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- EMDB-2043: Subtomogram averaging reconstruction of the Ebola virus nucleocapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2043
TitleSubtomogram averaging reconstruction of the Ebola virus nucleocapsid
Map dataReconstruction of the Ebola virus nucleocapsid
Sample
  • Sample: Ebola virus nucleocapsid
  • Virus: Zaire ebolavirus
Keywordsebola virus / nucleocapsid / subtomogram averaging
Biological speciesZaire ebolavirus
Methodsubtomogram averaging / cryo EM / Resolution: 36.0 Å
AuthorsBharat TAM / Noda T / Riches JD / Kraehling V / Kolesnikova L / Becker S / Kawaoka Y / Briggs JAG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.
Authors: Tanmay A M Bharat / Takeshi Noda / James D Riches / Verena Kraehling / Larissa Kolesnikova / Stephan Becker / Yoshihiro Kawaoka / John A G Briggs /
Abstract: Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, ...Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.
History
DepositionFeb 8, 2012-
Header (metadata) releaseFeb 15, 2012-
Map releaseMar 8, 2012-
UpdateMar 8, 2012-
Current statusMar 8, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2043_emd_204...

emd_2043.jpg

Downloads & links

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Map

FileDownload / File: emd_2043.map.gz / Format: CCP4 / Size: 646.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Ebola virus nucleocapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.8 Å/pix.
x 40 pix.
= 392. Å		9.8 Å/pix.
x 65 pix.
= 637. Å		9.8 Å/pix.
x 65 pix.
= 637. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.51170313 - 0.45584902
Average (Standard dev.)-0.00006877 (±0.1078746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions656540
Spacing656540
CellA: 637.0 Å / B: 637.0 Å / C: 392.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.89.89.8
M x/y/z656540
origin x/y/z0.0000.0000.000
length x/y/z637.000637.000392.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS656540
D min/max/mean-0.5120.456-0.000

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Supplemental data

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Sample components

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Entire : Ebola virus nucleocapsid

EntireName: Ebola virus nucleocapsid
Components
  • Sample: Ebola virus nucleocapsid
  • Virus: Zaire ebolavirus

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Supramolecule #1000: Ebola virus nucleocapsid

SupramoleculeName: Ebola virus nucleocapsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Zaire ebolavirus

SupramoleculeName: Zaire ebolavirus / type: virus / ID: 1 / NCBI-ID: 186538 / Sci species name: Zaire ebolavirus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7 / Details: PBS buffer with 4% paraformaldehyde
GridDetails: 300 mesh holey carbon C-Flat grid with 2micron holes.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at high magnification.
Specialist opticsEnergy filter - Name: Gatan (GIF 2002)
DateJun 30, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 80 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -6.0 µm / Nominal defocus min: -4.0 µm / Nominal magnification: 27500
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsSubtomogram averaging reconstruction was carried out without imposition of any symmetry.
Final reconstructionApplied symmetry - Helical parameters - Δz: 6.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 30.5 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: OTHER / Software - Name: IMOD,AV3,Matlab

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