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- PDB-9ufa: phosphatidylcholine head group bound alpha-hemolysin heptameric p... -

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Basic information

Entry
Database: PDB / ID: 9ufa
Titlephosphatidylcholine head group bound alpha-hemolysin heptameric pore structure in the presence of RBC
ComponentsAlpha-hemolysin
KeywordsTOXIN / PC / PFT
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily
Similarity search - Domain/homology
PHOSPHOCHOLINE / Alpha-hemolysin
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDutta, S. / Chatterjee, A. / Roy, A.
Funding support India, 3items
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
CitationJournal: To Be Published
Title: phosphatidylcholine head group bound alpha-hemolysin heptameric pore structure in the presence of RBC
Authors: Dutta, S. / Chatterjee, A. / Roy, A.
History
DepositionApr 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Alpha-hemolysin
A: Alpha-hemolysin
B: Alpha-hemolysin
C: Alpha-hemolysin
D: Alpha-hemolysin
E: Alpha-hemolysin
F: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,31914
Polymers233,0307
Non-polymers1,2897
Water00
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
Alpha-hemolysin / Alpha-HL / Alpha-toxin


Mass: 33290.000 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hly, hla / Production host: Escherichia coli (E. coli) / References: UniProt: P09616
#2: Chemical
ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H15NO4P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: phosphatidylcholine head group bound alpha-hemolysin heptameric pore structure in the presence of RBC
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (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: 1250 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55213 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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