7QEP | pdb_00007qep

Cryo-EM structure of the ribosome from Encephalitozoon cuniculi

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V88
experimental model	PDB	6RM3

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.5906
f_angle_d	0.9431
f_chiral_restr	0.0529
f_bond_d	0.0089
f_plane_restr	0.0058

Sample
Ribosome from Encephalitozoon cuniculi
Sample Components
large subunit
small subunit

Specimen Preparation
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
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (4V88, 6RM3)
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/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (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

EM Software
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		260895	Particles were picked using Laplacian-of-Gaussian autopicking and reference-free 2D classification used to generate templates for further autopicking. The resulting particles were extracted with binning-by-4, and 2D and 3D classification performed to remove junk images