Prion diseases are associated with the conversion of the α-helix rich prion protein (PrP
C
) into a β-structure-rich insoluble conformer (PrP
Sc
) that is thought to be infectious. The mechanism for the PrP
C
→ PrP
Sc
conversion and its relationship with the pathological effects of prion diseases are poorly understood, partly because of our limited knowledge of the structure of PrP
Sc
. In particular, the way in which mutations in the
PRNP
gene yield variants that confer different susceptibilities to disease needs to be clarified. We report here the 2.5-Å-resolution crystal structures of three scrapie-susceptibility ovine PrP variants complexed with an antibody that binds to PrP
C
and to PrP
Sc
; they identify two important features of the PrP
C
→ PrP
Sc
conversion. First, the epitope of the antibody mainly consists of the last two turns of ovine PrP second α-helix. We show that this is a structural invariant in the PrP
C
→ PrP
Sc
conversion; taken together with biochemical data, this leads to a model of the conformational change in which the two PrP
C
C-terminal α-helices are conserved in PrP
Sc
, whereas secondary structure changes are located in the N-terminal α-helix. Second, comparison of the structures of scrapie-sensitivity variants defines local changes in distant parts of the protein that account for the observed differences of PrP
C
stability, resistant variants being destabilized compared with sensitive ones. Additive contributions of these sensitivity-modulating mutations to resistance suggest a possible causal relationship between scrapie resistance and lowered stability of the PrP protein.