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- EMDB-52058: In situ Dictyostelium discoideum 80S ribosome - hypoosmotic stres... -

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Basic information

Entry
Database: EMDB / ID: EMD-52058
TitleIn situ Dictyostelium discoideum 80S ribosome - hypoosmotic stress condition
Map data80S D. discoideum Ribosome hypoosmotic stress
Sample
  • Complex: In situ 80S D. discoideum ribosome in hypoosmotic stress condition
KeywordsDictyostelium discoideum / 80S ribosome / hyperosmotic stress / RIBOSOME
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 5.9 Å
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_52058.png

Downloads & links

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Map

FileDownload / File: emd_52058.map.gz / Format: CCP4 / Size: 127.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation80S D. discoideum Ribosome hypoosmotic stress
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 322 pix.
= 700.672 Å		2.18 Å/pix.
x 322 pix.
= 700.672 Å		2.18 Å/pix.
x 322 pix.
= 700.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.176 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0042
Minimum - Maximum-0.003941626 - 0.014684516
Average (Standard dev.)0.00008005068 (±0.00078155636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions322322322
Spacing322322322
CellA=B=C: 700.67206 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap2

Fileemd_52058_half_map_1.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1

Fileemd_52058_half_map_2.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ 80S D. discoideum ribosome in hypoosmotic stress condition

EntireName: In situ 80S D. discoideum ribosome in hypoosmotic stress condition
Components
  • Complex: In situ 80S D. discoideum ribosome in hypoosmotic stress condition

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Supramolecule #1: In situ 80S D. discoideum ribosome in hypoosmotic stress condition

SupramoleculeName: In situ 80S D. discoideum ribosome in hypoosmotic stress condition
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

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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 22999
ExtractionNumber tomograms: 98 / Number images used: 98000
Final angle assignmentType: OTHER

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