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Yorodumi- PDB-6qns: Crystal structure of the binding domain of Botulinum Neurotoxin t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qns | |||||||||
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Title | Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1a receptors | |||||||||
Components |
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Keywords | TOXIN / botulinum toxin | |||||||||
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: 2.4 Å | |||||||||
Authors | Masuyer, G. / Yin, L. / Zhang, S. / Miyashita, S.I. / Dong, M. / Stenmark, P. | |||||||||
Funding support | Sweden, 1items
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Citation | Journal: Plos Biol. / Year: 2020 Title: Characterization of a membrane binding loop leads to engineering botulinum neurotoxin B with improved therapeutic efficacy. Authors: Yin, L. / Masuyer, G. / Zhang, S. / Zhang, J. / Miyashita, S.I. / Burgin, D. / Lovelock, L. / Coker, S.F. / Fu, T.M. / Stenmark, P. / Dong, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qns.cif.gz | 210.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qns.ent.gz | 165.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qns_validation.pdf.gz | 800.2 KB | Display | wwPDB validaton report |
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Full document | 6qns_full_validation.pdf.gz | 805.7 KB | Display | |
Data in XML | 6qns_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6qns_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/6qns ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qns | HTTPS FTP |
-Related structure data
Related structure data | 4kbbS 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: 53186.824 Da / Num. of mol.: 1 / Mutation: I1248W, V1249W Source method: isolated from a genetically manipulated source Details: The N- and C-termini were not visible. Please keep sequence numbering of the full botulinum toxin, as per the uploaded PDB, so that it starts at N862 and terminates at E1291. Thank you. Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P10844, bontoxilysin |
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#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: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: 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: 2.6 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 20% v/v PEG6000, 0.1 M MES pH 6.0, 0.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→74.6 Å / Num. obs: 23939 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.054 / Rrim(I) all: 0.129 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1728 / CC1/2: 0.907 / Rpim(I) all: 0.676 / Rrim(I) all: 1.62 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KBB Resolution: 2.4→74.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 19.277 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.234
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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: 65.14 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→74.55 Å
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