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

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Entry
Database: EMDB / ID: EMD-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 != Chikungunya virus

Budding-arrestedChikungunya virus nucleocapsid-like particle

  • Virus: Chikungunya virus
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 36.0 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) releaseMay 16, 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
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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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7515_1.png

emd_7515_2.png

emd_7515_3.png

emd_7515_4.png

emd_7515_5.png

Downloads & links

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Map

FileDownload / File: emd_7515.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.16 Å/pix.
x 128 pix.
= 916.48 Å		7.16 Å/pix.
x 128 pix.
= 916.48 Å		7.16 Å/pix.
x 128 pix.
= 916.48 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 - Maximum-1.130406 - 10.189989000000001
Average (Standard dev.)0.17448513 (±0.8805925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-919-919-29
Dimensions128128128
Spacing128128128
CellA=B=C: 916.48 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-919-919-29
NC/NR/NS128128128
D min/max/mean-1.13010.1900.174

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Supplemental data

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Additional map: Subtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside...

Fileemd_7515_additional_1.map
AnnotationSubtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside...

Fileemd_7515_additional_2.map
AnnotationSubtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside...

Fileemd_7515_additional_3.map
AnnotationSubtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside...

Fileemd_7515_additional_4.map
AnnotationSubtomogram average of budding-arrested nucleocapsid-like particles (NCLPs) inside CHIKV-infected human cells.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Budding-arrestedChikungunya virus nucleocapsid-like particle

EntireName: Budding-arrestedChikungunya virus nucleocapsid-like particle
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: 181/clone 25 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
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
DetailsNeutralizing antibody treated U2OS cells that were infected with CHIKV vaccine strain 181/clone 25

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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 reconstructionNumber classes used: 5 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.21) / Number subtomograms used: 378
ExtractionNumber tomograms: 20 / Number images used: 1163 / 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 3D classificationNumber classes: 11 / Avg.num./class: 63
Details: Of 1163 extracted NCLP subtomograms, 763 were classified by size deriving their radius from radial density profile plots computed from spherically averaged subtomograms. Of these, 378 were ...Details: Of 1163 extracted NCLP subtomograms, 763 were classified by size deriving their radius from radial density profile plots computed from spherically averaged subtomograms. Of these, 378 were part of the final 5 converging averages uploaded to the EMDB.
Final angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 2.21)
Details: Initial models were created (reference-free, symmetry-free) using hierarchical ascendant classification. NCLPs within different size classes were iteratively refined until convergence (gold- ...Details: 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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