8VXJ | pdb_00008vxj

The crystal structure of human apolipoprotein A-I in complex with Fab 55201


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.298 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.268 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Literature

The Structure of the Apolipoprotein A-I Monomer Provides Insights Into Its Oligomerisation and Lipid-binding Mechanisms.

Tou, H.I.Rosenes, Z.Khandokar, Y.Zlatic, C.O.Metcalfe, R.D.Mok, Y.F.Morton, C.J.Gooley, P.R.Griffin, M.D.W.

(2025) J Mol Biology 437: 169394-169394

  • DOI: https://doi.org/10.1016/j.jmb.2025.169394
  • Primary Citation Related Structures: 
    8VXJ

  • PubMed Abstract: 

    Apolipoprotein A-I (apoA-I) plays important roles in clearing cholesterol and phospholipids from peripheral tissues, forming high-density lipoprotein (HDL). However, despite this important function, apoA-I has a propensity to form amyloid fibrils implicated in atherosclerosis and hereditary amyloidosis. Historically, structural determination of lipid-free or lipid-poor apoA-I has been difficult. Here, we obtained the crystal structure of the apoA-I monomer in complex with the antigen-binding fragment (Fab) of a monoclonal antibody. The structure reveals that the N-terminal domain (NTD, residues 1-184) of apoA-I is a compact four-helical bundle, whereas the C-terminal domain (CTD, residues 185-243) is unresolved in the structure. Molecular Dynamics (MD) simulations and small-angle X-ray scattering (SAXS) analysis revealed that the apoA-I NTD dimerises by domain-swapping and the dimer is elongated. Methionine (Met) oxidation in apoA-I destabilises both full-length apoA-I (apoA-I FL ) and C-terminally truncated apoA-I (apoA-I Δ185-243 ), causing dissociation of the domain-swapped dimer and fibril formation. Met oxidation also increased the lipid-binding ability of apoA-I Δ185-243 , while the amyloidogenic mutation, G26R, did not. Hydrogen-deuterium exchange coupled with nuclear magnetic resonance (HDX-NMR), SAXS, and MD analyses showed that triply Met-oxidised (3MetO) and G26R apoA-I Δ185-243 are both highly dynamic but remain partially folded. Based on these results, we propose that domain-swapping dimerisation also exists in apoA-I FL , with the CTD mediating further oligomerisation. We also propose that lipid-binding is promoted by increased global destabilisation in the protein structure, and/or driven by a specific local conformation that is induced by Met-oxidation but not the G26R mutation.


  • Organizational Affiliation
    • Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.

Macromolecule Content 

  • Total Structure Weight: 147.69 kDa 
  • Atom Count: 9,275 
  • Modeled Residue Count: 1,228 
  • Deposited Residue Count: 1,358 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apolipoprotein A-IA [auth C],
D
243Homo sapiensMutation(s): 0 
Gene Names: APOA1
UniProt & NIH Common Fund Data Resources
Find proteins for P02647 (Homo sapiens)
Explore P02647 
Go to UniProtKB:  P02647
PHAROS:  P02647
GTEx:  ENSG00000118137 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02647
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 55201 heavy chainB [auth H],
E [auth A]
224Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 55201 light chainC [auth L],
F [auth B]
212Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.298 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.268 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.53α = 90
b = 67.472β = 95.742
c = 167.123γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP170104046
Australian Research Council (ARC)AustraliaFT140100544

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references