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- EMDB-4209: Subtomogram average of Rift Valley fever virus hexamer at pH 5.0 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4209
TitleSubtomogram average of Rift Valley fever virus hexamer at pH 5.0 in absence of target membrane
Map dataSubtomogram average of Rift Valley fever virus hexamer without a target membrane at pH 5.0
Sample
  • Virus: Rift Valley fever virus
Biological speciesRift Valley fever virus
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsSai L / Huiskonen JT
CitationJournal: Nat Commun / Year: 2018
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
DepositionDec 14, 2017-
Header (metadata) releaseDec 27, 2017-
Map releaseFeb 7, 2018-
UpdateMay 9, 2018-
Current statusMay 9, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4209.png

Downloads & links

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Map

FileDownload / File: emd_4209.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Rift Valley fever virus hexamer without a target membrane at pH 5.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 128 pix.
= 345.6 Å		2.7 Å/pix.
x 128 pix.
= 345.6 Å		2.7 Å/pix.
x 128 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-6.2831903 - 5.7527657
Average (Standard dev.)-0.016341219 (±1.1383914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-6.2835.753-0.016

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Supplemental data

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Sample components

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Entire : Rift Valley fever virus

EntireName: Rift Valley fever virus
Components
  • Virus: Rift Valley fever virus

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Supramolecule #1: Rift Valley fever virus

SupramoleculeName: 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
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Glycoprotein shell / Diameter: 1100.0 Å / T number (triangulation number): 12

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 5 / Details: PBS
VitrificationCryogen name: ETHANE-PROPANE
DetailsUnfixed sample with added liposomes

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Electron microscopy

MicroscopeFEI TECNAI F30
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 2300
ExtractionNumber tomograms: 17 / Number images used: 2300
CTF correctionSoftware:
Namedetails
GctfDetermination
IMODCorrection
Final angle assignmentType: NOT APPLICABLE / Software - Name: Dynamo

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