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- EMDB-47078: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refi... -

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Basic information

Entry
Database: EMDB / ID: EMD-47078
TitleMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
Map dataMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
Sample
  • Complex: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
    • Protein or peptide: Ostreolysin A6
    • Protein or peptide: Pleurotolysin B
  • Ligand: N-oleoyl-D-erythro-sphingosylphosphorylcholine
Keywordsmembrane / pore formation / lipid interaction / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsSmothers J / Chen Z / Li Y / Han Y / Radhakrishnan A
Funding support United States, France, 5 items
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, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47078.png

Downloads & links

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Map

FileDownload / File: emd_47078.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.4 Å		0.83 Å/pix.
x 512 pix.
= 422.4 Å		0.83 Å/pix.
x 512 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.28769395 - 0.7669215
Average (Standard dev.)0.0005428777 (±0.009752974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_47078_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement half...

Fileemd_47078_half_map_1.map
AnnotationMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement half...

Fileemd_47078_half_map_2.map
AnnotationMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
Components
  • Complex: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
    • Protein or peptide: Ostreolysin A6
    • Protein or peptide: Pleurotolysin B
  • Ligand: N-oleoyl-D-erythro-sphingosylphosphorylcholine

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Supramolecule #1: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refi...

SupramoleculeName: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pleurotus ostreatus (oyster mushroom)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Ostreolysin A6

MacromoleculeName: Ostreolysin A6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pleurotus ostreatus (oyster mushroom)
Molecular weightTheoretical: 15.701361 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MAYAQWVIII IHNVGSQDVK IKNLKASWGK LHADGDKDAE VSASNYEGKI VKPDEKLQIN ASGRSDAAAG TTGTFDLVDP ADGDKQVRH FYWDSPWGSK TNTWTVSGSN TKWMIEYSGQ NLDSGALGTI TVDTLKKGEN LYFQ

UniProtKB: Ostreolysin A6

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Macromolecule #2: Pleurotolysin B

MacromoleculeName: Pleurotolysin B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pleurotus ostreatus (oyster mushroom)
Molecular weightTheoretical: 53.328695 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: HHHHHHHHSQ AGDTLNDVIQ DPTRRNKLIN DNNLLKGIIM GRDGPVPSSR ELIVRPDTLR AIINNRATIE TTTMEAEFTE TLMESNYNS ASVKVSAPFI TANSEYSESS SFKNTETEKS MYTSSRYLFP QGRIDFTTPD SGFDDVIKLS PQFTSGVQAA L AKATGTEK ...String:
HHHHHHHHSQ AGDTLNDVIQ DPTRRNKLIN DNNLLKGIIM GRDGPVPSSR ELIVRPDTLR AIINNRATIE TTTMEAEFTE TLMESNYNS ASVKVSAPFI TANSEYSESS SFKNTETEKS MYTSSRYLFP QGRIDFTTPD SGFDDVIKLS PQFTSGVQAA L AKATGTEK REALQNLFQE YGHVFRTKVH IGGVLSAHTM ETFSRSENET EVKQDVKAGL EGAVKGWGGG ATAGHGNTQG TI TTSQNRK LNVKYIVNVV DYTKIQNTEE WVASTNQSEH WRVIEVTEVT AVADLLPQPI RGQVKDLLKP LLGKWVDVEK VPG LESLPV SVYRPKGAIP AGWFWLGDTA DASKALLVKP TLPARSGRNP ALTSLHQGSG MTEQPFVDLP QYQYLSTYFG SFAH DTPPG STLRGLRPDH VLPGRYEMHG DTISTAVYVT RPVDVPFPED ECFDLKSLVR VKLPGSGNPP KPRSALKKSM VLFDS GEK

UniProtKB: Pleurotolysin B

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Macromolecule #3: N-oleoyl-D-erythro-sphingosylphosphorylcholine

MacromoleculeName: N-oleoyl-D-erythro-sphingosylphosphorylcholine / type: ligand / ID: 3 / Number of copies: 16 / Formula: A1A8R
Molecular weightTheoretical: 730.073 Da

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2357407
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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