ELECTRON MICROSCOPY

Sample

Ribosome from Encephalitozoon cuniculi

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details Quantifoil grids (R1.2/1.3, 400 mesh, copper) were glow discharged (10 mA, 30s, Quorum GloQube), and 3 microlitres of the crude sample of E. cuniculi ribosomes (300 nM) was pipetted onto a grid. Excess sample was immediately blotted off and vitrification was performed by plunging the grid into liquid nitrogen-cooled liquid ethane at 100% humidity and 4 degrees celsius using an FEI Vitrobot Mark IV (Thermo Fisher)
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 108005
Reported Resolution (Å) 2.7
Resolution Method FSC 0.143 CUT-OFF
Other Details The remaining particles were re-extracted without binning and aligned and refined in 3D, again using a 60 Angstrom low-passed filtered ab initio starting model. Rounds of CTF refinement and Bayesian polishing were performed until the map resolution stopped improving. 108,005 particles fed into the final 3D reconstruction of estimated resolution 2.7 Angstrom.
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol OTHER
Refinement Target correlation coefficient
Overall B Value ?
Fitting Procedure ?
Details The model was built using fragments of S. cerevisiae (pdb id 4v88) and V. necatrix ribosomes (pdb id 6rm3) as starting models that were edited using Coot using genomic sequences of the E. cuniculi strain GB-M1 to model rRNA and ribosomal proteins. For ribosomal proteins that are encoded by two alternative genes (with one gene coding for a zinc-coordinating protein and another gene coding for a zinc-free ribosomal protein), we used zinc-coordinating isoforms, because the cryo-EM map revealed the presence of these isoforms and not their zinc-free paralogs in the ribosome structure. The identity of protein msL2 in the ribosome structure was determined using the genomic sequence of the E. cuniculi strain GB-M1 and the cryo-EM map that revealed a unique combination of aromatic and bulky amino acids in its structure: the cryo-EM map showed that msL2 has a tyrosine residue at position 5, a tryptophan residue at position 9, and lysine or arginine residues at positions 10, 12 and 13. The only protein with this sequence was the hypothetical protein ECU06_1135, whose sequence and length were fully consistent with the cryo-EM map. The structure of E. cuniculi ribosomes was refined using Phenix real space refine and validated using MolProbity within Phenix and PDB OneDep. The parts of the model corresponding to the 60S, 40S body and 40S head were built and refined using the consensus map, 40S body multibody map and 40S head multibody map, respectively.
Data Acquisition
Detector Type FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å2) 60
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 800
Maximum Defocus (nm) 2600
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 96000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
IMAGE ACQUISITION EPU ?
CTF CORRECTION RELION 3.1
CTF CORRECTION CTFFIND 4.1
MODEL FITTING Coot 0.9
INITIAL EULER ASSIGNMENT RELION 3.1
FINAL EULER ASSIGNMENT RELION 3.1
CLASSIFICATION RELION 3.1
RECONSTRUCTION RELION 3.1
MODEL REFINEMENT PHENIX 1.14
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?