+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3184 | |||||||||
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Title | Localized reconstruction of rotavirus VP4 spike | |||||||||
Map data | Localized reconstruction of rotavirus VP4 spike calculated from a previously published dataset by Settembre et al. (2011) | |||||||||
Sample |
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Keywords | rotavirus / VP4 / spike / triple-layered particle | |||||||||
Biological species | Rhesus Rotavirus (RRV) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Ilca S / Kotecha A / Sun X / Poranen MP / Stuart DI / Huiskonen JT | |||||||||
Citation | Journal: EMBO J / Year: 2011 Title: Atomic model of an infectious rotavirus particle. Authors: Ethan C Settembre / James Z Chen / Philip R Dormitzer / Nikolaus Grigorieff / Stephen C Harrison / Abstract: Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling ...Non-enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped-virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus-penetration protein, and infectivity analyses of structure-based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single-particle analysis at about 4.3 Å resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8(*) and VP5(*)) retain their association after proteolytic cleavage, reveals multiple structural roles for the β-barrel domain of VP5(*), and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry. | |||||||||
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_3184.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-3184-v30.xml emd-3184.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3184_fsc.xml | 3.6 KB | Display | FSC data file |
Images | EMD-3184.jpg emd_3184.jpg | 81.9 KB 81.9 KB | ||
Masks | emd_3184_msk_1.map | 3.8 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3184 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3184 | HTTPS FTP |
-Related structure data
Related structure data | 3183C 3185C 3186C 3187C 5fj5C 5fj6C 5fj7C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3184.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Localized reconstruction of rotavirus VP4 spike calculated from a previously published dataset by Settembre et al. (2011) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: Localized reconstruction of rotavirus VP4 spike
Annotation | Localized reconstruction of rotavirus VP4 spike | ||||||||||||
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File | emd_3184_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rotavirus triple-layered particle
Entire | Name: Rotavirus triple-layered particle |
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Components |
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-Supramolecule #1000: Rotavirus triple-layered particle
Supramolecule | Name: Rotavirus triple-layered particle / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Rhesus Rotavirus (RRV)
Supramolecule | Name: Rhesus Rotavirus (RRV) / type: virus / ID: 1 / Name.synonym: Rotavirus / Sci species name: Rhesus Rotavirus (RRV) / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Rotavirus |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Experimental: 100 MDa |
Virus shell | Shell ID: 1 / Name: Virus shell 1 / Diameter: 800 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
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F30 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 56770 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Details | Cut-plate film holders to reduce electron back-scattering |
Date | Jan 1, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 110 / Average electron dose: 20 e/Å2 |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |