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Yorodumi- EMDB-3136: A Single Alpha Helix Drives Extensive Remodeling of the Proteasom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3136 | |||||||||
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Title | A Single Alpha Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly | |||||||||
Map data | Reconstruction of LP2 | |||||||||
Sample |
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Keywords | proteasome / ubiquitin / proteolysis / electron microscopy / mass spectrometry | |||||||||
Function / homology | Function and homology information protein deneddylation => GO:0000338 / molecular_function / SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth ...protein deneddylation => GO:0000338 / molecular_function / SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / mitochondrial fission / metal-dependent deubiquitinase activity / protein deubiquitination / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / proteasome binding / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome assembly / Ub-specific processing proteases / mRNA export from nucleus / enzyme regulator activity / protein folding chaperone / Neutrophil degranulation / proteasome complex / double-strand break repair via homologous recombination / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / structural molecule activity / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.0 Å | |||||||||
Authors | Tomko Jr RJ / Taylor DW / Chen ZA / Wang HW / Rappsilber J / Hochstrasser M | |||||||||
Citation | Journal: Cell / Year: 2015 Title: A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly. Authors: Robert J Tomko / David W Taylor / Zhuo A Chen / Hong-Wei Wang / Juri Rappsilber / Mark Hochstrasser / Abstract: Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis ...Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis culminates with the joining of two large subcomplexes, the lid and base. In yeast and mammals, the lid appears to assemble completely before attaching to the base, but how this hierarchical assembly is enforced has remained unclear. Using biochemical reconstitutions, quantitative cross-linking/mass spectrometry, and electron microscopy, we resolve the mechanistic basis for the linkage between lid biogenesis and lid-base joining. Assimilation of the final lid subunit, Rpn12, triggers a large-scale conformational remodeling of the nascent lid that drives RP assembly, in part by relieving steric clash with the base. Surprisingly, this remodeling is triggered by a single Rpn12 α helix. Such assembly-coupled conformational switching is reminiscent of viral particle maturation and may represent a commonly used mechanism to enforce hierarchical assembly in multisubunit complexes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3136.map.gz | 14.7 MB | EMDB map data format | |
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Header (meta data) | emd-3136-v30.xml emd-3136.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_3136.png | 149.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3136 | HTTPS FTP |
-Validation report
Summary document | emd_3136_validation.pdf.gz | 219.7 KB | Display | EMDB validaton report |
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Full document | emd_3136_full_validation.pdf.gz | 218.8 KB | Display | |
Data in XML | emd_3136_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3136 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3136 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3136.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of LP2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Recombinant LP2 (Lid Particle 2)
Entire | Name: Recombinant LP2 (Lid Particle 2) |
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Components |
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-Supramolecule #1000: Recombinant LP2 (Lid Particle 2)
Supramolecule | Name: Recombinant LP2 (Lid Particle 2) / type: sample / ID: 1000 / Details: The sample was monodisperse. Oligomeric state: 1 Rpn3: 1 Rpn5: 1 Rpn6: 1 Rpn7: 1 Rpn8: 1 Rpn9: 1 Rpn11: 1 Sem1 Number unique components: 8 |
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Molecular weight | Theoretical: 343 KDa |
-Macromolecule #1: 26S proteasome regulatory subunit RPN3
Macromolecule | Name: 26S proteasome regulatory subunit RPN3 / type: protein_or_peptide / ID: 1 / Name.synonym: RPN3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 64 KDa |
