Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly.
Journal, issue, pages	Nucleic Acids Res, Vol. 53, Issue 20, Year 2025
Publish date	Oct 28, 2025
Authors	Amal Seffouh / Dominic Arpin / Kaustuv Basu / Joaquin Ortega /
PubMed Abstract	The maturation of the functional core of the 50S ribosomal subunit in Bacillus subtilis is assisted by assembly factors that enhance the efficiency of the process. Two essential assembly factors, the ...The maturation of the functional core of the 50S ribosomal subunit in Bacillus subtilis is assisted by assembly factors that enhance the efficiency of the process. Two essential assembly factors, the GTPases RbgA and YphC, bind at or near the functional sites of the 50S subunit to promote the folding of ribosomal RNA helices that play key functional roles. YsxC is another GTPase involved in the maturation of the 50S subunit, whose function remains unknown. We demonstrate that YsxC aids 50S assembly through a drastically different mechanism. YsxC binds in the body of the 44.5S large ribosome assembly intermediate, occupying the site where uL2 binds and controls the timing in the folding of rRNA helices forming the binding site for uL2. It creates a "primordial" binding site that includes six out of the eleven rRNA helices forming the uL2 mature binding site. Once YsxC is released, uL2 binds to this "primordial" binding site, and the remaining helices that stabilize uL2 fold, and the entire region adopts the mature conformation. This role of YsxC functioning as a placeholder factor for ribosomal protein uL2 provides the first example of such a factor's involvement in the ribosome assembly process in bacteria.
External links	Nucleic Acids Res / PubMed:41148149 / PubMed Central
Methods	EM (single particle)
Resolution	2.5 - 3.4 Å
Structure data	EMDB-71096: 44.5SYsxC particles isolated from YsxC-depleted cells. Class 1. Method: EM (single particle) / Resolution: 2.9 Å EMDB-71098: 44.5SYsxC particles isolated from YsxC-depleted cells. Class 3. Method: EM (single particle) / Resolution: 2.9 Å EMDB-71099: 44.5SYsxC particles isolated from YsxC-depleted cells. Class 2. Method: EM (single particle) / Resolution: 2.7 Å EMDB-71102: YsxC-GMPPNP treated 44.5SYsxC particles. Class 2. Method: EM (single particle) / Resolution: 2.9 Å EMDB-71103: YsxC-GMPPNP treated 44.5SYsxC particles. Class 3. Method: EM (single particle) / Resolution: 3.0 Å EMDB-71104: YsxC-GTP treated 44.5SYsxC particles. Class 1. Method: EM (single particle) / Resolution: 3.0 Å EMDB-71105: YsxC-GTP treated 44.5SYsxC particles. Class 2. Method: EM (single particle) / Resolution: 2.9 Å EMDB-71106: YsxC-GTP treated 44.5SYsxC particles. Class 3 Method: EM (single particle) / Resolution: 2.9 Å EMDB-71107: YsxC-GTP treated 44.5SYsxC particles. Class 4. Method: EM (single particle) / Resolution: 2.8 Å EMDB-71109: 44.5SYsxC particles after incubation at 37 oC for 15 min. Class 1 Method: EM (single particle) / Resolution: 3.4 Å EMDB-71110: 44.5SYsxC particles after incubation at 37 oC for 15 min. Class 2. Method: EM (single particle) / Resolution: 3.1 Å EMDB-71111: 44.5SYsxC particles after incubation at 37 oC for 15 min. Class 3. Method: EM (single particle) / Resolution: 2.9 Å 71238 9p38 EMDB-71238, PDB-9p38: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1. Method: EM (single particle) / Resolution: 2.5 Å 71268 9p4i EMDB-71268, PDB-9p4i: YsxC-GTP treated 44.5SYsxC particles. Class 5. Method: EM (single particle) / Resolution: 2.8 Å
Source	bacillus subtilis (bacteria)
Keywords	RIBOSOME / 44.5S particle / YsxC