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- EMDB-45937: Bacteriophage PhiTE mature capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-45937
TitleBacteriophage PhiTE mature capsid
Map data
Sample
  • Virus: Pectobacterium phage phiTE (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Head stabilization/decoration protein
Keywordscapsid / head / MCP / PhiTE / Virus / Phage / VIRAL PROTEIN / decoration / icosahedral
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / host cell cytoplasm / Putative major head protein / Head stabilization/decoration protein
Function and homology information
Biological speciesPectobacterium phage phiTE (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHodgkinson-Bean J / Ayala R
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
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
DepositionJul 26, 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_45937.png

Downloads & links

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Map

FileDownload / File: emd_45937.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.54 Å/pix.
x 808 pix.
= 1248.3 Å		1.54 Å/pix.
x 808 pix.
= 1248.3 Å		1.54 Å/pix.
x 808 pix.
= 1248.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.54493 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.3167783 - 3.6731915
Average (Standard dev.)-0.0020880857 (±0.23873194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808808808
Spacing808808808
CellA=B=C: 1248.2999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45937_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45937_half_map_2.map
Projections & Slices
AxesZYX

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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: Major capsid protein
    • Protein or peptide: Head stabilization/decoration 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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 37.596047 KDa
SequenceString: MQNGDFQILD YTGLISTMPR VDTLLQSMNL FTEHFGRTTV ARIERLDDGA GDIKAVQRGG VRQHLANDRK KIVNLNIPFF PLDRSIDRA DIQNFREFGT ENAPATVDAE VQRHMARIRR SHAILKSKAM YAALKGTSWS PDDPVSDYNY YDVWGATQTT A DVDFTKLG ...String:
MQNGDFQILD YTGLISTMPR VDTLLQSMNL FTEHFGRTTV ARIERLDDGA GDIKAVQRGG VRQHLANDRK KIVNLNIPFF PLDRSIDRA DIQNFREFGT ENAPATVDAE VQRHMARIRR SHAILKSKAM YAALKGTSWS PDDPVSDYNY YDVWGATQTT A DVDFTKLG VDPIEVLEAE ARAHIIDWAG DNGDNYEIVV LASRQWFSAL IAHPQVTGAY SQYPSTQEIL RRRLGGNANN RI FEHKNIL FIEDISGNIP AGEAYIFPRG ISRMFEIYYA PSDTLRDANQ AAQELYVFFK ESNYLREAKI ESETSFLTVN NRP ELVVKS TGKFTA

UniProtKB: Putative major head protein

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Macromolecule #2: Head stabilization/decoration protein

MacromoleculeName: Head stabilization/decoration protein / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 15.552637 KDa
SequenceString:
MAKAHVATLE GNYSDIVLGR VVAFGDTGWN FKEVDMTFIA DDADADSKTT LFAGVLVGED GTPATAAAGV FGVLVDRKVL PGVDHYIGV FEPGEKVPMV LAVRGLTLNQ LKLKYADGTA IDAAGIQALE AQGNQVTDKI VGTQFIGSVL

UniProtKB: Head stabilization/decoration protein

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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-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

Startup modelType of model: OTHER / Details: Ab initio helical model generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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