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- EMDB-44852: YphC-treated 45SYphC particle. Class 2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-44852
TitleYphC-treated 45SYphC particle. Class 2
Map data
Sample
  • Complex: 50S assembly intermediate 45SYphC Class 1
KeywordsRibosome / ribosome assembly / YphC
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsArpin D / Ortega J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nucleic Acids Res / Year: 2025
Title: The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.
Authors: Dominic Arpin / Armando Palacios / Kaustuv Basu / Joaquin Ortega /
Abstract: The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play ...The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial intermediate known as the 45S particle. RbgA and YphC, play pivotal roles in completing the maturation of the functional sites in the 45S particle. In this work, we found that RbgA and YphC can independently bind the 45S particle with high affinity, but when RbgA binds first to the particle, it significantly increases the binding affinity of YphC. Using cryo-electron microscopy, we determined that the changes exerted by RbgA and YphC when binding independently closely resemble those observed when the two factors bind to the 45S particle simultaneously. However, the structural analysis revealed that RbgA binding causes a conformational change that uncovers the binding site for YphC, thus increasing its binding affinity. We concluded that the functional interplay between RbgA and YphC primarily revolves around one factor promoting the binding of the other, rather than the binding of the two factors inducing entirely new conformational changes compared with those induced by the factors individually. These results highlight the synergic mechanism between two essential assembly factors, underscoring the intricate mechanism bacteria use to maximize the efficiency of the ribosome assembly process.
History
DepositionMay 12, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44852.png

Downloads & links

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Map

FileDownload / File: emd_44852.map.gz / Format: CCP4 / Size: 290.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 424 pix.
= 362.52 Å		0.86 Å/pix.
x 424 pix.
= 362.52 Å		0.86 Å/pix.
x 424 pix.
= 362.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.291
Minimum - Maximum-0.22887655 - 1.0341995
Average (Standard dev.)0.0061269826 (±0.050093308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions424424424
Spacing424424424
CellA=B=C: 362.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_44852_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_44852_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44852_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : 50S assembly intermediate 45SYphC Class 1

EntireName: 50S assembly intermediate 45SYphC Class 1
Components
  • Complex: 50S assembly intermediate 45SYphC Class 1

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Supramolecule #1: 50S assembly intermediate 45SYphC Class 1

SupramoleculeName: 50S assembly intermediate 45SYphC Class 1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus subtilis (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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.75 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109492
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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