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

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Basic information

Database: EMDB / ID: 2026
TitleStructure of the proteasome subunit Rpn1
Map dataMap of the proteasome subunit Rpn1 from S. cerevisiae
Keywordsproteasome / rpn1 / 19S subunit
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / negative staining / 25 Å resolution
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.
DateDeposition: Jan 9, 2012 / Header (metadata) release: Jan 20, 2012 / Map release: Apr 13, 2012 / Last update: Aug 26, 2015

Structure visualization

  • 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:
Supplemental images

Downloads & links


Fileemd_2026.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.17 Å/pix.
= 278.144 Å
128 pix
2.17 Å/pix.
= 278.144 Å
128 pix
2.17 Å/pix.
= 278.144 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.173 Å
Contour Level:5.5 (by author), 5.5 (movie #1):
Minimum - Maximum-11.30645084 - 36.75227737
Average (Standard dev.)0E-8 (1.00000012)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 278.144 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-64-64-64
D min/max/mean-11.30636.752-0.000

Supplemental data

Sample components

Entire Rpn1

EntireName: Rpn1 / Number of components: 1
MassTheoretical: 109.492 kDa

Component #1: protein, Rpn1

ProteinName: Rpn1 / a.k.a: Rpn1 / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 109.492 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.1 mg/ml
Support filmCarbon film on quantifoil
Staining2% uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 800 - 900 nm
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 71 / Bit depth: 16

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: Imagic / Resolution: 25 Å / Resolution method: FSC 0.5

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