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- EMDB-58456: Electron tomogram of the postmitotic nuclear envelope following a... -

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Basic information

Entry
Database: EMDB / ID: EMD-58456
TitleElectron tomogram of the postmitotic nuclear envelope following acute Nup62 depletion
Map data
Sample
  • Cell: HeLa Kyoto cell
KeywordsNuclear pore complex / nuclear envelope / postmitotic assembly / Nup62 / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / negative staining
AuthorsZhang W / Ellenberg J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Electron tomogram of the postmitotic nuclear envelope following acute Nup62 depletion
Authors: Zhang W / Ellenberg J
History
DepositionJun 9, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58456.png

Downloads & links

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Map

FileDownload / File: emd_58456.map.gz / Format: CCP4 / Size: 2.5 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.3 Å/pix.
x 330 pix.
= 3398.34 Å		10.3 Å/pix.
x 2032 pix.
= 20925.537 Å		10.3 Å/pix.
x 2032 pix.
= 20925.537 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.298 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2266.0 - 2516.0
Average (Standard dev.)404.292399999999986 (±311.258849999999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-165
Dimensions20322032330
Spacing20322032330
CellA: 20925.537 Å / B: 20925.537 Å / C: 3398.34 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HeLa Kyoto cell

EntireName: HeLa Kyoto cell
Components
  • Cell: HeLa Kyoto cell

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Supramolecule #1: HeLa Kyoto cell

SupramoleculeName: HeLa Kyoto cell / type: cell / ID: 1 / Parent: 0
Details: High-pressure frozen and freeze-substituted HeLa Kyoto cells embedded in Epon resin and analyzed during mitotic exit following acute Nup62 depletion.
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl acetate and lead citrate
Sugar embeddingMaterial: Epon 812
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is HPM 010; BalTec. This is not in a list of allowed values {'LEICA EM HPM100', 'BAL-TEC HPM 010', 'OTHER', 'EMS-002 RAPID IMMERSION ...Details: The value given for _em_high_pressure_freezing.instrument is HPM 010; BalTec. This is not in a list of allowed values {'LEICA EM HPM100', 'BAL-TEC HPM 010', 'OTHER', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'LEICA EM PACT2'} so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Leica ultracut UC7 / Ultramicrotomy - Temperature: 295 K / Ultramicrotomy - Final thickness: 300

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: OTHER / Average electron dose: 200.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.5.6) / Number images used: 121
CTF correctionType: NONE

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