9UMH | pdb_00009umh

V-type (V2-type) amyloid fibril (40) of Tottori (D7N) mutant

  • Classification: PROTEIN FIBRIL
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2025-04-22 Released: 2025-07-09 
  • 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: 3.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Microgravity-Assisted Exploration of the Conformational Space of Amyloid beta Affected by Tottori-Type Familial Mutation D7N.

Yagi-Utsumi, M.Yanaka, S.Burton-Smith, R.N.Song, C.Ganser, C.Yamazaki, C.Kasahara, H.Shimazu, T.Uchihashi, T.Murata, K.Kato, K.

(2025) ACS Chem Neurosci 16: 2682-2690

  • DOI: https://doi.org/10.1021/acschemneuro.5c00217
  • Primary Citation of Related Structures:  
    9M5P, 9M5Q, 9M5R, 9UMH

  • PubMed Abstract: 

    The amyloid β (Aβ) Tottori variant (D7N) exhibits unique aggregation behaviors and altered fibril formation, posing challenges for structural characterization. To overcome this, the microgravity environment on the International Space Station was employed to study Tottori-type Aβ40 fibril formation and structure. Under Earth gravity, Tottori-type Aβ40 primarily formed nonfibrillar aggregates, hindering detailed structural analysis. In contrast, microgravity significantly enhanced fibril formation and minimized amorphous aggregates. Cryo-electron microscopy revealed two structurally distinct fibril types, each comprising different protomer conformations. In both types, the N-terminal segment was disordered and nor resolved in the density maps. The D7N mutation disrupts the protection of the core by the N-terminal segment often observed in wild-type Aβ40 fibrils, enhancing the hydrophobicity-mediated aggregation propensity. However, microgravity suppressed kinetic traps and facilitated high-quality fibril formation suitable for structural studies that can explore the free energy landscape of Aβ fibril formation. These findings demonstrate the utility of microgravity for studying familial Aβ variants and potentially accelerate our understanding of Aβ aggregation mechanisms in Alzheimer's disease.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid-beta protein 4040Homo sapiensMutation(s): 1 
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: 3.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

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Currently 9UMH does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP24ama121005

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references