+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41993 | |||||||||
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Title | Proteasome 20S Core Particle from Beta 3 D205 deletion | |||||||||
Map data | Map of Proteasome 20S core particle from B3 D205 deletion | |||||||||
Sample |
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Keywords | Proteasome / 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: 2.16 Å | |||||||||
Authors | Walsh Jr RM / Rawson S / Velez B / Blickling M / Razi A / Hanna J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Mechanism of autocatalytic activation during proteasome assembly. Authors: Benjamin Velez / Richard M Walsh / Shaun Rawson / Aida Razi / Lea Adams / Erignacio Fermin Perez / Fenglong Jiao / Marie Blickling / Tamayanthi Rajakumar / Darlene Fung / Lan Huang / John Hanna / Abstract: Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the ...Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the proteasome, where protein degradation occurs, its six active sites are simultaneously activated via cleavage of N-terminal propeptides. Such activation is autocatalytic and coupled to fusion of two half-CP intermediates, which protects cells by preventing activation until enclosure of the active sites within the CP interior. Here we uncover key mechanistic aspects of autocatalytic activation, which proceeds through alignment of the β5 and β2 catalytic triad residues, respectively, with these triads being misaligned before fusion. This mechanism contrasts with most other zymogens, in which catalytic centers are preformed. Our data also clarify the mechanism by which individual subunits can be added in a precise, temporally ordered manner. This work informs two decades-old mysteries in the proteasome field, with broader implications for protease biology and multisubunit complex assembly. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41993.map.gz | 159.3 MB | EMDB map data format | |
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Header (meta data) | emd-41993-v30.xml emd-41993.xml | 33.6 KB 33.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41993_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_41993.png | 25.6 KB | ||
Filedesc metadata | emd-41993.cif.gz | 8.8 KB | ||
Others | emd_41993_half_map_1.map.gz emd_41993_half_map_2.map.gz | 157.1 MB 157.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41993 | HTTPS FTP |
-Validation report
Summary document | emd_41993_validation.pdf.gz | 955.9 KB | Display | EMDB validaton report |
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Full document | emd_41993_full_validation.pdf.gz | 955.6 KB | Display | |
Data in XML | emd_41993_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_41993_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41993 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41993 | HTTPS FTP |
-Related structure data
Related structure data | 8u7uMC 8u6yC C: citing same article (ref.) M: atomic model generated by this map |
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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_41993.map.gz / Format: CCP4 / Size: 169.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map of Proteasome 20S core particle from B3 D205 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
-Half map: Half Map B of Proteasome 20S core particle from B3 D205 deletion
File | emd_41993_half_map_1.map | ||||||||||||
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Annotation | Half Map B of Proteasome 20S core particle from B3 D205 deletion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A of Proteasome 20S core particle...
File | emd_41993_half_map_2.map | ||||||||||||
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Annotation | Half Map A of Proteasome 20S core particle from B3 D205 deletionMap of Proteasome 20S core particle from B3 D205 deletion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Proteasome 20S Core Particle from Beta 3 D205 deletion mutant
+Supramolecule #1: Proteasome 20S Core Particle from Beta 3 D205 deletion mutant
+Macromolecule #1: Proteasome subunit alpha type-5
+Macromolecule #2: Proteasome subunit alpha type-2
+Macromolecule #3: Proteasome subunit beta type-1
+Macromolecule #4: Proteasome subunit alpha type-6
+Macromolecule #5: Proteasome subunit beta type-6
+Macromolecule #6: Proteasome subunit beta type-4
+Macromolecule #7: Proteasome subunit alpha type-7
+Macromolecule #8: Proteasome subunit beta type-7
+Macromolecule #9: Proteasome subunit beta type-2
+Macromolecule #10: Proteasome subunit beta type-5
+Macromolecule #11: Proteasome subunit alpha type-3
+Macromolecule #12: Proteasome subunit alpha type-1
+Macromolecule #13: Proteasome subunit beta type-3
+Macromolecule #14: Proteasome subunit alpha type-4
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.48 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: Fluorinated Fos-Choline was added immediately prior to deposition on a grid for plunge freezing. | ||||||||||||
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 / Number real images: 7461 / Average exposure time: 3.995 sec. / Average electron dose: 57.0 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 |