8PIX

Cryo EM structure of the type 3C polymorph of alpha-synuclein at low pH.

Summary for 8PIX

• Entry DOI: 10.2210/pdb8pix/pdb
• Related: 8PIC
• EMDB information: 17693
• Descriptor: Alpha-synuclein (1 entity in total)
• Functional Keywords: amyloid, polymorphism, protein fibril
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 10
• Total formula weight: 144761.08

Authors

Frey, L.,Qureshi, B.M.,Kwiatkowski, W.,Rhyner, D.,Greenwald, J.,Riek, R. (deposition date: 2023-06-22, release date: 2024-05-29, Last modification date: 2024-09-11)

Primary citation

Frey, L.,Ghosh, D.,Qureshi, B.M.,Rhyner, D.,Guerrero-Ferreira, R.,Pokharna, A.,Kwiatkowski, W.,Serdiuk, T.,Picotti, P.,Riek, R.,Greenwald, J.
On the pH-dependence of alpha-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation.
Elife, 12:-, 2024

PubMed Abstract: The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.

PubMed: 39196271
DOI: 10.7554/eLife.93562

Experimental method

ELECTRON MICROSCOPY (3.41 Å)