8CE0 | pdb_00008ce0

N-terminal domain of human apolipoprotein E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer's Disease drug candidate.

Nemergut, M.Marques, S.M.Uhrik, L.Vanova, T.Nezvedova, M.Gadara, D.C.Jha, D.Tulis, J.Novakova, V.Planas-Iglesias, J.Kunka, A.Legrand, A.Hribkova, H.Pospisilova, V.Sedmik, J.Raska, J.Prokop, Z.Damborsky, J.Bohaciakova, D.Spacil, Z.Hernychova, L.Bednar, D.Marek, M.

(2023) Mol Neurodegener 18: 38-38

  • DOI: https://doi.org/10.1186/s13024-023-00620-9
  • Primary Citation Related Structures: 
    8AX8, 8AX9, 8CDY, 8CE0

  • PubMed Abstract: 

    Apolipoprotein E (ApoE) ε4 genotype is the most prevalent risk factor for late-onset Alzheimer's Disease (AD). Although ApoE4 differs from its non-pathological ApoE3 isoform only by the C112R mutation, the molecular mechanism of its proteinopathy is unknown. Here, we reveal the molecular mechanism of ApoE4 aggregation using a combination of experimental and computational techniques, including X-ray crystallography, site-directed mutagenesis, hydrogen-deuterium mass spectrometry (HDX-MS), static light scattering and molecular dynamics simulations. Treatment of ApoE ε3/ε3 and ε4/ε4 cerebral organoids with tramiprosate was used to compare the effect of tramiprosate on ApoE4 aggregation at the cellular level. We found that C112R substitution in ApoE4 induces long-distance (> 15 Å) conformational changes leading to the formation of a V-shaped dimeric unit that is geometrically different and more aggregation-prone than the ApoE3 structure. AD drug candidate tramiprosate and its metabolite 3-sulfopropanoic acid induce ApoE3-like conformational behavior in ApoE4 and reduce its aggregation propensity. Analysis of ApoE ε4/ε4 cerebral organoids treated with tramiprosate revealed its effect on cholesteryl esters, the storage products of excess cholesterol. Our results connect the ApoE4 structure with its aggregation propensity, providing a new druggable target for neurodegeneration and ageing.


  • Organizational Affiliation
    • Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 75.21 kDa 
  • Atom Count: 1,335 
  • Modeled Residue Count: 143 
  • Deposited Residue Count: 675 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Apolipoprotein E675Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malENCTC8450_00456NCTC9775_03059APOE
UniProt & NIH Common Fund Data Resources
Find proteins for P02649 (Homo sapiens)
Explore P02649 
Go to UniProtKB:  P02649
PHAROS:  P02649
GTEx:  ENSG00000130203 
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP02649P0AEX9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.215 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.529α = 90
b = 53.085β = 90
c = 73.171γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicGA22-09853S

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Database references