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- EMDB-51199: Contracted phiCD508 tail -

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Basic information

Entry
Database: EMDB / ID: EMD-51199
TitleContracted phiCD508 tail
Map dataContracted phiCD508 tail sharpened map (B-factor = -178.5A)
Sample
  • Complex: Contracted phiCD508 tail
    • Protein or peptide: Phage tail sheath protein
KeywordsBacteriophage / virus / needle / baseplate
Function / homologyPhage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Phage tail sheath protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsWilson JS / Fagan RP / Bullough PA
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
DepositionJul 29, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51199.png

Downloads & links

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Map

FileDownload / File: emd_51199.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContracted phiCD508 tail sharpened map (B-factor = -178.5A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. 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: 0.193
Minimum - Maximum-0.32374844 - 0.8573504
Average (Standard dev.)0.017883167 (±0.065261595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Contracted phiCD508 tail unsharpened map

Fileemd_51199_additional_1.map
AnnotationContracted phiCD508 tail unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Contracted phiCD508 tail half map A

Fileemd_51199_half_map_1.map
AnnotationContracted phiCD508 tail half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Contracted phiCD508 tail half map B

Fileemd_51199_half_map_2.map
AnnotationContracted phiCD508 tail half 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 : Contracted phiCD508 tail

EntireName: Contracted phiCD508 tail
Components
  • Complex: Contracted phiCD508 tail
    • Protein or peptide: Phage tail sheath protein

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Supramolecule #1: Contracted phiCD508 tail

SupramoleculeName: Contracted phiCD508 tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117

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Macromolecule #1: Phage tail sheath protein

MacromoleculeName: Phage tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 53.016762 KDa
SequenceString: MATGTWNEKE RKEIPGFYNR FKTQAEKSTN TGLKGRLAMP IRANWGDVGK VVTIKNDLRQ LKNLFGDDMN YSAFKLGKLA LLGNVKELL LYRLVDGNQK KGTLTLKDTT ENSAKDVIKL ETKYPTARNF NVTIKSNLVD SDKKDFIFFE NTKQLFSSSI K GTIDEIVL ...String:
MATGTWNEKE RKEIPGFYNR FKTQAEKSTN TGLKGRLAMP IRANWGDVGK VVTIKNDLRQ LKNLFGDDMN YSAFKLGKLA LLGNVKELL LYRLVDGNQK KGTLTLKDTT ENSAKDVIKL ETKYPTARNF NVTIKSNLVD SDKKDFIFFE NTKQLFSSSI K GTIDEIVL EINSNLDNEY VIATKVADSD TILANVVNQA LEGGNDGCTS ITNESYLKAL EEFERYSFDS FVLDGVADEA LQ ETTKAWV AKNKELGKDI LLFLGGKTED NIKQINDKSK SFNDENIVNV GSSAYYENIK YTPSEVAVYI AALSVSKGIT GSI CNAKTI FEEVEPRLSQ SEVKECLKSG TLVLDFDDGD VIIVDDVNTF KKYVDDKNEA MGYISNIMFI NTINKDTSLK RKEF VGKIF NDATGQTTVI CALKKYFEEL MSQGIISEFN VDIDTELQAT AKADEFYWKW DAVKVDVMKK IYGTGYLG

UniProtKB: Phage tail sheath protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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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: 31.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 33.9 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48919
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: MAXIMUM LIKELIHOOD

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