9QYL | pdb_00009qyl

Alpha-synuclein fibril type 1A polymorph in the presence of ATP

  • Classification: NEUROPEPTIDE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2025-04-18 Released: 2025-10-29 
  • Deposition Author(s): Frey, L., Riek, R., Wittung Stafshede, P.
  • Funding Organization(s): ETH Zurich, Knut and Alice Wallenberg Foundation (PWS), Swedish Research Council, The Swedish Cancer Foundation (PWS), Swiss National Science Foundation, The Synapsis Foundation Switzerland (RR)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 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

ATP Hydrolysis by alpha-Synuclein Amyloids is Mediated by Enclosing beta-Strand.

Frey, L.Buratti, F.A.Horvath, I.Parate, S.Kumar, R.Riek, R.Wittung-Stafshede, P.

(2025) Adv Sci (Weinh) : e08441-e08441

  • DOI: https://doi.org/10.1002/advs.202508441
  • Primary Citation of Related Structures:  
    9QYL, 9QYN

  • PubMed Abstract: 

    Pathological amyloids, like those formed by α-synuclein in Parkinson's disease, are recently found to catalyze the hydrolysis of model substrates in vitro. Here it is reported that the universal energy molecule ATP is another substrate for α-synuclein amyloid chemical catalysis. To reveal the underlying mechanism, the high-resolution cryo-EM structure of the amyloids in the presence of ATP is solved. The structure reveals a type 1A amyloid fold with an additional β-strand involving residues 16-22 that wraps around the ATP, creating an enclosed cavity at the interface of the protofilaments. Mutations of putative ATP-interacting residues in the cavity and the additional β-strand showed that replacing any one of Lys21, Lys23, Lys43, Lys45, and Lys60 with Ala reduced amyloid-mediated ATPase activity. High-resolution structural analysis of Lys21Ala α-synuclein amyloids in the presence of ATP reveals the same fold as wild-type α-synuclein amyloids but without the extra β-strand and with ATP oriented differently. It is concluded that positively-charged side chains, along with ordering of the N-terminal part into a β-strand, enclosing the cavity, are essential parameters governing ATP hydrolysis by α-synuclein amyloids. Amyloid-catalyzed ATP hydrolysis may hamper ATP-dependent rescue systems near amyloid deposits in vivo.


  • Organizational Affiliation
    • ETH Zürich, Institute of Molecular Physical Science, Zürich, 8092, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-synuclein140Homo 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: 3.08 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ETH ZurichSwitzerland--
Knut and Alice Wallenberg Foundation (PWS)--
Swedish Research Council--
The Swedish Cancer Foundation (PWS)--
Swiss National Science Foundation--
The Synapsis Foundation Switzerland (RR)--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release