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- EMDB-16767: In situ STA of rotavirus enveloped DLP (penton) -

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Basic information

Entry
Database: EMDB / ID: EMD-16767
TitleIn situ STA of rotavirus enveloped DLP (penton)
Map dataconsensus average
Sample
  • Virus: Rotavirus A
Biological speciesRotavirus A
Methodsubtomogram averaging / cryo EM / Resolution: 10.2 Å
AuthorsShah PNM / Stuart DI
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Wellcome Trust03141/Z/16/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: Cell Host Microbe / Year: 2023
Title: Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography
Authors: Shah PN / Gilchrist JB / Forsberg BO / Burt A / Howe A / Mosalaganti S / Wan W / Radecke J / Chaban Y / Sutton G / Stuart DI / Boyce M
History
DepositionFeb 24, 2023-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16767.png

Downloads & links

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Map

FileDownload / File: emd_16767.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 210 pix.
= 413.7 Å		1.97 Å/pix.
x 210 pix.
= 413.7 Å		1.97 Å/pix.
x 210 pix.
= 413.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00409
Minimum - Maximum-0.010787673 - 0.01896788
Average (Standard dev.)0.0001852184 (±0.0017678109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 413.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half1

Fileemd_16767_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_16767_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rotavirus A

EntireName: Rotavirus A
Components
  • Virus: Rotavirus A

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Supramolecule #1: Rotavirus A

SupramoleculeName: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 28875 / Sci species name: Rotavirus A / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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: 7.5
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Number subtomograms used: 138
ExtractionNumber tomograms: 85 / Number images used: 138 / Software - Name: crYOLO (ver. 1.8.2)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)

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