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Yorodumi- EMDB-19448: Alpha-synuclein amyloid fibrils with DNAJB1-Helix V mutant, HSC70... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19448 | ||||||||||||
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Title | Alpha-synuclein amyloid fibrils with DNAJB1-Helix V mutant, HSC70, HSP110 and ATP | ||||||||||||
Map data | Tomogram of alpha-synuclein amyloid fibrils incubated with a variant of DNAJB1 mutated in helix V, Hsc70, Hsp110 and ATP | ||||||||||||
Sample |
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Keywords | Chaperones / amyloid fibril / disaggregation / PROTEIN FIBRIL | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Saibil HR / Monistrol J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Biorxiv / Year: 2024 Title: Stepwise recruitment of Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibre disassembly Authors: Monistrol J / Beton JG / Johnston EC / Saibil HR | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19448.map.gz | 6 GB | EMDB map data format | |
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Header (meta data) | emd-19448-v30.xml emd-19448.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_19448.png | 181.2 KB | ||
Filedesc metadata | emd-19448.cif.gz | 4.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19448 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19448 | HTTPS FTP |
-Validation report
Summary document | emd_19448_validation.pdf.gz | 425.8 KB | Display | EMDB validaton report |
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Full document | emd_19448_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | emd_19448_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_19448_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19448 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19448 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19448.map.gz / Format: CCP4 / Size: 6.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Tomogram of alpha-synuclein amyloid fibrils incubated with a variant of DNAJB1 mutated in helix V, Hsc70, Hsp110 and ATP | ||||||||||||||||||||
Voxel size | X=Y=Z: 3.8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Alpha-synuclein amyloid fibrils incubated with a helix V mutant o...
Entire | Name: Alpha-synuclein amyloid fibrils incubated with a helix V mutant of DNAJB1, HSC70, HSP110 and ATP |
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Components |
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-Supramolecule #1: Alpha-synuclein amyloid fibrils incubated with a helix V mutant o...
Supramolecule | Name: Alpha-synuclein amyloid fibrils incubated with a helix V mutant of DNAJB1, HSC70, HSP110 and ATP type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: LEICA EM GP | ||||||||||||||||||||||||
Sectioning | Other: NO SECTIONING | ||||||||||||||||||||||||
Fiducial marker | Manufacturer: EMS / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 116.0 e/Å2 Details: Note: the original pixel size for the tomogram recording was 1.94 A/pixel. This was subsequently rounded to 1.9 A/pixel and the 2x binned tomogram deposited here is listed as 3.8 A/pixel. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.4 µm / Nominal defocus min: 2.0 µm |
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
Details | Note: the original tomogram was recorded at 1.94 A/pixel, but this was rounded to 1.9 A/pixel, so the 2x binned tomogram provided here is at 3.8 A/pixel |
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Final reconstruction | Software - Name: RELION (ver. 4) / Number images used: 121 |