+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15365 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Vairimorpha necatrix 20S proteasome from spores | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Peptidase Activity / Reductive Evolution / Bound Peptide / Microsporidia / HYDROLASE | |||||||||
Biological species | Vairimorpha necatrix (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||
Authors | Jespersen N / Ehrenbolger K / Winiger R / Svedberg D / Vossbrinck CR / Barandun J | |||||||||
Funding support | Sweden, European Union, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores. Authors: Nathan Jespersen / Kai Ehrenbolger / Rahel R Winiger / Dennis Svedberg / Charles R Vossbrinck / Jonas Barandun / Abstract: Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis in environments with limited resources. In microsporidia, divergent ...Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis in environments with limited resources. In microsporidia, divergent parasites with extraordinarily streamlined genomes, the proteasome complexity and structure are unknown, which limits our understanding of how these unique pathogens adapt and compact essential eukaryotic complexes. We present cryo-electron microscopy structures of the microsporidian 20S and 26S proteasome isolated from dormant or germinated Vairimorpha necatrix spores. The discovery of PI31-like peptides, known to inhibit proteasome activity, bound simultaneously to all six active sites within the central cavity of the dormant spore proteasome, suggests reduced activity in the environmental stage. In contrast, the absence of the PI31-like peptides and the existence of 26S particles post-germination in the presence of ATP indicates that proteasomes are reactivated in nutrient-rich conditions. Structural and phylogenetic analyses reveal that microsporidian proteasomes have undergone extensive reductive evolution, lost at least two regulatory proteins, and compacted nearly every subunit. The highly derived structure of the microsporidian proteasome, and the minimized version of PI31 presented here, reinforce the feasibility of the development of specific inhibitors and provide insight into the unique evolution and biology of these medically and economically important pathogens. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_15365.map.gz | 230.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-15365-v30.xml emd-15365.xml | 33.9 KB 33.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15365_fsc.xml | 13.1 KB | Display | FSC data file |
Images | emd_15365.png | 187.3 KB | ||
Filedesc metadata | emd-15365.cif.gz | 8.2 KB | ||
Others | emd_15365_half_map_1.map.gz emd_15365_half_map_2.map.gz | 226 MB 226 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15365 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15365 | HTTPS FTP |
-Validation report
Summary document | emd_15365_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_15365_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_15365_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_15365_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15365 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15365 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_15365.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.042 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_15365_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15365_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : 20S proteasome
+Supramolecule #1: 20S proteasome
+Macromolecule #1: Proteasome Inhibitor 31-Like
+Macromolecule #2: Proteasome subunit alpha type-2
+Macromolecule #3: Proteasome subunit alpha type-3
+Macromolecule #4: Proteasome subunit alpha type-4
+Macromolecule #5: Proteasome subunit alpha type-5
+Macromolecule #6: Proteasome subunit alpha type-6
+Macromolecule #7: Proteasome subunit alpha type-7
+Macromolecule #8: Proteasome subunit alpha type-1
+Macromolecule #9: Proteasome subunit beta type-2
+Macromolecule #10: Proteasome subunit beta type-3
+Macromolecule #11: Proteasome subunit beta type-4
+Macromolecule #12: Proteasome subunit beta type-5
+Macromolecule #13: Proteasome subunit beta type-6
+Macromolecule #14: Proteasome subunit beta type-7
+Macromolecule #15: Proteasome subunit beta type-1
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Number grids imaged: 1 / #0 - Average exposure time: 5.0 sec. / #0 - Average electron dose: 35.01 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Detector mode: COUNTING / #1 - Number grids imaged: 1 / #1 - Average exposure time: 5.0 sec. / #1 - Average electron dose: 36.334 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 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 |