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- EMDB-45235: Subtomogram average (C1) of fatty acid synthase from S.cerevisiae... -

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Basic information

Entry
Database: EMDB / ID: EMD-45235
TitleSubtomogram average (C1) of fatty acid synthase from S.cerevisiae prepared using cryo-plasmaFIB milling
Map datacryoDRGN-ET selected C1 refined sub volumes
Sample
  • Complex: Yeast fatty acid synthase complex
KeywordsComplex / LIPID BINDING PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 8.8 Å
AuthorsFeathers JR / Zhong ED / Khavnekar S
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
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
DepositionJun 7, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45235.png

Downloads & links

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Map

FileDownload / File: emd_45235.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoDRGN-ET selected C1 refined sub volumes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 300 pix.
= 588. Å		1.96 Å/pix.
x 300 pix.
= 588. Å		1.96 Å/pix.
x 300 pix.
= 588. 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: 0.581
Minimum - Maximum-0.60020196 - 1.4108478
Average (Standard dev.)-0.0026832297 (±0.11097476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45235_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: RELION Postprocess sharpened map with B-factor -100

Fileemd_45235_additional_1.map
AnnotationRELION Postprocess sharpened map with B-factor -100
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: Half map 1

Fileemd_45235_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_45235_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast fatty acid synthase complex

EntireName: Yeast fatty acid synthase complex
Components
  • Complex: Yeast fatty acid synthase complex

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Supramolecule #1: Yeast fatty acid synthase complex

SupramoleculeName: Yeast fatty acid synthase complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2 MDa

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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: 1.5 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: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 5239
ExtractionNumber tomograms: 263 / Number images used: 33492
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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