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- EMDB-57921: Siphohage OE33PA upon binding to its Gram+ host cell surface (view 6) -

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Basic information

Entry
Database: EMDB / ID: EMD-57921
TitleSiphohage OE33PA upon binding to its Gram+ host cell surface (view 6)
Map dataprocessed tomogram (IMOD deconvolution strength 0.5, reduce 4)
Sample
  • Complex: Phage OE33PA bound to its host Oenococcus oeni
    • Complex: phage OE33PA
    • Organelle or cellular component: Oenococcus oeni
Keywordsphage-cell interaction / adhesion device / siphophage / Gram-positive bacterium / VIRUS
Biological speciesOenococcus phage phiOE33PA (virus) / Oenococcus oeni (bacteria)
Methodelectron tomography / cryo EM
AuthorsGoulet A / Ptchelkine D
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0018-01 France
CitationJournal: bioRxiv / Year: 2026
Title: Dynamic adhesion device of phage OE33PA drives Gram-positive host recognition.
Authors: Laura Schmitt / Amel Chaïb / Denis Ptchelkine / Eaazhisai Kandiah / Claire Le Marrec / Christian Cambillau / Adeline Goulet
Abstract: Bacteriophages (phages) infecting Gram-positive bacteria must bind to host receptors across thick cell walls to initiate infection, yet the underlying structural mechanisms remain unclear. Here, we ...Bacteriophages (phages) infecting Gram-positive bacteria must bind to host receptors across thick cell walls to initiate infection, yet the underlying structural mechanisms remain unclear. Here, we report cryo-electron microscopy structures of the siphophage OE33PA, providing the first atomic resolution view of a phage infecting this bacterium important for the wine industry. While the overall virion architecture is conserved, the adhesion device displays distinctive features. Its receptor-binding proteins adopt multiple orientations, revealing an intrinsically dynamic assembly. cryo-electron tomography captures distinct conformations upon host attachment, providing rare structural insight into interactions with Gram-positive hosts. Additionally, functional assays show that a highly mobile carbohydrate-binding module in the distal tail protein mediates host-specific binding. Furthermore, the tape measure protein, central to phage assembly and infectivity, adopts a hexameric organization, updating the prevailing trimeric model in siphophages. Together, these findings reveal a dynamic adhesion device in a phage infecting Gram-positive bacteria and highlight the structural and functional diversity of phages.
History
DepositionMay 7, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57921.png

Downloads & links

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Map

FileDownload / File: emd_57921.map.gz / Format: CCP4 / Size: 101.7 MB / Type: IMAGE STORED AS SIGNED BYTE
Annotationprocessed tomogram (IMOD deconvolution strength 0.5, reduce 4)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.81 Å/pix.
x 147 pix.
= 1442.07 Å		9.81 Å/pix.
x 837 pix.
= 8210.971 Å		9.81 Å/pix.
x 867 pix.
= 8505.271 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9.81 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 87.0
Average (Standard dev.)0.0982377 (±4.7397137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin162132-138
Dimensions837867147
Spacing867837147
CellA: 8505.2705 Å / B: 8210.971 Å / C: 1442.0701 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Phage OE33PA bound to its host Oenococcus oeni

EntireName: Phage OE33PA bound to its host Oenococcus oeni
Components
  • Complex: Phage OE33PA bound to its host Oenococcus oeni
    • Complex: phage OE33PA
    • Organelle or cellular component: Oenococcus oeni

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Supramolecule #1: Phage OE33PA bound to its host Oenococcus oeni

SupramoleculeName: Phage OE33PA bound to its host Oenococcus oeni / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: phage OE33PA

SupramoleculeName: phage OE33PA / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Oenococcus phage phiOE33PA (virus)

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Supramolecule #3: Oenococcus oeni

SupramoleculeName: Oenococcus oeni / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Oenococcus oeni (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 800 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 40
CTF correctionType: PHASE FLIPPING ONLY

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