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Yorodumi- EMDB-1301: Electron cryomicroscopy comparison of the architectures of the en... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1301 | |||||||||
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Title | Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8. | |||||||||
Map data | 3D reconstruction of the bacteriophage Phi6 virion. | |||||||||
Sample |
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Biological species | Pseudomonas phage phi6 (bacteriophage) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Jaalinoja HT / Huiskonen JT / Butcher SJ | |||||||||
Citation | Journal: Structure / Year: 2007 Title: Electron cryomicroscopy comparison of the architectures of the enveloped bacteriophages phi6 and phi8. Authors: Harri T Jäälinoja / Juha T Huiskonen / Sarah J Butcher / Abstract: The enveloped dsRNA bacteriophages phi6 and phi8 are the two most distantly related members of the Cystoviridae family. Their structure and function are similar to that of the Reoviridae but their ...The enveloped dsRNA bacteriophages phi6 and phi8 are the two most distantly related members of the Cystoviridae family. Their structure and function are similar to that of the Reoviridae but their assembly can be conveniently studied in vitro. Electron cryomicroscopy and three-dimensional icosahedral reconstruction were used to determine the structures of the phi6 virion (14 A resolution), phi8 virion (18 A resolution), and phi8 core (8.5 A resolution). Spikes protrude 2 nm from the membrane bilayer in phi6 and 7 nm in phi8. In the phi6 nucleocapsid, 600 copies of P8 and 72 copies of P4 interact with the membrane, whereas in phi8 it is only P4 and 60 copies of a minor protein. The major polymerase complex protein P1 forms a dodecahedral shell from 60 asymmetric dimers in both viruses, but the alpha-helical fold has apparently diverged. These structural differences reflect the different host ranges and entry and assembly mechanisms of the two viruses. | |||||||||
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_1301.map.gz | 55.5 MB | EMDB map data format | |
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Header (meta data) | emd-1301-v30.xml emd-1301.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | 1301.gif | 22 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1301 | HTTPS FTP |
-Validation report
Summary document | emd_1301_validation.pdf.gz | 288.2 KB | Display | EMDB validaton report |
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Full document | emd_1301_full_validation.pdf.gz | 287.4 KB | Display | |
Data in XML | emd_1301_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1301 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1301 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1301.map.gz / Format: CCP4 / Size: 127.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of the bacteriophage Phi6 virion. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 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 Phi6 virion
Entire | Name: Bacteriophage Phi6 virion |
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Components |
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-Supramolecule #1000: Bacteriophage Phi6 virion
Supramolecule | Name: Bacteriophage Phi6 virion / type: sample / ID: 1000 / Oligomeric state: complete virion / Number unique components: 1 |
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-Supramolecule #1: Pseudomonas phage phi6
Supramolecule | Name: Pseudomonas phage phi6 / type: virus / ID: 1 / Name.synonym: Cystovirus Phi6 virion / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: Cystovirus Phi6 virion |
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Host (natural) | Organism: Pseudomonads syringae / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Name: Nucleocapsid / Diameter: 550 Å / T number (triangulation number): 13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | Details: 10 mM potassium phosphate pH 7.5, 1 mM MgCl2 |
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Grid | Details: 400 mesh copper grid, Quantifoil R2/2 holey |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: EMBL design Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 90 K / Max: 94 K / Average: 93 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 23 / Details: The data was processed at 2.8 ??/pixel sampling. / Bits/pixel: 12 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 49300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle, wiener factor 0.1 |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: pft2, em3dr2, POR, P3DR / Number images used: 517 |