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- EMDB-63088: Pore-like heptameric T201A Vibrio cholerae cytolysin mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-63088
TitlePore-like heptameric T201A Vibrio cholerae cytolysin mutant
Map dataPore-like heptameric state of T201A Vibrio cholerae cytolysin mutant in liposome
Sample
  • Complex: Pore-like heptameric state of T201A Vibrio cholerae cytolysin mutant in liposome
    • Protein or peptide: Cytolysin VCC
KeywordsMembrane Protein / Heptameric Pore-like / VCC mutant / Pore-forming toxin / TOXIN
Function / homology
Function and homology information


cytolysis in another organism / extracellular region
Similarity search - Function
Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Jacalin-like lectin domain superfamily ...Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Jacalin-like lectin domain superfamily / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsChatterjee A / Dutta S / Chattopadhyay K / 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: 2025
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 11, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63088.png

Downloads & links

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Map

FileDownload / File: emd_63088.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPore-like heptameric state of T201A 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: 0.0663
Minimum - Maximum-0.80433506 - 1.2538052
Average (Standard dev.)0.00070467783 (±0.03326493)
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 pore-like heptameric state of T201A...

Fileemd_63088_half_map_1.map
AnnotationHalf map of pore-like heptameric state of T201A 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 pore-like heptameric state of T201A...

Fileemd_63088_half_map_2.map
AnnotationHalf map of pore-like heptameric state of T201A 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 : Pore-like heptameric state of T201A Vibrio cholerae cytolysin mut...

EntireName: Pore-like heptameric state of T201A Vibrio cholerae cytolysin mutant in liposome
Components
  • Complex: Pore-like heptameric state of T201A Vibrio cholerae cytolysin mutant in liposome
    • Protein or peptide: Cytolysin VCC

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Supramolecule #1: Pore-like heptameric state of T201A Vibrio cholerae cytolysin mut...

SupramoleculeName: Pore-like heptameric state of T201A Vibrio cholerae cytolysin mutant in liposome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: Cytolysin VCC

MacromoleculeName: Cytolysin VCC / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 64.571082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TNTLPHVAFY ISVNRAISDE ECTFNNSWLW KNEKGSRPFC KDANISLIYR VNLERSLQYG IVGSAAPDAK IVRISLDDDS TGAGIHLND QLGYRQFGAS YTTLDAYFRE WSTDAIAQDY RFVFNASNNK AQILKTFPVD NINEKFERKE VSGFALGVTG G VEVSGDGP ...String:
TNTLPHVAFY ISVNRAISDE ECTFNNSWLW KNEKGSRPFC KDANISLIYR VNLERSLQYG IVGSAAPDAK IVRISLDDDS TGAGIHLND QLGYRQFGAS YTTLDAYFRE WSTDAIAQDY RFVFNASNNK AQILKTFPVD NINEKFERKE VSGFALGVTG G VEVSGDGP KAKLEARASY TQSRWLTYNT QDYRIERNAK NAQAVSFTWN RQQYATAESL LNRSTDALWV NTYPVDVNRI SP LSYASFV PKMDVIYKAS ATETGSTDFI IDSSVNIRPI YNGAYKHYYV VGAHQFYHGF EDTPRRRITK SASFTVDWDH PVF TGGRPV NLQLASFNNR CIQVDAQGRL AANTCDSQQS AQSFIYDQLG RYVSASNTKL CLDGEALDAL QPCNQNLTQR WEWR KGTDE LTNVYSGESL GHDKQTGELG LYASSNDAVS LRTITAYTDV FNAQESSPIL GYTQGKMNQQ RVGQDHRLYV RAGAA IDAL GSASDLLVGG NGGSLSSVDL SGVKSITATS GDFQYGGQQL VALTFTYQDG RQQTVGSKAY VTNAHEDRFD LPAAAK ITQ LKIWSDDWLV KGVQFDLN

UniProtKB: Cytolysin VCC

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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: 47.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136870
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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