9RKU | pdb_00009rku

Agrobacterium phage 7-7-1 baseplate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into the structure and initial host attachment of the flagellotropic bacteriophage 7-7-1.

Noteborn, W.E.M.Ouyang, R.Hoeksma, T.Sidi Mabrouk, A.Esteves, N.C.Pelt, D.M.Scharf, B.E.Briegel, A.

(2025) Commun Biol 9: 55-55

  • DOI: https://doi.org/10.1038/s42003-025-09319-7
  • Primary Citation of Related Structures:  
    9HZ7, 9HZ8, 9RKQ, 9RKR, 9RKS, 9RKT, 9RKU, 9RKV

  • PubMed Abstract: 

    Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. Using single particle analysis (SPA) cryo-electron microscopy (cryo-EM), we determined the capsid, neck region, tail, and baseplate complex structures. Combined with cryo-electron tomography (cryo-ET) and machine learning methodologies, our findings indicate that phage 7-7-1 uses capsid fibers to establish initial contact with the host flagellum, followed by subsequent attachment to cell surface receptors. The study also demonstrated that capsid fibers are flexible and can interact with other phages and host flagella, suggesting a cooperative infection strategy. These results provide crucial structural insights and may open avenues for developing phage-based therapeutics against resistant bacterial pathogens.


  • Organizational Affiliation
    • Netherlands Centre for Electron Nanoscopy, Leiden University, Leiden, The Netherlands.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate proteinA [auth Ac],
B [auth Ad],
C [auth Ae]
189Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FAQ1 (Agrobacterium phage 7-7-1)
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Go to UniProtKB:  J7FAQ1
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UniProt GroupJ7FAQ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tail biosynthetic proteinD [auth Af],
E [auth Ag],
F [auth Ah]
454Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F9D2 (Agrobacterium phage 7-7-1)
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UniProt GroupJ7F9D2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein286Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FAD9 (Agrobacterium phage 7-7-1)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate protein396Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F8X4 (Agrobacterium phage 7-7-1)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tail biosynthetic protein398Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FAD8 (Agrobacterium phage 7-7-1)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Putative structural protein178Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FA56 (Agrobacterium phage 7-7-1)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tail sheath protein503Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FA80 (Agrobacterium phage 7-7-1)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein136Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F8Z8 (Agrobacterium phage 7-7-1)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands184.034.014

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-21
    Changes: Data collection, Database references