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Open data
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Basic information
Entry | Database: PDB / ID: 7qve | ||||||
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Title | Spinach 20S proteasome | ||||||
![]() | (Proteasome subunit ...) x 14 | ||||||
![]() | PLANT PROTEIN / PROTEASOME / UPS / PLANT / SPINACH | ||||||
Function / homology | ![]() proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Kandolf, S. / Grishkovskaya, I. / Meinhart, A. / Haselbach, D. | ||||||
Funding support | 1items
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![]() | ![]() Title: Cryo-EM structure of the plant 26S proteasome. Authors: Susanne Kandolf / Irina Grishkovskaya / Katarina Belačić / Derek L Bolhuis / Sascha Amann / Brent Foster / Richard Imre / Karl Mechtler / Alexander Schleiffer / Hemant D Tagare / Ellen D ...Authors: Susanne Kandolf / Irina Grishkovskaya / Katarina Belačić / Derek L Bolhuis / Sascha Amann / Brent Foster / Richard Imre / Karl Mechtler / Alexander Schleiffer / Hemant D Tagare / Ellen D Zhong / Anton Meinhart / Nicholas G Brown / David Haselbach / ![]() ![]() ![]() Abstract: Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin- ...Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin-proteasome system. Thus, proteolysis by the 26S proteasome is vital to development, immunity, and cell division. Although the yeast and animal proteasomes are well characterized, there is only limited information on the plant proteasome. We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 Å. We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast. Nevertheless, we noticed a structural difference in the proteolytic active β1 subunit. Furthermore, we uncovered an unseen compression state by characterizing the proteasome's conformational landscape. We suspect that this new conformation of the 20S core protease, in correlation with a partial opening of the unoccupied gate, may contribute to peptide release after proteolysis. Our data provide a structural basis for the plant proteasome, which is crucial for further studies. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 877.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 700.3 KB | Display | ![]() |
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Full document | ![]() | 724.3 KB | Display | |
Data in XML | ![]() | 121.6 KB | Display | |
Data in CIF | ![]() | 185.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14175MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data #1: Unaligned multi-frame micrographs of spinach 26S proteasome [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs of spinach 26S proteasome [micrographs - multiframe] Data #3: Unaligned multi-frame micrographs of spinach 26S proteasome [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Proteasome subunit ... , 14 types, 28 molecules iCjDkElFmGnXBhoapbqcrdsetfug
#1: Protein | Mass: 25588.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 27504.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 26844.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 26027.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 29932.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 27322.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 27211.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 25324.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 29404.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 22847.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 22950.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 29652.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: O24361, proteasome endopeptidase complex #13: Protein | Mass: 24835.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 27098.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
Component | Name: Spinach 26S proteasome / Type: COMPLEX / Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.7 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||||||||
Electron gun | Electron source: ![]() | ||||||||||||||||||
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU | ||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||
Image recording |
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Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 951422 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 951422 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 109.9 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MSB |