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- EMDB-51196: Extended phiCD508 portal -

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Basic information

Entry
Database: EMDB / ID: EMD-51196
TitleExtended phiCD508 portal
Map dataC12 reconstruction extended phiCD508 portal sharpened map (B-factor =-114.6A)
Sample
  • Complex: Extended phiCD508 portal
    • Protein or peptide: gp45 - Portal protein
Keywordsbacteriophage / virus / portal / VIRAL PROTEIN
Function / homologyPortal protein / Phage portal protein, SPP1 Gp6-like / Putative portal protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 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_51196.png

Downloads & links

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Map

FileDownload / File: emd_51196.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC12 reconstruction extended phiCD508 portal sharpened map (B-factor =-114.6A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. 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: 0.303
Minimum - Maximum-1.179948 - 2.3209739
Average (Standard dev.)0.022863753 (±0.11924579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: C12 reconstruction extended phiCD508 portal unsharpened map

Fileemd_51196_additional_1.map
AnnotationC12 reconstruction extended phiCD508 portal unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C12 reconstruction extended phiCD508 portal half map A

Fileemd_51196_half_map_1.map
AnnotationC12 reconstruction extended phiCD508 portal half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C12 reconstruction extended phiCD508 portal half map B

Fileemd_51196_half_map_2.map
AnnotationC12 reconstruction extended phiCD508 portal 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 : Extended phiCD508 portal

EntireName: Extended phiCD508 portal
Components
  • Complex: Extended phiCD508 portal
    • Protein or peptide: gp45 - Portal protein

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Supramolecule #1: Extended phiCD508 portal

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

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Macromolecule #1: gp45 - Portal protein

MacromoleculeName: gp45 - Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
Molecular weightTheoretical: 57.239852 KDa
SequenceString: MGIISYVKKL FKRPAGEIMR MSSGNIGVYK LDDSRVDYEL ARELYQNKNA NYKLGSSFVR PIVNSTTGFM GVPHFQIEDE EAQYILDEF VLDNTSKMLK THTDSLKQGD CYIWITREER ENPLYPDKKV RLIYNFISPE EVKEIILDPT TKEPIAYILE S QNEWTDLG ...String:
MGIISYVKKL FKRPAGEIMR MSSGNIGVYK LDDSRVDYEL ARELYQNKNA NYKLGSSFVR PIVNSTTGFM GVPHFQIEDE EAQYILDEF VLDNTSKMLK THTDSLKQGD CYIWITREER ENPLYPDKKV RLIYNFISPE EVKEIILDPT TKEPIAYILE S QNEWTDLG ENKRKAKVKQ IITAESRFVE VEGDKIEGLE EGETPNVWGF IPIIHFKNEA DETLKYGQSD IEPIEPLLKA YH DVMLHAL KGSKMHSTPK LKLKLTDVAS FLAHNFGVED PVKFAKEGGK INLDGHEILF LNKDEEAEFV EVKSAIGDAK ELL KLLFYC IVDVSETPEF IFGVHTPSAL ASVKEQMPIM VNKIRRKREQ FTNSWQLLAR MVLIMSSNSS GMKYSSYDVT IGWD EVNPR DDKELAETLE KVCCALDKAL EGGFISEEST VNFLAQYIDT MSNYISDDPE REGEREKIIK TKMLKYRLDD SQGLN DESN EIEKEINKIK DNNGNG

UniProtKB: Putative portal 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: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38968
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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