8TUL | pdb_00008tul

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

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q9HD23-F1

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.639
f_angle_d	0.475
f_chiral_restr	0.039
f_plane_restr	0.006
f_bond_d	0.004

Sample
Cryo-EM structure of the pentameric human MRS2 magnesium channel under Mg2+ condition at an average resolution of 2.8 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. 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	450554
Reported Resolution (Å)	2.8
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Non-uniform refinement was performed with 450,554 selected particles, followed by local motion correction and CTF refinement to correct for beam-tilt, spherical aberrations, and per-particle defocus parameters. Non-uniform refinement with polished particles resulted in maps at 2.8 A (with C5 symmetry applied) and 3.1 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	2
Refinement Space	REAL	REAL
Refinement Protocol	RIGID BODY FIT	FLEXIBLE FIT
Refinement Target
Overall B Value	141	141
Fitting Procedure
Details		The model was then manually rebuilt in COOT v.0.9.7 using the local resolution filtered map, which was generated from refinement with C5 applied. The Mg2+ ions assigned in the pore regions were confirmed in the C1 map. Loop regions (residues 174-181, 273-287) were built with the unsharpened map. Iterative rounds of manual refinement in COOT and real-space refinement in Phenix v.1.20.1-4487 were performed.

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
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.2
CLASSIFICATION	cryoSPARC	3.3.2
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL FITTING	Coot
MODEL REFINEMENT	Coot
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	Patch CTF	1568444	Good 2D class averages generated from ~1,000 manually picked particles served as templates for automatic particle picking.