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- EMDB-26451: Cytosolic nucleocapsid intermediate from CHIKV-infected cells -

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Basic information

Entry
Database: EMDB / ID: EMD-26451
TitleCytosolic nucleocapsid intermediate from CHIKV-infected cells
Map data
Sample
  • Virus: Chikungunya virus
Keywordsalphavirus / icosahedral / enveloped virus / VIRUS
Biological speciesChikungunya virus
Methodsubtomogram averaging / cryo EM / Resolution: 47.6 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) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26451.png

Downloads & links

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Map

FileDownload / File: emd_26451.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 4.05
Minimum - Maximum-12.055375 - 10.915651
Average (Standard dev.)0.0020923375 (±0.97034264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-36-36-36
Dimensions727272
Spacing727272
CellA=B=C: 1019.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26451_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26451_half_map_2.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 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) / 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 reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 47.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 188
ExtractionNumber tomograms: 185 / Number images used: 188
Final angle assignmentType: PROJECTION MATCHING

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