+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2064 | |||||||||
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Title | A 3-D cryo-electron structure of bacteriophage phi92 baseplate | |||||||||
Map data | Reconstruction of bacteriophage phi92 baseplate | |||||||||
Sample |
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Keywords | Bacteriophage / coliphage / phi92 / single particle / cryo-electron / baseplate | |||||||||
Biological species | Staphylococcus phage 92 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Browning C / Nazarov S / Bowman VD / Leiman PG | |||||||||
Citation | Journal: J Virol / Year: 2012 Title: A multivalent adsorption apparatus explains the broad host range of phage phi92: a comprehensive genomic and structural analysis. Authors: David Schwarzer / Falk F R Buettner / Christopher Browning / Sergey Nazarov / Wolfgang Rabsch / Andrea Bethe / Astrid Oberbeck / Valorie D Bowman / Katharina Stummeyer / Martina Mühlenhoff ...Authors: David Schwarzer / Falk F R Buettner / Christopher Browning / Sergey Nazarov / Wolfgang Rabsch / Andrea Bethe / Astrid Oberbeck / Valorie D Bowman / Katharina Stummeyer / Martina Mühlenhoff / Petr G Leiman / Rita Gerardy-Schahn / Abstract: Bacteriophage phi92 is a large, lytic myovirus isolated in 1983 from pathogenic Escherichia coli strains that carry a polysialic acid capsule. Here we report the genome organization of phi92, the ...Bacteriophage phi92 is a large, lytic myovirus isolated in 1983 from pathogenic Escherichia coli strains that carry a polysialic acid capsule. Here we report the genome organization of phi92, the cryoelectron microscopy reconstruction of its virion, and the reinvestigation of its host specificity. The genome consists of a linear, double-stranded 148,612-bp DNA sequence containing 248 potential open reading frames and 11 putative tRNA genes. Orthologs were found for 130 of the predicted proteins. Most of the virion proteins showed significant sequence similarities to proteins of myoviruses rv5 and PVP-SE1, indicating that phi92 is a new member of the novel genus of rv5-like phages. Reinvestigation of phi92 host specificity showed that the host range is not limited to polysialic acid-encapsulated Escherichia coli but includes most laboratory strains of Escherichia coli and many Salmonella strains. Structure analysis of the phi92 virion demonstrated the presence of four different types of tail fibers and/or tailspikes, which enable the phage to use attachment sites on encapsulated and nonencapsulated bacteria. With this report, we provide the first detailed description of a multivalent, multispecies phage armed with a host cell adsorption apparatus resembling a nanosized Swiss army knife. The genome, structure, and, in particular, the organization of the baseplate of phi92 demonstrate how a bacteriophage can evolve into a multi-pathogen-killing agent. | |||||||||
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_2064.map.gz | 11.5 MB | EMDB map data format | |
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Header (meta data) | emd-2064-v30.xml emd-2064.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | EMD-2064.png | 74.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2064 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2064 | HTTPS FTP |
-Validation report
Summary document | emd_2064_validation.pdf.gz | 242.9 KB | Display | EMDB validaton report |
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Full document | emd_2064_full_validation.pdf.gz | 242 KB | Display | |
Data in XML | emd_2064_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2064 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2064 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2064.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of bacteriophage phi92 baseplate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.216 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 : Base plate-tail complex of bacteriophage phi92
Entire | Name: Base plate-tail complex of bacteriophage phi92 |
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Components |
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-Supramolecule #1000: Base plate-tail complex of bacteriophage phi92
Supramolecule | Name: Base plate-tail complex of bacteriophage phi92 / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: Baseplate-tail complex
Macromolecule | Name: Baseplate-tail complex / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Staphylococcus phage 92 (virus) / synonym: coliphage phi92 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | Details: 50mM TrisCl pH 7.5, 100mM NaCl, 8mM MgSO4 |
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Staining | Type: NEGATIVE / Details: vitrification in liquid ethane |
Grid | Details: holey carbon grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 113 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Date | May 30, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 38 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: PHILIPS ROTATION HOLDER |
-Image processing
Details | The reconstruction was performed by imposing 6-fold symmetry averaging. The 6-fold axis is along Z. |
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CTF correction | Details: Each Micrograph |
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, EMAN / Number images used: 985 |
Final two d classification | Number classes: 10 |