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- EMDB-15366: Vairimorpha necatrix 26S proteasome from sporoplasms -

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Basic information

Entry
Database: EMDB / ID: EMD-15366
TitleVairimorpha necatrix 26S proteasome from sporoplasms
Map data
Sample
  • Complex: 26S proteasomeProteasome
KeywordsPeptidase Activity / Reductive Evolution / Bound Peptide / Microsporidia / HYDROLASE
Biological speciesVairimorpha necatrix (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsJespersen N / Ehrenbolger K / Winiger R / Svedberg D / Vossbrinck CR / Barandun J
Funding support Sweden, European Union, 2 items
OrganizationGrant numberCountry
Swedish Research Council2019-02011 Sweden
European Research Council (ERC)948655European Union
CitationJournal: 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
DepositionJul 9, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15366.png

Downloads & links

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Map

FileDownload / File: emd_15366.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 400 pix.
= 598. Å		1.5 Å/pix.
x 400 pix.
= 598. Å		1.5 Å/pix.
x 400 pix.
= 598. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.495 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.5319203 - 1.7381142
Average (Standard dev.)0.0070050647 (±0.09603073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 598.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15366_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15366_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : 26S proteasome

EntireName: 26S proteasomeProteasome
Components
  • Complex: 26S proteasomeProteasome

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Supramolecule #1: 26S proteasome

SupramoleculeName: 26S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14 / Details: Purified from sporoplasms
Source (natural)Organism: Vairimorpha necatrix (fungus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris-HClTris
100.0 mMSodium ChlorideNaClSodium chloride
1.0 mMDTT
10.0 mMMagnesium ChlorideMgCl2
20.0 mMATPAdenosine triphosphate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 8.78 sec. / Average electron dose: 40.0 e/Å2

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 6442
FSC plot (resolution estimation)

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