+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40944 | |||||||||
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Title | Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant | |||||||||
Map data | Final Map of Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant | |||||||||
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 / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...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 / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Walsh Jr RM / Rawson S / Schnell H / Velez B / Hanna J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure of the preholoproteasome reveals late steps in proteasome core particle biogenesis. Authors: Richard M Walsh / Shaun Rawson / Helena M Schnell / Benjamin Velez / Tamayanthi Rajakumar / John Hanna / Abstract: Assembly of the proteasome's core particle (CP), a barrel-shaped chamber of four stacked rings, requires five chaperones and five subunit propeptides. Fusion of two half-CP precursors yields a ...Assembly of the proteasome's core particle (CP), a barrel-shaped chamber of four stacked rings, requires five chaperones and five subunit propeptides. Fusion of two half-CP precursors yields a complete structure but remains immature until active site maturation. Here, using Saccharomyces cerevisiae, we report a high-resolution cryogenic electron microscopy structure of preholoproteasome, a post-fusion assembly intermediate. Our data reveal how CP midline-spanning interactions induce local changes in structure, facilitating maturation. Unexpectedly, we find that cleavage may not be sufficient for propeptide release, as residual interactions with chaperones such as Ump1 hold them in place. We evaluated previous models proposing that dynamic conformational changes in chaperones drive CP fusion and autocatalytic activation by comparing preholoproteasome to pre-fusion intermediates. Instead, the data suggest a scaffolding role for the chaperones Ump1 and Pba1/Pba2. Our data clarify key aspects of CP assembly, suggest that undiscovered mechanisms exist to explain CP fusion/activation, and have relevance for diseases of defective CP biogenesis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40944.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-40944-v30.xml emd-40944.xml | 33.4 KB 33.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40944_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_40944.png | 33.1 KB | ||
Filedesc metadata | emd-40944.cif.gz | 8.7 KB | ||
Others | emd_40944_half_map_1.map.gz emd_40944_half_map_2.map.gz | 165.3 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40944 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40944 | HTTPS FTP |
-Related structure data
Related structure data | 8t0mMC 8t08C 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_40944.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Final Map of Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant | ||||||||||||||||||||
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 A of Proteasome 20S core particle...
File | emd_40944_half_map_1.map | ||||||||||||
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Annotation | Half Map A of Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B of Proteasome 20S core particle...
File | emd_40944_half_map_2.map | ||||||||||||
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Annotation | Half Map B of Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant
+Supramolecule #1: Proteasome 20S core particle from Pre1-1 Pre4-1 Double mutant
+Macromolecule #1: Proteasome subunit alpha type-1
+Macromolecule #2: Proteasome subunit alpha type-2
+Macromolecule #3: Proteasome subunit alpha type-3
+Macromolecule #4: Proteasome subunit alpha type-4
+Macromolecule #5: Proteasome subunit alpha type-5
+Macromolecule #6: Proteasome subunit alpha type-6
+Macromolecule #7: Proteasome subunit alpha type-7
+Macromolecule #8: Proteasome subunit beta type-1
+Macromolecule #9: Proteasome subunit beta type-2
+Macromolecule #10: Proteasome subunit beta type-3
+Macromolecule #11: Proteasome subunit beta type-4
+Macromolecule #12: Proteasome subunit beta type-5
+Macromolecule #13: Proteasome subunit beta type-6
+Macromolecule #14: Proteasome subunit beta type-7
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.4 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 | ||||||||||||
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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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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 33116 / Average exposure time: 3.8 sec. / Average electron dose: 54.3 e/Å2 |
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-8t0m: |