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- PDB-9gb4: Contracted phiCD508 portal -

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Basic information

Entry
Database: PDB / ID: 9gb4
TitleContracted phiCD508 portal
Componentsgp45 - Portal protein
KeywordsVIRAL PROTEIN / bacteriophage / virus / portal
Function / homologyPortal protein / Phage portal protein, SPP1 Gp6-like / Putative portal protein
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 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 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: gp45 - Portal protein
A: gp45 - Portal protein
B: gp45 - Portal protein
C: gp45 - Portal protein
D: gp45 - Portal protein
E: gp45 - Portal protein
F: gp45 - Portal protein
G: gp45 - Portal protein
H: gp45 - Portal protein
I: gp45 - Portal protein
J: gp45 - Portal protein
K: gp45 - Portal protein


Theoretical massNumber of molelcules
Total (without water)686,87812
Polymers686,87812
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
gp45 - Portal protein


Mass: 57239.852 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Clostridioides difficile (bacteria) / Strain: CD117 / References: UniProt: A0A069A478
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 portal / 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 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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26404 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 111.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003743836
ELECTRON MICROSCOPYf_angle_d0.589759124
ELECTRON MICROSCOPYf_chiral_restr0.04476528
ELECTRON MICROSCOPYf_plane_restr0.00387620
ELECTRON MICROSCOPYf_dihedral_angle_d4.9725700

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