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- EMDB-52054: Cryo-tomogram of Dictyostelium discoideum cell - hyperosmotic str... -

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Basic information

Entry
Database: EMDB / ID: EMD-52054
TitleCryo-tomogram of Dictyostelium discoideum cell - hyperosmotic stress condition (+0.4 M sorbitol), related to Figure 1b
Map datacryo-tomogram D.discoideum - hyper OS, tomogram 029
Sample
  • Cell: Cryo-tomogram of cryo-FIB milled D. discoideum cell under hyperosmotic stress
Keywordsin situ tomogram / nuclear pore complex / hyperosmotic stress / NUCLEAR PROTEIN
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodelectron tomography / cryo EM
AuthorsHoffmann PC / Kim H / Obarska-Kosinska A / Kreysing JP / Andino-Frydman E / Cruz-Leon S / Margiotta E / Cernikova L / Kosinski J / Turonova B ...Hoffmann PC / Kim H / Obarska-Kosinska A / Kreysing JP / Andino-Frydman E / Cruz-Leon S / Margiotta E / Cernikova L / Kosinski J / Turonova B / Hummer G / Beck M
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)101054823European Union
European Molecular Biology Organization (EMBO)ALTF 33-2021European Union
CitationJournal: Mol Cell / Year: 2025
Title: Nuclear pore permeability and fluid flow are modulated by its dilation state.
Authors: Patrick C Hoffmann / Hyuntae Kim / Agnieszka Obarska-Kosinska / Jan Philipp Kreysing / Eli Andino-Frydman / Sergio Cruz-León / Erica Margiotta / Lenka Cernikova / Jan Kosinski / Beata ...Authors: Patrick C Hoffmann / Hyuntae Kim / Agnieszka Obarska-Kosinska / Jan Philipp Kreysing / Eli Andino-Frydman / Sergio Cruz-León / Erica Margiotta / Lenka Cernikova / Jan Kosinski / Beata Turoňová / Gerhard Hummer / Martin Beck /
Abstract: Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in ...Changing environmental conditions necessitate rapid adaptation of cytoplasmic and nuclear volumes. We use the slime mold Dictyostelium discoideum, known for its ability to tolerate extreme changes in osmolarity, to assess which role nuclear pore complexes (NPCs) play in achieving nuclear volume adaptation and relieving mechanical stress. We capitalize on the unique properties of D. discoideum to quantify fluid flow across NPCs. D. discoideum has an elaborate NPC structure in situ. Its dilation state affects NPC permeability for nucleocytosolic flow. Based on mathematical concepts adapted from hydrodynamics, we conceptualize this phenomenon as porous flow across NPCs, which is distinct from canonically characterized modes of nucleocytoplasmic transport because of its dependence on pressure. Viral NPC blockage decreased nucleocytosolic flow. Our results may be relevant for any biological conditions that entail rapid nuclear size adaptation, including metastasizing cancer cells, migrating cells, or differentiating tissues.
History
DepositionNov 11, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52054.png

Downloads & links

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Map

FileDownload / File: emd_52054.map.gz / Format: CCP4 / Size: 378.1 MB / Type: IMAGE STORED AS SIGNED BYTE
Annotationcryo-tomogram D.discoideum - hyper OS, tomogram 029
Voxel sizeX=Y=Z: 8.704 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)9.64012 (±22.839445000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9897-115
Dimensions14401016271
Spacing10161440271
CellA: 8843.265 Å / B: 12533.761 Å / C: 2358.7842 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-tomogram of cryo-FIB milled D. discoideum cell under hyperos...

EntireName: Cryo-tomogram of cryo-FIB milled D. discoideum cell under hyperosmotic stress
Components
  • Cell: Cryo-tomogram of cryo-FIB milled D. discoideum cell under hyperosmotic stress

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Supramolecule #1: Cryo-tomogram of cryo-FIB milled D. discoideum cell under hyperos...

SupramoleculeName: Cryo-tomogram of cryo-FIB milled D. discoideum cell under hyperosmotic stress
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE
DetailsHyperosmotic stress in HL5 + 0.4M sorbitol applied for approx. 1 min prior to plunge freezing
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 91 K / Focused ion beam - Initial thickness: 5000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: for details please see material and methods section of the paper. The value given for _em_focused_ion_beam.instrument is TFS Aquilos2 cryo-FIB/SEM. This is not in a list ...Focused ion beam - Details: for details please see material and methods section of the paper. The value given for _em_focused_ion_beam.instrument is TFS Aquilos2 cryo-FIB/SEM. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.3 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 reconstructionDetails: alignment with patch-tracking and reconstruction in etomo, bin4 backprojection with SIRT-like filtering
Number images used: 59

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