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- EMDB-67197: E.coli delta lepA 30S ribosomal subunit class C -

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Basic information

Entry
Database: EMDB / ID: EMD-67197
TitleE.coli delta lepA 30S ribosomal subunit class C
Map data
Sample
  • Complex: E.coli delta lepA 30S ribosomal subunit class C
Keywords30S subunit maturation / LepA / cryo-EM / ribosome assembly / RIBOSOME
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsKravchenko OV / Maksimova EM / Baymukhametov TN / Stolboushkina EA
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2026
Title: The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly.
Authors: Olesya Kravchenko / Elena Maksimova / Timur Baymukhametov / Irina Eliseeva / Elena Stolboushkina /
Abstract: The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal ...The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an strain with a deleted gene. The cryo-EM maps for ∆ 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3' end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of Δ 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3' domain of the 30S subunit during ribosome assembly.
History
DepositionNov 22, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67197.png

Downloads & links

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Map

FileDownload / File: emd_67197.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 440 pix.
= 379.72 Å		0.86 Å/pix.
x 440 pix.
= 379.72 Å		0.86 Å/pix.
x 440 pix.
= 379.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.863 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.42657757 - 1.9746296
Average (Standard dev.)-0.0002254261 (±0.038146816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 379.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67197_msk_1.map
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Additional map: #1

Fileemd_67197_additional_1.map
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Half map: #1

Fileemd_67197_half_map_1.map
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Half map: #2

Fileemd_67197_half_map_2.map
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Sample components

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Entire : E.coli delta lepA 30S ribosomal subunit class C

EntireName: E.coli delta lepA 30S ribosomal subunit class C
Components
  • Complex: E.coli delta lepA 30S ribosomal subunit class C

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Supramolecule #1: E.coli delta lepA 30S ribosomal subunit class C

SupramoleculeName: E.coli delta lepA 30S ribosomal subunit class C / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.1) / Number images used: 771814
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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