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- PDB-9cc7: Bacteriophage PhiTE extended connector complex -

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Basic information

Entry
Database: PDB / ID: 9cc7
TitleBacteriophage PhiTE extended connector complex
Components
  • PhiTE adaptor protein
  • PhiTE head completion protein
  • PhiTE tail terminator protein
  • Portal protein
  • Tail sheath protein
  • Tail tube protein
KeywordsVIRAL PROTEIN / connector / neck / sheath / tube / PhiTE / virus / phage / adaptor / tail terminator / head completion / portal
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsHodgkinson-Bean, J. / Ayala, R.
Funding support Japan, 2items
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, 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

Downloads & links

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Assembly

Deposited unit
D: PhiTE adaptor protein
E: PhiTE head completion protein
F: PhiTE tail terminator protein
G: Tail tube protein
H: Tail tube protein
C: PhiTE adaptor protein
I: Tail sheath protein
J: Tail sheath protein
A: Portal protein
B: Portal protein


Theoretical massNumber of molelcules
Total (without water)329,33110
Polymers329,33110
Non-polymers00
Water00
1
D: PhiTE adaptor protein
E: PhiTE head completion protein
F: PhiTE tail terminator protein
G: Tail tube protein
H: Tail tube protein
C: PhiTE adaptor protein
I: Tail sheath protein
J: Tail sheath protein
A: Portal protein
B: Portal protein
x 6


Theoretical massNumber of molelcules
Total (without water)1,975,98460
Polymers1,975,98460
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

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Protein , 6 types, 10 molecules DCEFGHIJAB

#1: Protein PhiTE adaptor protein


Mass: 20132.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L3Y0
#2: Protein PhiTE head completion protein


Mass: 16585.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L551
#3: Protein PhiTE tail terminator protein


Mass: 25622.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L5Q6
#4: Protein Tail tube protein


Mass: 17280.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L3Y2
#5: Protein Tail sheath protein


Mass: 50647.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L4E9
#6: Protein Portal protein


Mass: 55500.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage phiTE (virus) / References: UniProt: K9L587

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Details

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: Pectobacterium phage phiTE / Type: VIRUS / Entity ID: #2, #1, #3-#6 / 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
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14858 / Symmetry type: POINT

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