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- EMDB-58189: Subtomogram average of H. sapiens 13-protofilament microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-58189
TitleSubtomogram average of H. sapiens 13-protofilament microtubule
Map data
Sample
  • Cell: cryoFIB lamellae of mycophenolic acid-treated H. sapiens (HeLa) cells
Keywordsprotofilament / microtubule / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 4.6 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 19, 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_58189.png

Downloads & links

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Map

FileDownload / File: emd_58189.map.gz / Format: CCP4 / Size: 71.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 266 pix.
= 399. Å		1.5 Å/pix.
x 266 pix.
= 399. Å		1.5 Å/pix.
x 266 pix.
= 399. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00124
Minimum - Maximum-0.0012170433 - 0.003993534
Average (Standard dev.)0.000074548734 (±0.0003452788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions266266266
Spacing266266266
CellA=B=C: 399.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58189_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_58189_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58189_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 : cryoFIB lamellae of mycophenolic acid-treated H. sapiens (HeLa) cells

EntireName: cryoFIB lamellae of mycophenolic acid-treated H. sapiens (HeLa) cells
Components
  • Cell: cryoFIB lamellae of mycophenolic acid-treated H. sapiens (HeLa) cells

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Supramolecule #1: cryoFIB lamellae of mycophenolic acid-treated H. sapiens (HeLa) cells

SupramoleculeName: cryoFIB lamellae of mycophenolic acid-treated H. sapiens (HeLa) cells
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE
DetailsHeLa cells were seeded on plasma treated R2/1 Quantifoil 200 mesh gold grids in DMEM supplemented with 10% fetal bovine serum and 100 U/mL penicillin and streptomycin, under normal culture conditions (5% CO2, 37 C). After 24 hours we added mycophenolic acid to a final concentration of 100 micromolar and incubated the culture for another 16 hours before plunging grids into liquid ethane.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 4.6 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: 2.5 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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M (ver. 2.0.0dev36) / Number subtomograms used: 49400
ExtractionNumber tomograms: 621 / Number images used: 3800 / 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: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0-dev)

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