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Yorodumi- EMDB-25847: Cryo-EM structure of the 20S Alpha 3 Deletion proteasome core particle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25847 | |||||||||
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Title | Cryo-EM structure of the 20S Alpha 3 Deletion proteasome core particle | |||||||||
Map data | Final Map For 20S Alpha 3 Deletion | |||||||||
Sample |
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Keywords | PI31 / Fub1 / core particle / HYDROLASE | |||||||||
Function / homology | Function and homology information proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||
Authors | Walsh Jr RM / Rawson S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Yeast PI31 inhibits the proteasome by a direct multisite mechanism. Authors: Shaun Rawson / Richard M Walsh / Benjamin Velez / Helena M Schnell / Fenglong Jiao / Marie Blickling / Jessie Ang / Meera K Bhanu / Lan Huang / John Hanna / Abstract: Proteasome inhibitors are widely used as therapeutics and research tools, and typically target one of the three active sites, each present twice in the proteasome complex. An endogeneous proteasome ...Proteasome inhibitors are widely used as therapeutics and research tools, and typically target one of the three active sites, each present twice in the proteasome complex. An endogeneous proteasome inhibitor, PI31, was identified 30 years ago, but its inhibitory mechanism has remained unclear. Here, we identify the mechanism of Saccharomyces cerevisiae PI31, also known as Fub1. Using cryo-electron microscopy (cryo-EM), we show that the conserved carboxy-terminal domain of Fub1 is present inside the proteasome's barrel-shaped core particle (CP), where it simultaneously interacts with all six active sites. Targeted mutations of Fub1 disrupt proteasome inhibition at one active site, while leaving the other sites unaffected. Fub1 itself evades degradation through distinct mechanisms at each active site. The gate that allows substrates to access the CP is constitutively closed, and Fub1 is enriched in mutant CPs with an abnormally open gate, suggesting that Fub1 may function to neutralize aberrant proteasomes, thereby ensuring the fidelity of proteasome-mediated protein degradation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25847.map.gz | 168.2 MB | EMDB map data format | |
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Header (meta data) | emd-25847-v30.xml emd-25847.xml | 28 KB 28 KB | Display Display | EMDB header |
Images | emd_25847.png | 37.9 KB | ||
Filedesc metadata | emd-25847.cif.gz | 8.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25847 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25847 | HTTPS FTP |
-Validation report
Summary document | emd_25847_validation.pdf.gz | 576.2 KB | Display | EMDB validaton report |
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Full document | emd_25847_full_validation.pdf.gz | 575.7 KB | Display | |
Data in XML | emd_25847_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_25847_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25847 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25847 | HTTPS FTP |
-Related structure data
Related structure data | 7tejMC 7teoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25847.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Final Map For 20S Alpha 3 Deletion | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : 20S proteasome from alpha3delta proteasome mutant
+Supramolecule #1: 20S proteasome from alpha3delta proteasome mutant
+Macromolecule #1: Proteasome subunit beta type-6
+Macromolecule #2: Proteasome subunit beta type-7
+Macromolecule #3: Proteasome subunit alpha type-1
+Macromolecule #4: Proteasome subunit alpha type-2
+Macromolecule #5: Proteasome subunit alpha type-4
+Macromolecule #6: Proteasome subunit alpha type-5
+Macromolecule #7: Proteasome subunit alpha type-6
+Macromolecule #8: Proteasome subunit alpha type-7
+Macromolecule #9: Proteasome subunit beta type-1
+Macromolecule #10: Proteasome subunit beta type-2
+Macromolecule #11: Proteasome subunit beta type-3
+Macromolecule #12: Proteasome subunit beta type-4
+Macromolecule #13: Proteasome subunit beta type-5
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.8 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
Details: Fluorinated Fos-Choline was added to the sample immediately prior to deposition on a grid for plunge freezing. | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 30 s glow discharge at 15 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 4.0 sec. / Average electron dose: 53.85 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 47169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7tej: |