Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
cryo-EM structure of full-length and internally HIS-tagged yeast E3 ubiquitin ligase Tom1p, in a closed-conformation state with helical repeat solenoid architecture
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
5.901
f_angle_d
0.545
f_chiral_restr
0.036
f_plane_restr
0.005
f_bond_d
0.003
Sample
yeast E3 ubiquitin ligase Tom1p
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK I
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
142020
Reported Resolution (Å)
3.97
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
Id
1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
40
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
-800
Maximum Defocus (nm)
-2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
MODEL REFINEMENT
PHENIX
1.20.1_4487
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
Movies were motion-corrected for all 3 datasets using CryoSPARC Patch Motion Correction. CTF estimation was performed on motion-corrected micrographs using CryoSPARC Patch CTF with default parameters applied.
3,522 of 3,630 micrographs were selected for particle picking from grids containing Tom1pHis. Initial blob picks were curated via 2D-classification and 3D ab initio jobs to create 60 2D templates for template-picking. 1,434,189 template-picked particles (lowpass filter 15 A) were narrowed through 6 rounds of 2D classification to give 201,930 particles, which were input to ab initio volume creation with 4 classes. 41,253 particles from one of these classes were used to refine the open/intermediate conformations and 160,667 total particles from the remaining 3 classes were combined for further refinement of the closed conformation map.