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- EMDB-63070: Pre-pore state (without transmembrane barrel) of Y194A Vibrio cho... -

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Entry
Database: EMDB / ID: EMD-63070
TitlePre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
Map datapre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
Sample
  • Complex: Heptameric Pre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
KeywordsMembrane Protein / Heptameric Prepore / VCC mutant / Pore-forming toxin / TOXIN
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.57 Å
AuthorsChattopadhyay K / Dutta S / Chatterjee A / Naskar P / Singh M
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
Council of Scientific & Industrial Research (CSIR)09/0079(13652)/2022-EMR-I India
Science and Engineering Research Board (SERB)CRG/2022/002674 India
Science and Engineering Research Board (SERB)STR/2022/000006 India
CitationJournal: Structure / Year: 2026
Title: Cradle loop regulates β-barrel pore-formation mechanism of Vibrio cholerae cytolysin.
Authors: Mahendra Singh / Arnab Chatterjee / Ananya Nayak / Prasenjit Naskar / Gurvinder Kaur / Jagannath Mondal / Somnath Dutta / Kausik Chattopadhyay /
Abstract: Vibrio cholerae cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). The membrane insertion of its pore-forming "pre-stem" motif is the most crucial step in the pore-formation mechanism. In ...Vibrio cholerae cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). The membrane insertion of its pore-forming "pre-stem" motif is the most crucial step in the pore-formation mechanism. In the soluble monomeric form, pre-stem remains clamped against the central cytolysin domain by the so-called cradle loop. In the course of oligomeric pore-formation in the target membranes, the cradle loop gets detached from the pre-stem and reorients, thus allowing the pre-stem to extend and insert into the membrane. Here, we show that the specific cradle loop residue(s) play crucial roles in governing the pore-formation mechanism of VCC by establishing decisive interactions with the neighboring structural domains/modules. The alteration of the cradle loop residue, Y194 in particular, compromises the membrane-insertion of the pre-stem, and tends to arrest the membrane-bound toxin in the pre-pore-like oligomeric states. Our study suggests that the native cradle loop architecture, with its intact contacts with the surrounding interaction partners, is essential for VCC pore-formation.
History
DepositionJan 10, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63070.png

Downloads & links

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Map

FileDownload / File: emd_63070.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 320 pix.
= 294.4 Å		0.92 Å/pix.
x 320 pix.
= 294.4 Å		0.92 Å/pix.
x 320 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0318
Minimum - Maximum-0.27186188 - 0.26171517
Average (Standard dev.)-0.00009740884 (±0.010964971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of pre-pore state (without transmembrane barrel)...

Fileemd_63070_half_map_1.map
AnnotationHalf map of pre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of pre-pore state (without transmembrane barrel)...

Fileemd_63070_half_map_2.map
AnnotationHalf map of pre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heptameric Pre-pore state (without transmembrane barrel) of Y194A...

EntireName: Heptameric Pre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
Components
  • Complex: Heptameric Pre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.

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Supramolecule #1: Heptameric Pre-pore state (without transmembrane barrel) of Y194A...

SupramoleculeName: Heptameric Pre-pore state (without transmembrane barrel) of Y194A Vibrio cholerae cytolysin mutant in liposome.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio cholerae (bacteria)

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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) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.5 µm / Nominal defocus min: 1.75 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

31972

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33590
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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