Cryo-EM structure for the mouse LEPR-CRH2:Leptin:LEPR-Ig complex following symmetry expansion in combination with local refinement
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
9.827
f_angle_d
0.6111
f_chiral_restr
0.0425
f_plane_restr
0.0041
f_bond_d
0.0024
Sample
Mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
163914
Reported Resolution (Å)
4.02
Resolution Method
FSC 0.143 CUT-OFF
Other Details
To address the breakage of symmetry in the ring-like core region of the complex and possibly revolve the mLEP-RCRH2:mLeptin:mLEP-RCRH1-IgCRH2 subcompl ...
To address the breakage of symmetry in the ring-like core region of the complex and possibly revolve the mLEP-RCRH2:mLeptin:mLEP-RCRH1-IgCRH2 subcomplex at higher resolution, the pseudo-C3 symmetric volume following consenus refinement was aligned to the pseudo-C3 symmetry axis via the Volume Alignment Tool job in cryoSPARC. The associated particle set was re-extracted without binning and symmetry expanded around the C3 axis resulting in 163,914 particles. Using the molmap function in Chimera, a volume blurred to 25 Angstrom around one mLEP-RCRH2:mLeptin:mLEP-RCRH1-IgCRH2 subcomplex was generated, and transformed into a mask with the Volume Tools job in cryoSPARC. Local refinement was performed by limiting the rotation and shift search extent around the original consensus refinement. The center of mass of the mask was used as a fulcrum point. This approach resulted in a cryo-EM map with an FSC0.143 resolution of 4.02 Angstrom in which the crystallographic model for the mLEP-RCRH2:mLeptin:mLEP-R_IgCRH2' complex was fitted using Chimera and real-space refined in Phenix using reference restraints to the starting model.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
The crystallographic model for the mLEP-RCRH2:mLeptin:mLEP-R_IgCRH2' complex (pdb 7z3r) was fitted in the cryo-EM map using Chimera and real-space re ...
The crystallographic model for the mLEP-RCRH2:mLeptin:mLEP-R_IgCRH2' complex (pdb 7z3r) was fitted in the cryo-EM map using Chimera and real-space refined in Phenix using reference restraints to the starting model.
