|Entry||Database: EMDB / ID: 3824|
|Title||Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1|
|Sample||Tra1 - Transcription-associated protein 1|
|Source||Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /|
|Method||single particle reconstruction, at 3.7 Å resolution|
|Authors||Diaz-Santin LM / Lukoyanova N|
|Citation||Elife, 2017, 6|
|Validation Report||PDB-ID: 5ojs|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 24, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Jan 31, 2018|
Downloads & links
|File||emd_3824.map.gz (map file in CCP4 format, 97557 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.06 Å|
CCP4 map header:
-Entire Tra1 - Transcription-associated protein 1
|Entire||Name: Tra1 - Transcription-associated protein 1 / Number of components: 2|
|Mass||Theoretical: 433 kDa|
-Component #1: protein, Tra1 - Transcription-associated protein 1
|Protein||Name: Tra1 - Transcription-associated protein 1 / Recombinant expression: No|
|Mass||Theoretical: 433 kDa|
|Source||Species: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /|
|Source (engineered)||Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /|
-Component #2: protein, Transcription-associated protein 1
|Protein||Name: Transcription-associated protein 1 / Recombinant expression: No|
|Mass||Theoretical: 436.527281 kDa|
|Source (engineered)||Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /|
|Sample solution||Specimen conc.: 0.1 mg/ml / pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 94 %|
Details: Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting after first application and 5 sec blotting after the second.
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: OTHER|
|Lens||Cs: 2.7 mm / Imaging mode: OTHER / Defocus: 1500 - 3500 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 182285|
|3D reconstruction||Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
-Atomic model buiding
-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
-Jul 12, 2017. Major update of PDB
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