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- EMDB-2026: Structure of the proteasome subunit Rpn1 -

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Basic information

Entry
Database: EMDB / ID: EMD-2026
TitleStructure of the proteasome subunit Rpn1
Map dataMap of the proteasome subunit Rpn1 from S. cerevisiae
Sample
  • Sample: Rpn1
  • Protein or peptide: Rpn1
Keywordsproteasome / rpn1 / 19S subunit
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsHe J / Kulkarni K / daFonseca P / Krutauz D / Glickman M / Barford D / Morris E
CitationJournal: 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
DepositionJan 9, 2012-
Header (metadata) releaseJan 20, 2012-
Map releaseApr 13, 2012-
UpdateAug 26, 2015-
Current statusAug 26, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-2026.png

Downloads & links

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Map

FileDownload / File: emd_2026.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the proteasome subunit Rpn1 from S. cerevisiae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 128 pix.
= 278.144 Å		2.17 Å/pix.
x 128 pix.
= 278.144 Å		2.17 Å/pix.
x 128 pix.
= 278.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.173 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-11.30645084 - 36.752277370000002
Average (Standard dev.)0.0 (±1.00000012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 278.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1732.1732.173
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z278.144278.144278.144
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-11.30636.752-0.000

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Supplemental data

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Sample components

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Entire : Rpn1

EntireName: Rpn1
Components
  • Sample: Rpn1
  • Protein or peptide: Rpn1

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Supramolecule #1000: Rpn1

SupramoleculeName: Rpn1 / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 109.492 KDa

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Macromolecule #1: Rpn1

MacromoleculeName: Rpn1 / type: protein_or_peptide / ID: 1 / Name.synonym: Rpn1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 109.492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
StainingType: NEGATIVE / Details: 2% uranyl acetate
GridDetails: Carbon film on quantifoil
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: 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 beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied 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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