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- EMDB-54136: 2.5 A structure of the E.coli 50S ribosomal subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-54136
Title2.5 A structure of the E.coli 50S ribosomal subunit
Map dataEM-map of 50S ribosomal subunit, control
Sample
  • Complex: E.coli 50S ribosomal subunit
Keywords50S / ribosome / ribosomal subunit
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsCurtis WA / Hruby J / Krueger CR / Barrass SV / Drabbels M / Lorenz UJ
Funding support Switzerland, United States, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMCG-2_213773 Switzerland
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U54AI170752 United States
CitationJournal: Nat Commun / Year: 2026
Title: Ultrathin liquid cells for microsecond time-resolved cryo-EM.
Authors: Wyatt A Curtis / Jakub Wenz / Constantin R Krüger / Sarah V Barrass / Marcel Drabbels / Ulrich J Lorenz /
Abstract: Microsecond time-resolved cryo-electron microscopy promises to significantly advance our understanding of protein function by rendering cryo-electron microscopy (cryo-EM) fast enough to observe ...Microsecond time-resolved cryo-electron microscopy promises to significantly advance our understanding of protein function by rendering cryo-electron microscopy (cryo-EM) fast enough to observe proteins at work. This emerging technique involves flash melting a cryo sample with a laser beam to provide a brief time window during which dynamics are initiated. When the laser is switched off, the sample revitrifies, arresting the proteins in their transient configurations. However, observations have so far been limited to tens of microseconds only, due to the instability of the thin liquid film under laser irradiation. Here, we seal samples between two ultrathin, vapor-deposited silicon dioxide membranes to extend the observation window by an order of magnitude. These membranes not only allow for reconstructions with near-atomic spatial resolution, but can also be used to eliminate preferred particle orientation. We showcase our technology by performing a time-resolved temperature jump experiment on the 50S ribosomal subunit that provides new insights into the conformational landscape of the L1 stalk. Our experiments significantly expand the capabilities of microsecond time-resolved cryo-EM and promise to bridge the gap to the millisecond timescale, which can already be addressed with traditional approaches.
History
DepositionJun 23, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54136.png

Downloads & links

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Map

FileDownload / File: emd_54136.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM-map of 50S ribosomal subunit, control
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 784 pix.
= 569.184 Å		0.73 Å/pix.
x 784 pix.
= 569.184 Å		0.73 Å/pix.
x 784 pix.
= 569.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0639
Minimum - Maximum-0.36144227 - 1.0336965
Average (Standard dev.)-0.00075172883 (±0.025724867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions784784784
Spacing784784784
CellA=B=C: 569.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM Half-map A of 50S ribosomal subunit, control

Fileemd_54136_half_map_1.map
AnnotationEM Half-map A of 50S ribosomal subunit, control
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM Half-map B of 50S ribosomal subunit, control

Fileemd_54136_half_map_2.map
AnnotationEM Half-map B of 50S ribosomal subunit, control
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E.coli 50S ribosomal subunit

EntireName: E.coli 50S ribosomal subunit
Components
  • Complex: E.coli 50S ribosomal subunit

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Supramolecule #1: E.coli 50S ribosomal subunit

SupramoleculeName: E.coli 50S ribosomal subunit / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli K-12 (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
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: OTHER / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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 correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65020
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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