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- EMDB-17118: 20S proteasome & CBR3 complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-17118
Title20S proteasome & CBR3 complex
Map dataRat 20S proteasome & Human CBR3 complex
Sample
  • Complex: Rat 20S proteasome complex with CBR3
    • Complex: Human CBR3
KeywordsComplex / PROTEIN BINDING
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsDeshmukh FK / Sharon M
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation300/17 Israel
CitationJournal: Nat Commun / Year: 2023
Title: Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family.
Authors: Fanindra Kumar Deshmukh / Gili Ben-Nissan / Maya A Olshina / Maria G Füzesi-Levi / Caley Polkinghorn / Galina Arkind / Yegor Leushkin / Irit Fainer / Sarel J Fleishman / Dan Tawfik / Michal Sharon /
Abstract: Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the degradation routes involves the uncapped 20S ...Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the degradation routes involves the uncapped 20S proteasome, which cleaves proteins with a partially unfolded region, including those that are damaged or contain intrinsically disordered regions. This degradation route is tightly controlled by a recently discovered family of proteins named Catalytic Core Regulators (CCRs). Here, we show that CCRs function through an allosteric mechanism, coupling the physical binding of the PSMB4 β-subunit with attenuation of the complex's three proteolytic activities. In addition, by dissecting the structural properties that are required for CCR-like function, we could recapitulate this activity using a designed protein that is half the size of natural CCRs. These data uncover an allosteric path that does not involve the proteasome's enzymatic subunits but rather propagates through the non-catalytic subunit PSMB4. This way of 20S proteasome-specific attenuation opens avenues for decoupling the 20S and 26S proteasome degradation pathways as well as for developing selective 20S proteasome inhibitors.
History
DepositionApr 13, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17118.png

Downloads & links

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Map

FileDownload / File: emd_17118.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRat 20S proteasome & Human CBR3 complex
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.0022
Minimum - Maximum-0.029417533 - 0.060780037
Average (Standard dev.)0.00012266039 (±0.0032198436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 476.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17118_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17118_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rat 20S proteasome complex with CBR3

EntireName: Rat 20S proteasome complex with CBR3
Components
  • Complex: Rat 20S proteasome complex with CBR3
    • Complex: Human CBR3

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Supramolecule #1: Rat 20S proteasome complex with CBR3

SupramoleculeName: Rat 20S proteasome complex with CBR3 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #2: Human CBR3

SupramoleculeName: Human CBR3 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number real images: 596 / Average exposure time: 60.0 sec. / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4r3o

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30273
FSC plot (resolution estimation)

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