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E3 ubiquitin ligase HUWE1 homolog Tom1p in closed-conformation with internal Acidic Domain deletion
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.945
f_angle_d
0.601
f_chiral_restr
0.055
f_plane_restr
0.005
f_bond_d
0.004
Sample
Yeast E3 ubiquitin ligase Tom1p with an internal truncation at the acidic domain (residues 1873-2131).
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK I
Cryogen Name
ETHANE
Sample Vitrification Details
Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA. The detergent sample was concentrated to 8.1 mg/mL ...
Specimens were prepared on Quantifoil R 2/2 Cu300 grids after glow discharge for 1 minute at 25 mA. The detergent sample was concentrated to 8.1 mg/mL in 0.01% CHAPS and 0.05% NP-40. 2.5 uL of sample was applied to grids and blotted for 2.5 seconds before vitrification by plunging into liquid ethane. For samples without detergent, protein was concentrated to 0.44 mg/mL and blotted for 1.5 seconds before vitrification.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
462711
Reported Resolution (Å)
3.07
Resolution Method
FSC 0.143 CUT-OFF
Other Details
The separately processed dataset #1 and #2 particles were combined for a total of 531,549 starting particles for further processing and refinement. A ...
The separately processed dataset #1 and #2 particles were combined for a total of 531,549 starting particles for further processing and refinement. A round of 2D classification resulted in selection of 477,889 particles, which were Fourier cropped from a box size of 680 to 320 pixels for further processing. Two-component 3DVA was performed after map refinement of the combined dataset with a filter resolution of 4 A. 3DVA display was subsequently run to give 8 intermediates along the first principal component at a filter resolution of 5 A. The top 4 intermediates with the highest number of particles were combined to yield 462,711 and refined using non-uniform refinement to an estimated overall resolution of 3.07 A.