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- EMDB-31261: RNPs within intact virions -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-31261
TitleRNPs within intact virions
Map data
Sample
  • Complex: RNPs within intact virions
Biological speciesPorcine epidemic diarrhea virus CV777
Methodsubtomogram averaging / cryo EM / Resolution: 35.5 Å
AuthorsHe J / Liao J
CitationJournal: To Be Published
Title: The supramolecular structure of porcine epidemic diarrhea virus characterized by cryo-electron tomography
Authors: He J / Liao J
History
DepositionMay 1, 2021-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31261.png

Downloads & links

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Map

FileDownload / File: emd_31261.map.gz / Format: CCP4 / Size: 162.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.07 Å/pix.
x 32 pix.
= 322.304 Å		10.07 Å/pix.
x 36 pix.
= 362.592 Å		10.07 Å/pix.
x 36 pix.
= 362.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.34
Minimum - Maximum-4.9023843 - 3.5416858
Average (Standard dev.)1.0100962e-08 (±0.8888939)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions363632
Spacing363632
CellA: 362.59198 Å / B: 362.59198 Å / C: 322.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RNPs within intact virions

EntireName: RNPs within intact virions
Components
  • Complex: RNPs within intact virions

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Supramolecule #1: RNPs within intact virions

SupramoleculeName: RNPs within intact virions / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Porcine epidemic diarrhea virus CV777

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 1398
ExtractionNumber tomograms: 24 / Number images used: 4326
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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