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- EMDB-58163: Subtomogram average of gamma tubulin ring complex capping microtu... -

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Basic information

Entry
Database: EMDB / ID: EMD-58163
TitleSubtomogram average of gamma tubulin ring complex capping microtubule minus ends from purified S. uvarum spindle pole bodies
Map data
Sample
  • Organelle or cellular component: Spindle pole body
Keywordsgamma-tubulin ring complex / microtubule nucleation / microtubule minus end / spindle pole body / STRUCTURAL PROTEIN
Biological speciesSaccharomyces uvarum (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 23.6 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_58163.png

Downloads & links

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Map

FileDownload / File: emd_58163.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
8 Å/pix.
x 96 pix.
= 768. Å		8 Å/pix.
x 96 pix.
= 768. Å		8 Å/pix.
x 96 pix.
= 768. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.25
Minimum - Maximum-2.11385 - 3.6517286
Average (Standard dev.)0.03421436 (±0.44122672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 768.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58163_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_58163_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58163_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Spindle pole body

EntireName: Spindle pole body
Components
  • Organelle or cellular component: Spindle pole body

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Supramolecule #1: Spindle pole body

SupramoleculeName: Spindle pole body / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces uvarum (yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.71 e/Å2
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: 2.0 µm
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: 23.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M (ver. 2.0.0dev36) / Number subtomograms used: 701
ExtractionNumber tomograms: 109 / Number images used: 2841 / Software - Name: Warp
Software - details: NOTE: we used easymode (github.com/mgflast/easymode) and Ais (github.com/bionanopatterning/Ais) but these are not in the list.
CTF correctionType: PHASE FLIPPING ONLY
Final 3D classificationNumber classes: 4 / Avg.num./class: 710 / Software - Name: RELION (ver. 5.0.0-dev)
Final angle assignmentType: OTHER

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