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- PDB-8adn: Vairimorpha necatrix 20S proteasome from spores -

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Basic information

Entry
Database: PDB / ID: 8adn
TitleVairimorpha necatrix 20S proteasome from spores
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • Proteasome Inhibitor 31-Like
KeywordsHYDROLASE / Peptidase Activity / Reductive Evolution / Bound Peptide / Microsporidia
Biological speciesVairimorpha necatrix (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsJespersen, N. / Ehrenbolger, K. / Winiger, R. / Svedberg, D. / Vossbrinck, C.R. / Barandun, J.
Funding support Sweden, European Union, 2items
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 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
3: Proteasome Inhibitor 31-Like
4: Proteasome Inhibitor 31-Like
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1


Theoretical massNumber of molelcules
Total (without water)757,79530
Polymers757,79530
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area122160 Å2
ΔGint-535 kcal/mol
Surface area202680 Å2
MethodPISA

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Components

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Protein , 1 types, 2 molecules 34

#1: Protein Proteasome Inhibitor 31-Like /


Mass: 17070.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)

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Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#2: Protein Proteasome subunit alpha type-2 /


Mass: 25849.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#3: Protein Proteasome subunit alpha type-3 /


Mass: 26848.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#4: Protein Proteasome subunit alpha type-4 /


Mass: 25596.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#5: Protein Proteasome subunit alpha type-5 /


Mass: 26520.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#6: Protein Proteasome subunit alpha type-6 /


Mass: 26297.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#7: Protein Proteasome subunit alpha type-7 /


Mass: 27835.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#8: Protein Proteasome subunit alpha type-1 /


Mass: 26308.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#9: Protein Proteasome subunit beta type-2 / PSMB2


Mass: 24776.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#10: Protein Proteasome subunit beta type-3 / PSMB3


Mass: 23016.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#11: Protein Proteasome subunit beta type-4 / PSMB4


Mass: 21945.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#12: Protein Proteasome subunit beta type-5 / PSMB5


Mass: 25290.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#13: Protein Proteasome subunit beta type-6 /


Mass: 34081.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#14: Protein Proteasome subunit beta type-7 /


Mass: 23806.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)
#15: Protein Proteasome subunit beta type-1 / PSMB1


Mass: 23654.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vairimorpha necatrix (fungus) / Production host: Vairimorpha necatrix (fungus)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 20S proteasomeProteasome / Type: COMPLEX / Details: Purified from spores / Entity ID: all / Source: NATURAL
Source (natural)Organism: Vairimorpha necatrix (fungus)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HClTris1
2300 mMSodium ChlorideNaClSodium chloride1
35 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Detector modeFilm or detector modelNum. of grids imaged
11535.01COUNTINGGATAN K2 QUANTUM (4k x 4k)1
21536.334COUNTINGGATAN K2 QUANTUM (4k x 4k)1

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.14CTF correction
7Cootmodel fitting
9RELION3.1initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
11cryoSPARC3.3.2classification
12cryoSPARC3.3.23D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52679 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 5CZ4

5cz4


Accession code: 5CZ4 / Source name: PDB / Type: experimental model

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