9GB5 | pdb_00009gb5

Contracted phiCD508 neck


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.

Wilson, J.S.Fortier, L.C.Fagan, R.P.Bullough, P.A.

(2025) Life Sci Alliance 8

  • DOI: https://doi.org/10.26508/lsa.202403088
  • Primary Citation of Related Structures:  
    9G8S, 9GAY, 9GAZ, 9GB0, 9GB1, 9GB2, 9GB3, 9GB4, 9GB5, 9GB6, 9GB7, 9GB8

  • PubMed Abstract: 

    The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S-layers. Here, we reveal the extended and contracted atomic structures of an intact contractile-tailed phage (φCD508) that binds to and penetrates the protective S-layer of the Gram-positive human pathogen Clostridioides difficile The tail is unusually long (225 nm), and it is also notable that the tail contracts less than those studied in related contractile injection systems such as the model phage T4 (∼20% compared with ∼50%). Surprisingly, we find no evidence of auxiliary enzymatic domains that other phages exploit in cell wall penetration, suggesting that sufficient energy is released upon tail contraction to penetrate the S-layer and the thick cell wall without enzymatic activity. Instead, the unusually long tail length, which becomes more flexible upon contraction, likely contributes toward the required free energy release for envelope penetration.


  • Organizational Affiliation

    Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK j.s.wilson@sheffield.ac.uk.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
gp56 - Tail tube protein
A, B, C, D, E
A, B, C, D, E, F
137Clostridioides difficileMutation(s): 0 
UniProt
Find proteins for A0A9X8RMX9 (Clostridioides difficile)
Explore A0A9X8RMX9 
Go to UniProtKB:  A0A9X8RMX9
Entity Groups  
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UniProt GroupA0A9X8RMX9
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
gp51 - Neck valve protein
G, K, M, O, Q
G, K, M, O, Q, X
125Clostridioides difficileMutation(s): 0 
UniProt
Find proteins for A0A9X8WSH7 (Clostridioides difficile)
Explore A0A9X8WSH7 
Go to UniProtKB:  A0A9X8WSH7
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X8WSH7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
gp53 - Tail adaptor protein273Clostridioides difficileMutation(s): 0 
UniProt
Find proteins for A0A9X8WSH1 (Clostridioides difficile)
Explore A0A9X8WSH1 
Go to UniProtKB:  A0A9X8WSH1
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UniProt GroupA0A9X8WSH1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
gp50 - Portal adaptor protein112Clostridioides difficileMutation(s): 0 
UniProt
Find proteins for A0A9X8WSI0 (Clostridioides difficile)
Explore A0A9X8WSI0 
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UniProt GroupA0A9X8WSI0
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
gp55 - Tail sheath protein473Clostridioides difficileMutation(s): 0 
UniProt
Find proteins for A0A9X8RMY4 (Clostridioides difficile)
Explore A0A9X8RMY4 
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UniProt GroupA0A9X8RMY4
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
gp45 - Portal protein500Clostridioides difficileMutation(s): 0 
UniProt
Find proteins for A0A9X8RMZ9 (Clostridioides difficile)
Explore A0A9X8RMZ9 
Go to UniProtKB:  A0A9X8RMZ9
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UniProt GroupA0A9X8RMZ9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P02002X/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references