8XWD | pdb_00008xwd

Croy-EM structure of alpha synuclein fibril with EGCG

• PDB DOI: https://doi.org/10.2210/pdb8XWD/pdb
• EM Map EMD-38733: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-01-16 Released: 2025-02-26 
• Deposition Author(s): Li, X., Liu, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Single-Molecule Insight Into alpha-Synuclein Fibril Structure and Mechanics Modulated by Chemical Compounds.

Li, X., Bi, L., Zhang, S., Xu, Q., Xia, W., Tao, Y., Wu, S., Li, Y., Le, W., Kang, W., Li, D., Sun, B., Liu, C.

(2025) Adv Sci (Weinh) 12: e2416721-e2416721

• PubMed: 39951335 
• DOI: https://doi.org/10.1002/advs.202416721
• Primary Citation Related Structures: 
  8XWD


• PubMed Abstract: 
  

  α-Syn fibrils, a key pathological hallmark of Parkinson's disease, is closely associated with disease initiation and progression. Several small molecules are found to bind or dissolve α-syn fibrils, offering potential therapeutic applications. Here, an innovative optical tweezers-based, fluorescence-combined approach is developed to probe the mechanical characteristics of α-syn fibrils at the single-molecule level. When subjected to axial stretching, local deformation within α-syn fibrils appeared at forces above 50 pN. These structural alternations occurred stepwise and are irreversible, suggesting unfolding of individual α-syn molecules or subdomains. Additionally, α-syn fibrils exhibits high heterogeneity in lateral disruption, with rupture force ranging from 50 to 500 pN. The impact of different compounds on the structure and mechanical features of α-syn fibrils is further examined. Notably, epigallocatechin gallate (EGCG) generally attenuates the rupture force of fibrils by wedging into the N-terminal polar groove and induces fibril dissociation. Conversely, copper chlorophyllin A (CCA) attaches to four different sites wrapping around the fibril core, reinforcing the stability of the fibril against rupture forces. The work offers an effective method for characterizing single-fibril properties and bridges compound-induced structural alternations with mechanical response. These insights are valuable for understanding amyloid fibril mechanics and their regulation by small molecules.

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Organizational Affiliation: 
• Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 201203, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China.
Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, 201318, China.
Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
Shanghai Academy of Natural Sciences (SANS), Fudan University, Shanghai, 200433, China.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 89.61 kDa 
• Atom Count: 2,670 
• Modeled Residue Count: 360 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	A [auth C], B [auth D], C [auth E], D [auth A], E [auth F], F [auth B]	140	Homo sapiens	Mutation(s): 0  Gene Names: SNCA, NACP, PARK1
UniProt & NIH Common Fund Data Resources
Find proteins for P37840 (Homo sapiens) Explore P37840  Go to UniProtKB:  P37840
PHAROS:  P37840 GTEx:  ENSG00000145335

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KDH (Subject of Investigation/LOI)	G [auth C], H [auth D], I [auth E], J [auth A], K [auth F], L [auth B]	(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate C22 H18 O11 WMBWREPUVVBILR-WIYYLYMNSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Li, X., Liu, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Data collection, Database references
• Version 1.2: 2025-04-30
  Changes: Data collection, Database references