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- EMDB-5124: Cryo-EM of Rift Valley fever virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5124
TitleCryo-EM of Rift Valley fever virus
Map datathis is RVFV map in 2-fold orientation
Sample
  • Sample: Rift Valley fever virus, RVFV vaccine strain MP-12
  • Virus: Rift Valley fever virus
Keywordscryo-electron microscopy / single particle averaging / Rift valley fever / bunyaviridae / inter-capsomer contacts
Biological speciesRift Valley fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 27.0 Å
AuthorsSherman MB / Freiberg AN / Holbrook AM / Watowich SJ
Citation
Journal: Virology / Year: 2009
Title: Single-particle cryo-electron microscopy of Rift Valley fever virus.
Authors: Michael B Sherman / Alexander N Freiberg / Michael R Holbrook / Stanley J Watowich /
Abstract: Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human and veterinary pathogen causing acute hepatitis in ruminants and has the potential to cause hemorrhagic fever in humans. ...Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human and veterinary pathogen causing acute hepatitis in ruminants and has the potential to cause hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit vaccines.
#1: Journal: J.VIROL. / Year: 2008
Title: Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography
Authors: Freiberg AN / Sherman MB / Morais MC / Holbrook MR / Watowich SJ
History
DepositionJul 20, 2009-
Header (metadata) releaseJul 24, 2009-
Map releaseJul 24, 2009-
UpdateJul 8, 2011-
Current statusJul 8, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 7.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5124_1.png

Downloads & links

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Map

FileDownload / File: emd_5124.map.gz / Format: CCP4 / Size: 341.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is RVFV map in 2-fold orientation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3 Å/pix.
x 451 pix.
= 1353. Å		3 Å/pix.
x 451 pix.
= 1353. Å		3 Å/pix.
x 451 pix.
= 1353. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 7.3
Minimum - Maximum-26.283200000000001 - 37.412500000000001
Average (Standard dev.)0.675954 (±6.08815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-225-225-225
Dimensions451451451
Spacing451451451
CellA=B=C: 1353 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z451451451
origin x/y/z0.0000.0000.000
length x/y/z1353.0001353.0001353.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-225-225-225
NC/NR/NS451451451
D min/max/mean-26.28337.4120.676

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Supplemental data

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Sample components

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Entire : Rift Valley fever virus, RVFV vaccine strain MP-12

EntireName: Rift Valley fever virus, RVFV vaccine strain MP-12
Components
  • Sample: Rift Valley fever virus, RVFV vaccine strain MP-12
  • Virus: Rift Valley fever virus

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Supramolecule #1000: Rift Valley fever virus, RVFV vaccine strain MP-12

SupramoleculeName: Rift Valley fever virus, RVFV vaccine strain MP-12 / type: sample / ID: 1000 / Details: monodisperse sample / Oligomeric state: single virions / Number unique components: 8

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Supramolecule #1: Rift Valley fever virus

SupramoleculeName: Rift Valley fever virus / type: virus / ID: 1 / Name.synonym: RVFV / Details: 100 nm particles / NCBI-ID: 11588 / Sci species name: Rift Valley fever virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: RVFV
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 1000 Å / T number (triangulation number): 12

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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

Concentration0.1 mg/mL
BufferpH: 7.2 / Details: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA
GridDetails: 200 mesh copper Qauntifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 95 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: pneumatic plunger / Method: blot 2 sec before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureMin: 99 K / Max: 99 K / Average: 99 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Legacy - Electron beam tilt params: 0
Specialist opticsEnergy filter - Name: omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateNov 1, 2007
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 93 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: OTHER / Software - Name: PFT / Details: Final map calculated from 108 particles / Number images used: 108
Final two d classificationNumber classes: 1

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