9K0F | pdb_00009k0f

Cryo-EM structure of Amyloid-beta42-4b polymorph 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

An O-glycopeptide participates in the formation of distinct A beta 42 fibril structures and attenuates A beta 42 neurotoxicity.

Wei, Q.Liu, D.Xia, W.Wang, F.Huang, L.Zhang, J.Wang, X.Xu, Z.He, C.Li, W.Shi, X.Wang, C.Liu, Y.Liu, C.Dong, S.

(2025) Nat Commun 16: 5815-5815

  • DOI: https://doi.org/10.1038/s41467-025-60978-w
  • Primary Citation of Related Structures:  
    9K0D, 9K0E, 9K0F

  • PubMed Abstract: 

    The self-assembly of biomolecules through noncovalent interactions is critical in both physiological and pathological processes, as exemplified by the assembly of amyloid β peptide (Aβ) into oligomers or fibrils in Alzheimer's disease (AD). Developing molecules that can modulate this assembly process holds significant mechanistic and therapeutic potential. In this study, we identified glycopeptides as a class of protein aggregation modulators, showing that β-N-acetylgalactosamine (β-GalNAc)-modified Aβ 9-21 promotes Aβ 42 fibrillation while reducing its toxic oligomers. Using biochemical assays, cryo-EM, and molecular dynamics simulations, we demonstrated that β-GalNAc-modified Aβ 9-21 coassembles with Aβ 42 , forming unique fibril structures stabilized by both hydrophobic interactions and an organized hydrogen bond network facilitated by the glycopeptide. Importantly, β-GalNAc-modified Aβ 9-21 can alleviate the neurotoxicity of Aβ 42 in neuronal cells and an AD male mouse model. These findings underscore the potential of glycopeptides in regulating amyloid aggregation and provide structural insights for designing molecules targeting amyloid-related pathologies.


  • Organizational Affiliation
    • State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid-beta A4 protein42Homo sapiensMutation(s): 0 
UniProt
Find proteins for B4DMD5 (Homo sapiens)
Explore B4DMD5 
Go to UniProtKB:  B4DMD5
Entity Groups  
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UniProt GroupB4DMD5
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid-beta protein 40D [auth K],
H [auth N],
L [auth O]
13Homo 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: 2.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15.2_3472:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release