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- EMDB-31974: Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31974
TitleCryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer- State 2
Map dataCryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer
Sample
  • Complex: Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer- State 2
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsSengupta N / Mondal AK / Mishra S / Chattopadhyay K / Dutta S
Funding support India, 5 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Science and Engineering Research Board (SERB)SB/S2/RJN-145/2015 India
Science and Engineering Research Board (SERB)SERB-EMR/2016/000608 India
Department of Biotechnology (DBT, India)BT/PR25580/BRB/10/1619/2017 India
CitationJournal: J Cell Biol / Year: 2021
Title: Single-particle cryo-EM reveals conformational variability of the oligomeric VCC β-barrel pore in a lipid bilayer.
Authors: Nayanika Sengupta / Anish Kumar Mondal / Suman Mishra / Kausik Chattopadhyay / Somnath Dutta /
Abstract: Vibrio cholerae cytolysin (VCC) is a water-soluble, membrane-damaging, pore-forming toxin (PFT) secreted by pathogenic V. cholerae, which causes eukaryotic cell death by altering the plasma membrane ...Vibrio cholerae cytolysin (VCC) is a water-soluble, membrane-damaging, pore-forming toxin (PFT) secreted by pathogenic V. cholerae, which causes eukaryotic cell death by altering the plasma membrane permeability. VCC self-assembles on the cell surface and undergoes a dramatic conformational change from prepore to heptameric pore structure. Over the past few years, several high-resolution structures of detergent-solubilized PFTs have been characterized. However, high-resolution structural characterization of small β-PFTs in a lipid environment is still rare. Therefore, we used single-particle cryo-EM to characterize the structure of the VCC oligomer in large unilamellar vesicles, which is the first atomic-resolution cryo-EM structure of VCC. From our study, we were able to provide the first documented visualization of the rim domain amino acid residues of VCC interacting with lipid membrane. Furthermore, cryo-EM characterization of lipid bilayer-embedded VCC suggests interesting conformational variabilities, especially in the transmembrane channel, which could have a potential impact on the pore architecture and assist us in understanding the pore formation mechanism.
History
DepositionSep 16, 2021-
Header (metadata) releaseSep 29, 2021-
Map releaseSep 29, 2021-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31974.png

Downloads & links

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Map

FileDownload / File: emd_31974.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 176 pix.
= 205.92 Å		1.17 Å/pix.
x 176 pix.
= 205.92 Å		1.17 Å/pix.
x 176 pix.
= 205.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0054 / Movie #1: 0.0054
Minimum - Maximum-0.02143925 - 0.045396034
Average (Standard dev.)0.000103350896 (±0.003790828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 205.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.171.171.17
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z205.920205.920205.920
α/β/γ90.00090.00090.000
start NX/NY/NZ139118109
NX/NY/NZ123164187
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS176176176
D min/max/mean-0.0210.0450.000

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Supplemental data

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Sample components

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Entire : Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially ...

EntireName: Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer- State 2
Components
  • Complex: Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer- State 2

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Supramolecule #1: Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially ...

SupramoleculeName: Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer- State 2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio cholerae (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36849
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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