The structural basis of lipid interactions in lipovitellin, a soluble lipoprotein

Background: The conformation and assembly of lipoproteins, proteins containing large amounts of noncovalently bound lipid, is poorly understood. Lipoproteins present an unusual challenge as they often contain varying loads of lipid and are not readily crystallized. Lipovitellin is a large crystallizable oocyte protein of approximately 1300 residues that contains about 16% w/w lipid. Lipovitellin contains two large domains that appear to be conserved in both microsomal triglyceride transfer protein and apolipoprotein B-100. To gain insight into the conformation of a lipoprotein and the potential modes of binding of both neutral and phospholipid, the crystal structure of lamprey lipovitellin has been determined. Results: We report here the refined crystal structure of lipovitellin at 2.8 Å resolution. The structure contains 1129 amino acid residues located on five peptide chains, one 40-atom phosphatidylcholine, and one 13-atom hydrocarbon chain. The protein contains a funnel-shaped cavity formed primarily by two β sheets and lined predominantly by hydrophobic residues. Conclusions: Using the crystal structure as a template, a model for the bound lipid is proposed. The lipid-binding cavity is formed primarily by a single-thickness β-sheet structure which is stabilized by bound lipid. This cavity appears to be flexible, allowing lipid to be loaded or unloaded.