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- EMDB-4204: Subtomogram average of Rift Valley fever virus pentamer at pH 7.5... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4204 | |||||||||
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Title | Subtomogram average of Rift Valley fever virus pentamer at pH 7.5 in absence of target membrane | |||||||||
![]() | Subtomogram average of Rift Valley fever virus pentamer without a target membrane at pH 7.5 | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 17.0 Å | |||||||||
![]() | Sai L / Huiskonen JT | |||||||||
![]() | ![]() Title: Shielding and activation of a viral membrane fusion protein. Authors: Steinar Halldorsson / Sai Li / Mengqiu Li / Karl Harlos / Thomas A Bowden / Juha T Huiskonen / ![]() ![]() Abstract: Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. ...Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. Here, we address the fusion mechanism of Rift Valley fever virus. We determine the crystal structure of the Gn glycoprotein and fit it with the Gc fusion protein into cryo-electron microscopy reconstructions of the virion. Our analysis reveals how the Gn shields the hydrophobic fusion loops of the Gc, preventing premature fusion. Electron cryotomography of virions interacting with membranes under acidic conditions reveals how the fusogenic Gc is activated upon removal of the Gn shield. Repositioning of the Gn allows extension of Gc and insertion of fusion loops in the outer leaflet of the target membrane. These data show early structural transitions that enveloped viruses undergo during host cell entry and indicate that analogous shielding mechanisms are utilized across diverse virus families. | |||||||||
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 | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.9 KB 9.9 KB | Display Display | ![]() |
Images | ![]() | 50.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4197C ![]() 4198C ![]() 4199C ![]() 4200C ![]() 4201C ![]() 4202C ![]() 4203C ![]() 4205C ![]() 4206C ![]() 4207C ![]() 4208C ![]() 4209C ![]() 4210C ![]() 4211C ![]() 6f8pC ![]() 6f9bC ![]() 6f9cC ![]() 6f9dC ![]() 6f9eC ![]() 6f9fC 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 | Subtomogram average of Rift Valley fever virus pentamer without a target membrane at pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 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 : Rift Valley fever virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Rift Valley fever virus
Supramolecule | Name: Rift Valley fever virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Cultured in Vero cells / NCBI-ID: 11588 / Sci species name: Rift Valley fever virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: Glycoprotein shell / Diameter: 1100.0 Å / T number (triangulation number): 12 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: PBS |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Details | Unfixed sample with added liposomes |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-8 / Average exposure time: 3.2 sec. / Average electron dose: 150.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 903 | ||||||
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Extraction | Number tomograms: 17 / Number images used: 903 | ||||||
CTF correction | Software:
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Final angle assignment | Type: NOT APPLICABLE / Software - Name: Dynamo |