9IIO | pdb_00009iio

J-shaped conformer of amyloid beta (1-40)

  • Classification: PROTEIN FIBRIL
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-06-21 Released: 2025-02-26 
  • Deposition Author(s): Burton-Smith, R.N., Murata, K.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9IIO

This is version 1.0 of the entry. See complete history

Literature

Elucidating the Unique J-Shaped Protomer Structure of Amyloid-beta (1-40) Fibril with Cryo-Electron Microscopy.

Burton-Smith, R.N.Yagi-Utsumi, M.Yanaka, S.Song, C.Murata, K.Kato, K.

(2025) Int J Mol Sci 26

  • DOI: https://doi.org/10.3390/ijms26031179
  • Primary Citation Related Structures: 
    9IIO

  • PubMed Abstract: 

    Although the structural diversity of amyloid-β (Aβ) fibrils plays a critical role in the pathology of Alzheimer's disease (AD), the mechanisms underlying this diversity remain poorly understood. In this study, we report the discovery of a novel J-shaped protomer structure of Aβ40 fibrils, resolved at 3.3 Å resolution using cryo-electron microscopy. Under controlled conditions (20 mM sodium phosphate buffer, pH 8.0) designed to emphasize intra-protomer interactions and slow fibril elongation, the J-shaped structure revealed distinct salt bridges (e.g., D1-K28, R5-E22) that stabilize the fibril core. These findings expand our understanding of the free energy landscape of fibril formation, shedding light on how specific environmental factors, such as pH and ionic strength, may influence fibril polymorphism. Importantly, the unique features of the J-shaped protomer provide insights into the structural basis of amyloid plaque diversity in AD and suggest potential therapeutic strategies targeting intra-protomer interactions. This study underscores the importance of fibril polymorphism in AD pathology and offers a foundation for future research into fibril-targeted therapies.


  • Organizational Affiliation
    • Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan.

Macromolecule Content 

  • Total Structure Weight: 173.43 kDa 
  • Atom Count: 12,240 
  • Modeled Residue Count: 1,600 
  • Deposited Residue Count: 1,600 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Amyloid-beta protein 4040Homo 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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release