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- EMDB-3588: Cryo-EM map of the tetanus neurotoxin -

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Basic information

Entry
Database: EMDB / ID: EMD-3588
TitleCryo-EM map of the tetanus neurotoxin
Map dataCryo-EM structure of the Tetanus Neurotoxin.
Sample
  • Organelle or cellular component: Tetanus neurotoxinTetanospasmin
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
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium tetani (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsConrad J / Masuyer G / Stenmark P
CitationJournal: 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
DepositionFeb 12, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseJun 21, 2017-
UpdateNov 22, 2017-
Current statusNov 22, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.066
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.066
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3588.png

Downloads & links

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Map

FileDownload / File: emd_3588.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the Tetanus Neurotoxin.
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.066 / Movie #1: 0.066
Minimum - Maximum-0.1345851 - 0.2030454
Average (Standard dev.)0.000043009255 (±0.009299137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 219.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z219.200219.200219.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1350.2030.000

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Supplemental data

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Half map: Half-map of the cryo-EM structure of the Tetanus Neurotoxin.

Fileemd_3588_half_map_1.map
AnnotationHalf-map of the cryo-EM structure of the Tetanus Neurotoxin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of the cryo-EM structure of the Tetanus Neurotoxin.

Fileemd_3588_half_map_2.map
AnnotationHalf-map of the cryo-EM structure of the Tetanus Neurotoxin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetanus neurotoxin

EntireName: Tetanus neurotoxinTetanospasmin
Components
  • Organelle or cellular component: Tetanus neurotoxinTetanospasmin

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Supramolecule #1: Tetanus neurotoxin

SupramoleculeName: Tetanus neurotoxin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Catalytically inactive variant of the tetanus neurotoxin (R372A/Y375F)
Source (natural)Organism: Clostridium tetani (bacteria)
Molecular weightTheoretical: 150 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pET28a

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Component:
ConcentrationFormulaName
0.2 MNaClSodium chloridesodium chloride
0.02 MC8H18N2O4Shepes
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.35 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5n0b

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.1)
Details: The actual resolution of the cryo-EM map is lower than 4.5A, as the map suffers bias due to the preferred distribution of particle orientations.
Number images used: 197000
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsFitting was performed manually using the X-ray crystal structure of the Tetanus neurotoxin (PDB 5n0b) by docking the two domains (catalytic and translocation domains) expected to be a 'rigid body' and then refined using the 'Fit in Map' logarithm of the Chimera software. A similar approach was used to fit in the binding domain.
RefinementProtocol: RIGID BODY FIT

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