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- EMDB-7004: Eilat virus/eastern equine encephalitis virus chimeric vaccine ca... -

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Basic information

Entry
Database: EMDB / ID: 7004
TitleEilat virus/eastern equine encephalitis virus chimeric vaccine candidate
SampleEilat virus
SourceEilat virus / virus
Map dataEilat virus/eastern equine encephalitis virus chimeric vaccine candidate
Methodsingle particle (icosahedral) reconstruction, at 11 Å resolution
AuthorsSherman MB / Erasmus JH / Frolov I / Weaver SC / Nasar F
CitationJ. Virol., 2017

J. Virol., 2017 Yorodumi Papers
Novel insect-specific Eilat virus-based chimeric vaccine candidates provide durable, mono- and multi-valent, single dose protection against lethal alphavirus challenge.
Jesse H Erasmus / Robert L Seymour / Jason T Kaelber / Dal Y Kim / Grace Leal / Michael B Sherman / Ilya Frolov / Wah Chiu / Scott C Weaver / Farooq Nasar

DateDeposition: Aug 31, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Nov 22, 2017 / Last update: Dec 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0045
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_7004.map.gz (map file in CCP4 format, 364501 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
450 pix
2.35 Å/pix.
= 1057.5 Å
450 pix
2.35 Å/pix.
= 1057.5 Å
450 pix
2.35 Å/pix.
= 1057.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.35 Å
Density
Contour Level:0.0045 (by author), 0.0045 (movie #1):
Minimum - Maximum-0.005502032 - 0.010450059
Average (Standard dev.)0.00027772094 (0.0010883694)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions450450450
Origin-225-225-225
Limit224224224
Spacing450450450
CellA=B=C: 1057.5 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.352.352.35
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z1057.5001057.5001057.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS450450450
D min/max/mean-0.0060.0100.000

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Supplemental data

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Sample components

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Entire Eilat virus

EntireName: Eilat virus / Number of components: 1
MassTheoretical: 42 MDa

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Component #1: virus, Eilat virus

VirusName: Eilat virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: OTHER
MassTheoretical: 42 MDa
SpeciesSpecies: Eilat virus / virus
Source (engineered)Expression System: Aedes albopictus / arthropod / image: Aedes aegypti
Cell of expression system: C7/10
Source (natural)Host Species: Aedes / arthropod / image: Aedes aegypti

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: Omega
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 126

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2145
3D reconstructionAlgorithm: FOURIER SPACE / Software: IMAGIC / Resolution: 11 Å / Resolution method: FSC 0.5 CUT-OFF

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External links: The 2017 Nobel Prize in Chemistry - Press Release

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