+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19461 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Alpha-synuclein amyloid fibrils with WT DNAJB1 | ||||||||||||
Map data | Postprocessed map of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1 | ||||||||||||
Sample |
| ||||||||||||
Keywords | Chaperones / amyloid fibril / disaggregation / PROTEIN FIBRIL | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 11.16 Å | ||||||||||||
Authors | Saibil HR / Monistrol J | ||||||||||||
Funding support | United Kingdom, 3 items
| ||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_19461.map.gz | 932.6 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-19461-v30.xml emd-19461.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_19461.png | 29.1 KB | ||
Masks | emd_19461_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-19461.cif.gz | 4.2 KB | ||
Others | emd_19461_half_map_1.map.gz emd_19461_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19461 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19461 | HTTPS FTP |
-Validation report
Summary document | emd_19461_validation.pdf.gz | 601.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_19461_full_validation.pdf.gz | 600.9 KB | Display | |
Data in XML | emd_19461_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | emd_19461_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19461 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19461 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_19461.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Postprocessed map of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.575 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_19461_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Unfiltered half map #1 of the complex formed...
File | emd_19461_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unfiltered half map #1 of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Unfiltered half map #2 of the complex formed...
File | emd_19461_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unfiltered half map #2 of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Alpha-synuclein amyloid fibril with WT DNAJB1
Entire | Name: Alpha-synuclein amyloid fibril with WT DNAJB1 |
---|---|
Components |
|
-Supramolecule #1: Alpha-synuclein amyloid fibril with WT DNAJB1
Supramolecule | Name: Alpha-synuclein amyloid fibril with WT DNAJB1 / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Component:
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: C-flat-2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 40.0 Å Applied symmetry - Helical parameters - Δ&Phi: -7.2 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 11.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199136 |
---|---|
Startup model | Type of model: OTHER Details: relion_helix_inimodel2d using fibre crossover distance |
Final angle assignment | Type: NOT APPLICABLE |