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- EMDB-2369: The Respiratory Syncytial Virus nucleoprotein-RNA complex forms a... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2369 | |||||||||
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Title | The Respiratory Syncytial Virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid. | |||||||||
![]() | Sub-tomogram average of purified RSV nucleocapsid | |||||||||
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![]() | Respiratory Syncytial Virus / nucleocapsid / cryo-electron tomography / sub-tomogram averaging | |||||||||
Function / homology | ![]() Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / helical viral capsid / RSV-host interactions / Respiratory syncytial virus genome replication / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / symbiont-mediated suppression of host PKR/eIFalpha signaling / Translation of respiratory syncytial virus mRNAs / protein serine/threonine kinase inhibitor activity / helical viral capsid / RSV-host interactions / Respiratory syncytial virus genome replication / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / PKR-mediated signaling / Evasion by RSV of host interferon responses / viral capsid / viral nucleocapsid / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / : / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / negative staining | |||||||||
![]() | Bakker SE / Duquerroy S / Galloux M / Loney C / Conner E / Eleouet JF / Rey FA / Bhella D | |||||||||
![]() | ![]() Title: The respiratory syncytial virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid. Authors: Saskia E Bakker / Stéphane Duquerroy / Marie Galloux / Colin Loney / Edward Conner / Jean-François Eléouët / Félix A Rey / David Bhella / ![]() ![]() Abstract: Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical ...Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC helix would be right-handed, as the N-N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a left-handed helix. We further show that the contacts in the ring can be distorted to maintain key N-N-protein interactions in a left-handed helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 217.8 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.4 KB 11.4 KB | Display Display | ![]() |
Images | ![]() | 47.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 200.4 KB | Display | ![]() |
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Full document | ![]() | 199.5 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bkkMC ![]() 2370C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sub-tomogram average of purified RSV nucleocapsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Purified recombinant RSV nucleocapsids.
Entire | Name: Purified recombinant RSV nucleocapsids. |
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Components |
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-Supramolecule #1000: Purified recombinant RSV nucleocapsids.
Supramolecule | Name: Purified recombinant RSV nucleocapsids. / type: sample / ID: 1000 / Oligomeric state: variable helices / Number unique components: 1 |
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-Supramolecule #1: Respiratory syncytial virus
Supramolecule | Name: Respiratory syncytial virus / type: virus / ID: 1 / Name.synonym: RSV / Details: Purified recombinant nucleocapsid / NCBI-ID: 12814 / Sci species name: Respiratory syncytial virus / Virus type: OTHER / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: RSV |
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Host (natural) | Organism: ![]() |
Host system | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | subtomogram averaging |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 / Details: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 10 mM EDTA |
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Staining | Type: NEGATIVE Details: Protein preparations were mixed with 10 nm colloidal gold and loaded onto freshly glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.). Grids were then washed in 0.1% ...Details: Protein preparations were mixed with 10 nm colloidal gold and loaded onto freshly glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.). Grids were then washed in 0.1% trehalose, and stained using 5% ammonium molybdate (pH 7.4) and 0.1% trehalose, drained and allowed to dry in air |
Grid | Details: Glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.) |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | JEOL 2200FSC |
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Temperature | Min: 97 K / Max: 293 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 100k times mag in digital micrograph |
Specialist optics | Energy filter - Name: Jeol / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV |
Details | Room temperature stained grids imaged at LN2 temperatures. |
Date | Jul 15, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 9 / Average electron dose: 131 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
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Image processing
Details | Subtomograms were manually picked. A starting model was obtained by manually aligning 100 subtomograms, all subtomograms were aligned to this starting model. To mitigate missing wedge artefacts, the orientations around the helical axis were randomised before further alignment. |
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Final reconstruction | Algorithm: OTHER / Software - Name: Etomo, Dynamo / Details: Subtomograms were picked from nine tomograms. / Number subtomograms used: 911 |
Final 3D classification | Number classes: 1 |