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- EMDB-51192: Contracted phiCD508 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-51192
TitleContracted phiCD508 capsid
Map dataContracted phiCD508 capsid sharpened map (B-factor =-146.9A)
Sample
  • Complex: Contracted phiCD508 capsid
    • Protein or peptide: gp49 - Major capsid protein
    • Protein or peptide: gp48 - Minor capsid protein
KeywordsBacteriophage / virus / capsid
Function / homologyBacteriophage VT1-Sakai, H0018 / Phage cement protein / Uncharacterized protein / Uncharacterized conserved protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 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_51192.png

Downloads & links

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Map

FileDownload / File: emd_51192.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContracted phiCD508 capsid sharpened map (B-factor =-146.9A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 800 pix.
= 1060. Å		1.33 Å/pix.
x 800 pix.
= 1060. Å		1.33 Å/pix.
x 800 pix.
= 1060. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.466
Minimum - Maximum-1.2872066 - 3.239826
Average (Standard dev.)0.002389281 (±0.13870722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1060.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Contracted phiCD508 capsid unsharpened map

Fileemd_51192_additional_1.map
AnnotationContracted phiCD508 capsid unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Contracted phiCD508 capsid half map B

Fileemd_51192_half_map_1.map
AnnotationContracted phiCD508 capsid half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Contracted phiCD508 capsid half map B

Fileemd_51192_half_map_2.map
AnnotationContracted phiCD508 capsid 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 capsid

EntireName: Contracted phiCD508 capsid
Components
  • Complex: Contracted phiCD508 capsid
    • Protein or peptide: gp49 - Major capsid protein
    • Protein or peptide: gp48 - Minor capsid protein

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Supramolecule #1: Contracted phiCD508 capsid

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

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Macromolecule #1: gp49 - Major capsid protein

MacromoleculeName: gp49 - Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 39.059477 KDa
SequenceString: MAFKVISQEN LLEQKRKETL QEDIPFIVNG EMEYVTKKIS NGEMETLELN KPLGEMMTFS STSNLKELLR KVVLDVELGR EQVQLLYKP IYDSIADSNL PQVMDAKWAL QGNCVFLEHI EGEEIKFGTI NAENGPVARI QTYATGFEYT KEMKDFNQTF S VEILNKSI ...String:
MAFKVISQEN LLEQKRKETL QEDIPFIVNG EMEYVTKKIS NGEMETLELN KPLGEMMTFS STSNLKELLR KVVLDVELGR EQVQLLYKP IYDSIADSNL PQVMDAKWAL QGNCVFLEHI EGEEIKFGTI NAENGPVARI QTYATGFEYT KEMKDFNQTF S VEILNKSI GESYNALLNH IHLSPIINFN YKASNKTAFK GETNDPIWLG IWRTLTQAQK DTVIAKRQGN ILMASSADQI EI EMALNGG HLLNGSMYPS IKNISTVIYY DGWEVTVGKK TYSYKGVTPG KGYLIRPKRG FKELIKRDLT TEVGNADLSK LVE NQIVGH CYRGAFAAVE ENVQEISFR

UniProtKB: Uncharacterized protein

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Macromolecule #2: gp48 - Minor capsid protein

MacromoleculeName: gp48 - Minor capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 14.115739 KDa
SequenceString:
MAFKGQPTPS TITQITRAKI SDGKSVRVIL SEGESTKTQQ FYLINGFFGV AMQDGEKGDE VTLQIEQAEY ETDNIVTSEA FEAGKLIYW DNTAKKFTTT SASNRLVGRV TDGKDSNNVI WFILLPQQ

UniProtKB: Uncharacterized conserved protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38654
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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