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Yorodumi- EMDB-50077: Cryo EM map of the type 2B polymorph of alpha-synuclein at pH 7.0. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50077 | |||||||||
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Title | Cryo EM map of the type 2B polymorph of alpha-synuclein at pH 7.0. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | amyloid / polymorphism / PROTEIN FIBRIL | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | Frey L / Qureshi BM / Kwiatkowski W / Rhyner D / Greenwald J / Riek R | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: Elife / Year: 2023 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 / Pokharna A / Guerrero-Ferreira R / Kwiatkowski W / Serdiuk T / Picotti P / Riek R / Greenwald J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50077.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-50077-v30.xml emd-50077.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50077_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_50077.png | 53.9 KB | ||
Filedesc metadata | emd-50077.cif.gz | 4.8 KB | ||
Others | emd_50077_half_map_1.map.gz emd_50077_half_map_2.map.gz | 22.3 MB 22.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50077 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50077 | HTTPS FTP |
-Validation report
Summary document | emd_50077_validation.pdf.gz | 701.5 KB | Display | EMDB validaton report |
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Full document | emd_50077_full_validation.pdf.gz | 701.1 KB | Display | |
Data in XML | emd_50077_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_50077_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50077 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50077 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50077.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_50077_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50077_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : alpha-synuclein amyloid fibril
Entire | Name: alpha-synuclein amyloid fibril |
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Components |
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-Supramolecule #1: alpha-synuclein amyloid fibril
Supramolecule | Name: alpha-synuclein amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: alpha-synuclein
Macromolecule | Name: alpha-synuclein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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