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- EMDB-64636: In situ cryo-electron tomogram of 4days rpn9deltaN nucleus -

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Basic information

Entry
Database: EMDB / ID: EMD-64636
TitleIn situ cryo-electron tomogram of 4days rpn9deltaN nucleus
Map data
Sample
  • Cell: 26S proteasome trimer
Keywordsproteasome / trimer / complex / PSG / paracrystalline / HYDROLASE
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodelectron tomography / cryo EM
AuthorsQu L / Tang XM / Baumeister W
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
Jung Foundation Germany
CitationJournal: Cell / Year: 2026
Title: Metabolically regulated proteasome supramolecular organization in situ.
Authors: Xiaomeng Tang / Lu Qu / Florian Wilfling / Florian Beck / Oliver P Ernst / Brenda A Schulman / Wolfgang Baumeister / Cordula Enenkel /
Abstract: Many proteins localize in membraneless organelles. However, understanding the steps along membraneless organelle formation-and the structural impact on granule constituents-has been hindered by ...Many proteins localize in membraneless organelles. However, understanding the steps along membraneless organelle formation-and the structural impact on granule constituents-has been hindered by limited resolution of intracellular data. We address these challenges through in situ cryo-electron tomography (cryo-ET) along with formation of yeast proteasome storage granules (PSGs). During the transition from proliferation to quiescence, doubly capped 26S proteasomes arrested in an inactive state arrange into ∼7.5 MDa trimeric units, dispersed in the nucleoplasm and congregated along the nuclear envelope near the nuclear pore. 9-Å-resolution cryo-ET structures reveal that cytoplasmic PSGs formed in various energy-limiting conditions are paracrystalline arrays of bundled fibers, assembled from stacking of proteasome trimers. The paracrystalline arrangement maintains a pool of fully assembled inactive 26S proteasomes that are released in energy-rich conditions. Overall, our data reveal structural steps along the assembly of an intracellular membraneless organelle in situ and quinary structure formation controlling a major eukaryotic regulatory machine.
History
DepositionMay 16, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64636.png

Downloads & links

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Map

FileDownload / File: emd_64636.map.gz / Format: CCP4 / Size: 525.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.96 Å/pix.
x 320 pix.
= 4467.2 Å		13.96 Å/pix.
x 928 pix.
= 12954.88 Å		13.96 Å/pix.
x 928 pix.
= 12954.88 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: 13.96 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-9909.0 - 8565.0
Average (Standard dev.)803.560899999999947 (±880.379940000000033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928320
Spacing928928320
CellA: 12954.88 Å / B: 12954.88 Å / C: 4467.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 26S proteasome trimer

EntireName: 26S proteasome trimer
Components
  • Cell: 26S proteasome trimer

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Supramolecule #1: 26S proteasome trimer

SupramoleculeName: 26S proteasome trimer / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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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: 6.8 / Details: YPD buffer
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 5 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 500 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 37
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

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