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- EMDB-58159: RBP trimer bound to a monomer of the distal tail protein of the p... -

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Basic information

Entry
Database: EMDB / ID: EMD-58159
TitleRBP trimer bound to a monomer of the distal tail protein of the phage OE33PA
Map datasharpened map
Sample
  • Virus: Oenococcus phage phiOE33PA (virus)
    • Protein or peptide: distal tail protein
    • Protein or peptide: receptor-binding protein
Keywordsreceptor-binding protein / distal tail protein / STRUCTURAL PROTEIN / VIRAL PROTEIN
Biological speciesOenococcus phage phiOE33PA (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_58159.png

Downloads & links

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Map

FileDownload / File: emd_58159.map.gz / Format: CCP4 / Size: 244.1 MB / 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 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 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: 0.18
Minimum - Maximum-0.4643446 - 0.73770475
Average (Standard dev.)0.00245625 (±0.023813697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map

Fileemd_58159_additional_1.map
Annotationraw map
Projections & Slices
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Half map: #2

Fileemd_58159_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_58159_half_map_2.map
Projections & Slices
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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: distal tail protein
    • Protein or peptide: receptor-binding 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: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: distal tail protein

MacromoleculeName: distal tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oenococcus phage phiOE33PA (virus)
Molecular weightTheoretical: 71.7455 KDa
SequenceString: MFKLTNARGE TVDLNTNSLR AYTPTGLGLT LKNTYSAYQS AFIKTHTQID DPASNPLQLY IKFGDVKSHS YQSFSDFSEF LAYPPYTLA YTTDAGTWYR KANLQSITKT EIGGSTIIAA DRLNEAFILE FYTAWYQLQS EEYVSYSNDP NLGLYGKIYN T SIKRNATD ...String:
MFKLTNARGE TVDLNTNSLR AYTPTGLGLT LKNTYSAYQS AFIKTHTQID DPASNPLQLY IKFGDVKSHS YQSFSDFSEF LAYPPYTLA YTTDAGTWYR KANLQSITKT EIGGSTIIAA DRLNEAFILE FYTAWYQLQS EEYVSYSNDP NLGLYGKIYN T SIKRNATD DSVSFPDQTL INSSGIDLAS IHDNGSATGT IQVSGSSEIQ NALVSVKDND GNIVGSQQLN TLPNPDQTVA AP SDTIIIH DNSDGSSTLS TKVTAGQSIQ LTQNTVGLIY SQANLGYNNL TADSEMLLGL QSASTAGWNS ANTISTILSG VYT DSVGKT HNAIQMASTS ASTSNVVVSK NIVPTLNSTY YWSVWYKVTG ALSTAASVHL EGRGIVSGSD AGTEAEALIS TTTA VGNWI QLTGSFTPTS SSTTYLRLRF QNLGTGTILF SEPMINSGSQ LNAYISDTVD ATQWSLKVTD GYLYLMEINA HEVDF TVLP QNTGYNFNFT FPHASGNYIF DNGSETFAFI LGSNLNYLFP YTYIESGRNL NQKAIPVSNS SEYFGLQNGS PCLITI TGP TTTNVSWEVL QNGITIASDA FDVTLTDNQQ LVVSSYPEDQ YARIYNPDGS YVNISQYQDI TKTNYILIPE GDSTIVF YI DKTAGVQLTY KEERLLV

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Macromolecule #2: receptor-binding protein

MacromoleculeName: receptor-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oenococcus phage phiOE33PA (virus)
Molecular weightTheoretical: 27.131156 KDa
SequenceString: MAITMYQADR NFVSPANDAA LYSAILNNTS GVLANRGNNF ALTIDGLVVS IDTGQAVIGG RLIEITALES VTVPANSSGS ICLVVDLTK TNTVTGNAGD TTYSVAVNQV YTSAVTGSLT QDDLNDGGFI YELPLASFVS TATSVTLTDT TGYLNDTGWL T LPNATGLV ...String:
MAITMYQADR NFVSPANDAA LYSAILNNTS GVLANRGNNF ALTIDGLVVS IDTGQAVIGG RLIEITALES VTVPANSSGS ICLVVDLTK TNTVTGNAGD TTYSVAVNQV YTSAVTGSLT QDDLNDGGFI YELPLASFVS TATSVTLTDT TGYLNDTGWL T LPNATGLV IGSGGFTKYR VKNNVVYIRL QALDTSKTTN ANQIGTIPSK YAPSITFMAA GMDDSSGTPY GIELHVQTSG LI YANYVSP HNGGIGGTIT YPLG

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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35755
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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