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- EMDB-58347: C. difficile phage phiCD508 tail tube in spontaneously contracted... -

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Basic information

Entry
Database: EMDB / ID: EMD-58347
TitleC. difficile phage phiCD508 tail tube in spontaneously contracted state
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Tail tube assembly
    • Protein or peptide: gp56 - Tail tube protein
Keywordsbacteriophage / phage tail / myophage / contractile injection system / S-layer / virus / 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)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsBullough PA / Wilson JS / Berry HL / Fagan RP
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P02002X/1 United Kingdom
CitationJournal: 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, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58347.png

Downloads & links

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Map

FileReleased
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 343.44 Å		1.06 Å/pix.
x 324 pix.
= 343.44 Å		1.06 Å/pix.
x 324 pix.
= 343.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.5850315 - 5.3616014
Average (Standard dev.)0.02277809 (±0.1379776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 343.43997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_58347_half_map_1.map
AnnotationHalf_map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_58347_half_map_2.map
AnnotationHalf_map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tail tube assembly

EntireName: Tail tube assembly
Components
  • Complex: Tail tube assembly
    • Protein or peptide: gp56 - Tail tube protein

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Supramolecule #1: Tail tube assembly

SupramoleculeName: Tail tube assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Tail tube assembly in spontaneously contracted phage tail. Helical symmetry was enforced, this smearing out the sheath density.
Source (natural)Organism: Clostridioides difficile (bacteria)

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Macromolecule #1: gp56 - Tail tube protein

MacromoleculeName: gp56 - Tail tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 15.572538 KDa
SequenceString:
MYNDDYIEEA SFLNGSDVVI LIDGVEELYM EEIKADFEQD EQSIKLLGCQ NEISRVGTTK GSFSLNGYKT DSKFAKLGFR SFEIIYNLS NSETLGYESI RLKNCRLKKL PLINSKAGEI VKIEVEGSFR GYDLLNEL

UniProtKB: Protein of uncharacterized function (DUF2001)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 18.1 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 754052
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9gb1

Final angle assignmentType: NOT APPLICABLE

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