8FPT | pdb_00008fpt

STRUCTURE OF ALPHA-SYNUCLEIN FIBRILS DERIVED FROM HUMAN LEWY BODY DEMENTIA TISSUE

• PDB DOI: https://doi.org/10.2210/pdb8FPT/pdb
• BMRB: 31068

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


• Deposited: 2023-01-05 Released: 2023-02-22 
• Deposition Author(s): Barclay, A.M., Dhavale, D.D., Borcik, C.G., Rau, M.J., Basore, K., Milchberg, M.H., Warmuth, O.A., Kotzbauer, P.T., Rienstra, C.M., Schwieters, C.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 256 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue.

Dhavale, D.D., Barclay, A.M., Borcik, C.G., Basore, K., Berthold, D.A., Gordon, I.R., Liu, J., Milchberg, M.H., O'Shea, J.Y., Rau, M.J., Smith, Z., Sen, S., Summers, B., Smith, J., Warmuth, O.A., Perrin, R.J., Perlmutter, J.S., Chen, Q., Fitzpatrick, J.A.J., Schwieters, C.D., Tajkhorshid, E., Rienstra, C.M., Kotzbauer, P.T.

(2024) Nat Commun 15: 2750-2750

• PubMed: 38553463 
• DOI: https://doi.org/10.1038/s41467-024-46832-5
• Primary Citation Related Structures: 
  8FPT


• PubMed Abstract: 
  

  The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural characterization of LBD Asyn fibrils and approaches for studying disease mechanisms, imaging agents and therapeutics targeting Asyn.

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Organizational Affiliation: 
• Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA.
Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
Department of Radiology, Neuroscience, Physical Therapy and Occupational Therapy, Washington University School of Medicine, St. Louis, MO, 63110, USA.
Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. [e-mail].
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA. [e-mail].
Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 144.76 kDa 
• Atom Count: 5,140 
• Modeled Residue Count: 740 
• Deposited Residue Count: 1,400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-synuclein	A, B, C, D, E, F, G, H, I, J	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

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 256 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Barclay, A.M., Dhavale, D.D., Borcik, C.G., Rau, M.J., Basore, K., Milchberg, M.H., Warmuth, O.A., Kotzbauer, P.T., Rienstra, C.M., Schwieters, C.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references
• Version 1.2: 2024-12-11
  Changes: Data collection, Database references, Structure summary