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- PDB-31es: C. difficile phage phiCD508 tail tube in spontaneously contracted... -

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Basic information

Entry
Database: PDB / ID: 31es
TitleC. difficile phage phiCD508 tail tube in spontaneously contracted state
Componentsgp56 - Tail tube protein
KeywordsVIRUS / bacteriophage / phage tail / myophage / contractile injection system / S-layer / helical assembly
Function / homologyPhage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Protein of uncharacterized function (DUF2001)
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsBullough, P.A. / Wilson, J.S. / Berry, H.L. / Fagan, R.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P02002X/1 United Kingdom
Citation
Journal: IUCrJ / Year: 2026
Title: How cryoEM has advanced our understanding of bacteriophages and bacteriocins targeting Clostridioides difficile.
Authors: Per A Bullough / Jason S Wilson / Hannah L Berry / Robert P Fagan /
Abstract: We 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.
#1: Journal: Life Sci Alliance / Year: 2025
Title: Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.
Authors: Jason S Wilson / Louis-Charles Fortier / Robert P Fagan / Per A Bullough /
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- ...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 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.
History
DepositionMay 30, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: gp56 - Tail tube protein
A: gp56 - Tail tube protein
B: gp56 - Tail tube protein
C: gp56 - Tail tube protein
D: gp56 - Tail tube protein
E: gp56 - Tail tube protein
F: gp56 - Tail tube protein
H: gp56 - Tail tube protein
I: gp56 - Tail tube protein
J: gp56 - Tail tube protein
K: gp56 - Tail tube protein
L: gp56 - Tail tube protein
M: gp56 - Tail tube protein
N: gp56 - Tail tube protein
O: gp56 - Tail tube protein
P: gp56 - Tail tube protein
Q: gp56 - Tail tube protein
R: gp56 - Tail tube protein


Theoretical massNumber of molelcules
Total (without water)280,30618
Polymers280,30618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
gp56 - Tail tube protein


Mass: 15572.538 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / References: UniProt: A0A9X8RMX9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Tail tube assembly / Type: COMPLEX
Details: Tail tube assembly in spontaneously contracted phage tail. Helical symmetry was enforced, this smearing out the sheath density.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Clostridioides difficile (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 18.1 ° / Axial rise/subunit: 39.3 Å / Axial symmetry: C6
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 754052 / Symmetry type: HELICAL
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318738
ELECTRON MICROSCOPYf_angle_d0.51225092
ELECTRON MICROSCOPYf_dihedral_angle_d4.3212502
ELECTRON MICROSCOPYf_chiral_restr0.0432808
ELECTRON MICROSCOPYf_plane_restr0.0023240

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