The structural history of Eukarya.

A proteome-scale structural similarity phylogeny of 1542 eukaryotic species (SHE) reveals a bipartite evolutionary model with a Strict Core and a plastic Operational Engine.

• Why it matters: Sequence markers have left the global evolutionary landscape of protein architecture largely unexplored, limiting how well structural evolution can inform eukaryotic phylogeny and function.
• What they did: SHE builds an all-vs-all structural similarity-derived phylogeny from proteome-level comparisons totaling nearly 300 trillion pairwise protein alignments across 1542 eukaryotic species.
• The result: The analysis supports a Strict Core dominated by cytoskeletal architecture and an Operational Engine centered on translational machinery, enables proteome-wide functional annotation, and provides quantitative model-organism selection.