The flagellate Giardia is reportedly (and controversially) the most primitive eukaryotic organism known to us. The trophozoite is without organelles but has an extensive cytoskeleton of microtubules and associated structural proteins. We have cloned and sequenced overlapping cDNAs and genomic DNAs for a 101,000 M(r) protein involved in microtubule bundling in the median body of G. lamblia cells. The polypeptide chain appears to be mainly alpha-helical with the repeating amphipathic heptapeptides characteristic of a coiled coil molecule, but without homology to known microtubule-associated proteins. Domain analysis suggests a structure in which a rod of three linked coils spans 695 residues (approximately 103 nm), with the ends of the chain forming compact globular head and tail domains of approximately 11 kDa and approximately 7 kDa. The rod domain has internal sequence repeats of 24 residues caused by multiple phase shifts in the coiled coil heptapeptide positions. These repeats have a conserved side-chain pattern which contributes the most significant periodicities in Fourier transforms of the linear distributions of apolar and charged residues. Our best alignment of the pattern has 21 complete repeats of 24 residues and 9 partial repeats of 21 or fewer residues. The apolar residue phase shifts will produce a regular stutter in the hydrophobic core of the coiled coil. This structure is reminiscent of beta-giardin, another coiled coil protein with a broken seam found in the Giardia cytoskeleton. Although the underlying sequence motif is different for the two proteins, the general feature of being regularly divided into segments might relate to a similar mechanism of interaction with microtubules.