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- EMDB-18232: CryoDRGN Reconstruction of 80S Ribosome in Unrotated State from S... -

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Basic information

Entry
Database: EMDB / ID: EMD-18232
TitleCryoDRGN Reconstruction of 80S Ribosome in Unrotated State from S.cerevisiae Prepared using Cryo-plasmaFIB Milling
Map dataTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated
Sample
  • Complex: 80S S. cerevisiae
Keywordsyeast 80S / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 4.5 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: Nat Methods / Year: 2024
Title: CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells.
Authors: Ramya Rangan / Ryan Feathers / Sagar Khavnekar / Adam Lerer / Jake D Johnston / Ron Kelley / Martin Obr / Abhay Kotecha / Ellen D Zhong /
Abstract: Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal ...Advances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecules in native cellular environments. While cryo-ET can reveal structures at molecular resolution, image processing algorithms remain a bottleneck in resolving the heterogeneity of biomolecular structures in situ. Here, we introduce cryoDRGN-ET for heterogeneous reconstruction of cryo-ET subtomograms. CryoDRGN-ET learns a deep generative model of three-dimensional density maps directly from subtomogram tilt-series images and can capture states diverse in both composition and conformation. We validate this approach by recovering the known translational states in Mycoplasma pneumoniae ribosomes in situ. We then perform cryo-ET on cryogenic focused ion beam-milled Saccharomyces cerevisiae cells. CryoDRGN-ET reveals the structural landscape of S. cerevisiae ribosomes during translation and captures continuous motions of fatty acid synthase complexes inside cells. This method is openly available in the cryoDRGN software.
History
DepositionAug 16, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18232.png

Downloads & links

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Map

FileDownload / File: emd_18232.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 256 pix.
= 501.76 Å		1.96 Å/pix.
x 256 pix.
= 501.76 Å		1.96 Å/pix.
x 256 pix.
= 501.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.049523044 - 0.103514686
Average (Standard dev.)0.000000000355217 (±0.005969104)
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_18232_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 80S yeast unrotated

Fileemd_18232_half_map_1.map
AnnotationTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated
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 80S yeast unrotated

Fileemd_18232_half_map_2.map
AnnotationTOMOMAN-STOPGAP-Warp-Relion-M CryoDRGN-ET 80S yeast unrotated
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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoDRGN / Software - details: Electron Tomography / Number subtomograms used: 30657
ExtractionNumber tomograms: 250 / Number images used: 250000
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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