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- PDB-8ch5: Cryo-EM structure of the fd bacteriophage capsid major coat prote... -

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Basic information

Entry
Database: PDB / ID: 8ch5
TitleCryo-EM structure of the fd bacteriophage capsid major coat protein pVIII
ComponentsMajor capsid protein pVIII
KeywordsVIRUS / Bacteriophage / fd / inovirus / ff / helical / phage / filamentous
Function / homologyPhage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBoehning, J. / Bharat, T.A.M.
Funding support United Kingdom, France, United States, European Union, 7items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/31 United Kingdom
Human Frontier Science Program (HFSP)RGY0074/2021 France
The Vallee Foundation Inc.Vallee Scholarship United States
Leverhulme TrustPhilip Leverhulme Prize United Kingdom
European Molecular Biology Organization (EMBO)EMBO YIPEuropean Union
The Lister Institute of Preventive MedicineLister Prize United Kingdom
UK Research and Innovation (UKRI)MR/V022385/1 United Kingdom
Citation
Journal: Nat Commun / Year: 2023
Title: Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa.
Authors: Jan Böhning / Miles Graham / Suzanne C Letham / Luke K Davis / Ulrike Schulze / Phillip J Stansfeld / Robin A Corey / Philip Pearce / Abul K Tarafder / Tanmay A M Bharat /
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 ...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.
#1: Journal: Biorxiv / Year: 2023
Title: Biophysical basis of phage liquid crystalline droplet-mediated antibiotic tolerance in pathogenic bacteria
Authors: Bohning, J. / Graham, M. / Letham, S. / Davis, L. / Schulze, U. / Stansfeld, P. / Corey, R. / Pearce, P. / Tarafder, A. / Bharat, T.
History
DepositionFeb 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_author_list
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_author_list.author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein pVIII


Theoretical massNumber of molelcules
Total (without water)5,2441
Polymers5,2441
Non-polymers00
Water0
1
A: Major capsid protein pVIII
x 50


Theoretical massNumber of molelcules
Total (without water)262,20050
Polymers262,20050
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation49

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Components

#1: Protein/peptide Major capsid protein pVIII / Coat protein B / Gene 8 protein / G8P / Major coat protein


Mass: 5244.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P69539

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Enterobacteria phage fd / Type: VIRUS
Details: Purified by PEG precipitation from the supernatant of infected E. coli cells.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Enterobacteria phage fd (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7.4 / Details: Phosphate-buffered saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: fd phage in PBS
Specimen supportDetails: 15 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2EPU2.9image acquisition
4CTFFIND4CTF correction
7Coot0.9model fitting
9PHENIX1.2model refinement
13RELION3.13D reconstruction
CTF correctionDetails: Performed in RELION 3.1 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -35.46 ° / Axial rise/subunit: 16.62 Å / Axial symmetry: C5
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84458 / Details: Relion 3.1 / Symmetry type: HELICAL
Atomic model buildingB value: 79.94 / Protocol: AB INITIO MODEL / Space: REAL

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