The structure of apolipoprotein B100 from human low-density lipoprotein

Zachary T. Berndsen () and C. Keith Cassidy ()
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Zachary T. Berndsen: University of Missouri
C. Keith Cassidy: University of Missouri

Nature, 2025, vol. 638, issue 8051, 836-843

Abstract: Abstract Low-density lipoprotein (LDL) has a central role in lipid and cholesterol metabolism and is a key agent in the development and progression of atherosclerosis, the leading cause of mortality worldwide1,2. Apolipoprotein B100 (apoB100), one of the largest proteins in the genome, is the primary structural and functional component of LDL, yet its size and complex lipid associations have posed major challenges for structural studies3. Here we present the structure of apoB100 resolved to subnanometre resolution in most regions using an integrative approach of cryo-electron microscopy, AlphaFold24 and molecular-dynamics-based refinement5. The structure consists of a large globular N-terminal domain and an approximately 61-nm-long continuous amphipathic β-sheet that wraps around the LDL particle like a belt. Distributed quasi-symmetrically across the two sides of the β-belt are nine strategically located interstrand inserts that extend across the lipid surface to provide additional structural support through a network of long-range interactions. We further compare our structure to a comprehensive list of more than 200 intramolecular cross-links and find close agreement between the two. These results suggest a mechanism for how the various domains of apoB100 act in concert to maintain LDL shape and cohesion across a range of particle sizes. More generally, they advance our fundamental understanding of LDL synthesis, form and function, and will help to accelerate the design of potential therapeutics.

Date: 2025
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DOI: 10.1038/s41586-024-08467-w

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