule / chromaffin granule membrane / calcium ion sensor activity / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / calcium ion-regulated exocytosis of neurotransmitter / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / vesicle docking / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / regulation of exocytosis / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / synaptic vesicle endocytosis / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / clathrin-coated endocytic vesicle membrane / synaptic vesicle membrane / calcium-dependent protein binding / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dominguez, M.J. / Bradberry, M.M. / Chapman, E.R. / Sutton, R.B. | ||||||
![]() | ![]() Title: Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder. Authors: Bradberry, M.M. / Courtney, N.A. / Dominguez, M.J. / Lofquist, S.M. / Knox, A.T. / Sutton, R.B. / Chapman, E.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 86.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tz3C ![]() 6u41C ![]() 6u4uC ![]() 1uowS 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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Unit cell |
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Components
#1: Protein | Mass: 17893.846 Da / Num. of mol.: 1 / Mutation: D366E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.6 M Ammonium Sulfate, 0.1 M Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→27.91 Å / Num. obs: 35752 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 12.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.082 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1747 / CC1/2: 0.698 / Rrim(I) all: 1.499 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UOW Resolution: 1.4→27.91 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7741 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: 21.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→27.91 Å
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Refine LS restraints |
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LS refinement shell |
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