2M9R

3D NMR structure of a complex between the amyloid beta peptide (1-40) and the polyphenol epsilon-viniferin glucoside


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

3D NMR structure of a complex between the amyloid beta peptide (1-40) and the polyphenol epsilon-viniferin glucoside: Implications in Alzheimer's disease.

Richard, T.Papastamoulis, Y.Pierre, W.T.Monti, J.P.

(2013) Biochim Biophys Acta 1830: 5068-5074

  • DOI: https://doi.org/10.1016/j.bbagen.2013.06.031
  • Primary Citation of Related Structures:  
    2M9R, 2M9S

  • PubMed Abstract: 

    Alzheimer's disease (AD) is a progressive neurodegenerative disorder. There is a consensus that Aβ is a pathologic agent and that its toxic effects, which are at present incompletely understood, may occur through several potential mechanisms. Polyphenols are known to have wide-ranging properties with regard to health and for helping to prevent various diseases like neurodegenerative disorders. Thus inhibiting the formation of toxic Aβ assemblies is a reasonable hypothesis to prevent and perhaps treat AD METHODS: Solution NMR and molecular modeling were used to obtain more information about the interaction between the Aβ1-40 and the polyphenol ε-viniferin glucoside (EVG) and particularly the Aβ residues involved in the complex. The study demonstrates the formation of a complex between two EVG molecules and Aβ1-40 in peptide characteristic regions that could be in agreement with the inhibition of aggregation. Indeed, in previous studies, we reported that EVG strongly inhibited in vitro the fibril formation of the full length peptides Aβ1-40 and Aβ1-42, and had a strong protective effect against PC12 cell death induced by these peptides. For the full length peptide Aβ1-40, the binding sites observed could explain the EVG inhibitory effect on fibrillization and thus prevent amyloidogenic neurotoxicity. Even though this interaction might be important at the biological level to explain the protective effect of polyphenols in neurodegenerative diseases, caution is required when extrapolating this in vitro model to human physiology.


  • Organizational Affiliation

    GESVAB EA 3675, ISVV Université de Bordeaux Victor Segalen, 146 rue Léo Saignat, 33076 Bordeaux cedex, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid beta A4 protein40Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
GTEx:  ENSG00000142192 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
23Y
Query on 23Y

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
(2S,3S)-3-(3,5-dihydroxyphenyl)-2-(4-hydroxyphenyl)-4-[(E)-2-(4-hydroxyphenyl)ethenyl]-2,3-dihydro-1-benzofuran-6-yl beta-D-glucopyranoside
C34 H32 O11
NHYFNLFVNSLRES-YNVKLIFMSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations