- EMDB-71268: YsxC-GTP treated 44.5SYsxC particles. Class 5. -
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Basic information
Entry
Database: EMDB / ID: EMD-71268
Title
YsxC-GTP treated 44.5SYsxC particles. Class 5.
Map data
YsxC-GMPPNP treated 44.5SYsxC particles. Class 1
Sample
Complex: YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.
RNA: x 1 types
Protein or peptide: x 16 types
RNA: x 1 types
Protein or peptide: x 5 types
Keywords
Ribosome / 44.5S particle / YsxC
Function / homology
Function and homology information
large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm Similarity search - Function
Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / : / Ribosomal protein L18, bacterial-type ...Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / : / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L24 signature. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L24/L26, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14p/L23e / Ribosomal protein L14P Similarity search - Domain/homology
Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 ...Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL29 Similarity search - Component
Biological species
Bacillus subtilis (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 2.8 Å
Journal: Nucleic Acids Res / Year: 2025 Title: YsxC is a placeholder for ribosomal protein uL2 during 50S ribosomal subunit assembly. Authors: Amal Seffouh / Dominic Arpin / Kaustuv Basu / Joaquin Ortega / 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.
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Movie
Controller
Open data
Basic information
Map data
Sample
Keywords
Function and homology information
Bacillus subtilis (bacteria)
Authors
Canada, 1 items 
Citation
Structure visualization
Downloads & links
emd_71268.png
http://ftp.pdbj.org/pub/emdb/structures/EMD-71268
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Sample components
Processing
Electron microscopy
FIELD EMISSION GUN
