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Yorodumi- PDB-6g5k: Crystal structure of the binding domain of Botulinum Neurotoxin t... -
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-Basic information
Entry | Database: PDB / ID: 6g5k | |||||||||
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Title | Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 | |||||||||
Components |
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Keywords | TOXIN / botulinum toxin / neurotoxin / protein engineering / receptor binding | |||||||||
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 / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / bontoxilysin / host cell presynaptic membrane / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / host cell cytoplasmic vesicle / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / host cell cytosol / 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 / lipid binding / calcium ion binding / host cell plasma membrane / Golgi apparatus / proteolysis / zinc ion binding / extracellular region / membrane / 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 Å | |||||||||
Authors | Masuyer, G. / Elliot, M. / Favre-Guilmard, C. / Liu, S.M. / Maignel, J. / Beard, M. / Carre, D. / Kalinichev, M. / Lezmi, S. / Mir, I. ...Masuyer, G. / Elliot, M. / Favre-Guilmard, C. / Liu, S.M. / Maignel, J. / Beard, M. / Carre, D. / Kalinichev, M. / Lezmi, S. / Mir, I. / Nicoleau, C. / Palan, S. / Perier, C. / Raban, E. / Dong, M. / Krupp, J. / Stenmark, P. | |||||||||
Funding support | Sweden, 1items
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Citation | Journal: Sci Adv / Year: 2019 Title: Engineered botulinum neurotoxin B with improved binding to human receptors has enhanced efficacy in preclinical models. Authors: Elliott, M. / Favre-Guilmard, C. / Liu, S.M. / Maignel, J. / Masuyer, G. / Beard, M. / Boone, C. / Carre, D. / Kalinichev, M. / Lezmi, S. / Mir, I. / Nicoleau, C. / Palan, S. / Perier, C. / ...Authors: Elliott, M. / Favre-Guilmard, C. / Liu, S.M. / Maignel, J. / Masuyer, G. / Beard, M. / Boone, C. / Carre, D. / Kalinichev, M. / Lezmi, S. / Mir, I. / Nicoleau, C. / Palan, S. / Perier, C. / Raban, E. / Zhang, S. / Dong, M. / Stenmark, P. / Krupp, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g5k.cif.gz | 209 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g5k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6g5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5k ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5k | HTTPS FTP |
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-Related structure data
Related structure data | 6g5fC 6g5gC 4kbbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55157.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Binding domain of Botulinum Neurotoxin type B expressed with a N-terminal poly-His tag Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10844, bontoxilysin #2: Protein/peptide | Mass: 2471.825 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic peptide corresponding to human synaptotagmin 1 residues [33-53] Source: (synth.) Homo sapiens (human) / References: UniProt: P21579 #3: 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: 2.5 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→70.93 Å / Num. obs: 71658 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.065 / Rrim(I) all: 0.122 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 1.31 / Num. unique obs: 5300 / CC1/2: 0.681 / Rpim(I) all: 0.815 / Rrim(I) all: 1.546 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KBB Resolution: 2→53.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.198 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.992 Å2
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Refinement step | Cycle: 1 / Resolution: 2→53.25 Å
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