+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5728 | |||||||||
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Title | Icosahedrally-averaged bacteriophage Sf6 virion | |||||||||
Map data | icosahedral reconstruction of phage Sf6 virion | |||||||||
Sample |
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Biological species | Shigella phage Sf6 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Parent KN / Gilcrease EB / Casjens SR / Baker TS / Tang J | |||||||||
Citation | Journal: Virology / Year: 2012 Title: Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures. Authors: Kristin N Parent / Eddie B Gilcrease / Sherwood R Casjens / Timothy S Baker / Abstract: Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig- ...Coat proteins of tailed, dsDNA phages and in herpesviruses include a conserved core similar to the bacteriophage HK97 subunit. This core is often embellished with other domains such as the telokin Ig-like domain of phage P22. Eighty-six P22-like phages and prophages with sequenced genomes share a similar set of virion assembly genes and, based on comparisons of twelve viral assembly proteins (structural and assembly/packaging chaperones), these phages are classified into three groups (P22-like, Sf6-like, and CUS-3-like). We used cryo-electron microscopy and 3D image reconstruction to determine the structures of Sf6 procapsids and virions (~7Å resolution), and the structure of the entire, asymmetric Sf6 virion (16-Å resolution). The Sf6 coat protein is similar to that of P22 yet it has differences in the telokin domain and in its overall quaternary organization. Thermal stability and agarose gel experiments show that Sf6 virions are slightly less stable than those of P22. Finally, bacterial host outer membrane proteins A and C were identified in lipid vesicles that co-purify with Sf6 particles, but are not components of the capsid. | |||||||||
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_5728.map.gz | 754.1 MB | EMDB map data format | |
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Header (meta data) | emd-5728-v30.xml emd-5728.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_5728_1.png | 2.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5728 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5728 | HTTPS FTP |
-Validation report
Summary document | emd_5728_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_5728_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_5728_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5728 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5728 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5728.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | icosahedral reconstruction of phage Sf6 virion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : phage Sf6 virion
Entire | Name: phage Sf6 virion |
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Components |
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-Supramolecule #1000: phage Sf6 virion
Supramolecule | Name: phage Sf6 virion / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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-Supramolecule #1: Shigella phage Sf6
Supramolecule | Name: Shigella phage Sf6 / type: virus / ID: 1 / NCBI-ID: 10761 / Sci species name: Shigella phage Sf6 / Sci species strain: clear mutant / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Shigella flexneri (bacteria) / Strain: PE577 / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.6 / Details: 10mM Tris, 10mM MgCl2 |
Grid | Details: 400 mesh Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 5 seconds before plunging. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 89 K / Max: 91 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at high magnification |
Date | Sep 30, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 1.07 µm / Number real images: 469 / Average electron dose: 22 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 58050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.95 µm / Nominal defocus min: 0.53 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | the reconstruction was performed with Auto3dem. |
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CTF correction | Details: Robem |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 15483 |