21BQ | pdb_000021bq

Cryo-EM structure of ex vivo Sup35 prion fibrils from yeast carrying "strong" [PSI+] variant

• PDB DOI: https://doi.org/10.2210/pdb21BQ/pdb
• EM Map EMD-67558: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2025-12-06 Released: 2026-07-22 
• Deposition Author(s): Chesnokov, Y.M., Burtseva, A.D., Dergalev, A.A., Baimukhametov, T.N., Kushnirov, V.V., Popov, V.O., Boyko, K.M.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: other

Literature

Cryo-EM structure of ex vivo Sup35 yeast prion and the factors defining prion phenotype.

Dergalev, A.A., Chesnokov, Y.M., Burtseva, A.D., Mitkevich, O.V., Baymukhametov, T.N., Popov, V.O., Boyko, K.M., Kushnirov, V.V.

(2026) Nat Commun 17

• PubMed: 42901901 
• DOI: https://doi.org/10.1038/s41467-026-77823-3


• PubMed Abstract: 
  

  Human prions and amyloids exhibit structural diversity that correlates with different pathological manifestations. Yeast prions represent a convenient model for studying fundamental properties of prions and their strain diversity. The Sup35 yeast prion has multiple structural variants, divided into "strong" and "weak" groups differing in frequency of fibril fragmentation and resulting nonsense-suppression. The molecular origin of these distinctions remains unclear. Here, we show that the different frequency of prion fragmentation is determined by their stability, rather than the efficiency of chaperone binding. The fully protease-resistant part (residues 2-32) of the Sup35 prion core is a key for the prion phenotype and maintenance, whereas partially resistant part (33-72) is less important. We established the cryo-EM structure of a strong Sup35 prion variant purified from yeast, comprising residues 2-64, with 2.7 Å resolution. Comparison of this structure with that of Sup35 amyloid formed in vitro at 4˚C revealed their significant difference.

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Organizational Affiliation: 
• Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia. [e-mail].
National Research Center "Kurchatov Institute", Moscow, Russia.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
Moscow Center for Advanced Studies, Moscow, Russia.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia. [e-mail].
Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 89.98 kDa 
• Atom Count: 2,580 
• Modeled Residue Count: 320 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid of yeast prion Sup35	A, B, C, D, E	160	Saccharomyces cerevisiae	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-22 
Deposition Author(s): Chesnokov, Y.M., Burtseva, A.D., Dergalev, A.A., Baimukhametov, T.N., Kushnirov, V.V., Popov, V.O., Boyko, K.M.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	23-74-00062

Revision History  

• Version 1.0: 2026-07-22
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Data collection, Database references
• Version 1.2: 2026-11-04
  Changes: Data collection, Database references