8J47 | pdb_00008j47

CryoEM Structure of 40-Residue Arctic (E22G) Beta-Amyloid Fibril Derived by Co-Analysis with Solid-State NMR | E22G Abeta40

• PDB DOI: https://doi.org/10.2210/pdb8J47/pdb
• EM Map EMD-35972: EMDB EMDataResource

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


• Deposited: 2023-04-19 Released: 2024-09-11 
• Deposition Author(s): Tehrani, M.J., Matsuda, I., Yamagata, A., Matsunaga, T., Sato, M., Toyooka, K., Shirouzu, M., Ishii, Y., Kodama, Y., McElheny, D., Kobayashi, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

E22G A beta 40 fibril structure and kinetics illuminate how A beta 40 rather than A beta 42 triggers familial Alzheimer's.

Tehrani, M.J., Matsuda, I., Yamagata, A., Kodama, Y., Matsunaga, T., Sato, M., Toyooka, K., McElheny, D., Kobayashi, N., Shirouzu, M., Ishii, Y.

(2024) Nat Commun 15: 7045-7045

• PubMed: 39147751 
• DOI: https://doi.org/10.1038/s41467-024-51294-w
• Primary Citation Related Structures: 
  8J47


• PubMed Abstract: 
  

  Arctic (E22G) mutation in amyloid-β (Aβ enhances Aβ40 fibril accumulation in Alzheimer's disease (AD). Unlike sporadic AD, familial AD (FAD) patients with the mutation exhibit more Aβ40 in the plaque core. However, structural details of E22G Aβ40 fibrils remain elusive, hindering therapeutic progress. Here, we determine a distinctive W-shaped parallel β-sheet structure through co-analysis by cryo-electron microscopy (cryoEM) and solid-state nuclear magnetic resonance (SSNMR) of in-vitro-prepared E22G Aβ40 fibrils. The E22G Aβ40 fibrils displays typical amyloid features in cotton-wool plaques in the FAD, such as low thioflavin-T fluorescence and a less compact unbundled morphology. Furthermore, kinetic and MD studies reveal previously unidentified in-vitro evidence that E22G Aβ40, rather than Aβ42, may trigger Aβ misfolding in the FAD, and prompt subsequent misfolding of wild-type (WT) Aβ40/Aβ42 via cross-seeding. The results provide insight into how the Arctic mutation promotes AD via Aβ40 accumulation and cross-propagation.

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Organizational Affiliation: 
• School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St, Chicago, IL, 60607, USA.
School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan. [e-mail].
RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 42.64 kDa 
• Atom Count: 2,080 
• Modeled Residue Count: 290 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E22G Amyloid-beta	A [auth D], B [auth C], C [auth F], D [auth E], E [auth B], F [auth A], G [auth H], H [auth G], I [auth J], J [auth I]	40	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for B7Z313 (Homo sapiens) Explore B7Z313  Go to UniProtKB:  B7Z313

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Tehrani, M.J., Matsuda, I., Yamagata, A., Matsunaga, T., Sato, M., Toyooka, K., Shirouzu, M., Ishii, Y., Kodama, Y., McElheny, D., Kobayashi, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5U01GM098033
Japan Science and Technology	Japan	JPMJMI17A2, Japan
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K18328, Japan
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H05733

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2024-09-18
  Changes: Data collection, Database references