+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2026 | |||||||||
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Title | Structure of the proteasome subunit Rpn1 | |||||||||
Map data | Map of the proteasome subunit Rpn1 from S. cerevisiae | |||||||||
Sample |
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Keywords | proteasome / rpn1 / 19S subunit | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | He J / Kulkarni K / daFonseca P / Krutauz D / Glickman M / Barford D / Morris E | |||||||||
Citation | Journal: Structure / Year: 2012 Title: The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings. Authors: Jun He / Kiran Kulkarni / Paula C A da Fonseca / Dasha Krutauz / Michael H Glickman / David Barford / Edward P Morris / Abstract: The 26S proteasome proteolyses ubiquitylated proteins and is assembled from a 20S proteolytic core and two 19S regulatory particles (19S-RP). The 19S-RP scaffolding subunits Rpn1 and Rpn2 function to ...The 26S proteasome proteolyses ubiquitylated proteins and is assembled from a 20S proteolytic core and two 19S regulatory particles (19S-RP). The 19S-RP scaffolding subunits Rpn1 and Rpn2 function to engage ubiquitin receptors. Rpn1 and Rpn2 are characterized by eleven tandem copies of a 35-40 amino acid repeat motif termed the proteasome/cyclosome (PC) repeat. Here, we reveal that the eleven PC repeats of Rpn2 form a closed toroidal structure incorporating two concentric rings of α helices encircling two axial α helices. A rod-like N-terminal domain consisting of 17 stacked α helices and a globular C-terminal domain emerge from one face of the toroid. Rpn13, an ubiquitin receptor, binds to the C-terminal 20 residues of Rpn2. Rpn1 adopts a similar conformation to Rpn2 but differs in the orientation of its rod-like N-terminal domain. These findings have implications for understanding how 19S-RPs recognize, unfold, and deliver ubiquitylated substrates to the 20S core. | |||||||||
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_2026.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-2026-v30.xml emd-2026.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
Images | emd-2026.png | 115.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2026 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2026 | HTTPS FTP |
-Validation report
Summary document | emd_2026_validation.pdf.gz | 179.6 KB | Display | EMDB validaton report |
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Full document | emd_2026_full_validation.pdf.gz | 178.7 KB | Display | |
Data in XML | emd_2026_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2026 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2026 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2026.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of the proteasome subunit Rpn1 from S. cerevisiae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.173 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 : Rpn1
Entire | Name: Rpn1 |
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Components |
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-Supramolecule #1000: Rpn1
Supramolecule | Name: Rpn1 / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 109.492 KDa |
-Macromolecule #1: Rpn1
Macromolecule | Name: Rpn1 / type: protein_or_peptide / ID: 1 / Name.synonym: Rpn1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Theoretical: 109.492 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Staining | Type: NEGATIVE / Details: 2% uranyl acetate |
Grid | Details: Carbon film on quantifoil |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 71 / Average electron dose: 100 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic |
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