[English] 日本語
Yorodumi
- EMDB-13876: Cryo-EM structure of the octameric pore of Clostridium perfringen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13876
TitleCryo-EM structure of the octameric pore of Clostridium perfringens beta-toxin.
Map datapostprocessed map CPB
Sample
  • Complex: octamer of beta toxin in SMALP
    • Protein or peptide: Clostridium perfringens beta toxin
Keywordspore forming toxin / hemolysin / octamer / TOXIN
Biological speciesClostridium perfringens (bacteria) / Clostridium perfringens CPE (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsIacovache I / Zuber B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation179520 Switzerland
CitationJournal: 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
DepositionNov 15, 2021-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13876.png

Downloads & links

-
Map

FileDownload / File: emd_13876.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map CPB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.2 Å		1.31 Å/pix.
x 200 pix.
= 261.2 Å		1.31 Å/pix.
x 200 pix.
= 261.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.306 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.20037964 - 0.43193036
Average (Standard dev.)0.0015350543 (±0.016621862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-99-99-99
Dimensions200200200
Spacing200200200
CellA=B=C: 261.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half1

Fileemd_13876_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2

Fileemd_13876_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : octamer of beta toxin in SMALP

EntireName: octamer of beta toxin in SMALP
Components
  • Complex: octamer of beta toxin in SMALP
    • Protein or peptide: Clostridium perfringens beta toxin

-
Supramolecule #1: octamer of beta toxin in SMALP

SupramoleculeName: octamer of beta toxin in SMALP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium perfringens (bacteria) / Strain: C
Molecular weightTheoretical: 250 KDa

-
Macromolecule #1: Clostridium perfringens beta toxin

MacromoleculeName: Clostridium perfringens beta toxin / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Clostridium perfringens CPE (bacteria)
Molecular weightTheoretical: 34.89375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8 / Component:
ConcentrationName
20.0 mMTris
150.0 mMNaCl
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3b07

Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260481
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3b07


Chain - Chain ID: B / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-7q9y:
Cryo-EM structure of the octameric pore of Clostridium perfringens beta-toxin.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more