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- EMDB-45420: Bacteriophage PhiTE contracted tail -

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Basic information

Entry
Database: EMDB / ID: EMD-45420
TitleBacteriophage PhiTE contracted tail
Map dataPhiTE contracted tail full map with helical and C6 symmetry imposed.
Sample
  • Virus: Pectobacterium phage phiTE (virus)
    • Protein or peptide: Structural protein
KeywordsTail / Sheath / PhiTE / Virus / Phage / VIRAL PROTEIN
Function / homologyStructural protein
Function and homology information
Biological speciesPectobacterium phage phiTE (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsHodgkinson-Bean J / Ayala R
Funding support Japan, Russian Federation, China, 4 items
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, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45420.png

Downloads & links

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Map

FileDownload / File: emd_45420.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhiTE contracted tail full map with helical and C6 symmetry imposed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.56
Minimum - Maximum-0.5910179 - 1.6271594
Average (Standard dev.)0.021648057 (±0.117037125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 554.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: PhiTE contracted tail half map A.

Fileemd_45420_half_map_1.map
AnnotationPhiTE contracted tail half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PhiTE contracted tail half map B.

Fileemd_45420_half_map_2.map
AnnotationPhiTE contracted tail half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pectobacterium phage phiTE

EntireName: Pectobacterium phage phiTE (virus)
Components
  • Virus: Pectobacterium phage phiTE (virus)
    • Protein or peptide: Structural protein

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Supramolecule #1: Pectobacterium phage phiTE

SupramoleculeName: Pectobacterium phage phiTE / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1116482 / Sci species name: Pectobacterium phage phiTE / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pectobacterium atrosepticum (bacteria)
Virus shellShell ID: 1 / Diameter: 1000.0 Å / T number (triangulation number): 13

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Macromolecule #1: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 50.647766 KDa
SequenceString: MAEYQDKVVD VEVSLGTQPI DTVGFETPMF LAMHGNFPER IRFYVSTAGM VADGFAVGSP AYQFATNAFA GNFAPQRVAI GRMSIDSSK VDFTGTTNTE QVVVNITLNK VVKAVKINVL PGNTPAQIAT ALADAVTADA DLTGKATAVA TGTYVTVTAV S PNVVSVGK ...String:
MAEYQDKVVD VEVSLGTQPI DTVGFETPMF LAMHGNFPER IRFYVSTAGM VADGFAVGSP AYQFATNAFA GNFAPQRVAI GRMSIDSSK VDFTGTTNTE QVVVNITLNK VVKAVKINVL PGNTPAQIAT ALADAVTADA DLTGKATAVA TGTYVTVTAV S PNVVSVGK GAGVYKIVNE SSETVATVLP SVIAENHNWY FLATEARSDA DIVAAAEFAK ANYKLHIYNS TDVDAYAPEN SA ASVFDTL KSLSYDSLGT SDAGADVDFT EGSVIGAMAA NDPSYGDSLH LKTMPGMVPF AGSDTQRSNA WSRNANIYRG LYG GGSYIE GKTSSGQYVD VIRFSHWVKF RMEESVFAYM KRRSDMGLSM KMSDEDLPVL KSVLMNNPIN IGIRNGGILT GYDT ENKVS YDPTIIIPKR ANIPTNDLAA RILRDVKVEL VYNNSLHYVK IRASVVLDRP AGQSTNAQTP MSSSAVGV

UniProtKB: Structural protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.426 Å
Applied symmetry - Helical parameters - Δ&Phi: 32.670 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18653
Startup modelType of model: OTHER / Details: Ab initio helical model generated in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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