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- EMDB-58147: In situ subtomogram average of filamentous IMPDH in mycophenolic ... -

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Basic information

Entry
Database: EMDB / ID: EMD-58147
TitleIn situ subtomogram average of filamentous IMPDH in mycophenolic acid-treated HeLa cells
Map data
Sample
  • Cell: cryoFIB-milled lamellae of mycophenolic-acid treated HeLa cells
Keywordspurine synthesis / octamer / filament / mycophenolic acid / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 4.0 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_58147.png

Downloads & links

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Map

FileDownload / File: emd_58147.map.gz / Format: CCP4 / Size: 96.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 294 pix.
= 458.64 Å		1.56 Å/pix.
x 294 pix.
= 458.64 Å		1.56 Å/pix.
x 294 pix.
= 458.64 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.008360003 - 0.014998876
Average (Standard dev.)0.000004215407 (±0.0004612018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions294294294
Spacing294294294
CellA=B=C: 458.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58147_msk_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_58147_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58147_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cryoFIB-milled lamellae of mycophenolic-acid treated HeLa cells

EntireName: cryoFIB-milled lamellae of mycophenolic-acid treated HeLa cells
Components
  • Cell: cryoFIB-milled lamellae of mycophenolic-acid treated HeLa cells

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Supramolecule #1: cryoFIB-milled lamellae of mycophenolic-acid treated HeLa cells

SupramoleculeName: cryoFIB-milled lamellae of mycophenolic-acid treated 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 statefilament

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Sample preparation

BufferpH: 7.4
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: 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: 2.0 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: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M (ver. 2.0.0dev36) / Number subtomograms used: 9568
ExtractionNumber tomograms: 19 / Number images used: 9568 / Reference model: EMD-20701 / Software - Name: Warp (ver. 2.0.0dev36)
Software - details: NOTE: I used easymode (github.com/mgflast/easymode) and Ais (github.com/bionanopatterning/Ais) but these are not available in the list.
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: NOT APPLICABLE
Software: (Name: Warp (ver. 2.0.0dev36), RELION (ver. 5.0.0-dev), M (ver. 2.0.0dev36))

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