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- EMDB-60961: 26S proteasome trimer close to nuclear envelope -

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Basic information

Entry
Database: EMDB / ID: EMD-60961
Title26S proteasome trimer close to nuclear envelope
Map data
Sample
  • Complex: 26S proteasome trimer
Keywordsproteasome / trimer / complex / PSG / paracrystalline / HYDROLASE
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 27.4 Å
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_60961.png

Downloads & links

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Map

FileDownload / File: emd_60961.map.gz / Format: CCP4 / Size: 3.4 MB / 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 96 pix.
= 890.88 Å		9.28 Å/pix.
x 96 pix.
= 890.88 Å		9.28 Å/pix.
x 96 pix.
= 890.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.4325538 - 1.9887737
Average (Standard dev.)-0.00035192218 (±0.21472548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 890.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60961_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60961_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60961_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.8 / Details: YPD buffer
VitrificationCryogen name: ETHANE-PROPANE

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 27.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 201
ExtractionNumber tomograms: 73 / Number images used: 1700
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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