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- EMDB-18231: CryoDRGN Reconstruction of 80S Ribosome in Rotated State from S.c... -

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Basic information

Entry
Database: EMDB / ID: EMD-18231
TitleCryoDRGN Reconstruction of 80S Ribosome in Rotated State from S.cerevisiae Prepared using Cryo-plasmaFIB Milling
Map dataTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast
Sample
  • Complex: 80S S. cerevisiae
Keywordsyeast 80S / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 4.7 Å
AuthorsRangan R / Khavnekar S / Lerer A / Johnston J / Kelley R / Obr M / Kotecha A / Zhong ED
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
Other private
CitationJournal: To Be Published
Title: Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells
Authors: Rangan R / Khavnekar S / Lerer A / Johnston J / Kelley R / Obr M / Kotecha A / Zhong ED
History
DepositionAug 16, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18231.png

Downloads & links

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Map

FileDownload / File: emd_18231.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast
Voxel sizeX=Y=Z: 1.96 Å
Density
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.039299782 - 0.08681587
Average (Standard dev.)0.000000000360709 (±0.004951836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 501.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18231_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast

Fileemd_18231_half_map_1.map
AnnotationTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast

Fileemd_18231_half_map_2.map
AnnotationTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET rotated 80S yeast
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S S. cerevisiae

EntireName: 80S S. cerevisiae
Components
  • Complex: 80S S. cerevisiae

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Supramolecule #1: 80S S. cerevisiae

SupramoleculeName: 80S S. cerevisiae / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 250 / Number images used: 250000
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoDRGN / Software - details: Electron Tomography / Number subtomograms used: 62624
FSC plot (resolution estimation)

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