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Structure paper

TitleStructure of apolipoprotein B100 bound to the low-density lipoprotein receptor.
Journal, issue, pagesNature, Year 2024
Publish dateDec 11, 2024
AuthorsMart Reimund / Altaira D Dearborn / Giorgio Graziano / Haotian Lei / Anthony M Ciancone / Ashish Kumar / Ronald Holewinski / Edward B Neufeld / Francis J O'Reilly / Alan T Remaley / Joseph Marcotrigiano /
PubMed AbstractApolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR). Mutations in apoB100 or in LDLR cause familial ...Apolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR). Mutations in apoB100 or in LDLR cause familial hypercholesterolaemia, an autosomal dominant disease that is characterized by a marked increase in LDL cholesterol (LDL-C) and a higher risk of cardiovascular disease. The structure of apoB100 on LDL and its interaction with LDLR are poorly understood. Here we present the cryo-electron microscopy structures of apoB100 on LDL bound to the LDLR and a nanobody complex, which can form a C-symmetric, higher-order complex. Using local refinement, we determined high-resolution structures of the interfaces between apoB100 and LDLR. One binding interface is formed between several small-ligand-binding modules of LDLR and a series of basic patches that are scattered along a β-belt formed by apoB100, encircling LDL. The other binding interface is formed between the β-propeller domain of LDLR and the N-terminal domain of apoB100. Our results reveal how both interfaces are involved in LDL dimer formation, and how LDLR cycles between LDL- and self-bound conformations. In addition, known mutations in either apoB100 or LDLR, associated with high levels of LDL-C, are located at the LDL-LDLR interface.
External linksNature / PubMed:39663455
MethodsEM (single particle)
Resolution3.73 - 8.6 Å
Structure data

EMDB-44442: Dimeric form of LDL, LDL receptor and Legobody
Method: EM (single particle) / Resolution: 8.6 Å

44443

9bd1

EMDB-44443, PDB-9bd1:
beta/alpha1 region of ApoB 100
Method: EM (single particle) / Resolution: 5.4 Å

44446

9bd8

EMDB-44446, PDB-9bd8:
ApoB 100 beta barrel bound to LDLR beta propeller
Method: EM (single particle) / Resolution: 4.8 Å

44450

9bde

EMDB-44450, PDB-9bde:
Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor
Method: EM (single particle) / Resolution: 4.18 Å

44469

9bdt

EMDB-44469, PDB-9bdt:
Apolipoprotein B 100 bound to LDL receptor and legobody
Method: EM (single particle) / Resolution: 5.4 Å

45787

9coo

EMDB-45787, PDB-9coo:
Nanobody 4 bound to Apolipoprotein B 100
Method: EM (single particle) / Resolution: 3.73 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-CA:
Unknown entry

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
  • escherichia coli (E. coli)
  • streptococcus sp. 'group g' (bacteria)
  • camelus bactrianus (Bactrian camel)
  • staphylococcus aureus (bacteria)
KeywordsLIPID TRANSPORT / Apolipoprotien B 100 / alpha/beta 1 region / LDL / Low density lipoprotein / LDL receptor / Apolipoprotein B 100 / ApoB100 / LDLreceptor

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