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Yorodumi- EMDB-13876: Cryo-EM structure of the octameric pore of Clostridium perfringen... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13876 | |||||||||
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Title | Cryo-EM structure of the octameric pore of Clostridium perfringens beta-toxin. | |||||||||
Map data | postprocessed map CPB | |||||||||
Sample |
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Keywords | pore forming toxin / hemolysin / octamer / TOXIN | |||||||||
Biological species | Clostridium perfringens (bacteria) / Clostridium perfringens CPE (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.84 Å | |||||||||
Authors | Iacovache I / Zuber B | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: EMBO Rep / Year: 2022 Title: Cryo-EM structure of the octameric pore of Clostridium perfringens β-toxin. Authors: Julia Bruggisser / Ioan Iacovache / Samuel C Musson / Matteo T Degiacomi / Horst Posthaus / Benoît Zuber / Abstract: Clostridium perfringens is one of the most widely distributed and successful pathogens producing an impressive arsenal of toxins. One of the most potent toxins produced is the C. perfringens β-toxin ...Clostridium perfringens is one of the most widely distributed and successful pathogens producing an impressive arsenal of toxins. One of the most potent toxins produced is the C. perfringens β-toxin (CPB). This toxin is the main virulence factor of type C strains. We describe the cryo-electron microscopy (EM) structure of CPB oligomer. We show that CPB forms homo-octameric pores like the hetero-oligomeric pores of the bi-component leukocidins, with important differences in the receptor binding region and the N-terminal latch domain. Intriguingly, the octameric CPB pore complex contains a second 16-stranded β-barrel protrusion atop of the cap domain that is formed by the N-termini of the eight protomers. We propose that CPB, together with the newly identified Epx toxins, is a member a new subclass of the hemolysin-like family. In addition, we show that the β-barrel protrusion domain can be modified without affecting the pore-forming ability, thus making the pore particularly attractive for macromolecule sensing and nanotechnology. The cryo-EM structure of the octameric pore of CPB will facilitate future developments in both nanotechnology and basic research. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13876.map.gz | 4.9 MB | EMDB map data format | |
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Header (meta data) | emd-13876-v30.xml emd-13876.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13876_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_13876.png | 47.4 KB | ||
Filedesc metadata | emd-13876.cif.gz | 5.6 KB | ||
Others | emd_13876_half_map_1.map.gz emd_13876_half_map_2.map.gz | 20.1 MB 20.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13876 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13876 | HTTPS FTP |
-Validation report
Summary document | emd_13876_validation.pdf.gz | 649.7 KB | Display | EMDB validaton report |
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Full document | emd_13876_full_validation.pdf.gz | 649.3 KB | Display | |
Data in XML | emd_13876_validation.xml.gz | 13 KB | Display | |
Data in CIF | emd_13876_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13876 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13876 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13876.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | postprocessed map CPB | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.306 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half1
File | emd_13876_half_map_1.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_13876_half_map_2.map | ||||||||||||
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Annotation | half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : octamer of beta toxin in SMALP
Entire | Name: octamer of beta toxin in SMALP |
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Components |
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-Supramolecule #1: octamer of beta toxin in SMALP
Supramolecule | Name: octamer of beta toxin in SMALP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Clostridium perfringens (bacteria) / Strain: C |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Clostridium perfringens beta toxin
Macromolecule | Name: Clostridium perfringens beta toxin / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium perfringens CPE (bacteria) |
Molecular weight | Theoretical: 34.89375 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: NDIGKTTTIT RNKTSDGYTI ITQNDKQIIS YQSVDSSSKN EDGFTASIDA RFIDDKYSSE MTTLINLTGF MSSKKEDVIK KYNLHDVTN STAINFPVRY SISILNESIN ENVKIVDSIP KNTISQKTVS NTMGYKIGGS IEIEENKPKA SIESEYAESS T IEYVQPDF ...String: NDIGKTTTIT RNKTSDGYTI ITQNDKQIIS YQSVDSSSKN EDGFTASIDA RFIDDKYSSE MTTLINLTGF MSSKKEDVIK KYNLHDVTN STAINFPVRY SISILNESIN ENVKIVDSIP KNTISQKTVS NTMGYKIGGS IEIEENKPKA SIESEYAESS T IEYVQPDF STIQTDHSTS KASWDTKFTE TTRGNYNLKS NNPVYGNEMF MYGRYTNVPA TENIIPDYQM SKLITGGLNP NM SVVLTAP NGTEESIIKV KMERERNCYY LNWNGANWVG QVYSRLAFDT PNVDSHIFTF KINWLTHKVT AI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.25 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |