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Structure paper

TitleHow cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile.
Journal, issue, pagesIucrj, Year 2026
Publish dateMay 31, 2026
AuthorsPer A Bullough / Jason S Wilson / Hannah L Berry / Robert P Fagan /
PubMed AbstractWe review the structural and functional characteristics of bacteriophages and bacteriocins (diffocins) that specifically target Clostridioides difficile, a significant healthcare concern due to its ...We review the structural and functional characteristics of bacteriophages and bacteriocins (diffocins) that specifically target Clostridioides difficile, a significant healthcare concern due to its role in nosocomial infections. The advent of modern cryogenic electron microscopy (cryoEM) has revolutionized our understanding of these contractile injection systems, providing high-resolution insights into their mechanisms. We compare the structures of C. difficile phages and diffocins, highlighting their adaptations for penetrating the Gram-positive bacterial cell envelope - including the cell membrane, cell wall and proteinaceous surface layer. Diffocins, simpler in structure, utilize a combination of mechanical and enzymatic strategies, while some phages like ΦCD508 may rely on mechanical force alone. This review delves into the assembly and function of key components such as the contractile sheath, baseplate and receptor-binding proteins, offering a framework for engineering precision antimicrobials. We also present new experimental results, including refined cryoEM structures of the ΦCD508 pre- and post-contracted tail, a novel spontaneously contracted conformation and an X-ray crystal structure of a phage receptor-binding protein domain. This work underscores the potential of cryoEM in advancing our understanding of phage biology and its applications in developing targeted therapies against C. difficile.
External linksIucrj / PubMed:42334192 / PubMed Central
MethodsEM (helical sym.) / X-ray diffraction
Resolution1.42 - 4.3 Å
Structure data

58347
EMDB Unreleased entry

31es

EMDB-58347, PDB-31es:
C. difficile phage phiCD508 tail tube in spontaneously contracted state
Method: EM (helical sym.) / Resolution: 2.4 Å

58348
EMDB Unreleased entry

31eu

EMDB-58348, PDB-31eu:
C. difficile phage phiCD508 tail sheath in spontaneously contracted state
Method: EM (helical sym.) / Resolution: 4.3 Å

58350
EMDB Unreleased entry

31ev

EMDB-58350, PDB-31ev:
Extended tail of C. difficile phage phiCD508 subjected to 3D variability analysis
Method: EM (helical sym.) / Resolution: 2.7 Å

PDB-31he:
Xray crystal structure of PtsM receptor binding protein
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

Chemicals

ChemComp-NA:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-HOH:
WATER

Source
  • clostridioides difficile (bacteria)
  • clostridioides difficile r20291 (bacteria)
KeywordsVIRUS / bacteriophage / phage tail / myophage / contractile injection system / S-layer / helical assembly / VIRAL PROTEIN / phage / C. difficile / helical array / Receptor binding protein / RBP

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