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- PDB-9cba: Bacteriophage PhiTE contracted tail -

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Basic information

Entry
Database: PDB / ID: 9cba
TitleBacteriophage PhiTE contracted tail
ComponentsStructural protein
KeywordsVIRAL PROTEIN / Tail / Sheath / PhiTE / Virus / Phage
Function / homologyStructural protein
Function and homology information
Biological speciesPectobacterium phage phiTE (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsHodgkinson-Bean, J. / Ayala, R.
Funding support Japan, Russian Federation, China, 4items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
Russian Science Foundation21-44-07002 Russian Federation
National Natural Science Foundation of China (NSFC)32250410316 China
CitationJournal: Nat Commun / Year: 2025
Title: Global structural survey of the flagellotropic myophage φTE infecting agricultural pathogen Pectobacterium atrosepticum.
Authors: James Hodgkinson-Bean / Rafael Ayala / Nadishka Jayawardena / Georgia L Rutter / Bridget N J Watson / David Mayo-Muñoz / James Keal / Peter C Fineran / Matthias Wolf / Mihnea Bostina /
Abstract: Bacteriophages offer a promising alternative to drug-based treatments due to their effectiveness and host specificity. This is particularly important in agriculture as a biocontrol agent of plant ...Bacteriophages offer a promising alternative to drug-based treatments due to their effectiveness and host specificity. This is particularly important in agriculture as a biocontrol agent of plant diseases. Phage engineering is facilitated by structural knowledge. However, structural information regarding bacteriophages infecting plant pathogens is limited. Here, we present the cryo-EM structure of bacteriophage φTE that infects plant pathogen Pectobacterium atrosepticum. The structure reveals a distinct neck topology compared with other myophages, where tail terminator proteins compensate for reduced connectivity between sheath subunits. A contact network between tail fibers, the sheath initiator, and baseplate wedge proteins provides insights into triggers that transduce conformational changes from the baseplate to the sheath to orchestrate contraction. We observe two distinct oligomeric states of the tape measure protein (TMP), which is six-fold in regions proximal to the N-terminus and throughout most of the tail, while three-fold at the C-terminus, indicating that the TMP may be proteolytically cleaved. Our results provide a structural atlas of the model bacteriophage φTE, enhancing future interpretation of phage host interactions in pectobacteria. We anticipate that our structure will inform rational design of biocontrol agents against plant pathogens that cause diseases such as soft rot and blackleg disease in potatoes.
History
DepositionJun 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural protein


Theoretical massNumber of molelcules
Total (without water)50,6481
Polymers50,6481
Non-polymers00
Water00
1
A: Structural protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,038,86660
Polymers3,038,86660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation1_555x,y,z1
helical symmetry operation59
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 16.426 Å / Rotation per n subunits: 32.67 °)

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Components

#1: Protein Structural protein


Mass: 50647.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L4E9
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pectobacterium phage phiTE / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pectobacterium atrosepticum
Virus shellDiameter: 1000 nm / Triangulation number (T number): 13
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 32.67 ° / Axial rise/subunit: 16.426 Å / Axial symmetry: C6
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18653 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033459
ELECTRON MICROSCOPYf_angle_d0.4884709
ELECTRON MICROSCOPYf_dihedral_angle_d4.385488
ELECTRON MICROSCOPYf_chiral_restr0.044549
ELECTRON MICROSCOPYf_plane_restr0.004610

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