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Yorodumi- EMDB-1859: Visualising a viral RNA genome poised for release from its recept... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1859 | |||||||||
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Title | Visualising a viral RNA genome poised for release from its receptor complex. | |||||||||
Map data | This is an image of a surface rendered side view of the bacteriophage MS2 in complex with an F-pilus | |||||||||
Sample |
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Keywords | MS2 / F-pili / virus-receptor complex | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Enterobacterio phage MS2 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Toropova K / Stockley PG / Ranson NA | |||||||||
Citation | Journal: J Mol Biol / Year: 2011 Title: Visualising a viral RNA genome poised for release from its receptor complex. Authors: Katerina Toropova / Peter G Stockley / Neil A Ranson / Abstract: We describe the cryo-electron microscopy structure of bacteriophage MS2 bound to its receptor, the bacterial F-pilus. The virus contacts the pilus at a capsid 5-fold vertex, thus locating the surface- ...We describe the cryo-electron microscopy structure of bacteriophage MS2 bound to its receptor, the bacterial F-pilus. The virus contacts the pilus at a capsid 5-fold vertex, thus locating the surface-accessible portion of the single copy of the pilin-binding maturation protein present in virions. This arrangement allows a 5-fold averaged map to be calculated, showing for the first time in any virus-receptor complex the nonuniform distribution of RNA within the capsid. Strikingly, at the vertex that contacts the pilus, a rod of density that may include contributions from both genome and maturation protein sits above a channel that goes through the capsid to the outside. This density is reminiscent of the DNA density observed in the exit channel of double-stranded DNA phages, suggesting that the RNA-maturation protein complex is poised to leave the capsid as the first step of the infection process. | |||||||||
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_1859.map.gz | 71.4 MB | EMDB map data format | |
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Header (meta data) | emd-1859-v30.xml emd-1859.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | 1859EMDB_MS2-pili-C5map.jpg | 107.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1859 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1859 | HTTPS FTP |
-Validation report
Summary document | emd_1859_validation.pdf.gz | 195.1 KB | Display | EMDB validaton report |
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Full document | emd_1859_full_validation.pdf.gz | 194.2 KB | Display | |
Data in XML | emd_1859_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1859 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1859 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1859.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an image of a surface rendered side view of the bacteriophage MS2 in complex with an F-pilus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.96 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 MS2 in complex with F-pilus
Entire | Name: Bacteriophage MS2 in complex with F-pilus |
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Components |
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-Supramolecule #1000: Bacteriophage MS2 in complex with F-pilus
Supramolecule | Name: Bacteriophage MS2 in complex with F-pilus / type: sample / ID: 1000 Details: The reconstruction was 5-fold rotationally (C5) averaged Oligomeric state: Heterodimer / Number unique components: 2 |
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-Supramolecule #1: Enterobacterio phage MS2
Supramolecule | Name: Enterobacterio phage MS2 / type: virus / ID: 1 / Name.synonym: MS2 / Details: MS2 in complex with F-pilus / NCBI-ID: 12022 / Sci species name: Enterobacterio phage MS2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: MS2 |
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Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Diameter: 280 Å / T number (triangulation number): 3 |
-Supramolecule #2: F-PILUS
Supramolecule | Name: F-PILUS / type: organelle_or_cellular_component / ID: 2 / Name.synonym: F-PILUS / Oligomeric state: helical multimer / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: BW22246 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 / Details: 0.1 M Tris-HCl, 0.5 mM EDTA |
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Grid | Details: Lacey carbon copper mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 22 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Double sided custom pneumatic blotter Method: 1.6s blot |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 9.88 µm / Number real images: 252 / Average electron dose: 18 e/Å2 / Od range: 1 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Phase flipping each particle |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 2739 |
Final two d classification | Number classes: 96 |