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- EMDB-50860: Cryo EM map of the type 2A polymorph of alpha-synuclein at pH 7.0. -

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Basic information

Entry
Database: EMDB / ID: EMD-50860
TitleCryo EM map of the type 2A polymorph of alpha-synuclein at pH 7.0.
Map data
Sample
  • Complex: alpha-synuclein amyloid fibril
    • Protein or peptide: alpha-synuclein
Keywordsamyloid / polymorphism / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsFrey L / Qureshi BM / Kwiatkowski W / Rhyner D / Greenwald J / Riek R
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Other government
CitationJournal: Elife / Year: 2024
Title: On the pH-dependence of alpha-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation
Authors: Frey L / Ghosh D / Qureshi BM / Rhyner D / Guerrero-Ferreira R / Pokharna A / Kwiatkowski W / Serdiuk T / Picotti P / Riek R / Greenwald J
History
DepositionJul 3, 2024-
SupersessionJul 17, 2024ID: EMD-50076
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50860.png

Downloads & links

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Map

FileDownload / File: emd_50860.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.089811124 - 0.18602459
Average (Standard dev.)0.00075981213 (±0.008253986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50860_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50860_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha-synuclein amyloid fibril

EntireName: alpha-synuclein amyloid fibril
Components
  • Complex: alpha-synuclein amyloid fibril
    • Protein or peptide: alpha-synuclein

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Supramolecule #1: alpha-synuclein amyloid fibril

SupramoleculeName: alpha-synuclein amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: alpha-synuclein

MacromoleculeName: alpha-synuclein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFMKGLSK AKEGVVAAA E KTKQGVAE AA GKTKEGV LYV GSKTKE GVVH GVATV AEKTK EQVT NVGGAV VTG VTAVAQK TV EGAGSIAA A TGFVKKDQL GKNEEGAPQE GILEDMPVD P DNEAYEMP SE EGYQDYE PEA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMPO4Phosphate
137.0 mMNaClSodium Chloride
2.7 mMKClPotassiu Chloride
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1339 / Average exposure time: 1.0 sec. / Average electron dose: 58.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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 reconstructionApplied symmetry - Helical parameters - Δz: 4.82 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.80 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 91238
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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