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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: Nat Struct Mol Biol / Year: 2026
Title: Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.
Authors: Wanlu Zhang / Andrew P Latham / Paolo Ronchi / Sebastian Schnorrenberg / Jean-Karim Hériché / Ziqiang Huang / Catherine Sue / M Julius Hossain / Natalia Rosalia Morero / Hannah Pflaumer / ...Authors: Wanlu Zhang / Andrew P Latham / Paolo Ronchi / Sebastian Schnorrenberg / Jean-Karim Hériché / Ziqiang Huang / Catherine Sue / M Julius Hossain / Natalia Rosalia Morero / Hannah Pflaumer / Merle Hantsche-Grininger / Yannick Schwab / Andrej Sali / Jan Ellenberg /
Abstract: Nuclear envelope (NE) reformation after mitosis is essential for daughter cell viability and requires tightly coordinated nuclear pore complex (NPC) assembly and nuclear membrane reformation. Here we ...Nuclear envelope (NE) reformation after mitosis is essential for daughter cell viability and requires tightly coordinated nuclear pore complex (NPC) assembly and nuclear membrane reformation. Here we combined acute molecular perturbations in live cells with correlative three-dimensional electron tomography or MINFLUX super-resolution microscopy to show that degrading Nup62 during mitosis arrests NPC assembly at an intermediate step with smaller membrane pores and removes the whole central transport channel. Molecular dynamics simulations predicted that 32 copies of the central channel subcomplex, recruited into the previously unoccupied pore center, can self-associate through hydrophobic interactions to occupy and expand pore volume, exerting an outward-pushing force; indeed, disrupting these interactions during NPC assembly blocked pore dilation. Later in mitotic exit, perturbed cells exhibited impaired nuclear import, smaller nuclei and looser NE spacing. Acute inhibition of nuclear import recapitulated these NE defects without affecting NPC assembly. Together, our findings reveal a two-step molecular mechanism linking NPC assembly and NE reformation. First, hydrophobic FG-nucleoporins dilate the assembling nuclear pore by forming the central transport channel, which then allows nuclear-import-driven nuclear expansion, leading to tight, regular NE membrane spacing.
History
DepositionJun 9, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 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 {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'LEICA EM HPM100', ...Details: The value given for _em_high_pressure_freezing.instrument is HPM 010; BalTec. This is not in a list of allowed values {'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM PACT', 'LEICA EM HPM100', 'BAL-TEC HPM 010', 'OTHER', '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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