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Yorodumi- PDB-6utg: Allosteric coupling between alpha-rings of the 20S proteasome, 20... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6utg | ||||||
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Title | Allosteric coupling between alpha-rings of the 20S proteasome, 20S singly capped with a PA26/V230F | ||||||
Components |
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Keywords | HYDROLASE / proteasome / PA26/V230F / singly-capped | ||||||
Function / homology | Function and homology information proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / endopeptidase activity / ubiquitin-dependent protein catabolic process / proteolysis ...proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / endopeptidase activity / ubiquitin-dependent protein catabolic process / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) Trypanosoma brucei (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Yu, Z. / Cheng, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Allosteric coupling between α-rings of the 20S proteasome. Authors: Zanlin Yu / Yadong Yu / Feng Wang / Alexander G Myasnikov / Philip Coffino / Yifan Cheng / Abstract: Proteasomal machinery performs essential regulated protein degradation in eukaryotes. Classic proteasomes are symmetric, with a regulatory ATPase docked at each end of the cylindrical 20S. Asymmetric ...Proteasomal machinery performs essential regulated protein degradation in eukaryotes. Classic proteasomes are symmetric, with a regulatory ATPase docked at each end of the cylindrical 20S. Asymmetric complexes are also present in cells, either with a single ATPase or with an ATPase and non-ATPase at two opposite ends. The mechanism that populates these different proteasomal complexes is unknown. Using archaea homologs, we construct asymmetric forms of proteasomes. We demonstrate that the gate conformation of the two opposite ends of 20S are coupled: binding one ATPase opens a gate locally, and also opens the opposite gate allosterically. Such allosteric coupling leads to cooperative binding of proteasomal ATPases to 20S and promotes formation of proteasomes symmetrically configured with two identical ATPases. It may also promote formation of asymmetric complexes with an ATPase and a non-ATPase at opposite ends. We propose that in eukaryotes a similar mechanism regulates the composition of the proteasomal population. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6utg.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6utg.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6utg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6utg_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6utg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6utg_validation.xml.gz | 174 KB | Display | |
Data in CIF | 6utg_validation.cif.gz | 249.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/6utg ftp://data.pdbj.org/pub/pdb/validation_reports/ut/6utg | HTTPS FTP |
-Related structure data
Related structure data | 20878MC 6utfC 6uthC 6utiC 6utjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 22294.848 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB, Ta0612 / Production host: Escherichia phage EcSzw-2 (virus) References: UniProt: P28061, proteasome endopeptidase complex #2: Protein | Mass: 25125.619 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia phage EcSzw-2 (virus) References: UniProt: P25156, proteasome endopeptidase complex #3: Protein | Mass: 24995.404 Da / Num. of mol.: 7 / Mutation: V230F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9U8G2 #4: Protein | Mass: 24718.178 Da / Num. of mol.: 7 / Mutation: K66A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia phage EcSzw-2 (virus) References: UniProt: P25156, proteasome endopeptidase complex |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The complex of Archaea 20S singly capped by one PA26/V230F Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Source (recombinant) | Organism: Escherichia phage EcSzw-2 (virus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50000 / Symmetry type: POINT | ||||||||||||||||||||||||
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