9CUY | pdb_00009cuy

Bacteriophage PhiTE extended baseplate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Global structural survey of the flagellotropic myophage phi TE infecting agricultural pathogen Pectobacterium atrosepticum.

Hodgkinson-Bean, J.Ayala, R.Jayawardena, N.Rutter, G.L.Watson, B.N.J.Mayo-Munoz, D.Keal, J.Fineran, P.C.Wolf, M.Bostina, M.

(2025) Nat Commun 16: 3257-3257

  • DOI: https://doi.org/10.1038/s41467-025-58514-x
  • Primary Citation of Related Structures:  
    9CB9, 9CBA, 9CC7, 9CUL, 9CUY, 9MJN

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Wedge 2 proteinA [auth T],
B [auth S],
R,
T [auth U]
494Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L596 (Pectobacterium phage phiTE)
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Go to UniProtKB:  K9L596
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UniProt GroupK9L596
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tail sheath protein473Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L4E9 (Pectobacterium phage phiTE)
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UniProt GroupK9L4E9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tube proteinF [auth J],
G [auth H],
K [auth I],
L [auth G]
156Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L3Y2 (Pectobacterium phage phiTE)
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UniProt GroupK9L3Y2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tube initiator proteinM [auth K],
N [auth L]
284Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L594 (Pectobacterium phage phiTE)
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UniProt GroupK9L594
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Hub proteinO [auth X]330Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L5R2 (Pectobacterium phage phiTE)
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UniProt GroupK9L5R2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative baseplate assembly proteinP [auth Y]247Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L4F2 (Pectobacterium phage phiTE)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Wedge 1 proteinQ [auth O],
S [auth P]
165Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L561 (Pectobacterium phage phiTE)
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UniProt GroupK9L561
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Spacer proteinU [auth N],
V [auth M]
112Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L557 (Pectobacterium phage phiTE)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Sheath initiator proteinW [auth n],
X [auth m]
163Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L3Y6 (Pectobacterium phage phiTE)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tail fiber protein793Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L5R6 (Pectobacterium phage phiTE)
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UniProt GroupK9L5R6
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Short tail fiber554Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L5R4 (Pectobacterium phage phiTE)
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UniProt GroupK9L5R4
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tape measure proteinEA [auth W]811Pectobacterium phage phiTEMutation(s): 0 
UniProt
Find proteins for K9L3Y4 (Pectobacterium phage phiTE)
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UniProt GroupK9L3Y4
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Agriculture, Forestry and Fisheries (MAFF)JapanGD0696J004
Japan Society for the Promotion of Science (JSPS)Japan21K20645

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release