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- PDB-9dob: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refi... -

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Basic information

Entry
Database: PDB / ID: 9dob
TitleMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
Components
  • Ostreolysin A6
  • Pleurotolysin B
KeywordsMEMBRANE PROTEIN / membrane / pore formation / lipid interaction
Function / homology
Function and homology information


symbiont-mediated hemolysis of host erythrocyte
Similarity search - Function
Pleurotolysin B, C-terminal / : / Pleurotolysin B C-terminal domain / Fungal MACPF-like domain / Hemolysin, aegerolysin type / Aegerolysin / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain
Similarity search - Domain/homology
: / Ostreolysin A6 / Pleurotolysin B
Similarity search - Component
Biological speciesPleurotus ostreatus (oyster mushroom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsSmothers, J. / Chen, Z. / Li, Y. / Han, Y. / Radhakrishnan, A.
Funding support United States, France, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL160487 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM131963 United States
Welch FoundationI-1793 United States
Leducq Foundation19CVD04 France
CitationJournal: To Be Published
Title: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
Authors: Smothers, J. / Chen, Z. / Li, Y. / Han, Y. / Radhakrishnan, A.
History
DepositionSep 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ostreolysin A6
B: Ostreolysin A6
C: Pleurotolysin B
L: Ostreolysin A6
M: Ostreolysin A6
N: Pleurotolysin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,14422
Polymers169,4636
Non-polymers11,68116
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
Ostreolysin A6


Mass: 15701.361 Da / Num. of mol.: 4 / Mutation: E69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Gene: OlyA6
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P83467
#2: Protein Pleurotolysin B


Mass: 53328.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus ostreatus (oyster mushroom) / Gene: plyB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5W9E8
#3: Chemical
ChemComp-A1A8R / N-oleoyl-D-erythro-sphingosylphosphorylcholine / N-(9Z-octadecenoyl)-sphing-4-enine-1-phosphocholine / N-Oleoylsphingomyelin


Mass: 730.073 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C41H82N2O6P / 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: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Pleurotus ostreatus (oyster mushroom)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2357407 / Symmetry type: POINT

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