|Entry||Database: EMDB / ID: 1992|
|Title||The Saccharomyces cerevisiae 26S proteasome at subnanometer resolution|
|Keywords||26S / 19S / proteasome / regulatory particle / ubiquitin recognition / deubiquitination / AAA-ATPase|
|Source||Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /|
|Map data||26 proteasome|
|Method||single particle reconstruction, at 9 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_1992.map.gz (map file in CCP4 format, 65537 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.17 Å|
CCP4 map header:
-Entire 26S Proteasome
|Entire||Name: 26S Proteasome / Details: monodisperse / Number of components: 1 / Oligomeric State: holoenzyme|
|Mass||Theoretical: 1.5 MDa / Experimental: 1.5 MDa / Measured by: Mass Spectrometry|
-Component #1: protein, 26S Proteasome
|Protein||Name: 26S Proteasome / a.k.a: 26S Proteasome / Oligomeric Details: monomer / Details: Endogenous 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 / yeast / サッカロミセス・セレビシエ / |
|External references||InterPro: InterPro: 001353 / Gene Ontology: GO: 0005838|
|Sample solution||Specimen conc.: 1.7 mg/ml|
Buffer solution: 20mM HEPES, 50mM NaCl, 50mM KCl, 1mM ATP, 1mM DTT, 0.05% NP40
|Support film||400-mesh C-flats, 2um holes with 2um spacing (Protochips Inc.)|
|Staining||C-flat grids made hydrophilic with Solarus Plasma cleaner, 4 uL of sample applied, blotted in Vitrobot for 3 seconds with offset -1, plunged into liquid ethane|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 86 K / Humidity: 100 % / Method: Blot 3 seconds with -2 offset / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20 / Date: Sep 11, 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: 100000 X (nominal)|
Astigmatism: objective lens astigmatism was corrected at 210,000 times magnification
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2600 nm
|Specimen Holder||Holder: Side-entry cryostage / Model: GATAN LIQUID NITROGEN / Temperature: 78 K ( 78 - 78 K)|
|Camera||Detector: GENERIC GATAN (4k x 4k)|
|Image acquisition||Number of digital images: 9153|
|Processing||Method: single particle reconstruction / Number of projections: 93679|
Details: Image processing performed in the Appion processing environment. 3D reconstruction performed using EMAN2 and SPARX libraries
Applied symmetry: C2 (2 fold cyclic)
|3D reconstruction||Algorithm: Projection matching / Software: EMAN2 SPARX / CTF correction: whole micrograph|
Details: Final map filtered to local resolution using the blocfilt function in Bsoft
Resolution: 9 Å / Resolution method: FSC 0.5
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- 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.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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