8P12 | pdb_00008p12

Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EN0
experimental model	PDB	6CMO
experimental model	PDB	6CRK
experimental model	PDB	1GOT
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.659
f_angle_d	1.045
f_chiral_restr	0.048
f_bond_d	0.008
f_plane_restr	0.006

Sample
Rhodopsin-Gi-Fab13 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
Immunoglobin G light chain and Immunoglobin G heavy chain FAB fragment

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	587113
Reported Resolution (Å)	3.21
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (5EN0, 6CMO, 6CRK, 6CMO, 1GOT, 1GOT)
Refinement Space	REAL
Refinement Protocol	AB INITIO MODEL
Refinement Target	cross-correlation coefficient
Overall B Value	150
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	66

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.31
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC
MODEL FITTING	UCSF Chimera	1.16
MODEL REFINEMENT	PHENIX	1.20-4487

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		3752145

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.