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- EMDB-25099: Electron cryo-tomography of CHIKV assembly intermediates in human... -

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Basic information

Entry
Database: EMDB / ID: EMD-25099
TitleElectron cryo-tomography of CHIKV assembly intermediates in human U2OS cells
Map dataCHIKV nucleocapsid-like particle from virus-infected human U2OS cells
Sample
  • Virus: Chikungunya virus
Keywordsalphavirus / enveloped virus / virus assembly and budding / cryogenic electron tomography / subtomogram averaging / VIRUS
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 43.5 Å
AuthorsChmielewski D / Schmid MF / Simmons G / Jin J / Chiu W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: In situ Alphavirus Assembly and Budding Mechanism Revealed by Cellular CryoET
Authors: Chmielewski D / Schmid M / Simmons G / Jin J / Chiu W
History
DepositionOct 4, 2021-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25099.png

Downloads & links

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Map

FileDownload / File: emd_25099.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCHIKV nucleocapsid-like particle from virus-infected human U2OS cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.16 Å/pix.
x 72 pix.
= 1019.52 Å		14.16 Å/pix.
x 72 pix.
= 1019.52 Å		14.16 Å/pix.
x 72 pix.
= 1019.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 14.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.36
Minimum - Maximum-7.1301317 - 9.46345
Average (Standard dev.)0.008952861 (±0.9792923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 1019.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Chikungunya virus

EntireName: Chikungunya virus
Components
  • Virus: Chikungunya virus

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / Parent: 0
Details: CHIKV nucleocapsid-like particle from virus-infected human U2OS cells
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

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 43.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 185
ExtractionNumber tomograms: 185 / Number images used: 185
Final angle assignmentType: PROJECTION MATCHING

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