+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2165 | |||||||||
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Title | Cryo-EM reconstruction of the yeast 26S proteasome | |||||||||
Map data | Reconstruction of Saccharomyces cerevisiase 26S proteasome | |||||||||
Sample |
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Keywords | 26S proteasome / AAA-ATPases / protein degradation / ubiquitin-proteasome pathway | |||||||||
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 / KEAP1-NFE2L2 pathway / peptide catabolic process / proteasome binding / 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 / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / positive regulation of transcription elongation by RNA polymerase II / ERAD pathway / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / nucleotide-excision repair / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / peroxisome / protein-macromolecule adaptor activity / endopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / chromatin remodeling / regulation of cell cycle / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
Authors | Beck F / Unverdorben P / Bohn S / Schweitzer A / Pfeifer G / Sakata E / Nickell S / Plitzko JM / Villa E / Baumeister W / Forster F | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Near-atomic resolution structural model of the yeast 26S proteasome. Authors: Florian Beck / Pia Unverdorben / Stefan Bohn / Andreas Schweitzer / Günter Pfeifer / Eri Sakata / Stephan Nickell / Jürgen M Plitzko / Elizabeth Villa / Wolfgang Baumeister / Friedrich Förster / Abstract: The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or ...The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits. | |||||||||
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_2165.map.gz | 78.4 MB | EMDB map data format | |
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Header (meta data) | emd-2165-v30.xml emd-2165.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | 2165_26S_cerevisiae.tif | 160.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2165 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2165 | HTTPS FTP |
-Validation report
Summary document | emd_2165_validation.pdf.gz | 309.9 KB | Display | EMDB validaton report |
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Full document | emd_2165_full_validation.pdf.gz | 309.5 KB | Display | |
Data in XML | emd_2165_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2165 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2165 | HTTPS FTP |
-Related structure data
Related structure data | 3j47M 4cr2M 4b4t M: atomic model generated by this map |
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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_2165.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Saccharomyces cerevisiase 26S proteasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.99 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 : Saccharomyes cerevisiae 26S proteasome
Entire | Name: Saccharomyes cerevisiae 26S proteasome |
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Components |
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-Supramolecule #1000: Saccharomyes cerevisiae 26S proteasome
Supramolecule | Name: Saccharomyes cerevisiae 26S proteasome / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Supramolecule #1: 26S proteasome
Supramolecule | Name: 26S proteasome / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.1 Details: 4 mM ATP, 10mM MgCl2, 50mM Tris[pH7.1], 10% glycerol |
Grid | Details: quantifoil holey carbon |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80 K / Max: 81 K / Average: 80.5 K |
Date | Mar 15, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 63126 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 156784 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 150000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program. |
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CTF correction | Details: micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP / Number images used: 2464694 |