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Yorodumi- PDB-6zvn: Botulinum neurotoxin B2 binding domain in complex with human syna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zvn | |||||||||
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Title | Botulinum neurotoxin B2 binding domain in complex with human synaptotagmin I | |||||||||
Components |
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Keywords | TOXIN / botulinum neurotoxin / ganglioside / gt1b / bont / b2 | |||||||||
Function / homology | Function and homology information clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway ...clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / negative regulation of neurotransmitter secretion / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / excitatory synapse / synaptic vesicle endocytosis / protein transmembrane transporter activity / 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 / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / toxin activity / chemical synaptic transmission / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / proteolysis / zinc ion binding / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Clostridium botulinum (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Davies, J.R. / Masuyer, G. / Stenmark, P. | |||||||||
Citation | Journal: Toxins / Year: 2020 Title: Structural and Biochemical Characterization of Botulinum Neurotoxin Subtype B2 Binding to Its Receptors. Authors: Davies, J.R. / Masuyer, G. / Stenmark, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zvn.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zvn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/6zvn ftp://data.pdbj.org/pub/pdb/validation_reports/zv/6zvn | HTTPS FTP |
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-Related structure data
Related structure data | 6zvmC 4kbbS 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: 52464.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bontb / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GR96 |
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#2: Protein/peptide | Mass: 2471.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21579 |
#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: 2.53 Å3/Da / Density % sol: 46.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→106.7 Å / Num. obs: 18223 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 46.89 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.082 / Rrim(I) all: 0.267 / Χ2: 0.97 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 11 % / Rmerge(I) obs: 2.563 / Num. unique obs: 2009 / CC1/2: 0.447 / Rpim(I) all: 0.799 / Rrim(I) all: 2.687 / Χ2: 0.92 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4kbb Resolution: 2.5→50.79 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.246 / Average fsc free: 0.8278 / Average fsc work: 0.8471 / Cross valid method: FREE R-VALUE / ESU R: 0.779 / ESU R Free: 0.333 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50.79 Å
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Refine LS restraints |
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LS refinement shell |
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