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- EMDB-5210: The structure of the recombinant alphavirus, Western equine encep... -

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Basic information

Entry
Database: EMDB / ID: EMD-5210
TitleThe structure of the recombinant alphavirus, Western equine encephalitis virus, revealed by cryoelectron microscopy
Map dataThis is a 3D map of Western equine encephalitis virus
Sample
  • Sample: Western equine encephalitis virus
  • Virus: Western equine encephalomyelitis virus
Keywordsalphavirus / cryoEM / structure / 3D reconstruction
Biological speciesWestern equine encephalomyelitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsSherman MB / Weaver SC
CitationJournal: J Virol / Year: 2010
Title: Structure of the recombinant alphavirus Western equine encephalitis virus revealed by cryoelectron microscopy.
Authors: Michael B Sherman / Scott C Weaver /
Abstract: Western equine encephalitis virus (WEEV; Togaviridae, Alphavirus) is an enveloped RNA virus that is typically transmitted to vertebrate hosts by infected mosquitoes. WEEV is an important cause of ...Western equine encephalitis virus (WEEV; Togaviridae, Alphavirus) is an enveloped RNA virus that is typically transmitted to vertebrate hosts by infected mosquitoes. WEEV is an important cause of viral encephalitis in humans and horses in the Americas, and infection results in a range of disease, from mild flu-like illnesses to encephalitis, coma, and death. In addition to spreading via mosquito vectors, human WEEV infections can potentially occur directly via aerosol transmission. Due to its aerosol infectivity and virulence, WEEV is thus classified as a biological safety level 3 (BSL-3) agent. Because of its highly infectious nature and containment requirements, it has not been possible to investigate WEEV's structure or assembly mechanism using standard structural biology techniques. Thus, to image WEEV and other BSL-3 agents, we have constructed a first-of-its-kind BSL-3 cryoelectron microscopy (cryoEM) containment facility. cryoEM images of WEEV were used to determine the first three-dimensional structure of this important human pathogen. The overall organization of WEEV is similar to those of other alphaviruses, consistent with the high sequence similarity among alphavirus structural proteins. Surprisingly, the nucleocapsid of WEEV, a New World virus, is more similar to the Old World alphavirus Sindbis virus than to other New World alphaviruses.
History
DepositionJul 7, 2010-
Header (metadata) releaseJul 16, 2010-
Map releaseSep 9, 2010-
UpdateApr 2, 2012-
Current statusApr 2, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 80
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 80
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5210.map.gz / Format: CCP4 / Size: 175.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3D map of Western equine encephalitis virus
Voxel sizeX=Y=Z: 2.3 Å
Density
Contour LevelBy AUTHOR: 80.0 / Movie #1: 80
Minimum - Maximum-298.084136960000023 - 340.75912476000002
Average (Standard dev.)9.37805367 (±57.561008450000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions361361361
Spacing361361361
CellA=B=C: 830.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z361361361
origin x/y/z0.0000.0000.000
length x/y/z830.300830.300830.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS361361361
D min/max/mean-298.084340.7599.378

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Supplemental data

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Sample components

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Entire : Western equine encephalitis virus

EntireName: Western equine encephalitis virus
Components
  • Sample: Western equine encephalitis virus
  • Virus: Western equine encephalomyelitis virus

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Supramolecule #1000: Western equine encephalitis virus

SupramoleculeName: Western equine encephalitis virus / type: sample / ID: 1000
Oligomeric state: 80 trimers of E1-E2 glycoproteins, 240 copies of capsid protein, vRNA
Number unique components: 4

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Supramolecule #1: Western equine encephalomyelitis virus

SupramoleculeName: Western equine encephalomyelitis virus / type: virus / ID: 1 / Name.synonym: WEEV / NCBI-ID: 11039 / Sci species name: Western equine encephalomyelitis virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: WEEV
Host (natural)Organism: Equus caballus (horse) / synonym: VERTEBRATES
Molecular weightExperimental: 52 MDa / Theoretical: 52 MDa
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 #1

Preparation ID1
BufferpH: 7.4
Details: TEN buffer: 0.05 M Tris-HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA
GridDetails: R2/2 Quantifoil grids, C-flat grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: Blot for 2s

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Sample preparation #2

Preparation ID2
BufferpH: 7.4
Details: TEN buffer: 0.05 M Tris-HCl, pH 7.4, 0.1 M NaCl, 0.001 M EDTA
GridDetails: R2/2 Quantifoil grids, C-flat grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: Blot for 2s

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 1.85 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Eucentric, side entry Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 89 K / Max: 95 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: 300,000x magnification / Legacy - Electron beam tilt params: 0
DateNov 15, 2007
Image recordingCategory: FILM / Film or detector model: GENERIC CCD / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 2.1 µm / Number real images: 49 / Average electron dose: 20 e/Å2 / Od range: 0.9 / Bits/pixel: 16

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PIF / Number images used: 4586

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