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- EMDB-2035: 8.4 A single-particle reconstruction of the 26S Proteasome from S... -

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Basic information

Entry
Database: EMDB / ID: EMD-2035
Title8.4 A single-particle reconstruction of the 26S Proteasome from Schizosaccharomyces pombe
Map dataThis is an image of a surface rendered S.pombe 26S proteasome
Sample
  • Sample: 26S proteasomes purified from S.pombe cells
  • Organelle or cellular component: 26S proteasome
Keywords26S proteasome / AAA-ATPase / PCI-domain / solenoid
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsBohn S / Beck F / Lasker K / Forster F / Walzthoeni T / Villa E / Unverdorben P / Aebersold R / Sali A / Baumeister W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach.
Authors: Keren Lasker / Friedrich Förster / Stefan Bohn / Thomas Walzthoeni / Elizabeth Villa / Pia Unverdorben / Florian Beck / Ruedi Aebersold / Andrej Sali / Wolfgang Baumeister /
Abstract: The 26S proteasome is at the executive end of the ubiquitin-proteasome pathway for the controlled degradation of intracellular proteins. While the structure of its 20S core particle (CP) has been ...The 26S proteasome is at the executive end of the ubiquitin-proteasome pathway for the controlled degradation of intracellular proteins. While the structure of its 20S core particle (CP) has been determined by X-ray crystallography, the structure of the 19S regulatory particle (RP), which recruits substrates, unfolds them, and translocates them to the CP for degradation, has remained elusive. Here, we describe the molecular architecture of the 26S holocomplex determined by an integrative approach based on data from cryoelectron microscopy, X-ray crystallography, residue-specific chemical cross-linking, and several proteomics techniques. The "lid" of the RP (consisting of Rpn3/5/6/7/8/9/11/12) is organized in a modular fashion. Rpn3/5/6/7/9/12 form a horseshoe-shaped heterohexamer, which connects to the CP and roofs the AAA-ATPase module, positioning the Rpn8/Rpn11 heterodimer close to its mouth. Rpn2 is rigid, supporting the lid, while Rpn1 is conformationally variable, positioned at the periphery of the ATPase ring. The ubiquitin receptors Rpn10 and Rpn13 are located in the distal part of the RP, indicating that they were recruited to the complex late in its evolution. The modular structure of the 26S proteasome provides insights into the sequence of events prior to the degradation of ubiquitylated substrates.
History
DepositionJan 12, 2012-
Header (metadata) releaseJan 27, 2012-
Map releaseFeb 2, 2012-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emdb2035_26S...

Downloads & links

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Map

FileDownload / File: emd_2035.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered S.pombe 26S proteasome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.22 Å/pix.
x 256 pix.
= 568.32 Å		2.22 Å/pix.
x 256 pix.
= 568.32 Å		2.22 Å/pix.
x 256 pix.
= 568.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.0224666 - 0.07053044
Average (Standard dev.)0.00034878 (±0.002872468671329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.222.222.22
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z568.320568.320568.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0220.0710.000

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Supplemental data

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Segmentation: This is a binary mask of the 26S proteasome

AnnotationThis is a binary mask of the 26S proteasome
Fileemd_2035_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 26S proteasomes purified from S.pombe cells

EntireName: 26S proteasomes purified from S.pombe cells
Components
  • Sample: 26S proteasomes purified from S.pombe cells
  • Organelle or cellular component: 26S proteasome

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Supramolecule #1000: 26S proteasomes purified from S.pombe cells

SupramoleculeName: 26S proteasomes purified from S.pombe cells / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1
Molecular weightExperimental: 2.5 MDa / Theoretical: 2.5 MDa

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Supramolecule #1: 26S proteasome

SupramoleculeName: 26S proteasome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: 26S proteasome / Recombinant expression: No
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / synonym: Fission yeast

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP / Number images used: 380000

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