|Entry||Database: PDB / ID: 5oej|
|Title||Structure of Tra1 subunit within the chromatin modifying complex SAGA|
|Components||Tra1 subunit within the chromatin modifying complex SAGA|
|Keywords||TRANSCRIPTION / yeast / Tra1 / SAGA / activator target|
|Specimen source||Komagataella pastoris / fungus|
|Method||Electron microscopy (5.7 Å resolution / Particle / Single particle)|
|Authors||Sharov, G. / Voltz, K. / Durand, A. / Kolesnikova, O. / Papai, G. / Myasnikov, A.G. / Dejaegere, A. / Ben-Shem, A. / Schultz, P.|
|Citation||Nat Commun, 2017, 8, 1556-1556|
Nat Commun, 2017, 8, 1556-1556 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Jul 7, 2017 / Release: Aug 2, 2017|
Downloads & links
B: Tra1 subunit within the chromatin modifying complex SAGA
|#1: Protein/peptide|| |
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Tra1 subunit of SAGA complex / Type: COMPLEX / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Value: 0.4 deg. / Units: MEGADALTONS / Experimental value: NO|
|Source (natural)||Organism: Komagataella pastoris|
|Buffer solution||pH: 8|
|Specimen||Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/2|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 kelvins / Details: Blot for 1 second before plunging|
-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: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 59000 / Calibrated magnification: 127272 / Nominal defocus max: 3400 nm / Nominal defocus min: 1400 nm / Calibrated defocus min: 1400 nm / Calibrated defocus max: 3400 nm / Cs: 0.001 mm / C2 aperture diameter: 100 mm / Alignment procedure: ZEMLIN TABLEAU|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 kelvins / Temperature (min): 70 kelvins|
|Image recording||Average exposure time: 1 sec. / Electron dose: 60 e/Å2|
Details: Images were collected in movie-mode at 17 frames per second, frame 1 was not acquired. Every two frames were joined together, producing 8 frames per second.
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 4 / Number of real images: 8505
|EM imaging optics||Sph aberration corrector: Microscope has a Cs corrector|
|Image scans||Sampling size: 14 microns / Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 8 / Used frames/image: 2-8|
|CTF correction||Details: Full CTF correction in Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 264901|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 105916 / Algorithm: FOURIER SPACE / Symmetry type: POINT|
|Atomic model building||Details: Secondary structure restraints were applied in Phenix.|
Ref protocol: RIGID BODY FIT / Ref space: REAL
|Atomic model building||PDB-ID: 4JSN|
Pdb chain ID: B / Pdb chain residue range: 1385-2549
|Least-squares process||Highest resolution: 5.7 Å|
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