|Entry||Database: EMDB / ID: 5668|
|Title||26S proteasome Rpn11AXA Rpn13-delta mutant|
|Map data||Reconstruction of the Rpn11AXA Rpn13-delta yeast 26S proteasome in the absence of substrate|
|Sample||Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome:|
|Keywords||26S proteasome / 19S regulatory particle / Rpn11 / deubiquitination / AAA+ ATPase / protein translocation / cryoEM / UPS|
|Function / homology||proteasome regulatory particle / Proteasome, subunit alpha/beta|
Function and homology information
|Source||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / cryo EM / 9 Å resolution|
|Authors||Matyskiela ME / Lander GC / Martin A|
|Citation||Journal: 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
|Date||Deposition: May 8, 2013 / Header (metadata) release: May 22, 2013 / Map release: Jun 19, 2013 / Last update: Jul 17, 2013|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5668.map.gz (map file in CCP4 format, 54001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.17 Å|
CCP4 map header:
-Entire Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome
|Entire||Name: Yeast Rpn11AXA Rpn13-delta mutant 26S proteasome / Details: mutant proteasome was purified from yeast / Number of components: 1 / Oligomeric State: holoenzyme|
|Mass||Theoretical: 1.5 MDa / Experimental: 1.5 MDa / Measured by: Sedimentation|
-Component #1: protein, 26S proteasome
|Protein||Name: 26S proteasome / a.k.a: proteasome / Oligomeric Details: monomer / Details: Mutant proteasome was purified from yeast / Recombinant expression: No / Number of Copies: 1|
|Mass||Theoretical: 1.5 MDa / Experimental: 1.5 MDa|
|Source||Species: Saccharomyces cerevisiae (baker's yeast) / Strain: yAM11|
|Source (natural)||Location in cell: cytoplasm|
|External references||InterPro: Proteasome, subunit alpha/beta / Gene Ontology: proteasome regulatory particle|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 2 mg/ml|
Buffer solution: 60mM HEPES, 50mM NaCl, 50mM KCl, 5mM MgCl2, 0.5mM EDTA, 1mM DTT, 2mM ATP, 0.05% NP40
|Support film||400-mesh C-flats, 2 um holes with 2 um spacing (Protochips Inc.)|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 86 K / Humidity: 50 % / Method: Blot 3 seconds with -1 offset|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20 / Date: Sep 10, 2012 / Details: Data acquired with Leginon|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Holder: Gatan 626, 70 degree cryoholder / Model: GATAN LIQUID NITROGEN / Temperature: 79 K ( 78 - 80 K)|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 4740|
|Processing||Method: 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 reconstruction||Algorithm: 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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