6TUP

Cryo-EM structure of Pf4 bacteriophage coat protein with single-stranded DNA


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 1.2 of the entry. See complete history


Literature

Phage liquid crystalline droplets form occlusive sheaths that encapsulate and protect infectious rod-shaped bacteria.

Tarafder, A.K.von Kugelgen, A.Mellul, A.J.Schulze, U.Aarts, D.G.A.L.Bharat, T.A.M.

(2020) Proc Natl Acad Sci U S A 117: 4724-4731

  • DOI: 10.1073/pnas.1917726117
  • Primary Citation of Related Structures:  
    6TUP, 6TUQ

  • PubMed Abstract: 
  • The opportunistic pathogen Pseudomonas aeruginosa is a major cause of antibiotic-tolerant infections in humans. P. aeruginosa evades antibiotics in bacterial biofilms by up-regulating expression of a symbiotic filamentous inoviral prophage, Pf4 ...

    The opportunistic pathogen Pseudomonas aeruginosa is a major cause of antibiotic-tolerant infections in humans. P. aeruginosa evades antibiotics in bacterial biofilms by up-regulating expression of a symbiotic filamentous inoviral prophage, Pf4. We investigated the mechanism of phage-mediated antibiotic tolerance using biochemical reconstitution combined with structural biology and high-resolution cellular imaging. We resolved electron cryomicroscopy atomic structures of Pf4 with and without its linear single-stranded DNA genome, and studied Pf4 assembly into liquid crystalline droplets using optical microscopy and electron cryotomography. By biochemically replicating conditions necessary for antibiotic protection, we found that phage liquid crystalline droplets form phase-separated occlusive compartments around rod-shaped bacteria leading to increased bacterial survival. Encapsulation by these compartments was observed even when inanimate colloidal rods were used to mimic rod-shaped bacteria, suggesting that shape and size complementarity profoundly influences the process. Filamentous inoviruses are pervasive across prokaryotes, and in particular, several Gram-negative bacterial pathogens including Neisseria meningitidis , Vibrio cholerae, and Salmonella enterica harbor these prophages. We propose that biophysical occlusion mediated by secreted filamentous molecules such as Pf4 may be a general strategy of bacterial survival in harsh environments.


    Organizational Affiliation

    Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, OX1 3RE Oxford, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein B of bacteriophage Pf1A46Pseudomonas virus Pf1Mutation(s): 0 
Gene Names: VIII
UniProt
Find proteins for P03621 (Pseudomonas phage Pf1)
Explore P03621 
Go to UniProtKB:  P03621
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*AP*AP*AP*AP*A)-3')B [auth z]6Pseudomonas aeruginosa PAO1
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

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

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Wellcome TrustUnited Kingdom202231/Z/16/Z

    Revision History  (Full details and data files)

    • Version 1.0: 2020-02-26
      Type: Initial release
    • Version 1.1: 2020-03-04
      Changes: Data collection, Database references, Source and taxonomy
    • Version 1.2: 2020-03-11
      Changes: Database references