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- EMDB-51745: Cryo-EM map of revitrified T20S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-51745
TitleCryo-EM map of revitrified T20S proteasome
Map dataMap of revitrified T20S sample
Sample
  • Complex: T20S Proteasome
KeywordsProtein degradation / UNKNOWN FUNCTION
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsStraub MS / Harder OF / Mowry NJ / Barrass SV / Hruby J / Drabbels M / Lorenz UJ
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation213773 Switzerland
CitationJournal: bioRxiv / Year: 2024
Title: Laser Flash Melting Cryo-EM Samples to Overcome Preferred Orientation.
Authors: Monique S Straub / Oliver F Harder / Nathan J Mowry / Sarah V Barrass / Jakub Hruby / Marcel Drabbels / Ulrich J Lorenz /
Abstract: Sample preparation remains a bottleneck for protein structure determination by cryo-electron microscopy. A frequently encountered issue is that proteins adsorb to the air-water interface of the ...Sample preparation remains a bottleneck for protein structure determination by cryo-electron microscopy. A frequently encountered issue is that proteins adsorb to the air-water interface of the sample in a limited number of orientations. This makes it challenging to obtain high-resolution reconstructions or may even cause projects to fail altogether. We have previously observed that laser flash melting and revitrification of cryo samples reduces preferred orientation for large, symmetric particles. Here, we demonstrate that our method can in fact be used to scramble the orientation of proteins of a range of sizes and symmetries. The effect can be enhanced for some proteins by increasing the heating rate during flash melting or by depositing amorphous ice onto the sample prior to revitrification. This also allows us to shed light onto the underlying mechanism. Our experiments establish a set of tools for overcoming preferred orientation that can be easily integrated into existing workflows.
History
DepositionOct 8, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51745.png

Downloads & links

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Map

FileDownload / File: emd_51745.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of revitrified T20S sample
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 333.312 Å		0.65 Å/pix.
x 512 pix.
= 333.312 Å		0.65 Å/pix.
x 512 pix.
= 333.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.173
Minimum - Maximum-0.6091316 - 0.8961932
Average (Standard dev.)0.000028546763 (±0.034569647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 333.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51745_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A to revitrified T20S map

Fileemd_51745_half_map_1.map
AnnotationHalf map A to revitrified T20S map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B to revitrified T20S map

Fileemd_51745_half_map_2.map
AnnotationHalf map B to revitrified T20S 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 : T20S Proteasome

EntireName: T20S Proteasome
Components
  • Complex: T20S Proteasome

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Supramolecule #1: T20S Proteasome

SupramoleculeName: T20S Proteasome / type: complex / ID: 1 / Parent: 0 / Details: conventional sample
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)
Molecular weightTheoretical: 750 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

Concentration3.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
150.0 mMNaClsodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6105 / Average exposure time: 1.3 sec. / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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