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- EMDB-47079: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore -

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Basic information

Entry
Database: EMDB / ID: EMD-47079
TitleMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
Map dataMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
Sample
  • Complex: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
    • Protein or peptide: OlyA E69A
    • Protein or peptide: PlyB Hinge-lock
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: 2.4 Å
AuthorsSmothers J / Han Y / Chen Z / Li 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_47079.png

Downloads & links

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Map

FileDownload / File: emd_47079.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
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: 0.09
Minimum - Maximum-0.16701211 - 0.49800274
Average (Standard dev.)0.0011829605 (±0.019753812)
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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Half map: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore half map 2

Fileemd_47079_half_map_1.map
AnnotationMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore 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 half map 1

Fileemd_47079_half_map_2.map
AnnotationMembrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore 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

EntireName: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
Components
  • Complex: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore
    • Protein or peptide: OlyA E69A
    • Protein or peptide: PlyB Hinge-lock

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

SupramoleculeName: Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pleurotus ostreatus (oyster mushroom)
Molecular weightTheoretical: 2.3 MDa

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Macromolecule #1: OlyA E69A

MacromoleculeName: OlyA E69A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
MAYAQWVIII IHNVGSQDVK IKNLKASWGK LHADGDKDAE VSASNYEGKI VKPDEKLQIN ASGRSDAAAG TTGTFDLVDP ADGDKQVRHF YWDSPWGSKT NTWTVSGSNT KWMIEYSGQN LDSGALGTIT VDTLKKGENL YFQ

UniProtKB: Ostreolysin A6

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Macromolecule #2: PlyB Hinge-lock

MacromoleculeName: PlyB Hinge-lock / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
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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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

MicroscopeFEI TITAN 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: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181339
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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