8CH5

Cryo-EM structure of the fd bacteriophage capsid major coat protein pVIII

  • Classification: VIRUS
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-02-07 Released: 2023-12-20 
  • Deposition Author(s): Boehning, J., Bharat, T.A.M.
  • Funding Organization(s): UK Research and Innovation (UKRI), Human Frontier Science Program (HFSP), The Vallee Foundation Inc., Leverhulme Trust, European Molecular Biology Organization (EMBO), The Lister Institute of Preventive Medicine

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa.

Bohning, J.Graham, M.Letham, S.C.Davis, L.K.Schulze, U.Stansfeld, P.J.Corey, R.A.Pearce, P.Tarafder, A.K.Bharat, T.A.M.

(2023) Nat Commun 14: 8429-8429

  • DOI: https://doi.org/10.1038/s41467-023-44160-8
  • Primary Citation of Related Structures:  
    8CH5

  • PubMed Abstract: 

    Inoviruses are filamentous phages infecting numerous prokaryotic phyla. Inoviruses can self-assemble into mesoscale structures with liquid-crystalline order, termed tactoids, which protect bacterial cells in Pseudomonas aeruginosa biofilms from antibiotics. Here, we investigate the structural, biophysical, and protective properties of tactoids formed by the P. aeruginosa phage Pf4 and Escherichia coli phage fd. A cryo-EM structure of the capsid from fd revealed distinct biochemical properties compared to Pf4. Fd and Pf4 formed tactoids with different morphologies that arise from differing phage geometries and packing densities, which in turn gave rise to different tactoid emergent properties. Finally, we showed that tactoids formed by either phage protect rod-shaped bacteria from antibiotic treatment, and that direct association with a tactoid is required for protection, demonstrating the formation of a diffusion barrier by the tactoid. This study provides insights into how filamentous molecules protect bacteria from extraneous substances in biofilms and in host-associated infections.


  • Organizational Affiliation

    Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein pVIII50Escherichia coliMutation(s): 0 
UniProt
Find proteins for P69539 (Enterobacteria phage fd)
Explore P69539 
Go to UniProtKB:  P69539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69539
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMC_UP_1201/31
Human Frontier Science Program (HFSP)FranceRGY0074/2021
The Vallee Foundation Inc.United StatesVallee Scholarship
Leverhulme TrustUnited KingdomPhilip Leverhulme Prize
European Molecular Biology Organization (EMBO)European UnionEMBO YIP
The Lister Institute of Preventive MedicineUnited KingdomLister Prize
UK Research and Innovation (UKRI)United KingdomMR/V022385/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Structure summary