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- PDB-9gb8: Contracted phiCD508 tail -

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Basic information

Entry
Database: PDB / ID: 9gb8
TitleContracted phiCD508 tail
ComponentsPhage tail sheath protein
KeywordsVIRUS / Bacteriophage / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.11 Å
AuthorsWilson, J.S. / Fagan, R.P. / Bullough, P.A.
Funding support United Kingdom, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Phage tail sheath protein
K: Phage tail sheath protein
L: Phage tail sheath protein
M: Phage tail sheath protein
N: Phage tail sheath protein
O: Phage tail sheath protein
P: Phage tail sheath protein
Q: Phage tail sheath protein
R: Phage tail sheath protein
S: Phage tail sheath protein
T: Phage tail sheath protein
U: Phage tail sheath protein
V: Phage tail sheath protein
W: Phage tail sheath protein
X: Phage tail sheath protein
Y: Phage tail sheath protein
Z: Phage tail sheath protein
a: Phage tail sheath protein


Theoretical massNumber of molelcules
Total (without water)954,30218
Polymers954,30218
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
Phage tail sheath protein


Mass: 53016.762 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A9X8RMY4
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Contracted phiCD508 tail / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: CD117
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 magnification: 81000 X / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48919 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00466150
ELECTRON MICROSCOPYf_angle_d0.65289226
ELECTRON MICROSCOPYf_dihedral_angle_d6.458730
ELECTRON MICROSCOPYf_chiral_restr0.04410296
ELECTRON MICROSCOPYf_plane_restr0.00411394

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