Architectural principles of the ribosomal large subunit revealed by A-helix spatial organization

Abstract

The ribosome, biology’s universal translation apparatus, is one of the deepest molecular imprints of life’s early evolution. Among its structural motifs, the RNA A-helix is the most abundant and fundamental architectural element. Here, we investigate how A-helices collectively shape the three-dimensional organization of the large ribosomal subunit (LSU) across bacteria, archaea, eukaryotes, and mitochondria. By mapping each A-helix onto a centroid-based geometric framework, we identify a conserved peak-centered radial distribution of A-helices that characterizes the spatial organization of LSUs. Applying this approach across diverse ribosomes reveals reproducible architectural states while accommodating lineage-specific structural variation. Notably, mitochondrial LSUs exhibit remodeled radial distributions while retaining the core architectural pattern, consistent with extensive structural adaptation accompanying mitochondrial ribosome evolution. Together, these findings establish the A-helix as a fundamental architectural element of the LSU and provide a generalizable framework for describing ribosomal structure across evolutionary diversity.