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- EMDB-55124: Structure of 70S ribosome-apramycin complex with tRNAs in hybrid ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55124
TitleStructure of 70S ribosome-apramycin complex with tRNAs in hybrid state 1 (H1)
Map data
Sample
  • Complex: Structure of the 70S ribosome complex with tRNAs in classic state (C)
KeywordsEF-G / robosome / 70S / apramycin / translocation / RIBOSOME / mutation
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsGhosh Dastidar N / Freyer N / Petrychenko V / Schwarzer AC / Peng BZ / Samatova E / Kothe C / Schmidt M / Peske F / Politi A ...Ghosh Dastidar N / Freyer N / Petrychenko V / Schwarzer AC / Peng BZ / Samatova E / Kothe C / Schmidt M / Peske F / Politi A / Urlaub H / Fischer N / Rodnina MV / Wohlgemuth I
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Leibniz Prize (to M.V.R.) & SFB 860 Germany
Max Planck Society Germany
CitationJournal: To Be Published / Year: 2025
Title: Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides
Authors: Ghosh Dastidar N / Freyer N / Petrychenko V / Schwarzer AC / Peng BZ / Samatova E / Kothe C / Schmidt M / Peske F / Politi A / Urlaub H / Fischer N / Rodnina MV / Wohlgemuth I
History
DepositionSep 23, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55124.png

Downloads & links

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Map

FileDownload / File: emd_55124.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.16 Å/pix.
x 288 pix.
= 334.08 Å		1.16 Å/pix.
x 288 pix.
= 334.08 Å		1.16 Å/pix.
x 288 pix.
= 334.08 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25
Minimum - Maximum-4.90243 - 11.725702999999999
Average (Standard dev.)0.000000000005665 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 334.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55124_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_55124_additional_1.map
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Half map: #1

Fileemd_55124_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_55124_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Structure of the 70S ribosome complex with tRNAs in classic state (C)

EntireName: Structure of the 70S ribosome complex with tRNAs in classic state (C)
Components
  • Complex: Structure of the 70S ribosome complex with tRNAs in classic state (C)

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Supramolecule #1: Structure of the 70S ribosome complex with tRNAs in classic state (C)

SupramoleculeName: Structure of the 70S ribosome complex with tRNAs in classic state (C)
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
Details: 50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1753901
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

10906

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 10677
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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