+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8869 | |||||||||
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Title | Bacteriophage Sf14 Capsid | |||||||||
Map data | Icosahedrally averaged map of capsid of phage Sf14. | |||||||||
Sample |
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Biological species | Bacteriophage Sf14 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.2 Å | |||||||||
Authors | Doore SM / Schrad JR / Dean WF / Dover JA / Parent KN | |||||||||
Funding support | United States, 2 items
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Citation | Journal: J Virol / Year: 2018 Title: Shigella Phages Isolated during a Dysentery Outbreak Reveal Uncommon Structures and Broad Species Diversity. Authors: Sarah M Doore / Jason R Schrad / William F Dean / John A Dover / Kristin N Parent / Abstract: In 2016, Michigan experienced the largest outbreak of shigellosis, a type of bacillary dysentery caused by spp., since 1988. Following this outbreak, we isolated 16 novel -infecting bacteriophages ...In 2016, Michigan experienced the largest outbreak of shigellosis, a type of bacillary dysentery caused by spp., since 1988. Following this outbreak, we isolated 16 novel -infecting bacteriophages (viruses that infect bacteria) from environmental water sources. Most well-known bacteriophages infect the common laboratory species and , and these phages have built the foundation of molecular and bacteriophage biology. Until now, comparatively few bacteriophages were known to infect spp., which are close relatives of We present a comprehensive analysis of these phages' host ranges, genomes, and structures, revealing genome sizes and capsid properties that are shared by very few previously described phages. After sequencing, a majority of the phages were found to have genomes of an uncommon size, shared by only 2% of all reported phage genomes. To investigate the structural implications of this unusual genome size, we used cryo-electron microscopy to resolve their capsid structures. We determined that these bacteriophage capsids have similarly uncommon geometry. Only two other viruses with this capsid structure have been described. Since most well-known bacteriophages infect or , our understanding of bacteriophages has been limited to a subset of well-described systems. Continuing to isolate phages using nontraditional strains of bacteria can fill gaps that currently exist in bacteriophage biology. In addition, the prevalence of phages during a shigellosis outbreak may suggest a potential impact of human health epidemics on local microbial communities. spp. bacteria are causative agents of dysentery and affect more than 164 million people worldwide every year. Despite the need to combat antibiotic-resistant strains, relatively few -infecting bacteriophages have been described. By specifically looking for -infecting phages, this work has identified new isolates that (i) may be useful to combat infections and (ii) fill gaps in our knowledge of bacteriophage biology. The rare qualities of these new isolates emphasize the importance of isolating phages on "nontraditional" laboratory strains of bacteria to more fully understand both the basic biology and diversity of bacteriophages. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8869.map.gz | 453.9 MB | EMDB map data format | |
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Header (meta data) | emd-8869-v30.xml emd-8869.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_8869.png | 234.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8869 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8869 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8869.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedrally averaged map of capsid of phage Sf14. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bacteriophage Sf14
Entire | Name: Bacteriophage Sf14 (virus) |
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Components |
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-Supramolecule #1: Bacteriophage Sf14
Supramolecule | Name: Bacteriophage Sf14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 38018 / Sci species name: Bacteriophage Sf14 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Shigella flexneri (bacteria) / Strain: PE577 |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 786.0 Å / T number (triangulation number): 9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER | |||||||||
Details | 1.8 x 10^12 phage/mL |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.9 µm / Calibrated defocus min: 0.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm / Nominal magnification: 25000 |
Specialist optics | Energy filter - Name: JEOL Omega / Energy filter - Lower energy threshold: 35 eV / Energy filter - Upper energy threshold: 35 eV |
Sample stage | Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER Cooling holder cryogen: NITROGEN |
Temperature | Min: 83.0 K / Max: 83.0 K |
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4866 pixel / Digitization - Dimensions - Height: 3411 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 44 / Average exposure time: 1.0 sec. / Average electron dose: 10.9 e/Å2 |
-Image processing
Particle selection | Number selected: 278 |
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CTF correction | Software - Name: Auto3DEM (ver. 4.05.1) |
Startup model | Type of model: OTHER / Details: Random Model Computation |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: Auto3DEM (ver. 4.05.1) |
Final angle assignment | Type: PROJECTION MATCHING Projection matching processing - Number reference projections: 60 Projection matching processing - Angular sampling: 1.0 degrees Software - Name: Auto3DEM (ver. 4.05.1) Details: Iterative procedure starting at 1 degree sampling, ending at 0.4 degrees imposing icosahedral symmetry. |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3DEM (ver. 4.05.1) / Number images used: 276 |