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- EMDB-16657: Cryo-EM structure of the fd bacteriophage capsid major coat prote... -
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Open data
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Basic information
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Title | Cryo-EM structure of the fd bacteriophage capsid major coat protein pVIII | ||||||||||||||||||||||||
![]() | Cryo-EM map of the intact fd bacteriophage capsid | ||||||||||||||||||||||||
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![]() | Bacteriophage / fd / inovirus / ff / helical / phage / filamentous / VIRUS | ||||||||||||||||||||||||
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![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||||||||
![]() | Boehning J / Bharat TAM | ||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() 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: ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 101.5 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 81.1 MB 80.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 997.6 KB | Display | ![]() |
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Full document | ![]() | 997.2 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ch5MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the intact fd bacteriophage capsid | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.092 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map 2
File | emd_16657_half_map_1.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_16657_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Enterobacteria phage fd
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Enterobacteria phage fd
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Major capsid protein pVIII
Macromolecule | Name: Major capsid protein pVIII / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 5.244 KDa |
Sequence | String: AEGDDPAKAA FDSLQASATE YIGYAWAMVV VIVGATIGIK LFKKFTSKAS UniProtKB: Capsid protein G8P |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 / Details: Phosphate-buffered saline |
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Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
Details | fd phage in PBS |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 53.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 79.94 |
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Output model | ![]() PDB-8ch5: |