|Entry||Database: EMDB / ID: 8274|
|Title||YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase-associated region, and functional core of the 50S ribosomal subunit|
|Map data||50S ribosomal subunit assembly intermediate obtained upon depletion of YsxC protein in Bacillus subtilis|
|Sample||Assembly intermediate of the 50S subunit, Class I:|
|Source||Bacillus subtilis (bacteria)|
|Method||single particle reconstruction / cryo EM / 5.8 Å resolution|
|Authors||Ni X / Davis JH / Jain N / Razi A / Benlekbir S / McArthur AG / Rubinstein JR / Britton RA / Williamson JR / Ortega J|
|Citation||Journal: Nucleic Acids Res. / Year: 2016|
Title: YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit.
Authors: Xiaodan Ni / Joseph H Davis / Nikhil Jain / Aida Razi / Samir Benlekbir / Andrew G McArthur / John L Rubinstein / Robert A Britton / James R Williamson / Joaquin Ortega
Abstract: YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we ...YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45SYphC and 44.5SYsxC particles. Quantitative mass spectrometry analysis and the 5-6 Å resolution cryo-EM maps of the 45SYphC and 44.5SYsxC particles revealed that the two GTPases participate in the maturation of the central protuberance, GTPase associated region and key RNA helices in the A, P and E functional sites of the 50S subunit. We observed that YphC and YsxC bind specifically to the two immature particles, suggesting that they represent either on-pathway intermediates or that their structure has not significantly diverged from that of the actual substrate. These results describe the nature of these immature particles, a widely used tool to study the assembly process of the ribosome. They also provide the first insights into the function of YphC and YsxC in 50S subunit assembly and are consistent with this process occurring through multiple parallel pathways, as it has been described for the 30S subunit.
|Date||Deposition: Jun 30, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: Aug 17, 2016 / Last update: Oct 12, 2016|
|Structure viewer||EM map: |
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|File||emd_8274.map.gz (map file in CCP4 format, 55297 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.45 Å|
CCP4 map header:
-Entire Assembly intermediate of the 50S subunit, Class I
|Entire||Name: Assembly intermediate of the 50S subunit, Class I / Details: Obtained upon depletion of YsxC protein / Number of components: 1|
-Component #1: protein, Assembly intermediate of the 50S subunit, Class I
|Protein||Name: Assembly intermediate of the 50S subunit, Class I / Details: Obtained upon depletion of YsxC protein / Recombinant expression: No|
|Source||Species: Bacillus subtilis (bacteria)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE|
Details: Plunged into liquid ethane (FEI VITROBOT MARK III).
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
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