+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14084 | ||||||||||||||||||
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Title | 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / peroxisome fission / negative regulation of proteasomal protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay ...SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / peroxisome fission / negative regulation of proteasomal protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / protein-containing complex localization / mitochondrial fission / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked polyubiquitin modification-dependent protein binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / peptide catabolic process / female gonad development / proteasome binding / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / proteasome storage granule / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / enzyme regulator activity / mRNA export from nucleus / energy homeostasis / regulation of neuron apoptotic process / : / protein folding chaperone / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Neutrophil degranulation / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / proteasome complex / Translesion synthesis by POLI Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) / Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | ||||||||||||||||||
Authors | Hung KYS / Klumpe S / Eisele MR / Elsasser S / Geng TT / Cheng TC / Joshi T / Rudack T / Sakata E / Finley D | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Commun / Year: 2022 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_14084.map.gz | 180.7 MB | EMDB map data format | |
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Header (meta data) | emd-14084-v30.xml emd-14084.xml | 57.9 KB 57.9 KB | Display Display | EMDB header |
Images | emd_14084.png | 106.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14084 | HTTPS FTP |
-Related structure data
Related structure data | 7qo5MC 7qo3C 7qo6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14084.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
+Entire : 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state
+Supramolecule #1: 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state
+Supramolecule #2: yeast Rpt1-RK 26S proteasome in si state
+Supramolecule #3: Ubp6-UbVS complex
+Macromolecule #1: Proteasome subunit alpha type-1
+Macromolecule #2: Proteasome subunit alpha type-2
+Macromolecule #3: Proteasome subunit alpha type-3
+Macromolecule #4: Proteasome subunit alpha type-4
+Macromolecule #5: Proteasome subunit alpha type-5
+Macromolecule #6: Proteasome subunit alpha type-6
+Macromolecule #7: Probable proteasome subunit alpha type-7
+Macromolecule #8: Proteasome subunit beta type-1
+Macromolecule #9: Proteasome subunit beta type-2
+Macromolecule #10: Proteasome subunit beta type-3
+Macromolecule #11: Proteasome subunit beta type-4
+Macromolecule #12: Proteasome subunit beta type-5
+Macromolecule #13: Proteasome subunit beta type-6
+Macromolecule #14: Proteasome subunit beta type-7
+Macromolecule #15: 26S proteasome regulatory subunit RPN10
+Macromolecule #16: Ubiquitin carboxyl-terminal hydrolase RPN11
+Macromolecule #17: 26S proteasome regulatory subunit RPN12
+Macromolecule #18: 26S proteasome regulatory subunit RPN13
+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 6
+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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64766 |