+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28878 | |||||||||
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Title | Thermoplasma acidophilum 20S proteasome - wild type | |||||||||
Map data | WT T20S EM Density Map | |||||||||
Sample |
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Keywords | Protease / threonine protease / endopeptidase activity / HYDROLASE | |||||||||
Function / homology | Function and homology information proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.06 Å | |||||||||
Authors | Chuah J / Smith D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2023 Title: High resolution structures define divergent and convergent mechanisms of archaeal proteasome activation. Authors: Janelle J Y Chuah / Matthew S Rexroad / David M Smith / Abstract: Considering the link between neurodegenerative diseases and impaired proteasome function, and the neuro-protective impact of enhanced proteasome activity in animal models, it's crucial to understand ...Considering the link between neurodegenerative diseases and impaired proteasome function, and the neuro-protective impact of enhanced proteasome activity in animal models, it's crucial to understand proteasome activation mechanisms. A hydrophobic-tyrosine-any residue (HbYX) motif on the C-termini of proteasome-activating complexes independently triggers gate-opening of the 20S core particle for protein degradation; however, the causal allosteric mechanism remains unclear. Our study employs a structurally irreducible dipeptide HbYX mimetic to investigate the allosteric mechanism of gate-opening in the archaeal proteasome. High-resolution cryo-EM structures pinpoint vital residues and conformational changes in the proteasome α-subunit implicated in HbYX-dependent activation. Using point mutations, we simulated the HbYX-bound state, providing support for our mechanistic model. We discerned four main mechanistic elements triggering gate-opening: 1) back-loop rearrangement adjacent to K66, 2) intra- and inter- α subunit conformational changes, 3) occupancy of the hydrophobic pocket, and 4) a highly conserved isoleucine-threonine pair in the 20S channel stabilizing the open and closed states, termed the "IT switch." Comparison of different complexes unveiled convergent and divergent mechanism of 20S gate-opening among HbYX-dependent and independent activators. This study delivers a detailed molecular model for HbYX-dependent 20S gate-opening, enabling the development of small molecule proteasome activators that hold promise to treat neurodegenerative diseases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28878.map.gz | 255.6 MB | EMDB map data format | |
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Header (meta data) | emd-28878-v30.xml emd-28878.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28878_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_28878.png | 58.8 KB | ||
Others | emd_28878_half_map_1.map.gz emd_28878_half_map_2.map.gz | 474.8 MB 474.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28878 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28878 | HTTPS FTP |
-Validation report
Summary document | emd_28878_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_28878_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_28878_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | emd_28878_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28878 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28878 | HTTPS FTP |
-Related structure data
Related structure data | 8f6aMC 8f66C 8f7kC 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_28878.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | WT T20S EM Density Map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.54 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: WT T20S EM Density Map Half B
File | emd_28878_half_map_1.map | ||||||||||||
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Annotation | WT T20S EM Density Map Half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: WT T20S EM Density Map Half A
File | emd_28878_half_map_2.map | ||||||||||||
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Annotation | WT T20S EM Density Map Half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Wild-type Thermoplasma acidophilum 20S proteasome
Entire | Name: Wild-type Thermoplasma acidophilum 20S proteasome |
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Components |
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-Supramolecule #1: Wild-type Thermoplasma acidophilum 20S proteasome
Supramolecule | Name: Wild-type Thermoplasma acidophilum 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 700 kDa/nm |
-Macromolecule #1: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 23.169811 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MNQTLETGTT TVGITLKDAV IMATERRVTM ENFIMHKNGK KLFQIDTYTG MTIAGLVGDA QVLVRYMKAE LELYRLQRRV NMPIEAVAT LLSNMLNQVK YMPYMVQLLV GGIDTAPHVF SIDAAGGSVE DIYASTGSGS PFVYGVLESQ YSEKMTVDEG V DLVIRAIS ...String: MNQTLETGTT TVGITLKDAV IMATERRVTM ENFIMHKNGK KLFQIDTYTG MTIAGLVGDA QVLVRYMKAE LELYRLQRRV NMPIEAVAT LLSNMLNQVK YMPYMVQLLV GGIDTAPHVF SIDAAGGSVE DIYASTGSGS PFVYGVLESQ YSEKMTVDEG V DLVIRAIS AAKQRDSASG GMIDVAVITR KDGYVQLPTD QIESRIRKLG LIL UniProtKB: Proteasome subunit beta |
-Macromolecule #2: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 25.829447 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MQQGQMAYDR AITVFSPDGR LFQVEYAREA VKKGSTALGM KFANGVLLIS DKKVRSRLIE QNSIEKIQLI DDYVAAVTSG LVADARVLV DFARISAQQE KVTYGSLVNI ENLVKRVADQ MQQYTQYGGV RPYGVSLIFA GIDQIGPRLF DCDPAGTINE Y KATAIGSG ...String: MQQGQMAYDR AITVFSPDGR LFQVEYAREA VKKGSTALGM KFANGVLLIS DKKVRSRLIE QNSIEKIQLI DDYVAAVTSG LVADARVLV DFARISAQQE KVTYGSLVNI ENLVKRVADQ MQQYTQYGGV RPYGVSLIFA GIDQIGPRLF DCDPAGTINE Y KATAIGSG KDAVVSFLER EYKENLPEKE AVTLGIKALK SSLEEGEELK APEIASITVG NKYRIYDQEE VKKFL UniProtKB: Proteasome subunit alpha |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8f6a: |