+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4789 | |||||||||
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Title | The pore structure of Clostridium perfringens epsilon toxin | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Epsilon toxin / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / : / toxin activity / Epsilon-toxin type B Function and homology information | |||||||||
Biological species | Clostridium perfringens B (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Savva CG / Clark AR / Naylor CE / Popoff MR / Moss DS / Basak AK / Titball RW / Bokori-Brown M | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: The pore structure of Clostridium perfringens epsilon toxin. Authors: Christos G Savva / Alice R Clark / Claire E Naylor / Michel R Popoff / David S Moss / Ajit K Basak / Richard W Titball / Monika Bokori-Brown / Abstract: Epsilon toxin (Etx), a potent pore forming toxin (PFT) produced by Clostridium perfringens, is responsible for the pathogenesis of enterotoxaemia of ruminants and has been suggested to play a role in ...Epsilon toxin (Etx), a potent pore forming toxin (PFT) produced by Clostridium perfringens, is responsible for the pathogenesis of enterotoxaemia of ruminants and has been suggested to play a role in multiple sclerosis in humans. Etx is a member of the aerolysin family of β-PFTs (aβ-PFTs). While the Etx soluble monomer structure was solved in 2004, Etx pore structure has remained elusive due to the difficulty of isolating the pore complex. Here we show the cryo-electron microscopy structure of Etx pore assembled on the membrane of susceptible cells. The pore structure explains important mutant phenotypes and suggests that the double β-barrel, a common feature of the aβ-PFTs, may be an important structural element in driving efficient pore formation. These insights provide the framework for the development of novel therapeutics to prevent human and animal infections, and are relevant for nano-biotechnology applications. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4789.map.gz | 4.2 MB | EMDB map data format | |
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Header (meta data) | emd-4789-v30.xml emd-4789.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_4789.png | 197.5 KB | ||
Others | emd_4789_half_map_1.map.gz emd_4789_half_map_2.map.gz | 31.3 MB 31.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4789 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4789 | HTTPS FTP |
-Related structure data
Related structure data | 6rb9MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4789.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4789_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4789_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Epsilon toxin
Entire | Name: Epsilon toxin |
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Components |
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-Supramolecule #1: Epsilon toxin
Supramolecule | Name: Epsilon toxin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Clostridium perfringens B (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta 2 / Recombinant plasmid: pHis-Parallel1 |
Molecular weight | Theoretical: 225.4 KDa |
-Macromolecule #1: Epsilon-toxin type B
Macromolecule | Name: Epsilon-toxin type B / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium perfringens B (bacteria) |
Molecular weight | Theoretical: 32.234695 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMASYD NVDTLIEKGR YNTKYNYLKR MEKYYPNAMA YFDKVTINPQ GNDFYINNPK VELDGEPSM NYLEDVYVGK ALLTNDTQQE QKLKSQSFTC KNTDTVTATT THTVGTSIQA TAKFTVPFNE TGVSLTTSYS F ANTNTNTN ...String: MSYYHHHHHH DYDIPTTENL YFQGAMASYD NVDTLIEKGR YNTKYNYLKR MEKYYPNAMA YFDKVTINPQ GNDFYINNPK VELDGEPSM NYLEDVYVGK ALLTNDTQQE QKLKSQSFTC KNTDTVTATT THTVGTSIQA TAKFTVPFNE TGVSLTTSYS F ANTNTNTN SKEITHNVPS QDILVPANTT VEVIAYLKKV NVKGNVKLVG QVSGSEWGEI PSYLAFPRDG YKFSLSDTVN KS DLNEDGT ININGKGNYS AVMGDELIVK VRNLNTNNVQ EYVIPVDKK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.013 mg/mL |
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Buffer | pH: 7.1 Details: DPBS containing 20 mM imidazole and 0.02% (w/v) DDM |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 40 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 75000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE Chromatic aberration corrector: Volta phase plate was used. Just prior to data collection, the phase plate was inserted and the un-scattered beam was made parallel by observing the Ronchigram in the ...Chromatic aberration corrector: Volta phase plate was used. Just prior to data collection, the phase plate was inserted and the un-scattered beam was made parallel by observing the Ronchigram in the back focal plane of the objective |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | AutoCTF |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 835 / Average exposure time: 60.0 sec. / Average electron dose: 32.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 263672 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Atomic model low-pass filtered and scaled to match EM data. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 25525 |
-Atomic model buiding 1
Details | A model was built into the 3.2 A map by initially docking the receptor-binding domain of the wild type Etx crystal structure (PDB: 1UYJ) and then extending this, building ab initio using Coot. |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-6rb9: |