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- PDB-9ue9: Heptameric pore structure of Vibrio cholerae Cytolysin (VCC) embe... -

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Basic information

Entry
Database: PDB / ID: 9ue9
TitleHeptameric pore structure of Vibrio cholerae Cytolysin (VCC) embedded in lipid bilayer
ComponentsHlyA
KeywordsTOXIN / Vibrio cholerae Cytolysin (VCC) / Pore-forming 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsDutta, S. / Chatterjee, A.
Funding support India, 4items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2022/002674 India
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
CitationJournal: To Be Published
Title: Heptameric pore structure of Vibrio cholerae Cytolysin (VCC) embedded in lipid bilayer
Authors: Dutta, S. / Chatterjee, A.
History
DepositionApr 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Source and taxonomy / Category: em_entity_assembly_naturalsource / entity_src_gen
Item: _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism ..._em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HlyA
B: HlyA
C: HlyA
D: HlyA
E: HlyA
F: HlyA
G: HlyA


Theoretical massNumber of molelcules
Total (without water)452,2367
Polymers452,2367
Non-polymers00
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
HlyA


Mass: 64605.098 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P1DZZ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vibrio cholerae Cytolysin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117427 / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00431784
ELECTRON MICROSCOPYf_angle_d0.46243313
ELECTRON MICROSCOPYf_dihedral_angle_d11.29511053
ELECTRON MICROSCOPYf_chiral_restr0.0414784
ELECTRON MICROSCOPYf_plane_restr0.0035754

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