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Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FUF experimental model PDB 6QNO in silico model AlphaFold experimental model PDB 6CRK
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.09 f_angle_d 1.071 f_chiral_restr 0.055 f_plane_restr 0.007 f_bond_d 0.005
Sample Rhodopsin-Gi-scFv16-Fab79 complex Sample Components Rhodopsin Guanine nucleotide-binding protein G(i) subunit alpha-1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 and Guanine nucleotide-binding protein G(T) subunit gamma-T1 single-chain Fv 16 Immunoglobin G heavy chain FAB fragment and Immunoglobin G light chain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 98000 Reported Resolution (Å) 5.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6FUF, 6QNO, 6QNO, 6QNO, 6QNO, 6CRK) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target cross-correlation coefficient Overall B Value 360 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (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) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU MODEL FITTING UCSF Chimera 1.16 MODEL REFINEMENT PHENIX 1.20.1-4487 INITIAL EULER ASSIGNMENT cryoSPARC 2.13 RECONSTRUCTION RELION 3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 7026029