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- EMDB-15583: Cryo-electron tomogram of chikungunya virus spherules at plasma m... -

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Basic information

Entry
Database: EMDB / ID: EMD-15583
TitleCryo-electron tomogram of chikungunya virus spherules at plasma membrane
Map dataCryo-electron tomogram of chikungunya virus spherules at the plasma membrane
Sample
  • Cell: BHK cell transduced with chikungunya viral replicon particles
Biological speciesChikungunya virus
Methodelectron tomography / cryo EM
AuthorsLaurent T / Carlson LA
Funding support Sweden, France, 4 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Human Frontier Science Program (HFSP)CDA00047/2017-C France
Swedish Research Council2018-05851 Sweden
Swedish Research Council2021-01145 Sweden
CitationJournal: Elife / Year: 2022
Title: Architecture of the chikungunya virus replication organelle.
Authors: Timothée Laurent / Pravin Kumar / Susanne Liese / Farnaz Zare / Mattias Jonasson / Andreas Carlson / Lars-Anders Carlson /
Abstract: are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the s chikungunya virus (CHIKV) has spread explosively in the last 20 years, and ... are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the s chikungunya virus (CHIKV) has spread explosively in the last 20 years, and there is no approved treatment for chikungunya fever. On the plasma membrane of the infected cell, CHIKV generates dedicated organelles for viral RNA replication, so-called spherules. Whereas structures exist for several viral proteins that make up the spherule, the architecture of the full organelle is unknown. Here, we use cryo-electron tomography to image CHIKV spherules in their cellular context. This reveals that the viral protein nsP1 serves as a base for the assembly of a larger protein complex at the neck of the membrane bud. Biochemical assays show that the viral helicase-protease nsP2, while having no membrane affinity on its own, is recruited to membranes by nsP1. The tomograms further reveal that full-sized spherules contain a single copy of the viral genome in double-stranded form. Finally, we present a mathematical model that explains the membrane remodeling of the spherule in terms of the pressure exerted on the membrane by the polymerizing RNA, which provides a good agreement with the experimental data. The energy released by RNA polymerization is found to be sufficient to remodel the membrane to the characteristic spherule shape.
History
DepositionAug 12, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_15583.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of chikungunya virus spherules at the plasma membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
17.16 Å/pix.
x 512 pix.
= 8785.92 Å
17.16 Å/pix.
x 927 pix.
= 15907.32 Å
17.16 Å/pix.
x 959 pix.
= 16456.439 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 17.16 Å
Density
Minimum - Maximum-8247.437 - 5051.044
Average (Standard dev.)84.742775 (±307.2547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616256
Dimensions927959512
Spacing959927512
CellA: 16456.44 Å / B: 15907.32 Å / C: 8785.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : BHK cell transduced with chikungunya viral replicon particles

EntireName: BHK cell transduced with chikungunya viral replicon particles
Components
  • Cell: BHK cell transduced with chikungunya viral replicon particles

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Supramolecule #1: BHK cell transduced with chikungunya viral replicon particles

SupramoleculeName: BHK cell transduced with chikungunya viral replicon particles
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chikungunya virus

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: CMC-Utrecht / Diameter: 5 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: CTFFIND (ver. 4), CTFPHASEFLIP)
Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 61

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