Proteolytically active calpain-3/p94 is clearly vital for normal muscle function, since its absence leads to limb girdle muscular dystrophy 2A, but its function and regulatory control are poorly understood. Here we use single muscle fibers, individually skinned by microdissection, to investigate the diffusibility and autolytic activation of calpain-3 in situ. Virtually all calpain-3 present in mature muscle fibers is tightly bound in the vicinity of the titin N2A line and triad junctions and remains so irrespective of fiber stretching or raised [Ca(2+)]. Most calpain-3 is evidently bound within the contractile filament lattice, because (i) its slow diffusional loss is slowed further by locking myosin and actin into rigor and (ii) detergent dispersion of membranes causes rapid washout of most ryanodine receptors and sarcoplasmic reticulum Ca(2+) pumps with little accompanying washout of calpain-3. Calpain-3 autolyzes (becoming proteolytically active) in a tightly calcium-dependent manner. It remains in its nonactivated full-length form if [Ca(2+)] is maintained at < or = 50 nm, the normal resting level, even with brief increases to 2-20 mum during repeated tetanic contractions, but it becomes active (though still bound) if [Ca(2+)] is kept slightly elevated at 200 nm ( approximately 20% autolysis in 1 h). Calpain-3 did not spontaneously autolyze even when free in solution with 200 nm Ca(2+) for up to 60 min. These findings explain why calpain-3 remains quiescent with normal exercise but is activated following eccentric (stretching) contractions, when resting [Ca(2+)] is elevated, and how a protease such as calpain-3 can be very Ca(2+)-sensitive yet highly specific in its actions.