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- EMDB-58166: Subtomogram average of the D. discoideum vault complex using D39 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-58166
TitleSubtomogram average of the D. discoideum vault complex using D39 symmetry (from EMPIAR-11845)
Map data
Sample
  • Cell: D. discoideum lamella (EMPIAR-11845)
Keywordsvault complex / D39 / cytoplasm / CYTOSOLIC PROTEIN
Biological speciesDictyostelium discoideum (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 13.8 Å
AuthorsSo-Last MGF / Allegretti MA
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF-721-2024European Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/29 United Kingdom
CitationJournal: To Be Published
Title: Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging
Authors: So-Last MGF / Hale T / Burt A / Allegretti MA
History
DepositionMay 18, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58166.png

Downloads & links

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Map

FileDownload / File: emd_58166.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 350 pix.
= 1400. Å		4 Å/pix.
x 350 pix.
= 1400. Å		4 Å/pix.
x 350 pix.
= 1400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0049
Minimum - Maximum-0.0054000816 - 0.01896853
Average (Standard dev.)-0.000041020172 (±0.000787959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 1400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58166_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58166_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58166_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : D. discoideum lamella (EMPIAR-11845)

EntireName: D. discoideum lamella (EMPIAR-11845)
Components
  • Cell: D. discoideum lamella (EMPIAR-11845)

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Supramolecule #1: D. discoideum lamella (EMPIAR-11845)

SupramoleculeName: D. discoideum lamella (EMPIAR-11845) / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Dictyostelium discoideum (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: 7.2
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.3 e/Å2
Details: We did not acquire the data. We used the data from EMPIAR-11845.
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D39 (2x39 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 13.8 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: M (ver. 2.0.0dev36), RELION (ver. 5.0.0-dev))
Number subtomograms used: 384
ExtractionNumber tomograms: 150 / Number images used: 384 / Software - Name: Warp
Software - details: NOTE: we used easymode (github.com/mgflast/easymode) and Ais (github.com/bionanopatterning/Ais)
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: RANDOM ASSIGNMENT

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