|Entry||Database: EMDB / ID: 8276|
|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||Assembly intermediate of the 50S subunit|
|Sample||Assembly intermediate of the 50S ribosomal subunit:|
|Source||Bacillus subtilis (bacteria)|
|Method||single particle reconstruction / cryo EM / 6.5 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: |
Downloads & links
|File||emd_8276.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 ribosomal subunit
|Entire||Name: Assembly intermediate of the 50S ribosomal subunit / Details: Obtained upon depletion of YphC protein / Number of components: 1|
-Component #1: protein, Assembly intermediate of the 50S ribosomal subunit
|Protein||Name: Assembly intermediate of the 50S ribosomal subunit / Details: Obtained upon depletion of YphC 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)|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi