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Yorodumi- PDB-6utf: Allosteric coupling between alpha-rings of the 20S proteasome, ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6utf | ||||||
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Title | Allosteric coupling between alpha-rings of the 20S proteasome, archaea 20S proteasome singly capped with a PAN complex | ||||||
Components |
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Keywords | HYDROLASE / proteasome / PAN / singly-capped | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Cheng, Y. / Yu, Z. | ||||||
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 | 6utf.cif.gz | 975.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6utf.ent.gz | 825.9 KB | Display | PDB format |
PDBx/mmJSON format | 6utf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6utf_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6utf_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6utf_validation.xml.gz | 158.2 KB | Display | |
Data in CIF | 6utf_validation.cif.gz | 218.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/6utf ftp://data.pdbj.org/pub/pdb/validation_reports/ut/6utf | HTTPS FTP |
-Related structure data
Related structure data | 20877MC 6utgC 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: 23169.811 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: 25067.518 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 #3: Protein | Mass: 25081.584 Da / Num. of mol.: 7 / Mutation: R28L 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: proteasome singly capped with a PAN complex together with GFPssRA as a substrate 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: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 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: 33000 / Symmetry type: POINT | ||||||||||||||||||||||||
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