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- EMDB-58150: Capsid-connector assembly of the phage OE33PA -

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Basic information

Entry
Database: EMDB / ID: EMD-58150
TitleCapsid-connector assembly of the phage OE33PA
Map datasharpened map
Sample
  • Virus: Oenococcus phage phiOE33PA (virus)
    • Protein or peptide: portal protein
    • Protein or peptide: Major Capsid Protein
KeywordsMajor capsid protein / portal protein / connector assembly / siphophage / VIRAL PROTEIN
Biological speciesOenococcus phage phiOE33PA (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGoulet A / Cambillau C
Funding support France, 3 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0018-01 France
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 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 18, 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_58150.png

Downloads & links

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Map

FileDownload / File: emd_58150.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 672 pix.
= 563.808 Å		0.84 Å/pix.
x 672 pix.
= 563.808 Å		0.84 Å/pix.
x 672 pix.
= 563.808 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.24914767 - 0.43511593
Average (Standard dev.)0.0013654806 (±0.028938213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 563.808 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map

Fileemd_58150_additional_1.map
Annotationraw map
Projections & Slices
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Half map: #2

Fileemd_58150_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_58150_half_map_2.map
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Sample components

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Entire : Oenococcus phage phiOE33PA

EntireName: Oenococcus phage phiOE33PA (virus)
Components
  • Virus: Oenococcus phage phiOE33PA (virus)
    • Protein or peptide: portal protein
    • Protein or peptide: Major Capsid Protein

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Supramolecule #1: Oenococcus phage phiOE33PA

SupramoleculeName: Oenococcus phage phiOE33PA / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2201414 / Sci species name: Oenococcus phage phiOE33PA / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: portal protein

MacromoleculeName: portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Oenococcus phage phiOE33PA (virus)
Molecular weightTheoretical: 42.652609 KDa
SequenceString: MPLFNSNFHI RDSTTEYPIS TSQWSQVLSS VDPYGGHYIS AWKALRNPDI QSAVTQLAGD LGSAKLKANM PRAQGILDNP SKLSNPRTF WVTMFAQMIL GGEAFAYRWR NANGIDDHWE YLRPSQVQIF ELSDGSGLVY TVSFDEPDIG IVENIPSSDM I HFRYFSMN ...String:
MPLFNSNFHI RDSTTEYPIS TSQWSQVLSS VDPYGGHYIS AWKALRNPDI QSAVTQLAGD LGSAKLKANM PRAQGILDNP SKLSNPRTF WVTMFAQMIL GGEAFAYRWR NANGIDDHWE YLRPSQVQIF ELSDGSGLVY TVSFDEPDIG IVENIPSSDM I HFRYFSMN GMTGISPLYS LLTTLNIKKQ SDQLTIKALS QSVVASSVLS EPTRVSDKYA LGRAKTLKKQ LESADGIPVV LM PEETFTP LEMKSNIANL LGQVDWTSTQ IAKAFQIPDS YLNGQGDQQS SITDISGLYA NTLNRDMNMV LSELNWQLSA NIA ADIRQA IDPLGNNYAT ALLGSKNLSA DQVSFALQQN GYLPSGMPKA PVATSTTTTS VANNPPQEGE DDD

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Macromolecule #2: Major Capsid Protein

MacromoleculeName: Major Capsid Protein / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Oenococcus phage phiOE33PA (virus)
Molecular weightTheoretical: 45.461793 KDa
SequenceString: MDLNKLNQAF TDAGQQVSDA QDARQKMVFE NIAEPGKHSD KELSDLKNKI DNLVATRDAA KDVLEDARKN AVVLPPKDGK DKESNLNNS DKENNKKLDF VKNVRGLIRG DHKVLDMATS STDESGNAIG LVIPQDIQTA IHTLIRQYDD LQQYVNVENV T TQTGSRVY ...String:
MDLNKLNQAF TDAGQQVSDA QDARQKMVFE NIAEPGKHSD KELSDLKNKI DNLVATRDAA KDVLEDARKN AVVLPPKDGK DKESNLNNS DKENNKKLDF VKNVRGLIRG DHKVLDMATS STDESGNAIG LVIPQDIQTA IHTLIRQYDD LQQYVNVENV T TQTGSRVY EKWTDVTPLA EITEEGATIG DNDDPDLQTV KYIIRRFAGI TTATNSLLSD SDQNILAWLE GWISKKVVVT RN AQIIAVF NALPNKPTLA KYDDILDLTY TGIDPAIQST AFFLTNQSGC NALHKVKNAD GDYLLQPNPQ NPMEMLMNGK QIK MVADRW LPSAGTTAAP VFPLYYGDAK QAATLFDRQN MSLLSTNIGA GSFETDTTKI RVIDRFDVKP TDTDAFVAAS FSAI ADQPA KIVVQSAS

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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: 7.5
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: 40.0 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: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5819
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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