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- EMDB-27268: In situ structure of the non-replicative Chikungunya virus nonstr... -

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Basic information

Entry
Database: EMDB / ID: EMD-27268
TitleIn situ structure of the non-replicative Chikungunya virus nonstructural protein complex
Map dataSubtomogram average of nsp1-2-4 ring
Sample
  • Complex: Chikungunya virus replicase complex
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 9.9 Å
AuthorsYaw Bia T / Chmielewski D / Yien Law MC / Zhang K / He Y / Chen M / Jin J / Luo D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R01AI148382 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)S10OD021600 United States
CitationJournal: Sci Adv / Year: 2022
Title: Molecular architecture of the Chikungunya virus replication complex.
Authors: Yaw Bia Tan / David Chmielewski / Michelle Cheok Yien Law / Kuo Zhang / Yu He / Muyuan Chen / Jing Jin / Dahai Luo /
Abstract: To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we ...To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we determined both the high-resolution structure of the core RNA replicase of chikungunya virus and the native RC architecture in its cellular context at subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase, the viral polymerase nsP4, which is in complex with nsP2 helicase-protease, sits in the central pore of the membrane-anchored nsP1 RNA-capping ring. The addition of a large cytoplasmic ring next to the C terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses.
History
DepositionJun 11, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27268.png

Downloads & links

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Map

FileDownload / File: emd_27268.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of nsp1-2-4 ring
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.54 Å/pix.
x 128 pix.
= 453.12 Å		3.54 Å/pix.
x 128 pix.
= 453.12 Å		3.54 Å/pix.
x 128 pix.
= 453.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.21
Minimum - Maximum-125.02666 - 38.069702
Average (Standard dev.)0.06429815 (±0.94976336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 453.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: even half map

Fileemd_27268_half_map_1.map
Annotationeven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: odd half map

Fileemd_27268_half_map_2.map
Annotationodd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chikungunya virus replicase complex

EntireName: Chikungunya virus replicase complex
Components
  • Complex: Chikungunya virus replicase complex

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Supramolecule #1: Chikungunya virus replicase complex

SupramoleculeName: Chikungunya virus replicase complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Chikungunya virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.76 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 5707
ExtractionNumber tomograms: 30 / Number images used: 5707
Final angle assignmentType: PROJECTION MATCHING

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