+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3537 | ||||||||||||
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Title | 26S proteasome in presence of BeFx (s4) | ||||||||||||
Map data | 26S proteasome in presence of BeFx (s4) | ||||||||||||
Sample |
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Keywords | Macromolecular complex / 26S proteasome / Protease / Hydrolase | ||||||||||||
Function / homology | Function and homology information SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / Metalloprotease DUBs / peroxisome fission / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation ...SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / Metalloprotease DUBs / peroxisome fission / regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / regulation of proteasomal protein catabolic process / 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 S288c (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.7 Å | ||||||||||||
Authors | Wehmer M / Rudack T | ||||||||||||
Funding support | Germany, United States, 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Authors: Marc Wehmer / Till Rudack / Florian Beck / Antje Aufderheide / Günter Pfeifer / Jürgen M Plitzko / Friedrich Förster / Klaus Schulten / Wolfgang Baumeister / Eri Sakata / Abstract: In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where ...In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis. | ||||||||||||
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_3537.map.gz | 23.7 MB | EMDB map data format | |
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Header (meta data) | emd-3537-v30.xml emd-3537.xml | 54.5 KB 54.5 KB | Display Display | EMDB header |
Images | emd_3537.png | 54.6 KB | ||
Filedesc metadata | emd-3537.cif.gz | 14.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3537 | HTTPS FTP |
-Validation report
Summary document | emd_3537_validation.pdf.gz | 219.5 KB | Display | EMDB validaton report |
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Full document | emd_3537_full_validation.pdf.gz | 218.6 KB | Display | |
Data in XML | emd_3537_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3537 | HTTPS FTP |
-Related structure data
Related structure data | 5mpcMC 3534C 3535C 3536C 5mp9C 5mpaC 5mpbC 5mpdC 5mpeC 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_3537.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 26S proteasome in presence of BeFx (s4) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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 of Saccharomyces cerevisiae in presence of BeFx (s4)
+Supramolecule #1: 26S proteasome of Saccharomyces cerevisiae in presence of BeFx (s4)
+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 protease regulatory subunit 7 homolog
+Macromolecule #16: 26S protease regulatory subunit 4 homolog
+Macromolecule #17: 26S protease regulatory subunit 6B homolog
+Macromolecule #18: 26S protease subunit RPT4
+Macromolecule #19: 26S protease regulatory subunit 6A
+Macromolecule #20: 26S protease regulatory subunit 8 homolog
+Macromolecule #21: 26S proteasome regulatory subunit RPN10
+Macromolecule #22: Ubiquitin carboxyl-terminal hydrolase RPN11
+Macromolecule #23: 26S proteasome regulatory subunit RPN12
+Macromolecule #24: 26S proteasome regulatory subunit RPN13
+Macromolecule #25: 26S proteasome complex subunit SEM1
+Macromolecule #26: 26S proteasome regulatory subunit RPN1
+Macromolecule #27: 26S proteasome regulatory subunit RPN2
+Macromolecule #28: 26S proteasome regulatory subunit RPN3
+Macromolecule #29: 26S proteasome regulatory subunit RPN5
+Macromolecule #30: 26S proteasome regulatory subunit RPN6
+Macromolecule #31: 26S proteasome regulatory subunit RPN7
+Macromolecule #32: 26S proteasome regulatory subunit RPN8
+Macromolecule #33: 26S proteasome regulatory subunit RPN9
+Macromolecule #34: Ubiquitin carboxyl-terminal hydrolase 6
+Macromolecule #35: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: 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 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
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 | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 27600 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |