8TUL | pdb_00008tul

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


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q9HD23-F1 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d3.639
f_angle_d0.475
f_chiral_restr0.039
f_plane_restr0.006
f_bond_d0.004
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 StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details400-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 MethodSINGLE PARTICLE
Number of Particles450554
Reported Resolution (Å)2.8
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsNon-uniform refinement was performed with 450,554 selected particles, followed by local motion correction and CTF refinement to correct for beam-tilt, ...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 TypePOINT
Point SymmetryC5
Map-Model Fitting and Refinement
Id12
Refinement SpaceREALREAL
Refinement ProtocolRIGID BODY FITFLEXIBLE FIT
Refinement Target
Overall B Value141141
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 ...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 TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.2
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONcryoSPARC3.3.2
MODEL FITTINGUCSF Chimera1.16
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC3.3.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC3.3.2
MODEL FITTINGCoot
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX1.20.1-4487
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTIONPatch CTF1568444Good 2D class averages generated from ~1,000 manually picked particles served as templates for automatic particle picking.