The mitochondrial ATP synthase beta subunit is encoded by a nuclear gene and assembled with the other subunits encoded by both mitochondrial and nuclear genes. As the next step in the analysis of the molecular mechanisms coordinating the two genetic systems, the gene for the human beta subunit was cloned, and its structure was determined. The gene contains 10 exons, with the first exon corresponding to the noncoding region and most of the presequence which targets this protein to the mitochondria. Eight Alu repeating sequences including inverted repeats were found in the 5' upstream region and introns. An S1 nuclease protection experiment revealed two initiation sites for the transcription. A typical TATA box was not present at about 30 base pairs upstream from either initiation site. Three CAT boxes (CCAAT) were found between the two initiation sites. In addition, one CAT box was found 41 base pairs upstream from the first initiation site. Two GC boxes (potential Sp1 binding sites) were located in the 5' upstream region, one of them linked to Alu repeating sequences. For determination of the promoter activity, fragments of various length from the 5' upstream region were fused to a chloramphenicol acetyltransferase gene and transfected into cultured cells. This experiment showed the existence of an enhancing, structure(s) for transcription between nucleotide -400 and -1100 in the upstream region.