One of the mysteries in prion research is the structure of the infectious form of mammalian prion protein PrP(Sc). Here we used mass spectrometry analysis of hydrogen-deuterium exchange to examine brain-derived PrP(Sc). Our data indicate that, contrary to popular models, prion-protein conversion involves refolding of the entire region from residue ~80-90 to the C-terminus, which in PrP(Sc) consists of β-strands and relatively short turns and/or loops, with no native α-helices present.