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- EMDB-1550: Three-dimensional icosahedral reconstruction of Rift Valley Fever... -

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Basic information

Entry
Database: EMDB / ID: EMD-1550
TitleThree-dimensional icosahedral reconstruction of Rift Valley Fever virus at pH 7.4
Map dataRift Valley Fever virus at pH 7.4Rift Valley fever
Sample
  • Sample: Rift Valley Fever virusRift Valley fever
  • Virus: Rift Valley fever virus
Biological speciesRift Valley fever virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å
AuthorsHuiskonen JT / Overby AK / Weber F / Gruenewald K
CitationJournal: J Virol / Year: 2009
Title: Electron cryo-microscopy and single-particle averaging of Rift Valley fever virus: evidence for GN-GC glycoprotein heterodimers.
Authors: Juha T Huiskonen / Anna K Overby / Friedemann Weber / Kay Grünewald /
Abstract: Rift Valley fever virus (RVFV) is a member of the genus Phlebovirus within the family Bunyaviridae. It is a mosquito-borne zoonotic agent that can cause hemorrhagic fever in humans. The enveloped ...Rift Valley fever virus (RVFV) is a member of the genus Phlebovirus within the family Bunyaviridae. It is a mosquito-borne zoonotic agent that can cause hemorrhagic fever in humans. The enveloped RVFV virions are known to be covered by capsomers of the glycoproteins G(N) and G(C), organized on a T=12 icosahedral lattice. However, the structural units forming the RVFV capsomers have not been determined. Conflicting biochemical results for another phlebovirus (Uukuniemi virus) have indicated the existence of either G(N) and G(C) homodimers or G(N)-G(C) heterodimers in virions. Here, we have studied the structure of RVFV using electron cryo-microscopy combined with three-dimensional reconstruction and single-particle averaging. The reconstruction at 2.2-nm resolution revealed the organization of the glycoprotein shell, the lipid bilayer, and a layer of ribonucleoprotein (RNP). Five- and six-coordinated capsomers are formed by the same basic structural unit. Molecular-mass measurements suggest a G(N)-G(C) heterodimer as the most likely candidate for this structural unit. Both leaflets of the lipid bilayer were discernible, and the glycoprotein transmembrane densities were seen to modulate the curvature of the lipid bilayer. RNP densities were situated directly underneath the transmembrane densities, suggesting an interaction between the glycoprotein cytoplasmic tails and the RNPs. The success of the single-particle averaging approach taken in this study suggests that it is applicable in the study of other phleboviruses, as well, enabling higher-resolution description of these medically important pathogens.
History
DepositionSep 5, 2008-
Header (metadata) releaseSep 8, 2008-
Map releaseApr 21, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1550.png

Downloads & links

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Map

FileDownload / File: emd_1550.map.gz / Format: CCP4 / Size: 127.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRift Valley Fever virus at pH 7.4
Voxel sizeX=Y=Z: 4 Å
Density
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-7.75936 - 7.01066
Average (Standard dev.)-0.00000180378 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-162-162-162
Dimensions325325325
Spacing325325325
CellA=B=C: 1300 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z325325325
origin x/y/z0.0000.0000.000
length x/y/z1300.0001300.0001300.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-162-162-162
NC/NR/NS325325325
D min/max/mean-7.7597.011-0.000

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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
  • Sample: Rift Valley Fever virusRift Valley fever
  • Virus: Rift Valley fever virus

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Supramolecule #1000: Rift Valley Fever virus

SupramoleculeName: Rift Valley Fever virus / type: sample / ID: 1000
Details: The sample was fixed with glutaraldehyde at pH 7.4 prior to virus purification
Number unique components: 1

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Supramolecule #1: Rift Valley fever virus

SupramoleculeName: Rift Valley fever virus / type: virus / ID: 1 / Name.synonym: RVFV / Details: clone 13 / NCBI-ID: 11588 / Sci species name: Rift Valley fever virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: RVFV
Host (natural)Organism: Ovis aries (sheep) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: glycoprotein layer / Diameter: 1060 Å / T number (triangulation number): 12

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 50 mM Tris-HCl pH 7.4, 100 mM NaCl
StainingType: NEGATIVE / Details: unstained sample
GridDetails: 200 mesh copper C-flat
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: MPI Biochemisty plunger / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 112000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification
DetailsLow dose imaging
DateJun 30, 2008
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 15 µm / Number real images: 19 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each image, phases flipped
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT2, EM3DR2 / Number images used: 113
DetailsThe particles were selected using an automatic selection program ETHAN

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