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- EMDB-54137: 2.4 A structure of the SiO2-sealed and revitrified (30 us) E.coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-54137
Title2.4 A structure of the SiO2-sealed and revitrified (30 us) E.coli 50S ribosomal subunit
Map dataEM map of the SiO2-sealed and revitrified (30 us) E.coli 50S ribosomal subunit
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: To Be Published
Title: Ultrathin Liquid Cells for Microsecond Time-Resolved Cryo-EM
Authors: Curtis WA / Hruby J / Krueger CR / Barrass SV / Drabbels M / Lorenz UJ
History
DepositionJun 23, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54137.png

Downloads & links

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Map

FileDownload / File: emd_54137.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of the SiO2-sealed and revitrified (30 us) E.coli 50S ribosomal subunit
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: 0.0536
Minimum - Maximum-0.3120091 - 0.9384545
Average (Standard dev.)0.00021950624 (±0.02075183)
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 B of the SiO2-sealed and revitrified...

Fileemd_54137_half_map_1.map
AnnotationEM Half-map B of the SiO2-sealed and revitrified (30 us) E.coli 50S ribosomal subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM Half-map A of the SiO2-sealed and revitrified...

Fileemd_54137_half_map_2.map
AnnotationEM Half-map A of the SiO2-sealed and revitrified (30 us) E.coli 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 : 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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