To screen for proteins interacting with ataxin-3 by yeast two-hybrid system 3, and to discuss the function of ataxin-3 and pathogenesis of spinocerebellar ataxia type 3 and Machado-Joseph disease (SCA3/MJD).First we sub-cloned the full reading frame of both wild-type and mutant ataxin-3 into carrier pGBKT7 (ataxin-3-bait), and then screened human brain cDNA library with ataxin-3-bait.We found five positive clones in 6.5 x 10(6) transformers. After sequencing, we knew all of them were novel ataxin-3 interacting proteins. Three were corresponded to the known sequences coding the known proteins, which were human Rho GDP dissociation inhibitor alpha, small ubiquitin-like modifier 1, and human neuronal amiloride-sensitive cation channel 2. Another two of the five were unknown.Small ubiquitin-like modifier 1 probably interacted with ataxin-3, suggesting that the sumoylation probably participated in post-translation modifying of ataxin-3 and pathogenesis of SCA3/MJD.