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- EMDB-16139: E.coli 70S ribosome subtomogram average from multishot acquisitio... -

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Basic information

Entry
Database: EMDB / ID: EMD-16139
TitleE.coli 70S ribosome subtomogram average from multishot acquisition on cryo-FIB lamellae
Map dataE.coli multishot 3 70s subtomo average map tomoman-stopgap
Sample
  • Cell: E.coli
Keywordscytoplasm / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 8.8 Å
AuthorsKhavnekar S / Plitzko JM / Erdmann PSE
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J Struct Biol / Year: 2023
Title: Multishot tomography for high-resolution in situ subtomogram averaging.
Authors: S Khavnekar / W Wan / P Majumder / W Wietrzynski / P S Erdmann / J M Plitzko /
Abstract: Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can ...Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.
History
DepositionNov 15, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16139.png

Downloads & links

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Map

FileDownload / File: emd_16139.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE.coli multishot 3 70s subtomo average map tomoman-stopgap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.58 Å/pix.
x 128 pix.
= 458.24 Å		3.58 Å/pix.
x 128 pix.
= 458.24 Å		3.58 Å/pix.
x 128 pix.
= 458.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.475
Minimum - Maximum-0.6415358 - 1.6256485
Average (Standard dev.)-0.0005083384 (±0.15325102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 458.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16139_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: E.coli multishot 3 70s subtomo average half map 1 tomoman-stopgap

Fileemd_16139_half_map_1.map
AnnotationE.coli multishot 3 70s subtomo average half map 1 tomoman-stopgap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: E.coli multishot 3 70s subtomo average half map 2 tomoman-stopgap

Fileemd_16139_half_map_2.map
AnnotationE.coli multishot 3 70s subtomo average half map 2 tomoman-stopgap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E.coli

EntireName: E.coli (others)
Components
  • Cell: E.coli

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Supramolecule #1: E.coli

SupramoleculeName: E.coli / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / 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: 8000
ExtractionNumber tomograms: 27 / Number images used: 12000
Final angle assignmentType: OTHER

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