9BD1 | pdb_00009bd1

beta/alpha1 region of ApoB 100


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9BD1

This is version 1.1 of the entry. See complete history

Literature

Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor.

Reimund, M.Dearborn, A.D.Graziano, G.Lei, H.Ciancone, A.M.Kumar, A.Holewinski, R.Neufeld, E.B.O'Reilly, F.J.Remaley, A.T.Marcotrigiano, J.

(2025) Nature 638: 829-835

  • DOI: https://doi.org/10.1038/s41586-024-08223-0
  • Primary Citation Related Structures: 
    9BD1, 9BD8, 9BDE, 9BDT, 9COO

  • PubMed Abstract: 

    Apolipoprotein B100 (apoB100) is a structural component of low-density lipoprotein (LDL) and a ligand for the LDL receptor (LDLR) 1 . 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 2 . 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 2 -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.


  • Organizational Affiliation
    • Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 516.39 kDa 
  • Atom Count: 6,868 
  • Modeled Residue Count: 935 
  • Deposited Residue Count: 4,563 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apolipoprotein B-1004,563Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04114 (Homo sapiens)
Explore P04114 
Go to UniProtKB:  P04114
PHAROS:  P04114
GTEx:  ENSG00000084674 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04114
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P04114-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Data collection, Database references