8TUP | pdb_00008tup

Cryo-EM structure of the human MRS2 magnesium channel under Mg2+-free condition

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8TUL

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.094
f_angle_d	0.372
f_chiral_restr	0.036
f_plane_restr	0.003
f_bond_d	0.002

Sample
Cryo-EM structure of the pentameric human MRS2 magnesium channel under Mg2+-free condition at an average resolution of 3.3 A, filtered to local resolution, C5

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	400-mesh R1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for 60 seconds with a current of 15 mA in a PELCO easiGlow system. T ...	400-mesh R1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for 60 seconds with a current of 15 mA in a PELCO easiGlow system. The cryo grids were produced using a Leica EM GP2 (Leica). The chamber was kept at 4 C and set to 95% humidity. 3 microliter sample at 0.5 mg/ml was applied to a glow-discharged holey grid, blotted for 6 s, and plunge frozen into liquid ethane and stored in liquid nitrogen.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1744117
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Final non-uniform refinement by using 1,744,117 particles yielded maps at 3.3 A (with C5 symmetry applied) and 3.6 A (with C1 symmetry applied) acco ...	Final non-uniform refinement by using 1,744,117 particles yielded maps at 3.3 A (with C5 symmetry applied) and 3.6 A (with C1 symmetry applied) according to gold-standard FSC = 0.143 criterion.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C5

Map-Model Fitting and Refinement
Id	1 (8TUL)	2 (8TUL)
Refinement Space	REAL	REAL
Refinement Protocol	RIGID BODY FIT	FLEXIBLE FIT
Refinement Target
Overall B Value	141	141
Fitting Procedure
Details		For the MRS2-EDTA structures, models were generated from multiple rounds of manual refinement and real-space refinements with the final model of MRS2- ...	For the MRS2-EDTA structures, models were generated from multiple rounds of manual refinement and real-space refinements with the final model of MRS2-Mg2+ as initial model.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2000
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.3.2
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	3.3.2
MODEL FITTING	UCSF Chimera	1.16
MODEL FITTING	Coot
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX	1.20.1-4487
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.2
CLASSIFICATION	cryoSPARC	3.3.2
RECONSTRUCTION	cryoSPARC	3.3.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Patch CTF	4802706	Good 2D class averages generated from ~1,000 manually picked particles served as templates for automatic particle picking.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.