9G8S | pdb_00009g8s

C3 reconstruction of extended phiCD508 needle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 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

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
Baseplate J family protein378Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp23
UniProt
Find proteins for J9QE72 (Clostridium phage phiMMP02)
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Go to UniProtKB:  J9QE72
Entity Groups  
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UniProt GroupJ9QE72
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XkdT-related protein157Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp24
UniProt
Find proteins for J9QE20 (Clostridium phage phiMMP02)
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Go to UniProtKB:  J9QE20
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UniProt GroupJ9QE20
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan-binding LysM protein223Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp19
UniProt
Find proteins for J9QE19 (Clostridium phage phiMMP02)
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UniProt GroupJ9QE19
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
XkdM-related protein130Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp14
UniProt
Find proteins for J9QE18 (Clostridium phage phiMMP02)
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UniProt GroupJ9QE18
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tail sheath460Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp13
UniProt
Find proteins for J9QE70 (Clostridium phage phiMMP02)
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UniProt GroupJ9QE70
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
XkdS-related protein125Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp22
UniProt
Find proteins for J9QEB8 (Clostridium phage phiMMP02)
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UniProt GroupJ9QEB8
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Phage proteinQA [auth r],
RA [auth v],
TA [auth s]
112Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp21
UniProt
Find proteins for J9QD14 (Clostridium phage phiMMP02)
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UniProt GroupJ9QD14
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
XkdQ-related proteinSA [auth q],
UA [auth t],
VA [auth u]
316Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp20
UniProt
Find proteins for J9QDX2 (Clostridium phage phiMMP02)
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UniProt GroupJ9QDX2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tape measureWA [auth w],
XA [auth x],
YA [auth y]
1,424Clostridioides phage phiCD508Mutation(s): 0 
Gene Names: phiMMP02_gp17
UniProt
Find proteins for J9QEB7 (Clostridium phage phiMMP02)
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UniProt GroupJ9QEB7
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.96 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: 2025-04-09
    Type: Initial release