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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-14085 | ||||||||||||||||||
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Title | 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state | ||||||||||||||||||
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Function / homology | ![]() SAGA complex localization to transcription regulatory region / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) ...SAGA complex localization to transcription regulatory region / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / filamentous growth / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / 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 / protein deubiquitination / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / 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 / modification-dependent protein catabolic process / protein tag activity / metallopeptidase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / protein ubiquitination / ubiquitin protein ligase binding / structural molecule activity / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | ||||||||||||||||||
![]() | Hung KYS / Klumpe S / Eisele MR / Elsasser S / Geng TT / Cheng TC / Joshi T / Rudack T / Sakata E / Finley D | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric control of Ubp6 and the proteasome via a bidirectional switch. Authors: Ka Ying Sharon Hung / Sven Klumpe / Markus R Eisele / Suzanne Elsasser / Geng Tian / Shuangwu Sun / Jamie A Moroco / Tat Cheung Cheng / Tapan Joshi / Timo Seibel / Duco Van Dalen / Xin-Hua ...Authors: Ka Ying Sharon Hung / Sven Klumpe / Markus R Eisele / Suzanne Elsasser / Geng Tian / Shuangwu Sun / Jamie A Moroco / Tat Cheung Cheng / Tapan Joshi / Timo Seibel / Duco Van Dalen / Xin-Hua Feng / Ying Lu / Huib Ovaa / John R Engen / Byung-Hoon Lee / Till Rudack / Eri Sakata / Daniel Finley / ![]() ![]() ![]() ![]() ![]() Abstract: The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by ...The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome. | ||||||||||||||||||
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 | ![]() | 185 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 51.3 KB 51.3 KB | Display Display | ![]() |
Images | ![]() | 110.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qo6MC ![]() 7qo3C ![]() 7qo5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 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 : 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state
+Supramolecule #1: 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state
+Macromolecule #1: BJ4_G0020160.mRNA.1.CDS.1
+Macromolecule #2: HLJ1_G0039880.mRNA.1.CDS.1
+Macromolecule #3: BJ4_G0021480.mRNA.1.CDS.1
+Macromolecule #4: HLJ1_G0048980.mRNA.1.CDS.1
+Macromolecule #5: EM14S01-3B_G0035190.mRNA.1.CDS.1
+Macromolecule #6: BJ4_G0043800.mRNA.1.CDS.1
+Macromolecule #7: Probable proteasome subunit alpha type-7
+Macromolecule #8: Proteasome subunit beta type-1
+Macromolecule #9: Proteasome endopeptidase complex
+Macromolecule #10: Proteasome endopeptidase complex
+Macromolecule #11: Proteasome subunit beta
+Macromolecule #12: Proteasome subunit beta type-5
+Macromolecule #13: HLJ1_G0013750.mRNA.1.CDS.1
+Macromolecule #14: Proteasome subunit beta type-7
+Macromolecule #15: 26S proteasome regulatory subunit RPN10
+Macromolecule #16: 26S proteasome regulatory subunit RPN11
+Macromolecule #17: EM14S01-3B_G0050020.mRNA.1.CDS.1
+Macromolecule #18: HLJ1_G0030700.mRNA.1.CDS.1
+Macromolecule #19: 26S proteasome complex subunit SEM1
+Macromolecule #20: 26S proteasome regulatory subunit RPN1
+Macromolecule #21: 26S proteasome regulatory subunit RPN2
+Macromolecule #22: 26S proteasome regulatory subunit RPN3
+Macromolecule #23: 26S proteasome regulatory subunit RPN5
+Macromolecule #24: 26S proteasome regulatory subunit RPN6
+Macromolecule #25: 26S proteasome regulatory subunit RPN7
+Macromolecule #26: 26S proteasome regulatory subunit RPN8
+Macromolecule #27: 26S proteasome regulatory subunit RPN9
+Macromolecule #28: 26S proteasome regulatory subunit 7 homolog
+Macromolecule #29: 26S proteasome regulatory subunit 4 homolog
+Macromolecule #30: 26S proteasome regulatory subunit 6B homolog
+Macromolecule #31: 26S proteasome subunit RPT4
+Macromolecule #32: 26S proteasome regulatory subunit 6A
+Macromolecule #33: 26S proteasome regulatory subunit 8 homolog
+Macromolecule #34: Ubiquitin carboxyl-terminal hydrolase
+Macromolecule #35: Polyubiquitin-B
+Macromolecule #36: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74842 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |