+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4323 | |||||||||
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Title | 26S proteasome, s5 state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 26S proteasome / AAA+ ATPase / hydrolase | |||||||||
Function / homology | Function and homology information SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / protein-containing complex localization / proteasome-activating activity / mitochondrial fission / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / nonfunctional rRNA decay / K48-linked polyubiquitin modification-dependent protein binding / 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 / proteasome binding / peptide catabolic process / 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 / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / 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 / Ub-specific processing proteases / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / ERAD pathway / Neutrophil degranulation / protein folding chaperone / proteasome complex / ubiquitin binding / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / peroxisome / 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 / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Eisele MR / Reed RG | |||||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Authors: Markus R Eisele / Randi G Reed / Till Rudack / Andreas Schweitzer / Florian Beck / Istvan Nagy / Günter Pfeifer / Jürgen M Plitzko / Wolfgang Baumeister / Robert J Tomko / Eri Sakata / Abstract: The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive ...The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber. | |||||||||
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_4323.map.gz | 202.4 MB | EMDB map data format | |
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Header (meta data) | emd-4323-v30.xml emd-4323.xml | 49.4 KB 49.4 KB | Display Display | EMDB header |
Images | emd_4323.png | 54.6 KB | ||
Filedesc metadata | emd-4323.cif.gz | 13.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4323 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4323 | HTTPS FTP |
-Validation report
Summary document | emd_4323_validation.pdf.gz | 301.2 KB | Display | EMDB validaton report |
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Full document | emd_4323_full_validation.pdf.gz | 300.4 KB | Display | |
Data in XML | emd_4323_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4323 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4323 | HTTPS FTP |
-Related structure data
Related structure data | 6fvxMC 4321C 4322C 4324C 6fvtC 6fvuC 6fvvC 6fvwC 6fvyC 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_4323.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
+Supramolecule #1: 26S proteasome
+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: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146519 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |