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- EMDB-7513: Subtomogram average of mature CHIKV virion budded from human cells -

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Basic information

Entry
Database: EMDB / ID: EMD-7513
TitleSubtomogram average of mature CHIKV virion budded from human cells
Map dataMature CHIKV virion budded from human cells
Sample
  • Virus: Chikungunya virus
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 34.0 Å
AuthorsGalaz-Montoya JG / Jin J / Sherman MB
CitationJournal: Cell Host Microbe / Year: 2018
Title: Neutralizing Antibodies Inhibit Chikungunya Virus Budding at the Plasma Membrane.
Authors: Jing Jin / Jesús G Galaz-Montoya / Michael B Sherman / Stella Y Sun / Cynthia S Goldsmith / Eileen T O'Toole / Larry Ackerman / Lars-Anders Carlson / Scott C Weaver / Wah Chiu / Graham Simmons /
Abstract: Neutralizing antibodies (NAbs) are traditionally thought to inhibit virus infection by preventing virion entry into target cells. In addition, antibodies can engage Fc receptors (FcRs) on immune ...Neutralizing antibodies (NAbs) are traditionally thought to inhibit virus infection by preventing virion entry into target cells. In addition, antibodies can engage Fc receptors (FcRs) on immune cells to activate antiviral responses. We describe a mechanism by which NAbs inhibit chikungunya virus (CHIKV), the most common alphavirus infecting humans, by preventing virus budding from infected human cells and activating IgG-specific Fcγ receptors. NAbs bind to CHIKV glycoproteins on the infected cell surface and induce glycoprotein coalescence, preventing budding of nascent virions and leaving structurally heterogeneous nucleocapsids arrested in the cytosol. Furthermore, NAbs induce clustering of CHIKV replication spherules at sites of budding blockage. Functionally, these densely packed glycoprotein-NAb complexes on infected cells activate Fcγ receptors, inducing a strong, antibody-dependent, cell-mediated cytotoxicity response from immune effector cells. Our findings describe a triply functional antiviral pathway for NAbs that might be broadly applicable across virus-host systems, suggesting avenues for therapeutic innovation through antibody design.
History
DepositionMar 2, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseJan 9, 2019-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7513.png

Downloads & links

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Map

FileDownload / File: emd_7513.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMature CHIKV virion budded from human cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.16 Å/pix.
x 180 pix.
= 1288.8 Å		7.16 Å/pix.
x 180 pix.
= 1288.8 Å		7.16 Å/pix.
x 180 pix.
= 1288.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum0.0 - 12.174003000000001
Average (Standard dev.)0.18559761 (±0.9999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-919-919-33
Dimensions180180180
Spacing180180180
CellA=B=C: 1288.7999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.167.167.16
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z1288.8001288.8001288.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-919-919-33
NC/NR/NS180180180
D min/max/mean0.00012.1740.186

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Supplemental data

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Sample components

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Entire : Chikungunya virus

EntireName: Chikungunya virus
Components
  • Virus: Chikungunya virus

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: vaccine strain 181/clone 25 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / Strain: vaccine strain 181/clone 25
Virus shellShell ID: 1 / Diameter: 698.0 Å / T number (triangulation number): 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
DetailsCHIKV vaccine strain 181/clone 25 infected U2OS cells.

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average exposure time: 0.6 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

DetailsIMOD was used to align the tiltseries. ICON-GPU was used to reconstruct the aligned tiltseries into tomograms.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.21) / Number subtomograms used: 35
ExtractionNumber tomograms: 20 / Number images used: 47 / Software - Name: EMAN2 (ver. 2.21)
CTF correctionSoftware - Name: EMAN2 (ver. 2.21)
Details: Not all images were CTF corrected; only those images and those tiltseries with clear CTF ripples in the power spectrum.
Final angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 2.21)
Details: Self-symmetry search was used to create an initial model. All particles were iterative refined in 3D against such model.
FSC plot (resolution estimation)

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