|Entry||Database: EMDB / ID: 1994|
|Title||Negative stain reconstruction of the Saccharomyces cerevisiae proteasome lid|
|Keywords||26S / 19S / proteasome / yeast lid / regulatory particle / ubiquitin recognition / deubiquitination / AAA-ATPase|
|Sample||Saccharomyces cerevisiae proteasome lid subcomplex|
|Source||Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /|
|Map data||map of endogenous Saccharomyces cerevisiae proteasome lid|
|Method||single particle reconstruction, at 15 Å resolution|
|Authors||Lander GC / Estrin E / Matyskiela M / Bashore C / Nogales E / Martin A|
|Citation||Nature, 2012, 482, 186-191|
|Date||Deposition: Nov 18, 2011 / Header (metadata) release: Jan 6, 2012 / Map release: Jan 6, 2012 / Last update: Feb 3, 2012|
Downloads & links
|File||emd_1994.map.gz (map file in CCP4 format, 8193 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.76 Å|
CCP4 map header:
-Entire Saccharomyces cerevisiae proteasome lid subcomplex
|Entire||Name: Saccharomyces cerevisiae proteasome lid subcomplex / Details: monodisperse / Number of components: 1 / Oligomeric State: 8 subunit complex|
|Mass||Theoretical: 361 kDa / Experimental: 361 kDa / Measured by: Mass Spectrometry|
-Component #1: protein, lid
|Protein||Name: lid / a.k.a: lid / Oligomeric Details: monomer|
Details: lid was purified from endogenous proteasome holoenzyme using a 1M salt wash
Recombinant expression: No / Number of Copies: 1
|Mass||Theoretical: 361 kDa / Experimental: 361 kDa|
|Source||Species: Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ / |
|External references||InterPro: InterPro: 002015 / Gene Ontology: GO: 0008541|
|Sample solution||Specimen conc.: 0.009 mg/ml|
Buffer solution: 60mM HEPES, 50mM NaCl, 50mM KCl, 5 mM MgCl2, 0.5mM EDTA, 1mM DTT, 10% glycerol
|Support film||200 mesh Cu grid|
|Staining||Protein adsorbed to grid for 1 minute, then passed over four 50uL drops of 2% w/v uranyl formate, 5 seconds on each drop|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20 / Date: Apr 2, 2011 / Details: Data acquired using Leginon|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 80000 X (nominal), 80000 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 1200 nm
|Specimen Holder||Holder: Room temp single tilt / Model: SIDE ENTRY, EUCENTRIC / Temperature: 78 K ( 78 - 78 K)|
|Camera||Detector: GENERIC GATAN (4k x 4k)|
|Image acquisition||Number of digital images: 250|
|Processing||Method: single particle reconstruction / Number of projections: 33478|
Details: Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
Applied symmetry: C1 (asymmetric)
|3D reconstruction||Algorithm: Projection matching / Software: EMAN2 SPARX / CTF correction: whole micrograph / Resolution: 15 Å / Resolution method: FSC 0.5|
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- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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