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- PDB-9krf: Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chai... -

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Basic information

Entry
Database: PDB / ID: 9krf
TitleAlpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC liposomes
ComponentsAlpha-hemolysin
KeywordsLIPID BINDING PROTEIN / PFT / Liposomes
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
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Alpha-hemolysin
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChatterjee, A. / Roy, A. / Dutta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: To Be Published
Title: Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC liposomes
Authors: Chatterjee, A. / Roy, A. / Dutta, S.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 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)236,99714
Polymers233,0307
Non-polymers3,9677
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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-P1O / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 566.728 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C28H57NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DDPC, phospholipid*YM
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: Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC liposomes
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: 3500 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 40 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127106 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00517108
ELECTRON MICROSCOPYf_angle_d0.45523128
ELECTRON MICROSCOPYf_dihedral_angle_d12.5316440
ELECTRON MICROSCOPYf_chiral_restr0.0422443
ELECTRON MICROSCOPYf_plane_restr0.0032961

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