Cryo-EM structure of ex vivo Sup35 yeast prion and the factors defining prion phenotype

Human prions and amyloids exhibit structural diversity that correlates with different pathology manifestations. Yeast prions represent a convenient model for studying basic properties of prions and their strain diversity. The yeast Sup35 prion has multiple structural variants divided into two groups, “strong” and “weak”, differing in the frequency of fibril fragmentation and resulting nonsense-suppressor phenotype. Yet, the molecular origin of these distinctions remains unclear. Here, we show that the difference in fragmentation between strong- and weak-type amyloid fibrils correlates with their stability, rather than with the efficiency of chaperone binding. The fully protease-resistant part (residues 2–32) of [ PSI+ ] fibril core is a key for the prion phenotype and maintenance, whereas partially resistant part (33–72) stabilizes the “strong” prion structure, and is less important for the weak variant. Using prion purified from yeast, we established the cryo-EM structure of the strong [ PSI+ ] variant, comprising residues 2–64, with 2.7 Å resolution. Using in silico modeling based on this atomic structure, we demonstrate that known anti-prion mutations in Sup35 N-domain decrease the thermodynamic stability of the structure. Comparison of ex vivo Sup35 prion structure with that of Sup35 amyloids formed in vitro shows that the latter differ significantly from the prion structure propagating in yeast cells.