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- PDB-30yv: Portal-adaptor asssembly of the phage OE33PA -

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Basic information

Entry
Database: PDB / ID: 30yv
TitlePortal-adaptor asssembly of the phage OE33PA
Components
  • adaptor protein
  • portal protein
KeywordsVIRAL PROTEIN / portal protein / adaptor protein / STRUCTURAL PROTEIN
Biological speciesOenococcus phage phiOE33PA (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGoulet, A. / Cambillau, C.
Funding support France, 3items
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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: portal protein
N: adaptor protein
B: portal protein
C: adaptor protein
D: portal protein
E: adaptor protein
F: portal protein
G: adaptor protein
H: portal protein
I: adaptor protein
J: portal protein
K: adaptor protein
L: portal protein
M: adaptor protein
O: portal protein
P: adaptor protein
Q: portal protein
R: adaptor protein
S: portal protein
T: adaptor protein
U: portal protein
V: adaptor protein
W: portal protein
X: adaptor protein


Theoretical massNumber of molelcules
Total (without water)663,05324
Polymers663,05324
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
portal protein


Mass: 42652.609 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Oenococcus phage phiOE33PA (virus)
#2: Protein
adaptor protein


Mass: 12601.828 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Oenococcus phage phiOE33PA (virus)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Oenococcus phage phiOE33PA / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Oenococcus phage phiOE33PA (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5319 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 66.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002239821
ELECTRON MICROSCOPYf_angle_d0.457354208
ELECTRON MICROSCOPYf_chiral_restr0.03846276
ELECTRON MICROSCOPYf_plane_restr0.00387019
ELECTRON MICROSCOPYf_dihedral_angle_d3.33695376

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