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- EMDB-63083: Half barrel Pre-pore state of Y194A Vibrio cholerae cytolysin mut... -

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Basic information

Entry
Database: EMDB / ID: EMD-63083
TitleHalf barrel Pre-pore state of Y194A Vibrio cholerae cytolysin mutant in liposome.
Map datahalf-barrel prepore of Y194A Vibrio cholerae cytolysin mutant in liposome
Sample
  • Complex: Half-barrel Heptameric Pre-pore state of Y194A Vibrio cholerae cytolysin mutant in liposome.
    • Protein or peptide: Cytolysin VCC
KeywordsMembrane Protein / Heptameric Half-barrel Prepore / 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: 3.51 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: To Be Published
Title: Half barrel Pre-pore state of Y194A Vibrio cholerae cytolysin mutant in liposome.
Authors: Chattopadhyay K / Dutta S / Chatterjee A / Naskar P / Singh M
History
DepositionJan 11, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63083.png

Downloads & links

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Map

FileDownload / File: emd_63083.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf-barrel prepore 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: 0.0239
Minimum - Maximum-0.20033087 - 0.32577747
Average (Standard dev.)0.0007508397 (±0.009826919)
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 half-barrel prepore Y194A Vibrio cholerae cytolysin...

Fileemd_63083_half_map_1.map
Annotationhalf-map of half-barrel prepore 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 half-barrel prepore Y194A Vibrio cholerae cytolysin...

Fileemd_63083_half_map_2.map
Annotationhalf-map of half-barrel prepore 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 : Half-barrel Heptameric Pre-pore state of Y194A Vibrio cholerae cy...

EntireName: Half-barrel Heptameric Pre-pore state of Y194A Vibrio cholerae cytolysin mutant in liposome.
Components
  • Complex: Half-barrel Heptameric Pre-pore state of Y194A Vibrio cholerae cytolysin mutant in liposome.
    • Protein or peptide: Cytolysin VCC

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Supramolecule #1: Half-barrel Heptameric Pre-pore state of Y194A Vibrio cholerae cy...

SupramoleculeName: Half-barrel Heptameric Pre-pore state of Y194A 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: 64.567043 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TNTLPHVAFY ISVNRAISDE ECTFNNSWLW KNEKGSRPFC KDANISLIYR VNLERSLQAG IVGSATPDAK IVRISLDDDS TGAGIHLND QLGYRQFGAS YTTLDAYFRE WSTDAIAQDY RFVFNASNNK AQILKTFPVD NINEKFERKE VSGFELGVTG G VEVSGDGP ...String:
TNTLPHVAFY ISVNRAISDE ECTFNNSWLW KNEKGSRPFC KDANISLIYR VNLERSLQAG IVGSATPDAK IVRISLDDDS TGAGIHLND QLGYRQFGAS YTTLDAYFRE WSTDAIAQDY RFVFNASNNK AQILKTFPVD NINEKFERKE VSGFELGVTG 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: 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: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70872
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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