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- EMDB-53039: Structure of 30S ribosomes determined by cryoEM prepared with foa... -

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Basic information

Entry
Database: EMDB / ID: EMD-53039
TitleStructure of 30S ribosomes determined by cryoEM prepared with foam film vitrification method
Map data
Sample
  • Complex: 30S ribosome from E. coli
Keywords30S ribosomes / small ribosomal subunit / cryo-EM structure / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsZhang Y / Nandy B / Sader K / Russo CJ / Lowe J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)BSF2-08 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Foam film vitrification for cryo-EM.
Authors: Yue Zhang / Biplob Nandy / Kasim Sader / Christopher J Russo / Jan Löwe /
Abstract: Electron cryomicroscopy (cryo-EM) has revolutionised structural biology, enhancing applicability, size limits and speed. Despite these successes, cryo-EM sample preparation remains a major bottleneck ...Electron cryomicroscopy (cryo-EM) has revolutionised structural biology, enhancing applicability, size limits and speed. Despite these successes, cryo-EM sample preparation remains a major bottleneck for routinely achieving high-resolution structures through single particle analysis. Challenges such as inconsistent ice thicknesses, air-water interface interactions and preferred particle orientation persist. Here, we introduce a blot-free vitrification method that uses free-standing surfactant-stabilised foam films to address some of these issues. The method achieves uniform ice thicknesses, enables thickness control of the foam film prior to vitrification, and for some specimens enhances orientation distribution efficiency. Furthermore, it reduces particle adsorption to carbon foil on the specimen support. The method simplifies cryo-EM specimen preparation, offering improved control over ice thickness and particle orientation, to help streamline and accelerate structure determination.
History
DepositionMar 7, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53039.png

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Map

FileDownload / File: emd_53039.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 432 pix.
= 355.968 Å		0.82 Å/pix.
x 432 pix.
= 355.968 Å		0.82 Å/pix.
x 432 pix.
= 355.968 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
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Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.019877601 - 0.032775443
Average (Standard dev.)0.000009430852 (±0.00082095526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 355.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53039_msk_1.map
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Half map: #1

Fileemd_53039_half_map_1.map
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Half map: #2

Fileemd_53039_half_map_2.map
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Sample components

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Entire : 30S ribosome from E. coli

EntireName: 30S ribosome from E. coli
Components
  • Complex: 30S ribosome from E. coli

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Supramolecule #1: 30S ribosome from E. coli

SupramoleculeName: 30S ribosome from E. coli / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 787 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

Concentration3.4 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 18 K / Instrument: HOMEMADE PLUNGER
Details: The sample is prepared with the foam film vitrification method..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9644 / Average exposure time: 2.6 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.4 µm / Calibrated defocus min: 0.6 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 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: 778822
CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39546
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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