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- EMDB-49493: 20S proteasome complex from D. discoideum -

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Basic information

Entry
Database: EMDB / ID: EMD-49493
Title20S proteasome complex from D. discoideum
Map data
Sample
  • Complex: 20S proteasome from D. discoideum
Keywordsproteostasis / CYTOSOLIC PROTEIN
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.52 Å
AuthorsHoogerbrugge G / Marcotte EM / Keatinge-Clay AT
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106112 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122480 United States
Department of Defense (DOD, United States)W911NF-12-1-0390 United States
Welch FoundationF-1712 United States
Welch FoundationF-1515 United States
CitationJournal: To Be Published
Title: Serendipity and the slime mold: a visual survey of megadalton protein assemblies reveals the structure of the polyketide synthase Pks16
Authors: Hoogerbrugge G / Keatinge-Clay AT / Marcotte EM
History
DepositionFeb 27, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49493.png

Downloads & links

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Map

FileDownload / File: emd_49493.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 360 pix.
= 477.696 Å		1.33 Å/pix.
x 360 pix.
= 477.696 Å		1.33 Å/pix.
x 360 pix.
= 477.696 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.269
Minimum - Maximum-0.41439396 - 0.68207186
Average (Standard dev.)0.0000014449032 (±0.034783788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 477.696 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49493_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49493_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49493_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 20S proteasome from D. discoideum

EntireName: 20S proteasome from D. discoideum
Components
  • Complex: 20S proteasome from D. discoideum

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Supramolecule #1: 20S proteasome from D. discoideum

SupramoleculeName: 20S proteasome from D. discoideum / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 549
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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