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- EMDB-26447: Docking NC CHIKV assembly/budding intermediate from virus-infecte... -

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Basic information

Entry
Database: EMDB / ID: EMD-26447
TitleDocking NC CHIKV assembly/budding intermediate from virus-infected human cells
Map dataSubtomogram average of early budding intermediate
Sample
  • Virus: Chikungunya virus
Keywordsalphavirus / icosahedral / enveloped virus / VIRUS / budding
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 43.7 Å
AuthorsChmielewski D / Schmid MF / Jin J / Simmons G / Chiu W
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI148382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI119056 United States
CitationJournal: To Be Published
Title: In situ Alphavirus Assembly and Budding Mechanism Revealed by Cellular CryoET
Authors: Chmielewski D / Schmid MF / Jin J / Simmons G / Chiu W
History
DepositionMar 17, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26447.png

Downloads & links

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Map

FileDownload / File: emd_26447.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of early budding intermediate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.16 Å/pix.
x 120 pix.
= 1699.2 Å		14.16 Å/pix.
x 120 pix.
= 1699.2 Å		14.16 Å/pix.
x 120 pix.
= 1699.2 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: 4.38
Minimum - Maximum-16.83502 - 14.240641
Average (Standard dev.)0.036103677 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin222
Dimensions120120120
Spacing120120120
CellA=B=C: 1699.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: odd half map

Fileemd_26447_half_map_1.map
Annotationodd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even half map

Fileemd_26447_half_map_2.map
Annotationeven 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

EntireName: Chikungunya virus
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 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Diameter: 700.0 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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -0.005 µm / Nominal defocus min: -0.002 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 43.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 197
ExtractionNumber tomograms: 144 / Number images used: 197

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