8AVE

Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric isoleucine GCN4 zipper (2:2 model)

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.1582
f_angle_d	0.9337
f_chiral_restr	0.0556
f_plane_restr	0.0101
f_bond_d	0.0039

Sample
Human leptin in complex with the human LEP-R ectodomain C-terminally fused to a trimeric GCN4 isoleucine zipper tag

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	91899
Reported Resolution (Å)	5.62
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Non-uniform refinement in cryoSPARC
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7Z3R, 7Z3Q)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Atomic models for the 2:2 and 3:3 hLeptin:hLEP-R complexes were created based on the Alphafold2 predictions for hLEP-R and hLeptin, and the mouse 3:3 ...	Atomic models for the 2:2 and 3:3 hLeptin:hLEP-R complexes were created based on the Alphafold2 predictions for hLEP-R and hLeptin, and the mouse 3:3 Leptin:LEP-RIgCRH2 complex (pdb 7z3r) and the human Leptin:LEP-RCRH2 complex (pdb 7z3q) and fitted in the cryo-EM maps via Chimera. Atomic models were further refined via real space refinement in Phenix using rigid body refinement and coordinate refinement with reference restraints to the starting model and hydrogen-bonding restraints across the site II and site III hLeptin:hLEP-R interface regions.

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	62.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL CRYO ARM 300
Minimum Defocus (nm)	800
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	OTHER
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
CTF CORRECTION	cryoSPARC	v3.1.0
MODEL FITTING	UCSF Chimera	1.17
INITIAL EULER ASSIGNMENT	cryoSPARC	v3.1.0
RECONSTRUCTION	cryoSPARC	v3.3.2
MODEL REFINEMENT	PHENIX	1.19.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		206218	Initial 2D-classes were obtained via template-based particle picking using 2D-classes for a mLeptin:mLEP-R-deltaFnIII-tGCN4 complex lowpass filtered to 20 Angstrom. These 2D classes were then used to seed template-based picking and neural network-based particle picking via Topaz 0.2.4. Junk particles were removed by multiple rounds of 2D classification resulting in a particle set of 206,218 particles. High-resolution 2D classes were selected for ab initio 3D classification followed by heterogeneous refinement and non-uniform refinement.

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 R01GM133198.