Cryo-EM structure of the human inward-rectifier potassium 2.1 channel (Kir2.1)
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
4.766
f_angle_d
0.828
f_chiral_restr
0.047
f_bond_d
0.003
f_plane_restr
0.003
Sample
Human inward-rectifier potassium channel 2.1 (Kir2.1)
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
63584
Reported Resolution (Å)
4.3
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C4
Map-Model Fitting and Refinement
Id
1 (1U4F)
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Correlation coefficient
Overall B Value
404.73
Fitting Procedure
Details
For structural fitting, it was used dock-in-map (available at PHENIX) that uses both SSM and convolution-based shape searches to find a part of a map ...
For structural fitting, it was used dock-in-map (available at PHENIX) that uses both SSM and convolution-based shape searches to find a part of a map that is similar to a model.
An initial in silico homology model of human Kir2.1 was generated using I-TASSER using the crystal structure of chicken Kir2.2 channel (PDB ID 3JYC) as a template. For building and refinement of the atomic model, the transmembrane domain (TMD, 55-184 region) of this in silico model was placed into the final sharpened cryo-EM map using the Dock in Map tool available in PHENIX. For the cytoplasmic domain (CTD; 188-367 region), the crystal structure of the CTD from mice Kir2.1 channel (PDB ID 1U4F) was placed into the final cryo-EM map using the same approach. Once the models were placed in the electron density, the loops that connect the two domains (185-187 region) and a N-terminal loop (41-54 region) absent in the in silico model were manually built using Coot.
