+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4092 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tomographic reconstruction of ex vivo mammalian prions | |||||||||
Map data | None | |||||||||
Sample |
| |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / negative staining | |||||||||
Authors | Terry C / Wenborn A / Gros N / Sells J / Joiner S / Hosszu LLP / Tattum MH / Panico S / Clare DK / Collinge J ...Terry C / Wenborn A / Gros N / Sells J / Joiner S / Hosszu LLP / Tattum MH / Panico S / Clare DK / Collinge J / Saibil HR / Wadsworth JDF | |||||||||
Citation | Journal: Open Biol / Year: 2016 Title: Ex vivo mammalian prions are formed of paired double helical prion protein fibrils. Authors: Cassandra Terry / Adam Wenborn / Nathalie Gros / Jessica Sells / Susan Joiner / Laszlo L P Hosszu / M Howard Tattum / Silvia Panico / Daniel K Clare / John Collinge / Helen R Saibil / Jonathan D F Wadsworth / Abstract: Mammalian prions are hypothesized to be fibrillar or amyloid forms of prion protein (PrP), but structures observed to date have not been definitively correlated with infectivity and the three- ...Mammalian prions are hypothesized to be fibrillar or amyloid forms of prion protein (PrP), but structures observed to date have not been definitively correlated with infectivity and the three-dimensional structure of infectious prions has remained obscure. Recently, we developed novel methods to obtain exceptionally pure preparations of prions from mouse brain and showed that pathogenic PrP in these high-titre preparations is assembled into rod-like assemblies. Here, we have used precise cell culture-based prion infectivity assays to define the physical relationship between the PrP rods and prion infectivity and have used electron tomography to define their architecture. We show that infectious PrP rods isolated from multiple prion strains have a common hierarchical assembly comprising twisted pairs of short fibres with repeating substructure. The architecture of the PrP rods provides a new structural basis for understanding prion infectivity and can explain the inability to systematically generate high-titre synthetic prions from recombinant PrP. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4092.map.gz | 17.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4092-v30.xml emd-4092.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_4092.png | 65.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4092 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4092 | HTTPS FTP |
-Validation report
Summary document | emd_4092_validation.pdf.gz | 262.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4092_full_validation.pdf.gz | 261.4 KB | Display | |
Data in XML | emd_4092_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4092 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4092 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4092.map.gz / Format: CCP4 / Size: 23.7 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.153 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Infectious prion rods
Entire | Name: Infectious prion rods |
---|---|
Components |
|
-Supramolecule #1: Infectious prion rods
Supramolecule | Name: Infectious prion rods / type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: Ex vivo, isolated from prion-infected mouse brain (prion strain ME7) |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / Strain: C57Bl/6 / Organ: Brain |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | electron tomography |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 Component:
| ||||||
---|---|---|---|---|---|---|---|
Staining | Type: NEGATIVE / Material: Uranyl Acetate / Details: 2% (w/v) | ||||||
Grid | Model: Electron Microscopy Sciences / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||
Details | Prions isolated from mouse brain, approximate concentration 3 ug/ml | ||||||
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TECNAI 12 |
---|---|
Image recording | Film or detector model: GATAN MULTISCAN / Digitization - Dimensions - Width: 1024 pixel / Digitization - Dimensions - Height: 1024 pixel / Digitization - Sampling interval: 15.0 µm / Number grids imaged: 1 / Number real images: 1 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2 Details: This is a representative tomogram of many samples and grids imaged. |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 58594 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: OTHER |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.3) / Number images used: 51 |
---|