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- PDB-21bq: Cryo-EM structure of ex vivo Sup35 prion fibrils from yeast carry... -

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Basic information

Entry
Database: PDB / ID: 21bq
TitleCryo-EM structure of ex vivo Sup35 prion fibrils from yeast carrying "strong" [PSI+] variant
ComponentsAmyloid of yeast prion Sup35
KeywordsPROTEIN FIBRIL / Amyloid / prion / yeast / in vivo / natural
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChesnokov, Y.M. / Burtseva, A.D. / Dergalev, A.A. / Baimukhametov, T.N. / Kushnirov, V.V. / Popov, V.O. / Boyko, K.M.
Funding support Russian Federation, 1items
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, A.A. / Chesnokov, Y.M. / Burtseva, A.D. / Kushnirov, V.V. / Boyko, K.M. / Popov, V.O.
History
DepositionDec 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid of yeast prion Sup35
B: Amyloid of yeast prion Sup35
C: Amyloid of yeast prion Sup35
D: Amyloid of yeast prion Sup35
E: Amyloid of yeast prion Sup35


Theoretical massNumber of molelcules
Total (without water)89,9775
Polymers89,9775
Non-polymers00
Water00
1


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

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Components

#1: Protein
Amyloid of yeast prion Sup35


Mass: 17995.439 Da / Num. of mol.: 5 / Source method: isolated from a natural source
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.
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: Strong [PSI+] variant strain
Has ligand of interestY
Has protein modificationY

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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: Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 14 kDa/nm / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: 74-D694
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H12ClNO31
2150 mMNaClNaCl1
334 mMsarcosylC15H28NNaO31
SpecimenConc.: 0.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Cs corrected, 3x3 holes (2 exposures per hole) image-shift data acquisition strategy
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 57937 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 700 nm / Calibrated defocus max: 2000 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 77 K
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: Cs image corrector (CEOS GmbH)
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9particle selection
2SerialEM4.055image acquisition
4CTFFIND4.1CTF correction
7PHENIX1.21.2_5419model fitting
9cryoSPARC4.6initial Euler assignment
10cryoSPARC4.6final Euler assignment
11cryoSPARC4.6classification
12cryoSPARC4.63D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.388 ° / Axial rise/subunit: 4.782 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 1259000
Details: Filaments were automatically picked with crYOLO using an inter-box step of 24 angstrom (five helical units per step).
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50658 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 59.7 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Maximum likelihood with map correlation
Details: A 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 ...Details: A 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.
Atomic model building
ID 3D fitting-IDChain-IDChain residue rangeDetails (eV)Source nameType
11A2-64Initial monomer built in CootOtherother
21B2-64Rigid-body copy of chain AOtherother
31C2-64Rigid-body copy of chain AOtherother
41D2-64Rigid-body copy of chain AOtherother
51E2-64Rigid-body copy of chain AOtherother
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0052640
ELECTRON MICROSCOPYf_angle_d0.4533565
ELECTRON MICROSCOPYf_dihedral_angle_d14.911965
ELECTRON MICROSCOPYf_chiral_restr0.035265
ELECTRON MICROSCOPYf_plane_restr0.002540

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