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Yorodumi- PDB-8ch5: Cryo-EM structure of the fd bacteriophage capsid major coat prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ch5 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the fd bacteriophage capsid major coat protein pVIII | ||||||||||||||||||||||||
Components | Major capsid protein pVIII | ||||||||||||||||||||||||
Keywords | VIRUS / Bacteriophage / fd / inovirus / ff / helical / phage / filamentous | ||||||||||||||||||||||||
Function / homology | Phage 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 species | Escherichia coli (E. coli) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||||||||
Authors | Boehning, J. / Bharat, T.A.M. | ||||||||||||||||||||||||
Funding support | United Kingdom, France, United States, European Union, 7items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ch5.cif.gz | 22.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ch5.ent.gz | 12.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ch5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ch5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ch5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ch5_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 8ch5_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/8ch5 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/8ch5 | HTTPS FTP |
-Related structure data
Related structure data | 16657MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein/peptide | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Enterobacteria phage fd / Type: VIRUS Details: Purified by PEG precipitation from the supernatant of infected E. coli cells. Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Enterobacteria phage fd (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Escherichia coli |
Buffer solution | pH: 7.4 / Details: Phosphate-buffered saline |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: fd phage in PBS |
Specimen support | Details: 15 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron 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 optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Details: Performed in RELION 3.1 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -35.46 ° / Axial rise/subunit: 16.62 Å / Axial symmetry: C5 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84458 / Details: Relion 3.1 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | B value: 79.94 / Protocol: AB INITIO MODEL / Space: REAL |