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- EMDB-3406: Eilat virus/Chikungunya virus chimeric vaccine candidate -

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Basic information

Entry
Database: EMDB / ID: EMD-3406
TitleEilat virus/Chikungunya virus chimeric vaccine candidate
Map dataIcosahedral reconstruction of virion of EILV/CHIKV chimera
Sample
  • Sample: Icosahedral reconstruction of virion of EILV/CHIKV chimera
  • Virus: Eilat virus/Chikungunya virus chimera
Keywordsalphavirus / virion / Togaviridae / vaccine
Biological speciesEilat virus/Chikungunya virus chimera
Methodsingle particle reconstruction / cryo EM / Resolution: 9.85 Å
AuthorsKaelber JT / Erasmus JH / Kim DY / Frolov I / Nasar F / Weaver SC / Chiu W
CitationJournal: Nat Med / Year: 2017
Title: A chikungunya fever vaccine utilizing an insect-specific virus platform.
Authors: Jesse H Erasmus / Albert J Auguste / Jason T Kaelber / Huanle Luo / Shannan L Rossi / Karla Fenton / Grace Leal / Dal Y Kim / Wah Chiu / Tian Wang / Ilya Frolov / Farooq Nasar / Scott C Weaver /
Abstract: Traditionally, vaccine development involves tradeoffs between immunogenicity and safety. Live-attenuated vaccines typically offer rapid and durable immunity but have reduced safety when compared to ...Traditionally, vaccine development involves tradeoffs between immunogenicity and safety. Live-attenuated vaccines typically offer rapid and durable immunity but have reduced safety when compared to inactivated vaccines. In contrast, the inability of inactivated vaccines to replicate enhances safety at the expense of immunogenicity, often necessitating multiple doses and boosters. To overcome these tradeoffs, we developed the insect-specific alphavirus, Eilat virus (EILV), as a vaccine platform. To address the chikungunya fever (CHIKF) pandemic, we used an EILV cDNA clone to design a chimeric virus containing the chikungunya virus (CHIKV) structural proteins. The recombinant EILV/CHIKV was structurally identical at 10 Å to wild-type CHIKV, as determined by single-particle cryo-electron microscopy, and it mimicked the early stages of CHIKV replication in vertebrate cells from attachment and entry to viral RNA delivery. Yet the recombinant virus remained completely defective for productive replication, providing a high degree of safety. A single dose of EILV/CHIKV produced in mosquito cells elicited rapid (within 4 d) and long-lasting (>290 d) neutralizing antibodies that provided complete protection in two different mouse models. In nonhuman primates, EILV/CHIKV elicited rapid and robust immunity that protected against viremia and telemetrically monitored fever. Our EILV platform represents the first structurally native application of an insect-specific virus in preclinical vaccine development and highlights the potential application of such viruses in vaccinology.
History
DepositionApr 7, 2016-
Header (metadata) releaseMay 4, 2016-
Map releaseFeb 1, 2017-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3406.png

Downloads & links

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Map

FileDownload / File: emd_3406.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of virion of EILV/CHIKV chimera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 384 pix.
= 756.48 Å		1.97 Å/pix.
x 384 pix.
= 756.48 Å		1.97 Å/pix.
x 384 pix.
= 756.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.74064136 - 1.54598391
Average (Standard dev.)-0.0071753 (±0.23466673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 756.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.971.971.97
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z756.480756.480756.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.7411.546-0.007

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Supplemental data

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Sample components

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Entire : Icosahedral reconstruction of virion of EILV/CHIKV chimera

EntireName: Icosahedral reconstruction of virion of EILV/CHIKV chimera
Components
  • Sample: Icosahedral reconstruction of virion of EILV/CHIKV chimera
  • Virus: Eilat virus/Chikungunya virus chimera

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Supramolecule #1000: Icosahedral reconstruction of virion of EILV/CHIKV chimera

SupramoleculeName: Icosahedral reconstruction of virion of EILV/CHIKV chimera
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Eilat virus/Chikungunya virus chimera

SupramoleculeName: Eilat virus/Chikungunya virus chimera / type: virus / ID: 1
Details: Contains structural proteins from Chikungunya strain 99659 isolated from the British Virgin Islands.
Sci species name: Eilat virus/Chikungunya virus chimera / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / T number (triangulation number): 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 10mM Tris-HCl 1mM EDTA 100mM NaCl
GridDetails: 200 mesh Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 94.9 K
Specialist opticsEnergy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV
DateOct 17, 2014
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Number real images: 348 / Average electron dose: 60 e/Å2
Details: 2s exposure at 16 frames per second. Movie corrected for motion and specimen damage with DE_process_frames.py written by Ben Bammes of Direct Electron, L.P.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 32487 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

DetailsRefined in independent halves starting from an initial model derived from low-resolution imaging on a JEM2010F
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.85 Å / Resolution method: OTHER / Software - Name: MPSA, EMAN2
Details: Boxing and CTF correction using EMAN2. Alignment and reconstruction using MPSA. Post-processing using EMAN2.
Number images used: 13455
FSC plot (resolution estimation)

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