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- EMDB-9043: Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9043 | |||||||||
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Title | Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state) | |||||||||
![]() | Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state) | |||||||||
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![]() | 26S Proteasome / ATPase / AAA+ / Protease / Motor protein / Ubiquitin | |||||||||
Function / homology | ![]() proteasome regulatory particle assembly / nonfunctional rRNA decay / mitotic cell cycle phase transition / cytosolic proteasome complex / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, base subcomplex / cyclin-dependent protein serine/threonine kinase regulator activity / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network ...proteasome regulatory particle assembly / nonfunctional rRNA decay / mitotic cell cycle phase transition / cytosolic proteasome complex / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, base subcomplex / cyclin-dependent protein serine/threonine kinase regulator activity / 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 / 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 / peptide catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / cyclin-dependent protein kinase holoenzyme complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / ERAD pathway / Neutrophil degranulation / proteasome complex / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / positive regulation of protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / chromatin remodeling / protein domain specific binding / cell division / mRNA binding / ubiquitin protein ligase binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.73 Å | |||||||||
![]() | de la Pena AH / Goodall EA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate-engaged 26 proteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation. Authors: Andres H de la Peña / Ellen A Goodall / Stephanie N Gates / Gabriel C Lander / Andreas Martin / ![]() Abstract: The 26 proteasome is the primary eukaryotic degradation machine and thus is critically involved in numerous cellular processes. The heterohexameric adenosine triphosphatase (ATPase) motor of the ...The 26 proteasome is the primary eukaryotic degradation machine and thus is critically involved in numerous cellular processes. The heterohexameric adenosine triphosphatase (ATPase) motor of the proteasome unfolds and translocates targeted protein substrates into the open gate of a proteolytic core while a proteasomal deubiquitinase concomitantly removes substrate-attached ubiquitin chains. However, the mechanisms by which ATP hydrolysis drives the conformational changes responsible for these processes have remained elusive. Here we present the cryo-electron microscopy structures of four distinct conformational states of the actively ATP-hydrolyzing, substrate-engaged 26 proteasome. These structures reveal how mechanical substrate translocation accelerates deubiquitination and how ATP-binding, -hydrolysis, and phosphate-release events are coordinated within the AAA+ (ATPases associated with diverse cellular activities) motor to induce conformational changes and propel the substrate through the central pore. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 13.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 56.5 KB 56.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() ![]() | 12.2 KB 12.2 KB 12.1 KB | Display Display Display | ![]() |
Images | ![]() | 94.4 KB | ||
Masks | ![]() ![]() ![]() | 149.9 MB 149.9 MB 149.9 MB | ![]() | |
Filedesc metadata | ![]() | 10.1 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 118.3 MB 118.5 MB 140.2 MB 118.3 MB 118.3 MB 140.4 MB 118.4 MB 118.4 MB 140.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 544.8 KB | Display | ![]() |
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Full document | ![]() | 544.4 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 7.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ef1MC ![]() 9042C ![]() 9044C ![]() 9045C ![]() 6ef0C ![]() 6ef2C ![]() 6ef3C C: citing same article ( M: atomic model generated by this map |
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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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Annotation | Yeast 26S proteasome bound to ubiquitinated substrate (5D motor state) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Additional map: Motor (half 2)
+Additional map: Motor (half 1)
+Additional map: Motor (sharpened)
+Additional map: Alpha ring (half 2)
+Additional map: Alpha ring (half 1)
+Additional map: Alpha ring (sharpened)
+Additional map: Global (half 2)
+Additional map: Global (half 1)
+Additional map: Global (sharpened)
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Sample components
+Entire : Substrate-engaged 26S proteasome in the 5D state (composite map)
+Supramolecule #1: Substrate-engaged 26S proteasome in the 5D state (composite map)
+Supramolecule #2: Proteasome
+Supramolecule #3: substrate
+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: 26S proteasome regulatory subunit 7 homolog
+Macromolecule #9: 26S proteasome regulatory subunit 4 homolog
+Macromolecule #10: 26S proteasome regulatory subunit 8 homolog
+Macromolecule #11: 26S proteasome regulatory subunit 6B homolog
+Macromolecule #12: 26S proteasome subunit RPT4
+Macromolecule #13: 26S proteasome regulatory subunit 6A
+Macromolecule #14: model substrate polypeptide
+Macromolecule #15: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #16: 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 | 25 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: specimens were manually blotted with Whatman #1 filter paper. | ||||||||||||||||||
Details | 26S proteasomes were diluted to a concentration of 20 micromolar in a buffer with an ATP regeneration system, and 6 mM ortho-phenanthroline. This solution was mixed with an equal volume of 50 micromolar ubiquitinated model substrate |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | images were acquired in nanoprobe mode |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 11656 / Average exposure time: 6.25 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: -3.0 µm / Calibrated defocus min: -1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |