|Entry||Database: PDB / ID: 5ojs|
|Title||Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1|
|Components||Transcription-associated protein 1|
|Keywords||TRANSCRIPTION / Coactivator / PIKK / SAGA / NuA4|
|Function / homology|
Function and homology information
ASTRA complex / SLIK (SAGA-like) complex / SAGA complex / NuA4 histone acetyltransferase complex / histone acetylation / transcription coregulator activity / DNA repair / protein phosphorylation / regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / nucleus
FAT domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Transcription-associated protein 1 / Armadillo-type fold / PIK-related kinase / Protein kinase-like domain superfamily / FATC domain / PIK-related kinase, FAT
Transcription-associated protein 1
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å|
|Authors||Diaz-Santin, L.M. / Lukoyanova, N. / Aciyan, E. / Cheung, A.C.M.|
|Funding support|| United Kingdom, 2items |
|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 /
Abstract: Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the ...Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair. The structure was fitted into an existing SAGA EM reconstruction and reveals limited contact surfaces to Tra1, hence it does not act as a molecular scaffold within SAGA. Mutations that affect activator targeting are distributed across the Tra1 structure, but also cluster within the N-terminal Finger region, indicating the presence of an activator interaction site. The structure of Tra1 is a key milestone in deciphering the mechanism of multiple coactivator complexes.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
T: Transcription-associated protein 1
|#1: Protein|| |
Mass: 436527.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TRA1, YHR099W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38811
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Tra1 - Transcription-associated protein 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Molecular weight||Value: 0.433 MDa / Experimental value: NO|
|Source (natural)||Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)|
|Source (recombinant)||Organism: Saccharomyces cerevisiae (baker's yeast)|
|Buffer solution||pH: 8|
|Specimen||Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid type: Agar Scientific|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 % / Chamber temperature: 277 K|
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 ...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
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER|
|Electron lens||Mode: OTHER / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Electron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Software||Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1 (asymmetric)|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182285 / Symmetry type: POINT|
|Atomic model building||Protocol: AB INITIO MODEL / Space: REAL|
|Refine LS restraints|
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