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Yorodumi- PDB-6g5f: Crystal structure of an engineered Botulinum Neurotoxin type B mu... -
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-Basic information
Entry | Database: PDB / ID: 6g5f | |||||||||
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Title | Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y 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 / 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 / bontoxilysin / host cell presynaptic membrane / positive regulation of dendrite extension / neurotransmitter secretion / host cell cytoplasmic vesicle / calcium-dependent phospholipid binding / neuron projection terminus / Neurexins and neuroligins / syntaxin-1 binding / host cell cytosol / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / synaptic vesicle endocytosis / excitatory synapse / protein transmembrane transporter activity / 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 / metalloendopeptidase activity / synaptic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / calcium-dependent protein binding / Clathrin-mediated endocytosis / synaptic vesicle / presynaptic membrane / chemical synaptic transmission / toxin activity / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / lipid binding / glutamatergic synapse / calcium ion binding / host cell plasma membrane / Golgi apparatus / proteolysis / zinc ion binding / extracellular region / identical protein binding / membrane / 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 | 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 | 6g5f.cif.gz | 566.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g5f.ent.gz | 456.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g5f_validation.pdf.gz | 483.1 KB | Display | wwPDB validaton report |
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Full document | 6g5f_full_validation.pdf.gz | 486 KB | Display | |
Data in XML | 6g5f_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 6g5f_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5f ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5f | HTTPS FTP |
-Related structure data
Related structure data | 6g5gC 6g5kC 1epwS 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: 151066.797 Da / Num. of mol.: 2 / Mutation: E231Q, H234Y Source method: isolated from a genetically manipulated source Details: Catalytic domain of an engineered inactive (mutations E231Q/H234Y) botulinum toxin type B mutant E1191M/S1199Y. Please note the protein is expressed as a single polypeptide which is post- ...Details: Catalytic domain of an engineered inactive (mutations E231Q/H234Y) botulinum toxin type B mutant E1191M/S1199Y. Please note the protein is expressed as a single polypeptide which is post-translationally cleaved into a di-chain molecule (light and heavy chains - chain A and B) 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.: 1 / Source method: obtained synthetically Details: Synthetic peptide corresponding to human synaptotagmin 1 residues [33-53] Source: (synth.) Homo sapiens (human) / References: UniProt: P21579 #3: Chemical | #4: Chemical | ChemComp-MLI / | #5: 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: 5.44 Å3/Da / Density % sol: 77.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1 M sodium malonate dibasic monohydrate, HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→98.5 Å / Num. obs: 113032 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.061 / Rrim(I) all: 0.117 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5535 / CC1/2: 0.492 / Rpim(I) all: 0.598 / Rrim(I) all: 1.124 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EPW Resolution: 2.5→98.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 18.852 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.189 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.562 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→98.5 Å
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Refine LS restraints |
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