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- PDB-9xbn: Cryo-EM structure of Sup35NM fibril formed at 4 degrees (Sc4) -

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Basic information

Entry
Database: PDB / ID: 9xbn
TitleCryo-EM structure of Sup35NM fibril formed at 4 degrees (Sc4)
ComponentsEukaryotic peptide chain release factor GTP-binding subunit
KeywordsPROTEIN FIBRIL / Yeast / Sup35NM / Amyloid
Function / homology
Function and homology information


Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytoplasmic stress granule / regulation of translation / ribosome binding ...Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytoplasmic stress granule / regulation of translation / ribosome binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / mRNA binding / GTPase activity / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / : / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain ...Eukaryotic peptide chain release factor GTP-binding subunit / : / GTP-eEF1A C-terminal domain-like / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNomura, T. / Boyer, D.R. / Tanaka, M.
Funding support Japan, France, United States, 11items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)21gm1410009 Japan
Japan Society for the Promotion of Science (JSPS)20H00501 Japan
Japan Society for the Promotion of Science (JSPS)24H00603 Japan
Japan Society for the Promotion of Science (JSPS)21H05257 Japan
Human Frontier Science Program (HFSP)RGP0010/2011 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032543 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG048120 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG070895 United States
Japan Society for the Promotion of Science (JSPS)22K15067 Japan
Japan Society for the Promotion of Science (JSPS)JP25830025 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R24GM154186 United States
CitationJournal: Res Sq / Year: 2025
Title: How Sup35 monomer conformation and amyloid fibril polymorphism determine yeast strain phenotypes.
Authors: Motomasa Tanaka / Takashi Nomura / David Boyer / Yusuke Komi / Peng Ge / Rodrigo A Maillard / Piere Rodriguez / Atsushi Yamagata / Mikako Shirouzu / Giuseppe Legname / Bruno Samori / David Eisenberg /
Abstract: In the [ ] prion system, the yeast prion protein Sup35 can form structurally distinct amyloid fibrils that lead to distinct transmissible prion states, or strains. However, our understanding of how ...In the [ ] prion system, the yeast prion protein Sup35 can form structurally distinct amyloid fibrils that lead to distinct transmissible prion states, or strains. However, our understanding of how different Sup35 fibril structures arise and translate to phenotypic variations is limited. Here, using cryo-EM and single-monomer force spectroscopy with optical tweezers, we reveal the structural basis of yeast prion propagation in four wild-type and S17R mutant variants of Sup35 that underlie different [ ] strains. Cryo-EM structures show that the four variants form strikingly distinct fibril structures, which exhibit varying stability and chaperone-accessibility. Force spectroscopy suggests the different distinct fibril structures are derived from distinct monomer conformational ensembles. Further, cryo-EM structures indicate that prion strain strength is correlated with enhanced fibril propagation caused by a combination of low fibril stability and a large separation between the Sup35 fibril core and the Ssa1/Sis1 chaperone-binding region. These results provide a structure-based mechanism for the yeast prion strain phenomenon with implications for understanding amyloid propagation in human neurodegenerative diseases.
History
DepositionOct 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic peptide chain release factor GTP-binding subunit
B: Eukaryotic peptide chain release factor GTP-binding subunit
C: Eukaryotic peptide chain release factor GTP-binding subunit
D: Eukaryotic peptide chain release factor GTP-binding subunit
E: Eukaryotic peptide chain release factor GTP-binding subunit


Theoretical massNumber of molelcules
Total (without water)147,5675
Polymers147,5675
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Eukaryotic peptide chain release factor GTP-binding subunit / ERF-3 / ERF3 / ERF2 / G1 to S phase transition protein 1 / Omnipotent suppressor protein 2 / PSI no ...ERF-3 / ERF3 / ERF2 / G1 to S phase transition protein 1 / Omnipotent suppressor protein 2 / PSI no more protein 2 / Polypeptide release factor 3 / Translation release factor 3


Mass: 29513.445 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUP35, GST1, PNM2, SAL3, SUF12, SUP2, YDR172W, YD9395.05
Production host: Escherichia coli (E. coli)
References: UniProt: P05453, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid fibril of Sup35NM Sc4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.21_5207model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.82 ° / Axial rise/subunit: 4.83 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86542 / Symmetry type: HELICAL
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0041660
ELECTRON MICROSCOPYf_angle_d0.5722225
ELECTRON MICROSCOPYf_dihedral_angle_d3.776225
ELECTRON MICROSCOPYf_chiral_restr0.036170
ELECTRON MICROSCOPYf_plane_restr0.006335

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