Sequence | UniProtKB: 26S proteasome regulatory subunit RPN3 GO: ubiquitin-dependent protein catabolic process, regulation of protein catabolic process, molecular_function, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: 26S proteasome regulatory subunit, C-terminal, Proteasome component (PCI) domain |
-Macromolecule #2: 26S proteasome regulatory subunit RPN5
Macromolecule | Name: 26S proteasome regulatory subunit RPN5 / type: protein_or_peptide / ID: 2 / Name.synonym: RPN5 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 52 KDa |
Sequence | UniProtKB: 26S proteasome regulatory subunit RPN5 GO: ubiquitin-dependent protein catabolic process, protein deneddylation => GO:0000338, molecular_function, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: Proteasome component (PCI) domain, ArsR-like helix-turn-helix domain |
-Macromolecule #3: 26S proteasome regulatory subunit RPN6
Macromolecule | Name: 26S proteasome regulatory subunit RPN6 / type: protein_or_peptide / ID: 3 / Name.synonym: RPN6 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 50 KDa |
Sequence | UniProtKB: 26S proteasome regulatory subunit RPN6 GO: ubiquitin-dependent protein catabolic process, structural molecule activity, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: Proteasome component (PCI) domain, INTERPRO: IPR013143 |
-Macromolecule #4: 26S proteasome regulatory subunit RPN7
Macromolecule | Name: 26S proteasome regulatory subunit RPN7 / type: protein_or_peptide / ID: 4 / Name.synonym: RPN7 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 49 KDa |
Sequence | UniProtKB: 26S proteasome regulatory subunit RPN7 GO: ubiquitin-dependent protein catabolic process, structural molecule activity, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1, Proteasome component (PCI) domain, INTERPRO: IPR013026 |
-Macromolecule #5: 26S proteasome regulatory subunit RPN8
Macromolecule | Name: 26S proteasome regulatory subunit RPN8 / type: protein_or_peptide / ID: 5 / Name.synonym: RPN8 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 38 KDa |
Sequence | UniProtKB: 26S proteasome regulatory subunit RPN8 GO: ubiquitin-dependent protein catabolic process, molecular_function, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: JAB1/MPN/MOV34 metalloenzyme domain, Rpn11/EIF3F, C-terminal |
-Macromolecule #6: 26S proteasome regulatory subunit RPN9
Macromolecule | Name: 26S proteasome regulatory subunit RPN9 / type: protein_or_peptide / ID: 6 / Name.synonym: RPN9 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 46 KDa |
Sequence | UniProtKB: 26S proteasome regulatory subunit RPN9 GO: ubiquitin-dependent protein catabolic process, structural molecule activity, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: Proteasome component (PCI) domain, ArsR-like helix-turn-helix domain |
-Macromolecule #7: 26S proteasome regulatory subunit RPN11
Macromolecule | Name: 26S proteasome regulatory subunit RPN11 / type: protein_or_peptide / ID: 7 / Name.synonym: RPN11 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 34 KDa |
Sequence | UniProtKB: Ubiquitin carboxyl-terminal hydrolase RPN11 GO: protein deubiquitination, mitochondrial fission, cysteine-type deubiquitinase activity, proteasome complex, proteasome regulatory particle, lid subcomplex InterPro: JAB1/MPN/MOV34 metalloenzyme domain, Rpn11/EIF3F, C-terminal |
-Macromolecule #8: 26S proteasome regulatory subunit Sem1
Macromolecule | Name: 26S proteasome regulatory subunit Sem1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Yeast |
Molecular weight | Theoretical: 10 KDa |
Sequence | UniProtKB: 26S proteasome complex subunit SEM1 GO: proteasome complex, proteasome regulatory particle, lid subcomplex, proteasome-mediated ubiquitin-dependent protein catabolic process, proteasome assembly InterPro: DSS1/SEM1 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.04 mg/mL |
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Buffer | pH: 7.5 Details: 50 mM Tris, 150 mM NaCl, 5 mM MgCl2, and 10% glycerol |
Staining | Type: NEGATIVE Details: Sample was negatively stained with six consecutive droplets of 2% uranyl acetate. |
Grid | Details: 400 mesh Cu grid with thin carbon, glow discharged with a sputter coater. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Details | Data acquired using Leginon. |
Date | Apr 26, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 600 / Average electron dose: 30 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: Each micrograph |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: EMAN2, SPARX / Number images used: 60000 |