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- EMDB-16657: Cryo-EM structure of the fd bacteriophage capsid major coat prote... -

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Basic information

Entry
Database: EMDB / ID: EMD-16657
TitleCryo-EM structure of the fd bacteriophage capsid major coat protein pVIII
Map dataCryo-EM map of the intact fd bacteriophage capsid
Sample
  • Virus: Enterobacteria phage fd (virus)
    • Protein or peptide: Major capsid protein pVIII
KeywordsBacteriophage / fd / inovirus / ff / helical / phage / filamentous / VIRUS
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) / Enterobacteria phage fd (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBoehning J / Bharat TAM
Funding support United Kingdom, France, United States, European Union, 7 items
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, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16657.png

Downloads & links

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Map

FileDownload / File: emd_16657.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the intact fd bacteriophage capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 327.6 Å		1.09 Å/pix.
x 300 pix.
= 327.6 Å		1.09 Å/pix.
x 300 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.092 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.027363125 - 0.07787412
Average (Standard dev.)0.00010592476 (±0.002854244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 2

Fileemd_16657_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_16657_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage fd

EntireName: Enterobacteria phage fd (virus)
Components
  • Virus: Enterobacteria phage fd (virus)
    • Protein or peptide: Major capsid protein pVIII

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Supramolecule #1: Enterobacteria phage fd

SupramoleculeName: Enterobacteria phage fd / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Purified by PEG precipitation from the supernatant of infected E. coli cells.
NCBI-ID: 10864 / Sci species name: Enterobacteria phage fd / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Major capsid protein pVIII

MacromoleculeName: Major capsid protein pVIII / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.244 KDa
SequenceString:
AEGDDPAKAA FDSLQASATE YIGYAWAMVV VIVGATIGIK LFKKFTSKAS

UniProtKB: Capsid protein G8P

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4 / Details: Phosphate-buffered saline
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Detailsfd phage in PBS

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 53.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 16.62 Å
Applied symmetry - Helical parameters - Δ&Phi: -35.46 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: Relion 3.1 / Number images used: 84458
Startup modelType of model: OTHER
Details: Cylindrical reference with no internal features (unbiased)
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 79.94
Output model

PDB-8ch5:
Cryo-EM structure of the fd bacteriophage capsid major coat protein pVIII

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