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

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Basic information

Database: EMDB / ID: EMD-7513
TitleSubtomogram average of mature CHIKV virion budded from human cells
Map data
SampleChikungunya virus:
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 34 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.
DepositionMar 2, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseJan 9, 2019-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

Structure visualization

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

Downloads & links


FileDownload / File: emd_7513.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.16 Å
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum0.0 - 12.174003000000001
Average (Standard dev.)0.18559761 (±0.9999999)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS-919-919-33
D min/max/mean0.00012.1740.186

Supplemental data

Sample components

Entire Chikungunya virus

EntireName: Chikungunya virus / Number of components: 1

Component #1: virus, Chikungunya virus

VirusName: Chikungunya virusChikungunya / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Chikungunya virus / Strain: vaccine strain 181/clone 25
Source (natural)Host Species: Homo sapiens (human) / Host species strain: vaccine strain 181/clone 25

Experimental details

Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter / Energy window: 0-20 eV
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 35
Details: IMOD was used to align the tiltseries. ICON-GPU was used to reconstruct the aligned tiltseries into tomograms.
3D reconstructionSoftware: EMAN2
CTF correction: Not all images were CTF corrected; only those images and those tiltseries with clear CTF ripples in the power spectrum.
Resolution: 34 Å / Resolution method: FSC 0.143 CUT-OFF
Euler angles: 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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