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- EMDB-45435: Bacteriophage PhiTE extended connector complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45435
TitleBacteriophage PhiTE extended connector complex
Map dataComposite PhiTE connector reconstruction half map 2 derived from C6 and C12 constituent reconstructions (deposited as individual related entries).
Sample
  • Virus: Pectobacterium phage phiTE (virus)
    • Protein or peptide: PhiTE head completion protein
    • Protein or peptide: PhiTE adaptor protein
    • Protein or peptide: PhiTE tail terminator protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Portal protein
Keywordsconnector / neck / sheath / tube / PhiTE / virus / phage / adaptor / tail terminator / head completion / portal / VIRAL PROTEIN
Function / homology
Function and homology information


Phage neck terminator protein / Structural protein ORF10, bacteriophage KPP10 / Bacteriophage PhiTE tail tube protein / Bacteriophage SPP1, head-tail adaptor / Phage head completion protein
Similarity search - Domain/homology
Uncharacterized protein / Structural protein / Structural protein / Uncharacterized protein / Portal protein / Uncharacterized protein
Similarity search - Component
Biological speciesPectobacterium phage phiTE (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 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
DepositionJun 20, 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_45435.png

Downloads & links

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Map

FileDownload / File: emd_45435.map.gz / Format: CCP4 / Size: 401.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite PhiTE connector reconstruction half map 2 derived from C6 and C12 constituent reconstructions (deposited as individual related entries).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.39 Å/pix.
x 472 pix.
= 654.664 Å		1.39 Å/pix.
x 472 pix.
= 654.664 Å		1.39 Å/pix.
x 472 pix.
= 654.664 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: 3.65
Minimum - Maximum-15.407377 - 31.771334
Average (Standard dev.)0.008807246 (±1.1115206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions472472472
Spacing472472472
CellA=B=C: 654.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Composite PhiTE connector reconstruction half map 2 derived...

Fileemd_45435_half_map_1.map
AnnotationComposite PhiTE connector reconstruction half map 2 derived from C6 and C12 constituent reconstructions (deposited as individual related entries).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Composite PhiTE connector reconstruction half map 2 derived...

Fileemd_45435_half_map_2.map
AnnotationComposite PhiTE connector reconstruction half map 2 derived from C6 and C12 constituent reconstructions (deposited as individual related entries).
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: PhiTE head completion protein
    • Protein or peptide: PhiTE adaptor protein
    • Protein or peptide: PhiTE tail terminator protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Portal protein

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Supramolecule #1: Pectobacterium phage phiTE

SupramoleculeName: Pectobacterium phage phiTE / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #3-#6 / 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: PhiTE adaptor protein

MacromoleculeName: PhiTE adaptor protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 20.13277 KDa
SequenceString:
MTNEQVIELV RVLLGGITTE EISDQTIIFF WTKWKLTYDL DNRPEKIPAA LYNTVVDCVR WLIVQEVSSG NSSIRERFEK IGDETISVK GGSSWESWKD FLDWLELNPD YIDPSLAFNS SLVIIGGVRK DEFFRVKNNP NSYNGFMEQG VYPTPAIPKQ S AWPCTAAR RSPWMVR

UniProtKB: Uncharacterized protein

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Macromolecule #2: PhiTE head completion protein

MacromoleculeName: PhiTE head completion protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 16.58576 KDa
SequenceString:
MARAYSLLSS RNRLIPRVEV QCRKREWVKT DPDSPFLNGG REVLYTPFTA VECTVQPMRG KAIRDQNNQL MIGGEEDYDS YTVYSETLL FRAREGTEHL SDQMLLPDSG GGQTWFTVMK ADMYPSSGVP RYRYYLIAVP VGTEGGL

UniProtKB: Uncharacterized protein

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Macromolecule #3: PhiTE tail terminator protein

MacromoleculeName: PhiTE tail terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 25.622951 KDa
SequenceString: MALPLDFTNS DVVMGALTKA VGRLCLDVTG YDVVEADETI PKPEGPYILV DLSLLTPLDW ATNEVVDEDG VVHTAHNYTA SYTLTAYRG KPHWALSRVH QAFGLPFLRE KYFPTGSPYA YSSTSNIARM RVPLNQQMFE NRARTIVTFN ATFVEKDLGT F EDIEHIII ...String:
MALPLDFTNS DVVMGALTKA VGRLCLDVTG YDVVEADETI PKPEGPYILV DLSLLTPLDW ATNEVVDEDG VVHTAHNYTA SYTLTAYRG KPHWALSRVH QAFGLPFLRE KYFPTGSPYA YSSTSNIARM RVPLNQQMFE NRARTIVTFN ATFVEKDLGT F EDIEHIII GIDVDNPSGP PIGIGADYDK GVKPGGDDPG LPPKPNPPIV YHDAIAQVCM ATPVIDKPAL ISDKTGE

UniProtKB: Uncharacterized protein

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Macromolecule #4: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 17.28042 KDa
SequenceString:
MLNQSKILTL QAYDPAKVLV FIGGQRVSGF AADTKIVITR NNDNISVHAG VDGEISNALS RDNTGVMTLS LQNTAKWNGY LAQWQRQAN VTGLIYLPVQ VEGSQGLSLN TIGWIQKQPD LSYGTEVGQM DWEIGVLDAW LSPDQIQGIA AGITGLLGLD Q

UniProtKB: Structural protein

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Macromolecule #5: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / 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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Macromolecule #6: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage phiTE (virus)
Molecular weightTheoretical: 55.500016 KDa
SequenceString: MSRKRNRNRS VQVAKATSEQ LNVSRMRMSE QGTFALAKVQ VDSERMKAEE IRWPHLIGTA ESMKQDATVA TGLDMLYTFV EKAFKDFKV IPGESEESKK AAKFIEYCLK NMEGQTLRQF ARDAATFNEY GLSVVEKVYT QIAVGEYVGK YKVKNLAFRP Q ASLSRTNP ...String:
MSRKRNRNRS VQVAKATSEQ LNVSRMRMSE QGTFALAKVQ VDSERMKAEE IRWPHLIGTA ESMKQDATVA TGLDMLYTFV EKAFKDFKV IPGESEESKK AAKFIEYCLK NMEGQTLRQF ARDAATFNEY GLSVVEKVYT QIAVGEYVGK YKVKNLAFRP Q ASLSRTNP IVYNSDGSAI VGIKQSLSAF QNYTASEIGV GGVSTRMSDV IIPISRVMLM NTGGSSSQAL GVSPLVGCYR AW REKILIE NLEVVGATKD MGGVIELKIP SQILNKAAMD PSSPEADMVR GLMSDAANAH SGEQSFFMLP SDTKDNAPQY SMT LKGIDG MGKQYSTAQL ISDRKKSILD RLGAGFINVG NDKGGSYNLS ESKQTIHTQF VQRVNEIILE ALNENLLPQL LALN DIRLP ETEMPYVKAG EIVDVDMEGF SKAIQRIGAV GYLPKTPKVI NRVLEVLGID EKIEEDISQE ELMKLLGEDT SRAGD GMTK GSSGNGTGKI SASRDNSAAN LDN

UniProtKB: Portal 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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