+Open data
-Basic information
Entry | Database: PDB / ID: 5n0b | |||||||||
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Title | Crystal structure of the tetanus neurotoxin in complex with GD1a | |||||||||
Components | Tetanus toxin | |||||||||
Keywords | TOXIN / Tetanus neurotoxin / tetanospasmin / tentoxilysin / clostridial toxin | |||||||||
Function / homology | Function and homology information tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Clostridium tetani (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Masuyer, G. / Conrad, J. / Stenmark, P. | |||||||||
Funding support | Sweden, 1items
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Citation | Journal: EMBO Rep / Year: 2017 Title: The structure of the tetanus toxin reveals pH-mediated domain dynamics. Authors: Geoffrey Masuyer / Julian Conrad / Pål Stenmark / Abstract: The tetanus neurotoxin (TeNT) is a highly potent toxin produced by that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the ...The tetanus neurotoxin (TeNT) is a highly potent toxin produced by that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the other clostridial neurotoxins by its unique ability to target the central nervous system by retrograde axonal transport. The crystal structure of the tetanus toxin reveals a "closed" domain arrangement stabilised by two disulphide bridges, and the molecular details of the toxin's interaction with its polysaccharide receptor. An integrative analysis combining X-ray crystallography, solution scattering and single particle electron cryo-microscopy reveals pH-mediated domain rearrangements that may give TeNT the ability to adapt to the multiple environments encountered during intoxication, and facilitate binding to distinct receptors. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n0b.cif.gz | 280.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n0b.ent.gz | 218.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n0b_validation.pdf.gz | 860.7 KB | Display | wwPDB validaton report |
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Full document | 5n0b_full_validation.pdf.gz | 868.6 KB | Display | |
Data in XML | 5n0b_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 5n0b_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0b ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0b | HTTPS FTP |
-Related structure data
Related structure data | 3588C 5n0cC 1fv2S 1z7hS 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: 152909.828 Da / Num. of mol.: 1 / Mutation: R372A, Y375F Source method: isolated from a genetically manipulated source Details: Catalytically inactive variant of the tetanus neurotoxin Source: (gene. exp.) Clostridium tetani (bacteria) / Gene: tetX, CTC_p60 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04958, tentoxilysin |
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#2: 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 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-PEG / |
#5: 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: 3.2 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% v/v polyethylene glycol 3350, 0.1M Bis-Tris propane pH 6.5, 0.2M potassium thiocyanate PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 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: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→68.5 Å / Num. obs: 58411 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.088 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.6→2.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.937 / Num. unique obs: 27187 / CC1/2: 0.307 / Rpim(I) all: 0.644 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z7H, 1FV2 Resolution: 2.6→68.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.355 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.48 / ESU R Free: 0.285 / 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: 64.736 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→68.5 Å
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Refine LS restraints |
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