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- EMDB-29336: Golden shiner reovirus tropical vertex missing TEC -

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Basic information

Entry
Database: EMDB / ID: EMD-29336
TitleGolden shiner reovirus tropical vertex missing TEC
Map datatropical without tec
Sample
  • Virus: Golden shiner reovirus
KeywordsdsRNA virus / aquareovirus / RNA-dependent RNA-polymerase / VIRUS
Biological speciesGolden shiner reovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhou ZH / Stevens AW
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007323 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116792 United States
National Institutes of Health/Office of the Director1S10OD018111
CitationJournal: Protein Cell / Year: 2023
Title: Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation.
Authors: Alexander Stevens / Yanxiang Cui / Sakar Shivakoti / Z Hong Zhou /
History
DepositionDec 29, 2022-
Header (metadata) releaseMar 15, 2023-
Map releaseMar 15, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29336.png

Downloads & links

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Map

FileDownload / File: emd_29336.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtropical without tec
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00973
Minimum - Maximum-0.019279374 - 0.03734499
Average (Standard dev.)0.00049092993 (±0.0030357146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29336_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_29336_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 : Golden shiner reovirus

EntireName: Golden shiner reovirus
Components
  • Virus: Golden shiner reovirus

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Supramolecule #1: Golden shiner reovirus

SupramoleculeName: Golden shiner reovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 / Details: Purified from infected cells / NCBI-ID: 185783 / Sci species name: Golden shiner reovirus / Sci species strain: AQRVC / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Notemigonus crysoleucas (golden shiner)
Molecular weightTheoretical: 47 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 750.0 Å / T number (triangulation number): 13

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: Phosphate buffered saline
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m99

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21844
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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