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- EMDB-57021: Optimal tilt-increment for cryo-ET -

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Basic information

Entry
Database: EMDB / ID: EMD-57021
TitleOptimal tilt-increment for cryo-ET
Map dataRibosome from Dictyostelium discoideum, from in-situ data using cryo-ET and STA. Acquired with a 3-degree tilt-increment. Refined with M.
Sample
  • Cell: Dictyostelium discoideum
KeywordsRibosome / cryo-electron tomography / subtomogram averaging
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 5.8 Å
AuthorsTuijtel MW / Beck M
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234666 United States
CitationJournal: Elife / Year: 2026
Title: Optimising the tilt-increment for in situ cryo-electron tomography
Authors: Tuijtel MW / Majtner T / Turonova B / Beck M
History
DepositionMar 3, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57021.png

Downloads & links

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Map

FileDownload / File: emd_57021.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRibosome from Dictyostelium discoideum, from in-situ data using cryo-ET and STA. Acquired with a 3-degree tilt-increment. Refined with M.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 356 pix.
= 701.676 Å		1.97 Å/pix.
x 356 pix.
= 701.676 Å		1.97 Å/pix.
x 356 pix.
= 701.676 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.971 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00275
Minimum - Maximum-0.0035371208 - 0.009554365
Average (Standard dev.)0.000028690183 (±0.00047960176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 701.67596 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 3-degree...

Fileemd_57021_additional_1.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 3-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 1-degree...

Fileemd_57021_additional_2.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 1-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 2-degree...

Fileemd_57021_additional_3.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 2-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 10-degree...

Fileemd_57021_additional_4.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 10-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 2-degree...

Fileemd_57021_additional_5.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 2-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 10-degree...

Fileemd_57021_additional_6.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 10-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 1-degree...

Fileemd_57021_additional_7.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 1-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 5-degree...

Fileemd_57021_additional_8.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 5-degree tilt-increment. Refined with M, local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: Ribosome from Dictyostelium discoideum. Acquired with a 5-degree...

Fileemd_57021_additional_9.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 5-degree tilt-increment. Refined with M.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: Ribosome from Dictyostelium discoideum. Acquired with a 3-degree...

Fileemd_57021_half_map_1.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 3-degree tilt-increment. Refined with M. Halfmap 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: Ribosome from Dictyostelium discoideum. Acquired with a 3-degree...

Fileemd_57021_half_map_2.map
AnnotationRibosome from Dictyostelium discoideum. Acquired with a 3-degree tilt-increment. Refined with M. Halfmap 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 : Dictyostelium discoideum

EntireName: Dictyostelium discoideum (eukaryote)
Components
  • Cell: Dictyostelium discoideum

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Supramolecule #1: Dictyostelium discoideum

SupramoleculeName: Dictyostelium discoideum / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)

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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 / Details: HL5 medium
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 38.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 21 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 6 / Average electron dose: 3.2 e/Å2
Details: Value for electron dose varied with the tilt-increment
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 10760
ExtractionNumber tomograms: 20 / Number images used: 22303 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD

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