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- EMDB-66736: In vitro structure of bacterial 50S ribosomes -

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Basic information

Entry
Database: EMDB / ID: EMD-66736
TitleIn vitro structure of bacterial 50S ribosomes
Map databest consensus
Sample
  • Complex: In vitro E. coli ribosome sample
Keywordsribosomes / 50S / in vitro / bacterial / RIBOSOME
Function / homology
Function and homology information


stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / cytosolic ribosome assembly / ribosome assembly / response to reactive oxygen species / assembly of large subunit precursor of preribosome / regulation of cell growth / response to radiation / DNA-templated transcription termination / mRNA 5'-UTR binding / large ribosomal subunit / transferase activity / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. ...Ribosomal protein L11, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / : / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28/L24 superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L28 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 ...Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWu F / Naschberger A
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Commun Biol / Year: 2025
Title: In situ structure of bacterial 50S ribosomes at 3.0 Å resolution from vitreous sections.
Authors: Ashraf Al-Amoudi / Rozbeh Baradaran / Xukun Yuan / Fēi Wú / Andreas Naschberger /
Abstract: In situ high-resolution structure determination is limited to samples thin enough to be penetrated by the electron beam during imaging. Sample thinning involves focused ion or plasma beam milling of ...In situ high-resolution structure determination is limited to samples thin enough to be penetrated by the electron beam during imaging. Sample thinning involves focused ion or plasma beam milling of specimens to produce lamellae with thicknesses as low as 100-150 nm. However, surface damage caused by the milling process can extend 30-60 nm deep, restricting the usable lamella thickness. This imposes limitations on single-particle analysis of macromolecular complexes due to elevated structural noise, which cannot be avoided in situ because of the dense cellular environment. Alternative methods capable of producing thinner samples are needed to reduce background. Here, we demonstrate that high-resolution structures at side-chain level, free of orientation bias, can be obtained from vitreous sections prepared by cryo-ultramicrotomy, both in vitro and in situ. We optimized the method to produce sections as thin as ~40 nm, free from significant surface damage. Using this approach, we determined the structure of the 50S ribosomal subunit in vitro at 2.8 Å and in situ at 3 Å from bacterial cells. These results lay the foundation for future in situ studies of smaller complexes using CEMOVIS, as well as for methodological advances aimed at achieving compression-free sectioning.
History
DepositionOct 26, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66736.png

Downloads & links

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Map

FileDownload / File: emd_66736.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbest consensus
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 500 pix.
= 364.5 Å		0.73 Å/pix.
x 500 pix.
= 364.5 Å		0.73 Å/pix.
x 500 pix.
= 364.5 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
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Contour LevelBy AUTHOR: 0.0032
Minimum - Maximum-0.02273245 - 0.030624162
Average (Standard dev.)-0.00021658186 (±0.0014159984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 364.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66736_msk_1.map
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Additional map: post

Fileemd_66736_additional_1.map
Annotationpost
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Half map: half

Fileemd_66736_half_map_1.map
Annotationhalf
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Half map: half

Fileemd_66736_half_map_2.map
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Sample components

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Entire : In vitro E. coli ribosome sample

EntireName: In vitro E. coli ribosome sample
Components
  • Complex: In vitro E. coli ribosome sample

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Supramolecule #1: In vitro E. coli ribosome sample

SupramoleculeName: In vitro E. coli ribosome sample / 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

BufferpH: 7.7
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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 81081
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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