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- EMDB-60950: In situ cryo-electron tomogram of 4days WT nucleus (PSG at NE) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60950
TitleIn situ cryo-electron tomogram of 4days WT nucleus (PSG at NE)
Map data
Sample
  • Complex: 26S proteasome trimer
Keywordsproteasome / trimer / complex / PSG / paracrystalline / HYDROLASE
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodelectron tomography / cryo EM
AuthorsQu L / Tang X
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
Jung foundation Germany
CitationJournal: To Be Published
Title: Metabolically regulated proteasome supramolecular organization
Authors: Tang X / Qu L / Florian W / Oliver PE / Brenda AS / Baumeister W / Cordula E
History
DepositionJul 25, 2024-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60950.png

Downloads & links

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Map

FileDownload / File: emd_60950.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.28 Å/pix.
x 320 pix.
= 2969.6 Å		9.28 Å/pix.
x 1024 pix.
= 9502.72 Å		9.28 Å/pix.
x 1024 pix.
= 9502.72 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: 9.28 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4516.0 - 4056.0
Average (Standard dev.)473.963840000000005 (±610.115800000000036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024320
Spacing10241024320
CellA: 9502.72 Å / B: 9502.72 Å / C: 2969.5999 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
  • Complex: 26S proteasome trimer

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Supramolecule #1: 26S proteasome trimer

SupramoleculeName: 26S proteasome trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
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 {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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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