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- EMDB-5668: 26S proteasome Rpn11AXA Rpn13-delta mutant -

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Basic information

Database: EMDB / ID: 5668
Title26S proteasome Rpn11AXA Rpn13-delta mutant
Map dataReconstruction of the Rpn11AXA Rpn13-delta yeast 26S proteasome in the absence of substrate
SampleYeast Rpn11AXA Rpn13-delta mutant 26S proteasome:
26S proteasome
Keywords26S proteasome / 19S regulatory particle / Rpn11 / deubiquitination / AAA+ ATPase / protein translocation / cryoEM / UPS
Function / homologyproteasome regulatory particle / Proteasome, subunit alpha/beta
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 9 Å resolution
AuthorsMatyskiela ME / Lander GC / Martin A
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2013
Title: Conformational switching of the 26S proteasome enables substrate degradation.
Authors: Mary E Matyskiela / Gabriel C Lander / Andreas Martin
DateDeposition: May 8, 2013 / Header (metadata) release: May 22, 2013 / Map release: Jun 19, 2013 / Last update: Jul 17, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

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Fileemd_5668.map.gz (map file in CCP4 format, 54001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
2.17 Å/pix.
= 520.8 Å
240 pix
2.17 Å/pix.
= 520.8 Å
240 pix
2.17 Å/pix.
= 520.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.17 Å
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-11.60969639 - 15.19638729
Average (Standard dev.)0.01988752 (0.59111792)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 520.80005 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z520.800520.800520.800
start NX/NY/NZ-132-122-147
MAP C/R/S123
start NC/NR/NS404040
D min/max/mean-11.61015.1960.020

Supplemental data

Sample components

Entire Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome

EntireName: Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome / Details: mutant proteasome was purified from yeast / Number of components: 1 / Oligomeric State: holoenzyme
MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa / Measured by: Sedimentation

Component #1: protein, 26S proteasome

ProteinName: 26S proteasome / a.k.a: proteasome / Oligomeric Details: monomer / Details: Mutant proteasome was purified from yeast / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 1.5 MDa / Experimental: 1.5 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: yAM11
Source (natural)Location in cell: cytoplasm
External referencesInterPro: Proteasome, subunit alpha/beta / Gene Ontology: proteasome regulatory particle

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml
Buffer solution: 60mM HEPES, 50mM NaCl, 50mM KCl, 5mM MgCl2, 0.5mM EDTA, 1mM DTT, 2mM ATP, 0.05% NP40
pH: 7.6
Support film400-mesh C-flats, 2 um holes with 2 um spacing (Protochips Inc.)
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 86 K / Humidity: 50 % / Method: Blot 3 seconds with -1 offset

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Sep 10, 2012 / Details: Data acquired with Leginon
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100000 X (nominal), 100000 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2500 nm
Specimen HolderHolder: Gatan 626, 70 degree cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 79 K ( 78 - 80 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 4740

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 80011
Details: 3D reconstruction with EMAN2/SPARX libraries; final alignment of particles with FREALIGN. Sharpened with SPIDER; low-pass filtered to local resolution with BSOFT.
3D reconstructionAlgorithm: Projection matching / Software: EMAN2/SPARX, FREALIGN / CTF correction: each particle
Details: Final map filtered to local resolution using the blocfilt function in Bsoft. Image processing performed in the Appion processing environment.
Resolution: 9 Å / Resolution method: FSC 0.5

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