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- EMDB-7515: Subtomogram averages of budding-arrested nucleocapsid-like partic... -

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Basic information

Database: EMDB / ID: 7515
TitleSubtomogram averages of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
Map dataSubtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
SampleBudding-arrestedChikungunya virus nucleocapsid-like particle:
SourceChikungunya virus
Methodsubtomogram averaging / cryo EM / 36 Å resolution
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.
DateDeposition: Mar 2, 2018 / Header (metadata) release: May 16, 2018 / Map release: Jan 9, 2019 / Last update: Jan 9, 2019

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


Fileemd_7515.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
7.16 Å/pix.
= 916.48 Å
128 pix
7.16 Å/pix.
= 916.48 Å
128 pix
7.16 Å/pix.
= 916.48 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.16 Å
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-1.130406 - 10.189989000000001
Average (Standard dev.)0.17448513 (0.8805925)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 916.48 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.167.167.16
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z916.480916.480916.480
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-919-919-29
D min/max/mean-1.13010.1900.174

Supplemental data

Sample components

Entire Budding-arrestedChikungunya virus nucleocapsid-like particle

EntireName: Budding-arrestedChikungunya virus nucleocapsid-like particle
Number of components: 1

Component #1: virus, Chikungunya virus

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

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 / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 378 / Number of class averages: 11
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: 36 Å / Resolution method: FSC 0.143 CUT-OFF
Euler angles: Initial models were created (reference-free, symmetry-free) using hierarchical ascendant classification. NCLPs within different size classes were iteratively refined until convergence (gold-standard, symmetry-free).
FSC plot
(resolution estimation)

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