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- EMDB-51751: Cryo-EM map of shaped pulse revitrified 50S ribosomal subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-51751
TitleCryo-EM map of shaped pulse revitrified 50S ribosomal subunit
Map dataMap of shaped pulse revitrified 50S ribosomal subunit
Sample
  • Complex: 50S ribosomal subunit
Keywords50S subunit / RIBOSOME
Biological speciesE.coli K12 BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_51751.png

Downloads & links

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Map

FileDownload / File: emd_51751.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of shaped pulse revitrified 50S ribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 784 pix.
= 510.384 Å		0.65 Å/pix.
x 784 pix.
= 510.384 Å		0.65 Å/pix.
x 784 pix.
= 510.384 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: 0.071
Minimum - Maximum-0.3532764 - 0.70608616
Average (Standard dev.)-0.00025912304 (±0.02358428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions784784784
Spacing784784784
CellA=B=C: 510.38403 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51751_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 shaped pulse revitrified 50S ribosomal subunit

Fileemd_51751_half_map_1.map
AnnotationHalf map A to shaped pulse revitrified 50S ribosomal subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B to shaped pulse revitrified 50S ribosomal subunit

Fileemd_51751_half_map_2.map
AnnotationHalf map B to shaped pulse revitrified 50S ribosomal subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 50S ribosomal subunit

EntireName: 50S ribosomal subunit
Components
  • Complex: 50S ribosomal subunit

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Supramolecule #1: 50S ribosomal subunit

SupramoleculeName: 50S ribosomal subunit / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: E.coli K12 BW25113 (bacteria)

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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: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClSodium Chloride
2.0 mMMgCl2Magnesium 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
Details40 OD260/ml

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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: 7725 / Average electron dose: 63.0 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: 1.6 µm / Nominal defocus min: 0.4 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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