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Open data
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Basic information
Entry | Database: PDB / ID: 5n0b | |||||||||
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Title | Crystal structure of the tetanus neurotoxin in complex with GD1a | |||||||||
![]() | Tetanus toxin | |||||||||
![]() | TOXIN / Tetanus neurotoxin / tetanospasmin / tentoxilysin / clostridial toxin | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Masuyer, G. / Conrad, J. / Stenmark, P. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.7 KB | Display | ![]() |
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PDB format | ![]() | 218.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 860.7 KB | Display | ![]() |
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Full document | ![]() | 868.6 KB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3588C ![]() 5n0cC ![]() 1fv2S ![]() 1z7hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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