|Entry||Database: EMDB / ID: 3824|
|Title||Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1|
|Sample||Tra1 - Transcription-associated protein 1:|
Transcription-associated protein 1
|Function / homology||FATC domain / PIK-related kinase / Ub-specific processing proteases / FATC domain profile. / FAT domain profile. / FAT domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Phosphatidylinositol 3-/4-kinase, catalytic domain / PIK-related kinase, FAT ...FATC domain / PIK-related kinase / Ub-specific processing proteases / FATC domain profile. / FAT domain profile. / FAT domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Phosphatidylinositol 3-/4-kinase, catalytic domain / PIK-related kinase, FAT / Armadillo-type fold / Protein kinase-like domain superfamily / SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / histone acetylation / kinase activity / DNA repair / positive regulation of transcription by RNA polymerase II / transcription, DNA-templated / nucleus / Transcription-associated protein 1|
Function and homology information
|Source||Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)|
|Method||single particle reconstruction / cryo EM / 3.7 Å resolution|
|Authors||Diaz-Santin LM / Lukoyanova N|
|Citation||Journal: Elife / Year: 2017|
Title: Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 at 3.7 angstrom resolution.
Authors: Luis Miguel Díaz-Santín / Natasha Lukoyanova / Emir Aciyan / Alan Cm Cheung
|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|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3824.map.gz (map file in CCP4 format, 97557 KB)|
|Projections & slices|
Images are generated by Spider.
|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 (baker's yeast)|
-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)|
|Specimen||Specimen state: particle / Method: cryo EM|
|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|
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