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Yorodumi- EMDB-2063: A 3-D cryo-electron microscopy structure of bacteriophage phi92 capsid -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2063 | |||||||||
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Title | A 3-D cryo-electron microscopy structure of bacteriophage phi92 capsid | |||||||||
Map data | Reconstruction ofbacteriophage phi92 capsid | |||||||||
Sample |
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Keywords | Bacteriophage / phi92 / capsid / single particle / cryo-electron / reconstruction | |||||||||
Biological species | Staphylococcus phage 92 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Browning C / Nazarov S / Bowman V / Leiman P | |||||||||
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_2063.map.gz | 105.2 MB | EMDB map data format | |
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Header (meta data) | emd-2063-v30.xml emd-2063.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 2063.png | 118.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2063 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2063 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2063.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction ofbacteriophage phi92 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.81 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 phi92
Entire | Name: Bacteriophage phi92 (virus) |
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Components |
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-Supramolecule #1000: Bacteriophage phi92
Supramolecule | Name: Bacteriophage phi92 / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Staphylococcus phage 92
Supramolecule | Name: Staphylococcus phage 92 / type: virus / ID: 1 / Name.synonym: bacteriophage phi92 / Details: Bacteriophage phi92 is a large lytic myovirus / NCBI-ID: 320849 / Sci species name: Staphylococcus phage 92 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage phi92 |
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Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / T number (triangulation number): 13 |
-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: 100 % / Chamber temperature: 113 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
-Image processing
CTF correction | Details: Each Micrograph |
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Final two d classification | Number classes: 10 |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 1137 |
Details | The icosahedral reconstruction the phi92 capsid was calculated from scratch. The initial model was constructed with a small subset of initial data. This model was then subjected to several rounds of refinement until convergence. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL |