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- EMDB-16180: 20S Proteasome subtomogram average from Singleshot acquisition on... -

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Basic information

Entry
Database: EMDB / ID: EMD-16180
Title20S Proteasome subtomogram average from Singleshot acquisition on mixed Riobsome-Proteasome sample
Map dataMultishot tomography Riboprot 20S bin1 tomoman-stopgap
Sample
  • Complex: T. acidophilum 20S Proteasome
Keywords20s Proteasome / PROTEIN BINDING
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsubtomogram averaging / cryo EM / Resolution: 4.7 Å
AuthorsKhavnekar S / Plitzko JM / Erdmann PSE
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J Struct Biol / Year: 2023
Title: Multishot tomography for high-resolution in situ subtomogram averaging.
Authors: S Khavnekar / W Wan / P Majumder / W Wietrzynski / P S Erdmann / J M Plitzko /
Abstract: Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can ...Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.
History
DepositionNov 21, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16180.png

Downloads & links

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Map

FileDownload / File: emd_16180.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMultishot tomography Riboprot 20S bin1 tomoman-stopgap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.636
Minimum - Maximum-0.8913874 - 1.7568465
Average (Standard dev.)0.00046464807 (±0.14207241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16180_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Multishot tomography Riboprot 20S bin1 tomoman-stopgap

Fileemd_16180_half_map_1.map
AnnotationMultishot tomography Riboprot 20S bin1 tomoman-stopgap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Multishot tomography Riboprot 20S bin1 tomoman-stopgap

Fileemd_16180_half_map_2.map
AnnotationMultishot tomography Riboprot 20S bin1 tomoman-stopgap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T. acidophilum 20S Proteasome

EntireName: T. acidophilum 20S Proteasome
Components
  • Complex: T. acidophilum 20S Proteasome

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Supramolecule #1: T. acidophilum 20S Proteasome

SupramoleculeName: T. acidophilum 20S Proteasome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightTheoretical: 750 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP / Number subtomograms used: 5000
ExtractionNumber tomograms: 25 / Number images used: 5000 / Software - Name: STOPGAP (ver. 0.7)
Final 3D classificationSoftware - Name: STOPGAP
Final angle assignmentType: OTHER / Software - Name: STOPGAP

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