Apolipoprotein B-100 (apoB-100) is the major protein in low-density lipoprotein (LDL) and contains the ligand for binding LDL to its cell surface receptor. Lipoprotein [a] (Lp[a]) is a lipoprotein that consists of LDL and apolipoprotein [a] (apo[a]). The primary structure of apoB-100 has been determined by a combination of recombinant DNA and protein sequencing methods. Using high-performance liquid chromatographic techniques, we have identified sulfhydryl and disulfide groups of apoB-100 from LDL. Sixteen of the 25 cysteine residues in apoB-100 exist in disulfide form. All 14 cysteine residues within the N terminal end of apoB-100 are linked in disulfide bridges. Using the fluorescent sulfhydryl probe, 5-iodoacetoamidofluoresceine, two free sulfhydryls of apoB-100 on LDL were identified at positions 3734 and 4190. Based on its differential susceptibility to trypsin, apoB-100 can be divided into five domains: domain 1 (residues 1-1000), largely trypsin-releasable (TR); domain 2 (residues 1001-1700), alternating TR and trypsin non-releasable (TN); domain 3 (residues 1701-3070), largely TN; domain 4 (residues 3071-4100), mainly TR and mixed; and domain 5 (residues 4101-4536), almost exclusively TN. Based on our data, we propose that the structure of apoB-100 in LDL is probably an elongated form that wraps around the LDL particle, and that Cys3734 of apoB-100 may be the cysteine residue linked to a cysteine of apo[a].