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- EMDB-16537: Optimizing Cryo-FIB Lamellas for sub-5 Angstrom in situ Structura... -

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Basic information

Entry
Database: EMDB / ID: EMD-16537
TitleOptimizing Cryo-FIB Lamellas for sub-5 Angstrom in situ Structural Biology : Subtomogram average of the Large Subunit of S.Cerevisiae 80S Ribosome
Map dataLocal resolution filtered map after M refinement Workflow: TOMOMAN-STOPGAP-Warp-Relion-M
Sample
  • Complex: S.Cerevisiae 80s ribosome large subunit
KeywordsS.Cerevisiae / 80S / Ribosome / FIB / insitu
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 4.6 Å
AuthorsKhavnekar S / Vrbovska V / Zaoralova M / KElley R / Beck F / Klumpe S / Kotech A / Plitzko JM / Erdmann PS
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Optimizing Cryo-FIB Lamellas for sub-5 Angstrom in situ Structural Biology : Large Subunit of S.Cerevisiae 80S Ribosome
Authors: Khavnekar S / Vrbovska V / Zaoralova M / KElley R / Beck F / Klumpe S / Kotech A / Plitzko JM / Erdmann PS
History
DepositionJan 24, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16537.png

Downloads & links

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Map

FileDownload / File: emd_16537.map.gz / Format: CCP4 / Size: 411.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map after M refinement Workflow: TOMOMAN-STOPGAP-Warp-Relion-M
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 476 pix.
= 761.6 Å		1.6 Å/pix.
x 476 pix.
= 761.6 Å		1.6 Å/pix.
x 476 pix.
= 761.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0028
Minimum - Maximum-0.01833069 - 0.024395237
Average (Standard dev.)0.000016939359 (±0.00036435347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions476476476
Spacing476476476
CellA=B=C: 761.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16537_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: From WARP/M

Fileemd_16537_half_map_1.map
AnnotationFrom WARP/M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: From WARP/M

Fileemd_16537_half_map_2.map
AnnotationFrom WARP/M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S.Cerevisiae 80s ribosome large subunit

EntireName: S.Cerevisiae 80s ribosome large subunit
Components
  • Complex: S.Cerevisiae 80s ribosome large subunit

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Supramolecule #1: S.Cerevisiae 80s ribosome large subunit

SupramoleculeName: S.Cerevisiae 80s ribosome large subunit / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 3.5 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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12500
ExtractionNumber tomograms: 91 / Number images used: 45500
Final angle assignmentType: MAXIMUM LIKELIHOOD

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