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- EMDB-67558: Cryo-EM structure of ex vivo Sup35 prion fibrils from yeast carry... -

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Basic information

Entry
Database: EMDB / ID: EMD-67558
TitleCryo-EM structure of ex vivo Sup35 prion fibrils from yeast carrying "strong" [PSI+] variant
Map data
Sample
  • Complex: Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant
    • Protein or peptide: Amyloid of yeast prion Sup35
KeywordsAmyloid / prion / yeast / in vivo / natural / PROTEIN FIBRIL
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChesnokov YM / Burtseva AD / Dergalev AA / Baimukhametov TN / Kushnirov VV / Popov VO / Boyko KM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: To Be Published
Title: CryoEM structure of ex vivo extracted Sup35 prion fibrils provides insights into [PSI+] prion phenotype determination and stability
Authors: Dergalev AA / Chesnokov YM / Burtseva AD / Kushnirov VV / Boyko KM / Popov VO
History
DepositionDec 6, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67558.png

Downloads & links

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Map

FileDownload / File: emd_67558.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 331.392 Å		1.29 Å/pix.
x 256 pix.
= 331.392 Å		1.29 Å/pix.
x 256 pix.
= 331.392 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2945 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-5.1244497 - 10.738823
Average (Standard dev.)0.011324733 (±0.2147306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.392 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67558_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67558_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_67558_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant

EntireName: Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant
Components
  • Complex: Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant
    • Protein or peptide: Amyloid of yeast prion Sup35

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Supramolecule #1: Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant

SupramoleculeName: Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 74-D694
Molecular weightTheoretical: 14 kDa/nm

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Macromolecule #1: Amyloid of yeast prion Sup35

MacromoleculeName: Amyloid of yeast prion Sup35 / type: protein_or_peptide / ID: 1
Details: Five identical Sup35 prion domain chains of an amyloid fibril with left-handed helical symmetry. Chains in the amyloid are related by staggered displacements and rotations along the fibril axis.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: Strong [PSI+] variant strain
Molecular weightTheoretical: 17.995439 KDa
SequenceString:
(ACE)SDSNQGNNQ QNYQQYSQNG NQQQGNNRYQ GYQAYNAQAQ PAGGYYQNYQ GYSGYQQGGY QQYNPDAGYQ QQYNPQ GGY QQYNPQGGYQ QQFNPQGDDD NEDSEEDDED GGPRGSRANA TKKVGTKPAE SDKKEEEKSA ETKEPTKEPT KVEEPVK KE EK

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.38 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC4H12ClNO3Tris-HCl
150.0 mMNaClNaCl
34.0 mMC15H28NNaO3sarcosyl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 80.0 K
Specialist opticsSpherical aberration corrector: Cs image corrector (CEOS GmbH)
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM (ver. 4.055)
DetailsCs corrected, 3x3 holes (2 exposures per hole) image-shift data acquisition strategy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 57937 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.782 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.388 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 50658
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 1259000 / Software - Name: crYOLO (ver. 1.9)
Details: Filaments were automatically picked with crYOLO using an inter-box step of 24 angstrom (five helical units per step).
Startup modelType of model: OTHER
Details: An initial ab initio 3D helical model was generated from 2D class averages using relion_helix_inimodel2d (RELION-5), assuming left-handed symmetry for the amyloid fibril.
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.6)
Details: Automatically determined during cryoSPARC helical refinement (no external angular assignments).
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
chain_id: A, residue_range: 2-64, source_name: Other, initial_model_type: otherInitial monomer built in Coot
chain_id: B, residue_range: 2-64, source_name: Other, initial_model_type: otherRigid-body copy of chain A
chain_id: C, residue_range: 2-64, source_name: Other, initial_model_type: otherRigid-body copy of chain A
chain_id: D, residue_range: 2-64, source_name: Other, initial_model_type: otherRigid-body copy of chain A
chain_id: E, residue_range: 2-64, source_name: Other, initial_model_type: otherRigid-body copy of chain A
SoftwareName: PHENIX (ver. 1.21.2_5419)
DetailsA single protomer was built de novo into the sharpened map in Coot, with unambiguous sequence assignment. The built protomer was stacked into a five-layer segment by rigid-body placement in UCSF Chimera, and the resulting model was refined in PHENIX real-space refine with NCS constraints between the five chains and individual ADPs.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 59.7 / Target criteria: Maximum likelihood with map correlation
Output model

PDB-21bq:
Cryo-EM structure of ex vivo Sup35 prion fibrils from yeast carrying "strong" [PSI+] variant

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