We have identified repeat motifs in the large proteasome-bin ding proteins PA200 and Ecm29 by applying a sensitive sequence profile method. These repeat motifs, especially those of PA200, resemble HEAT/ARM repeats in length and other properties but differ from them in the occupancy of certain positions. The HEAT motif consists of two alpha-helices and two turns: molecular modeling suggests that in the PA200 and Ecm29 repeats, the alpha-helices may be slightly turned relative to their orientations in typical HEAT repeats. Both PA200 and Ecm29 are composed almost entirely of such repeats, and therefore are likely to have alpha-helical solenoid structures. These observations lead us to speculate on how PA200 and Ecm29 may associate with proteasomes. (C) 2004 Published by Elsevier Inc.