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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5615 | |||||||||
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Title | Yeast 20S proteasome with C-terminal peptide of yeast Rpt5 | |||||||||
![]() | 3D density map of yeast 20S proteasome core particle with GST tag added to the C-terminus of beta-2 subunit in complex with the C-terminal peptide of yeast Rpt5 | |||||||||
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![]() | Yeast 20S proteasome / C-terminal peptide / yeast Rpt5 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
![]() | Li X / Kim HM / Cheng Y | |||||||||
![]() | ![]() Title: Reconfiguration of the proteasome during chaperone-mediated assembly. Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan ...Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan Cheng / Daniel Finley / ![]() Abstract: The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting ...The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting into pockets of the α-ring. Rpt ring assembly is mediated by four chaperones, each binding a distinct Rpt subunit. Here we report that the base subassembly of the Saccharomyces cerevisiae proteasome, which includes the Rpt ring, forms a high-affinity complex with the CP. This complex is subject to active dissociation by the chaperones Hsm3, Nas6 and Rpn14. Chaperone-mediated dissociation was abrogated by a non-hydrolysable ATP analogue, indicating that chaperone action is coupled to nucleotide hydrolysis by the Rpt ring. Unexpectedly, synthetic Rpt tail peptides bound α-pockets with poor specificity, except for Rpt6, which uniquely bound the α2/α3-pocket. Although the Rpt6 tail is not visualized within an α-pocket in mature proteasomes, it inserts into the α2/α3-pocket in the base-CP complex and is important for complex formation. Thus, the Rpt-CP interface is reconfigured when the lid complex joins the nascent proteasome to form the mature holoenzyme. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
Images | ![]() | 110.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.8 KB | Display | ![]() |
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Full document | ![]() | 77.9 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5593C ![]() 5611C ![]() 5612C ![]() 5613C ![]() 5614C ![]() 5616C ![]() 5617C ![]() 4jpoC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | 3D density map of yeast 20S proteasome core particle with GST tag added to the C-terminus of beta-2 subunit in complex with the C-terminal peptide of yeast Rpt5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Yeast 20S proteasome
Entire | Name: Yeast 20S proteasome |
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Components |
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-Supramolecule #1000: Yeast 20S proteasome
Supramolecule | Name: Yeast 20S proteasome / type: sample / ID: 1000 / Oligomeric state: 28mer / Number unique components: 1 |
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Molecular weight | Experimental: 700 KDa |
-Macromolecule #1: 20S proteasome
Macromolecule | Name: 20S proteasome / type: protein_or_peptide / ID: 1 / Details: GST tag was added to C-terminus of beta-2 subunit / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 700 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Grid | Details: Quantifoil grid |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Details | Low-dose procedure |
Date | Jan 1, 2010 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 25 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder: CT3500 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | FREALIGN |
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CTF correction | Details: Each Particle |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 58953 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |