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- EMDB-15769: A gap across the beta rings in 20S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-15769
TitleA gap across the beta rings in 20S proteasome
Map data20S proteasome Gap across beta rings Sharpened map
Sample
  • Complex: Untreated 20S proteasome
Keywords20S proteasome / Degradation / Proteolysis / HYDROLASE
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSzenkier N / Arie M / Matzov D / Sertchook R / Carmeli R / Cascio P / Stanhill A / Shalev Benami M / Navon A
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: To be published
Title: Bovine 20S proteasome, in its way to dissasembly
Authors: Szenkier N / Arie M / Matzov D / Sertchook R / Carmeli R / Cascio P / Stanhill A / Shalev Benami M / Navon A
History
DepositionSep 6, 2022-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15769.png

Downloads & links

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Map

FileDownload / File: emd_15769.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation20S proteasome Gap across beta rings Sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 440 pix.
= 378.4 Å		0.86 Å/pix.
x 440 pix.
= 378.4 Å		0.86 Å/pix.
x 440 pix.
= 378.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0791495 - 0.17635697
Average (Standard dev.)-0.00014310681 (±0.00865706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 378.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 20S proteasome Gap across beta rings Unsharpened map

Fileemd_15769_additional_1.map
Annotation20S proteasome Gap across beta rings Unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_15769_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_15769_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Untreated 20S proteasome

EntireName: Untreated 20S proteasome
Components
  • Complex: Untreated 20S proteasome

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Supramolecule #1: Untreated 20S proteasome

SupramoleculeName: Untreated 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Bos taurus (cattle) / Organ: Dyaphragma muscle
Molecular weightTheoretical: 700 KDa

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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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76516
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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