9RKS | pdb_00009rks

Agrobacterium phage 7-7-1 neck 2 + tail terminator + tail sheath + tail tube


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein179Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F9G5 (Agrobacterium phage 7-7-1)
Explore J7F9G5 
Go to UniProtKB:  J7F9G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7F9G5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein140Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FA79 (Agrobacterium phage 7-7-1)
Explore J7FA79 
Go to UniProtKB:  J7FA79
Entity Groups  
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UniProt GroupJ7FA79
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tail sheath protein503Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FA80 (Agrobacterium phage 7-7-1)
Explore J7FA80 
Go to UniProtKB:  J7FA80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7FA80
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein136Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F8Z8 (Agrobacterium phage 7-7-1)
Explore J7F8Z8 
Go to UniProtKB:  J7F8Z8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7F8Z8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 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