|Entry||Database: PDB / ID: 5ojs|
|Title||Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1|
|Descriptor||Transcription-associated protein 1|
|Keywords||TRANSCRIPTION / Coactivator / PIKK / SAGA / NuA4|
|Specimen source||Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /|
|Method||Electron microscopy (3.7 Å resolution / Particle / Single particle)|
|Authors||Diaz-Santin, L.M. / Lukoyanova, N. / Aciyan, E. / Cheung, A.C.M.|
|Citation||Elife, 2017, 6|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 24, 2017 / Release: Aug 9, 2017|
Downloads & links
T: Transcription-associated protein 1
Mass: 436527.281 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: P38811
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Tra1 - Transcription-associated protein 1 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Value: 0.433 deg. / Units: MEGADALTONS / Experimental value: NO|
|Source (natural)||Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)|
|Source (recombinant)||Organism: Saccharomyces cerevisiae|
|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 kelvins|
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||Microscope 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 / Specimen holder 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|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 182285 / Symmetry type: POINT|
|Atomic model building||Ref protocol: AB INITIO MODEL / Ref space: REAL|
|Refine LS restraints|
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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.
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- 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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