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- EMDB-54829: Cryo-EM map of 50S ribosomal subunit following ultrasonic excitation -

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Basic information

Entry
Database: EMDB / ID: EMD-54829
TitleCryo-EM map of 50S ribosomal subunit following ultrasonic excitation
Map dataSharpened consensus map
Sample
  • Complex: 50S ribosomal subunit
Keywords50S ribosomal subunit / preferred orientation / ultrasonic excitation / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWilliams HM / Curtis WA / Haubner M / Hruby J / Drabbels M / Lorenz UJ
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMCG-2_213773 Switzerland
CitationJournal: bioRxiv / Year: 2025
Title: Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification.
Authors: Harry M Williams / Wyatt A Curtis / Michal Haubner / Jakub Hruby / Marcel Drabbels / Ulrich J Lorenz /
Abstract: Preferred particle orientation remains a frequently encountered issue in cryo-electron microscopy that arises when proteins adsorb to the air-water interface in only a limited number of orientations. ...Preferred particle orientation remains a frequently encountered issue in cryo-electron microscopy that arises when proteins adsorb to the air-water interface in only a limited number of orientations. This can significantly increase the data acquisition time required to reach a desired resolution or even make it impossible to obtain a reconstruction altogether. Here, we show that preferred orientation can be overcome by continuously exciting the sample with ultrasonic waves during vitrification. Our experiments suggest that mechanical oscillations induced in the sample support continuously shake proteins loose form the air-water interface, thereby scrambling their orientations. The simple, physical nature of this mechanism should make it applicable to a wide range of proteins. Since our method can be easily implemented in existing vitrification devices, it should find widespread adoption.
History
DepositionAug 20, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54829.png

Downloads & links

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Map

FileDownload / File: emd_54829.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 784 pix.
= 650.72 Å		0.83 Å/pix.
x 784 pix.
= 650.72 Å		0.83 Å/pix.
x 784 pix.
= 650.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.703345 - 1.3172464
Average (Standard dev.)-0.000086613334 (±0.037056975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions784784784
Spacing784784784
CellA=B=C: 650.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54829_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

Fileemd_54829_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_54829_half_map_2.map
AnnotationHalf map B
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: Escherichia coli (E. coli)

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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

Concentration2.6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClSodium chloride
2.0 mMMgCl2Magnesium chloride

Details: 20 mM HEPES buffer, pH 7.5, 100 mM NaCl, 2 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K
Details: The sample was vitrified using our in-house Vitrobot Mark IV modified through the addition of a jetting assembly..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 96000
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

Particle selectionNumber selected: 625311
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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