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- EMDB-13879: Subtomogram average of D. melanogaster Ribosomes from tomograms c... -

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Basic information

Entry
Database: EMDB / ID: EMD-13879
TitleSubtomogram average of D. melanogaster Ribosomes from tomograms collected on a cryo-lift-out lamella
Map dataSubtomogram average
Sample
  • Complex: Drosophila melanogaster ribosome
Keywordscyro-FIB / cryo-electron tomography / Drosophila melanogaster / subtomogram average / RIBOSOME
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM / Resolution: 20.8 Å
AuthorsKlumpe S / Fung HKH / Goetz SK / Plitzko JM / Mahamid J
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726European Union
European Research Council (ERC)760067European Union
European Union (EU)871037European Union
CitationJournal: Elife / Year: 2021
Title: A modular platform for automated cryo-FIB workflows.
Authors: Sven Klumpe / Herman Kh Fung / Sara K Goetz / Ievgeniia Zagoriy / Bernhard Hampoelz / Xiaojie Zhang / Philipp S Erdmann / Janina Baumbach / Christoph W Müller / Martin Beck / Jürgen M ...Authors: Sven Klumpe / Herman Kh Fung / Sara K Goetz / Ievgeniia Zagoriy / Bernhard Hampoelz / Xiaojie Zhang / Philipp S Erdmann / Janina Baumbach / Christoph W Müller / Martin Beck / Jürgen M Plitzko / Julia Mahamid /
Abstract: Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ...Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.
History
DepositionNov 15, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13879.png

Downloads & links

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Map

FileDownload / File: emd_13879.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.04 Å/pix.
x 64 pix.
= 450.56 Å		7.04 Å/pix.
x 64 pix.
= 450.56 Å		7.04 Å/pix.
x 64 pix.
= 450.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.17
Minimum - Maximum-0.36189026 - 0.6313389
Average (Standard dev.)0.000000000203743 (±0.110145725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.047.047.04
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z450.560450.560450.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.3620.6310.000

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Supplemental data

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Mask #1

Fileemd_13879_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Subtomogram average filtered to resolution (~21 A)

Fileemd_13879_additional_1.map
AnnotationSubtomogram average filtered to resolution (~21 A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_13879_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_13879_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Drosophila melanogaster ribosome

EntireName: Drosophila melanogaster ribosome
Components
  • Complex: Drosophila melanogaster ribosome

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Supramolecule #1: Drosophila melanogaster ribosome

SupramoleculeName: Drosophila melanogaster ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 20284
ExtractionNumber tomograms: 8 / Number images used: 20284
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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