9Y0S | pdb_00009y0s

CryoEM structure of alpha-synuclein fibril induced by psychosine


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Leveraging bioorthogonal conjugation for alpha synuclein fibril surveillance.

Jenkins, R.A.Wu, S.Fujimura, G.Heredia, A.Flowers, C.W.Sun, C.Sawaya, M.R.Loo, J.A.Rodriguez, J.A.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.09.12.675751
  • Primary Citation of Related Structures:  
    9Y0S

  • PubMed Abstract: 

    Alpha synuclein (α-syn) amyloid fibrils are associated with various neurodegenerative diseases. To better understand the molecular and cellular basis for α-syn fibril persistence and spread, we implemented a fluorophore labeling strategy to surveil pre-formed α-syn fibrils in solution and in cells. We leveraged amber codon mediated incorporation of a tetrazine-based artificial amino acid (TetV2.0) to install a cyclooctene-conjugated Janeliaflour, JF549, at four sites on human α-syn: residues 4, 60, 96 and 136. Fast coupling occurred under mild buffer conditions and in the presence of the disease-associated cofactor and cytotoxic lipid, psychosine. Labeled fibrils retained their polymorphic features, seeded the growth of new fibrils in vitro , and induced the seeding of positive puncta in α-syn FRET biosensor HEK293T cells. This allowed simultaneous tracking of exogenous and endogenous α-syn aggregates in biosensor cells, and their localization within the cells. In doing so, our approach facilitates more detailed mechanistic investigation of α-syn aggregates.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center; University of California, Los Angeles (UCLA); Los Angeles, CA 90095, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-synuclein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
140Homo sapiensMutation(s): 0 
Gene Names: SNCANACPPARK1
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens)
Explore P37840 
Go to UniProtKB:  P37840
PHAROS:  P37840
GTEx:  ENSG00000145335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37840
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM128867
National Science Foundation (NSF, United States)United StatesDMR-1548924

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release