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- EMDB-19158: Asymmetric subunit of the Dictyostelium discoideum nuclear pore c... -

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Basic information

Entry
Database: EMDB / ID: EMD-19158
TitleAsymmetric subunit of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress
Map dataAsymmetric subunit - hypoosmotic stress
Sample
  • Complex: Nuclear pore complex
Keywordsnuclear pore complex / NUCLEAR PROTEIN
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 37.0 Å
AuthorsHoffmann PC / Kim H / Obarska-Kosinska A / Kreysing JP / Andino-Frydman E / Cruz-Leon S / Cernikova L / Kosinski J / Turonova B / Hummer G / Beck M
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
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
DepositionDec 14, 2023-
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_19158.png

Downloads & links

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Map

FileDownload / File: emd_19158.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric subunit - hypoosmotic stress
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.7 Å/pix.
x 120 pix.
= 1044.48 Å		8.7 Å/pix.
x 120 pix.
= 1044.48 Å		8.7 Å/pix.
x 120 pix.
= 1044.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.704 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.31688344 - 0.39339218
Average (Standard dev.)0.0006191065 (±0.059057336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 1044.4801 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Nuclear ring segment focused at basket attachment of...

Fileemd_19158_additional_1.map
AnnotationNuclear ring segment focused at basket attachment of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress
Projections & Slices
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Additional map: Cytoplasmic ring segment of the Dictyostelium discoideum nuclear...

Fileemd_19158_additional_2.map
AnnotationCytoplasmic ring segment of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress
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AxesZYX

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Additional map: Lumenal ring segment of the Dictyostelium discoideum nuclear...

Fileemd_19158_additional_3.map
AnnotationLumenal ring segment of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress
Projections & Slices
AxesZYX

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Additional map: Inner ring segment of the Dictyostelium discoideum nuclear...

Fileemd_19158_additional_4.map
AnnotationInner ring segment of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Nuclear ring segment of the Dictyostelium discoideum nuclear...

Fileemd_19158_additional_5.map
AnnotationNuclear ring segment of the Dictyostelium discoideum nuclear pore complex - hypoosmotic stress
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: half map A

Fileemd_19158_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Half map: half map B

Fileemd_19158_half_map_2.map
Annotationhalf map B
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AxesZYX

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Sample components

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Entire : Nuclear pore complex

EntireName: Nuclear pore complex
Components
  • Complex: Nuclear pore complex

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Supramolecule #1: Nuclear pore complex

SupramoleculeName: Nuclear pore complex / type: complex / 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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE
DetailsHypoosmotic stress in distilled water applied for approx. 1 min prior to plunge freezing

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Electron microscopy

MicroscopeFEI TITAN 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 969
ExtractionNumber tomograms: 74 / Number images used: 1192
Final angle assignmentType: NOT APPLICABLE

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