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 6RHY | pdb_00006rhy

Structure of pore-forming amyloid-beta tetramers


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 6RHY

This is version 1.3 of the entry. See complete history. 

Literature

A beta (1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage.

Ciudad, S., Puig, E., Botzanowski, T., Meigooni, M., Arango, A.S., Do, J., Mayzel, M., Bayoumi, M., Chaignepain, S., Maglia, G., Cianferani, S., Orekhov, V., Tajkhorshid, E., Bardiaux, B., Carulla, N.

(2020) Nat Commun 11: 3014-3014

  • DOI: https://doi.org/10.1038/s41467-020-16566-1
  • Primary Citation Related Structures: 
    6RHY

  • PubMed Abstract: 

    Formation of amyloid-beta (Aβ) oligomer pores in the membrane of neurons has been proposed to explain neurotoxicity in Alzheimer's disease (AD). Here, we present the three-dimensional structure of an Aβ oligomer formed in a membrane mimicking environment, namely an Aβ(1-42) tetramer, which comprises a six stranded β-sheet core. The two faces of the β-sheet core are hydrophobic and surrounded by the membrane-mimicking environment while the edges are hydrophilic and solvent-exposed. By increasing the concentration of Aβ(1-42) in the sample, Aβ(1-42) octamers are also formed, made by two Aβ(1-42) tetramers facing each other forming a β-sandwich structure. Notably, Aβ(1-42) tetramers and octamers inserted into lipid bilayers as well-defined pores. To establish oligomer structure-membrane activity relationships, molecular dynamics simulations were carried out. These studies revealed a mechanism of membrane disruption in which water permeation occurred through lipid-stabilized pores mediated by the hydrophilic residues located on the core β-sheets edges of the oligomers.


  • Organizational Affiliation: 
    • University of Bordeaux, CBMN (UMR 5248)-CNRS-IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.

Macromolecule Content 

  • Total Structure Weight: 18.08 kDa 
  • Atom Count: 1,276 
  • Modeled Residue Count: 168 
  • Deposited Residue Count: 168 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Amyloid beta A4 protein
A, B, C, D
42Homo sapiensMutation(s): 0 
Gene Names: APP, A4, AD1
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

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 15 
  • 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: 2019-09-25
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2024-06-19
    Changes: Data collection, Database references